From 38fa42776f16b676884ac94d4f540dffc69de245 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Wed, 11 Sep 2024 21:57:51 -0500 Subject: [PATCH 01/14] fix: try to solve #87 for non-scala components We have already had the algorithm for computing the gradients of the fitting group from the gradients of the main group. In cases that the gradients of the main group are not available, we can "intercept" the forces applied to the main group, and then use the same algorithm to convert the forces applied to the main group with the rotation to the forces applied to the fitting group. --- src/colvaratoms.cpp | 73 ++++++++++++++++++++++++++++++++++++ src/colvaratoms.h | 4 ++ src/colvarcomp_rotations.cpp | 37 +++++++++++------- 3 files changed, 100 insertions(+), 14 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index e15b9301a..f8f6c92f9 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1282,6 +1282,79 @@ void cvm::atom_group::calc_fit_gradients_impl() { } +template +std::vector cvm::atom_group::calc_fit_forces_impl(const std::vector& forces_on_main_group) const { + const cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; + std::vector forces_on_fitting_group(group_for_fit->size()); + // the center of geometry contribution to the gradients + cvm::rvector atom_grad; + // the rotation matrix contribution to the gradients + const auto rot_inv = rot.inverse().matrix(); + // temporary variables for computing and summing derivatives + cvm::real sum_dxdq[4] = {0, 0, 0, 0}; + cvm::vector1d dq0_1(4); + // loop 1: iterate over the current atom group + for (size_t i = 0; i < size(); i++) { + cvm::atom_pos pos_orig; + if (B_ag_center) { + atom_grad += forces_on_main_group[i]; + if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); + } else { + if (B_ag_rotate) pos_orig = atoms[i].pos; + } + if (B_ag_rotate) { + // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i + cvm::quaternion const dxdq = + rot.q.position_derivative_inner(pos_orig, forces_on_main_group[i]); + sum_dxdq[0] += dxdq[0]; + sum_dxdq[1] += dxdq[1]; + sum_dxdq[2] += dxdq[2]; + sum_dxdq[3] += dxdq[3]; + } + } + if (B_ag_center) { + if (B_ag_rotate) atom_grad = rot.inverse().matrix() * atom_grad; + atom_grad *= (-1.0)/(cvm::real(group_for_fit->size())); + } + // loop 2: iterate over the fitting group + if (B_ag_rotate) rot_deriv->prepare_derivative(rotation_derivative_dldq::use_dq); + for (size_t j = 0; j < group_for_fit->size(); j++) { + if (B_ag_center) { + forces_on_fitting_group[j] = atom_grad; + } + if (B_ag_rotate) { + rot_deriv->calc_derivative_wrt_group1(j, nullptr, &dq0_1); + // multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients + forces_on_fitting_group[j] += sum_dxdq[0] * dq0_1[0] + + sum_dxdq[1] * dq0_1[1] + + sum_dxdq[2] * dq0_1[2] + + sum_dxdq[3] * dq0_1[3]; + } + } + return forces_on_fitting_group; + // TODO +} + + +std::vector cvm::atom_group::calc_fit_forces(const std::vector& forces_on_main_group) const { + if (cvm::debug()) + cvm::log("Calculating fit forces.\n"); + + if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) + return calc_fit_forces_impl(forces_on_main_group); + if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) + return calc_fit_forces_impl(forces_on_main_group); + if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) + return calc_fit_forces_impl(forces_on_main_group); + if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) + return calc_fit_forces_impl(forces_on_main_group); + + if (cvm::debug()) + cvm::log("Done calculating fit forces.\n"); + return std::vector(); +} + + std::vector cvm::atom_group::positions() const { if (b_dummy) { diff --git a/src/colvaratoms.h b/src/colvaratoms.h index d16ca7bd5..613a36164 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -497,6 +497,8 @@ class colvarmodule::atom_group /// \brief Calculate the derivatives of the fitting transformation void calc_fit_gradients(); + std::vector calc_fit_forces(const std::vector& forces_on_main_group) const; + /*! @brief Actual implementation of `calc_fit_gradients`. The template is * used to avoid branching inside the loops in case that the CPU * branch prediction is broken (or further migration to GPU code). @@ -507,6 +509,8 @@ class colvarmodule::atom_group */ template void calc_fit_gradients_impl(); + template std::vector calc_fit_forces_impl(const std::vector& forces_on_main_group) const; + /// \brief Derivatives of the fitting transformation std::vector fit_gradients; diff --git a/src/colvarcomp_rotations.cpp b/src/colvarcomp_rotations.cpp index 9f401a5f2..f9c265808 100644 --- a/src/colvarcomp_rotations.cpp +++ b/src/colvarcomp_rotations.cpp @@ -137,21 +137,30 @@ void colvar::orientation::apply_force(colvarvalue const &force) if (!atoms->noforce) { rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq); cvm::vector1d dq0_2; - - if (atoms->is_enabled(f_ag_rotate)) { - auto const rot_inv = atoms->rot.inverse().matrix(); - for (size_t ia = 0; ia < atoms->size(); ia++) { - rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); - for (size_t i = 0; i < 4; i++) { - (*atoms)[ia].apply_force(rot_inv * (FQ[i] * dq0_2[i])); - } + std::vector main_group_forces; + const bool force_on_fitting_group = atoms->fitting_group == nullptr ? false : true; + cvm::rmatrix ag_rot; + if (force_on_fitting_group) { + ag_rot = atoms->rot.inverse().matrix(); + } + for (size_t ia = 0; ia < atoms->size(); ia++) { + rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); + const auto f_ia = FQ[0] * dq0_2[0] + + FQ[1] * dq0_2[1] + + FQ[2] * dq0_2[2] + + FQ[3] * dq0_2[3]; + if (force_on_fitting_group) { + main_group_forces.push_back(f_ia); + (*atoms)[ia].apply_force(ag_rot * f_ia); + } else { + (*atoms)[ia].apply_force(f_ia); } - } else { - for (size_t ia = 0; ia < atoms->size(); ia++) { - rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); - for (size_t i = 0; i < 4; i++) { - (*atoms)[ia].apply_force(FQ[i] * dq0_2[i]); - } + } + if (force_on_fitting_group) { + const std::vector fitting_group_forces = atoms->calc_fit_forces(main_group_forces); + if (fitting_group_forces.empty()) return; + for (size_t ia = 0; ia < atoms->fitting_group->size(); ia++) { + (*(atoms->fitting_group))[ia].apply_force(fitting_group_forces[ia]); } } } From b953421c640eb7340f8eab1732c0f3e346307803 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Thu, 12 Sep 2024 14:35:15 -0500 Subject: [PATCH 02/14] refactor: merge the implementation of calc_fit_gradients_impl and calc_fit_forces_impl --- src/colvaratoms.cpp | 100 +++++++++++------------------------ src/colvaratoms.h | 16 ++++-- src/colvarcomp.h | 5 ++ src/colvarcomp_rotations.cpp | 43 +++++++++++---- 4 files changed, 80 insertions(+), 84 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index f8f6c92f9..5ea1bb3d9 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1217,75 +1217,33 @@ void cvm::atom_group::calc_fit_gradients() if (cvm::debug()) cvm::log("Calculating fit gradients.\n"); + cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; + auto accessor = [](const std::vector& v, size_t i){return v[i].grad;}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); if (cvm::debug()) cvm::log("Done calculating fit gradients.\n"); } -template -void cvm::atom_group::calc_fit_gradients_impl() { - cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - // the center of geometry contribution to the gradients - cvm::rvector atom_grad; - // the rotation matrix contribution to the gradients - const auto rot_inv = rot.inverse().matrix(); - // temporary variables for computing and summing derivatives - cvm::real sum_dxdq[4] = {0, 0, 0, 0}; - cvm::vector1d dq0_1(4); - // loop 1: iterate over the current atom group - for (size_t i = 0; i < size(); i++) { - cvm::atom_pos pos_orig; - if (B_ag_center) { - atom_grad += atoms[i].grad; - if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); - } else { - if (B_ag_rotate) pos_orig = atoms[i].pos; - } - if (B_ag_rotate) { - // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i - cvm::quaternion const dxdq = - rot.q.position_derivative_inner(pos_orig, atoms[i].grad); - sum_dxdq[0] += dxdq[0]; - sum_dxdq[1] += dxdq[1]; - sum_dxdq[2] += dxdq[2]; - sum_dxdq[3] += dxdq[3]; - } - } - if (B_ag_center) { - if (B_ag_rotate) atom_grad = rot.inverse().matrix() * atom_grad; - atom_grad *= (-1.0)/(cvm::real(group_for_fit->size())); - } - // loop 2: iterate over the fitting group - if (B_ag_rotate) rot_deriv->prepare_derivative(rotation_derivative_dldq::use_dq); - for (size_t j = 0; j < group_for_fit->size(); j++) { - if (B_ag_center) { - group_for_fit->fit_gradients[j] = atom_grad; - } - if (B_ag_rotate) { - rot_deriv->calc_derivative_wrt_group1(j, nullptr, &dq0_1); - // multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients - group_for_fit->fit_gradients[j] += sum_dxdq[0] * dq0_1[0] + - sum_dxdq[1] * dq0_1[1] + - sum_dxdq[2] * dq0_1[2] + - sum_dxdq[3] * dq0_1[3]; - } - } -} - - -template -std::vector cvm::atom_group::calc_fit_forces_impl(const std::vector& forces_on_main_group) const { +template +void cvm::atom_group::calc_fit_forces_impl( + const main_force_container_T& forces_on_main_group, + std::vector& forces_on_fitting_group, + main_force_accessor_T accessor) const { const cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - std::vector forces_on_fitting_group(group_for_fit->size()); + if (forces_on_fitting_group.size() != group_for_fit->size()) { + forces_on_fitting_group.resize(group_for_fit->size()); + } // the center of geometry contribution to the gradients cvm::rvector atom_grad; // the rotation matrix contribution to the gradients @@ -1297,7 +1255,7 @@ std::vector cvm::atom_group::calc_fit_forces_impl(const std::vecto for (size_t i = 0; i < size(); i++) { cvm::atom_pos pos_orig; if (B_ag_center) { - atom_grad += forces_on_main_group[i]; + atom_grad += accessor(forces_on_main_group, i); if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); } else { if (B_ag_rotate) pos_orig = atoms[i].pos; @@ -1305,7 +1263,7 @@ std::vector cvm::atom_group::calc_fit_forces_impl(const std::vecto if (B_ag_rotate) { // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i cvm::quaternion const dxdq = - rot.q.position_derivative_inner(pos_orig, forces_on_main_group[i]); + rot.q.position_derivative_inner(pos_orig, accessor(forces_on_main_group, i)); sum_dxdq[0] += dxdq[0]; sum_dxdq[1] += dxdq[1]; sum_dxdq[2] += dxdq[2]; @@ -1313,7 +1271,7 @@ std::vector cvm::atom_group::calc_fit_forces_impl(const std::vecto } } if (B_ag_center) { - if (B_ag_rotate) atom_grad = rot.inverse().matrix() * atom_grad; + if (B_ag_rotate) atom_grad = rot_inv * atom_grad; atom_grad *= (-1.0)/(cvm::real(group_for_fit->size())); } // loop 2: iterate over the fitting group @@ -1331,23 +1289,27 @@ std::vector cvm::atom_group::calc_fit_forces_impl(const std::vecto sum_dxdq[3] * dq0_1[3]; } } - return forces_on_fitting_group; - // TODO } -std::vector cvm::atom_group::calc_fit_forces(const std::vector& forces_on_main_group) const { +std::vector cvm::atom_group::calc_fit_forces( + const std::vector& forces_on_main_group, + std::vector& forces_on_fitting_group) const { if (cvm::debug()) cvm::log("Calculating fit forces.\n"); - + auto accessor = [](const std::vector& v, size_t i){return v[i];}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - return calc_fit_forces_impl(forces_on_main_group); + calc_fit_forces_impl( + forces_on_main_group, forces_on_fitting_group, accessor); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - return calc_fit_forces_impl(forces_on_main_group); + calc_fit_forces_impl( + forces_on_main_group, forces_on_fitting_group, accessor); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - return calc_fit_forces_impl(forces_on_main_group); + calc_fit_forces_impl( + forces_on_main_group, forces_on_fitting_group, accessor); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - return calc_fit_forces_impl(forces_on_main_group); + calc_fit_forces_impl( + forces_on_main_group, forces_on_fitting_group, accessor); if (cvm::debug()) cvm::log("Done calculating fit forces.\n"); diff --git a/src/colvaratoms.h b/src/colvaratoms.h index 613a36164..1dced9a86 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -497,7 +497,9 @@ class colvarmodule::atom_group /// \brief Calculate the derivatives of the fitting transformation void calc_fit_gradients(); - std::vector calc_fit_forces(const std::vector& forces_on_main_group) const; + std::vector calc_fit_forces( + const std::vector& forces_on_main_group, + std::vector& forces_on_fitting_group) const; /*! @brief Actual implementation of `calc_fit_gradients`. The template is * used to avoid branching inside the loops in case that the CPU @@ -507,9 +509,15 @@ class colvarmodule::atom_group * @tparam B_ag_rotate Calculate the optimal rotation? This should follow * the value of `is_enabled(f_ag_rotate)`. */ - template void calc_fit_gradients_impl(); - - template std::vector calc_fit_forces_impl(const std::vector& forces_on_main_group) const; + // template void calc_fit_gradients_impl(); + + template + void calc_fit_forces_impl( + const main_force_container_T& forces_on_main_group, + std::vector& forces_on_fitting_group, + main_force_accessor_T accessor) const; /// \brief Derivatives of the fitting transformation std::vector fit_gradients; diff --git a/src/colvarcomp.h b/src/colvarcomp.h index 334fdc1f6..b740ff28a 100644 --- a/src/colvarcomp.h +++ b/src/colvarcomp.h @@ -1008,6 +1008,11 @@ class colvar::orientation struct rotation_derivative_impl_; std::unique_ptr rot_deriv_impl; + bool atom_rotated; + cvm::atom_group *group_for_fit; + std::vector main_group_forces; + std::vector fitting_group_forces; + public: orientation(); diff --git a/src/colvarcomp_rotations.cpp b/src/colvarcomp_rotations.cpp index f9c265808..9776b7f7b 100644 --- a/src/colvarcomp_rotations.cpp +++ b/src/colvarcomp_rotations.cpp @@ -22,7 +22,8 @@ struct colvar::orientation::rotation_derivative_impl_: public rotation_derivativ }; -colvar::orientation::orientation() +colvar::orientation::orientation(): + atom_rotated(false), group_for_fit(nullptr) { set_function_type("orientation"); rot_deriv_impl = std::unique_ptr(new rotation_derivative_impl_(this)); @@ -43,6 +44,12 @@ int colvar::orientation::init(std::string const &conf) return error_code | COLVARS_INPUT_ERROR; } ref_pos.reserve(atoms->size()); + main_group_forces.resize(atoms->size()); + atom_rotated = atoms->is_enabled(f_ag_rotate); + if (atom_rotated) { + group_for_fit = atoms->fitting_group ? atoms->fitting_group : atoms; + fitting_group_forces.resize(group_for_fit->size()); + } if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) { cvm::log("Using reference positions from input file.\n"); @@ -137,30 +144,44 @@ void colvar::orientation::apply_force(colvarvalue const &force) if (!atoms->noforce) { rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq); cvm::vector1d dq0_2; - std::vector main_group_forces; - const bool force_on_fitting_group = atoms->fitting_group == nullptr ? false : true; cvm::rmatrix ag_rot; - if (force_on_fitting_group) { + if (atom_rotated) { ag_rot = atoms->rot.inverse().matrix(); } + if (cvm::debug()) { + cvm::log("Force on main group:\n"); + } for (size_t ia = 0; ia < atoms->size(); ia++) { rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); const auto f_ia = FQ[0] * dq0_2[0] + FQ[1] * dq0_2[1] + FQ[2] * dq0_2[2] + FQ[3] * dq0_2[3]; - if (force_on_fitting_group) { - main_group_forces.push_back(f_ia); + if (atom_rotated) { + main_group_forces[ia] = f_ia; (*atoms)[ia].apply_force(ag_rot * f_ia); + if (cvm::debug()) { + cvm::log(cvm::to_str(ag_rot * f_ia)); + } } else { (*atoms)[ia].apply_force(f_ia); + if (cvm::debug()) { + cvm::log(cvm::to_str(f_ia)); + } } } - if (force_on_fitting_group) { - const std::vector fitting_group_forces = atoms->calc_fit_forces(main_group_forces); - if (fitting_group_forces.empty()) return; - for (size_t ia = 0; ia < atoms->fitting_group->size(); ia++) { - (*(atoms->fitting_group))[ia].apply_force(fitting_group_forces[ia]); + if (atom_rotated) { + atoms->calc_fit_forces(main_group_forces, fitting_group_forces); + if (cvm::debug()) { + cvm::log("Force on fitting group:\n"); + } + for (size_t ia = 0; ia < group_for_fit->size(); ia++) { + (*(group_for_fit))[ia].apply_force(fitting_group_forces[ia]); + if (cvm::debug()) { + cvm::log(cvm::to_str(fitting_group_forces[ia])); + } + // Clear the fitting group force + fitting_group_forces[ia] = 0; } } } From f513577b42d5b2e42cc742519f41132f80553b30 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Thu, 12 Sep 2024 14:48:49 -0500 Subject: [PATCH 03/14] fix: calculate the fit forces in cvm::atom_group::apply_force --- src/colvaratoms.cpp | 30 ++++++++++++++++++++++++++---- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 5ea1bb3d9..0f07c5045 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1242,7 +1242,7 @@ void cvm::atom_group::calc_fit_forces_impl( main_force_accessor_T accessor) const { const cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; if (forces_on_fitting_group.size() != group_for_fit->size()) { - forces_on_fitting_group.resize(group_for_fit->size()); + forces_on_fitting_group.assign(group_for_fit->size(), 0); } // the center of geometry contribution to the gradients cvm::rvector atom_grad; @@ -1488,12 +1488,34 @@ void cvm::atom_group::apply_force(cvm::rvector const &force) } if (is_enabled(f_ag_rotate)) { - + // TODO: What is the best way to avoid repeating the allocation?? + std::vector forces_on_main_group; const auto rot_inv = rot.inverse().matrix(); + if (cvm::debug()) { + cvm::log("Force on main group:\n"); + } for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->apply_force(rot_inv * ((ai->mass/total_mass) * force)); + const auto f = (ai->mass/total_mass) * force; + ai->apply_force(rot_inv * f); + if (cvm::debug()) { + cvm::log(cvm::to_str(rot_inv * f)); + } + forces_on_main_group.push_back(f); + } + if (cvm::debug()) { + cvm::log("Force on fitting group:\n"); + } + std::vector forces_on_fitting_group; + calc_fit_forces(forces_on_main_group, forces_on_fitting_group); + atom_group *group_for_fit = fitting_group ? fitting_group : this; + if (forces_on_fitting_group.size() == group_for_fit->size()) { + for (size_t j = 0; j < group_for_fit->size(); j++) { + (*group_for_fit)[j].apply_force(forces_on_fitting_group[j]); + if (cvm::debug()) { + cvm::log(cvm::to_str(forces_on_fitting_group[j])); + } + } } - } else { for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { From 842df8a68e019955b253607afe15f81ac3167b6b Mon Sep 17 00:00:00 2001 From: HanatoK Date: Thu, 12 Sep 2024 17:20:29 -0500 Subject: [PATCH 04/14] refactor: simplify the template and function parameters of calc_fit_forces_impl --- src/colvaratoms.cpp | 30 ++++++++++++------------------ src/colvaratoms.h | 2 -- 2 files changed, 12 insertions(+), 20 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 0f07c5045..1feadd1fc 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1218,15 +1218,15 @@ void cvm::atom_group::calc_fit_gradients() cvm::log("Calculating fit gradients.\n"); cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - auto accessor = [](const std::vector& v, size_t i){return v[i].grad;}; + auto accessor = [this](size_t i){return atoms[i].grad;}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl(atoms, group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); if (cvm::debug()) cvm::log("Done calculating fit gradients.\n"); @@ -1234,10 +1234,8 @@ void cvm::atom_group::calc_fit_gradients() template void cvm::atom_group::calc_fit_forces_impl( - const main_force_container_T& forces_on_main_group, std::vector& forces_on_fitting_group, main_force_accessor_T accessor) const { const cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; @@ -1255,7 +1253,7 @@ void cvm::atom_group::calc_fit_forces_impl( for (size_t i = 0; i < size(); i++) { cvm::atom_pos pos_orig; if (B_ag_center) { - atom_grad += accessor(forces_on_main_group, i); + atom_grad += accessor(i); if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); } else { if (B_ag_rotate) pos_orig = atoms[i].pos; @@ -1263,7 +1261,7 @@ void cvm::atom_group::calc_fit_forces_impl( if (B_ag_rotate) { // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i cvm::quaternion const dxdq = - rot.q.position_derivative_inner(pos_orig, accessor(forces_on_main_group, i)); + rot.q.position_derivative_inner(pos_orig, accessor(i)); sum_dxdq[0] += dxdq[0]; sum_dxdq[1] += dxdq[1]; sum_dxdq[2] += dxdq[2]; @@ -1297,19 +1295,15 @@ std::vector cvm::atom_group::calc_fit_forces( std::vector& forces_on_fitting_group) const { if (cvm::debug()) cvm::log("Calculating fit forces.\n"); - auto accessor = [](const std::vector& v, size_t i){return v[i];}; + auto accessor = [&forces_on_main_group](size_t i){return forces_on_main_group[i];}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl( - forces_on_main_group, forces_on_fitting_group, accessor); + calc_fit_forces_impl(forces_on_fitting_group, accessor); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl( - forces_on_main_group, forces_on_fitting_group, accessor); + calc_fit_forces_impl(forces_on_fitting_group, accessor); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl( - forces_on_main_group, forces_on_fitting_group, accessor); + calc_fit_forces_impl(forces_on_fitting_group, accessor); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl( - forces_on_main_group, forces_on_fitting_group, accessor); + calc_fit_forces_impl(forces_on_fitting_group, accessor); if (cvm::debug()) cvm::log("Done calculating fit forces.\n"); diff --git a/src/colvaratoms.h b/src/colvaratoms.h index 1dced9a86..2dbe66305 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -512,10 +512,8 @@ class colvarmodule::atom_group // template void calc_fit_gradients_impl(); template void calc_fit_forces_impl( - const main_force_container_T& forces_on_main_group, std::vector& forces_on_fitting_group, main_force_accessor_T accessor) const; From 87e5081786e0b9083b93a16be7a9abd9ee32b7e7 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 13 Sep 2024 10:05:54 -0500 Subject: [PATCH 05/14] refactor: unify the exertion of fitting group forces This commit introduces the group_force_object that unifies the exertion of atomic forces in an atom group. If a colvarcomp requires to apply forces individually on atoms in an atom group, now it can do ``` auto ag_force = atoms->get_group_force_object(); for (size_t ia = 0; ia < atoms->size(); ia++) { const f_ia = ...; ag_force.set_atom_force(ia, f_ia); } ``` If the optimal fitting is enabled for the atom group, group_force_object will "intercept" the forces applied to the main group, and then calculate the forces required on the fitting group by calling calc_fit_forces internally, and then apply the forces on destruction. --- src/colvaratoms.cpp | 92 ++++++++++++++++++++++++------------ src/colvaratoms.h | 19 +++++++- src/colvarcomp.h | 5 -- src/colvarcomp_distances.cpp | 3 +- src/colvarcomp_rotations.cpp | 44 ++--------------- 5 files changed, 84 insertions(+), 79 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 1feadd1fc..78d3047cb 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1290,7 +1290,7 @@ void cvm::atom_group::calc_fit_forces_impl( } -std::vector cvm::atom_group::calc_fit_forces( +void cvm::atom_group::calc_fit_forces( const std::vector& forces_on_main_group, std::vector& forces_on_fitting_group) const { if (cvm::debug()) @@ -1307,7 +1307,6 @@ std::vector cvm::atom_group::calc_fit_forces( if (cvm::debug()) cvm::log("Done calculating fit forces.\n"); - return std::vector(); } @@ -1481,39 +1480,70 @@ void cvm::atom_group::apply_force(cvm::rvector const &force) return; } - if (is_enabled(f_ag_rotate)) { - // TODO: What is the best way to avoid repeating the allocation?? - std::vector forces_on_main_group; - const auto rot_inv = rot.inverse().matrix(); - if (cvm::debug()) { - cvm::log("Force on main group:\n"); - } - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - const auto f = (ai->mass/total_mass) * force; - ai->apply_force(rot_inv * f); - if (cvm::debug()) { - cvm::log(cvm::to_str(rot_inv * f)); - } - forces_on_main_group.push_back(f); - } - if (cvm::debug()) { - cvm::log("Force on fitting group:\n"); + auto ag_force = get_group_force_object(); + for (size_t i = 0; i < size(); ++i) { + ag_force.set_atom_force(i, atoms[i].mass / total_mass * force); + } +} + +cvm::atom_group::group_force_object cvm::atom_group::get_group_force_object() { + return cvm::atom_group::group_force_object(this); +} + +cvm::atom_group::group_force_object::group_force_object(cvm::atom_group* ag): +m_ag(ag), m_group_for_fit(m_ag->fitting_group ? m_ag->fitting_group : m_ag), +m_has_fitting_force(m_ag->is_enabled(f_ag_center) || m_ag->is_enabled(f_ag_rotate)) { + if (m_has_fitting_force) { + if (m_ag->group_forces.size() != m_ag->size()) { + m_ag->group_forces.assign(m_ag->size(), 0); + } else { + std::fill(m_ag->group_forces.begin(), + m_ag->group_forces.end(), 0); } - std::vector forces_on_fitting_group; - calc_fit_forces(forces_on_main_group, forces_on_fitting_group); - atom_group *group_for_fit = fitting_group ? fitting_group : this; - if (forces_on_fitting_group.size() == group_for_fit->size()) { - for (size_t j = 0; j < group_for_fit->size(); j++) { - (*group_for_fit)[j].apply_force(forces_on_fitting_group[j]); - if (cvm::debug()) { - cvm::log(cvm::to_str(forces_on_fitting_group[j])); - } - } + if (m_ag->fitting_group_forces.size() != m_group_for_fit->size()) { + m_ag->fitting_group_forces.assign(m_group_for_fit->size(), 0); + } else { + std::fill(m_ag->fitting_group_forces.begin(), + m_ag->fitting_group_forces.end(), 0); } + } +} + +cvm::atom_group::group_force_object::~group_force_object() { + if (m_has_fitting_force) { + apply_force_with_fitting_group(); + } +} + +void cvm::atom_group::group_force_object::set_atom_force(size_t i, const cvm::rvector& force) { + if (m_has_fitting_force) { + m_ag->group_forces[i] = force; } else { + // Apply the force directly if we don't use fitting + (*m_ag)[i].apply_force(force); + } +} - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->apply_force((ai->mass/total_mass) * force); +void cvm::atom_group::group_force_object::apply_force_with_fitting_group() { + m_ag->calc_fit_forces(m_ag->group_forces, m_ag->fitting_group_forces); + const cvm::rmatrix rot_inv = m_ag->rot.inverse().matrix(); + if (cvm::debug()) { + cvm::log("Applying force on main group " + m_ag->name + ":\n"); + } + for (size_t ia = 0; ia < m_ag->size(); ++ia) { + const cvm::rvector f_ia = rot_inv * m_ag->group_forces[ia]; + (*m_ag)[ia].apply_force(f_ia); + if (cvm::debug()) { + cvm::log(cvm::to_str(f_ia)); + } + } + if (cvm::debug()) { + cvm::log("Applying force on the fitting group of main group" + m_ag->name + ":\n"); + } + for (size_t ia = 0; ia < m_group_for_fit->size(); ia++) { + (*(m_group_for_fit))[ia].apply_force(m_ag->fitting_group_forces[ia]); + if (cvm::debug()) { + cvm::log(cvm::to_str(m_ag->fitting_group_forces[ia])); } } } diff --git a/src/colvaratoms.h b/src/colvaratoms.h index 2dbe66305..bdc46cceb 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -257,8 +257,25 @@ class colvarmodule::atom_group /// \brief Index in the colvarproxy arrays (if the group is scalable) int index; + std::vector group_forces; + std::vector fitting_group_forces; + public: + class group_force_object { + public: + group_force_object(cvm::atom_group* ag); + ~group_force_object(); + void set_atom_force(size_t i, const cvm::rvector& force); + private: + cvm::atom_group* m_ag; + cvm::atom_group* m_group_for_fit; + bool m_has_fitting_force; + void apply_force_with_fitting_group(); + }; + + group_force_object get_group_force_object(); + inline cvm::atom & operator [] (size_t const i) { return atoms[i]; @@ -497,7 +514,7 @@ class colvarmodule::atom_group /// \brief Calculate the derivatives of the fitting transformation void calc_fit_gradients(); - std::vector calc_fit_forces( + void calc_fit_forces( const std::vector& forces_on_main_group, std::vector& forces_on_fitting_group) const; diff --git a/src/colvarcomp.h b/src/colvarcomp.h index b740ff28a..334fdc1f6 100644 --- a/src/colvarcomp.h +++ b/src/colvarcomp.h @@ -1008,11 +1008,6 @@ class colvar::orientation struct rotation_derivative_impl_; std::unique_ptr rot_deriv_impl; - bool atom_rotated; - cvm::atom_group *group_for_fit; - std::vector main_group_forces; - std::vector fitting_group_forces; - public: orientation(); diff --git a/src/colvarcomp_distances.cpp b/src/colvarcomp_distances.cpp index 6e97e276e..4245c3003 100644 --- a/src/colvarcomp_distances.cpp +++ b/src/colvarcomp_distances.cpp @@ -1401,11 +1401,12 @@ void colvar::cartesian::apply_force(colvarvalue const &force) size_t ia, j; if (!atoms->noforce) { cvm::rvector f; + auto ag_force = atoms->get_group_force_object(); for (ia = 0; ia < atoms->size(); ia++) { for (j = 0; j < dim; j++) { f[axes[j]] = force.vector1d_value[dim*ia + j]; } - (*atoms)[ia].apply_force(f); + ag_force.set_atom_force(ia, f); } } } diff --git a/src/colvarcomp_rotations.cpp b/src/colvarcomp_rotations.cpp index 9776b7f7b..7073b4230 100644 --- a/src/colvarcomp_rotations.cpp +++ b/src/colvarcomp_rotations.cpp @@ -22,8 +22,7 @@ struct colvar::orientation::rotation_derivative_impl_: public rotation_derivativ }; -colvar::orientation::orientation(): - atom_rotated(false), group_for_fit(nullptr) +colvar::orientation::orientation() { set_function_type("orientation"); rot_deriv_impl = std::unique_ptr(new rotation_derivative_impl_(this)); @@ -44,12 +43,6 @@ int colvar::orientation::init(std::string const &conf) return error_code | COLVARS_INPUT_ERROR; } ref_pos.reserve(atoms->size()); - main_group_forces.resize(atoms->size()); - atom_rotated = atoms->is_enabled(f_ag_rotate); - if (atom_rotated) { - group_for_fit = atoms->fitting_group ? atoms->fitting_group : atoms; - fitting_group_forces.resize(group_for_fit->size()); - } if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) { cvm::log("Using reference positions from input file.\n"); @@ -144,45 +137,14 @@ void colvar::orientation::apply_force(colvarvalue const &force) if (!atoms->noforce) { rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq); cvm::vector1d dq0_2; - cvm::rmatrix ag_rot; - if (atom_rotated) { - ag_rot = atoms->rot.inverse().matrix(); - } - if (cvm::debug()) { - cvm::log("Force on main group:\n"); - } + auto ag_force = atoms->get_group_force_object(); for (size_t ia = 0; ia < atoms->size(); ia++) { rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); const auto f_ia = FQ[0] * dq0_2[0] + FQ[1] * dq0_2[1] + FQ[2] * dq0_2[2] + FQ[3] * dq0_2[3]; - if (atom_rotated) { - main_group_forces[ia] = f_ia; - (*atoms)[ia].apply_force(ag_rot * f_ia); - if (cvm::debug()) { - cvm::log(cvm::to_str(ag_rot * f_ia)); - } - } else { - (*atoms)[ia].apply_force(f_ia); - if (cvm::debug()) { - cvm::log(cvm::to_str(f_ia)); - } - } - } - if (atom_rotated) { - atoms->calc_fit_forces(main_group_forces, fitting_group_forces); - if (cvm::debug()) { - cvm::log("Force on fitting group:\n"); - } - for (size_t ia = 0; ia < group_for_fit->size(); ia++) { - (*(group_for_fit))[ia].apply_force(fitting_group_forces[ia]); - if (cvm::debug()) { - cvm::log(cvm::to_str(fitting_group_forces[ia])); - } - // Clear the fitting group force - fitting_group_forces[ia] = 0; - } + ag_force.set_atom_force(ia, f_ia); } } } From dcf5a159275011397973a8571eee355e90673e1e Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 13 Sep 2024 10:26:28 -0500 Subject: [PATCH 06/14] fix: change the setting of force in group_force_object to accumulation This should better match what the existing apply_force does. --- src/colvaratoms.cpp | 6 +++--- src/colvaratoms.h | 2 +- src/colvarcomp_distances.cpp | 2 +- src/colvarcomp_rotations.cpp | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 78d3047cb..c0c2bba39 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1482,7 +1482,7 @@ void cvm::atom_group::apply_force(cvm::rvector const &force) auto ag_force = get_group_force_object(); for (size_t i = 0; i < size(); ++i) { - ag_force.set_atom_force(i, atoms[i].mass / total_mass * force); + ag_force.add_atom_force(i, atoms[i].mass / total_mass * force); } } @@ -1515,9 +1515,9 @@ cvm::atom_group::group_force_object::~group_force_object() { } } -void cvm::atom_group::group_force_object::set_atom_force(size_t i, const cvm::rvector& force) { +void cvm::atom_group::group_force_object::add_atom_force(size_t i, const cvm::rvector& force) { if (m_has_fitting_force) { - m_ag->group_forces[i] = force; + m_ag->group_forces[i] += force; } else { // Apply the force directly if we don't use fitting (*m_ag)[i].apply_force(force); diff --git a/src/colvaratoms.h b/src/colvaratoms.h index bdc46cceb..5c96b307e 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -266,7 +266,7 @@ class colvarmodule::atom_group public: group_force_object(cvm::atom_group* ag); ~group_force_object(); - void set_atom_force(size_t i, const cvm::rvector& force); + void add_atom_force(size_t i, const cvm::rvector& force); private: cvm::atom_group* m_ag; cvm::atom_group* m_group_for_fit; diff --git a/src/colvarcomp_distances.cpp b/src/colvarcomp_distances.cpp index 4245c3003..1c7267f1e 100644 --- a/src/colvarcomp_distances.cpp +++ b/src/colvarcomp_distances.cpp @@ -1406,7 +1406,7 @@ void colvar::cartesian::apply_force(colvarvalue const &force) for (j = 0; j < dim; j++) { f[axes[j]] = force.vector1d_value[dim*ia + j]; } - ag_force.set_atom_force(ia, f); + ag_force.add_atom_force(ia, f); } } } diff --git a/src/colvarcomp_rotations.cpp b/src/colvarcomp_rotations.cpp index 7073b4230..12dd90e33 100644 --- a/src/colvarcomp_rotations.cpp +++ b/src/colvarcomp_rotations.cpp @@ -144,7 +144,7 @@ void colvar::orientation::apply_force(colvarvalue const &force) FQ[1] * dq0_2[1] + FQ[2] * dq0_2[2] + FQ[3] * dq0_2[3]; - ag_force.set_atom_force(ia, f_ia); + ag_force.add_atom_force(ia, f_ia); } } } From b877ac708efca38892241d27597efaf23fe19783 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 13 Sep 2024 10:59:10 -0500 Subject: [PATCH 07/14] fix: check f_ag_fit_gradients when applying the force on the fitting group --- src/colvaratoms.cpp | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index c0c2bba39..e4a507ef5 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1525,7 +1525,6 @@ void cvm::atom_group::group_force_object::add_atom_force(size_t i, const cvm::rv } void cvm::atom_group::group_force_object::apply_force_with_fitting_group() { - m_ag->calc_fit_forces(m_ag->group_forces, m_ag->fitting_group_forces); const cvm::rmatrix rot_inv = m_ag->rot.inverse().matrix(); if (cvm::debug()) { cvm::log("Applying force on main group " + m_ag->name + ":\n"); @@ -1537,13 +1536,21 @@ void cvm::atom_group::group_force_object::apply_force_with_fitting_group() { cvm::log(cvm::to_str(f_ia)); } } - if (cvm::debug()) { - cvm::log("Applying force on the fitting group of main group" + m_ag->name + ":\n"); - } - for (size_t ia = 0; ia < m_group_for_fit->size(); ia++) { - (*(m_group_for_fit))[ia].apply_force(m_ag->fitting_group_forces[ia]); + // Gradients are only available with scalar components, so for a scalar component, + // if f_ag_fit_gradients is disabled, then the forces on the fitting group is not + // computed. For a vector component, we can only know the forces on the fitting + // group, but checking this flag can mimic results that the users expect (if + // "enableFitGradients no" then there is no force on the fitting group). + if (m_ag->is_enabled(f_ag_fit_gradients)) { + m_ag->calc_fit_forces(m_ag->group_forces, m_ag->fitting_group_forces); if (cvm::debug()) { - cvm::log(cvm::to_str(m_ag->fitting_group_forces[ia])); + cvm::log("Applying force on the fitting group of main group" + m_ag->name + ":\n"); + } + for (size_t ia = 0; ia < m_group_for_fit->size(); ia++) { + (*(m_group_for_fit))[ia].apply_force(m_ag->fitting_group_forces[ia]); + if (cvm::debug()) { + cvm::log(cvm::to_str(m_ag->fitting_group_forces[ia])); + } } } } From 544731c9d16a9ba75bedb5c9de417a847fb5f1c1 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 13 Sep 2024 11:22:53 -0500 Subject: [PATCH 08/14] tests: add tests for vector components with fitting forces --- .../AutoDiff/test.colvars.out | 6259 ++++++++++++++++ .../AutoDiff/test.colvars.state.stripped | 17 + .../AutoDiff/test.colvars.traj | 22 + .../AutoDiff/test.restart.colvars.out | 6309 +++++++++++++++++ .../test.restart.colvars.state.stripped | 17 + .../AutoDiff/test.restart.colvars.traj | 22 + .../namd-version.txt | 3 + .../test.in | 41 + .../AutoDiff/test.colvars.out | 4821 +++++++++++++ .../AutoDiff/test.colvars.state.stripped | 17 + .../AutoDiff/test.colvars.traj | 22 + .../AutoDiff/test.restart.colvars.out | 4871 +++++++++++++ .../test.restart.colvars.state.stripped | 17 + .../AutoDiff/test.restart.colvars.traj | 22 + .../namd-version.txt | 3 + .../test.in | 31 + 16 files changed, 22494 insertions(+) create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/namd-version.txt create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out new file mode 100644 index 000000000..315994e09 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out @@ -0,0 +1,6259 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Called colvarcript::init_commands() +colvars: Defined command "cv_addenergy", with help string: +colvars: Add an energy to the MD engine (no effect in VMD) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: E : float - Amount of energy to add +colvars: Defined command "cv_bias", with help string: +colvars: Prefix for bias-specific commands +colvars: Defined command "cv_colvar", with help string: +colvars: Prefix for colvar-specific commands +colvars: Defined command "cv_config", with help string: +colvars: Read configuration from the given string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf : string - Configuration string +colvars: Defined command "cv_configfile", with help string: +colvars: Read configuration from a file +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf_file : string - Path to configuration file +colvars: Defined command "cv_delete", with help string: +colvars: Delete this Colvars module instance (VMD only) +colvars: Defined command "cv_featurereport", with help string: +colvars: Return a summary of Colvars features used so far and their citations +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: report : string - Feature report and citations +colvars: +colvars: Defined command "cv_frame", with help string: +colvars: Get or set current frame number (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: frame : integer - Frame number (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: frame : integer - Frame number +colvars: +colvars: Defined command "cv_getatomappliedforces", with help string: +colvars: Get the list of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic forces +colvars: +colvars: Defined command "cv_getatomappliedforcesmax", with help string: +colvars: Get the maximum norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesmaxid", with help string: +colvars: Get the atom ID with the largest applied force +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: id : int - ID of the atom with the maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesrms", with help string: +colvars: Get the root-mean-square norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - RMS atomic force +colvars: +colvars: Defined command "cv_resetatomappliedforces", with help string: +colvars: Reset forces applied by Colvars to atoms +colvars: Defined command "cv_getatomids", with help string: +colvars: Get the list of indices of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "cv_getatomcharges", with help string: +colvars: Get the list of charges of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: charges : array of floats - Atomic charges +colvars: +colvars: Defined command "cv_getatommasses", with help string: +colvars: Get the list of masses of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: masses : array of floats - Atomic masses +colvars: +colvars: Defined command "cv_getatompositions", with help string: +colvars: Get the list of cached positions of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: positions : array of arrays of floats - Atomic positions +colvars: +colvars: Defined command "cv_getatomtotalforces", with help string: +colvars: Get the list of cached total forces of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic total foces +colvars: +colvars: Defined command "cv_getconfig", with help string: +colvars: Get the module's configuration string read so far +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "cv_getenergy", with help string: +colvars: Get the current Colvars energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Amount of energy (internal units) +colvars: +colvars: Defined command "cv_getnumactiveatomgroups", with help string: +colvars: Get the number of atom groups that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atom groups +colvars: +colvars: Defined command "cv_getnumactiveatoms", with help string: +colvars: Get the number of atoms that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getnumatoms", with help string: +colvars: Get the number of requested atoms, including those not in use now +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getstepabsolute", with help string: +colvars: Get the current step number of the simulation (including restarts) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Absolute step number +colvars: +colvars: Defined command "cv_getsteprelative", with help string: +colvars: Get the current step number from the start of this job +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Relative step number +colvars: +colvars: Defined command "cv_help", with help string: +colvars: Get the help string of the Colvars scripting interface +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "cv_languageversion", with help string: +colvars: Get the C++ language version number +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - C++ language version +colvars: +colvars: Defined command "cv_list", with help string: +colvars: Return a list of all variables or biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: param : string - "colvars" or "biases"; default is "colvars" (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of elements +colvars: +colvars: Defined command "cv_listcommands", with help string: +colvars: Get the list of script functions, prefixed with "cv_", "colvar_" or "bias_" +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of commands +colvars: +colvars: Defined command "cv_listindexfiles", with help string: +colvars: Get a list of the index files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of index file names +colvars: +colvars: Defined command "cv_listinputfiles", with help string: +colvars: Get a list of all input/configuration files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of file names +colvars: +colvars: Defined command "cv_load", with help string: +colvars: Load data from a state file into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Path to existing state file or input prefix +colvars: Defined command "cv_loadfromstring", with help string: +colvars: Load state data from a string into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "cv_molid", with help string: +colvars: Get or set the molecule ID on which Colvars is defined (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: molid : integer - New molecule ID; -1 means undefined (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: molid : integer - Current molecule ID +colvars: +colvars: Defined command "cv_printframe", with help string: +colvars: Return the values that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: values : string - The values +colvars: +colvars: Defined command "cv_printframelabels", with help string: +colvars: Return the labels that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Labels : string - The labels +colvars: +colvars: Defined command "cv_reset", with help string: +colvars: Delete all internal configuration +colvars: Defined command "cv_resetindexgroups", with help string: +colvars: Clear the index groups loaded so far, allowing to replace them +colvars: Defined command "cv_save", with help string: +colvars: Change the prefix of all output files and save them +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Output prefix with trailing ".colvars.state" gets removed) +colvars: Defined command "cv_savetostring", with help string: +colvars: Write the Colvars state to a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The saved state +colvars: +colvars: Defined command "cv_targettemperature", with help string: +colvars: Get/set target temperature, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: T : float - New target temperature in K (internal use) (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: T : float - Current target temperature in K +colvars: +colvars: Defined command "cv_timestep", with help string: +colvars: Get/set integration timestep, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: dt : float - New integration timestep in MD engine units (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: dt : float - Current integration timestep in MD engine units +colvars: +colvars: Defined command "cv_units", with help string: +colvars: Get or set the current Colvars unit system +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: units : string - The new unit system (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: units : string - The current unit system +colvars: +colvars: Defined command "cv_update", with help string: +colvars: Recalculate colvars and biases +colvars: Defined command "cv_version", with help string: +colvars: Get the Colvars Module version string +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - Colvars version +colvars: +colvars: Defined command "colvar_addforce", with help string: +colvars: Apply the given force onto this colvar (no effects outside run) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: force : float or array - Applied force; must match colvar dimensionality +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float or array - Applied force; matches colvar dimensionality +colvars: +colvars: Defined command "colvar_communicateforces", with help string: +colvars: Communicate bias forces from this colvar to atoms +colvars: Defined command "colvar_cvcflags", with help string: +colvars: Enable or disable individual components by setting their active flags +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: flags : integer array - Zero/nonzero value disables/enables the CVC +colvars: Defined command "colvar_delete", with help string: +colvars: Delete this colvar, along with all biases that depend on it +colvars: Defined command "colvar_get", with help string: +colvars: Get the value of the given feature for this colvar +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "colvar_getappliedforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Applied force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_resetbiasforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: Defined command "colvar_getatomgroups", with help string: +colvars: Return the atom indices used by this colvar as a list of lists +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: groups : array of arrays of ints - Atom indices +colvars: +colvars: Defined command "colvar_getatomids", with help string: +colvars: Return the list of atom indices used by this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "colvar_getconfig", with help string: +colvars: Return the configuration string of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "colvar_getgradients", with help string: +colvars: Return the atomic gradients of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: gradients : array of arrays of floats - Atomic gradients +colvars: +colvars: Defined command "colvar_gettotalforce", with help string: +colvars: Return the sum of internal and external forces to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Total force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_getvolmapids", with help string: +colvars: Return the list of volumetric map indices used by this colvar +colvars: Defined command "colvar_help", with help string: +colvars: Get a help summary or the help string of one colvar subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "colvar_modifycvcs", with help string: +colvars: Modify configuration of individual components by passing string arguments +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: confs : sequence of strings - New configurations; empty strings are skipped +colvars: Defined command "colvar_run_ave", with help string: +colvars: Get the current running average of the value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Averaged value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_set", with help string: +colvars: Set the given feature of this colvar to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "colvar_state", with help string: +colvars: Print a string representation of the feature state of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The feature state +colvars: +colvars: Defined command "colvar_type", with help string: +colvars: Get the type description of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type description +colvars: +colvars: Defined command "colvar_update", with help string: +colvars: Recompute this colvar and return its up-to-date value +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_value", with help string: +colvars: Get the current value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_width", with help string: +colvars: Get the width of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: width : float - Value of the width +colvars: +colvars: Defined command "bias_bin", with help string: +colvars: Get the current grid bin index (flattened if more than 1d) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: bin : integer - Bin index +colvars: +colvars: Defined command "bias_bincount", with help string: +colvars: Get the number of samples at the given grid bin (1D ABF only for now) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: index : integer - Grid index; defaults to current bin (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: samples : integer - Number of samples +colvars: +colvars: Defined command "bias_local_sample_count", with help string: +colvars: Get the number of samples around the current binsamples : integer - Number of samples +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: radius : integer - Sum over radius bins around current bin (optional) +colvars: Defined command "bias_binnum", with help string: +colvars: Get the total number of grid points of this bias (1D ABF only for now) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Bins : integer - Number of grid points +colvars: +colvars: Defined command "bias_delete", with help string: +colvars: Delete this bias +colvars: Defined command "bias_energy", with help string: +colvars: Get the current energy of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Defined command "bias_get", with help string: +colvars: Get the value of the given feature for this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "bias_getconfig", with help string: +colvars: Return the configuration string of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "bias_help", with help string: +colvars: Get a help summary or the help string of one bias subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "bias_load", with help string: +colvars: Load data into this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Read from a file with this name or prefix +colvars: Defined command "bias_loadfromstring", with help string: +colvars: Load state data into this bias from a string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "bias_save", with help string: +colvars: Save data from this bias into a file with the given prefix +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Prefix for the state file of this bias +colvars: Defined command "bias_savetostring", with help string: +colvars: Save data from this bias into a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The bias state +colvars: +colvars: Defined command "bias_set", with help string: +colvars: Set the given feature of this bias to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "bias_share", with help string: +colvars: Share bias information with other replicas (multiple-walker scheme) +colvars: Defined command "bias_state", with help string: +colvars: Print a string representation of the feature state of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - String representation of the bias features +colvars: +colvars: Defined command "bias_type", with help string: +colvars: Print the type of this bias object +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type of this bias object (e.g. metadynamics) +colvars: +colvars: Defined command "bias_update", with help string: +colvars: Recompute this bias and return its up-to-date energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Called script run with 3 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: configfile +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: test.in +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: Executing script function "cv_configfile" +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: Looking for the keyword "logLevel" and its value. +colvars: Keyword "logLevel" not found. +colvars: Looking for the keyword "units" and its value. +colvars: Keyword "units" not found. +colvars: # units = "" [default] +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword value = "index.ndx". +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword "indexFile" not found. +colvars: Looking for the keyword "smp" and its value. +colvars: Keyword "smp" not found. +colvars: # smp = on [default] +colvars: Looking for the keyword "analysis" and its value. +colvars: Keyword "analysis" not found. +colvars: Looking for the keyword "debugGradientsStepSize" and its value. +colvars: Keyword "debugGradientsStepSize" not found. +colvars: Looking for the keyword "monitorEigenvalueCrossing" and its value. +colvars: Keyword "monitorEigenvalueCrossing" not found. +colvars: Looking for the keyword "eigenvalueCrossingThreshold" and its value. +colvars: Keyword "eigenvalueCrossingThreshold" not found. +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword value = "1". +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword "colvarsTrajFrequency" not found. +colvars: # colvarsTrajFrequency = 1 +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword value = "10". +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword "colvarsRestartFrequency" not found. +colvars: # colvarsRestartFrequency = 10 +colvars: Looking for the keyword "scriptedColvarForces" and its value. +colvars: Keyword "scriptedColvarForces" not found. +colvars: # scriptedColvarForces = off [default] +colvars: Looking for the keyword "scriptingAfterBiases" and its value. +colvars: Keyword "scriptingAfterBiases" not found. +colvars: # scriptingAfterBiases = off [default] +colvars: Looking for the keyword "sourceTclFile" and its value. +colvars: Keyword "sourceTclFile" not found. +colvars: # sourceTclFile = "" [default] +colvars: Initializing the collective variables. +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "one" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword value = " +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Initializing a new "distanceDir" component, with configuration: +colvars: +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: unnamed cvc of type "distance" enabling "defined_lower_boundary" +colvars: DEPS: feature "defined_lower_boundary" in unnamed cvc of type "distance" enabled, ref_count = 1. +colvars: DEPS: unnamed cvc of type "distance" enabling "function_of_centers_of_mass" +colvars: DEPS: feature "function_of_centers_of_mass" in unnamed cvc of type "distance" enabled, ref_count = 1. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "function_of_centers_of_mass" +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "distanceDir" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "group1" and its value. +colvars: Keyword value = " +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" +colvars: scalable_calculation_of_centers_of_mass requires exclude explicit_gradient +colvars: scalable_calculation_of_centers_of_mass requires self scalable_calculation +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation" +colvars: scalable_calculation requires exclude explicit_gradient +colvars: DEPS: feature "scalable_calculation" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. +colvars: scalable_calculation_of_centers_of_mass requires self function_of_centers_of_mass +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "function_of_centers_of_mass" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "scalable_calculation_of_centers_of_mass" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. +colvars: Initializing atom group "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group group1 +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group group1 +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = on +colvars: DEPS: atom group group1 enabling "center_to_reference" +colvars: DEPS: feature "center_to_reference" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group group1 +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = on +colvars: DEPS: atom group group1 enabling "rotate_to_origin" +colvars: DEPS: feature "rotate_to_origin" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group1" +colvars: Adding atom 1 for collective variables calculation. +colvars: Adding atom 4 for collective variables calculation. +colvars: Adding atom 10 for collective variables calculation. +colvars: Adding atom 11 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "refPositionsGroup" and its value. +colvars: Keyword "refPositionsGroup" not found. +colvars: Looking for the keyword "fittingGroup" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Within atom group "group1": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Adding atom 6 for collective variables calculation. +colvars: Adding atom 12 for collective variables calculation. +colvars: Adding atom 14 for collective variables calculation. +colvars: Adding atom 16 for collective variables calculation. +colvars: Adding atom 20 for collective variables calculation. +colvars: Adding atom 21 for collective variables calculation. +colvars: Adding atom 22 for collective variables calculation. +colvars: Adding atom 24 for collective variables calculation. +colvars: Adding atom 26 for collective variables calculation. +colvars: Adding atom 30 for collective variables calculation. +colvars: Adding atom 31 for collective variables calculation. +colvars: Adding atom 32 for collective variables calculation. +colvars: Adding atom 34 for collective variables calculation. +colvars: Adding atom 36 for collective variables calculation. +colvars: Adding atom 40 for collective variables calculation. +colvars: Adding atom 41 for collective variables calculation. +colvars: Adding atom 42 for collective variables calculation. +colvars: Adding atom 44 for collective variables calculation. +colvars: Adding atom 46 for collective variables calculation. +colvars: Adding atom 50 for collective variables calculation. +colvars: Adding atom 51 for collective variables calculation. +colvars: Adding atom 52 for collective variables calculation. +colvars: Adding atom 54 for collective variables calculation. +colvars: Adding atom 56 for collective variables calculation. +colvars: Adding atom 60 for collective variables calculation. +colvars: Adding atom 61 for collective variables calculation. +colvars: Adding atom 62 for collective variables calculation. +colvars: Adding atom 64 for collective variables calculation. +colvars: Adding atom 66 for collective variables calculation. +colvars: Adding atom 70 for collective variables calculation. +colvars: Adding atom 71 for collective variables calculation. +colvars: Adding atom 72 for collective variables calculation. +colvars: Adding atom 74 for collective variables calculation. +colvars: Adding atom 76 for collective variables calculation. +colvars: Adding atom 80 for collective variables calculation. +colvars: Adding atom 81 for collective variables calculation. +colvars: Adding atom 82 for collective variables calculation. +colvars: Adding atom 84 for collective variables calculation. +colvars: Adding atom 86 for collective variables calculation. +colvars: Adding atom 90 for collective variables calculation. +colvars: Adding atom 91 for collective variables calculation. +colvars: Adding atom 92 for collective variables calculation. +colvars: Adding atom 93 for collective variables calculation. +colvars: Adding atom 94 for collective variables calculation. +colvars: Adding atom 97 for collective variables calculation. +colvars: Adding atom 99 for collective variables calculation. +colvars: Adding atom 101 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group group1 enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. +colvars: Warning: atom group "group1" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group group1 enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group group1 enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group group1 enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "group1". +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. +colvars: Configuration string for "group1": " +colvars: +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "group2" and its value. +colvars: Keyword value = " +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" +colvars: Initializing atom group "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group group2 +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group group2 +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = on +colvars: DEPS: atom group group2 enabling "center_to_reference" +colvars: DEPS: feature "center_to_reference" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group group2 +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = on +colvars: DEPS: atom group group2 enabling "rotate_to_origin" +colvars: DEPS: feature "rotate_to_origin" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group2" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "refPositionsGroup" and its value. +colvars: Keyword "refPositionsGroup" not found. +colvars: Looking for the keyword "fittingGroup" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Within atom group "group2": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group group2 enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: atom group "group2" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group group2 enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group group2 enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group group2 enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "group2". +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" +colvars: Configuration string for "group2": " +colvars: +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "oneSiteSystemForce" and its value. +colvars: Keyword "oneSiteSystemForce" not found. +colvars: # oneSiteSystemForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Looking for the keyword "oneSiteTotalForce" and its value. +colvars: Keyword "oneSiteTotalForce" not found. +colvars: # oneSiteTotalForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Configuration string for "distanceDir": " +colvars: +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: Initializing the collective variables biases. +colvars: Looking for the keyword "abf" and its value. +colvars: Keyword "abf" not found. +colvars: Looking for the keyword "abmd" and its value. +colvars: Keyword "abmd" not found. +colvars: Looking for the keyword "ALB" and its value. +colvars: Keyword "ALB" not found. +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword value = " +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "harmonic1" [default] +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword "colvars" not found. +colvars: # colvars = { one } +colvars: Applying this bias to collective variable "one". +colvars: Looking for the keyword "stepZeroData" and its value. +colvars: Keyword "stepZeroData" not found. +colvars: # stepZeroData = off [default] +colvars: DEPS: disabling feature "step_zero_data" in bias harmonic1 +colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword "outputEnergy" not found. +colvars: # outputEnergy = off [default] +colvars: Looking for the keyword "outputFreq" and its value. +colvars: Keyword "outputFreq" not found. +colvars: # outputFreq = 10 [default] +colvars: Looking for the keyword "bypassExtendedLagrangian" and its value. +colvars: Keyword "bypassExtendedLagrangian" not found. +colvars: DEPS: disabling feature "bypass_extended_Lagrangian_coordinates" in bias harmonic1 +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "scaledBiasingForce" and its value. +colvars: Keyword "scaledBiasingForce" not found. +colvars: DEPS: disabling feature "scale_biasing_force" in bias harmonic1 +colvars: DEPS: bias harmonic1 enabling "active" +colvars: DEPS: colvar one testing "active" +colvars: DEPS: re-enabling children's active +colvars: DEPS: colvar one enabling "active" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in bias harmonic1 enabled, ref_count = 1. +colvars: Features of "bias harmonic1" (refcount) +colvars: - ON active +colvars: - awake +colvars: - step_zero_data +colvars: - apply_force +colvars: - bypass_extended_Lagrangian_coordinates +colvars: - obtain_total_force +colvars: - output_accumulated_work +colvars: - history_dependent +colvars: - time_dependent +colvars: - require_scalar_variables +colvars: - calculate_a_PMF +colvars: - calculate_TI_samples +colvars: - write_TI_samples_ +colvars: - write_TI_PMF +colvars: - scale_biasing_force +colvars: - Bias on extended-Lagrangian variables +colvars: * child 1 +colvars: Features of "colvar one" (refcount) +colvars: - ON active (1) +colvars: - awake +colvars: - gradient +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - total_force +colvars: - total_force_calculation +colvars: - subtract_applied_force_from_total_force +colvars: - Jacobian_derivative +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - output_total_force +colvars: - lower_boundary +colvars: - upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - scalar +colvars: - ON linear (1) +colvars: - ON homogeneous +colvars: - multiple_timestep +colvars: * child 1 +colvars: Features of "cvc "distanceDir0001" of type "distanceDir"" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - ON defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON explicit_atom_groups +colvars: - gradient +colvars: - explicit_gradient +colvars: - inverse_gradient +colvars: - Jacobian_derivative +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - ON function_of_centers_of_mass (1) +colvars: - ON scalable_calculation (1) +colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids +colvars: * child 1 +colvars: Features of "atom group group1" (refcount) +colvars: - active +colvars: - ON center_to_reference +colvars: - center_to_origin +colvars: - ON rotate_to_origin +colvars: - ON fitting_group +colvars: - ON explicit_atom_gradient (1) +colvars: - ON fit_gradients +colvars: - atomic_forces +colvars: - scalable_group +colvars: - scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: * child 2 +colvars: Features of "atom group group2" (refcount) +colvars: - active +colvars: - ON center_to_reference +colvars: - center_to_origin +colvars: - ON rotate_to_origin +colvars: - ON fitting_group +colvars: - ON explicit_atom_gradient (1) +colvars: - ON fit_gradients +colvars: - atomic_forces +colvars: - scalable_group +colvars: - scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: DEPS: bias harmonic1 enabling "apply_force" +colvars: DEPS: colvar one enabling "gradient" +colvars: DEPS: cvc "distanceDir0001" of type "distanceDir" enabling "gradient" +colvars: DEPS: feature "gradient" in cvc "distanceDir0001" of type "distanceDir" enabled, ref_count = 1. +colvars: DEPS: feature "gradient" in colvar one enabled, ref_count = 1. +colvars: DEPS: feature "apply_force" in bias harmonic1 enabled, ref_count = 1. +colvars: Looking for the keyword "writeTISamples" and its value. +colvars: Keyword "writeTISamples" not found. +colvars: # writeTISamples = off [default] +colvars: DEPS: disabling feature "write_TI_samples_" in bias harmonic1 +colvars: Looking for the keyword "writeTIPMF" and its value. +colvars: Keyword "writeTIPMF" not found. +colvars: # writeTIPMF = off [default] +colvars: DEPS: disabling feature "write_TI_PMF" in bias harmonic1 +colvars: Initializing a new restraint bias. +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword value = "(1.0, 0.1, 0.2)". +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword "centers" not found. +colvars: # centers = { ( 0.9759 , 0.09759 , 0.19518 ) } +colvars: colvarbias_restraint: parsing initial centers, i = 0. +colvars: colvarbias_restraint: parsing target centers. +colvars: Looking for the keyword "targetCenters" and its value. +colvars: Keyword "targetCenters" not found. +colvars: # targetCenters = { ( 0.9759 , 0.09759 , 0.19518 ) } [default] +colvars: Looking for the keyword "outputCenters" and its value. +colvars: Keyword "outputCenters" not found. +colvars: # outputCenters = off [default] +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword value = "10.0". +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword "forceConstant" not found. +colvars: # forceConstant = 10 +colvars: Looking for the keyword "decoupling" and its value. +colvars: Keyword "decoupling" not found. +colvars: # decoupling = off [default] +colvars: Looking for the keyword "targetForceConstant" and its value. +colvars: Keyword "targetForceConstant" not found. +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 40 according to the specified width (0.5). +colvars: Configuration string for "harmonic": " +colvars: +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: ". +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword "harmonic" not found. +colvars: Looking for the keyword "harmonicWalls" and its value. +colvars: Keyword "harmonicWalls" not found. +colvars: Looking for the keyword "histogram" and its value. +colvars: Keyword "histogram" not found. +colvars: Looking for the keyword "histogramRestraint" and its value. +colvars: Keyword "histogramRestraint" not found. +colvars: Looking for the keyword "linear" and its value. +colvars: Keyword "linear" not found. +colvars: Looking for the keyword "metadynamics" and its value. +colvars: Keyword "metadynamics" not found. +colvars: Looking for the keyword "reweightaMD" and its value. +colvars: Keyword "reweightaMD" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: Configuration string for "colvarmodule": " +colvars: colvarsTrajFrequency 1 +colvars: colvarsRestartFrequency 10 +colvars: indexFile index.ndx +colvars: colvar { +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 0 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 0, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 0, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 0, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 0, atoms_positions[size = 51] = { ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 ), ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 ), ( 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 ), ( 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ), ( 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 ), ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 ), ( 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 ), ( 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 ), ( 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 ), ( 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ), ( 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 ), ( 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 ), ( 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 ), ( 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 ), ( 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 ), ( 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 ), ( 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 ), ( 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 ), ( 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 ), ( 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 ), ( 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 ), ( 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 ), ( 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 ), ( 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 ), ( -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 ), ( 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 ), ( 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 ), ( 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 ), ( -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 ), ( -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 ), ( -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 ), ( -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 ), ( -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 ), ( -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 ), ( -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 ), ( -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 ), ( -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 ), ( -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 ), ( -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 ), ( -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 ), ( -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 ), ( -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 ), ( -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 ), ( -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 ), ( -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 ), ( -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 ), ( -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 ), ( -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 ), ( -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 ), ( -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ), ( -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) } +colvars: Step 0, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atom_groups_ids[size = 0] = +colvars: Step 0, atom_groups_refcount[size = 0] = +colvars: Step 0, atom_groups_masses[size = 0] = +colvars: Step 0, atom_groups_charges[size = 0] = +colvars: Step 0, atom_groups_coms[size = 0] = +colvars: Step 0, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 0, volmaps_ids[size = 0] = +colvars: Step 0, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 0 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.3141 , 1.79667 , -14.9057 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.3141 , 1.79667 , -14.9057 ) to colvar "one". +colvars: Adding total bias energy: 45.892 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.3141 , 1.79667 , -14.9057 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.83605 , -0.57345 , -1.60798 ) +colvars: ( -4.14691 , -0.491734 , -1.37884 ) +colvars: ( -4.14691 , -0.491734 , -1.37884 ) +colvars: ( -5.5238 , -0.655003 , -1.83666 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.904449 , 0.192195 , 0.652965 ) +colvars: ( 0.781455 , 0.264196 , 0.679172 ) +colvars: ( 0.767414 , 0.256567 , 0.660103 ) +colvars: ( 0.665192 , 0.266597 , 0.612546 ) +colvars: ( 0.652998 , 0.200174 , 0.512746 ) +colvars: ( 0.575103 , 0.345124 , 0.667639 ) +colvars: ( 0.463397 , 0.360776 , 0.622201 ) +colvars: ( 0.383597 , 0.459129 , 0.711085 ) +colvars: ( 0.380393 , 0.316766 , 0.510988 ) +colvars: ( 0.343708 , 0.275912 , 0.432042 ) +colvars: ( 0.352206 , 0.321644 , 0.500814 ) +colvars: ( 0.280154 , 0.279134 , 0.398279 ) +colvars: ( 0.254339 , 0.307672 , 0.422468 ) +colvars: ( 0.345014 , 0.180479 , 0.299985 ) +colvars: ( 0.284533 , 0.137844 , 0.204238 ) +colvars: ( 0.471912 , 0.141938 , 0.322704 ) +colvars: ( 0.547075 , 0.0496465 , 0.239467 ) +colvars: ( 0.681454 , 0.0269033 , 0.288679 ) +colvars: ( 0.553916 , 0.0184719 , 0.200189 ) +colvars: ( 0.53773 , -0.0463997 , 0.100148 ) +colvars: ( 0.573618 , 0.0668172 , 0.279343 ) +colvars: ( 0.56998 , 0.0514399 , 0.255748 ) +colvars: ( 0.605964 , 0.116347 , 0.367755 ) +colvars: ( 0.441227 , 0.0575265 , 0.186736 ) +colvars: ( 0.433486 , 0.00196018 , 0.10473 ) +colvars: ( 0.336494 , 0.12415 , 0.216447 ) +colvars: ( 0.207874 , 0.134227 , 0.15307 ) +colvars: ( 0.114014 , 0.220808 , 0.217104 ) +colvars: ( 0.180185 , 0.0603279 , 0.0335389 ) +colvars: ( 0.128667 , 0.0249964 , -0.0466463 ) +colvars: ( 0.216875 , 0.0336433 , 0.0184743 ) +colvars: ( 0.203893 , -0.0392063 , -0.0907449 ) +colvars: ( 0.242516 , -0.0437657 , -0.0738479 ) +colvars: ( 0.280911 , -0.125759 , -0.164876 ) +colvars: ( 0.235718 , -0.178415 , -0.265371 ) +colvars: ( 0.39894 , -0.141798 , -0.116172 ) +colvars: ( 0.478044 , -0.217851 , -0.174433 ) +colvars: ( 0.61295 , -0.221787 , -0.0987231 ) +colvars: ( 0.427261 , -0.221063 , -0.209465 ) +colvars: ( 0.432715 , -0.289069 , -0.300847 ) +colvars: ( 0.375506 , -0.146693 , -0.137089 ) +colvars: ( 0.317642 , -0.139121 , -0.161371 ) +colvars: ( 0.299087 , -0.0517292 , -0.0508885 ) +colvars: ( 0.190821 , -0.146631 , -0.248146 ) +colvars: ( 0.164689 , -0.187988 , -0.321443 ) +colvars: ( -0.0132844 , -0.191347 , -0.433224 ) +colvars: ( -0.106835 , -0.20819 , -0.512969 ) +colvars: ( 0.0914093 , -0.242821 , -0.441871 ) +colvars: ( 0.107821 , -0.105612 , -0.240998 ) +colvars: ( -0.0147712 , -0.108801 , -0.319215 ) +colvars: ( -0.105785 , -0.0274413 , -0.260735 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.83605 , 0.57345 , 1.60798 ) +colvars: ( 4.14691 , 0.491734 , 1.37884 ) +colvars: ( 4.14691 , 0.491734 , 1.37884 ) +colvars: ( 5.5238 , 0.655003 , 1.83666 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.628624 , -0.0803095 , -0.404496 ) +colvars: ( -0.562979 , -0.162306 , -0.377749 ) +colvars: ( -0.517226 , -0.140683 , -0.3212 ) +colvars: ( -0.5184 , -0.190034 , -0.346132 ) +colvars: ( -0.50878 , -0.132262 , -0.30863 ) +colvars: ( -0.488908 , -0.281012 , -0.360168 ) +colvars: ( -0.450514 , -0.321339 , -0.340852 ) +colvars: ( -0.424599 , -0.427271 , -0.36569 ) +colvars: ( -0.387357 , -0.287046 , -0.260655 ) +colvars: ( -0.380307 , -0.262436 , -0.241701 ) +colvars: ( -0.340884 , -0.281609 , -0.211169 ) +colvars: ( -0.280874 , -0.245749 , -0.133392 ) +colvars: ( -0.235212 , -0.260495 , -0.094436 ) +colvars: ( -0.3036 , -0.143978 , -0.107338 ) +colvars: ( -0.270682 , -0.115574 , -0.0604717 ) +colvars: ( -0.362639 , -0.0868482 , -0.13939 ) +colvars: ( -0.392639 , 0.0101283 , -0.12298 ) +colvars: ( -0.448566 , 0.0577244 , -0.156481 ) +colvars: ( -0.426859 , 0.0248658 , -0.1504 ) +colvars: ( -0.415349 , 0.0805584 , -0.111992 ) +colvars: ( -0.467947 , -0.0281639 , -0.217356 ) +colvars: ( -0.49836 , -0.0296841 , -0.24876 ) +colvars: ( -0.546 , -0.0937884 , -0.327654 ) +colvars: ( -0.441259 , -0.0599455 , -0.205735 ) +colvars: ( -0.446751 , -0.0166987 , -0.190462 ) +colvars: ( -0.383423 , -0.133561 , -0.18283 ) +colvars: ( -0.321416 , -0.165078 , -0.13546 ) +colvars: ( -0.268688 , -0.25422 , -0.125177 ) +colvars: ( -0.282277 , -0.0936367 , -0.0616093 ) +colvars: ( -0.266256 , -0.0756726 , -0.0368075 ) +colvars: ( -0.267497 , -0.0492663 , -0.0253521 ) +colvars: ( -0.234777 , 0.0241484 , 0.042974 ) +colvars: ( -0.218877 , 0.0503727 , 0.0716291 ) +colvars: ( -0.280428 , 0.109829 , 0.0381639 ) +colvars: ( -0.2529 , 0.150602 , 0.0855471 ) +colvars: ( -0.352048 , 0.138136 , -0.0204457 ) +colvars: ( -0.402129 , 0.213447 , -0.034713 ) +colvars: ( -0.476749 , 0.236408 , -0.0989201 ) +colvars: ( -0.408333 , 0.193606 , -0.0505178 ) +colvars: ( -0.412792 , 0.253389 , -0.026247 ) +colvars: ( -0.408149 , 0.108199 , -0.0914308 ) +colvars: ( -0.409781 , 0.0781684 , -0.107528 ) +colvars: ( -0.427537 , -0.013667 , -0.169626 ) +colvars: ( -0.339772 , 0.0663524 , -0.0426067 ) +colvars: ( -0.340591 , 0.0920225 , -0.0310805 ) +colvars: ( -0.179083 , 0.0973929 , 0.134389 ) +colvars: ( -0.127239 , 0.098679 , 0.187293 ) +colvars: ( -0.211393 , 0.169106 , 0.136312 ) +colvars: ( -0.277077 , 0.025872 , 0.00114273 ) +colvars: ( -0.207386 , 0.0117805 , 0.064647 ) +colvars: ( -0.151761 , -0.0703734 , 0.0812133 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 0. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 0. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atoms_new_colvar_forces = { ( -4.56022301351998e+00 , -4.61564888436068e-01 , -1.35951177988766e+00 ), ( -3.92843445711296e+00 , -3.89843112362469e-01 , -1.07742000515632e+00 ), ( -4.00011804015036e+00 , -4.15171281383325e-01 , -1.11243026024849e+00 ), ( -5.37958662474869e+00 , -5.87092156407929e-01 , -1.63254351293296e+00 ), ( 2.50188227787937e-01 , 1.15884548440611e-01 , 3.38902821897569e-01 ), ( 4.92224252104192e+00 , 6.37562353004536e-01 , 1.91545290434692e+00 ), ( 4.15979249713217e+00 , 5.31170028110173e-01 , 1.66019271046701e+00 ), ( -4.10013245486699e-02 , 3.18580111145642e-02 , 3.45394759111406e-01 ), ( 4.13994655920834e+00 , 5.21453476411363e-01 , 1.62917699767166e+00 ), ( 5.48720654003203e+00 , 6.68479365021477e-01 , 2.02700010370679e+00 ), ( 1.13228880308536e-02 , 4.00342907390078e-02 , 2.89645605122908e-01 ), ( -7.20125311565400e-04 , 3.33850914918679e-02 , 2.64887654827042e-01 ), ( 1.91272371136485e-02 , 4.71768859623820e-02 , 3.28032369661851e-01 ), ( 4.14145638066024e-02 , 3.65005871821940e-02 , 1.92646338795725e-01 ), ( 1.38509087206640e-02 , 2.22695518224478e-02 , 1.43766826482371e-01 ), ( 1.09272369395027e-01 , 5.50900822328472e-02 , 1.83313711879413e-01 ), ( 1.54435579943054e-01 , 5.97748101103748e-02 , 1.16487245422154e-01 ), ( 2.32887859519156e-01 , 8.46277010294356e-02 , 1.32198685408501e-01 ), ( 1.27056649533084e-01 , 4.33377389098029e-02 , 4.97892768769213e-02 ), ( 1.22381753985573e-01 , 3.41586847326240e-02 , -1.18445110129732e-02 ), ( 1.05671464855148e-01 , 3.86532894199961e-02 , 6.19869217567546e-02 ), ( 7.16203311743855e-02 , 2.17558192616861e-02 , 6.98849025123255e-03 ), ( 5.99640138968076e-02 , 2.25588560215600e-02 , 4.01011154373220e-02 ), ( -3.25542195704354e-05 , -2.41900197301183e-03 , -1.89984337550084e-02 ), ( -1.32647221593366e-02 , -1.47384674205409e-02 , -8.57328888562245e-02 ), ( -4.69295810825941e-02 , -9.41129292941427e-03 , 3.36169882557587e-02 ), ( -1.13541921192049e-01 , -3.08516894386112e-02 , 1.76094573558321e-02 ), ( -1.54674308412988e-01 , -3.34118168784681e-02 , 9.19268829537772e-02 ), ( -1.02091982823549e-01 , -3.33087248294972e-02 , -2.80703710993668e-02 ), ( -1.37588732745389e-01 , -5.06762598547442e-02 , -8.34537828360104e-02 ), ( -5.06218660559404e-02 , -1.56230283335258e-02 , -6.87781890768321e-03 ), ( -3.08839705592416e-02 , -1.50579525809766e-02 , -4.77709840365084e-02 ), ( 2.36395155405980e-02 , 6.60692129558478e-03 , -2.21885338022018e-03 ), ( 4.83354967454996e-04 , -1.59296729329767e-02 , -1.26712034451445e-01 ), ( -1.71815952692567e-02 , -2.78131275404488e-02 , -1.79824148452554e-01 ), ( 4.68922585797591e-02 , -3.66288751900909e-03 , -1.36617896790793e-01 ), ( 7.59151612564729e-02 , -4.40440718034790e-03 , -2.09145936861076e-01 ), ( 1.36201758070916e-01 , 1.46213983056402e-02 , -1.97643193338638e-01 ), ( 1.89282960943429e-02 , -2.74573869374166e-02 , -2.59983219655275e-01 ), ( 1.99223584509793e-02 , -3.56791693618768e-02 , -3.27093827759356e-01 ), ( -3.26432516920732e-02 , -3.84943911025121e-02 , -2.28519445694830e-01 ), ( -9.21394164551950e-02 , -6.09521307976269e-02 , -2.68898187169678e-01 ), ( -1.28449800819388e-01 , -6.53962493000429e-02 , -2.20514316951765e-01 ), ( -1.48950313055385e-01 , -8.02780675198336e-02 , -2.90752958515001e-01 ), ( -1.75902205718680e-01 , -9.59657763030266e-02 , -3.52523528143139e-01 ), ( -1.92367142029188e-01 , -9.39544201238159e-02 , -2.98835600202562e-01 ), ( -2.34073918659256e-01 , -1.09511474765624e-01 , -3.25676026667567e-01 ), ( -1.19983779327036e-01 , -7.37153221787298e-02 , -3.05559177101654e-01 ), ( -1.69256110911622e-01 , -7.97398200384644e-02 , -2.39855584707409e-01 ), ( -2.22157552370696e-01 , -9.70207445613183e-02 , -2.54568081838475e-01 ), ( -2.57546357186263e-01 , -9.78147696285256e-02 , -1.79521501278274e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 0, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 1 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 1, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 1, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 1, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 1, atoms_positions[size = 51] = { ( 8.42020860115927e+00 , 4.21991772440572e-02 , -7.45620320908196e-01 ), ( 7.00356168021470e+00 , -4.79961273240136e-01 , -6.79276268523547e-01 ), ( 6.23767829724485e+00 , -2.51247056733134e-01 , 6.26723013266982e-01 ), ( 5.02836760689927e+00 , -2.08045498598506e-01 , 6.39279949863210e-01 ), ( 7.03907190853467e+00 , -2.00682955930526e+00 , -1.03762126887887e+00 ), ( 6.90865762910286e+00 , -2.67402193238485e-01 , 1.77894374849930e+00 ), ( 6.18212607952751e+00 , -1.31162942641700e-01 , 3.03990487109687e+00 ), ( 7.19806650022761e+00 , -3.16977124704912e-01 , 4.30310525801892e+00 ), ( 5.30277106614921e+00 , 1.14009027458730e+00 , 3.26020429141508e+00 ), ( 4.09168799566628e+00 , 1.07931872502458e+00 , 3.60441862233567e+00 ), ( 5.87383598445601e+00 , 2.34423023509440e+00 , 2.94316659460719e+00 ), ( 5.23330840410800e+00 , 3.60157582019048e+00 , 2.87824077887178e+00 ), ( 6.32195899986517e+00 , 4.64361828650942e+00 , 2.47418830211963e+00 ), ( 3.90567262185191e+00 , 3.68544878849974e+00 , 2.03017213713226e+00 ), ( 2.93268290479868e+00 , 4.11879115223505e+00 , 2.57740403700341e+00 ), ( 3.81729626779150e+00 , 3.24363106424524e+00 , 7.83854251329338e-01 ), ( 2.65736293095857e+00 , 3.20810250854710e+00 , -6.18612205529565e-02 ), ( 3.04748223300176e+00 , 2.73697170209860e+00 , -1.57072865932818e+00 ), ( 1.65396529802342e+00 , 2.17247883063761e+00 , 5.62166269959855e-01 ), ( 4.23522803585828e-01 , 2.41894531818558e+00 , 5.75950510780766e-01 ), ( 1.99311747302112e+00 , 9.90200204878183e-01 , 1.06367245965403e+00 ), ( 1.11563866641463e+00 , 1.72485962153876e-02 , 1.68771527836420e+00 ), ( 2.01680432847577e+00 , -1.21223508026317e+00 , 2.02283227251816e+00 ), ( 4.93808100313684e-01 , 5.72993726796709e-01 , 3.01393255407714e+00 ), ( -6.88662684141346e-01 , 3.95917856413356e-01 , 3.20168916817509e+00 ), ( 1.26635423078224e+00 , 1.30187284743042e+00 , 3.82424713040866e+00 ), ( 8.02055999729061e-01 , 1.87550275041104e+00 , 5.08797241823521e+00 ), ( 2.07403821144199e+00 , 2.57688573350060e+00 , 5.62065001861050e+00 ), ( -3.48560203228005e-01 , 2.92052155004377e+00 , 4.98852924984934e+00 ), ( -1.18494600718505e+00 , 3.01232061184074e+00 , 5.89678764769942e+00 ), ( -3.82031855792474e-01 , 3.70595279193985e+00 , 3.87941565006141e+00 ), ( -1.45082110565174e+00 , 4.62175504315960e+00 , 3.53071333627421e+00 ), ( -7.75724398501387e-01 , 5.37503394369413e+00 , 2.40305640723820e+00 ), ( -2.70209506676955e+00 , 3.89870945597851e+00 , 2.94981388354107e+00 ), ( -3.85031566372397e+00 , 4.39752350986476e+00 , 2.87664301725662e+00 ), ( -2.54961285801488e+00 , 2.62499766609283e+00 , 2.51165344297249e+00 ), ( -3.73779778375935e+00 , 1.87724750734948e+00 , 2.08367054576034e+00 ), ( -3.40254393652096e+00 , 7.87407333184051e-01 , 1.02115029402814e+00 ), ( -4.34988393963124e+00 , 1.12609477459219e+00 , 3.21266592727085e+00 ), ( -5.52818384628272e+00 , 9.52475239449865e-01 , 3.35258498212062e+00 ), ( -3.48967721875033e+00 , 6.30398567215183e-01 , 4.18272134653624e+00 ), ( -3.74839312960716e+00 , 1.02522560825697e-01 , 5.46548357801744e+00 ), ( -2.45559644797203e+00 , -4.43402837804419e-01 , 6.12151759153573e+00 ), ( -4.45577146937068e+00 , 1.02426407947902e+00 , 6.42056265889269e+00 ), ( -5.32862086963481e+00 , 5.86032714410330e-01 , 7.17433883244170e+00 ), ( -6.29033006805714e+00 , 3.54932222936094e+00 , 6.69033999722774e+00 ), ( -6.93486349092612e+00 , 4.31932173934529e+00 , 7.41926550612646e+00 ), ( -6.77302656697589e+00 , 3.20630978062096e+00 , 5.49497885507638e+00 ), ( -4.07615678740045e+00 , 2.28779023613822e+00 , 6.46796989327310e+00 ), ( -4.91096621861803e+00 , 3.24745840702887e+00 , 7.21735263439854e+00 ), ( -4.05359762454723e+00 , 4.48287939172511e+00 , 7.26229858930884e+00 ) } +colvars: Step 1, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atom_groups_ids[size = 0] = +colvars: Step 1, atom_groups_refcount[size = 0] = +colvars: Step 1, atom_groups_masses[size = 0] = +colvars: Step 1, atom_groups_charges[size = 0] = +colvars: Step 1, atom_groups_coms[size = 0] = +colvars: Step 1, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 1, volmaps_ids[size = 0] = +colvars: Step 1, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 1 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.39359239792396e-01 , 6.97253156444326e-03 , 9.40631006384071e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.39359239792396e-01 , 6.97253156444326e-03 , 9.40631006384071e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.3052 , 1.81235 , -14.909 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.3052 , 1.81235 , -14.909 ) to colvar "one". +colvars: Adding total bias energy: 45.8763 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.3052 , 1.81235 , -14.909 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.83683 , -0.573221 , -1.60667 ) +colvars: ( -4.14758 , -0.491537 , -1.37772 ) +colvars: ( -4.14758 , -0.491537 , -1.37772 ) +colvars: ( -5.5247 , -0.654741 , -1.83516 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.903993 , 0.192289 , 0.652417 ) +colvars: ( 0.781088 , 0.264308 , 0.678501 ) +colvars: ( 0.76699 , 0.256656 , 0.659382 ) +colvars: ( 0.664952 , 0.266705 , 0.611922 ) +colvars: ( 0.652774 , 0.20025 , 0.512255 ) +colvars: ( 0.574956 , 0.345265 , 0.666906 ) +colvars: ( 0.463377 , 0.360922 , 0.621494 ) +colvars: ( 0.383656 , 0.459317 , 0.710222 ) +colvars: ( 0.380415 , 0.316875 , 0.510353 ) +colvars: ( 0.343791 , 0.276006 , 0.431519 ) +colvars: ( 0.352193 , 0.321737 , 0.50012 ) +colvars: ( 0.280168 , 0.279191 , 0.397647 ) +colvars: ( 0.254311 , 0.307723 , 0.421727 ) +colvars: ( 0.344972 , 0.180495 , 0.29952 ) +colvars: ( 0.284546 , 0.137834 , 0.203871 ) +colvars: ( 0.471756 , 0.141947 , 0.322278 ) +colvars: ( 0.546856 , 0.0496184 , 0.239198 ) +colvars: ( 0.681101 , 0.0268724 , 0.288403 ) +colvars: ( 0.553753 , 0.0184455 , 0.200036 ) +colvars: ( 0.537588 , -0.0464574 , 0.100124 ) +colvars: ( 0.573487 , 0.0668284 , 0.279141 ) +colvars: ( 0.569914 , 0.0514594 , 0.255635 ) +colvars: ( 0.605908 , 0.116412 , 0.367553 ) +colvars: ( 0.441286 , 0.0575401 , 0.186656 ) +colvars: ( 0.43358 , 0.00195342 , 0.104781 ) +colvars: ( 0.336623 , 0.12418 , 0.216247 ) +colvars: ( 0.208119 , 0.134251 , 0.152885 ) +colvars: ( 0.114315 , 0.220858 , 0.216757 ) +colvars: ( 0.180422 , 0.0603052 , 0.0334676 ) +colvars: ( 0.128974 , 0.0249581 , -0.0466157 ) +colvars: ( 0.217024 , 0.0335967 , 0.0183899 ) +colvars: ( 0.204019 , -0.0392982 , -0.0907238 ) +colvars: ( 0.242544 , -0.0438727 , -0.0738891 ) +colvars: ( 0.280998 , -0.125878 , -0.164685 ) +colvars: ( 0.235845 , -0.178563 , -0.265071 ) +colvars: ( 0.398949 , -0.141907 , -0.115956 ) +colvars: ( 0.478016 , -0.217981 , -0.174063 ) +colvars: ( 0.612818 , -0.221902 , -0.098366 ) +colvars: ( 0.427337 , -0.221184 , -0.209021 ) +colvars: ( 0.432801 , -0.289218 , -0.300262 ) +colvars: ( 0.375661 , -0.146774 , -0.136737 ) +colvars: ( 0.317902 , -0.139189 , -0.160966 ) +colvars: ( 0.299397 , -0.051749 , -0.0506101 ) +colvars: ( 0.191183 , -0.146717 , -0.247707 ) +colvars: ( 0.165106 , -0.188089 , -0.320888 ) +colvars: ( -0.0128421 , -0.1915 , -0.432746 ) +colvars: ( -0.106316 , -0.208362 , -0.512442 ) +colvars: ( 0.0917321 , -0.242996 , -0.441349 ) +colvars: ( 0.108209 , -0.105699 , -0.240659 ) +colvars: ( -0.0142897 , -0.108905 , -0.318854 ) +colvars: ( -0.105257 , -0.0275227 , -0.260534 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.83683 , 0.573221 , 1.60667 ) +colvars: ( 4.14758 , 0.491537 , 1.37772 ) +colvars: ( 4.14758 , 0.491537 , 1.37772 ) +colvars: ( 5.5247 , 0.654741 , 1.83516 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.628373 , -0.0803096 , -0.404156 ) +colvars: ( -0.562768 , -0.162435 , -0.377206 ) +colvars: ( -0.516859 , -0.140734 , -0.3205 ) +colvars: ( -0.518305 , -0.190229 , -0.34562 ) +colvars: ( -0.508681 , -0.132365 , -0.308245 ) +colvars: ( -0.488918 , -0.281371 , -0.359533 ) +colvars: ( -0.450653 , -0.321788 , -0.340237 ) +colvars: ( -0.42483 , -0.427905 , -0.364904 ) +colvars: ( -0.387449 , -0.287422 , -0.260022 ) +colvars: ( -0.380468 , -0.262789 , -0.241201 ) +colvars: ( -0.340853 , -0.28194 , -0.210376 ) +colvars: ( -0.280782 , -0.246001 , -0.132571 ) +colvars: ( -0.234992 , -0.260733 , -0.0934018 ) +colvars: ( -0.303441 , -0.144057 , -0.106704 ) +colvars: ( -0.270545 , -0.11561 , -0.0599066 ) +colvars: ( -0.362401 , -0.086826 , -0.138848 ) +colvars: ( -0.392337 , 0.0103139 , -0.122623 ) +colvars: ( -0.448151 , 0.0580048 , -0.156152 ) +colvars: ( -0.426686 , 0.0250386 , -0.150249 ) +colvars: ( -0.415174 , 0.0808204 , -0.111965 ) +colvars: ( -0.467892 , -0.0281086 , -0.217242 ) +colvars: ( -0.498444 , -0.0296691 , -0.248821 ) +colvars: ( -0.546188 , -0.0939051 , -0.327712 ) +colvars: ( -0.441439 , -0.0599934 , -0.205787 ) +colvars: ( -0.446978 , -0.0166911 , -0.190677 ) +colvars: ( -0.383628 , -0.133723 , -0.18269 ) +colvars: ( -0.321695 , -0.165299 , -0.135281 ) +colvars: ( -0.268983 , -0.254577 , -0.124763 ) +colvars: ( -0.282468 , -0.093719 , -0.0614744 ) +colvars: ( -0.266517 , -0.0757416 , -0.0367823 ) +colvars: ( -0.267531 , -0.0492391 , -0.0251369 ) +colvars: ( -0.234713 , 0.0243191 , 0.0431483 ) +colvars: ( -0.218644 , 0.0506275 , 0.0719412 ) +colvars: ( -0.280361 , 0.110129 , 0.0381004 ) +colvars: ( -0.252838 , 0.150968 , 0.0853995 ) +colvars: ( -0.351976 , 0.138471 , -0.0206253 ) +colvars: ( -0.402067 , 0.213892 , -0.0351229 ) +colvars: ( -0.476649 , 0.236888 , -0.0993991 ) +colvars: ( -0.408431 , 0.19398 , -0.0510639 ) +colvars: ( -0.412899 , 0.253854 , -0.026951 ) +colvars: ( -0.408376 , 0.108407 , -0.0919166 ) +colvars: ( -0.410166 , 0.0782913 , -0.10812 ) +colvars: ( -0.428039 , -0.0137189 , -0.170142 ) +colvars: ( -0.340193 , 0.0664573 , -0.0431592 ) +colvars: ( -0.341087 , 0.0921493 , -0.0317796 ) +colvars: ( -0.179362 , 0.0976022 , 0.134041 ) +colvars: ( -0.127545 , 0.0988906 , 0.186951 ) +colvars: ( -0.211539 , 0.169456 , 0.135918 ) +colvars: ( -0.277448 , 0.025934 , 0.000791771 ) +colvars: ( -0.207783 , 0.0118233 , 0.0643523 ) +colvars: ( -0.152155 , -0.0704514 , 0.0811613 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 1. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 1. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atoms_new_colvar_forces = { ( -4.56121296830658e+00 , -4.61241353827074e-01 , -1.35840638133783e+00 ), ( -3.92926416259046e+00 , -3.89663782249164e-01 , -1.07642270018368e+00 ), ( -4.00093646166547e+00 , -4.15060921777743e-01 , -1.11141506274544e+00 ), ( -5.38060802928969e+00 , -5.86855187741701e-01 , -1.63114963622738e+00 ), ( 2.50130489904713e-01 , 1.15921831227305e-01 , 3.38882353346319e-01 ), ( 4.92287015525418e+00 , 6.37114670971567e-01 , 1.91404037546853e+00 ), ( 4.16030699965575e+00 , 5.30670341810993e-01 , 1.65897480365853e+00 ), ( -4.11742060744669e-02 , 3.14122235304719e-02 , 3.45318167522374e-01 ), ( 4.14054924899995e+00 , 5.20990230072956e-01 , 1.62804834803012e+00 ), ( 5.48802414203826e+00 , 6.67957628124025e-01 , 2.02547787152414e+00 ), ( 1.13401367888580e-02 , 3.97968575512088e-02 , 2.89743590064456e-01 ), ( -6.13429998875925e-04 , 3.31904585487345e-02 , 2.65076285639856e-01 ), ( 1.93189132040426e-02 , 4.69906894317092e-02 , 3.28324792571684e-01 ), ( 4.15310107971116e-02 , 3.64372642432776e-02 , 1.92815524833123e-01 ), ( 1.40014331258611e-02 , 2.22243632771206e-02 , 1.43964433073201e-01 ), ( 1.09355673121523e-01 , 5.51208045376686e-02 , 1.83430053208428e-01 ), ( 1.54518940908901e-01 , 5.99322715671118e-02 , 1.16574711662165e-01 ), ( 2.32949880910387e-01 , 8.48772135203020e-02 , 1.32250608109155e-01 ), ( 1.27067186507369e-01 , 4.34840848401806e-02 , 4.97865198257480e-02 ), ( 1.22413872360718e-01 , 3.43629960831720e-02 , -1.18407958674590e-02 ), ( 1.05594346949082e-01 , 3.87197923562023e-02 , 6.18992448292895e-02 ), ( 7.14691535860895e-02 , 2.17903102851525e-02 , 6.81407061135675e-03 ), ( 5.97209641981943e-02 , 2.25071296417359e-02 , 3.98410799496707e-02 ), ( -1.53110558083924e-04 , -2.45333152116743e-03 , -1.91318682968406e-02 ), ( -1.33985293929014e-02 , -1.47376676480654e-02 , -8.58964055168903e-02 ), ( -4.70048825419079e-02 , -9.54275314410222e-03 , 3.35569101122025e-02 ), ( -1.13575193091344e-01 , -3.10487005981428e-02 , 1.76041991738181e-02 ), ( -1.54667891555866e-01 , -3.37194469106931e-02 , 9.19939515909655e-02 ), ( -1.02045936431039e-01 , -3.34138341929289e-02 , -2.80068672415610e-02 ), ( -1.37542540797621e-01 , -5.07835025888675e-02 , -8.33979922915723e-02 ), ( -5.05074127724774e-02 , -1.56424153031696e-02 , -6.74701525473648e-03 ), ( -3.06936455782306e-02 , -1.49790441228229e-02 , -4.75755526079221e-02 ), ( 2.39000305306330e-02 , 6.75481445114764e-03 , -1.94799258460876e-03 ), ( 6.37144587265381e-04 , -1.57489830272470e-02 , -1.26584734390641e-01 ), ( -1.69929924153842e-02 , -2.75956164402141e-02 , -1.79671034076676e-01 ), ( 4.69730059885827e-02 , -3.43618896392178e-03 , -1.36581244707262e-01 ), ( 7.59492983355819e-02 , -4.08946030671814e-03 , -2.09185780341426e-01 ), ( 1.36168129122491e-01 , 1.49856831637182e-02 , -1.97765073724213e-01 ), ( 1.89063730085664e-02 , -2.72042479706727e-02 , -2.60084439073423e-01 ), ( 1.99018506305078e-02 , -3.53633903280922e-02 , -3.27212801214469e-01 ), ( -3.27154388013418e-02 , -3.83669120876546e-02 , -2.28653734204113e-01 ), ( -9.22637240513290e-02 , -6.08979080427851e-02 , -2.69086145709003e-01 ), ( -1.28641601578139e-01 , -6.54678727585377e-02 , -2.20752217137649e-01 ), ( -1.49009988673130e-01 , -8.02600661059803e-02 , -2.90865913646557e-01 ), ( -1.75980595287395e-01 , -9.59396265372952e-02 , -3.52667928620230e-01 ), ( -1.92204196160349e-01 , -9.38979806873025e-02 , -2.98704791488973e-01 ), ( -2.33861549390566e-01 , -1.09471039414501e-01 , -3.25491120340965e-01 ), ( -1.19806713205189e-01 , -7.35403764057818e-02 , -3.05431270609309e-01 ), ( -1.69238240580481e-01 , -7.97645301640516e-02 , -2.39867247275705e-01 ), ( -2.22072836915525e-01 , -9.70814311455297e-02 , -2.54501227948042e-01 ), ( -2.57412102810795e-01 , -9.79740872238340e-02 , -1.79372920140549e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 1, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 2 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 2, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 2, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 2, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 2, atoms_positions[size = 51] = { ( 8.41230217581484e+00 , 4.24326733536878e-02 , -7.47569490176025e-01 ), ( 7.00089513421555e+00 , -4.83663699546571e-01 , -6.72804704936553e-01 ), ( 6.24367623868857e+00 , -2.51597399688398e-01 , 6.35902751887321e-01 ), ( 5.02199310371592e+00 , -2.08647537136810e-01 , 6.45327524407029e-01 ), ( 7.03875423602966e+00 , -2.01024090894622e+00 , -1.03297768688768e+00 ), ( 6.90728101575796e+00 , -2.68409594185841e-01 , 1.78553096211824e+00 ), ( 6.17984674260531e+00 , -1.29067444864042e-01 , 3.04264192791274e+00 ), ( 7.19403104814050e+00 , -3.17368222969422e-01 , 4.30320854269290e+00 ), ( 5.30491583043216e+00 , 1.13376171120378e+00 , 3.26705018916841e+00 ), ( 4.08866819057517e+00 , 1.07659208744573e+00 , 3.60871383769025e+00 ), ( 5.87394211299741e+00 , 2.33800746103373e+00 , 2.95025840533623e+00 ), ( 5.23075710856745e+00 , 3.59958439514760e+00 , 2.87915965088407e+00 ), ( 6.32630915491025e+00 , 4.63549135662606e+00 , 2.47116449869166e+00 ), ( 3.90153079829527e+00 , 3.69481371251487e+00 , 2.02631829831871e+00 ), ( 2.92849868300238e+00 , 4.11702537266563e+00 , 2.57104338554592e+00 ), ( 3.81753045166978e+00 , 3.24384573133083e+00 , 7.83691308238158e-01 ), ( 2.66012692529136e+00 , 3.20111572487056e+00 , -6.86003878622946e-02 ), ( 3.04893081854912e+00 , 2.73309481829466e+00 , -1.57997395201901e+00 ), ( 1.64933960432362e+00 , 2.16482434474135e+00 , 5.69612675768092e-01 ), ( 4.24921990500371e-01 , 2.42605373880924e+00 , 5.70944354578611e-01 ), ( 1.98623149883073e+00 , 9.97645952529453e-01 , 1.06028397478289e+00 ), ( 1.12204224960049e+00 , 1.47142447093945e-02 , 1.68718091217601e+00 ), ( 2.01639805450803e+00 , -1.20568292550127e+00 , 2.02326698950649e+00 ), ( 4.98103216842537e-01 , 5.80679823587245e-01 , 3.01308846211547e+00 ), ( -6.84829676640720e-01 , 3.90833079255459e-01 , 3.19685945568519e+00 ), ( 1.27432015398850e+00 , 1.30473014901260e+00 , 3.82336698286764e+00 ), ( 8.08601410185370e-01 , 1.88137209556391e+00 , 5.08538325715984e+00 ), ( 2.07182119428108e+00 , 2.58031798980506e+00 , 5.62057423330987e+00 ), ( -3.51856598997225e-01 , 2.92077064179559e+00 , 4.98737393872034e+00 ), ( -1.18280182786636e+00 , 3.01570881875917e+00 , 5.89917061211271e+00 ), ( -3.87794274194742e-01 , 3.70427748455740e+00 , 3.87474110532419e+00 ), ( -1.45631640972632e+00 , 4.61459319965596e+00 , 3.53258775067119e+00 ), ( -7.71525256388986e-01 , 5.37658883982654e+00 , 2.40420584478656e+00 ), ( -2.70490428847905e+00 , 3.89833439606985e+00 , 2.94596721752849e+00 ), ( -3.85265652977568e+00 , 4.40316722845360e+00 , 2.87069810170517e+00 ), ( -2.55585210102612e+00 , 2.62089197346870e+00 , 2.50849831177278e+00 ), ( -3.73243894282155e+00 , 1.88635397507806e+00 , 2.08117958634558e+00 ), ( -3.40440145433502e+00 , 7.90661523283313e-01 , 1.01489749289712e+00 ), ( -4.34244223157238e+00 , 1.12117998375176e+00 , 3.21348381567827e+00 ), ( -5.52935798388581e+00 , 9.45031041354011e-01 , 3.35102684162587e+00 ), ( -3.48508740061830e+00 , 6.29273187233610e-01 , 4.17782066610908e+00 ), ( -3.75586810994823e+00 , 1.04520729936072e-01 , 5.46864564339515e+00 ), ( -2.44525456155645e+00 , -4.36565563433725e-01 , 6.12524646328179e+00 ), ( -4.45857770956377e+00 , 1.01874257320945e+00 , 6.41862259580145e+00 ), ( -5.32722304597339e+00 , 5.89222557864481e-01 , 7.17650762843785e+00 ), ( -6.29285957437603e+00 , 3.54731449624820e+00 , 6.69277829408017e+00 ), ( -6.92913918708456e+00 , 4.31545557739325e+00 , 7.41850538938275e+00 ), ( -6.76638490706359e+00 , 3.20728509611946e+00 , 5.49812757005705e+00 ), ( -4.07643470196769e+00 , 2.29036157014482e+00 , 6.47113725812446e+00 ), ( -4.91331138905739e+00 , 3.24680974286670e+00 , 7.21653939356896e+00 ), ( -4.05852930675624e+00 , 4.48539530316559e+00 , 7.26244311964441e+00 ) } +colvars: Step 2, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atom_groups_ids[size = 0] = +colvars: Step 2, atom_groups_refcount[size = 0] = +colvars: Step 2, atom_groups_masses[size = 0] = +colvars: Step 2, atom_groups_charges[size = 0] = +colvars: Step 2, atom_groups_coms[size = 0] = +colvars: Step 2, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 2, volmaps_ids[size = 0] = +colvars: Step 2, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 2 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.38680441300733e-01 , 6.30491679893380e-03 , 9.40880336017551e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.38680441300733e-01 , 6.30491679893380e-03 , 9.40880336017551e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.2916 , 1.8257 , -14.914 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.2916 , 1.8257 , -14.914 ) to colvar "one". +colvars: Adding total bias energy: 45.8505 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.2916 , 1.8257 , -14.914 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.83825 , -0.572725 , -1.60415 ) +colvars: ( -4.1488 , -0.491112 , -1.37556 ) +colvars: ( -4.1488 , -0.491112 , -1.37556 ) +colvars: ( -5.52632 , -0.654175 , -1.83229 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.903535 , 0.192419 , 0.651664 ) +colvars: ( 0.780731 , 0.264443 , 0.67763 ) +colvars: ( 0.766569 , 0.256779 , 0.658479 ) +colvars: ( 0.664736 , 0.266819 , 0.611113 ) +colvars: ( 0.652573 , 0.200335 , 0.511595 ) +colvars: ( 0.574848 , 0.345396 , 0.665979 ) +colvars: ( 0.463412 , 0.361039 , 0.620604 ) +colvars: ( 0.383782 , 0.459461 , 0.709164 ) +colvars: ( 0.380494 , 0.316955 , 0.509564 ) +colvars: ( 0.343936 , 0.276062 , 0.430853 ) +colvars: ( 0.352233 , 0.321808 , 0.499285 ) +colvars: ( 0.280237 , 0.279227 , 0.396903 ) +colvars: ( 0.254334 , 0.307761 , 0.420883 ) +colvars: ( 0.344972 , 0.180501 , 0.298957 ) +colvars: ( 0.284608 , 0.137811 , 0.203424 ) +colvars: ( 0.47163 , 0.141963 , 0.321743 ) +colvars: ( 0.546655 , 0.0496105 , 0.238828 ) +colvars: ( 0.680748 , 0.0268805 , 0.288013 ) +colvars: ( 0.553613 , 0.0184308 , 0.199777 ) +colvars: ( 0.537467 , -0.0465024 , 0.100013 ) +colvars: ( 0.573383 , 0.066842 , 0.278811 ) +colvars: ( 0.569881 , 0.0514707 , 0.255387 ) +colvars: ( 0.605891 , 0.116462 , 0.367187 ) +colvars: ( 0.441394 , 0.0575291 , 0.186457 ) +colvars: ( 0.433723 , 0.00191955 , 0.104723 ) +colvars: ( 0.336812 , 0.124174 , 0.215933 ) +colvars: ( 0.208438 , 0.134224 , 0.152605 ) +colvars: ( 0.1147 , 0.220846 , 0.216313 ) +colvars: ( 0.180728 , 0.0602387 , 0.0333285 ) +colvars: ( 0.129356 , 0.0248684 , -0.0466406 ) +colvars: ( 0.217231 , 0.0335218 , 0.0182484 ) +colvars: ( 0.204197 , -0.0394093 , -0.0907342 ) +colvars: ( 0.242613 , -0.0439831 , -0.0739554 ) +colvars: ( 0.281128 , -0.126008 , -0.164523 ) +colvars: ( 0.236018 , -0.178725 , -0.264779 ) +colvars: ( 0.398992 , -0.142018 , -0.115788 ) +colvars: ( 0.478014 , -0.218106 , -0.173742 ) +colvars: ( 0.612698 , -0.222 , -0.098081 ) +colvars: ( 0.42745 , -0.221316 , -0.208626 ) +colvars: ( 0.432923 , -0.289376 , -0.299715 ) +colvars: ( 0.375865 , -0.146882 , -0.136452 ) +colvars: ( 0.318224 , -0.139301 , -0.160631 ) +colvars: ( 0.299778 , -0.0518247 , -0.0504242 ) +colvars: ( 0.191617 , -0.146859 , -0.247312 ) +colvars: ( 0.165601 , -0.18825 , -0.32037 ) +colvars: ( -0.0123199 , -0.191709 , -0.432251 ) +colvars: ( -0.10571 , -0.208597 , -0.511879 ) +colvars: ( 0.0921189 , -0.243208 , -0.44081 ) +colvars: ( 0.108675 , -0.105843 , -0.240352 ) +colvars: ( -0.0137199 , -0.109076 , -0.318501 ) +colvars: ( -0.104631 , -0.0276806 , -0.260342 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.83825 , 0.572725 , 1.60415 ) +colvars: ( 4.1488 , 0.491112 , 1.37556 ) +colvars: ( 4.1488 , 0.491112 , 1.37556 ) +colvars: ( 5.52632 , 0.654175 , 1.83229 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.628038 , -0.0803205 , -0.403541 ) +colvars: ( -0.562504 , -0.162549 , -0.376391 ) +colvars: ( -0.516435 , -0.140783 , -0.319547 ) +colvars: ( -0.518187 , -0.190392 , -0.344857 ) +colvars: ( -0.50856 , -0.132447 , -0.30764 ) +colvars: ( -0.488933 , -0.281669 , -0.358633 ) +colvars: ( -0.450828 , -0.322155 , -0.33937 ) +colvars: ( -0.42512 , -0.428424 , -0.363842 ) +colvars: ( -0.387594 , -0.287721 , -0.259182 ) +colvars: ( -0.380692 , -0.263066 , -0.240514 ) +colvars: ( -0.340876 , -0.282201 , -0.209392 ) +colvars: ( -0.280756 , -0.24619 , -0.131601 ) +colvars: ( -0.234841 , -0.26091 , -0.0922247 ) +colvars: ( -0.303329 , -0.144104 , -0.105948 ) +colvars: ( -0.270469 , -0.115615 , -0.0592513 ) +colvars: ( -0.362176 , -0.0867935 , -0.138171 ) +colvars: ( -0.392027 , 0.0104813 , -0.122151 ) +colvars: ( -0.447692 , 0.0582447 , -0.15569 ) +colvars: ( -0.426508 , 0.025196 , -0.149984 ) +colvars: ( -0.414997 , 0.0810551 , -0.111854 ) +colvars: ( -0.467834 , -0.0280515 , -0.216979 ) +colvars: ( -0.498531 , -0.0296447 , -0.24873 ) +colvars: ( -0.546374 , -0.0939945 , -0.327573 ) +colvars: ( -0.441655 , -0.0600148 , -0.205713 ) +colvars: ( -0.447244 , -0.016664 , -0.190785 ) +colvars: ( -0.383895 , -0.133835 , -0.182423 ) +colvars: ( -0.322068 , -0.165454 , -0.135001 ) +colvars: ( -0.269397 , -0.254844 , -0.124237 ) +colvars: ( -0.282755 , -0.0937551 , -0.0612828 ) +colvars: ( -0.266887 , -0.0757627 , -0.0367231 ) +colvars: ( -0.267647 , -0.0491851 , -0.024878 ) +colvars: ( -0.234727 , 0.0244956 , 0.0433257 ) +colvars: ( -0.218475 , 0.050872 , 0.0722516 ) +colvars: ( -0.280353 , 0.110411 , 0.0380266 ) +colvars: ( -0.252846 , 0.151309 , 0.0852086 ) +colvars: ( -0.351936 , 0.138778 , -0.0207893 ) +colvars: ( -0.402017 , 0.214287 , -0.0355247 ) +colvars: ( -0.47653 , 0.237306 , -0.0998371 ) +colvars: ( -0.408558 , 0.19432 , -0.0516044 ) +colvars: ( -0.413034 , 0.254271 , -0.0276744 ) +colvars: ( -0.408651 , 0.10861 , -0.092371 ) +colvars: ( -0.410618 , 0.0784253 , -0.108681 ) +colvars: ( -0.428619 , -0.0137323 , -0.170588 ) +colvars: ( -0.340712 , 0.0665832 , -0.0437158 ) +colvars: ( -0.341689 , 0.0922962 , -0.0325006 ) +colvars: ( -0.17978 , 0.0978275 , 0.133604 ) +colvars: ( -0.128013 , 0.0991234 , 0.186489 ) +colvars: ( -0.211793 , 0.169794 , 0.135432 ) +colvars: ( -0.277934 , 0.0260275 , 0.000425854 ) +colvars: ( -0.208326 , 0.0119073 , 0.0640095 ) +colvars: ( -0.152718 , -0.0704656 , 0.081068 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 2. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 2. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atoms_new_colvar_forces = { ( -4.56275591432568e+00 , -4.60626201406985e-01 , -1.35602921553252e+00 ), ( -3.93057432356231e+00 , -3.89218540353453e-01 , -1.07432085574555e+00 ), ( -4.00225225577945e+00 , -4.14684542315428e-01 , -1.10930365840729e+00 ), ( -5.38231018573623e+00 , -5.86287786085435e-01 , -1.62833067766371e+00 ), ( 2.50133161932021e-01 , 1.15996383439220e-01 , 3.38932431945268e-01 ), ( 4.92416773946919e+00 , 6.36452457626012e-01 , 1.91149846005699e+00 ), ( 4.16138500265152e+00 , 5.29996299679700e-01 , 1.65679341661957e+00 ), ( -4.13386379963794e-02 , 3.10363702515917e-02 , 3.45321802947897e-01 ), ( 4.14170174373320e+00 , 5.20345366926022e-01 , 1.62594137310275e+00 ), ( 5.48956688633158e+00 , 6.67171491848512e-01 , 2.02262452634672e+00 ), ( 1.13572538101830e-02 , 3.96069067900944e-02 , 2.89892874903251e-01 ), ( -5.18992402491980e-04 , 3.30363442557886e-02 , 2.65302472716106e-01 ), ( 1.94934753306099e-02 , 4.68502764998364e-02 , 3.28657895366362e-01 ), ( 4.16436497949736e-02 , 3.63979047739679e-02 , 1.93008539238330e-01 ), ( 1.41385702217975e-02 , 2.21958752053348e-02 , 1.44173170879472e-01 ), ( 1.09453693916134e-01 , 5.51691320542270e-02 , 1.83572631283874e-01 ), ( 1.54627155519217e-01 , 6.00918449323470e-02 , 1.16676694421352e-01 ), ( 2.33056290670824e-01 , 8.51252625753025e-02 , 1.32322949487176e-01 ), ( 1.27104485771322e-01 , 4.36268377333083e-02 , 4.97931884745996e-02 ), ( 1.22469588881520e-01 , 3.45527297063639e-02 , -1.18411614465137e-02 ), ( 1.05548588130028e-01 , 3.87905064186184e-02 , 6.18318922172304e-02 ), ( 7.13498720750871e-02 , 2.18259599675757e-02 , 6.65707447147101e-03 ), ( 5.95169456640540e-02 , 2.24672160196834e-02 , 3.96137239089935e-02 ), ( -2.60767644603088e-04 , -2.48569559566528e-03 , -1.92565272867681e-02 ), ( -1.35207607822719e-02 , -1.47444722739935e-02 , -8.60621405897303e-02 ), ( -4.70825964826798e-02 , -9.66096510064252e-03 , 3.35101085101995e-02 ), ( -1.13630006285656e-01 , -3.12309114222545e-02 , 1.76042896158294e-02 ), ( -1.54696522040518e-01 , -3.39975897931801e-02 , 9.20754644045805e-02 ), ( -1.02027239087699e-01 , -3.35163749467409e-02 , -2.79542940474772e-02 ), ( -1.37531391006204e-01 , -5.08943593481360e-02 , -8.33636581276309e-02 ), ( -5.04163089596834e-02 , -1.56632782600083e-02 , -6.62965293435192e-03 ), ( -3.05302955123607e-02 , -1.49136379461020e-02 , -4.74085257795145e-02 ), ( 2.41379870386027e-02 , 6.88894780305944e-03 , -1.70374332627504e-03 ), ( 7.74988081106043e-04 , -1.55965123551653e-02 , -1.26496207176680e-01 ), ( -1.68277988227925e-02 , -2.74152433603144e-02 , -1.79570128967291e-01 ), ( 4.70558577979064e-02 , -3.24048717205680e-03 , -1.36577244444368e-01 ), ( 7.59971083401451e-02 , -3.81848829811693e-03 , -2.09266474286324e-01 ), ( 1.36168663308619e-01 , 1.53053615391257e-02 , -1.97918154817217e-01 ), ( 1.88916709109832e-02 , -2.69961088695052e-02 , -2.60230730369980e-01 ), ( 1.98888151078248e-02 , -3.51041763993108e-02 , -3.27389242672573e-01 ), ( -3.27865049719737e-02 , -3.82722054379483e-02 , -2.28822806188803e-01 ), ( -9.23943646511856e-02 , -6.08756444697767e-02 , -2.69311625873086e-01 ), ( -1.28840678665156e-01 , -6.55570021994047e-02 , -2.21012340430644e-01 ), ( -1.49095358557464e-01 , -8.02753353134499e-02 , -2.91027575172649e-01 ), ( -1.76088459354702e-01 , -9.59539844029730e-02 , -3.52870718355002e-01 ), ( -1.92100235430595e-01 , -9.38818108222520e-02 , -2.98647260389017e-01 ), ( -2.33722560153824e-01 , -1.09473757572936e-01 , -3.25389876174375e-01 ), ( -1.19674155785813e-01 , -7.34140642627520e-02 , -3.05378508384878e-01 ), ( -1.69258950149056e-01 , -7.98153405417789e-02 , -2.39926417106925e-01 ), ( -2.22045455872506e-01 , -9.71687672132796e-02 , -2.54491942785526e-01 ), ( -2.57348474469147e-01 , -9.81461925066468e-02 , -1.79273616435353e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 2, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 3 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 3, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 3, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 3, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 3, atoms_positions[size = 51] = { ( 8.40432537347079e+00 , 4.27023523143084e-02 , -7.49794923258072e-01 ), ( 6.99827921913924e+00 , -4.88099279872046e-01 , -6.66623615895143e-01 ), ( 6.24916457435144e+00 , -2.53048519132688e-01 , 6.44402643797318e-01 ), ( 5.01528146738013e+00 , -2.08801464651714e-01 , 6.51168343880958e-01 ), ( 7.03895372542554e+00 , -2.01326453297722e+00 , -1.02798237640550e+00 ), ( 6.90599022218291e+00 , -2.69083020729788e-01 , 1.79259469596826e+00 ), ( 6.17819898214310e+00 , -1.26840925294146e-01 , 3.04742788378711e+00 ), ( 7.18887437910556e+00 , -3.18190833806877e-01 , 4.30239979123681e+00 ), ( 5.30617195835321e+00 , 1.12821582441797e+00 , 3.27354885186499e+00 ), ( 4.08708135560753e+00 , 1.07380406152037e+00 , 3.61286819362922e+00 ), ( 5.87428867854682e+00 , 2.33046793187875e+00 , 2.95718497242407e+00 ), ( 5.22756350482070e+00 , 3.59806525574326e+00 , 2.87989514418974e+00 ), ( 6.33004307020987e+00 , 4.62660812393183e+00 , 2.46802154801930e+00 ), ( 3.89875238684539e+00 , 3.70379061870336e+00 , 2.02347113410718e+00 ), ( 2.92333152941826e+00 , 4.11580387576656e+00 , 2.56498423514490e+00 ), ( 3.81870278458513e+00 , 3.24371694954947e+00 , 7.82492593993091e-01 ), ( 2.66310947197167e+00 , 3.19306357098013e+00 , -7.50220870549412e-02 ), ( 3.04938643337800e+00 , 2.72950976483335e+00 , -1.58743687892350e+00 ), ( 1.64232873722823e+00 , 2.15864496476834e+00 , 5.75792927917045e-01 ), ( 4.27089418257113e-01 , 2.43325458247010e+00 , 5.66066287421235e-01 ), ( 1.98044090530470e+00 , 1.00388484796073e+00 , 1.05723688588043e+00 ), ( 1.12901883607008e+00 , 1.29164702929013e-02 , 1.68724131837110e+00 ), ( 2.01590185879845e+00 , -1.19931648648901e+00 , 2.02325086478451e+00 ), ( 5.02873254555376e-01 , 5.87789153957021e-01 , 3.01035426063972e+00 ), ( -6.81444668247382e-01 , 3.85824447391906e-01 , 3.19254280514024e+00 ), ( 1.28185479878008e+00 , 1.30770660347493e+00 , 3.82341380909578e+00 ), ( 8.15487463448196e-01 , 1.88749925503596e+00 , 5.08218900980267e+00 ), ( 2.06839167547174e+00 , 2.58346656952317e+00 , 5.62073869300250e+00 ), ( -3.54751879904785e-01 , 2.92076574274276e+00 , 4.98648026571535e+00 ), ( -1.18059724189041e+00 , 3.01914654867617e+00 , 5.90115838004479e+00 ), ( -3.94242642986330e-01 , 3.70183887701549e+00 , 3.87005057704240e+00 ), ( -1.46136750440668e+00 , 4.60679196136818e+00 , 3.53446350406840e+00 ), ( -7.67375645143352e-01 , 5.37852585060086e+00 , 2.40557761823244e+00 ), ( -2.70861286210308e+00 , 3.89781603149094e+00 , 2.94244721299768e+00 ), ( -3.85397037061724e+00 , 4.40886783867621e+00 , 2.86514694670063e+00 ), ( -2.56238553987727e+00 , 2.61704026388775e+00 , 2.50463334676025e+00 ), ( -3.72731744273190e+00 , 1.89477473704136e+00 , 2.07834151690659e+00 ), ( -3.40648322734221e+00 , 7.94791140868560e-01 , 1.00822925596241e+00 ), ( -4.33411907667829e+00 , 1.11540771527026e+00 , 3.21619006920151e+00 ), ( -5.53124186056364e+00 , 9.37678491175850e-01 , 3.34931219584712e+00 ), ( -3.48029058481271e+00 , 6.29573843203298e-01 , 4.17165746663140e+00 ), ( -3.76293160038971e+00 , 1.04890509942572e-01 , 5.47218972935680e+00 ), ( -2.43524421545893e+00 , -4.28568742802307e-01 , 6.12917392570417e+00 ), ( -4.46137453930486e+00 , 1.01289730291090e+00 , 6.41730615543044e+00 ), ( -5.32588941289969e+00 , 5.92469724995526e-01 , 7.17853966797247e+00 ), ( -6.29516516770400e+00 , 3.54677363850763e+00 , 6.69521066423102e+00 ), ( -6.92401100227964e+00 , 4.31155236642489e+00 , 7.41786634158487e+00 ), ( -6.76023033797462e+00 , 3.20798202034655e+00 , 5.50142984649732e+00 ), ( -4.07780765935896e+00 , 2.29340417035688e+00 , 6.47431154141452e+00 ), ( -4.91395609424947e+00 , 3.24498075683916e+00 , 7.21568507981577e+00 ), ( -4.06366753987422e+00 , 4.48963350668488e+00 , 7.26344888853188e+00 ) } +colvars: Step 3, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atom_groups_ids[size = 0] = +colvars: Step 3, atom_groups_refcount[size = 0] = +colvars: Step 3, atom_groups_masses[size = 0] = +colvars: Step 3, atom_groups_charges[size = 0] = +colvars: Step 3, atom_groups_coms[size = 0] = +colvars: Step 3, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 3, volmaps_ids[size = 0] = +colvars: Step 3, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 3 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.37759603496395e-01 , 5.75914840711148e-03 , 9.41214790818537e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.37759603496395e-01 , 5.75914840711148e-03 , 9.41214790818537e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.2732 , 1.83662 , -14.9207 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.2732 , 1.83662 , -14.9207 ) to colvar "one". +colvars: Adding total bias energy: 45.8141 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.2732 , 1.83662 , -14.9207 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.84033 , -0.571928 , -1.60039 ) +colvars: ( -4.15058 , -0.490428 , -1.37234 ) +colvars: ( -4.15058 , -0.490428 , -1.37234 ) +colvars: ( -5.52869 , -0.653265 , -1.82799 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.903074 , 0.192581 , 0.6507 ) +colvars: ( 0.780384 , 0.264594 , 0.676557 ) +colvars: ( 0.766151 , 0.256931 , 0.65739 ) +colvars: ( 0.664546 , 0.266933 , 0.610115 ) +colvars: ( 0.652397 , 0.200421 , 0.510762 ) +colvars: ( 0.57478 , 0.345509 , 0.664858 ) +colvars: ( 0.463502 , 0.36112 , 0.619527 ) +colvars: ( 0.383978 , 0.459551 , 0.707907 ) +colvars: ( 0.380632 , 0.316998 , 0.508619 ) +colvars: ( 0.344144 , 0.276077 , 0.430041 ) +colvars: ( 0.352328 , 0.321851 , 0.498309 ) +colvars: ( 0.280362 , 0.279236 , 0.396046 ) +colvars: ( 0.254409 , 0.307779 , 0.419935 ) +colvars: ( 0.345018 , 0.180496 , 0.298293 ) +colvars: ( 0.284718 , 0.137772 , 0.202897 ) +colvars: ( 0.471532 , 0.141983 , 0.321097 ) +colvars: ( 0.54647 , 0.0496204 , 0.238356 ) +colvars: ( 0.680396 , 0.0269253 , 0.287507 ) +colvars: ( 0.553494 , 0.0184252 , 0.19941 ) +colvars: ( 0.537367 , -0.0465365 , 0.09981 ) +colvars: ( 0.573307 , 0.0668544 , 0.278348 ) +colvars: ( 0.569884 , 0.05147 , 0.254999 ) +colvars: ( 0.605913 , 0.116491 , 0.366652 ) +colvars: ( 0.441552 , 0.0574899 , 0.186135 ) +colvars: ( 0.433918 , 0.00185543 , 0.104552 ) +colvars: ( 0.337063 , 0.124129 , 0.215504 ) +colvars: ( 0.208832 , 0.134142 , 0.152227 ) +colvars: ( 0.115172 , 0.22077 , 0.21577 ) +colvars: ( 0.181105 , 0.0601262 , 0.0331193 ) +colvars: ( 0.129816 , 0.024725 , -0.0467234 ) +colvars: ( 0.217497 , 0.0334169 , 0.0180474 ) +colvars: ( 0.204427 , -0.0395403 , -0.0907781 ) +colvars: ( 0.242723 , -0.0440971 , -0.0740483 ) +colvars: ( 0.281303 , -0.126149 , -0.164391 ) +colvars: ( 0.236237 , -0.178898 , -0.264498 ) +colvars: ( 0.399068 , -0.142132 , -0.115671 ) +colvars: ( 0.478039 , -0.218225 , -0.173473 ) +colvars: ( 0.612593 , -0.222081 , -0.0978724 ) +colvars: ( 0.427601 , -0.221458 , -0.208287 ) +colvars: ( 0.433081 , -0.289542 , -0.29921 ) +colvars: ( 0.37612 , -0.147017 , -0.136236 ) +colvars: ( 0.31861 , -0.139457 , -0.160368 ) +colvars: ( 0.300234 , -0.0519593 , -0.0503347 ) +colvars: ( 0.192127 , -0.147055 , -0.246965 ) +colvars: ( 0.166176 , -0.188473 , -0.319892 ) +colvars: ( -0.0117145 , -0.191974 , -0.431741 ) +colvars: ( -0.105012 , -0.208896 , -0.51128 ) +colvars: ( 0.0925722 , -0.243456 , -0.440256 ) +colvars: ( 0.109222 , -0.106045 , -0.240081 ) +colvars: ( -0.0130582 , -0.109316 , -0.318161 ) +colvars: ( -0.103904 , -0.0279159 , -0.260159 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.84033 , 0.571928 , 1.60039 ) +colvars: ( 4.15058 , 0.490428 , 1.37234 ) +colvars: ( 4.15058 , 0.490428 , 1.37234 ) +colvars: ( 5.52869 , 0.653265 , 1.82799 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.627615 , -0.0803386 , -0.402643 ) +colvars: ( -0.562184 , -0.162644 , -0.375296 ) +colvars: ( -0.515953 , -0.140825 , -0.318333 ) +colvars: ( -0.518047 , -0.190518 , -0.343837 ) +colvars: ( -0.508418 , -0.132507 , -0.306808 ) +colvars: ( -0.488952 , -0.281898 , -0.357461 ) +colvars: ( -0.451039 , -0.322432 , -0.338247 ) +colvars: ( -0.425473 , -0.428821 , -0.362499 ) +colvars: ( -0.387791 , -0.287939 , -0.258132 ) +colvars: ( -0.38098 , -0.263262 , -0.239637 ) +colvars: ( -0.340955 , -0.282387 , -0.208214 ) +colvars: ( -0.2808 , -0.246314 , -0.130479 ) +colvars: ( -0.23476 , -0.261025 , -0.0909025 ) +colvars: ( -0.303266 , -0.144114 , -0.105067 ) +colvars: ( -0.270457 , -0.115588 , -0.0585038 ) +colvars: ( -0.361966 , -0.0867489 , -0.137354 ) +colvars: ( -0.39171 , 0.0106314 , -0.121561 ) +colvars: ( -0.447187 , 0.0584443 , -0.155089 ) +colvars: ( -0.426325 , 0.0253396 , -0.1496 ) +colvars: ( -0.414817 , 0.0812633 , -0.111655 ) +colvars: ( -0.467772 , -0.0279898 , -0.216562 ) +colvars: ( -0.49862 , -0.0296075 , -0.24848 ) +colvars: ( -0.54656 , -0.0940514 , -0.327231 ) +colvars: ( -0.441907 , -0.0600057 , -0.205507 ) +colvars: ( -0.447549 , -0.0166137 , -0.190782 ) +colvars: ( -0.384226 , -0.133894 , -0.182027 ) +colvars: ( -0.322539 , -0.16554 , -0.134618 ) +colvars: ( -0.269934 , -0.255015 , -0.123599 ) +colvars: ( -0.283142 , -0.0937417 , -0.061033 ) +colvars: ( -0.267372 , -0.0757326 , -0.036629 ) +colvars: ( -0.267846 , -0.0491024 , -0.0245742 ) +colvars: ( -0.234822 , 0.0246784 , 0.0435066 ) +colvars: ( -0.218371 , 0.0511056 , 0.0725609 ) +colvars: ( -0.280406 , 0.110676 , 0.0379434 ) +colvars: ( -0.252924 , 0.151626 , 0.0849745 ) +colvars: ( -0.351927 , 0.139056 , -0.0209354 ) +colvars: ( -0.401979 , 0.214633 , -0.0359157 ) +colvars: ( -0.476388 , 0.237661 , -0.10023 ) +colvars: ( -0.408716 , 0.194626 , -0.0521367 ) +colvars: ( -0.413196 , 0.254641 , -0.0284146 ) +colvars: ( -0.408976 , 0.108808 , -0.0927914 ) +colvars: ( -0.411141 , 0.0785735 , -0.109209 ) +colvars: ( -0.429281 , -0.0137024 , -0.170961 ) +colvars: ( -0.341333 , 0.0667333 , -0.0442755 ) +colvars: ( -0.342402 , 0.0924665 , -0.0332427 ) +colvars: ( -0.180342 , 0.0980697 , 0.133075 ) +colvars: ( -0.128647 , 0.099378 , 0.185903 ) +colvars: ( -0.212159 , 0.170121 , 0.134852 ) +colvars: ( -0.278541 , 0.026155 , 4.52214e-05 ) +colvars: ( -0.209019 , 0.0120352 , 0.0636175 ) +colvars: ( -0.153454 , -0.070413 , 0.080932 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 3. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 3. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atoms_new_colvar_forces = { ( -4.56487061011886e+00 , -4.59685831895255e-01 , -1.35233694819707e+00 ), ( -3.93238146654361e+00 , -3.88478641659634e-01 , -1.07107701968183e+00 ), ( -4.00408244135132e+00 , -4.14012759563741e-01 , -1.10605930645938e+00 ), ( -5.38471609876755e+00 , -5.85350253472914e-01 , -1.62403928539813e+00 ), ( 2.50197518083188e-01 , 1.16105599315324e-01 , 3.39056906872779e-01 ), ( 4.92615705354908e+00 , 6.35538871221162e-01 , 1.90779136990955e+00 ), ( 4.16304480640670e+00 , 5.29116839520988e-01 , 1.65361772228232e+00 ), ( -4.14949383727183e-02 , 3.07305285718129e-02 , 3.45408411279225e-01 ), ( 4.14342185132284e+00 , 5.19487842965588e-01 , 1.62282443813380e+00 ), ( 5.49185857422559e+00 , 6.66080075257598e-01 , 2.01839684326895e+00 ), ( 1.13735276396146e-02 , 3.94637412988196e-02 , 2.90095116759329e-01 ), ( -4.37980711462616e-04 , 3.29219895556979e-02 , 2.65567142933957e-01 ), ( 1.96493372913084e-02 , 4.67544004734959e-02 , 3.29032608954994e-01 ), ( 4.17517513185083e-02 , 3.63815161495367e-02 , 1.93226093065388e-01 ), ( 1.42613454118347e-02 , 2.21833393193577e-02 , 1.44393101146810e-01 ), ( 1.09566380540977e-01 , 5.52336030720906e-02 , 1.83742711865076e-01 ), ( 1.54760666636931e-01 , 6.02518219830255e-02 , 1.16794349329711e-01 ), ( 2.33208169185079e-01 , 8.53695062893084e-02 , 1.32417563596404e-01 ), ( 1.27169303485221e-01 , 4.37648180459563e-02 , 4.98102976435282e-02 ), ( 1.22549673285161e-01 , 3.47268139157361e-02 , -1.18451040129114e-02 ), ( 1.05535179110596e-01 , 3.88646125237500e-02 , 6.17863190148528e-02 ), ( 7.12637190605996e-02 , 2.18625136619909e-02 , 6.51885003976191e-03 ), ( 5.93534652820759e-02 , 2.24391092563474e-02 , 3.94210417867065e-02 ), ( -3.54900192036711e-04 , -2.51577365533177e-03 , -1.93718318195105e-02 ), ( -1.36306602564206e-02 , -1.47582898551569e-02 , -8.62299095607836e-02 ), ( -4.71627870611054e-02 , -9.76542623030544e-03 , 3.34769198330712e-02 ), ( -1.13707074495827e-01 , -3.13973323221215e-02 , 1.76093197346190e-02 ), ( -1.54761587457910e-01 , -3.42451509648487e-02 , 9.21709637097256e-02 ), ( -1.02036789446135e-01 , -3.36155506237409e-02 , -2.79137093293044e-02 ), ( -1.37556306244541e-01 , -5.10076308736129e-02 , -8.33523807337776e-02 ), ( -5.03494574316361e-02 , -1.56854513186011e-02 , -6.52673962942850e-03 ), ( -3.03949427132665e-02 , -1.48618314992314e-02 , -4.72714612957865e-02 ), ( 2.43523124840560e-02 , 7.00851641007569e-03 , -1.48746276996539e-03 ), ( 8.96461779929136e-04 , -1.54723804513230e-02 , -1.26448067123199e-01 ), ( -1.66866040324639e-02 , -2.72719594462136e-02 , -1.79523664908714e-01 ), ( 4.71411047327051e-02 , -3.07609723793698e-03 , -1.36606863263470e-01 ), ( 7.60594961592974e-02 , -3.59179757849404e-03 , -2.09388962054148e-01 ), ( 1.36205003469239e-01 , 1.55797619110987e-02 , -1.98102552728792e-01 ), ( 1.88850720429327e-02 , -2.68325710041684e-02 , -2.60423364304162e-01 ), ( 1.98842994345018e-02 , -3.49010102631597e-02 , -3.27624815446407e-01 ), ( -3.28557809917819e-02 , -3.82093859713364e-02 , -2.29027780483115e-01 ), ( -9.25307546435023e-02 , -6.08837585106190e-02 , -2.69576051073301e-01 ), ( -1.29046508739680e-01 , -6.56616889443625e-02 , -2.21295666946355e-01 ), ( -1.49206511158328e-01 , -8.03219299582977e-02 , -2.91240214591351e-01 ), ( -1.76225841867150e-01 , -9.60065163528050e-02 , -3.53134587891629e-01 ), ( -1.92056714839460e-01 , -9.39041113894416e-02 , -2.98666867374924e-01 ), ( -2.33658882296404e-01 , -1.09517546841951e-01 , -3.25376851383054e-01 ), ( -1.19587084081475e-01 , -7.33352095500071e-02 , -3.05404423424871e-01 ), ( -1.69318973902053e-01 , -7.98904179788683e-02 , -2.40035638596806e-01 ), ( -2.22076815170801e-01 , -9.72806075816354e-02 , -2.54543565760879e-01 ), ( -2.57357559050462e-01 , -9.83289077236454e-02 , -1.79226994917502e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 3, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 4 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 4, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 4, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 4, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 4, atoms_positions[size = 51] = { ( 8.39630587064579e+00 , 4.29943465782394e-02 , -7.52199108723305e-01 ), ( 6.99593233779914e+00 , -4.93189643592685e-01 , -6.60809448212279e-01 ), ( 6.25334620052430e+00 , -2.55576423048625e-01 , 6.52134952756242e-01 ), ( 5.00863481394510e+00 , -2.08509189081610e-01 , 6.56823873951176e-01 ), ( 7.03960944147393e+00 , -2.01594374016989e+00 , -1.02263212502426e+00 ), ( 6.90486605359888e+00 , -2.69474731448735e-01 , 1.79995455816582e+00 ), ( 6.17721298300845e+00 , -1.24592364672657e-01 , 3.05436709893728e+00 ), ( 7.18263050000036e+00 , -3.19480526235659e-01 , 4.30079231053380e+00 ), ( 5.30638862165417e+00 , 1.12357846240288e+00 , 3.27971835376572e+00 ), ( 4.08699891438005e+00 , 1.07094504461034e+00 , 3.61687655216301e+00 ), ( 5.87480603087758e+00 , 2.32183540838686e+00 , 2.96384694642444e+00 ), ( 5.22401915265732e+00 , 3.59700412458860e+00 , 2.88057747926707e+00 ), ( 6.33313533401084e+00 , 4.61702887256776e+00 , 2.46480269594214e+00 ), ( 3.89738305245604e+00 , 3.71211781175670e+00 , 2.02161270713417e+00 ), ( 2.91712091159561e+00 , 4.11519986001302e+00 , 2.55927131780976e+00 ), ( 3.82085076072587e+00 , 3.24332122198801e+00 , 7.80298010083329e-01 ), ( 2.66609412663421e+00 , 3.18393292087782e+00 , -8.09732098745300e-02 ), ( 3.04893607098911e+00 , 2.72636467572710e+00 , -1.59291650460730e+00 ), ( 1.63335066410015e+00 , 2.15440563920939e+00 , 5.80232627280548e-01 ), ( 4.29818984818214e-01 , 2.44050626812841e+00 , 5.61388467671019e-01 ), ( 1.97583065645857e+00 , 1.00857630417830e+00 , 1.05487824551291e+00 ), ( 1.13634226071496e+00 , 1.23089593893438e-02 , 1.68772194611812e+00 ), ( 2.01544817887602e+00 , -1.19309537116505e+00 , 2.02278050366493e+00 ), ( 5.08048336175847e-01 , 5.94101137645552e-01 , 3.00574686454125e+00 ), ( -6.78412934869142e-01 , 3.80967717896477e-01 , 3.18874653147992e+00 ), ( 1.28890187333229e+00 , 1.31089121022321e+00 , 3.82435149915531e+00 ), ( 8.22534449637726e-01 , 1.89379486709480e+00 , 5.07838479055152e+00 ), ( 2.06389289096600e+00 , 2.58645934212356e+00 , 5.62114574845432e+00 ), ( -3.57121046548542e-01 , 2.92054171335235e+00 , 4.98576532871696e+00 ), ( -1.17836314763820e+00 , 3.02261193921792e+00 , 5.90276985343399e+00 ), ( -4.01301426275823e-01 , 3.69849913582816e+00 , 3.86545359028066e+00 ), ( -1.46590819015392e+00 , 4.59865726720223e+00 , 3.53615951568706e+00 ), ( -7.63234155976260e-01 , 5.38072815661016e+00 , 2.40731489624795e+00 ), ( -2.71331069827867e+00 , 3.89707543976032e+00 , 2.93922599438776e+00 ), ( -3.85425520137104e+00 , 4.41458103160539e+00 , 2.85997009027781e+00 ), ( -2.56891327231543e+00 , 2.61382709061189e+00 , 2.50018343044392e+00 ), ( -3.72280990264342e+00 , 1.90196009531901e+00 , 2.07499763501250e+00 ), ( -3.40868018825125e+00 , 7.99802390159160e-01 , 1.00115989809505e+00 ), ( -4.32545326123900e+00 , 1.10899602039969e+00 , 3.22040107072979e+00 ), ( -5.53351212628670e+00 , 9.30424355623366e-01 , 3.34744388032221e+00 ), ( -3.47526168876013e+00 , 6.31186970943236e-01 , 4.16470822933633e+00 ), ( -3.76916025366485e+00 , 1.03561979531401e-01 , 5.47575484720759e+00 ), ( -2.42579310007635e+00 , -4.19509630099199e-01 , 6.13327791685099e+00 ), ( -4.46410471486241e+00 , 1.00719118603773e+00 , 6.41671194409057e+00 ), ( -5.32471233100479e+00 , 5.95667181679337e-01 , 7.18047936707207e+00 ), ( -6.29683336764235e+00 , 3.54744147510084e+00 , 6.69753385518659e+00 ), ( -6.91965812216361e+00 , 4.30777659601339e+00 , 7.41750168295901e+00 ), ( -6.75473038539063e+00 , 3.20844432219158e+00 , 5.50482636834567e+00 ), ( -4.08019852473436e+00 , 2.29656195202179e+00 , 6.47727219430328e+00 ), ( -4.91287960219249e+00 , 3.24198162568352e+00 , 7.21486613348559e+00 ), ( -4.06885052697904e+00 , 4.49555549485688e+00 , 7.26530725052506e+00 ) } +colvars: Step 4, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atom_groups_ids[size = 0] = +colvars: Step 4, atom_groups_refcount[size = 0] = +colvars: Step 4, atom_groups_masses[size = 0] = +colvars: Step 4, atom_groups_charges[size = 0] = +colvars: Step 4, atom_groups_coms[size = 0] = +colvars: Step 4, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 4, volmaps_ids[size = 0] = +colvars: Step 4, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 4 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.36592560477046e-01 , 5.33466425476265e-03 , 9.41635274184647e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.36592560477046e-01 , 5.33466425476265e-03 , 9.41635274184647e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.2499 , 1.84511 , -14.9291 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.2499 , 1.84511 , -14.9291 ) to colvar "one". +colvars: Adding total bias energy: 45.7669 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.2499 , 1.84511 , -14.9291 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.84306 , -0.570804 , -1.59539 ) +colvars: ( -4.15292 , -0.489465 , -1.36805 ) +colvars: ( -4.15292 , -0.489465 , -1.36805 ) +colvars: ( -5.53182 , -0.651981 , -1.82228 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.902607 , 0.192767 , 0.649526 ) +colvars: ( 0.780045 , 0.264756 , 0.67528 ) +colvars: ( 0.765734 , 0.257105 , 0.656115 ) +colvars: ( 0.664379 , 0.267042 , 0.608928 ) +colvars: ( 0.652243 , 0.200504 , 0.509757 ) +colvars: ( 0.574751 , 0.345598 , 0.663541 ) +colvars: ( 0.463648 , 0.36116 , 0.618264 ) +colvars: ( 0.384243 , 0.459583 , 0.706454 ) +colvars: ( 0.380828 , 0.317001 , 0.507517 ) +colvars: ( 0.344416 , 0.276046 , 0.429083 ) +colvars: ( 0.352477 , 0.321861 , 0.497191 ) +colvars: ( 0.280541 , 0.279216 , 0.395076 ) +colvars: ( 0.254535 , 0.307776 , 0.418884 ) +colvars: ( 0.345106 , 0.180475 , 0.297529 ) +colvars: ( 0.284877 , 0.137714 , 0.202288 ) +colvars: ( 0.471463 , 0.142003 , 0.320337 ) +colvars: ( 0.546302 , 0.0496451 , 0.237779 ) +colvars: ( 0.680042 , 0.0270031 , 0.286884 ) +colvars: ( 0.553398 , 0.018426 , 0.198934 ) +colvars: ( 0.537287 , -0.0465617 , 0.099515 ) +colvars: ( 0.573259 , 0.0668623 , 0.277753 ) +colvars: ( 0.569922 , 0.0514542 , 0.254472 ) +colvars: ( 0.605975 , 0.116495 , 0.365948 ) +colvars: ( 0.441761 , 0.0574199 , 0.185692 ) +colvars: ( 0.434165 , 0.00175912 , 0.104268 ) +colvars: ( 0.337376 , 0.124041 , 0.214957 ) +colvars: ( 0.209303 , 0.134004 , 0.15175 ) +colvars: ( 0.115732 , 0.220625 , 0.21513 ) +colvars: ( 0.181554 , 0.0599665 , 0.0328395 ) +colvars: ( 0.130354 , 0.0245276 , -0.0468646 ) +colvars: ( 0.217823 , 0.0332811 , 0.0177865 ) +colvars: ( 0.204712 , -0.0396912 , -0.0908564 ) +colvars: ( 0.242875 , -0.044215 , -0.0741694 ) +colvars: ( 0.281522 , -0.126301 , -0.164292 ) +colvars: ( 0.236504 , -0.179083 , -0.26423 ) +colvars: ( 0.39918 , -0.142248 , -0.115607 ) +colvars: ( 0.47809 , -0.21834 , -0.173259 ) +colvars: ( 0.612502 , -0.222146 , -0.0977414 ) +colvars: ( 0.427791 , -0.221611 , -0.208003 ) +colvars: ( 0.433276 , -0.289716 , -0.298749 ) +colvars: ( 0.376428 , -0.147181 , -0.136092 ) +colvars: ( 0.319062 , -0.139658 , -0.160177 ) +colvars: ( 0.300766 , -0.0521534 , -0.0503418 ) +colvars: ( 0.192714 , -0.147306 , -0.246666 ) +colvars: ( 0.166833 , -0.188756 , -0.319455 ) +colvars: ( -0.0110242 , -0.192291 , -0.431218 ) +colvars: ( -0.104221 , -0.209253 , -0.510647 ) +colvars: ( 0.0930934 , -0.243737 , -0.439689 ) +colvars: ( 0.109852 , -0.106305 , -0.239846 ) +colvars: ( -0.0123028 , -0.109622 , -0.317833 ) +colvars: ( -0.103074 , -0.0282269 , -0.259987 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.84306 , 0.570804 , 1.59539 ) +colvars: ( 4.15292 , 0.489465 , 1.36805 ) +colvars: ( 4.15292 , 0.489465 , 1.36805 ) +colvars: ( 5.53182 , 0.651981 , 1.82228 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.627104 , -0.0803608 , -0.401461 ) +colvars: ( -0.561809 , -0.162717 , -0.373921 ) +colvars: ( -0.515412 , -0.14086 , -0.31686 ) +colvars: ( -0.517883 , -0.190604 , -0.34256 ) +colvars: ( -0.508255 , -0.13254 , -0.305749 ) +colvars: ( -0.488975 , -0.282057 , -0.356018 ) +colvars: ( -0.451287 , -0.322617 , -0.336868 ) +colvars: ( -0.425887 , -0.429092 , -0.360877 ) +colvars: ( -0.388043 , -0.288072 , -0.256872 ) +colvars: ( -0.381332 , -0.263374 , -0.238572 ) +colvars: ( -0.341089 , -0.282497 , -0.206842 ) +colvars: ( -0.280912 , -0.246372 , -0.129207 ) +colvars: ( -0.234749 , -0.261076 , -0.0894365 ) +colvars: ( -0.303251 , -0.144089 , -0.104062 ) +colvars: ( -0.270507 , -0.115529 , -0.0576641 ) +colvars: ( -0.36177 , -0.086691 , -0.136397 ) +colvars: ( -0.391384 , 0.0107654 , -0.120851 ) +colvars: ( -0.446637 , 0.0586049 , -0.154349 ) +colvars: ( -0.426137 , 0.0254712 , -0.149096 ) +colvars: ( -0.414634 , 0.0814467 , -0.111367 ) +colvars: ( -0.467706 , -0.0279212 , -0.21599 ) +colvars: ( -0.498712 , -0.0295545 , -0.248072 ) +colvars: ( -0.546745 , -0.0940725 , -0.326685 ) +colvars: ( -0.442197 , -0.0599633 , -0.20517 ) +colvars: ( -0.447893 , -0.0165373 , -0.190668 ) +colvars: ( -0.384622 , -0.133898 , -0.1815 ) +colvars: ( -0.323109 , -0.165552 , -0.134132 ) +colvars: ( -0.270594 , -0.255088 , -0.12285 ) +colvars: ( -0.283628 , -0.0936773 , -0.0607249 ) +colvars: ( -0.26797 , -0.0756497 , -0.0364999 ) +colvars: ( -0.26813 , -0.0489899 , -0.024225 ) +colvars: ( -0.234999 , 0.0248681 , 0.0436921 ) +colvars: ( -0.218332 , 0.0513285 , 0.0728703 ) +colvars: ( -0.28052 , 0.110925 , 0.0378527 ) +colvars: ( -0.253073 , 0.151919 , 0.0846994 ) +colvars: ( -0.351951 , 0.139306 , -0.0210618 ) +colvars: ( -0.401953 , 0.214932 , -0.0362933 ) +colvars: ( -0.476225 , 0.237957 , -0.100575 ) +colvars: ( -0.408904 , 0.1949 , -0.0526585 ) +colvars: ( -0.413387 , 0.254965 , -0.0291688 ) +colvars: ( -0.409351 , 0.109005 , -0.0931761 ) +colvars: ( -0.411734 , 0.0787388 , -0.109701 ) +colvars: ( -0.430024 , -0.0136259 , -0.17126 ) +colvars: ( -0.342057 , 0.0669099 , -0.0448369 ) +colvars: ( -0.343224 , 0.0926625 , -0.0340042 ) +colvars: ( -0.181048 , 0.0983297 , 0.132455 ) +colvars: ( -0.129447 , 0.0996551 , 0.185195 ) +colvars: ( -0.212637 , 0.170437 , 0.134181 ) +colvars: ( -0.279269 , 0.0263186 , -0.000349039 ) +colvars: ( -0.209862 , 0.0122083 , 0.0631773 ) +colvars: ( -0.154364 , -0.0702927 , 0.0807534 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 4. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 4. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atoms_new_colvar_forces = { ( -4.56755970043401e+00 , -4.58398711848707e-01 , -1.34732300742556e+00 ), ( -3.93468791836226e+00 , -3.87426465624286e-01 , -1.06668606236787e+00 ), ( -4.00642888403167e+00 , -4.13027385595220e-01 , -1.10167706048978e+00 ), ( -5.38782761704673e+00 , -5.84016677733107e-01 , -1.61826841698039e+00 ), ( 2.50321504886440e-01 , 1.16245295489213e-01 , 3.39255398975650e-01 ), ( 4.92883736981228e+00 , 6.34345651122820e-01 , 1.90291170887934e+00 ), ( 4.16528605368736e+00 , 5.28007727220982e-01 , 1.64944100269517e+00 ), ( -4.16437368020444e-02 , 3.04913040696692e-02 , 3.45576187807646e-01 ), ( 4.14570946719244e+00 , 5.18393800215361e-01 , 1.61869086476715e+00 ), ( 5.49489950751797e+00 , 6.64653134297239e-01 , 2.01278646669079e+00 ), ( 1.13883455696422e-02 , 3.93643843013007e-02 , 2.90349004028925e-01 ), ( -3.70807556216823e-04 , 3.28447072483438e-02 , 2.65869032407028e-01 ), ( 1.97859397429609e-02 , 4.66996762106549e-02 , 3.29447457923400e-01 ), ( 4.18548301059438e-02 , 3.63860215155832e-02 , 1.93467465381695e-01 ), ( 1.43695494209841e-02 , 2.21852577237395e-02 , 1.44623595784099e-01 ), ( 1.09692872721714e-01 , 5.53120347165737e-02 , 1.83939950194680e-01 ), ( 1.54918505135066e-01 , 6.04105659645602e-02 , 1.16927864882144e-01 ), ( 2.33404078254006e-01 , 8.56079164497673e-02 , 1.32534946989211e-01 ), ( 1.27260876156989e-01 , 4.38971456075600e-02 , 4.98382262109091e-02 ), ( 1.22653529168925e-01 , 3.48850093387145e-02 , -1.18519795553965e-02 ), ( 1.05553360591133e-01 , 3.89411671411217e-02 , 6.17627536192067e-02 ), ( 7.12101521699346e-02 , 2.18996851388409e-02 , 6.39972885720105e-03 ), ( 5.92298878883137e-02 , 2.24222184028202e-02 , 3.92631636924738e-02 ), ( -4.35588411519083e-04 , -2.54337581643551e-03 , -1.94776782216607e-02 ), ( -1.37281194031207e-02 , -1.47782136067391e-02 , -8.63993568512332e-02 ), ( -4.72453442307985e-02 , -9.85634197974009e-03 , 3.34569676626325e-02 ), ( -1.13805860803223e-01 , -3.15478085997175e-02 , 1.76186612653798e-02 ), ( -1.54862439390776e-01 , -3.44626087716927e-02 , 9.22792674757840e-02 ), ( -1.02073944256152e-01 , -3.37107738130019e-02 , -2.78854802297323e-02 ), ( -1.37616345424722e-01 , -5.11220622448815e-02 , -8.33644381165563e-02 ), ( -5.03064636035201e-02 , -1.57087122606304e-02 , -6.43850145005012e-03 ), ( -3.02871431291500e-02 , -1.48230430191508e-02 , -4.71643061872050e-02 ), ( 2.45431398711071e-02 , 7.11348030937944e-03 , -1.29905709631239e-03 ), ( 1.00196235262762e-03 , -1.53752966528304e-02 , -1.26439733331159e-01 ), ( -1.65687790100254e-02 , -2.71638812066232e-02 , -1.79530900424476e-01 ), ( 4.72288447177213e-02 , -2.94176658105896e-03 , -1.36669240405971e-01 ), ( 7.61365023631097e-02 , -3.40748521546808e-03 , -2.09551895307170e-01 ), ( 1.36276780675960e-01 , 1.58104907876680e-02 , -1.98316673595567e-01 ), ( 1.88869653133905e-02 , -2.67110483526931e-02 , -2.60661022091157e-01 ), ( 1.98888205232494e-02 , -3.47506266933952e-02 , -3.27917879997113e-01 ), ( -3.29227145289210e-02 , -3.81760368618233e-02 , -2.29267730012848e-01 ), ( -9.26719967181926e-02 , -6.09192490450635e-02 , -2.69878585659409e-01 ), ( -1.29258162337561e-01 , -6.57793184853189e-02 , -2.21601756566605e-01 ), ( -1.49342140870217e-01 , -8.03964576088819e-02 , -2.91503175829467e-01 ), ( -1.76391190701122e-01 , -9.60931232258814e-02 , -3.53458718354442e-01 ), ( -1.92071864528452e-01 , -9.39612737579393e-02 , -2.98763154821138e-01 ), ( -2.33668423067563e-01 , -1.09598401532826e-01 , -3.25451669556599e-01 ), ( -1.19544086295381e-01 , -7.33003482140267e-02 , -3.05508177947573e-01 ), ( -1.69416922526762e-01 , -7.99868253862246e-02 , -2.40194602873481e-01 ), ( -2.22165149877229e-01 , -9.74137079021122e-02 , -2.54655982572481e-01 ), ( -2.57437502491945e-01 , -9.85196456364392e-02 , -1.79233471872105e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 4, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 5 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 5, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 5, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 5, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 5, atoms_positions[size = 51] = { ( 8.38826312441025e+00 , 4.32888237930165e-02 , -7.54675773037975e-01 ), ( 6.99401820014457e+00 , -4.98814692882301e-01 , -6.55412617370388e-01 ), ( 6.25553939543217e+00 , -2.59136807844394e-01 , 6.59061145245593e-01 ), ( 5.00241331038846e+00 , -2.07780021618727e-01 , 6.62310517785252e-01 ), ( 7.04065218160799e+00 , -2.01833631588376e+00 , -1.01694795435808e+00 ), ( 6.90394945934699e+00 , -2.69627423956689e-01 , 1.80743544886632e+00 ), ( 6.17687930822337e+00 , -1.22440873196289e-01 , 3.06343563573041e+00 ), ( 7.17537831251022e+00 , -3.21243267443331e-01 , 4.29853733458758e+00 ), ( 5.30553815329920e+00 , 1.11989718325646e+00 , 3.28558165082311e+00 ), ( 4.08841558874180e+00 , 1.06801273878407e+00 , 3.62074729123617e+00 ), ( 5.87539437014727e+00 , 2.31240698981955e+00 , 2.97013979692365e+00 ), ( 5.22045553148862e+00 , 3.59633905368878e+00 , 2.88134102962379e+00 ), ( 6.33556785019079e+00 , 4.60686978260033e+00 , 2.46153202451686e+00 ), ( 3.89733815963180e+00 , 3.71958256211498e+00 , 2.02068427507450e+00 ), ( 2.90986815591977e+00 , 4.11525632332891e+00 , 2.55392464879702e+00 ), ( 3.82401942445680e+00 , 3.24274539244656e+00 , 7.77213156482582e-01 ), ( 2.66882752044054e+00 , 3.17373646269596e+00 , -8.63455684056099e-02 ), ( 3.04771552949509e+00 , 2.72378753594042e+00 , -1.59629639528942e+00 ), ( 1.62300085673154e+00 , 2.15239258201508e+00 , 5.82562684490643e-01 ), ( 4.32822116349314e-01 , 2.44779921445653e+00 , 5.56964352470077e-01 ), ( 1.97245902367590e+00 , 1.01153179605837e+00 , 1.05347444161927e+00 ), ( 1.14378127395772e+00 , 1.32526980536757e-02 , 1.68846421958047e+00 ), ( 2.01515457557546e+00 , -1.18697461776164e+00 , 2.02187446643857e+00 ), ( 5.13510131564253e-01 , 5.99454131544490e-01 , 2.99941530739477e+00 ), ( -6.75608864846344e-01 , 3.76333381606639e-01 , 3.18545385099906e+00 ), ( 1.29542211863670e+00 , 1.31432351581721e+00 , 3.82604713879422e+00 ), ( 8.29534604581958e-01 , 1.90018079264796e+00 , 5.07401854513477e+00 ), ( 2.05856363564941e+00 , 2.58942602120153e+00 , 5.62179434951341e+00 ), ( -3.58859976297028e-01 , 2.92014631902862e+00 , 4.98512722536177e+00 ), ( -1.17612766767868e+00 , 3.02608003185974e+00 , 5.90402944495260e+00 ), ( -4.08861565874776e-01 , 3.69412626548260e+00 , 3.86107612713235e+00 ), ( -1.46993085000088e+00 , 4.59050357313592e+00 , 3.53748159806234e+00 ), ( -7.59061023216564e-01 , 5.38308591896450e+00 , 2.40952232961719e+00 ), ( -2.71897816168511e+00 , 3.89602914930668e+00 , 2.93626552401718e+00 ), ( -3.85356068716273e+00 , 4.42028349637097e+00 , 2.85514810456908e+00 ), ( -2.57516889268564e+00 , 2.61161662691592e+00 , 2.49527974380284e+00 ), ( -3.71923442891987e+00 , 1.90738900127391e+00 , 2.07104008103557e+00 ), ( -3.41086464468343e+00 , 8.05652926698358e-01 , 9.93708353839769e-01 ), ( -4.31703059699794e+00 , 1.10221203230376e+00 , 3.22564085779991e+00 ), ( -5.53582774533983e+00 , 9.23270006620592e-01 , 3.34544140351197e+00 ), ( -3.46995064414351e+00 , 6.33935530671426e-01 , 4.15753540802055e+00 ), ( -3.77419317548219e+00 , 1.00549858819052e-01 , 5.47895461462770e+00 ), ( -2.41708481082698e+00 , -4.09546097586824e-01 , 6.13752475430754e+00 ), ( -4.46669955995532e+00 , 1.00204957729110e+00 , 6.41689844970049e+00 ), ( -5.32378814837926e+00 , 5.98706771018336e-01 , 7.18237841153734e+00 ), ( -6.29749438766859e+00 , 3.54903428818487e+00 , 6.69965967371175e+00 ), ( -6.91624074182789e+00 , 4.30429019871442e+00 , 7.41755872782235e+00 ), ( -6.75003990259343e+00 , 3.20870922124133e+00 , 5.50823685204315e+00 ), ( -4.08349342960840e+00 , 2.29945882106867e+00 , 6.47979179303521e+00 ), ( -4.91012602716345e+00 , 3.23790127696191e+00 , 7.21413892695397e+00 ), ( -4.07391902579364e+00 , 4.50301961064101e+00 , 7.26796867056682e+00 ) } +colvars: Step 5, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atom_groups_ids[size = 0] = +colvars: Step 5, atom_groups_refcount[size = 0] = +colvars: Step 5, atom_groups_masses[size = 0] = +colvars: Step 5, atom_groups_charges[size = 0] = +colvars: Step 5, atom_groups_coms[size = 0] = +colvars: Step 5, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 5, volmaps_ids[size = 0] = +colvars: Step 5, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 5 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.35182699996778e-01 , 5.02452781962055e-03 , 9.42139751705160e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.35182699996778e-01 , 5.02452781962055e-03 , 9.42139751705160e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.2217 , 1.85131 , -14.9392 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.2217 , 1.85131 , -14.9392 ) to colvar "one". +colvars: Adding total bias energy: 45.7091 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.2217 , 1.85131 , -14.9392 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.84643 , -0.569343 , -1.58917 ) +colvars: ( -4.15581 , -0.488211 , -1.36271 ) +colvars: ( -4.15581 , -0.488211 , -1.36271 ) +colvars: ( -5.53566 , -0.650312 , -1.81517 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.90213 , 0.19297 , 0.648149 ) +colvars: ( 0.779712 , 0.264921 , 0.673806 ) +colvars: ( 0.765315 , 0.257295 , 0.654659 ) +colvars: ( 0.664234 , 0.267138 , 0.607557 ) +colvars: ( 0.652109 , 0.20058 , 0.508584 ) +colvars: ( 0.574758 , 0.345658 , 0.662034 ) +colvars: ( 0.463847 , 0.361153 , 0.61682 ) +colvars: ( 0.384576 , 0.459552 , 0.704808 ) +colvars: ( 0.38108 , 0.31696 , 0.506263 ) +colvars: ( 0.344749 , 0.275966 , 0.427983 ) +colvars: ( 0.352677 , 0.321836 , 0.495935 ) +colvars: ( 0.280774 , 0.279164 , 0.393995 ) +colvars: ( 0.25471 , 0.307747 , 0.417731 ) +colvars: ( 0.345236 , 0.180437 , 0.296666 ) +colvars: ( 0.285082 , 0.137636 , 0.201598 ) +colvars: ( 0.471419 , 0.142021 , 0.319468 ) +colvars: ( 0.546147 , 0.0496815 , 0.237101 ) +colvars: ( 0.679683 , 0.0271096 , 0.286145 ) +colvars: ( 0.55332 , 0.0184306 , 0.198352 ) +colvars: ( 0.537227 , -0.0465799 , 0.0991299 ) +colvars: ( 0.573237 , 0.0668629 , 0.277029 ) +colvars: ( 0.569993 , 0.0514208 , 0.253808 ) +colvars: ( 0.606074 , 0.116471 , 0.365081 ) +colvars: ( 0.442019 , 0.057318 , 0.18513 ) +colvars: ( 0.434463 , 0.00163008 , 0.103875 ) +colvars: ( 0.33775 , 0.12391 , 0.214297 ) +colvars: ( 0.20985 , 0.13381 , 0.151178 ) +colvars: ( 0.116377 , 0.220413 , 0.214393 ) +colvars: ( 0.182074 , 0.0597604 , 0.0324908 ) +colvars: ( 0.13097 , 0.0242779 , -0.0470627 ) +colvars: ( 0.218208 , 0.0331147 , 0.0174665 ) +colvars: ( 0.205048 , -0.0398613 , -0.0909691 ) +colvars: ( 0.243066 , -0.0443367 , -0.0743187 ) +colvars: ( 0.281785 , -0.126462 , -0.164225 ) +colvars: ( 0.236816 , -0.179277 , -0.263975 ) +colvars: ( 0.399324 , -0.142366 , -0.115595 ) +colvars: ( 0.478166 , -0.218449 , -0.173096 ) +colvars: ( 0.612422 , -0.222196 , -0.0976857 ) +colvars: ( 0.42802 , -0.221774 , -0.207772 ) +colvars: ( 0.433508 , -0.289896 , -0.29833 ) +colvars: ( 0.376788 , -0.147371 , -0.136015 ) +colvars: ( 0.319579 , -0.139901 , -0.160058 ) +colvars: ( 0.301373 , -0.0524053 , -0.050442 ) +colvars: ( 0.193379 , -0.147609 , -0.246415 ) +colvars: ( 0.167573 , -0.189094 , -0.319056 ) +colvars: ( -0.0102493 , -0.192656 , -0.430682 ) +colvars: ( -0.103337 , -0.209665 , -0.509981 ) +colvars: ( 0.093682 , -0.244047 , -0.439109 ) +colvars: ( 0.110564 , -0.10662 , -0.239645 ) +colvars: ( -0.0114541 , -0.109991 , -0.317518 ) +colvars: ( -0.10214 , -0.0286097 , -0.259825 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.84643 , 0.569343 , 1.58917 ) +colvars: ( 4.15581 , 0.488211 , 1.36271 ) +colvars: ( 4.15581 , 0.488211 , 1.36271 ) +colvars: ( 5.53566 , 0.650312 , 1.81517 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.626509 , -0.0803844 , -0.400005 ) +colvars: ( -0.56138 , -0.162767 , -0.372276 ) +colvars: ( -0.514815 , -0.140885 , -0.315136 ) +colvars: ( -0.517698 , -0.19065 , -0.341035 ) +colvars: ( -0.508071 , -0.132545 , -0.304472 ) +colvars: ( -0.489004 , -0.282145 , -0.354315 ) +colvars: ( -0.451571 , -0.322711 , -0.335245 ) +colvars: ( -0.426362 , -0.42924 , -0.358989 ) +colvars: ( -0.388347 , -0.288123 , -0.25541 ) +colvars: ( -0.381747 , -0.263404 , -0.237326 ) +colvars: ( -0.341276 , -0.282532 , -0.205284 ) +colvars: ( -0.281091 , -0.246364 , -0.12779 ) +colvars: ( -0.234806 , -0.261066 , -0.0878318 ) +colvars: ( -0.303283 , -0.144028 , -0.102935 ) +colvars: ( -0.270618 , -0.115437 , -0.0567348 ) +colvars: ( -0.361587 , -0.086619 , -0.135305 ) +colvars: ( -0.391049 , 0.0108852 , -0.120025 ) +colvars: ( -0.446043 , 0.0587294 , -0.153471 ) +colvars: ( -0.425943 , 0.0255928 , -0.148475 ) +colvars: ( -0.414448 , 0.081608 , -0.110991 ) +colvars: ( -0.467636 , -0.0278437 , -0.215269 ) +colvars: ( -0.498806 , -0.0294836 , -0.247509 ) +colvars: ( -0.546931 , -0.0940559 , -0.325943 ) +colvars: ( -0.442522 , -0.0598865 , -0.204704 ) +colvars: ( -0.448276 , -0.0164332 , -0.190445 ) +colvars: ( -0.38508 , -0.133845 , -0.180848 ) +colvars: ( -0.323774 , -0.165494 , -0.133546 ) +colvars: ( -0.271374 , -0.255066 , -0.121994 ) +colvars: ( -0.284211 , -0.0935622 , -0.06036 ) +colvars: ( -0.268679 , -0.0755144 , -0.0363361 ) +colvars: ( -0.268493 , -0.0488475 , -0.0238308 ) +colvars: ( -0.235253 , 0.0250653 , 0.0438838 ) +colvars: ( -0.218354 , 0.0515414 , 0.0731819 ) +colvars: ( -0.280692 , 0.11116 , 0.0377568 ) +colvars: ( -0.253289 , 0.15219 , 0.0843872 ) +colvars: ( -0.352005 , 0.139532 , -0.0211668 ) +colvars: ( -0.401939 , 0.215188 , -0.0366553 ) +colvars: ( -0.476041 , 0.238197 , -0.100872 ) +colvars: ( -0.409123 , 0.195147 , -0.0531677 ) +colvars: ( -0.413605 , 0.255249 , -0.0299338 ) +colvars: ( -0.409775 , 0.109203 , -0.0935246 ) +colvars: ( -0.412396 , 0.0789234 , -0.110159 ) +colvars: ( -0.430848 , -0.0135015 , -0.171487 ) +colvars: ( -0.342879 , 0.0671146 , -0.0453985 ) +colvars: ( -0.344154 , 0.0928863 , -0.0347829 ) +colvars: ( -0.181891 , 0.0986082 , 0.131751 ) +colvars: ( -0.130408 , 0.0999549 , 0.184372 ) +colvars: ( -0.213223 , 0.170743 , 0.133424 ) +colvars: ( -0.280113 , 0.0265189 , -0.000755106 ) +colvars: ( -0.210852 , 0.0124267 , 0.0626921 ) +colvars: ( -0.155442 , -0.0701059 , 0.0805347 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 5. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 5. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atoms_new_colvar_forces = { ( -4.57080684447655e+00 , -4.56757474205258e-01 , -1.34102307171331e+00 ), ( -3.93747933215641e+00 , -3.86057338789111e-01 , -1.06117980046159e+00 ), ( -4.00927585857282e+00 , -4.11723324486918e-01 , -1.09618838089752e+00 ), ( -5.39162219427185e+00 , -5.82277485042152e-01 , -1.61105752315784e+00 ), ( 2.50499884075726e-01 , 1.16409947280580e-01 , 3.39523401748820e-01 ), ( 4.93218264419087e+00 , 6.32855477223542e-01 , 1.89688596676198e+00 ), ( 4.16808727784256e+00 , 5.26653504109717e-01 , 1.64428538084388e+00 ), ( -4.17860487363991e-02 , 3.03117103968229e-02 , 3.45818921212498e-01 ), ( 4.14854415606074e+00 , 5.17048519073003e-01 , 1.61356370786374e+00 ), ( 5.49866324358008e+00 , 6.62873647003371e-01 , 2.00582619307530e+00 ), ( 1.14012440143183e-02 , 3.93035748419776e-02 , 2.90650467510932e-01 ), ( -3.17040350262143e-04 , 3.27998909670149e-02 , 2.66204944764889e-01 ), ( 1.99039043264463e-02 , 4.66806301700874e-02 , 3.29898912273345e-01 ), ( 4.19527538390151e-02 , 3.64083238256336e-02 , 1.93730700466022e-01 ), ( 1.44638449731704e-02 , 2.21994295576479e-02 , 1.44863533841288e-01 ), ( 1.09831626893484e-01 , 5.54016538627385e-02 , 1.84162532551469e-01 ), ( 1.55098431698864e-01 , 6.05666978079027e-02 , 1.17076539039485e-01 ), ( 2.33640235017002e-01 , 8.58390448148273e-02 , 1.32674281012204e-01 ), ( 1.27377000149962e-01 , 4.40233800636930e-02 , 4.98767088688037e-02 ), ( 1.22779275317610e-01 , 3.50280548828395e-02 , -1.18610391719648e-02 ), ( 1.05600645114430e-01 , 3.90191934872285e-02 , 6.17601479328360e-02 ), ( 7.11868109790795e-02 , 2.19371933538081e-02 , 6.29890121668214e-03 ), ( 5.91433406710006e-02 , 2.24153630278143e-02 , 3.91381972993816e-02 ), ( -5.03685952378485e-04 , -2.56847520689389e-03 , -1.95745320550648e-02 ), ( -1.38137677312026e-02 , -1.48030671154608e-02 , -8.65701004571590e-02 ), ( -4.73300457103983e-02 , -9.93470162873675e-03 , 3.34491547077175e-02 ), ( -1.13924654194938e-01 , -3.16831573457569e-02 , 1.76315017947849e-02 ), ( -1.54996461323862e-01 , -3.46521916242989e-02 , 9.23985997100513e-02 ), ( -1.02136551133698e-01 , -3.38017646487173e-02 , -2.78692317279842e-02 ), ( -1.37708661800939e-01 , -5.12364765932485e-02 , -8.33987592573597e-02 ), ( -5.02856010121193e-02 , -1.57328062474774e-02 , -6.36429116155157e-03 ), ( -3.02049049275266e-02 , -1.47959889480401e-02 , -4.70852908917164e-02 ), ( 2.47119619522573e-02 , 7.20466392188440e-03 , -1.13681819999997e-03 ), ( 1.09277549907982e-03 , -1.53025068800609e-02 , -1.26468416302199e-01 ), ( -1.64724043297200e-02 , -2.70872431561396e-02 , -1.79588114525385e-01 ), ( 4.73190353632281e-02 , -2.83458982824220e-03 , -1.36761747937318e-01 ), ( 7.62273370426887e-02 , -3.26132908138688e-03 , -2.09751788637767e-01 ), ( 1.36381644721633e-01 , 1.60015897261400e-02 , -1.98557429325506e-01 ), ( 1.88972130932885e-02 , -2.66267328650469e-02 , -2.60940000748580e-01 ), ( 1.99023246462202e-02 , -3.46469713197062e-02 , -3.28263746013194e-01 ), ( -3.29869544103972e-02 , -3.81682488079819e-02 , -2.29539878144585e-01 ), ( -9.28170291224147e-02 , -6.09778122526505e-02 , -2.70216370990327e-01 ), ( -1.29474503398891e-01 , -6.59067902809915e-02 , -2.21928981664928e-01 ), ( -1.49499695039101e-01 , -8.04942388469761e-02 , -2.91813060961600e-01 ), ( -1.76581536684527e-01 , -9.62081310288704e-02 , -3.53839012520408e-01 ), ( -1.92140739724632e-01 , -9.40480253856186e-02 , -2.98931372311928e-01 ), ( -2.33745114138208e-01 , -1.09710568743338e-01 , -3.25609015287589e-01 ), ( -1.19541366284067e-01 , -7.33037889823187e-02 , -3.05684612691047e-01 ), ( -1.69549392593515e-01 , -8.01006867640513e-02 , -2.40400237740579e-01 ), ( -2.22305627275974e-01 , -9.75639286307687e-02 , -2.54825659835956e-01 ), ( -2.57582595709948e-01 , -9.87156446620556e-02 , -1.79290409704149e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 5, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 6 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 6, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 6, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 6, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 6, atoms_positions[size = 51] = { ( 8.38021201992906e+00 , 4.35622795205877e-02 , -7.57115549324088e-01 ), ( 6.99262075636104e+00 , -5.04815880767098e-01 , -6.50451452925487e-01 ), ( 6.25524799500166e+00 , -2.63667412648881e-01 , 6.65189730502905e-01 ), ( 4.99690128414275e+00 , -2.06630997050247e-01 , 6.67638995185915e-01 ), ( 7.04200716597089e+00 , -2.02050994511587e+00 , -1.01097403828471e+00 ), ( 6.90323517761355e+00 , -2.69573324907610e-01 , 1.81488311154711e+00 ), ( 6.17714731650717e+00 , -1.20515781462237e-01 , 3.07447537163275e+00 ), ( 7.16724113885896e+00 , -3.23458232146617e-01 , 4.29582213736862e+00 ), ( 5.30371594464467e+00 , 1.11714457836753e+00 , 3.29116469814723e+00 ), ( 4.09124849388116e+00 , 1.06501228412928e+00 , 3.62450262691055e+00 ), ( 5.87592866731547e+00 , 2.30253352539849e+00 , 2.97596071644480e+00 ), ( 5.21721389427611e+00 , 3.59596879390688e+00 , 2.88231338201453e+00 ), ( 6.33732766261078e+00 , 4.59629301054931e+00 , 2.45820200815087e+00 ), ( 3.89841652616976e+00 , 3.72602361681020e+00 , 2.02059671909465e+00 ), ( 2.90163811499207e+00 , 4.11598602240834e+00 , 2.54893878749135e+00 ), ( 3.82824919667602e+00 , 3.24208207942299e+00 , 7.73397951419180e-01 ), ( 2.67104733587927e+00 , 3.16251592386761e+00 , -9.10789941855962e-02 ), ( 3.04589936923495e+00 , 2.72187283946001e+00 , -1.59753742891037e+00 ), ( 1.61199981524947e+00 , 2.15269245744589e+00 , 5.82542052598303e-01 ), ( 4.35751799960440e-01 , 2.45515498134900e+00 , 5.52825511508801e-01 ), ( 1.97036780896963e+00 , 1.01273359174694e+00 , 1.05319136812280e+00 ), ( 1.15110250994451e+00 , 1.59855514824167e-02 , 1.68932967303409e+00 ), ( 2.01511729620419e+00 , -1.18091189184246e+00 , 2.02057383850610e+00 ), ( 5.19105471671030e-01 , 6.03751819725599e-01 , 2.99163240110414e+00 ), ( -6.72886335070202e-01 , 3.71984468858815e-01 , 3.18262593486689e+00 ), ( 1.30139050900177e+00 , 1.31799183325441e+00 , 3.82827802807958e+00 ), ( 8.36262416995475e-01 , 1.90659178940060e+00 , 5.06918797411790e+00 ), ( 2.05272790066819e+00 , 2.59249147938586e+00 , 5.62268788668921e+00 ), ( -3.59893314125172e-01 , 2.91963533099828e+00 , 4.98445769700446e+00 ), ( -1.17391249997732e+00 , 3.02952357363619e+00 , 5.90496283539945e+00 ), ( -4.16789831385964e-01 , 3.68860637085030e+00 , 3.85705143789314e+00 ), ( -1.47348624273045e+00 , 4.58263341198187e+00 , 3.53823008437198e+00 ), ( -7.54821420980561e-01 , 5.38550361473275e+00 , 2.41225635423488e+00 ), ( -2.72548455940354e+00 , 3.89460562853851e+00 , 2.93352283387009e+00 ), ( -3.85198517324324e+00 , 4.42597164355928e+00 , 2.85066191943228e+00 ), ( -2.58094023964050e+00 , 2.61071842582377e+00 , 2.49004794895700e+00 ), ( -3.71683196204322e+00 , 1.91061848615932e+00 , 2.06642203885726e+00 ), ( -3.41290123558981e+00 , 8.12251625818482e-01 , 9.85897670341821e-01 ), ( -4.30943088113364e+00 , 1.09535078280136e+00 , 3.23137618348510e+00 ), ( -5.53785685645807e+00 , 9.16210965946274e-01 , 3.34334002368099e+00 ), ( -3.46429849587187e+00 , 6.37594506320484e-01 , 4.15073901356801e+00 ), ( -3.77774838928890e+00 , 9.59601976211820e-02 , 5.48141661971274e+00 ), ( -2.40925846838727e+00 , -3.98892124368813e-01 , 6.14186628363733e+00 ), ( -4.46908183155242e+00 , 9.97824625721238e-01 , 6.41787423491210e+00 ), ( -5.32321128737128e+00 , 6.01484903984397e-01 , 7.18429115422948e+00 ), ( -6.29685375196358e+00 , 3.55127290010162e+00 , 6.70152734031360e+00 ), ( -6.91388693893618e+00 , 4.30123660545722e+00 , 7.41816638381674e+00 ), ( -6.74629264999051e+00 , 3.20880368173676e+00 , 5.51156283491087e+00 ), ( -4.08754871373955e+00 , 2.30173173767669e+00 , 6.48165063911067e+00 ), ( -4.90580092458475e+00 , 3.23290383832168e+00 , 7.21354073589404e+00 ), ( -4.07873592871374e+00 , 4.51178543035802e+00 , 7.27132768660334e+00 ) } +colvars: Step 6, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_ids[size = 0] = +colvars: Step 6, atom_groups_refcount[size = 0] = +colvars: Step 6, atom_groups_masses[size = 0] = +colvars: Step 6, atom_groups_charges[size = 0] = +colvars: Step 6, atom_groups_coms[size = 0] = +colvars: Step 6, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 6, volmaps_ids[size = 0] = +colvars: Step 6, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 6 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.33541437426750e-01 , 4.81523415673580e-03 , 9.42723142306008e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.33541437426750e-01 , 4.81523415673580e-03 , 9.42723142306008e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.1888 , 1.8555 , -14.9509 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.1888 , 1.8555 , -14.9509 ) to colvar "one". +colvars: Adding total bias energy: 45.6413 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.1888 , 1.8555 , -14.9509 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.85038 , -0.567546 , -1.5818 ) +colvars: ( -4.1592 , -0.486671 , -1.35639 ) +colvars: ( -4.1592 , -0.486671 , -1.35639 ) +colvars: ( -5.54018 , -0.648259 , -1.80676 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.901641 , 0.193183 , 0.646578 ) +colvars: ( 0.779379 , 0.265084 , 0.672145 ) +colvars: ( 0.764888 , 0.257493 , 0.653031 ) +colvars: ( 0.664104 , 0.267219 , 0.606012 ) +colvars: ( 0.651991 , 0.200643 , 0.507252 ) +colvars: ( 0.574797 , 0.345684 , 0.660348 ) +colvars: ( 0.464093 , 0.361099 , 0.615206 ) +colvars: ( 0.384969 , 0.459456 , 0.702981 ) +colvars: ( 0.381382 , 0.316874 , 0.504866 ) +colvars: ( 0.345139 , 0.275836 , 0.426748 ) +colvars: ( 0.352924 , 0.321772 , 0.494547 ) +colvars: ( 0.281055 , 0.279078 , 0.392807 ) +colvars: ( 0.25493 , 0.30769 , 0.416479 ) +colvars: ( 0.345404 , 0.180378 , 0.295708 ) +colvars: ( 0.285329 , 0.137537 , 0.200832 ) +colvars: ( 0.471397 , 0.142033 , 0.318494 ) +colvars: ( 0.546003 , 0.0497262 , 0.236327 ) +colvars: ( 0.679318 , 0.0272402 , 0.285298 ) +colvars: ( 0.553258 , 0.0184365 , 0.197669 ) +colvars: ( 0.537182 , -0.0465929 , 0.0986598 ) +colvars: ( 0.573236 , 0.0668538 , 0.276184 ) +colvars: ( 0.570093 , 0.0513687 , 0.253018 ) +colvars: ( 0.606206 , 0.116419 , 0.364061 ) +colvars: ( 0.442321 , 0.0571844 , 0.184457 ) +colvars: ( 0.434807 , 0.00146932 , 0.103379 ) +colvars: ( 0.33818 , 0.123737 , 0.213531 ) +colvars: ( 0.210467 , 0.133562 , 0.150515 ) +colvars: ( 0.117104 , 0.220136 , 0.213566 ) +colvars: ( 0.182661 , 0.0595102 , 0.0320774 ) +colvars: ( 0.131661 , 0.0239791 , -0.047314 ) +colvars: ( 0.218647 , 0.0329188 , 0.0170909 ) +colvars: ( 0.205434 , -0.0400493 , -0.0911145 ) +colvars: ( 0.243294 , -0.0444622 , -0.0744956 ) +colvars: ( 0.282088 , -0.126633 , -0.164188 ) +colvars: ( 0.237173 , -0.179479 , -0.263732 ) +colvars: ( 0.3995 , -0.142487 , -0.115631 ) +colvars: ( 0.478266 , -0.218552 , -0.172983 ) +colvars: ( 0.612353 , -0.22223 , -0.0977002 ) +colvars: ( 0.428284 , -0.221944 , -0.207592 ) +colvars: ( 0.433774 , -0.290079 , -0.297949 ) +colvars: ( 0.377195 , -0.147585 , -0.136002 ) +colvars: ( 0.320158 , -0.140183 , -0.160003 ) +colvars: ( 0.302051 , -0.0527111 , -0.0506283 ) +colvars: ( 0.194117 , -0.147958 , -0.246205 ) +colvars: ( 0.168392 , -0.189483 , -0.318693 ) +colvars: ( -0.00939214 , -0.193064 , -0.430133 ) +colvars: ( -0.102361 , -0.210124 , -0.509284 ) +colvars: ( 0.094336 , -0.244381 , -0.438516 ) +colvars: ( 0.111355 , -0.106983 , -0.239476 ) +colvars: ( -0.0105149 , -0.110415 , -0.317213 ) +colvars: ( -0.101108 , -0.0290579 , -0.259673 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.85038 , 0.567546 , 1.5818 ) +colvars: ( 4.1592 , 0.486671 , 1.35639 ) +colvars: ( 4.1592 , 0.486671 , 1.35639 ) +colvars: ( 5.54018 , 0.648259 , 1.80676 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.625835 , -0.0804071 , -0.398294 ) +colvars: ( -0.560902 , -0.162793 , -0.37038 ) +colvars: ( -0.514164 , -0.1409 , -0.313178 ) +colvars: ( -0.517493 , -0.190657 , -0.339281 ) +colvars: ( -0.507867 , -0.132524 , -0.302991 ) +colvars: ( -0.489037 , -0.282167 , -0.352372 ) +colvars: ( -0.451889 , -0.322721 , -0.333395 ) +colvars: ( -0.426892 , -0.429274 , -0.356855 ) +colvars: ( -0.388699 , -0.288097 , -0.253762 ) +colvars: ( -0.38222 , -0.263357 , -0.235911 ) +colvars: ( -0.341512 , -0.282498 , -0.203554 ) +colvars: ( -0.28133 , -0.246297 , -0.126237 ) +colvars: ( -0.234925 , -0.261 , -0.0860976 ) +colvars: ( -0.303358 , -0.143934 , -0.101695 ) +colvars: ( -0.270783 , -0.115314 , -0.0557208 ) +colvars: ( -0.361416 , -0.0865334 , -0.134086 ) +colvars: ( -0.390706 , 0.0109931 , -0.119088 ) +colvars: ( -0.445407 , 0.0588221 , -0.152464 ) +colvars: ( -0.425744 , 0.0257071 , -0.147744 ) +colvars: ( -0.414259 , 0.0817507 , -0.110531 ) +colvars: ( -0.467563 , -0.027756 , -0.214408 ) +colvars: ( -0.498903 , -0.0293939 , -0.246804 ) +colvars: ( -0.547117 , -0.0940021 , -0.325019 ) +colvars: ( -0.442882 , -0.0597757 , -0.20412 ) +colvars: ( -0.448696 , -0.0163008 , -0.190121 ) +colvars: ( -0.385596 , -0.133739 , -0.180079 ) +colvars: ( -0.324528 , -0.165367 , -0.132869 ) +colvars: ( -0.272264 , -0.254954 , -0.121039 ) +colvars: ( -0.284882 , -0.0933989 , -0.0599412 ) +colvars: ( -0.269489 , -0.075329 , -0.036139 ) +colvars: ( -0.268931 , -0.0486762 , -0.0233934 ) +colvars: ( -0.235578 , 0.0252706 , 0.0440836 ) +colvars: ( -0.218432 , 0.0517461 , 0.0734982 ) +colvars: ( -0.280917 , 0.111383 , 0.0376588 ) +colvars: ( -0.253567 , 0.152443 , 0.0840435 ) +colvars: ( -0.352088 , 0.139737 , -0.0212495 ) +colvars: ( -0.401936 , 0.215405 , -0.0370002 ) +colvars: ( -0.475837 , 0.23839 , -0.10112 ) +colvars: ( -0.409369 , 0.195371 , -0.0536629 ) +colvars: ( -0.413849 , 0.255498 , -0.0307062 ) +colvars: ( -0.410244 , 0.109405 , -0.0938378 ) +colvars: ( -0.413122 , 0.0791291 , -0.110582 ) +colvars: ( -0.431746 , -0.0133296 , -0.171647 ) +colvars: ( -0.343793 , 0.0673481 , -0.0459587 ) +colvars: ( -0.345184 , 0.0931388 , -0.035576 ) +colvars: ( -0.182863 , 0.0989059 , 0.13097 ) +colvars: ( -0.131518 , 0.100277 , 0.183445 ) +colvars: ( -0.213909 , 0.171044 , 0.132591 ) +colvars: ( -0.281066 , 0.0267554 , -0.00117054 ) +colvars: ( -0.211976 , 0.0126889 , 0.0621667 ) +colvars: ( -0.156676 , -0.0698563 , 0.0802804 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 6. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 6. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atoms_new_colvar_forces = { ( -4.57457590091407e+00 , -4.54769792276199e-01 , -1.33351707855332e+00 ), ( -3.94072400108378e+00 , -3.84380271113976e-01 , -1.05462859139149e+00 ), ( -4.01258945124985e+00 , -4.10109375456033e-01 , -1.08966275115916e+00 ), ( -5.39605214643696e+00 , -5.80140582968099e-01 , -1.60249485637283e+00 ), ( 2.50724548660147e-01 , 1.16592979696714e-01 , 3.39852632993541e-01 ), ( 4.93614108413631e+00 , 6.31063238128868e-01 , 1.88977701154470e+00 ), ( 4.17140544998400e+00 , 5.25048525480392e-01 , 1.63820398799561e+00 ), ( -4.19233568377603e-02 , 3.01812045108948e-02 , 3.46126386938239e-01 ), ( 4.15188469720697e+00 , 5.15447446166591e-01 , 1.60749792277893e+00 ), ( 5.50309595182518e+00 , 6.60739122455141e-01 , 1.99759268427134e+00 ), ( 1.14119430284726e-02 , 3.92738611795704e-02 , 2.90993062355441e-01 ), ( -2.75358202559972e-04 , 3.27811062718754e-02 , 2.66570139588651e-01 ), ( 2.00051288091696e-02 , 4.66898393156434e-02 , 3.30381886686014e-01 ), ( 4.20458379946161e-02 , 3.64444128073375e-02 , 1.94012894368770e-01 ), ( 1.45458339541725e-02 , 2.22230271631906e-02 , 1.45111545271329e-01 ), ( 1.09980586478823e-01 , 5.54992517679401e-02 , 1.84407419045777e-01 ), ( 1.55297160248552e-01 , 6.07192690646057e-02 , 1.17238922544312e-01 ), ( 2.33910828741050e-01 , 8.60622613534296e-02 , 1.32833565871435e-01 ), ( 1.27514196804622e-01 , 4.41436407988194e-02 , 4.99248708458485e-02 ), ( 1.22923907696598e-01 , 3.51577700283853e-02 , -1.18714649727845e-02 ), ( 1.05672931481030e-01 , 3.90977730899397e-02 , 6.17761989815965e-02 ), ( 7.11895650300886e-02 , 2.19747986094425e-02 , 6.21434578213198e-03 ), ( 5.90887226343063e-02 , 2.24167941881323e-02 , 3.90421673496766e-02 ), ( -5.60854668515354e-04 , -2.59123290819695e-03 , -1.96635008192578e-02 ), ( -1.38890313213493e-02 , -1.48314610215812e-02 , -8.67418934573790e-02 ), ( -4.74166351608394e-02 , -1.00023195858622e-02 , 3.34516895036507e-02 ), ( -1.14060720473267e-01 , -3.18052610494058e-02 , 1.76468853341181e-02 ), ( -1.55159256123518e-01 , -3.48179780444641e-02 , 9.25267549914819e-02 ), ( -1.02221065357800e-01 , -3.38886349648099e-02 , -2.78638372939027e-02 ), ( -1.37828667250468e-01 , -5.13499038997308e-02 , -8.34529773880383e-02 ), ( -5.02838432334893e-02 , -1.57574706892050e-02 , -6.30253794941990e-03 ), ( -3.01446766030854e-02 , -1.47786917641173e-02 , -4.70309076154132e-02 ), ( 2.48617336337160e-02 , 7.28381713931851e-03 , -9.97329476770725e-04 ), ( 1.17111278742887e-03 , -1.52498038272826e-02 , -1.26529222394273e-01 ), ( -1.63942486188990e-02 , -2.70364317515549e-02 , -1.79688761882733e-01 ), ( 4.74115681131560e-02 , -2.74999557612118e-03 , -1.36880149751937e-01 ), ( 7.63304734857032e-02 , -3.14677873538044e-03 , -2.09983299662943e-01 ), ( 1.36515415149144e-01 , 1.61595861306180e-02 , -1.98820545958617e-01 ), ( 1.89151549537173e-02 , -2.65726554723585e-02 , -2.61254566381825e-01 ), ( 1.99241892300920e-02 , -3.45812794293266e-02 , -3.28655113023876e-01 ), ( -3.30484240030184e-02 , -3.81807226834966e-02 , -2.29839916874141e-01 ), ( -9.29647904685690e-02 , -6.10540128733924e-02 , -2.70584900912252e-01 ), ( -1.29694415948701e-01 , -6.60407161880313e-02 , -2.22274856383424e-01 ), ( -1.49675593189720e-01 , -8.06095207714782e-02 , -2.92164093126229e-01 ), ( -1.76792755195341e-01 , -9.63445469293042e-02 , -3.54268538508474e-01 ), ( -1.92255432658238e-01 , -9.41576450489818e-02 , -2.99162749866294e-01 ), ( -2.33879163494353e-01 , -1.09846797309254e-01 , -3.25838911485061e-01 ), ( -1.19572861011783e-01 , -7.33377688046537e-02 , -3.05924542942689e-01 ), ( -1.69711186872272e-01 , -8.02273904813037e-02 , -2.40646967816807e-01 ), ( -2.22490615695736e-01 , -9.77264749791153e-02 , -2.55045883517791e-01 ), ( -2.57783569993132e-01 , -9.89142087441336e-02 , -1.79392228103473e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 6, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 7 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 7, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 7, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 7, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 7, atoms_positions[size = 51] = { ( 8.37216689789659e+00 , 4.37901021565677e-02 , -7.59411723254822e-01 ), ( 6.99173054907958e+00 , -5.11003354462312e-01 , -6.45907471420836e-01 ), ( 6.25221119267448e+00 , -2.69091534483833e-01 , 6.70571886292195e-01 ), ( 4.99228195304877e+00 , -2.05086330889782e-01 , 6.72814098426171e-01 ), ( 7.04359599190517e+00 , -2.02253704031353e+00 , -1.00477459978557e+00 ), ( 6.90267241837949e+00 , -2.69335919735951e-01 , 1.82217587835446e+00 ), ( 6.17792876764567e+00 , -1.18953323080614e-01 , 3.08719841013444e+00 ), ( 7.15838402043010e+00 , -3.26081341049786e-01 , 4.29286456775614e+00 ), ( 5.30112870328665e+00 , 1.11522696219995e+00 , 3.29649468447787e+00 ), ( 4.09534266970237e+00 , 1.06195563949245e+00 , 3.62817802468735e+00 ), ( 5.87626839767972e+00 , 2.29259571261726e+00 , 2.98121564432398e+00 ), ( 5.21461288512338e+00 , 3.59576583004550e+00 , 2.88360626769294e+00 ), ( 6.33840920834483e+00 , 4.58549358015512e+00 , 2.45476724732243e+00 ), ( 3.90032408292894e+00 , 3.73133036989772e+00 , 2.02124029549192e+00 ), ( 2.89255588836865e+00 , 4.11737318509602e+00 , 2.54428457609364e+00 ), ( 3.83356219454626e+00 , 3.24142387567202e+00 , 7.69050780996117e-01 ), ( 2.67251421064126e+00 , 3.15034569878916e+00 , -9.51577527267812e-02 ), ( 3.04368512113888e+00 , 2.72066769781539e+00 , -1.59666941033504e+00 ), ( 1.60112724258352e+00 , 2.15518793050311e+00 , 5.80068295548032e-01 ), ( 4.38233270168014e-01 , 2.46262153981858e+00 , 5.48981598165023e-01 ), ( 1.96958751120776e+00 , 1.01234128829259e+00 , 1.05408371514749e+00 ), ( 1.15807522608227e+00 , 2.06027233883888e-02 , 1.69020068061949e+00 ), ( 2.01540564756394e+00 , -1.17487324590962e+00 , 2.01894159981868e+00 ), ( 5.24663007784567e-01 , 6.06965819914373e-01 , 2.98277643258594e+00 ), ( -6.70090969972222e-01 , 3.67974474617330e-01 , 3.18020553481106e+00 ), ( 1.30679036128140e+00 , 1.32183633270117e+00 , 3.83074757279869e+00 ), ( 8.42488195596810e-01 , 1.91297572203268e+00 , 5.06403148238549e+00 ), ( 2.04677603931843e+00 , 2.59577348740326e+00 , 5.62384342827763e+00 ), ( -3.60180939664793e-01 , 2.91906679253784e+00 , 4.98365594086841e+00 ), ( -1.17172989361066e+00 , 3.03291389730550e+00 , 5.90559291049596e+00 ), ( -4.24939831007310e-01 , 3.68185624142305e+00 , 3.85350870437035e+00 ), ( -1.47667593349521e+00 , 4.57531737478610e+00 , 3.53820703004744e+00 ), ( -7.50487409870848e-01 , 5.38790604517640e+00 , 2.41552088477231e+00 ), ( -2.73259917625150e+00 , 3.89276123730311e+00 , 2.93095501406970e+00 ), ( -3.84966840439603e+00 , 4.43165783486031e+00 , 2.84649266920355e+00 ), ( -2.58608181826962e+00 , 2.61135617881768e+00 , 2.48459688257362e+00 ), ( -3.71575716909455e+00 , 1.91132912833534e+00 , 2.06115901113227e+00 ), ( -3.41465732316873e+00 , 8.19462590483590e-01 , 9.77757428708235e-01 ), ( -4.30317407348321e+00 , 1.08871154582173e+00 , 3.23705656315551e+00 ), ( -5.53930318891123e+00 , 9.09237161496671e-01 , 3.34118827929819e+00 ), ( -3.45825224147659e+00 , 6.41909647597761e-01 , 4.14490520440339e+00 ), ( -3.77963526796013e+00 , 8.99923158144878e-02 , 5.48281966476050e+00 ), ( -2.40241084597597e+00 , -3.87809119227215e-01 , 6.14623871747730e+00 ), ( -4.47116968586997e+00 , 9.94765591923464e-01 , 6.41959234942850e+00 ), ( -5.32306816356207e+00 , 6.03907780412336e-01 , 7.18626963175422e+00 ), ( -6.29471935298229e+00 , 3.55391001295303e+00 , 6.70311288498439e+00 ), ( -6.91268166174429e+00 , 4.29872678709487e+00 , 7.41942409497783e+00 ), ( -6.74358894487107e+00 , 3.20874084258452e+00 , 5.51469129648207e+00 ), ( -4.09219714159797e+00 , 2.30306276865046e+00 , 6.48264861014977e+00 ), ( -4.90006546259677e+00 , 3.22721863105854e+00 , 7.21309658831055e+00 ), ( -4.08320233912291e+00 , 4.52152873527003e+00 , 7.27521294593529e+00 ) } +colvars: Step 7, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_ids[size = 0] = +colvars: Step 7, atom_groups_refcount[size = 0] = +colvars: Step 7, atom_groups_masses[size = 0] = +colvars: Step 7, atom_groups_charges[size = 0] = +colvars: Step 7, atom_groups_coms[size = 0] = +colvars: Step 7, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 7, volmaps_ids[size = 0] = +colvars: Step 7, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 7 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.31688046920632e-01 , 4.68707413595258e-03 , 9.43377480580293e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.31688046920632e-01 , 4.68707413595258e-03 , 9.43377480580293e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.1518 , 1.85806 , -14.9639 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.1518 , 1.85806 , -14.9639 ) to colvar "one". +colvars: Adding total bias energy: 45.5643 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.1518 , 1.85806 , -14.9639 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.85485 , -0.565432 , -1.5734 ) +colvars: ( -4.16303 , -0.484858 , -1.34919 ) +colvars: ( -4.16303 , -0.484858 , -1.34919 ) +colvars: ( -5.54528 , -0.645845 , -1.79716 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.901133 , 0.193401 , 0.644831 ) +colvars: ( 0.779041 , 0.265239 , 0.670314 ) +colvars: ( 0.76445 , 0.257694 , 0.651244 ) +colvars: ( 0.663985 , 0.267279 , 0.604309 ) +colvars: ( 0.651883 , 0.200691 , 0.505776 ) +colvars: ( 0.574859 , 0.345676 , 0.658498 ) +colvars: ( 0.46438 , 0.360995 , 0.613435 ) +colvars: ( 0.385415 , 0.459294 , 0.700988 ) +colvars: ( 0.381729 , 0.316741 , 0.503336 ) +colvars: ( 0.345579 , 0.275658 , 0.425392 ) +colvars: ( 0.353211 , 0.321669 , 0.493039 ) +colvars: ( 0.281378 , 0.278957 , 0.391523 ) +colvars: ( 0.255188 , 0.307604 , 0.415137 ) +colvars: ( 0.345603 , 0.180299 , 0.294663 ) +colvars: ( 0.285614 , 0.137417 , 0.199996 ) +colvars: ( 0.471392 , 0.142036 , 0.317424 ) +colvars: ( 0.545865 , 0.049776 , 0.235465 ) +colvars: ( 0.678942 , 0.0273897 , 0.284351 ) +colvars: ( 0.553209 , 0.018442 , 0.196895 ) +colvars: ( 0.53715 , -0.0466022 , 0.098113 ) +colvars: ( 0.573252 , 0.0668338 , 0.275229 ) +colvars: ( 0.570216 , 0.0512977 , 0.252113 ) +colvars: ( 0.606365 , 0.116338 , 0.362902 ) +colvars: ( 0.442663 , 0.0570208 , 0.183683 ) +colvars: ( 0.435193 , 0.00127931 , 0.102791 ) +colvars: ( 0.33866 , 0.123523 , 0.212668 ) +colvars: ( 0.211149 , 0.133263 , 0.149772 ) +colvars: ( 0.117906 , 0.219797 , 0.212656 ) +colvars: ( 0.183309 , 0.0592197 , 0.0316057 ) +colvars: ( 0.13242 , 0.0236363 , -0.0476128 ) +colvars: ( 0.219137 , 0.0326958 , 0.0166649 ) +colvars: ( 0.205864 , -0.0402532 , -0.0912891 ) +colvars: ( 0.243556 , -0.044591 , -0.0746975 ) +colvars: ( 0.282429 , -0.126809 , -0.164177 ) +colvars: ( 0.237569 , -0.179685 , -0.263499 ) +colvars: ( 0.399702 , -0.142608 , -0.115709 ) +colvars: ( 0.478385 , -0.218648 , -0.172912 ) +colvars: ( 0.61229 , -0.22225 , -0.0977766 ) +colvars: ( 0.42858 , -0.222118 , -0.207454 ) +colvars: ( 0.43407 , -0.290263 , -0.2976 ) +colvars: ( 0.377647 , -0.14782 , -0.136044 ) +colvars: ( 0.320792 , -0.140498 , -0.160004 ) +colvars: ( 0.302795 , -0.0530645 , -0.0508904 ) +colvars: ( 0.194924 , -0.148346 , -0.246032 ) +colvars: ( 0.169284 , -0.189914 , -0.318358 ) +colvars: ( -0.00845748 , -0.193505 , -0.42957 ) +colvars: ( -0.1013 , -0.210621 , -0.508556 ) +colvars: ( 0.0950515 , -0.244734 , -0.437909 ) +colvars: ( 0.112219 , -0.107388 , -0.239335 ) +colvars: ( -0.00949102 , -0.110888 , -0.316915 ) +colvars: ( -0.099982 , -0.0295633 , -0.259527 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.85485 , 0.565432 , 1.5734 ) +colvars: ( 4.16303 , 0.484858 , 1.34919 ) +colvars: ( 4.16303 , 0.484858 , 1.34919 ) +colvars: ( 5.54528 , 0.645845 , 1.79716 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.625093 , -0.0804276 , -0.396358 ) +colvars: ( -0.560381 , -0.162799 , -0.368263 ) +colvars: ( -0.513465 , -0.140907 , -0.311013 ) +colvars: ( -0.51727 , -0.190629 , -0.337324 ) +colvars: ( -0.507647 , -0.132478 , -0.30133 ) +colvars: ( -0.489074 , -0.282131 , -0.350216 ) +colvars: ( -0.452237 , -0.322655 , -0.331346 ) +colvars: ( -0.427473 , -0.429208 , -0.354503 ) +colvars: ( -0.389093 , -0.288003 , -0.251948 ) +colvars: ( -0.382743 , -0.263241 , -0.234348 ) +colvars: ( -0.341791 , -0.282403 , -0.20167 ) +colvars: ( -0.281622 , -0.246177 , -0.124564 ) +colvars: ( -0.235095 , -0.260886 , -0.084247 ) +colvars: ( -0.303468 , -0.14381 , -0.100353 ) +colvars: ( -0.270996 , -0.115164 , -0.05463 ) +colvars: ( -0.361254 , -0.0864348 , -0.132753 ) +colvars: ( -0.390355 , 0.0110919 , -0.118052 ) +colvars: ( -0.444733 , 0.0588882 , -0.151341 ) +colvars: ( -0.425541 , 0.0258167 , -0.146914 ) +colvars: ( -0.414066 , 0.0818792 , -0.109995 ) +colvars: ( -0.467487 , -0.0276577 , -0.213421 ) +colvars: ( -0.499004 , -0.0292854 , -0.24597 ) +colvars: ( -0.547306 , -0.0939133 , -0.323933 ) +colvars: ( -0.443272 , -0.0596328 , -0.203429 ) +colvars: ( -0.449149 , -0.0161412 , -0.189706 ) +colvars: ( -0.386164 , -0.133585 , -0.179206 ) +colvars: ( -0.325359 , -0.16518 , -0.132108 ) +colvars: ( -0.273251 , -0.254763 , -0.119995 ) +colvars: ( -0.285632 , -0.0931916 , -0.0594732 ) +colvars: ( -0.27039 , -0.075098 , -0.0359107 ) +colvars: ( -0.269434 , -0.0484783 , -0.0229157 ) +colvars: ( -0.235966 , 0.0254846 , 0.0442931 ) +colvars: ( -0.218559 , 0.0519446 , 0.0738219 ) +colvars: ( -0.281189 , 0.111598 , 0.0375617 ) +colvars: ( -0.253899 , 0.152681 , 0.0836751 ) +colvars: ( -0.352196 , 0.139926 , -0.0213099 ) +colvars: ( -0.401942 , 0.215593 , -0.0373274 ) +colvars: ( -0.475618 , 0.238543 , -0.101324 ) +colvars: ( -0.40964 , 0.195579 , -0.0541433 ) +colvars: ( -0.414117 , 0.25572 , -0.0314825 ) +colvars: ( -0.410754 , 0.109613 , -0.0941181 ) +colvars: ( -0.413907 , 0.0793564 , -0.110974 ) +colvars: ( -0.432712 , -0.0131131 , -0.171746 ) +colvars: ( -0.34479 , 0.0676101 , -0.0465161 ) +colvars: ( -0.346304 , 0.0934199 , -0.0363803 ) +colvars: ( -0.183948 , 0.0992229 , 0.130125 ) +colvars: ( -0.132758 , 0.100623 , 0.182429 ) +colvars: ( -0.214682 , 0.171341 , 0.131694 ) +colvars: ( -0.282114 , 0.0270264 , -0.00159238 ) +colvars: ( -0.213219 , 0.012992 , 0.061608 ) +colvars: ( -0.158046 , -0.0695496 , 0.0799967 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 7. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 7. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atoms_new_colvar_forces = { ( -4.57881203862854e+00 , -4.52458345793086e-01 , -1.32492776682226e+00 ), ( -3.94437384767086e+00 , -3.82417843017137e-01 , -1.04713994835495e+00 ), ( -4.01631867516224e+00 , -4.08208157242501e-01 , -1.08220634144740e+00 ), ( -5.40104624412911e+00 , -5.77631414378630e-01 , -1.59271593308303e+00 ), ( 2.50984966528159e-01 , 1.16787110595548e-01 , 3.40231544502879e-01 ), ( 4.94063698000285e+00 , 6.28976582484485e-01 , 1.88168352904184e+00 ), ( 4.17517745135057e+00 , 5.23197450817813e-01 , 1.63128052240920e+00 ), ( -4.20576341559172e-02 , 3.00860374184086e-02 , 3.46484923582174e-01 ), ( 4.15567049794573e+00 , 5.13596645883970e-01 , 1.60057985982117e+00 ), ( 5.50811824623009e+00 , 6.58262060591907e-01 , 1.98820557210076e+00 ), ( 1.14203592291789e-02 , 3.92658818748587e-02 , 2.91368412510501e-01 ), ( -2.43584894888960e-04 , 3.27803392663165e-02 , 2.66958721176205e-01 ), ( 2.00927636844206e-02 , 4.67182343113446e-02 , 3.30890207317210e-01 ), ( 4.21348827655389e-02 , 3.64895436103206e-02 , 1.94310464858261e-01 ), ( 1.46180376589936e-02 , 2.22527232081962e-02 , 1.45366201047434e-01 ), ( 1.10137344647507e-01 , 5.56013586772384e-02 , 1.84670598380992e-01 ), ( 1.55510598512366e-01 , 6.08678727783858e-02 , 1.17412964942392e-01 ), ( 2.34208401915362e-01 , 8.62778847570254e-02 , 1.33009786672209e-01 ), ( 1.27667927087642e-01 , 4.42586584499522e-02 , 4.99812886998157e-02 ), ( 1.23083500300451e-01 , 3.52770442088739e-02 , -1.18824088660680e-02 ), ( 1.05764707525599e-01 , 3.91761163391697e-02 , 6.18074492802734e-02 ), ( 7.12126795258260e-02 , 2.20123250534493e-02 , 6.14286387951918e-03 ), ( 5.90588761872212e-02 , 2.24242570234704e-02 , 3.89691217501037e-02 ), ( -6.09530360472066e-04 , -2.61200572806048e-03 , -1.97463383138328e-02 ), ( -1.39561171330660e-02 , -1.48618650562138e-02 , -8.69147276533931e-02 ), ( -4.75048814931489e-02 , -1.00617973682600e-02 , 3.34621595037623e-02 ), ( -1.14210487647717e-01 , -3.19170509843065e-02 , 1.76637592968527e-02 ), ( -1.55344913649278e-01 , -3.49658124342954e-02 , 9.26612570797246e-02 ), ( -1.02322737878863e-01 , -3.39719229125203e-02 , -2.78674605719969e-02 ), ( -1.37970280897008e-01 , -5.14616706976876e-02 , -8.35235536373673e-02 ), ( -5.02969831431410e-02 , -1.57824537127487e-02 , -6.25077624580102e-03 ), ( -3.01014536880143e-02 , -1.47685444530168e-02 , -4.69960206071053e-02 ), ( 2.49968386091572e-02 , 7.35359067746522e-03 , -8.75526166746188e-04 ), ( 1.24006954608552e-03 , -1.52116641400138e-02 , -1.26615382461637e-01 ), ( -1.63298505474880e-02 , -2.70041779785319e-02 , -1.79823789126329e-01 ), ( 4.75063265139463e-02 , -2.68188527752566e-03 , -1.37018835573269e-01 ), ( 7.64437698499632e-02 , -3.05515994060623e-03 , -2.10239569080751e-01 ), ( 1.36672325487755e-01 , 1.62933078486417e-02 , -1.99100878528603e-01 ), ( 1.89396477903299e-02 , -2.65399369148128e-02 , -2.61597355036449e-01 ), ( 1.99532646554350e-02 , -3.45423922930599e-02 , -3.29082575762017e-01 ), ( -3.31073554508113e-02 , -3.82069868180719e-02 , -2.30162342620894e-01 ), ( -9.31143410004120e-02 , -6.11415380356488e-02 , -2.70978402664321e-01 ), ( -1.29916968755332e-01 , -6.61776222449396e-02 , -2.22636324356853e-01 ), ( -1.49865463946659e-01 , -8.07357596419478e-02 , -2.92548538421674e-01 ), ( -1.77019843655578e-01 , -9.64944012637901e-02 , -3.54738040576786e-01 ), ( -1.92405447073281e-01 , -9.42822745455138e-02 , -2.99444973862644e-01 ), ( -2.34057515354482e-01 , -1.09998681358580e-01 , -3.26127242550109e-01 ), ( -1.19630494885950e-01 , -7.33927701270712e-02 , -3.06215255951226e-01 ), ( -1.69895608366100e-01 , -8.03618298557150e-02 , -2.40927071349435e-01 ), ( -2.22710088160625e-01 , -9.78961594255737e-02 , -2.55307146559071e-01 ), ( -2.58028075821192e-01 , -9.91129022369759e-02 , -1.79530681601258e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 7, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 8 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 8, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 8, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 8, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 8, atoms_positions[size = 51] = { ( 8.36414562955246e+00 , 4.39491520117101e-02 , -7.61465752784014e-01 ), ( 6.99124365928816e+00 , -5.17168081148215e-01 , -6.41722339118265e-01 ), ( 6.24642810472991e+00 , -2.75322333841344e-01 , 6.75295340628177e-01 ), ( 4.98862323934973e+00 , -2.03175910272633e-01 , 6.77834882121448e-01 ), ( 7.04533790569600e+00 , -2.02448926271327e+00 , -9.98429050453915e-01 ), ( 6.90217139512517e+00 , -2.68933690729307e-01 , 1.82923166797993e+00 ), ( 6.17910591250209e+00 , -1.17889565169931e-01 , 3.10120127862239e+00 ), ( 7.14900881728461e+00 , -3.29048642728293e-01 , 4.28990368612928e+00 ), ( 5.29807241339890e+00 , 1.11399743146709e+00 , 3.30159846251327e+00 ), ( 4.10048248387142e+00 , 1.05886027048216e+00 , 3.63182068564134e+00 ), ( 5.87627128395544e+00 , 2.28297783431676e+00 , 2.98582534532623e+00 ), ( 5.21291751013209e+00 , 3.59559249648075e+00 , 2.88530813891945e+00 ), ( 6.33882055167443e+00 , 4.57468564952785e+00 , 2.45114548842214e+00 ), ( 3.90270476849195e+00 , 3.73543946966959e+00 , 2.02249299328080e+00 ), ( 2.88279899651480e+00 , 4.11937654924065e+00 , 2.53991298785212e+00 ), ( 3.83994916640648e+00 , 3.24085633863087e+00 , 7.64389773024474e-01 ), ( 2.67304378296441e+00 , 3.13733741515520e+00 , -9.86014610419304e-02 ), ( 3.04127619585192e+00 , 2.72015813917021e+00 , -1.59378650427401e+00 ), ( 1.59114910455646e+00 , 2.15957060798836e+00 , 5.75176375064758e-01 ), ( 4.39898768954398e-01 , 2.47026507927626e+00 , 5.45423000782526e-01 ), ( 1.97013573003170e+00 , 1.01068491768257e+00 , 1.05609300283235e+00 ), ( 1.16447767483790e+00 , 2.70492508108200e-02 , 1.69098108917443e+00 ), ( 2.01605815135543e+00 , -1.16883679388384e+00 , 2.01706039103549e+00 ), ( 5.30011373102028e-01 , 6.09134564598044e-01 , 2.97330411338839e+00 ), ( -6.67073156924597e-01 , 3.64345499449882e-01 , 3.17812208143694e+00 ), ( 1.31160615660600e+00 , 1.32575664901383e+00 , 3.83310879776563e+00 ), ( 8.47993750313544e-01 , 1.91929252820542e+00 , 5.05871476478534e+00 ), ( 2.04113716352292e+00 , 2.59938327267694e+00 , 5.62529864458867e+00 ), ( -3.59722350522117e-01 , 2.91849518036233e+00 , 4.98264198214745e+00 ), ( -1.16958058346025e+00 , 3.03622187083803e+00 , 5.90593641611715e+00 ), ( -4.33163554736300e-01 , 3.67383514574877e+00 , 3.85056023167338e+00 ), ( -1.47963774811415e+00 , 4.56877579992782e+00 , 3.53722432686352e+00 ), ( -7.46039498319265e-01 , 5.39024221562592e+00 , 2.41926953184947e+00 ), ( -2.74001310166305e+00 , 3.89049424798704e+00 , 2.92852320403613e+00 ), ( -3.84678053760197e+00 , 4.43736504431714e+00 , 2.84262148699286e+00 ), ( -2.59051894955208e+00 , 2.61364284712942e+00 , 2.47900930243999e+00 ), ( -3.71607674693391e+00 , 1.90935976894779e+00 , 2.05532296722771e+00 ), ( -3.41601193968398e+00 , 8.27113019808494e-01 , 9.69328172836758e-01 ), ( -4.29867066960749e+00 , 1.08257393526329e+00 , 3.24215630625605e+00 ), ( -5.53992972413454e+00 , 9.02333823848470e-01 , 3.33904409628711e+00 ), ( -3.45177678617437e+00 , 6.46618658489588e-01 , 4.14055635132178e+00 ), ( -3.77976112126359e+00 , 8.29345963562324e-02 , 5.48292537427215e+00 ), ( -2.39659991009518e+00 , -3.76593461979270e-01 , 6.15056380343767e+00 ), ( -4.47288185649612e+00 , 9.92997842083107e-01 , 6.42195032275813e+00 ), ( -5.32343113024443e+00 , 6.05896370513471e-01 , 7.18835870483030e+00 ), ( -6.29102177553357e+00 , 3.55675183621645e+00 , 6.70443456787512e+00 ), ( -6.91265869085218e+00 , 4.29682881912548e+00 , 7.42139316651740e+00 ), ( -6.74198079214409e+00 , 3.20851726934949e+00 , 5.51749927782646e+00 ), ( -4.09725344014070e+00 , 2.30320690324963e+00 , 6.48261488982570e+00 ), ( -4.89312829848055e+00 , 3.22112397688395e+00 , 7.21282981111052e+00 ), ( -4.08726624310037e+00 , 4.53186400797260e+00 , 7.27938796196023e+00 ) } +colvars: Step 8, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_ids[size = 0] = +colvars: Step 8, atom_groups_refcount[size = 0] = +colvars: Step 8, atom_groups_masses[size = 0] = +colvars: Step 8, atom_groups_charges[size = 0] = +colvars: Step 8, atom_groups_coms[size = 0] = +colvars: Step 8, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 8, volmaps_ids[size = 0] = +colvars: Step 8, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 8 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.29649003636170e-01 , 4.61519105247550e-03 , 9.44092280666053e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.29649003636170e-01 , 4.61519105247550e-03 , 9.44092280666053e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.111 , 1.8595 , -14.9782 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.111 , 1.8595 , -14.9782 ) to colvar "one". +colvars: Adding total bias energy: 45.4794 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.111 , 1.8595 , -14.9782 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.85975 , -0.563033 , -1.56411 ) +colvars: ( -4.16724 , -0.4828 , -1.34123 ) +colvars: ( -4.16724 , -0.4828 , -1.34123 ) +colvars: ( -5.55088 , -0.643104 , -1.78655 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.900602 , 0.193618 , 0.642932 ) +colvars: ( 0.778693 , 0.265381 , 0.668333 ) +colvars: ( 0.763996 , 0.25789 , 0.649319 ) +colvars: ( 0.66387 , 0.267317 , 0.602466 ) +colvars: ( 0.651779 , 0.200723 , 0.504174 ) +colvars: ( 0.574938 , 0.34563 , 0.656504 ) +colvars: ( 0.464696 , 0.360843 , 0.611528 ) +colvars: ( 0.385903 , 0.45907 , 0.69885 ) +colvars: ( 0.38211 , 0.316565 , 0.501691 ) +colvars: ( 0.346059 , 0.275434 , 0.423928 ) +colvars: ( 0.353531 , 0.321527 , 0.491424 ) +colvars: ( 0.281737 , 0.278802 , 0.390152 ) +colvars: ( 0.255478 , 0.307487 , 0.413714 ) +colvars: ( 0.345829 , 0.180199 , 0.293543 ) +colvars: ( 0.285931 , 0.137275 , 0.199098 ) +colvars: ( 0.471399 , 0.142029 , 0.316269 ) +colvars: ( 0.54573 , 0.0498282 , 0.234525 ) +colvars: ( 0.678552 , 0.0275533 , 0.283317 ) +colvars: ( 0.553166 , 0.0184456 , 0.196043 ) +colvars: ( 0.537125 , -0.0466086 , 0.0975006 ) +colvars: ( 0.573279 , 0.0668023 , 0.274178 ) +colvars: ( 0.570357 , 0.0512089 , 0.251109 ) +colvars: ( 0.606542 , 0.116229 , 0.361625 ) +colvars: ( 0.443036 , 0.0568301 , 0.182823 ) +colvars: ( 0.435612 , 0.00106392 , 0.102126 ) +colvars: ( 0.339181 , 0.123273 , 0.211722 ) +colvars: ( 0.211886 , 0.13292 , 0.148958 ) +colvars: ( 0.118772 , 0.219404 , 0.211675 ) +colvars: ( 0.184011 , 0.0588939 , 0.0310843 ) +colvars: ( 0.133238 , 0.0232558 , -0.0479516 ) +colvars: ( 0.21967 , 0.0324492 , 0.0161958 ) +colvars: ( 0.206335 , -0.0404701 , -0.0914884 ) +colvars: ( 0.243847 , -0.0447225 , -0.0749207 ) +colvars: ( 0.282803 , -0.12699 , -0.164187 ) +colvars: ( 0.238002 , -0.179893 , -0.263272 ) +colvars: ( 0.399927 , -0.142728 , -0.115822 ) +colvars: ( 0.47852 , -0.218735 , -0.172876 ) +colvars: ( 0.612231 , -0.222255 , -0.0979043 ) +colvars: ( 0.428902 , -0.222294 , -0.207351 ) +colvars: ( 0.434393 , -0.290442 , -0.297276 ) +colvars: ( 0.378135 , -0.14807 , -0.136132 ) +colvars: ( 0.321476 , -0.140839 , -0.160051 ) +colvars: ( 0.303594 , -0.0534576 , -0.0512158 ) +colvars: ( 0.195792 , -0.148765 , -0.245888 ) +colvars: ( 0.170242 , -0.190378 , -0.318045 ) +colvars: ( -0.00745225 , -0.193973 , -0.428992 ) +colvars: ( -0.100159 , -0.211147 , -0.507799 ) +colvars: ( 0.095823 , -0.245098 , -0.437288 ) +colvars: ( 0.113148 , -0.107827 , -0.239214 ) +colvars: ( -0.00839075 , -0.111399 , -0.316622 ) +colvars: ( -0.0987717 , -0.030116 , -0.259386 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.85975 , 0.563033 , 1.56411 ) +colvars: ( 4.16724 , 0.4828 , 1.34123 ) +colvars: ( 4.16724 , 0.4828 , 1.34123 ) +colvars: ( 5.55088 , 0.643104 , 1.78655 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.624295 , -0.0804454 , -0.394233 ) +colvars: ( -0.559823 , -0.162786 , -0.365959 ) +colvars: ( -0.512727 , -0.140905 , -0.308673 ) +colvars: ( -0.517032 , -0.190572 , -0.335196 ) +colvars: ( -0.507413 , -0.132411 , -0.299518 ) +colvars: ( -0.489115 , -0.282047 , -0.347882 ) +colvars: ( -0.452609 , -0.322528 , -0.329129 ) +colvars: ( -0.428094 , -0.42906 , -0.351971 ) +colvars: ( -0.389522 , -0.287852 , -0.249995 ) +colvars: ( -0.383309 , -0.263068 , -0.23266 ) +colvars: ( -0.342104 , -0.282258 , -0.199657 ) +colvars: ( -0.281955 , -0.246013 , -0.122788 ) +colvars: ( -0.235307 , -0.260731 , -0.0822969 ) +colvars: ( -0.303608 , -0.14366 , -0.0989237 ) +colvars: ( -0.271247 , -0.114991 , -0.0534722 ) +colvars: ( -0.3611 , -0.0863248 , -0.131322 ) +colvars: ( -0.389996 , 0.0111844 , -0.116929 ) +colvars: ( -0.444028 , 0.0589339 , -0.150118 ) +colvars: ( -0.425333 , 0.0259242 , -0.145999 ) +colvars: ( -0.413872 , 0.0819983 , -0.109394 ) +colvars: ( -0.467409 , -0.0275487 , -0.212329 ) +colvars: ( -0.499108 , -0.0291592 , -0.245029 ) +colvars: ( -0.547497 , -0.0937937 , -0.322713 ) +colvars: ( -0.443689 , -0.0594615 , -0.202649 ) +colvars: ( -0.44963 , -0.0159566 , -0.189215 ) +colvars: ( -0.386776 , -0.133389 , -0.178244 ) +colvars: ( -0.326256 , -0.164942 , -0.131277 ) +colvars: ( -0.274318 , -0.254507 , -0.118875 ) +colvars: ( -0.286446 , -0.0929464 , -0.0589619 ) +colvars: ( -0.271365 , -0.0748273 , -0.0356544 ) +colvars: ( -0.26999 , -0.0482567 , -0.0224016 ) +colvars: ( -0.236404 , 0.0257076 , 0.0445142 ) +colvars: ( -0.218724 , 0.0521399 , 0.0741557 ) +colvars: ( -0.281499 , 0.111808 , 0.0374689 ) +colvars: ( -0.254276 , 0.152911 , 0.08329 ) +colvars: ( -0.352323 , 0.140105 , -0.0213487 ) +colvars: ( -0.401956 , 0.215759 , -0.0376367 ) +colvars: ( -0.475385 , 0.238669 , -0.101488 ) +colvars: ( -0.409933 , 0.195776 , -0.0546091 ) +colvars: ( -0.414405 , 0.255925 , -0.0322594 ) +colvars: ( -0.411299 , 0.10983 , -0.094369 ) +colvars: ( -0.414741 , 0.0796053 , -0.111339 ) +colvars: ( -0.433735 , -0.0128565 , -0.171794 ) +colvars: ( -0.345856 , 0.0678991 , -0.0470693 ) +colvars: ( -0.347499 , 0.0937285 , -0.0371919 ) +colvars: ( -0.185126 , 0.0995592 , 0.129229 ) +colvars: ( -0.134105 , 0.10099 , 0.181342 ) +colvars: ( -0.215528 , 0.17164 , 0.130747 ) +colvars: ( -0.283243 , 0.0273287 , -0.00201727 ) +colvars: ( -0.214561 , 0.0133318 , 0.0610243 ) +colvars: ( -0.15953 , -0.0691937 , 0.0796911 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 8. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 8. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atoms_new_colvar_forces = { ( -4.58344434885704e+00 , -4.49860158678809e-01 , -1.31541615237951e+00 ), ( -3.94836672387277e+00 , -3.80205458682773e-01 , -1.03885454368685e+00 ), ( -4.02039792462075e+00 , -4.06055353329953e-01 , -1.07395808320483e+00 ), ( -5.40651315208959e+00 , -5.74792210794058e-01 , -1.58189861696530e+00 ), ( 2.51268730056784e-01 , 1.16984740749356e-01 , 3.40645929350380e-01 ), ( 4.94557440742433e+00 , 6.26616067403621e-01 , 1.87273677478185e+00 ), ( 4.17932315036328e+00 , 5.21115482468212e-01 , 1.62362651306334e+00 ), ( -4.21912554978746e-02 , 3.00100291342354e-02 , 3.46878154095955e-01 ), ( 4.15982453800690e+00 , 5.11512963645720e-01 , 1.59292438489359e+00 ), ( 5.51362904246052e+00 , 6.55469922523709e-01 , 1.97782338151619e+00 ), ( 1.14265985695535e-02 , 3.92688940204443e-02 , 2.91766646742411e-01 ), ( -2.18814736665685e-04 , 3.27884520916616e-02 , 2.67363940426838e-01 ), ( 2.01710328789859e-02 , 4.67556153602492e-02 , 3.31416923897180e-01 ), ( 4.22211241168671e-02 , 3.65385046560910e-02 , 1.94619332477587e-01 ), ( 1.46837581712214e-02 , 2.22848815686842e-02 , 1.45626079920616e-01 ), ( 1.10299267126576e-01 , 5.57044334535554e-02 , 1.84947293564009e-01 ), ( 1.55734063950428e-01 , 6.10126566180705e-02 , 1.17596118387542e-01 ), ( 2.34524245568810e-01 , 8.64871478696009e-02 , 1.33199069265361e-01 ), ( 1.27832833023067e-01 , 4.43697239750103e-02 , 5.00440650162387e-02 ), ( 1.23253416627463e-01 , 3.53896649196837e-02 , -1.18930374930429e-02 ), ( 1.05869341764032e-01 , 3.92535967111143e-02 , 6.18494720302165e-02 ), ( 7.12491199655274e-02 , 2.20496609093494e-02 , 6.08025480232838e-03 ), ( 5.90449651647699e-02 , 2.24351068203813e-02 , 3.89114551921695e-02 ), ( -6.52793404475660e-04 , -2.63132930808936e-03 , -1.98253468619322e-02 ), ( -1.40178933589912e-02 , -1.48926970356135e-02 , -8.70888270975484e-02 ), ( -4.75945938876590e-02 , -1.01163750495041e-02 , 3.34776604677360e-02 ), ( -1.14369738689893e-01 , -3.20223336783406e-02 , 1.76810302294982e-02 ), ( -1.55546331266055e-01 , -3.51029627420427e-02 , 9.27994864871048e-02 ), ( -1.02435867973602e-01 , -3.40525533251060e-02 , -2.78776543776639e-02 ), ( -1.38126250865608e-01 , -5.15714260733037e-02 , -8.36059651088255e-02 ), ( -5.03198562699047e-02 , -1.58075213240080e-02 , -6.20578071133937e-03 ), ( -3.00690419058648e-02 , -1.47624501626466e-02 , -4.69741442118032e-02 ), ( 2.51228587554857e-02 , 7.41739157852034e-03 , -7.64972945065112e-04 ), ( 1.30346671309423e-03 , -1.51815562046862e-02 , -1.26718612931018e-01 ), ( -1.62737474331351e-02 , -2.69819613950322e-02 , -1.79982117012514e-01 ), ( 4.76031994387484e-02 , -2.62297912456652e-03 , -1.37171117397487e-01 ), ( 7.65645931911323e-02 , -2.97616953392221e-03 , -2.10512579582090e-01 ), ( 1.36845339987936e-01 , 1.64133730704317e-02 , -1.99392676538652e-01 ), ( 1.89691374920026e-02 , -2.65182912392013e-02 , -2.61959755448783e-01 ), ( 1.99879490737617e-02 , -3.45173894265902e-02 , -3.29535113440665e-01 ), ( -3.31642689686467e-02 , -3.82397618534294e-02 , -2.30500739735148e-01 ), ( -9.32649038958296e-02 , -6.12335498914378e-02 , -2.71390132170575e-01 ), ( -1.30141459289913e-01 , -6.63141399704378e-02 , -2.23009909093778e-01 ), ( -1.50064368321367e-01 , -8.08659803519194e-02 , -2.92957107313791e-01 ), ( -1.77257176407694e-01 , -9.66491859286723e-02 , -3.55236419133693e-01 ), ( -1.92578245837911e-01 , -9.44133429746729e-02 , -2.99762839292360e-01 ), ( -2.34264533059651e-01 , -1.10157110915457e-01 , -3.26456503527616e-01 ), ( -1.19704597095965e-01 , -7.34580441687327e-02 , -3.06541184157487e-01 ), ( -1.70094809091255e-01 , -8.04986777869762e-02 , -2.41231085210268e-01 ), ( -2.22952147964946e-01 , -9.80676749608512e-02 , -2.55597650901597e-01 ), ( -2.58301335228226e-01 , -9.93096636368683e-02 , -1.79695298676914e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 8, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 9 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 9, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 9, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 9, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 9, atoms_positions[size = 51] = { ( 8.35617328958012e+00 , 4.40201111550499e-02 , -7.63192151632155e-01 ), ( 6.99097240602844e+00 , -5.23098682154020e-01 , -6.37797836607381e-01 ), ( 6.23815514520239e+00 , -2.82267287807500e-01 , 6.79477069875679e-01 ), ( 4.98587590394737e+00 , -2.00932986909559e-01 , 6.82695304324461e-01 ), ( 7.04715049340700e+00 , -2.02643209091800e+00 , -9.92025769775599e-01 ), ( 6.90161384614784e+00 , -2.68384744323356e-01 , 1.83601037032123e+00 ), ( 6.18054212321817e+00 , -1.17450447738679e-01 , 3.11598783394613e+00 ), ( 7.13934721123654e+00 , -3.32279104868168e-01 , 4.28718687453315e+00 ), ( 5.29490234909104e+00 , 1.11327202908185e+00 , 3.30650130783058e+00 ), ( 4.10640776207485e+00 , 1.05574731323172e+00 , 3.63548712960390e+00 ), ( 5.87580925869317e+00 , 2.27404129461307e+00 , 2.98972979204815e+00 ), ( 5.21231284290999e+00 , 3.59531799564475e+00 , 2.88747776096073e+00 ), ( 6.33859155764595e+00 , 4.56408994671179e+00 , 2.44722573395776e+00 ), ( 3.90517545640542e+00 , 3.73832953430805e+00 , 2.02422730802836e+00 ), ( 2.87258579891551e+00 , 4.12193333072030e+00 , 2.53576047562773e+00 ), ( 3.84735886677987e+00 , 3.24045019666927e+00 , 7.59633277859372e-01 ), ( 2.67253480373983e+00 , 3.12364501480597e+00 , -1.01452792510276e-01 ), ( 3.03886841154488e+00 , 2.72025863545469e+00 , -1.58904877234166e+00 ), ( 1.58274495770850e+00 , 2.16537127625444e+00 , 5.68027596240243e-01 ), ( 4.40423296023978e-01 , 2.47815927412273e+00 , 5.42125148164896e-01 ), ( 1.97200939263015e+00 , 1.00824310186052e+00 , 1.05905375799457e+00 ), ( 1.17010508599150e+00 , 3.51247468335211e-02 , 1.69159923058915e+00 ), ( 2.01708154865540e+00 , -1.16279420424218e+00 , 2.01502857453269e+00 ), ( 5.34997050289972e-01 , 6.10358356760984e-01 , 2.96371694185010e+00 ), ( -6.63700711229056e-01 , 3.61126800954301e-01 , 3.17629794481568e+00 ), ( 1.31581740276896e+00 , 1.32962342021575e+00 , 3.83499332809479e+00 ), ( 8.52588626285425e-01 , 1.92551209086982e+00 , 5.05341516621813e+00 ), ( 2.03624439154334e+00 , 2.60342652482486e+00 , 5.62711318893577e+00 ), ( -3.58558490625571e-01 , 2.91796618389863e+00 , 4.98136792635613e+00 ), ( -1.16745295221365e+00 , 3.03941892019623e+00 , 5.90600181805091e+00 ), ( -4.41322306075072e-01 , 3.66455474655012e+00 , 3.84828838059791e+00 ), ( -1.48252578938067e+00 , 4.56316356375946e+00 , 3.53511400940353e+00 ), ( -7.41468959412178e-01 , 5.39248644752632e+00 , 2.42341400340784e+00 ), ( -2.74736893011247e+00 , 3.88785555416379e+00 , 2.92619479610957e+00 ), ( -3.84350855686151e+00 , 4.44312079852304e+00 , 2.83902955175231e+00 ), ( -2.59424505987070e+00 , 2.61756475163911e+00 , 2.47333619260125e+00 ), ( -3.71777271979420e+00 , 1.90472692667774e+00 , 2.04903238796236e+00 ), ( -3.41686265392583e+00 , 8.35004039841956e-01 , 9.60666142566565e-01 ), ( -4.29618105174137e+00 , 1.07717611171578e+00 , 3.24621515370550e+00 ), ( -5.53957738113770e+00 , 8.95482826704819e-01 , 3.33696988539247e+00 ), ( -3.44486334884249e+00 , 6.51473089862034e-01 , 4.13810663291588e+00 ), ( -3.77813050514537e+00 , 7.51531857860098e-02 , 5.48160152246266e+00 ), ( -2.39184882813385e+00 , -3.65561141921903e-01 , 6.15475234122969e+00 ), ( -4.47414411182857e+00 , 9.92512844121139e-01 , 6.42479652659573e+00 ), ( -5.32435262549222e+00 , 6.07391462923434e-01 , 7.19059188262768e+00 ), ( -6.28582600349913e+00 , 3.55967174203309e+00 , 6.70555358996822e+00 ), ( -6.91379627624659e+00 , 4.29556210374275e+00 , 7.42409134891773e+00 ), ( -6.74145689380113e+00 , 3.20811190368739e+00 , 5.51986027101593e+00 ), ( -4.10251973193467e+00 , 2.30201306228987e+00 , 6.48141691185082e+00 ), ( -4.88523547828012e+00 , 3.21492618966655e+00 , 7.21277338851064e+00 ), ( -4.09092078104340e+00 , 4.54237014762350e+00 , 7.28356625152157e+00 ) } +colvars: Step 9, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_ids[size = 0] = +colvars: Step 9, atom_groups_refcount[size = 0] = +colvars: Step 9, atom_groups_masses[size = 0] = +colvars: Step 9, atom_groups_charges[size = 0] = +colvars: Step 9, atom_groups_coms[size = 0] = +colvars: Step 9, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 9, volmaps_ids[size = 0] = +colvars: Step 9, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 9 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.27457007407554e-01 , 4.57131359996204e-03 , 9.44855021361299e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.27457007407554e-01 , 4.57131359996204e-03 , 9.44855021361299e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.0671 , 1.86037 , -14.9935 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.0671 , 1.86037 , -14.9935 ) to colvar "one". +colvars: Adding total bias energy: 45.3881 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.0671 , 1.86037 , -14.9935 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.86498 , -0.560393 , -1.55412 ) +colvars: ( -4.17172 , -0.480537 , -1.33265 ) +colvars: ( -4.17172 , -0.480537 , -1.33265 ) +colvars: ( -5.55685 , -0.640089 , -1.77513 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.900044 , 0.193828 , 0.640905 ) +colvars: ( 0.778327 , 0.265507 , 0.666228 ) +colvars: ( 0.763521 , 0.258077 , 0.647278 ) +colvars: ( 0.663751 , 0.267332 , 0.600509 ) +colvars: ( 0.651672 , 0.200736 , 0.502468 ) +colvars: ( 0.575024 , 0.345549 , 0.65439 ) +colvars: ( 0.465033 , 0.360647 , 0.609507 ) +colvars: ( 0.386421 , 0.458787 , 0.696589 ) +colvars: ( 0.382517 , 0.316347 , 0.49995 ) +colvars: ( 0.34657 , 0.275169 , 0.422376 ) +colvars: ( 0.353873 , 0.321348 , 0.48972 ) +colvars: ( 0.282122 , 0.278613 , 0.388708 ) +colvars: ( 0.255793 , 0.30734 , 0.412222 ) +colvars: ( 0.346074 , 0.180078 , 0.292359 ) +colvars: ( 0.286273 , 0.137115 , 0.19815 ) +colvars: ( 0.471413 , 0.142011 , 0.315046 ) +colvars: ( 0.545593 , 0.0498805 , 0.233524 ) +colvars: ( 0.678147 , 0.0277263 , 0.282213 ) +colvars: ( 0.553125 , 0.0184466 , 0.195126 ) +colvars: ( 0.537104 , -0.0466127 , 0.0968358 ) +colvars: ( 0.57331 , 0.0667599 , 0.273051 ) +colvars: ( 0.570507 , 0.0511046 , 0.250025 ) +colvars: ( 0.60673 , 0.116096 , 0.36025 ) +colvars: ( 0.443432 , 0.0566168 , 0.181895 ) +colvars: ( 0.436056 , 0.000828193 , 0.101399 ) +colvars: ( 0.339734 , 0.122991 , 0.210709 ) +colvars: ( 0.212668 , 0.132538 , 0.148088 ) +colvars: ( 0.11969 , 0.218962 , 0.210635 ) +colvars: ( 0.184756 , 0.0585392 , 0.0305233 ) +colvars: ( 0.134107 , 0.0228453 , -0.0483214 ) +colvars: ( 0.220239 , 0.032183 , 0.0156924 ) +colvars: ( 0.206839 , -0.0406968 , -0.0917063 ) +colvars: ( 0.244163 , -0.0448557 , -0.0751602 ) +colvars: ( 0.283203 , -0.127172 , -0.164213 ) +colvars: ( 0.238465 , -0.180099 , -0.263048 ) +colvars: ( 0.400169 , -0.142845 , -0.115962 ) +colvars: ( 0.478667 , -0.218813 , -0.172864 ) +colvars: ( 0.612171 , -0.222246 , -0.0980705 ) +colvars: ( 0.429245 , -0.222467 , -0.207272 ) +colvars: ( 0.434736 , -0.290614 , -0.296967 ) +colvars: ( 0.378652 , -0.148329 , -0.136253 ) +colvars: ( 0.322198 , -0.141198 , -0.160132 ) +colvars: ( 0.304437 , -0.0538809 , -0.0515897 ) +colvars: ( 0.196709 , -0.149206 , -0.245763 ) +colvars: ( 0.171254 , -0.190863 , -0.317744 ) +colvars: ( -0.00638552 , -0.194456 , -0.428398 ) +colvars: ( -0.0989486 , -0.211691 , -0.507013 ) +colvars: ( 0.0966431 , -0.245467 , -0.436651 ) +colvars: ( 0.114132 , -0.108291 , -0.239107 ) +colvars: ( -0.00722485 , -0.111939 , -0.316329 ) +colvars: ( -0.0974884 , -0.030705 , -0.259247 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.86498 , 0.560393 , 1.55412 ) +colvars: ( 4.17172 , 0.480537 , 1.33265 ) +colvars: ( 4.17172 , 0.480537 , 1.33265 ) +colvars: ( 5.55685 , 0.640089 , 1.77513 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.623455 , -0.0804608 , -0.391963 ) +colvars: ( -0.559239 , -0.16276 , -0.363513 ) +colvars: ( -0.511959 , -0.140899 , -0.306199 ) +colvars: ( -0.516784 , -0.190494 , -0.332938 ) +colvars: ( -0.50717 , -0.132327 , -0.297589 ) +colvars: ( -0.489159 , -0.281927 , -0.345411 ) +colvars: ( -0.453001 , -0.322355 , -0.326785 ) +colvars: ( -0.428748 , -0.428851 , -0.349301 ) +colvars: ( -0.389977 , -0.28766 , -0.247935 ) +colvars: ( -0.383908 , -0.262853 , -0.230874 ) +colvars: ( -0.342442 , -0.282076 , -0.197543 ) +colvars: ( -0.28232 , -0.245818 , -0.12093 ) +colvars: ( -0.235548 , -0.260548 , -0.0802672 ) +colvars: ( -0.303768 , -0.143492 , -0.0974243 ) +colvars: ( -0.271526 , -0.114799 , -0.05226 ) +colvars: ( -0.360949 , -0.0862058 , -0.129814 ) +colvars: ( -0.38963 , 0.0112737 , -0.115738 ) +colvars: ( -0.443298 , 0.0589657 , -0.148816 ) +colvars: ( -0.425122 , 0.026032 , -0.145015 ) +colvars: ( -0.413675 , 0.0821126 , -0.108738 ) +colvars: ( -0.467331 , -0.0274302 , -0.211154 ) +colvars: ( -0.499216 , -0.0290179 , -0.244004 ) +colvars: ( -0.547693 , -0.0936495 , -0.321389 ) +colvars: ( -0.444126 , -0.0592667 , -0.201798 ) +colvars: ( -0.450134 , -0.0157506 , -0.188663 ) +colvars: ( -0.38742 , -0.133161 , -0.177214 ) +colvars: ( -0.327201 , -0.164664 , -0.13039 ) +colvars: ( -0.275446 , -0.2542 , -0.117696 ) +colvars: ( -0.28731 , -0.0926709 , -0.0584148 ) +colvars: ( -0.272396 , -0.0745244 , -0.0353736 ) +colvars: ( -0.270586 , -0.0480154 , -0.0218562 ) +colvars: ( -0.236879 , 0.0259398 , 0.0447484 ) +colvars: ( -0.218916 , 0.0523348 , 0.0745018 ) +colvars: ( -0.281838 , 0.112019 , 0.0373833 ) +colvars: ( -0.254685 , 0.153138 , 0.0828963 ) +colvars: ( -0.352467 , 0.14028 , -0.0213675 ) +colvars: ( -0.401977 , 0.215914 , -0.0379292 ) +colvars: ( -0.475144 , 0.238777 , -0.101619 ) +colvars: ( -0.410244 , 0.195971 , -0.0550606 ) +colvars: ( -0.41471 , 0.256121 , -0.0330337 ) +colvars: ( -0.411872 , 0.110058 , -0.0945951 ) +colvars: ( -0.415614 , 0.0798746 , -0.11168 ) +colvars: ( -0.434804 , -0.0125662 , -0.171802 ) +colvars: ( -0.346976 , 0.0682126 , -0.0476167 ) +colvars: ( -0.348753 , 0.0940626 , -0.0380068 ) +colvars: ( -0.186374 , 0.0999143 , 0.128299 ) +colvars: ( -0.135534 , 0.101378 , 0.180206 ) +colvars: ( -0.216428 , 0.171944 , 0.129766 ) +colvars: ( -0.284433 , 0.0276585 , -0.00244153 ) +colvars: ( -0.215979 , 0.0137028 , 0.0604248 ) +colvars: ( -0.161099 , -0.0687978 , 0.0793727 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 9. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 9. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atoms_new_colvar_forces = { ( -4.58838939552603e+00 , -4.47025406485466e-01 , -1.30517458629373e+00 ), ( -3.95262953610289e+00 , -3.77790051392105e-01 , -1.02994016022491e+00 ), ( -4.02475028214488e+00 , -4.03698360924690e-01 , -1.06508371318764e+00 ), ( -5.41234607372141e+00 , -5.71680551513149e-01 , -1.57025556500880e+00 ), ( 2.51562216889713e-01 , 1.17178376118225e-01 , 3.41079617991009e-01 ), ( 4.95084225672090e+00 , 6.24014982972654e-01 , 1.86309528259453e+00 ), ( 4.18374962124968e+00 , 5.18828422240018e-01 , 1.61537684187741e+00 ), ( -4.23267784255257e-02 , 2.99357634345412e-02 , 3.47287849172900e-01 ), ( 4.16425737827149e+00 , 5.09223970527797e-01 , 1.58467017776851e+00 ), ( 5.51951081381373e+00 , 6.52404708008969e-01 , 1.96663701025769e+00 ), ( 1.14309374908305e-02 , 3.92715412937946e-02 , 2.92176818157258e-01 ), ( -1.97626284989816e-04 , 3.27958376982011e-02 , 2.67778399480675e-01 ), ( 2.02449020889785e-02 , 4.67913698494855e-02 , 3.31954452118544e-01 ), ( 4.23060999561829e-02 , 3.65859673557188e-02 , 1.94935003509608e-01 ), ( 1.47468199500804e-02 , 2.23158061441952e-02 , 1.45889702940907e-01 ), ( 1.10463574728554e-01 , 5.58050595088237e-02 , 1.85232110153984e-01 ), ( 1.55962471079082e-01 , 6.11542297307415e-02 , 1.17785392145717e-01 ), ( 2.34848803626830e-01 , 8.66919870393438e-02 , 1.33396818480500e-01 ), ( 1.28003003150382e-01 , 4.44785301151353e-02 , 5.01109143233972e-02 ), ( 1.23428526411529e-01 , 3.54999806743200e-02 , -1.19025851190753e-02 ), ( 1.05979465254891e-01 , 3.93297450713575e-02 , 6.18971412911153e-02 ), ( 7.12909988965698e-02 , 2.20867361726002e-02 , 6.02163646700365e-03 ), ( 5.90370670778059e-02 , 2.24464791202778e-02 , 3.88604569920168e-02 ), ( -6.94140731715032e-04 , -2.64987447240094e-03 , -1.99031728324598e-02 ), ( -1.40776635980440e-02 , -1.49224245825257e-02 , -8.72645246846075e-02 ), ( -4.76855873423211e-02 , -1.01696705013155e-02 , 3.34949842275970e-02 ), ( -1.14533806333947e-01 , -3.21254569734481e-02 , 1.76976299207021e-02 ), ( -1.55755579574356e-01 , -3.52375175545587e-02 , 9.29387757429661e-02 ), ( -1.02554119821961e-01 , -3.41317207071895e-02 , -2.78915169926651e-02 ), ( -1.38288549138629e-01 , -5.16790984770918e-02 , -8.36949556710445e-02 ), ( -5.03466708133782e-02 , -1.58324531341675e-02 , -6.16381064425375e-03 ), ( -3.00404839183512e-02 , -1.47570375988996e-02 , -4.69578936620170e-02 ), ( 2.52461364857733e-02 , 7.47911462853162e-03 , -6.58367711261681e-04 ), ( 1.36556717716091e-03 , -1.51524177235188e-02 , -1.26829611284271e-01 ), ( -1.62198623073919e-02 , -2.69606235091154e-02 , -1.80151290106232e-01 ), ( 4.77020405271442e-02 , -2.56536827973369e-03 , -1.37329588016078e-01 ), ( 7.66899354199569e-02 , -2.89865855484989e-03 , -2.10793530067861e-01 ), ( 1.37026533235403e-01 , 1.65313564537396e-02 , -1.99689795007217e-01 ), ( 1.90017538023108e-02 , -2.64967761920840e-02 , -2.62332266474575e-01 ), ( 2.00262856142383e-02 , -3.44925295012664e-02 , -3.30000554065977e-01 ), ( -3.32199011481871e-02 , -3.82714658780087e-02 , -2.30848003170492e-01 ), ( -9.34158282033889e-02 , -6.13231263029747e-02 , -2.71812571879274e-01 ), ( -1.30367333523874e-01 , -6.64471755188303e-02 , -2.23391713824821e-01 ), ( -1.50267012108277e-01 , -8.09932006274197e-02 , -2.93379324869338e-01 ), ( -1.77498740239768e-01 , -9.68003745367784e-02 , -3.55751166841283e-01 ), ( -1.92759980965373e-01 , -9.45420930354249e-02 , -3.00099074615717e-01 ), ( -2.34482915509898e-01 , -1.10312817777597e-01 , -3.26806772145153e-01 ), ( -1.19784494264076e-01 , -7.35223318744086e-02 , -3.06884751428479e-01 ), ( -1.70300196712858e-01 , -8.06326849680640e-02 , -2.41548251140115e-01 ), ( -2.23203680393268e-01 , -9.82358675590512e-02 , -2.55903918425207e-01 ), ( -2.58586970064436e-01 , -9.95028280023367e-02 , -1.79873980219490e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 9, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 10 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 10, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 10, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 10, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 10, atoms_positions[size = 51] = { ( 8.34828490212455e+00 , 4.39894433023356e-02 , -7.64522375820389e-01 ), ( 6.99066540503349e+00 , -5.28601023906280e-01 , -6.34000486864719e-01 ), ( 6.22787719172293e+00 , -2.89831996815122e-01 , 6.83255367663832e-01 ), ( 4.98388392467191e+00 , -1.98391484362259e-01 , 6.87385272656312e-01 ), ( 7.04895001260948e+00 , -2.02841985382283e+00 , -9.85655084473563e-01 ), ( 6.90086556455800e+00 , -2.67711113006922e-01 , 1.84251244929543e+00 ), ( 6.18209256661512e+00 , -1.17740826747379e-01 , 3.13099931567514e+00 ), ( 7.12965186159977e+00 , -3.35676864764050e-01 , 4.28495453374987e+00 ), ( 5.29199820865372e+00 , 1.11284754163302e+00 , 3.31122615081410e+00 ), ( 4.11283309435019e+00 , 1.05263945814561e+00 , 3.63923997924621e+00 ), ( 5.87478417221971e+00 , 2.26610006058109e+00 , 2.99289064644132e+00 ), ( 5.21288515405497e+00 , 3.59483387029529e+00 , 2.89013831118651e+00 ), ( 6.33778100011006e+00 , 4.55392283929975e+00 , 2.44288214950251e+00 ), ( 3.90736158670035e+00 , 3.74001471462344e+00 , 2.02631562061012e+00 ), ( 2.86216126640952e+00 , 4.12496378479377e+00 , 2.53175509803549e+00 ), ( 3.85569108363366e+00 , 3.24025358116369e+00 , 7.54981812605449e-01 ), ( 2.67098973829651e+00 , 3.10946892730785e+00 , -1.03764678446356e-01 ), ( 3.03664326320571e+00 , 2.72080972454192e+00 , -1.58268844848001e+00 ), ( 1.57644296541130e+00 , 2.17200559816706e+00 , 5.58891174795041e-01 ), ( 4.39558011672441e-01 , 2.48637330476707e+00 , 5.39053206581799e-01 ), ( 1.97517386223124e+00 , 1.00560560902377e+00 , 1.06270749861102e+00 ), ( 1.17477948121920e+00 , 4.45000157290994e-02 , 1.69201394519546e+00 ), ( 2.01845353772129e+00 , -1.15675025686559e+00 , 2.01295487579453e+00 ), ( 5.39499967580355e-01 , 6.10790411480097e-01 , 2.95452398667484e+00 ), ( -6.59870110540155e-01 , 3.58333963239616e-01 , 3.17465537308870e+00 ), ( 1.31939556510853e+00 , 1.33329287373207e+00 , 3.83604298766876e+00 ), ( 8.56125141777084e-01 , 1.93161115115897e+00 , 5.04830601042540e+00 ), ( 2.03249704322438e+00 , 2.60800253069114e+00 , 5.62936319970994e+00 ), ( -3.56770742758726e-01 , 2.91751267018339e+00 , 4.97982558507318e+00 ), ( -1.16532359861227e+00 , 3.04247810993894e+00 , 5.90578872487953e+00 ), ( -4.49296030429180e-01 , 3.65408615124073e+00 , 3.84673383894858e+00 ), ( -1.48548772780184e+00 , 4.55855948345671e+00 , 3.53174132461905e+00 ), ( -7.36781504246551e-01 , 5.39463649316501e+00 , 2.42783688629379e+00 ), ( -2.75429472876099e+00 , 3.88495472413804e+00 , 2.92394328126824e+00 ), ( -3.84004154165180e+00 , 4.44895112862008e+00 , 2.83569853222850e+00 ), ( -2.59731427225162e+00 , 2.62297631579534e+00 , 2.46759561069813e+00 ), ( -3.72074920442391e+00 , 1.89762696393657e+00 , 2.04244110775780e+00 ), ( -3.41713011421728e+00 , 8.42923170279376e-01 , 9.51846315365505e-01 ), ( -4.29578789041755e+00 , 1.07269722121539e+00 , 3.24887402230753e+00 ), ( -5.53817683691649e+00 , 8.88664207121781e-01 , 3.33502724950635e+00 ), ( -3.43753460573195e+00 , 6.56258582345316e-01 , 4.13782656979711e+00 ), ( -3.77483687997640e+00 , 6.70731232223418e-02 , 5.47883543248952e+00 ), ( -2.38814976257285e+00 , -3.55030569804516e-01 , 6.15870945269310e+00 ), ( -4.47489688972547e+00 , 9.93170557498753e-01 , 6.42794280092462e+00 ), ( -5.32585979374457e+00 , 6.08358684041427e-01 , 7.19298823114831e+00 ), ( -6.27933301187145e+00 , 3.56261466069330e+00 , 6.70656970156401e+00 ), ( -6.91601696318481e+00 , 4.29489682897800e+00 , 7.42749128910578e+00 ), ( -6.74193048548450e+00 , 3.20748748801981e+00 , 5.52165326494754e+00 ), ( -4.10779169319408e+00 , 2.29943673434181e+00 , 6.47896963556771e+00 ), ( -4.87665888157469e+00 , 3.20893642721787e+00 , 7.21297894686708e+00 ), ( -4.09419104402405e+00 , 4.55261536958934e+00 , 7.28744062529414e+00 ) } +colvars: Step 10, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_ids[size = 0] = +colvars: Step 10, atom_groups_refcount[size = 0] = +colvars: Step 10, atom_groups_masses[size = 0] = +colvars: Step 10, atom_groups_charges[size = 0] = +colvars: Step 10, atom_groups_coms[size = 0] = +colvars: Step 10, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 10, volmaps_ids[size = 0] = +colvars: Step 10, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 10 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.25149814022648e-01 , 4.52596031009924e-03 , 9.45651687527870e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.25149814022648e-01 , 4.52596031009924e-03 , 9.45651687527870e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 26.021 , 1.86128 , -15.0094 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 26.021 , 1.86128 , -15.0094 ) to colvar "one". +colvars: Adding total bias energy: 45.292 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 26.021 , 1.86128 , -15.0094 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.87042 , -0.557571 , -1.5436 ) +colvars: ( -4.17638 , -0.478117 , -1.32364 ) +colvars: ( -4.17638 , -0.478117 , -1.32364 ) +colvars: ( -5.56306 , -0.636865 , -1.76313 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.899454 , 0.19403 , 0.638783 ) +colvars: ( 0.77794 , 0.265616 , 0.664028 ) +colvars: ( 0.763022 , 0.258252 , 0.645148 ) +colvars: ( 0.663621 , 0.267325 , 0.598464 ) +colvars: ( 0.651555 , 0.200731 , 0.500683 ) +colvars: ( 0.575107 , 0.345435 , 0.652183 ) +colvars: ( 0.46538 , 0.360411 , 0.607398 ) +colvars: ( 0.386955 , 0.458454 , 0.694233 ) +colvars: ( 0.382938 , 0.316093 , 0.498135 ) +colvars: ( 0.3471 , 0.274869 , 0.420757 ) +colvars: ( 0.35423 , 0.321135 , 0.487947 ) +colvars: ( 0.282525 , 0.278396 , 0.387209 ) +colvars: ( 0.256124 , 0.307164 , 0.410675 ) +colvars: ( 0.346331 , 0.179938 , 0.291127 ) +colvars: ( 0.286632 , 0.136937 , 0.197162 ) +colvars: ( 0.471428 , 0.141981 , 0.313769 ) +colvars: ( 0.545451 , 0.0499312 , 0.232476 ) +colvars: ( 0.677724 , 0.0279046 , 0.281056 ) +colvars: ( 0.553082 , 0.0184449 , 0.194164 ) +colvars: ( 0.537081 , -0.0466146 , 0.0961337 ) +colvars: ( 0.57334 , 0.0667081 , 0.271866 ) +colvars: ( 0.570659 , 0.0509882 , 0.248884 ) +colvars: ( 0.606919 , 0.115944 , 0.358803 ) +colvars: ( 0.443841 , 0.0563863 , 0.180916 ) +colvars: ( 0.436516 , 0.000578149 , 0.100627 ) +colvars: ( 0.340309 , 0.122685 , 0.209646 ) +colvars: ( 0.213482 , 0.132128 , 0.147176 ) +colvars: ( 0.120648 , 0.218483 , 0.209551 ) +colvars: ( 0.185534 , 0.058163 , 0.0299343 ) +colvars: ( 0.135015 , 0.0224134 , -0.0487122 ) +colvars: ( 0.220834 , 0.0319022 , 0.0151648 ) +colvars: ( 0.207368 , -0.04093 , -0.0919361 ) +colvars: ( 0.244498 , -0.0449898 , -0.0754104 ) +colvars: ( 0.283624 , -0.127352 , -0.164246 ) +colvars: ( 0.238953 , -0.1803 , -0.262821 ) +colvars: ( 0.400423 , -0.142958 , -0.116118 ) +colvars: ( 0.47882 , -0.218878 , -0.172867 ) +colvars: ( 0.612106 , -0.222221 , -0.0982612 ) +colvars: ( 0.429603 , -0.222634 , -0.207206 ) +colvars: ( 0.435093 , -0.290774 , -0.296664 ) +colvars: ( 0.37919 , -0.148593 , -0.136395 ) +colvars: ( 0.322948 , -0.141566 , -0.160234 ) +colvars: ( 0.305312 , -0.054324 , -0.0519959 ) +colvars: ( 0.197664 , -0.149658 , -0.245647 ) +colvars: ( 0.172308 , -0.191359 , -0.317448 ) +colvars: ( -0.0052684 , -0.194948 , -0.427787 ) +colvars: ( -0.09768 , -0.212243 , -0.506201 ) +colvars: ( 0.0975032 , -0.245834 , -0.435996 ) +colvars: ( 0.11516 , -0.10877 , -0.239006 ) +colvars: ( -0.00600621 , -0.112495 , -0.316031 ) +colvars: ( -0.0961462 , -0.0313186 , -0.259104 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.87042 , 0.557571 , 1.5436 ) +colvars: ( 4.17638 , 0.478117 , 1.32364 ) +colvars: ( 4.17638 , 0.478117 , 1.32364 ) +colvars: ( 5.56306 , 0.636865 , 1.76313 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.622591 , -0.0804752 , -0.389597 ) +colvars: ( -0.558639 , -0.162727 , -0.360972 ) +colvars: ( -0.511171 , -0.140891 , -0.303633 ) +colvars: ( -0.51653 , -0.190403 , -0.330592 ) +colvars: ( -0.506921 , -0.132233 , -0.295581 ) +colvars: ( -0.489206 , -0.281787 , -0.342849 ) +colvars: ( -0.453406 , -0.322155 , -0.324354 ) +colvars: ( -0.429422 , -0.428608 , -0.346538 ) +colvars: ( -0.390449 , -0.287442 , -0.245802 ) +colvars: ( -0.384527 , -0.262612 , -0.229023 ) +colvars: ( -0.342796 , -0.281873 , -0.19536 ) +colvars: ( -0.282702 , -0.245603 , -0.119014 ) +colvars: ( -0.235805 , -0.260349 , -0.0781804 ) +colvars: ( -0.30394 , -0.143311 , -0.0958746 ) +colvars: ( -0.271821 , -0.114595 , -0.051007 ) +colvars: ( -0.360801 , -0.0860808 , -0.12825 ) +colvars: ( -0.38926 , 0.0113623 , -0.114498 ) +colvars: ( -0.442551 , 0.0589901 , -0.147458 ) +colvars: ( -0.42491 , 0.0261421 , -0.143984 ) +colvars: ( -0.413477 , 0.0822271 , -0.108044 ) +colvars: ( -0.467252 , -0.0273039 , -0.209921 ) +colvars: ( -0.499328 , -0.0288647 , -0.242922 ) +colvars: ( -0.547894 , -0.0934882 , -0.319996 ) +colvars: ( -0.444578 , -0.0590547 , -0.200899 ) +colvars: ( -0.450654 , -0.0155278 , -0.188069 ) +colvars: ( -0.388087 , -0.13291 , -0.176135 ) +colvars: ( -0.328179 , -0.164359 , -0.129464 ) +colvars: ( -0.276612 , -0.253861 , -0.116474 ) +colvars: ( -0.288205 , -0.0923737 , -0.0578402 ) +colvars: ( -0.273463 , -0.0741982 , -0.0350726 ) +colvars: ( -0.271206 , -0.0477593 , -0.0212858 ) +colvars: ( -0.237377 , 0.0261811 , 0.0449965 ) +colvars: ( -0.219124 , 0.0525326 , 0.0748622 ) +colvars: ( -0.282193 , 0.112235 , 0.0373077 ) +colvars: ( -0.255115 , 0.153369 , 0.0825029 ) +colvars: ( -0.35262 , 0.140457 , -0.0213685 ) +colvars: ( -0.402003 , 0.216067 , -0.0382063 ) +colvars: ( -0.474899 , 0.23888 , -0.101725 ) +colvars: ( -0.410567 , 0.196169 , -0.0554991 ) +colvars: ( -0.415027 , 0.256319 , -0.0338025 ) +colvars: ( -0.412465 , 0.110298 , -0.0948017 ) +colvars: ( -0.416514 , 0.0801623 , -0.112004 ) +colvars: ( -0.435906 , -0.0122501 , -0.171781 ) +colvars: ( -0.348132 , 0.0685475 , -0.048157 ) +colvars: ( -0.350046 , 0.0944194 , -0.0388206 ) +colvars: ( -0.187668 , 0.100287 , 0.127352 ) +colvars: ( -0.137015 , 0.101786 , 0.179044 ) +colvars: ( -0.217362 , 0.172259 , 0.128769 ) +colvars: ( -0.285663 , 0.0280107 , -0.00286133 ) +colvars: ( -0.217445 , 0.014099 , 0.0598197 ) +colvars: ( -0.162722 , -0.0683725 , 0.0790507 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 10. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 10. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atoms_new_colvar_forces = { ( -4.59355517748052e+00 , -4.44015582373764e-01 , -1.29441814405527e+00 ), ( -3.95708173849547e+00 , -3.75228180486825e-01 , -1.02058421403536e+00 ), ( -4.02929122398260e+00 , -4.01194296213209e-01 , -1.05576841054788e+00 ), ( -5.41842798778098e+00 , -5.68367125599078e-01 , -1.55802487116354e+00 ), ( 2.51851372887664e-01 , 1.17361051476457e-01 , 3.41515291608866e-01 ), ( 4.95632002040441e+00 , 6.21218647463185e-01 , 1.85293826133283e+00 ), ( 4.18835600817839e+00 , 5.16372339342320e-01 , 1.60668415040966e+00 ), ( -4.24666245193869e-02 , 2.98460525351839e-02 , 3.47694943353193e-01 ), ( 4.16887175490274e+00 , 5.06767494651288e-01 , 1.57597385144500e+00 ), ( 5.52563560582053e+00 , 6.49121921402458e-01 , 1.95486160530762e+00 ), ( 1.14338044971929e-02 , 3.92627685380244e-02 , 2.92587354077863e-01 ), ( -1.76353895908199e-04 , 3.27931934186928e-02 , 2.68194224423467e-01 ), ( 2.03196459775179e-02 , 4.68153052057464e-02 , 3.32494641046370e-01 ), ( 4.23914640979515e-02 , 3.66268781596063e-02 , 1.95252610481756e-01 ), ( 1.48112287820190e-02 , 2.23420181197107e-02 , 1.46155393268324e-01 ), ( 1.10627414805206e-01 , 5.59001320634085e-02 , 1.85519171104405e-01 ), ( 1.56190520271940e-01 , 6.12934875812506e-02 , 1.17977390525700e-01 ), ( 2.35172116741031e-01 , 8.68947006454514e-02 , 1.33597866154505e-01 ), ( 1.28172272983708e-01 , 4.45869353089523e-02 , 5.01792661929765e-02 ), ( 1.23603441351940e-01 , 3.56124503587407e-02 , -1.19104122689279e-02 ), ( 1.06087434773844e-01 , 3.94042136454398e-02 , 6.19449742594518e-02 ), ( 7.13301364336489e-02 , 2.21234866110346e-02 , 5.96187343917060e-03 ), ( 5.90249315729242e-02 , 2.24554982023740e-02 , 3.88070281089110e-02 ), ( -7.37185733114432e-04 , -2.66838208090871e-03 , -1.99825276030163e-02 ), ( -1.41388668208941e-02 , -1.49496680985678e-02 , -8.74420666668334e-02 ), ( -4.77776168715920e-02 , -1.02253422823412e-02 , 3.35108529817474e-02 ), ( -1.14697783246846e-01 , -3.22308661056235e-02 , 1.77125899747320e-02 ), ( -1.55964318524189e-01 , -3.53776095124567e-02 , 9.30764924170915e-02 ), ( -1.02670899719694e-01 , -3.42107177704016e-02 , -2.79058955250904e-02 ), ( -1.38448839720594e-01 , -5.17848001772567e-02 , -8.37848463015384e-02 ), ( -5.03714226955432e-02 , -1.58570314938234e-02 , -6.12093541209686e-03 ), ( -3.00086115625056e-02 , -1.47489284659867e-02 , -4.69395684412112e-02 ), ( 2.53731877118849e-02 , 7.54278441208116e-03 , -5.48209286519691e-04 ), ( 1.43069654691069e-03 , -1.51172445636054e-02 , -1.26938667375671e-01 ), ( -1.61620144077224e-02 , -2.69311168224513e-02 , -1.80318274271151e-01 ), ( 4.78025904146258e-02 , -2.50120185002350e-03 , -1.37486543738285e-01 ), ( 7.68165274518192e-02 , -2.81160123981145e-03 , -2.11073250310744e-01 ), ( 1.37207528057790e-01 , 1.66587451843357e-02 , -1.99985892888856e-01 ), ( 1.90354178595755e-02 , -2.64646968483361e-02 , -2.62704873731052e-01 ), ( 2.00660700555651e-02 , -3.44543827886409e-02 , -3.30466067975266e-01 ), ( -3.32751058238674e-02 , -3.82948005392128e-02 , -2.31196550790619e-01 ), ( -9.35665127547106e-02 , -6.14037431164247e-02 , -2.72237598425034e-01 ), ( -1.30594036332267e-01 , -6.65740465220482e-02 , -2.23777346184272e-01 ), ( -1.50467976632238e-01 , -8.11108803068862e-02 , -2.93803922833369e-01 ), ( -1.77738387046901e-01 , -9.69399751611738e-02 , -3.56268826708945e-01 ), ( -1.92936389879557e-01 , -9.46601609724783e-02 , -3.00435337930446e-01 ), ( -2.34694823424672e-01 , -1.10456969420736e-01 , -3.27156893105670e-01 ), ( -1.19859255162479e-01 , -7.35747042567381e-02 , -3.07227390840892e-01 ), ( -1.70502911342417e-01 , -8.07589792449124e-02 , -2.41867029203612e-01 ), ( -2.23451131897684e-01 , -9.83959930751030e-02 , -2.56211521024765e-01 ), ( -2.58867996826473e-01 , -9.96910769369178e-02 , -1.80053743267714e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 10, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 11 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 11, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 11, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 11, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 11, atoms_positions[size = 51] = { ( 8.34052672881583e+00 , 4.38508509545042e-02 , -7.65407392242128e-01 ), ( 6.99003358745559e+00 , -5.33517344223640e-01 , -6.30171873135856e-01 ), ( 6.21625615191044e+00 , -2.97922534055335e-01 , 6.86781779786704e-01 ), ( 4.98240576208412e+00 , -1.95583496296942e-01 , 6.91891998399505e-01 ), ( 7.05065161917571e+00 , -2.03049166569140e+00 , -9.79402107372247e-01 ), ( 6.89978919361934e+00 , -2.66941748921589e-01 , 1.84877477574450e+00 ), ( 6.18361273865802e+00 , -1.18834935336737e-01 , 3.14564946586988e+00 ), ( 7.12018607770449e+00 , -3.39133444194479e-01 , 4.28342409989501e+00 ), ( 5.28972774565670e+00 , 1.11251939790860e+00 , 3.31579332456398e+00 ), ( 4.11946856705428e+00 , 1.04955885047178e+00 , 3.64314414480319e+00 ), ( 5.87314062584667e+00 , 2.25939982092709e+00 , 2.99529215588447e+00 ), ( 5.21461221236525e+00 , 3.59406567754698e+00 , 2.89327208680642e+00 ), ( 6.33647971926123e+00 , 4.54438634602907e+00 , 2.43799153373710e+00 ), ( 3.90893018123439e+00 , 3.74053771608229e+00 , 2.02863443162684e+00 ), ( 2.85178143029123e+00 , 4.12837607322095e+00 , 2.52782271173447e+00 ), ( 3.86479385176451e+00 , 3.24028536473171e+00 , 7.50603483927780e-01 ), ( 2.66852534664435e+00 , 3.09505731900435e+00 , -1.05589370912802e-01 ), ( 3.03476771861854e+00 , 2.72158829630843e+00 , -1.57501570121844e+00 ), ( 1.57256907379180e+00 , 2.17883113470269e+00 , 5.48121120390495e-01 ), ( 4.37157985028312e-01 , 2.49496004378577e+00 , 5.36166029002277e-01 ), ( 1.97955365004857e+00 , 1.00342201375213e+00 , 1.06672437926646e+00 ), ( 1.17836136809065e+00 , 5.47447152221373e-02 , 1.69222191033390e+00 ), ( 2.02012954087636e+00 , -1.15072095948188e+00 , 2.01095221725133e+00 ), ( 5.43445055480431e-01 , 6.10623986654365e-01 , 2.94620431664111e+00 ), ( -6.55515370594273e-01 , 3.55968869687285e-01 , 3.17312349336380e+00 ), ( 1.32230512468366e+00 , 1.33662322216111e+00 , 3.83594085279798e+00 ), ( 8.58510581431592e-01 , 1.93756947490075e+00 , 5.04354275866483e+00 ), ( 2.03022561426183e+00 , 2.61320004550326e+00 , 5.63213006966011e+00 ), ( -3.54477007570914e-01 , 2.91715217679086e+00 , 4.97804937059007e+00 ), ( -1.16315933060431e+00 , 3.04537524561224e+00 , 5.90528903163306e+00 ), ( -4.56990337670391e-01 , 3.64256325723145e+00 , 3.84588691845218e+00 ), ( -1.48864258329021e+00 , 4.55496162424248e+00 , 3.52701983361952e+00 ), ( -7.32001928779663e-01 , 5.39670861979645e+00 , 2.43240618541534e+00 ), ( -2.76043849975506e+00 , 3.88196022461464e+00 , 2.92174554398755e+00 ), ( -3.83655630145068e+00 , 4.45487516920878e+00 , 2.83261139928302e+00 ), ( -2.59983145788163e+00 , 2.62960630289858e+00 , 2.46177627650691e+00 ), ( -3.72484225979729e+00 , 1.88842135467647e+00 , 2.03572771512213e+00 ), ( -3.41676046733324e+00 , 8.50656873830850e-01 , 9.42962055798462e-01 ), ( -4.29738453201457e+00 , 1.06924562870131e+00 , 3.24990257230490e+00 ), ( -5.53575216260335e+00 , 8.81857604131008e-01 , 3.33327200415026e+00 ), ( -3.42984743988176e+00 , 6.60811055660684e-01 , 4.13981911095222e+00 ), ( -3.77004771139532e+00 , 5.91521031988681e-02 , 5.47473677954351e+00 ), ( -2.38546708128188e+00 , -3.45304623138144e-01 , 6.16234065583497e+00 ), ( -4.47510333484871e+00 , 9.94714080794383e-01 , 6.43118179611945e+00 ), ( -5.32795009589764e+00 , 6.08792548504162e-01 , 7.19555040150092e+00 ), ( -6.27187030467191e+00 , 3.56559208374733e+00 , 6.70761174381335e+00 ), ( -6.91919188498955e+00 , 4.29475861302874e+00 , 7.43152309603963e+00 ), ( -6.74323318420630e+00 , 3.20659487665074e+00 , 5.52277473089573e+00 ), ( -4.11286614873520e+00 , 2.29554357073650e+00 , 6.47524521982787e+00 ), ( -4.86768391437572e+00 , 3.20344925316398e+00 , 7.21352022461795e+00 ), ( -4.09711095439933e+00 , 4.56217863115927e+00 , 7.29072155849984e+00 ) } +colvars: Step 11, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_ids[size = 0] = +colvars: Step 11, atom_groups_refcount[size = 0] = +colvars: Step 11, atom_groups_masses[size = 0] = +colvars: Step 11, atom_groups_charges[size = 0] = +colvars: Step 11, atom_groups_coms[size = 0] = +colvars: Step 11, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 11, volmaps_ids[size = 0] = +colvars: Step 11, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 11 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.22768924320888e-01 , 4.45076971931406e-03 , 9.46467332844427e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.22768924320888e-01 , 4.45076971931406e-03 , 9.46467332844427e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.9734 , 1.86278 , -15.0257 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.9734 , 1.86278 , -15.0257 ) to colvar "one". +colvars: Adding total bias energy: 45.193 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.9734 , 1.86278 , -15.0257 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.87596 , -0.554631 , -1.53279 ) +colvars: ( -4.18113 , -0.475596 , -1.31437 ) +colvars: ( -4.18113 , -0.475596 , -1.31437 ) +colvars: ( -5.56939 , -0.633508 , -1.75077 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.898831 , 0.194221 , 0.636598 ) +colvars: ( 0.777528 , 0.265708 , 0.661764 ) +colvars: ( 0.762497 , 0.258412 , 0.642958 ) +colvars: ( 0.663476 , 0.267298 , 0.596359 ) +colvars: ( 0.651424 , 0.200712 , 0.498847 ) +colvars: ( 0.575181 , 0.345294 , 0.649914 ) +colvars: ( 0.465725 , 0.360144 , 0.60523 ) +colvars: ( 0.387493 , 0.458082 , 0.691812 ) +colvars: ( 0.383363 , 0.315812 , 0.49627 ) +colvars: ( 0.347637 , 0.274542 , 0.419092 ) +colvars: ( 0.354591 , 0.320896 , 0.486126 ) +colvars: ( 0.282937 , 0.278156 , 0.38567 ) +colvars: ( 0.256465 , 0.306965 , 0.409089 ) +colvars: ( 0.346593 , 0.179783 , 0.289863 ) +colvars: ( 0.287 , 0.136747 , 0.19615 ) +colvars: ( 0.471439 , 0.14194 , 0.312458 ) +colvars: ( 0.5453 , 0.049979 , 0.231398 ) +colvars: ( 0.677282 , 0.0280841 , 0.279865 ) +colvars: ( 0.553031 , 0.0184407 , 0.193172 ) +colvars: ( 0.537052 , -0.0466147 , 0.0954103 ) +colvars: ( 0.573362 , 0.0666491 , 0.270647 ) +colvars: ( 0.570804 , 0.0508636 , 0.247707 ) +colvars: ( 0.6071 , 0.115778 , 0.357313 ) +colvars: ( 0.444254 , 0.0561451 , 0.179908 ) +colvars: ( 0.43698 , 0.000320414 , 0.0998317 ) +colvars: ( 0.340894 , 0.122362 , 0.208552 ) +colvars: ( 0.214315 , 0.131698 , 0.146239 ) +colvars: ( 0.121631 , 0.217978 , 0.208438 ) +colvars: ( 0.186333 , 0.0577736 , 0.0293293 ) +colvars: ( 0.135947 , 0.0219692 , -0.0491135 ) +colvars: ( 0.221447 , 0.0316125 , 0.0146235 ) +colvars: ( 0.207915 , -0.041166 , -0.0921709 ) +colvars: ( 0.244846 , -0.0451237 , -0.0756655 ) +colvars: ( 0.284058 , -0.127529 , -0.164281 ) +colvars: ( 0.239458 , -0.180494 , -0.262588 ) +colvars: ( 0.400683 , -0.143065 , -0.11628 ) +colvars: ( 0.478975 , -0.218933 , -0.172873 ) +colvars: ( 0.612034 , -0.222183 , -0.0984613 ) +colvars: ( 0.429966 , -0.222791 , -0.207142 ) +colvars: ( 0.435457 , -0.29092 , -0.296356 ) +colvars: ( 0.379738 , -0.148854 , -0.136544 ) +colvars: ( 0.323715 , -0.141935 , -0.160342 ) +colvars: ( 0.306205 , -0.0547758 , -0.0524171 ) +colvars: ( 0.198645 , -0.150113 , -0.245531 ) +colvars: ( 0.173391 , -0.191856 , -0.317147 ) +colvars: ( -0.00411391 , -0.195438 , -0.427159 ) +colvars: ( -0.0963675 , -0.212793 , -0.505365 ) +colvars: ( 0.0983927 , -0.246193 , -0.435323 ) +colvars: ( 0.116217 , -0.109253 , -0.238903 ) +colvars: ( -0.0047496 , -0.113057 , -0.315725 ) +colvars: ( -0.094761 , -0.0319444 , -0.258956 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.87596 , 0.554631 , 1.53279 ) +colvars: ( 4.18113 , 0.475596 , 1.31437 ) +colvars: ( 4.18113 , 0.475596 , 1.31437 ) +colvars: ( 5.56939 , 0.633508 , 1.75077 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.621718 , -0.0804909 , -0.387185 ) +colvars: ( -0.558034 , -0.162695 , -0.358385 ) +colvars: ( -0.510374 , -0.140885 , -0.301022 ) +colvars: ( -0.516275 , -0.190309 , -0.328203 ) +colvars: ( -0.506671 , -0.132137 , -0.293534 ) +colvars: ( -0.489255 , -0.281642 , -0.340244 ) +colvars: ( -0.453819 , -0.321948 , -0.321882 ) +colvars: ( -0.430106 , -0.428356 , -0.343732 ) +colvars: ( -0.390929 , -0.287218 , -0.243631 ) +colvars: ( -0.385156 , -0.262361 , -0.227137 ) +colvars: ( -0.343155 , -0.281664 , -0.19314 ) +colvars: ( -0.283089 , -0.245383 , -0.117066 ) +colvars: ( -0.236064 , -0.260146 , -0.0760604 ) +colvars: ( -0.304114 , -0.143126 , -0.0942955 ) +colvars: ( -0.272119 , -0.114386 , -0.0497285 ) +colvars: ( -0.360651 , -0.0859532 , -0.126655 ) +colvars: ( -0.388887 , 0.0114524 , -0.113229 ) +colvars: ( -0.441797 , 0.0590135 , -0.146069 ) +colvars: ( -0.424697 , 0.026256 , -0.142926 ) +colvars: ( -0.413279 , 0.0823459 , -0.107326 ) +colvars: ( -0.467176 , -0.0271723 , -0.208659 ) +colvars: ( -0.499446 , -0.0287038 , -0.241811 ) +colvars: ( -0.548101 , -0.0933183 , -0.31857 ) +colvars: ( -0.445039 , -0.0588327 , -0.199974 ) +colvars: ( -0.451185 , -0.0152937 , -0.187453 ) +colvars: ( -0.388764 , -0.132649 , -0.17503 ) +colvars: ( -0.329172 , -0.16404 , -0.128514 ) +colvars: ( -0.277795 , -0.253509 , -0.115228 ) +colvars: ( -0.289112 , -0.0920643 , -0.0572469 ) +colvars: ( -0.274546 , -0.0738579 , -0.0347564 ) +colvars: ( -0.271835 , -0.0474935 , -0.0206969 ) +colvars: ( -0.237882 , 0.026431 , 0.0452591 ) +colvars: ( -0.219335 , 0.0527359 , 0.075238 ) +colvars: ( -0.282555 , 0.112459 , 0.0372444 ) +colvars: ( -0.255552 , 0.153609 , 0.0821179 ) +colvars: ( -0.352778 , 0.140641 , -0.0213547 ) +colvars: ( -0.402034 , 0.216228 , -0.0384702 ) +colvars: ( -0.474654 , 0.238989 , -0.101813 ) +colvars: ( -0.410898 , 0.196379 , -0.055926 ) +colvars: ( -0.415352 , 0.256529 , -0.0345629 ) +colvars: ( -0.413069 , 0.11055 , -0.0949945 ) +colvars: ( -0.417431 , 0.0804657 , -0.112315 ) +colvars: ( -0.437026 , -0.0119167 , -0.171745 ) +colvars: ( -0.349307 , 0.0688996 , -0.0486888 ) +colvars: ( -0.351361 , 0.0947951 , -0.0396287 ) +colvars: ( -0.18898 , 0.100677 , 0.126406 ) +colvars: ( -0.138516 , 0.102211 , 0.177879 ) +colvars: ( -0.218311 , 0.172588 , 0.127773 ) +colvars: ( -0.286911 , 0.0283797 , -0.00327288 ) +colvars: ( -0.218932 , 0.0145134 , 0.0592193 ) +colvars: ( -0.164367 , -0.0679289 , 0.0787349 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 11. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 11. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atoms_new_colvar_forces = { ( -4.59884513447972e+00 , -4.40900820867944e-01 , -1.28337506853621e+00 ), ( -3.96163887115342e+00 , -3.72583406983679e-01 , -1.01098544233917e+00 ), ( -4.03393239834945e+00 , -3.98607267392641e-01 , -1.04620861900968e+00 ), ( -5.42463701602936e+00 , -5.64932512498923e-01 , -1.54545968977434e+00 ), ( 2.52122600767734e-01 , 1.17526712350953e-01 , 3.41935437795740e-01 ), ( 4.96188382968194e+00 , 6.18282820313522e-01 , 1.84245832108118e+00 ), ( 4.19303858656264e+00 , 5.13792492554205e-01 , 1.59771267574707e+00 ), ( -4.26127345682579e-02 , 2.97254133625255e-02 , 3.48080688600381e-01 ), ( 4.17356734697521e+00 , 5.04190403647140e-01 , 1.56700347347154e+00 ), ( 5.53187126614492e+00 , 6.45688546426307e-01 , 1.94272759159626e+00 ), ( 1.14357699440463e-02 , 3.92327263640231e-02 , 2.92986597107914e-01 ), ( -1.51372103148639e-04 , 3.27722799696802e-02 , 2.68603304469462e-01 ), ( 2.04003955970579e-02 , 4.68184559794554e-02 , 3.33028914310537e-01 ), ( 4.24787983461165e-02 , 3.66568305659243e-02 , 1.95566998128986e-01 ), ( 1.48808118778211e-02 , 2.23605158788987e-02 , 1.46421157206805e-01 ), ( 1.10787960062394e-01 , 5.59870178408550e-02 , 1.85802306159689e-01 ), ( 1.56412927814132e-01 , 6.14314039279574e-02 , 1.18168388061017e-01 ), ( 2.35484338777458e-01 , 8.70975640996397e-02 , 1.33796672484103e-01 ), ( 1.28334568769220e-01 , 4.46967062211768e-02 , 5.02463943210389e-02 ), ( 1.23772787025132e-01 , 3.57311716871498e-02 , -1.19160624079119e-02 ), ( 1.06185848120741e-01 , 3.94767284527993e-02 , 6.19875167770056e-02 ), ( 7.13586731729734e-02 , 2.21598185424610e-02 , 5.89604027723398e-03 ), ( 5.89988047881739e-02 , 2.24594945422259e-02 , 3.87424590980556e-02 ), ( -7.85336772361367e-04 , -2.68758796431411e-03 , -2.00658935725362e-02 ), ( -1.42047598250104e-02 , -1.49732891714304e-02 , -8.76214225949302e-02 ), ( -4.78703133974230e-02 , -1.02867402626420e-02 , 3.35221731945086e-02 ), ( -1.14856764966572e-01 , -3.23426402810121e-02 , 1.77251173079882e-02 ), ( -1.56164265820016e-01 , -3.55306178344022e-02 , 9.32101362088979e-02 ), ( -1.02779777673893e-01 , -3.42907513475975e-02 , -2.79176158306193e-02 ), ( -1.38599004907390e-01 , -5.18887123716195e-02 , -8.38698931274176e-02 ), ( -5.03883490752813e-02 , -1.58810317266450e-02 , -6.07338679726589e-03 ), ( -2.99666445512997e-02 , -1.47350139960092e-02 , -4.69117871334710e-02 ), ( 2.55100756206192e-02 , 7.61217337109285e-03 , -4.27509143430649e-04 ), ( 1.50283291200376e-03 , -1.50696887306304e-02 , -1.27036342323648e-01 ), ( -1.60944744697057e-02 , -2.68852617720362e-02 , -1.80470346539109e-01 ), ( 4.79043970101733e-02 , -2.42338409384135e-03 , -1.37634460798546e-01 ), ( 7.69409680429476e-02 , -2.70507328915792e-03 , -2.11342681785463e-01 ), ( 1.37379981564062e-01 , 1.68058816156087e-02 , -2.00274676521168e-01 ), ( 1.90679535935423e-02 , -2.64125042132309e-02 , -2.63067504258520e-01 ), ( 2.01049607196809e-02 , -3.43909572427850e-02 , -3.30918761131843e-01 ), ( -3.33307589809503e-02 , -3.83033210706806e-02 , -2.31538599588535e-01 ), ( -9.37163462636916e-02 , -6.14697262270893e-02 , -2.72656723612530e-01 ), ( -1.30820877143099e-01 , -6.66925790424657e-02 , -2.24161892236045e-01 ), ( -1.50661997623523e-01 , -8.12133363018726e-02 , -2.94219328629125e-01 ), ( -1.77970142126282e-01 , -9.70610417104104e-02 , -3.56775566209909e-01 ), ( -1.93093795451497e-01 , -9.47601328613884e-02 , -3.00753355593030e-01 ), ( -2.34883133458497e-01 , -1.10581736122046e-01 , -3.27485825976173e-01 ), ( -1.19918516908678e-01 , -7.36053910619497e-02 , -3.07550702818950e-01 ), ( -1.70694370259342e-01 , -8.08733348585255e-02 , -2.42175707234071e-01 ), ( -2.23681388006602e-01 , -9.85439408538684e-02 , -2.56505928004477e-01 ), ( -2.59127939526269e-01 , -9.98733555627645e-02 , -1.80221569877279e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 11, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 12 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 12, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 12, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 12, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 12, atoms_positions[size = 51] = { ( 8.33295571895662e+00 , 4.36061656045469e-02 , -7.65818806317456e-01 ), ( 6.98877846778014e+00 , -5.37741483712509e-01 , -6.26144120316792e-01 ), ( 6.20406265157318e+00 , -3.06445668968316e-01 , 6.90213293377312e-01 ), ( 4.98114405786721e+00 , -1.92537607642435e-01 , 6.96201523086720e-01 ), ( 7.05216970222226e+00 , -2.03266865864220e+00 , -9.73340123141853e-01 ), ( 6.89825599504267e+00 , -2.66113724750723e-01 , 1.85486440943486e+00 ), ( 6.18496365955545e+00 , -1.20770477430784e-01 , 3.15936212167099e+00 ), ( 7.11121253656082e+00 , -3.42530652917635e-01 , 4.28277545291277e+00 ), ( 5.28841220037515e+00 , 1.11209820607442e+00 , 3.32022070845398e+00 ), ( 4.12604012509779e+00 , 1.04652528783029e+00 , 3.64726274554401e+00 ), ( 5.87087372721693e+00 , 2.25410236808351e+00 , 2.99694107228310e+00 ), ( 5.21736348697982e+00 , 3.59297928625683e+00 , 2.89681673047679e+00 ), ( 6.33480788548696e+00 , 4.53565809183101e+00 , 2.43245136361519e+00 ), ( 3.90961739436181e+00 , 3.73996287366647e+00 , 2.03106767909737e+00 ), ( 2.84169790894118e+00 , 4.13207118883219e+00 , 2.52389262293396e+00 ), ( 3.87446485100083e+00 , 3.24053076273417e+00 , 7.46624285597141e-01 ), ( 2.66537195679257e+00 , 3.08070250699176e+00 , -1.06970825269599e-01 ), ( 3.03339709044189e+00 , 2.72233175202439e+00 , -1.56641643435355e+00 ), ( 1.57121526890728e+00 , 2.18520968208356e+00 , 5.36130647529653e-01 ), ( 4.33201316981108e-01 , 2.50394567657911e+00 , 5.33418648401908e-01 ), ( 1.98502933817818e+00 , 1.00234124743323e+00 , 1.07073191094727e+00 ), ( 1.18076254581051e+00 , 6.53645310955235e-02 , 1.69226266857951e+00 ), ( 2.02205290769318e+00 , -1.14473097002340e+00 , 2.00913153765872e+00 ), ( 5.46808386891470e-01 , 6.10076055254844e-01 , 2.93917233454231e+00 ), ( -6.50613837447251e-01 , 3.54020578335481e-01 , 3.17164471336799e+00 ), ( 1.32450853334442e+00 , 1.33949134166068e+00 , 3.83443885250890e+00 ), ( 8.59715275247287e-01 , 1.94336563984750e+00 , 5.03925228208658e+00 ), ( 2.02966514880358e+00 , 2.61908990284665e+00 , 5.63548641588938e+00 ), ( -3.51825069730810e-01 , 2.91688608723441e+00 , 4.97611389187533e+00 ), ( -1.16092050531517e+00 , 3.04808993560574e+00 , 5.90448975522759e+00 ), ( -4.64340852385915e-01 , 3.63018167649035e+00 , 3.84568329380056e+00 ), ( -1.49206207655392e+00 , 4.55228924756019e+00 , 3.52092650506299e+00 ), ( -7.27178460610727e-01 , 5.39873008902098e+00 , 2.43698904581802e+00 ), ( -2.76549961074677e+00 , 3.87909298094911e+00 , 2.91957687931561e+00 ), ( -3.83320500718966e+00 , 4.46090103812986e+00 , 2.82975353569123e+00 ), ( -2.60194127387236e+00 , 2.63707560012780e+00 , 2.45584524632627e+00 ), ( -3.72983316266672e+00 , 1.87760732537601e+00 , 2.02908581185006e+00 ), ( -3.41572625315696e+00 , 8.58001699944253e-01 , 9.34120452580659e-01 ), ( -4.30068086593182e+00 , 1.06685373748620e+00 , 3.24921589040063e+00 ), ( -5.53241571682040e+00 , 8.75043424747895e-01 , 3.33175013181537e+00 ), ( -3.42189417280314e+00 , 6.65026977550348e-01 , 4.14400913502875e+00 ), ( -3.76398547140368e+00 , 5.18481619405909e-02 , 5.46953003321335e+00 ), ( -2.38373988627510e+00 , -3.36652890873889e-01 , 6.16555774885334e+00 ), ( -4.47475638623978e+00 , 9.96794401766116e-01 , 6.43430594146024e+00 ), ( -5.33058868219778e+00 , 6.08717875327609e-01 , 7.19826346543950e+00 ), ( -6.26387125422770e+00 , 3.56866870710881e+00 , 6.70882368927237e+00 ), ( -6.92314946980549e+00 , 4.29503765079163e+00 , 7.43608083062516e+00 ), ( -6.74511748440753e+00 , 3.20538001822847e+00 , 5.52315269871824e+00 ), ( -4.11755045843843e+00 , 2.29050371691807e+00 , 6.47028156112260e+00 ), ( -4.85859726047702e+00 , 3.19872694766136e+00 , 7.21448858099587e+00 ), ( -4.09969496157519e+00 , 4.57066698467727e+00 , 7.29317571082817e+00 ) } +colvars: Step 12, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_ids[size = 0] = +colvars: Step 12, atom_groups_refcount[size = 0] = +colvars: Step 12, atom_groups_masses[size = 0] = +colvars: Step 12, atom_groups_charges[size = 0] = +colvars: Step 12, atom_groups_coms[size = 0] = +colvars: Step 12, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 12, volmaps_ids[size = 0] = +colvars: Step 12, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 12 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.20358118183599e-01 , 4.32056543368708e-03 , 9.47286656101624e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.20358118183599e-01 , 4.32056543368708e-03 , 9.47286656101624e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.9252 , 1.86539 , -15.0421 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.9252 , 1.86539 , -15.0421 ) to colvar "one". +colvars: Adding total bias energy: 45.093 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.9252 , 1.86539 , -15.0421 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.88148 , -0.551647 , -1.52188 ) +colvars: ( -4.18587 , -0.473038 , -1.30501 ) +colvars: ( -4.18587 , -0.473038 , -1.30501 ) +colvars: ( -5.5757 , -0.6301 , -1.73832 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.898175 , 0.194402 , 0.634384 ) +colvars: ( 0.777089 , 0.265785 , 0.65947 ) +colvars: ( 0.761945 , 0.258557 , 0.640737 ) +colvars: ( 0.663309 , 0.267255 , 0.594227 ) +colvars: ( 0.651274 , 0.200681 , 0.496986 ) +colvars: ( 0.575238 , 0.345133 , 0.647614 ) +colvars: ( 0.466059 , 0.359857 , 0.603032 ) +colvars: ( 0.388024 , 0.457683 , 0.689357 ) +colvars: ( 0.383782 , 0.315512 , 0.494379 ) +colvars: ( 0.348171 , 0.274199 , 0.417406 ) +colvars: ( 0.354946 , 0.320639 , 0.48428 ) +colvars: ( 0.283349 , 0.277898 , 0.38411 ) +colvars: ( 0.256805 , 0.306747 , 0.40748 ) +colvars: ( 0.346853 , 0.179616 , 0.288582 ) +colvars: ( 0.28737 , 0.136547 , 0.195125 ) +colvars: ( 0.471441 , 0.141891 , 0.31113 ) +colvars: ( 0.545137 , 0.0500229 , 0.230307 ) +colvars: ( 0.676822 , 0.028261 , 0.278661 ) +colvars: ( 0.552969 , 0.0184345 , 0.192171 ) +colvars: ( 0.537014 , -0.0466133 , 0.0946818 ) +colvars: ( 0.573371 , 0.0665855 , 0.269414 ) +colvars: ( 0.570938 , 0.0507356 , 0.246519 ) +colvars: ( 0.607267 , 0.115605 , 0.355806 ) +colvars: ( 0.444661 , 0.0558999 , 0.178891 ) +colvars: ( 0.437441 , 6.18542e-05 , 0.0990312 ) +colvars: ( 0.341478 , 0.122032 , 0.207448 ) +colvars: ( 0.215155 , 0.131259 , 0.145293 ) +colvars: ( 0.122623 , 0.217459 , 0.207313 ) +colvars: ( 0.18714 , 0.0573797 , 0.0287208 ) +colvars: ( 0.136892 , 0.0215226 , -0.0495148 ) +colvars: ( 0.222066 , 0.0313196 , 0.014079 ) +colvars: ( 0.20847 , -0.0414012 , -0.0924042 ) +colvars: ( 0.245199 , -0.0452568 , -0.0759201 ) +colvars: ( 0.284498 , -0.1277 , -0.164309 ) +colvars: ( 0.239971 , -0.18068 , -0.262345 ) +colvars: ( 0.400942 , -0.143165 , -0.116437 ) +colvars: ( 0.479126 , -0.218976 , -0.17287 ) +colvars: ( 0.611952 , -0.222134 , -0.0986562 ) +colvars: ( 0.43033 , -0.222938 , -0.207068 ) +colvars: ( 0.435822 , -0.291051 , -0.296034 ) +colvars: ( 0.380288 , -0.149108 , -0.136687 ) +colvars: ( 0.324486 , -0.142298 , -0.160443 ) +colvars: ( 0.307103 , -0.0552255 , -0.0528358 ) +colvars: ( 0.199638 , -0.15056 , -0.245403 ) +colvars: ( 0.174487 , -0.192344 , -0.316831 ) +colvars: ( -0.0029368 , -0.195918 , -0.426513 ) +colvars: ( -0.0950272 , -0.213334 , -0.504508 ) +colvars: ( 0.0992999 , -0.246541 , -0.434632 ) +colvars: ( 0.117289 , -0.109732 , -0.23879 ) +colvars: ( -0.00347128 , -0.113615 , -0.315407 ) +colvars: ( -0.0933505 , -0.0325701 , -0.2588 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.88148 , 0.551647 , 1.52188 ) +colvars: ( 4.18587 , 0.473038 , 1.30501 ) +colvars: ( 4.18587 , 0.473038 , 1.30501 ) +colvars: ( 5.5757 , 0.6301 , 1.73832 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.620856 , -0.0805104 , -0.384779 ) +colvars: ( -0.557435 , -0.16267 , -0.355802 ) +colvars: ( -0.509582 , -0.140887 , -0.298413 ) +colvars: ( -0.516025 , -0.190223 , -0.325817 ) +colvars: ( -0.506426 , -0.132044 , -0.291488 ) +colvars: ( -0.489307 , -0.281509 , -0.337642 ) +colvars: ( -0.454232 , -0.321754 , -0.319413 ) +colvars: ( -0.43079 , -0.428122 , -0.340929 ) +colvars: ( -0.391406 , -0.287004 , -0.241461 ) +colvars: ( -0.385783 , -0.262119 , -0.22525 ) +colvars: ( -0.343509 , -0.281465 , -0.190917 ) +colvars: ( -0.283468 , -0.245172 , -0.115112 ) +colvars: ( -0.236314 , -0.259953 , -0.0739318 ) +colvars: ( -0.304283 , -0.142944 , -0.0927086 ) +colvars: ( -0.272411 , -0.114178 , -0.0484402 ) +colvars: ( -0.360499 , -0.0858269 , -0.125054 ) +colvars: ( -0.388512 , 0.011546 , -0.111953 ) +colvars: ( -0.441045 , 0.0590415 , -0.144673 ) +colvars: ( -0.424485 , 0.0263748 , -0.141862 ) +colvars: ( -0.413083 , 0.0824728 , -0.106601 ) +colvars: ( -0.467103 , -0.0270385 , -0.207394 ) +colvars: ( -0.499569 , -0.0285401 , -0.240699 ) +colvars: ( -0.548316 , -0.0931488 , -0.317147 ) +colvars: ( -0.445503 , -0.058608 , -0.199046 ) +colvars: ( -0.45172 , -0.0150543 , -0.186833 ) +colvars: ( -0.389442 , -0.132388 , -0.173921 ) +colvars: ( -0.330161 , -0.163724 , -0.127559 ) +colvars: ( -0.278971 , -0.253162 , -0.113975 ) +colvars: ( -0.290015 , -0.0917525 , -0.0566445 ) +colvars: ( -0.275624 , -0.0735136 , -0.0344299 ) +colvars: ( -0.272459 , -0.0472238 , -0.0200969 ) +colvars: ( -0.238379 , 0.0266885 , 0.0455361 ) +colvars: ( -0.219538 , 0.0529473 , 0.0756297 ) +colvars: ( -0.282913 , 0.112695 , 0.0371953 ) +colvars: ( -0.255983 , 0.153863 , 0.0817491 ) +colvars: ( -0.352935 , 0.140839 , -0.0213295 ) +colvars: ( -0.402066 , 0.216405 , -0.0387233 ) +colvars: ( -0.474416 , 0.239115 , -0.101894 ) +colvars: ( -0.411233 , 0.196605 , -0.056343 ) +colvars: ( -0.415681 , 0.256758 , -0.0353124 ) +colvars: ( -0.413676 , 0.110816 , -0.0951795 ) +colvars: ( -0.418351 , 0.0807814 , -0.112619 ) +colvars: ( -0.43815 , -0.0115757 , -0.171704 ) +colvars: ( -0.350482 , 0.0692644 , -0.049211 ) +colvars: ( -0.352675 , 0.0951855 , -0.0404267 ) +colvars: ( -0.190283 , 0.101082 , 0.125477 ) +colvars: ( -0.140005 , 0.102653 , 0.176734 ) +colvars: ( -0.219253 , 0.172934 , 0.126795 ) +colvars: ( -0.288156 , 0.0287593 , -0.00367274 ) +colvars: ( -0.220411 , 0.0149384 , 0.0586334 ) +colvars: ( -0.166001 , -0.0674787 , 0.0784344 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 12. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 12. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atoms_new_colvar_forces = { ( -4.60416200301848e+00 , -4.37756284700426e-01 , -1.27227691754553e+00 ), ( -3.96621596863790e+00 , -3.69922931911158e-01 , -1.00134529679591e+00 ), ( -4.03858528774981e+00 , -3.96004927783702e-01 , -1.03660358798177e+00 ), ( -5.43085162563976e+00 , -5.61462924506829e-01 , -1.53281752140938e+00 ), ( 2.52363689247368e-01 , 1.17670511959752e-01 , 3.42323432777615e-01 ), ( 4.96741230845689e+00 , 6.15270971905017e-01 , 1.83185400807489e+00 ), ( 4.19769564488300e+00 , 5.11141221197853e-01 , 1.58863191712320e+00 ), ( -4.27662929355598e-02 , 2.95612670755830e-02 , 3.48427877676948e-01 ), ( 4.17824538855081e+00 , 5.01546377407413e-01 , 1.55793193781718e+00 ), ( 5.53808746651970e+00 , 6.42179756465880e-01 , 1.93047144887531e+00 ), ( 1.14375417566049e-02 , 3.91734938130505e-02 , 2.93363468353129e-01 ), ( -1.19347846750439e-04 , 3.27265206291947e-02 , 2.68997676509169e-01 ), ( 2.04917499010411e-02 , 4.67937133134244e-02 , 3.33548614846786e-01 ), ( 4.25694709662555e-02 , 3.66723510925716e-02 , 1.95872932010920e-01 ), ( 1.49589089809564e-02 , 2.23689698419174e-02 , 1.46684679808794e-01 ), ( 1.10942559946892e-01 , 5.60636699505158e-02 , 1.86075351427912e-01 ), ( 1.56624720330733e-01 , 6.15688485861727e-02 , 1.18354490821199e-01 ), ( 2.35776330104741e-01 , 8.73025032542672e-02 , 1.33987616003798e-01 ), ( 1.28484285779145e-01 , 4.48093035207972e-02 , 5.03095763111477e-02 ), ( 1.23931515695198e-01 , 3.58594939211851e-02 , -1.19193045247740e-02 ), ( 1.06268060132023e-01 , 3.95470517957588e-02 , 6.20197301896569e-02 ), ( 7.13696518171053e-02 , 2.21955893176192e-02 , 5.81983461485280e-03 ), ( 5.89501894578733e-02 , 2.24561960891333e-02 , 3.86591357010410e-02 ), ( -8.41514629004392e-04 , -2.70815266962117e-03 , -2.01552831428085e-02 ), ( -1.42781456312115e-02 , -1.49924494423558e-02 , -8.78021804497830e-02 ), ( -4.79631559915603e-02 , -1.03566167906717e-02 , 3.35262719064853e-02 ), ( -1.15006131967528e-01 , -3.24641122952530e-02 , 1.77346578863561e-02 ), ( -1.56347702432740e-01 , -3.57025213484728e-02 , 9.33374664950721e-02 ), ( -1.02874919178057e-01 , -3.43727930989843e-02 , -2.79237118241520e-02 ), ( -1.38731690028093e-01 , -5.19909893725838e-02 , -8.39446687419543e-02 ), ( -5.03923572669588e-02 , -1.59042210930658e-02 , -6.01787372405616e-03 ), ( -2.99087347311788e-02 , -1.47126907452013e-02 , -4.68680712295294e-02 ), ( 2.56618747965985e-02 , 7.69047263856128e-03 , -2.90404569400160e-04 ), ( 1.58524766448676e-03 , -1.50045503741583e-02 , -1.27114139759477e-01 ), ( -1.60124616049861e-02 , -2.68163680344020e-02 , -1.80595986281854e-01 ), ( 4.80067747608525e-02 , -2.32614238032083e-03 , -1.37766493033706e-01 ), ( 7.70598843276784e-02 , -2.57104270572023e-03 , -2.11593424546662e-01 ), ( 1.37536095785058e-01 , 1.69811113976544e-02 , -2.00550226781543e-01 ), ( 1.90971989338418e-02 , -2.63325143667982e-02 , -2.63410591662629e-01 ), ( 2.01405894558621e-02 , -3.42926000685874e-02 , -3.31346404967134e-01 ), ( -3.33876932201316e-02 , -3.82918851108436e-02 , -2.31866561651735e-01 ), ( -9.38647083066095e-02 , -6.15165982123629e-02 , -2.73061494078509e-01 ), ( -1.31046987776956e-01 , -6.68011620217128e-02 , -2.24540057378766e-01 ), ( -1.50844297938520e-01 , -8.12960617680461e-02 , -2.94614300476024e-01 ), ( -1.78188578549210e-01 , -9.71580672763863e-02 , -3.57257930575860e-01 ), ( -1.93220098418491e-01 , -9.48359932665020e-02 , -3.01036128669544e-01 ), ( -2.35032678802051e-01 , -1.10680750129854e-01 , -3.27774055228857e-01 ), ( -1.19953280936978e-01 , -7.36064528570606e-02 , -3.07837674488556e-01 ), ( -1.70866846813936e-01 , -8.09723802475359e-02 , -2.42463108076809e-01 ), ( -2.23882676752656e-01 , -9.86764076408371e-02 , -2.56773434825889e-01 ), ( -2.59351961445597e-01 , -1.00048802953869e-01 , -1.80365290808875e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 12, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 13 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 13, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 13, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 13, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 13, atoms_positions[size = 51] = { ( 8.32563668862924e+00 , 4.32657320564243e-02 , -7.65748447617707e-01 ), ( 6.98661919936763e+00 , -5.41227563033319e-01 , -6.21758543748275e-01 ), ( 6.19209801346542e+00 , -3.15306580245825e-01 , 6.93705052961330e-01 ), ( 4.97978049326016e+00 , -1.89278595719519e-01 , 7.00300270066944e-01 ), ( 7.05341851019372e+00 , -2.03495284782903e+00 , -9.67525140668200e-01 ), ( 6.89615579853863e+00 , -2.65271694396097e-01 , 1.86087063899170e+00 ), ( 6.18601376492217e+00 , -1.23547653691593e-01 , 3.17160838459325e+00 ), ( 7.10298170551818e+00 , -3.45744813901811e-01 , 4.28313968504903e+00 ), ( 5.28829647670455e+00 , 1.11142363892930e+00 , 3.32452399627943e+00 ), ( 4.13230788771988e+00 , 1.04355492143894e+00 , 3.65165316687648e+00 ), ( 5.86803046994690e+00 , 2.25027637895970e+00 , 2.99786612839834e+00 ), ( 5.22090995318872e+00 , 3.59158121811476e+00 , 2.90066447440529e+00 ), ( 6.33290598194421e+00 , 4.52788068981783e+00 , 2.42619501232639e+00 ), ( 3.90924832418276e+00 , 3.73836971419749e+00 , 2.03350920492794e+00 ), ( 2.83214384561086e+00 , 4.13594770995655e+00 , 2.51990224649253e+00 ), ( 3.88445670732267e+00 , 3.24094017599406e+00 , 7.43123862429219e-01 ), ( 2.66186122446235e+00 , 3.06673144525553e+00 , -1.07940780309680e-01 ), ( 3.03267628080236e+00 , 2.72277183365063e+00 , -1.55733631745110e+00 ), ( 1.57223017446702e+00 , 2.19056819808818e+00 , 5.23365936649474e-01 ), ( 4.27797343425988e-01 , 2.51332171791790e+00 , 5.30763201286296e-01 ), ( 1.99144319024645e+00 , 1.00294925032535e+00 , 1.07434901335352e+00 ), ( 1.18195814860052e+00 , 7.58451142980359e-02 , 1.69221730557218e+00 ), ( 2.02416703905804e+00 , -1.13881127834980e+00 , 2.00759640101040e+00 ), ( 5.49617185678168e-01 , 6.09368571473590e-01 , 2.93374885372882e+00 ), ( -6.45188447181623e-01 , 3.52467064801428e-01 , 3.17017989878665e+00 ), ( 1.32597370357311e+00 , 1.34180807118143e+00 , 3.83137967123143e+00 ), ( 8.59775872582345e-01 , 1.94897297063648e+00 , 5.03552588557840e+00 ), ( 2.03094018947012e+00 , 2.62571564767449e+00 , 5.63948259151190e+00 ), ( -3.48983674247370e-01 , 2.91670045601694e+00 , 4.97412630730138e+00 ), ( -1.15856527598334e+00 , 3.05060646151493e+00 , 5.90337715179325e+00 ), ( -4.71314783134488e-01 , 3.61719276093745e+00 , 3.84600498612597e+00 ), ( -1.49575782198763e+00 , 4.55039130986648e+00 , 3.51351392910702e+00 ), ( -7.22385227454294e-01 , 5.40073011168207e+00 , 2.44146282214525e+00 ), ( -2.76925428816865e+00 , 3.87661302285524e+00 , 2.91740443128944e+00 ), ( -3.83010584362955e+00 , 4.46702339232755e+00 , 2.82711386484213e+00 ), ( -2.60381690422610e+00 , 2.64492564216005e+00 , 2.44975836915772e+00 ), ( -3.73546535960365e+00 , 1.86577767106548e+00 , 2.02271438672350e+00 ), ( -3.41402649543479e+00 , 8.64772982443447e-01 , 9.25433492011849e-01 ), ( -4.30522658520302e+00 , 1.06547933586241e+00 , 3.24687854450203e+00 ), ( -5.52835461462766e+00 , 8.68203672679641e-01 , 3.33049508088187e+00 ), ( -3.41380267786763e+00 , 6.68866823699580e-01 , 4.15014754048846e+00 ), ( -3.75690767903950e+00 , 4.55839844889497e-02 , 5.46353760075140e+00 ), ( -2.38288396029947e+00 , -3.29295031220147e-01 , 6.16828366291920e+00 ), ( -4.47388340590213e+00 , 9.99001790413945e-01 , 6.43712437824932e+00 ), ( -5.33370829992695e+00 , 6.08187134023306e-01 , 7.20109423386675e+00 ), ( -6.25584413419192e+00 , 3.57194274168611e+00 , 6.71034737659518e+00 ), ( -6.92768822243289e+00 , 4.29560122448252e+00 , 7.44103235347024e+00 ), ( -6.74726924123469e+00 , 3.20379273004767e+00 , 5.52276082551144e+00 ), ( -4.12167346184729e+00 , 2.28457680469545e+00 , 6.46418689653973e+00 ), ( -4.84967541764903e+00 , 3.19499187486762e+00 , 7.21597988933476e+00 ), ( -4.10191196539783e+00 , 4.57773057696201e+00 , 7.29465500401028e+00 ) } +colvars: Step 13, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_ids[size = 0] = +colvars: Step 13, atom_groups_refcount[size = 0] = +colvars: Step 13, atom_groups_masses[size = 0] = +colvars: Step 13, atom_groups_charges[size = 0] = +colvars: Step 13, atom_groups_coms[size = 0] = +colvars: Step 13, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 13, volmaps_ids[size = 0] = +colvars: Step 13, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 13 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.17961771860725e-01 , 4.11480979755661e-03 , 9.48094604971212e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.17961771860725e-01 , 4.11480979755661e-03 , 9.48094604971212e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.8772 , 1.8695 , -15.0583 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.8772 , 1.8695 , -15.0583 ) to colvar "one". +colvars: Adding total bias energy: 44.9939 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.8772 , 1.8695 , -15.0583 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.88688 , -0.548692 , -1.5111 ) +colvars: ( -4.1905 , -0.470504 , -1.29577 ) +colvars: ( -4.1905 , -0.470504 , -1.29577 ) +colvars: ( -5.58187 , -0.626724 , -1.726 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.897491 , 0.194571 , 0.632175 ) +colvars: ( 0.776624 , 0.26585 , 0.657177 ) +colvars: ( 0.761369 , 0.258688 , 0.638515 ) +colvars: ( 0.66312 , 0.267203 , 0.592097 ) +colvars: ( 0.651102 , 0.200643 , 0.49513 ) +colvars: ( 0.575274 , 0.344962 , 0.645314 ) +colvars: ( 0.466374 , 0.359562 , 0.600835 ) +colvars: ( 0.388536 , 0.457275 , 0.6869 ) +colvars: ( 0.384187 , 0.315206 , 0.492489 ) +colvars: ( 0.348691 , 0.273852 , 0.415723 ) +colvars: ( 0.355289 , 0.320372 , 0.482431 ) +colvars: ( 0.283751 , 0.277633 , 0.382546 ) +colvars: ( 0.257138 , 0.306519 , 0.405865 ) +colvars: ( 0.347103 , 0.179444 , 0.287301 ) +colvars: ( 0.287733 , 0.136344 , 0.194101 ) +colvars: ( 0.47143 , 0.141834 , 0.309803 ) +colvars: ( 0.544961 , 0.0500621 , 0.229222 ) +colvars: ( 0.676344 , 0.0284316 , 0.277462 ) +colvars: ( 0.552893 , 0.0184267 , 0.191179 ) +colvars: ( 0.536964 , -0.0466112 , 0.0939638 ) +colvars: ( 0.573364 , 0.0665204 , 0.26819 ) +colvars: ( 0.571056 , 0.0506088 , 0.245343 ) +colvars: ( 0.607413 , 0.115433 , 0.354311 ) +colvars: ( 0.445056 , 0.0556579 , 0.177886 ) +colvars: ( 0.43789 , -0.000190828 , 0.0982455 ) +colvars: ( 0.342052 , 0.121703 , 0.206352 ) +colvars: ( 0.215988 , 0.130824 , 0.144355 ) +colvars: ( 0.123611 , 0.216942 , 0.206191 ) +colvars: ( 0.187944 , 0.0569904 , 0.0281205 ) +colvars: ( 0.137835 , 0.0210832 , -0.0499059 ) +colvars: ( 0.222682 , 0.0310296 , 0.0135415 ) +colvars: ( 0.209024 , -0.0416324 , -0.0926299 ) +colvars: ( 0.245552 , -0.0453886 , -0.0761696 ) +colvars: ( 0.284935 , -0.127864 , -0.164326 ) +colvars: ( 0.240484 , -0.180857 , -0.262089 ) +colvars: ( 0.401195 , -0.143259 , -0.11658 ) +colvars: ( 0.479269 , -0.219011 , -0.17285 ) +colvars: ( 0.611857 , -0.222077 , -0.0988319 ) +colvars: ( 0.430686 , -0.223072 , -0.206973 ) +colvars: ( 0.43618 , -0.291168 , -0.295689 ) +colvars: ( 0.380831 , -0.14935 , -0.136811 ) +colvars: ( 0.325251 , -0.142647 , -0.160522 ) +colvars: ( 0.307992 , -0.0556623 , -0.0532347 ) +colvars: ( 0.200628 , -0.150992 , -0.245256 ) +colvars: ( 0.175582 , -0.192813 , -0.316493 ) +colvars: ( -0.00175316 , -0.196383 , -0.425851 ) +colvars: ( -0.0936769 , -0.213857 , -0.503636 ) +colvars: ( 0.100212 , -0.246873 , -0.433924 ) +colvars: ( 0.118362 , -0.110197 , -0.238661 ) +colvars: ( -0.00218851 , -0.114158 , -0.315073 ) +colvars: ( -0.0919338 , -0.0331834 , -0.258632 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.88688 , 0.548692 , 1.5111 ) +colvars: ( 4.1905 , 0.470504 , 1.29577 ) +colvars: ( 4.1905 , 0.470504 , 1.29577 ) +colvars: ( 5.58187 , 0.626724 , 1.726 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.620021 , -0.0805364 , -0.382427 ) +colvars: ( -0.556854 , -0.16266 , -0.353271 ) +colvars: ( -0.508805 , -0.140899 , -0.29585 ) +colvars: ( -0.515785 , -0.190154 , -0.323478 ) +colvars: ( -0.50619 , -0.131963 , -0.289483 ) +colvars: ( -0.489363 , -0.281404 , -0.335089 ) +colvars: ( -0.454642 , -0.321591 , -0.316991 ) +colvars: ( -0.431464 , -0.427931 , -0.338178 ) +colvars: ( -0.391874 , -0.286817 , -0.239325 ) +colvars: ( -0.386398 , -0.261902 , -0.223394 ) +colvars: ( -0.34385 , -0.281293 , -0.188723 ) +colvars: ( -0.283828 , -0.244982 , -0.113176 ) +colvars: ( -0.23654 , -0.259782 , -0.071819 ) +colvars: ( -0.304438 , -0.142773 , -0.0911351 ) +colvars: ( -0.272685 , -0.113978 , -0.0471576 ) +colvars: ( -0.360342 , -0.0857058 , -0.123471 ) +colvars: ( -0.388139 , 0.0116444 , -0.11069 ) +colvars: ( -0.440304 , 0.0590793 , -0.143297 ) +colvars: ( -0.424277 , 0.0264991 , -0.140813 ) +colvars: ( -0.412889 , 0.082611 , -0.105884 ) +colvars: ( -0.467035 , -0.0269055 , -0.206153 ) +colvars: ( -0.499698 , -0.0283782 , -0.239613 ) +colvars: ( -0.548541 , -0.0929887 , -0.31576 ) +colvars: ( -0.445964 , -0.0583885 , -0.198138 ) +colvars: ( -0.452252 , -0.0148158 , -0.186229 ) +colvars: ( -0.390108 , -0.13214 , -0.172831 ) +colvars: ( -0.33113 , -0.163422 , -0.126614 ) +colvars: ( -0.280119 , -0.25284 , -0.112734 ) +colvars: ( -0.290895 , -0.0914479 , -0.0560422 ) +colvars: ( -0.276676 , -0.0731749 , -0.0340985 ) +colvars: ( -0.273061 , -0.046956 , -0.0194933 ) +colvars: ( -0.238855 , 0.0269524 , 0.0458266 ) +colvars: ( -0.219719 , 0.0531687 , 0.076037 ) +colvars: ( -0.283255 , 0.112946 , 0.0371613 ) +colvars: ( -0.256396 , 0.154137 , 0.0814032 ) +colvars: ( -0.353086 , 0.141053 , -0.0212965 ) +colvars: ( -0.402098 , 0.216607 , -0.0389684 ) +colvars: ( -0.474188 , 0.239268 , -0.101976 ) +colvars: ( -0.411565 , 0.196853 , -0.0567524 ) +colvars: ( -0.416009 , 0.257016 , -0.0360491 ) +colvars: ( -0.414277 , 0.111093 , -0.0953628 ) +colvars: ( -0.419262 , 0.0811054 , -0.112922 ) +colvars: ( -0.439264 , -0.0112365 , -0.171672 ) +colvars: ( -0.351638 , 0.0696366 , -0.0497227 ) +colvars: ( -0.353971 , 0.0955855 , -0.041211 ) +colvars: ( -0.191552 , 0.1015 , 0.124582 ) +colvars: ( -0.141454 , 0.103108 , 0.175631 ) +colvars: ( -0.220168 , 0.173301 , 0.12585 ) +colvars: ( -0.289376 , 0.029143 , -0.00405802 ) +colvars: ( -0.221857 , 0.0153666 , 0.0580709 ) +colvars: ( -0.167594 , -0.0670334 , 0.0781573 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 13. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 13. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atoms_new_colvar_forces = { ( -4.60941152857979e+00 , -4.34657732283577e-01 , -1.26134882081779e+00 ), ( -3.97073083473694e+00 , -3.67313651566339e-01 , -9.91859389363031e-01 ), ( -4.04316472548736e+00 , -3.93454487430930e-01 , -1.02714696681659e+00 ), ( -5.43695557364111e+00 , -5.58045088291464e-01 , -1.52034955209816e+00 ), ( 2.52564673419413e-01 , 1.17788991033556e-01 , 3.42664670190256e-01 ), ( 4.97279195956864e+00 , 6.12250390674802e-01 , 1.82132229160582e+00 ), ( 4.20223194665849e+00 , 5.08474736142992e-01 , 1.57961024511043e+00 ), ( -4.29276074776823e-02 , 2.93446213700490e-02 , 3.48722012915199e-01 ), ( 4.18281293288223e+00 , 4.98892623958362e-01 , 1.54893034738508e+00 ), ( 5.54416128143707e+00 , 6.38674358062218e-01 , 1.91832647544192e+00 ), ( 1.14399585720751e-02 , 3.90794787476342e-02 , 2.93708226731225e-01 ), ( -7.74227782932568e-05 , 3.26513237297457e-02 , 2.69370076729104e-01 ), ( 2.05975207283844e-02 , 4.67361566095524e-02 , 3.34045608643490e-01 ), ( 4.26645761142326e-02 , 3.66710482458952e-02 , 1.96165462885331e-01 ), ( 1.50481746260900e-02 , 2.23658164168660e-02 , 1.46943492053965e-01 ), ( 1.11088946090217e-01 , 5.61286874900876e-02 , 1.86332573791074e-01 ), ( 1.56821586267231e-01 , 6.17064835141191e-02 , 1.18531904330075e-01 ), ( 2.36040288827892e-01 , 8.75109152017895e-02 , 1.34165376638010e-01 ), ( 1.28616670071091e-01 , 4.49257663790903e-02 , 5.03662776739318e-02 ), ( 1.24075243198848e-01 , 3.59998038770147e-02 , -1.19201499422995e-02 ), ( 1.06328632335919e-01 , 3.96149728507969e-02 , 6.20373291991009e-02 ), ( 7.13574773389903e-02 , 2.22306139835790e-02 , 5.72986097930586e-03 ), ( 5.88724090671617e-02 , 2.24438607366800e-02 , 3.85510442010033e-02 ), ( -9.07964480255985e-04 , -2.73061051878320e-03 , -2.02521081487401e-02 ), ( -1.43612030032016e-02 , -1.50066306082719e-02 , -8.79835825452684e-02 ), ( -4.80555049049832e-02 , -1.04369604238727e-02 , 3.35210763573743e-02 ), ( -1.15141857182860e-01 , -3.25976579414282e-02 , 1.77409353727871e-02 ), ( -1.56507975530757e-01 , -3.58975451284672e-02 , 9.34566598098229e-02 ), ( -1.02951477208506e-01 , -3.44575047755011e-02 , -2.79216233723472e-02 ), ( -1.38840804626506e-01 , -5.20917148981355e-02 , -8.40044277638193e-02 ), ( -5.03793616759529e-02 , -1.59263713413516e-02 , -5.95179953464081e-03 ), ( -2.98303562581878e-02 , -1.46800115534475e-02 , -4.68032765683968e-02 ), ( 2.58323416427286e-02 , 7.78008423467155e-03 , -1.32545044126964e-04 ), ( 1.68027528414161e-03 , -1.49180664151575e-02 , -1.27165078361497e-01 ), ( -1.59124803691898e-02 , -2.67195990972143e-02 , -1.80685652304989e-01 ), ( 4.81088347348926e-02 , -2.20534914566670e-03 , -1.37876936909011e-01 ), ( 7.71701297516348e-02 , -2.40380998444134e-03 , -2.11818312120294e-01 ), ( 1.37669110328292e-01 , 1.71903182358169e-02 , -2.00807409614685e-01 ), ( 1.91211137365860e-02 , -2.62193053405430e-02 , -2.63725732867441e-01 ), ( 2.01706741704832e-02 , -3.41524960997568e-02 , -3.31738275345898e-01 ), ( -3.34466762409990e-02 , -3.82568962355038e-02 , -2.32173567232608e-01 ), ( -9.40110524129654e-02 , -6.15412620828612e-02 , -2.73444075319582e-01 ), ( -1.31271417989929e-01 , -6.68987632847314e-02 , -2.24906537274629e-01 ), ( -1.51010948978680e-01 , -8.13559030288523e-02 , -2.94978697112032e-01 ), ( -1.78389231192939e-01 , -9.72272014198814e-02 , -3.57703764515572e-01 ), ( -1.93305620802337e-01 , -9.48833976742998e-02 , -3.01269082478313e-01 ), ( -2.35131299405755e-01 , -1.10749390328410e-01 , -3.28004908137406e-01 ), ( -1.19956549612358e-01 , -7.35721764200462e-02 , -3.08073831054048e-01 ), ( -1.71014019022640e-01 , -8.10537214557247e-02 , -2.42719349761469e-01 ), ( -2.24045387087126e-01 , -9.87910106647013e-02 , -2.57002091063096e-01 ), ( -2.59527876165445e-01 , -1.00216736055959e-01 , -1.80474404556519e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 13, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 14 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 14, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 14, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 14, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 14, atoms_positions[size = 51] = { ( 8.31863750519705e+00 , 4.28481966305417e-02 , -7.65206741939643e-01 ), ( 6.98331590064913e+00 , -5.43991075653974e-01 , -6.16884455522366e-01 ), ( 6.18111442627412e+00 , -3.24404099978712e-01 , 6.97403733346897e-01 ), ( 4.97801206783498e+00 , -1.85828863818795e-01 , 7.04176494016022e-01 ), ( 7.05431325902464e+00 , -2.03732785898560e+00 , -9.61992064451894e-01 ), ( 6.89340484043793e+00 , -2.64466142941914e-01 , 1.86689532454778e+00 ), ( 6.18663853782403e+00 , -1.27133089111293e-01 , 3.18194056005567e+00 ), ( 7.09572082235899e+00 , -3.48652736844465e-01 , 4.28459267746327e+00 ), ( 5.28952645252616e+00 , 1.11037466441903e+00 , 3.32871674110496e+00 ), ( 4.13808099528070e+00 , 1.04065956594520e+00 , 3.65636369414770e+00 ), ( 5.86470469300440e+00 , 2.24789547729248e+00 , 2.99811719126949e+00 ), ( 5.22494219944958e+00 , 3.58991350029252e+00 , 2.90466592388533e+00 ), ( 6.33092062020958e+00 , 4.52115114886205e+00 , 2.41920114776961e+00 ), ( 3.90774768740196e+00 , 3.73584735239143e+00 , 2.03586437430797e+00 ), ( 2.82332237875758e+00 , 4.13990616960905e+00 , 2.51580050247276e+00 ), ( 3.89448587872994e+00 , 3.24143183651133e+00 , 7.40136563845258e-01 ), ( 2.65840305240840e+00 , 3.05349047909279e+00 , -1.08518046424564e-01 ), ( 3.03273633519467e+00 , 2.72266970420083e+00 , -1.54825072249137e+00 ), ( 1.57523337633800e+00 , 2.19445215623750e+00 , 5.10280557617337e-01 ), ( 4.21182621729726e-01 , 2.52304005585736e+00 , 5.28148743679193e-01 ), ( 1.99861255663857e+00 , 1.00571244570487e+00 , 1.07722229584875e+00 ), ( 1.18199531938308e+00 , 8.56985360570121e-02 , 1.69219813070834e+00 ), ( 2.02642714277573e+00 , -1.13299810631360e+00 , 2.00643889685938e+00 ), ( 5.51943737918944e-01 , 6.08708944595558e-01 , 2.93014012300699e+00 ), ( -6.39306298584151e-01 , 3.51277656962935e-01 , 3.16871182423111e+00 ), ( 1.32668201217350e+00 , 1.34353055777980e+00 , 3.82671156457060e+00 ), ( 8.58793759228554e-01 , 1.95435624128480e+00 , 5.03241615749648e+00 ), ( 2.03406101961544e+00 , 2.63308418324986e+00 , 5.64413623984418e+00 ), ( -3.46131928142968e-01 , 2.91656829817748e+00 , 4.97221412870430e+00 ), ( -1.15605456019786e+00 , 3.05291443243522e+00 , 5.90194179828644e+00 ), ( -4.77909747478039e-01 , 3.60389260342203e+00 , 3.84668661004553e+00 ), ( -1.49967549984600e+00 , 4.54906058839603e+00 , 3.50491675486485e+00 ), ( -7.17721575937902e-01 , 5.40273099800795e+00 , 2.44572269188412e+00 ), ( -2.77157313701106e+00 , 3.87479971881634e+00 , 2.91518005527361e+00 ), ( -3.82733748016690e+00 , 4.47322294191850e+00 , 2.82468573954751e+00 ), ( -2.60564839500708e+00 , 2.65265533898342e+00 , 2.44347184607968e+00 ), ( -3.74146458335978e+00 , 1.85357453515159e+00 , 2.01680732864283e+00 ), ( -3.41168661134235e+00 , 8.70810771691938e-01 , 9.17006250189225e-01 ), ( -4.31045011776362e+00 , 1.06501267850850e+00 , 3.24309556219264e+00 ), ( -5.52380999153781e+00 , 8.61322541413432e-01 , 3.32952655005222e+00 ), ( -3.40573488210103e+00 , 6.72351857022020e-01 , 4.15783018513658e+00 ), ( -3.74908880178937e+00 , 4.07118213772935e-02 , 5.45715542794465e+00 ), ( -2.38279341493287e+00 , -3.23386240057656e-01 , 6.17045574130615e+00 ), ( -4.47254737130439e+00 , 1.00090046845871e+00 , 6.43947533768169e+00 ), ( -5.33721208135359e+00 , 6.07273663880178e-01 , 7.20399112266022e+00 ), ( -6.24833293180304e+00 , 3.57552261214592e+00 , 6.71230379498847e+00 ), ( -6.93259262162092e+00 , 4.29630801696207e+00 , 7.44623149775835e+00 ), ( -6.74932958271965e+00 , 3.20179591103569e+00 , 5.52162953840506e+00 ), ( -4.12509679092533e+00 , 2.27808818570299e+00 , 6.45713772268763e+00 ), ( -4.84117444611746e+00 , 3.19242576639085e+00 , 7.21807501097597e+00 ), ( -4.10366948633281e+00 , 4.58307875841315e+00 , 7.29510970661580e+00 ) } +colvars: Step 14, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_ids[size = 0] = +colvars: Step 14, atom_groups_refcount[size = 0] = +colvars: Step 14, atom_groups_masses[size = 0] = +colvars: Step 14, atom_groups_charges[size = 0] = +colvars: Step 14, atom_groups_coms[size = 0] = +colvars: Step 14, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 14, volmaps_ids[size = 0] = +colvars: Step 14, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 14 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.15622953688594e-01 , 3.81824775894985e-03 , 9.48877005775216e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.15622953688594e-01 , 3.81824775894985e-03 , 9.48877005775216e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.8305 , 1.87544 , -15.0739 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.8305 , 1.87544 , -15.0739 ) to colvar "one". +colvars: Adding total bias energy: 44.8977 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.8305 , 1.87544 , -15.0739 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.89206 , -0.545836 , -1.50063 ) +colvars: ( -4.19494 , -0.468054 , -1.28679 ) +colvars: ( -4.19494 , -0.468054 , -1.28679 ) +colvars: ( -5.58778 , -0.623462 , -1.71405 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.896784 , 0.19473 , 0.630006 ) +colvars: ( 0.776135 , 0.265906 , 0.65492 ) +colvars: ( 0.760773 , 0.258807 , 0.636322 ) +colvars: ( 0.662908 , 0.267148 , 0.589999 ) +colvars: ( 0.650909 , 0.200601 , 0.493307 ) +colvars: ( 0.575285 , 0.34479 , 0.643047 ) +colvars: ( 0.466665 , 0.359272 , 0.598669 ) +colvars: ( 0.389022 , 0.456875 , 0.684472 ) +colvars: ( 0.384569 , 0.314904 , 0.490624 ) +colvars: ( 0.349191 , 0.273513 , 0.414065 ) +colvars: ( 0.355613 , 0.320107 , 0.480602 ) +colvars: ( 0.284136 , 0.277369 , 0.380998 ) +colvars: ( 0.257454 , 0.306288 , 0.404258 ) +colvars: ( 0.347337 , 0.179272 , 0.286035 ) +colvars: ( 0.288081 , 0.136142 , 0.193091 ) +colvars: ( 0.471404 , 0.141775 , 0.308496 ) +colvars: ( 0.54477 , 0.0500958 , 0.228158 ) +colvars: ( 0.675852 , 0.028592 , 0.276287 ) +colvars: ( 0.552801 , 0.0184175 , 0.190212 ) +colvars: ( 0.536899 , -0.0466095 , 0.0932708 ) +colvars: ( 0.573338 , 0.0664566 , 0.266997 ) +colvars: ( 0.571153 , 0.0504875 , 0.244202 ) +colvars: ( 0.607537 , 0.115267 , 0.352857 ) +colvars: ( 0.445431 , 0.0554257 , 0.176913 ) +colvars: ( 0.43832 , -0.000431498 , 0.0974928 ) +colvars: ( 0.342606 , 0.121386 , 0.205283 ) +colvars: ( 0.216802 , 0.130404 , 0.143441 ) +colvars: ( 0.124579 , 0.21644 , 0.205088 ) +colvars: ( 0.188731 , 0.0566147 , 0.0275399 ) +colvars: ( 0.138762 , 0.0206604 , -0.0502775 ) +colvars: ( 0.223283 , 0.0307484 , 0.0130203 ) +colvars: ( 0.209567 , -0.0418568 , -0.0928429 ) +colvars: ( 0.245894 , -0.0455188 , -0.07641 ) +colvars: ( 0.285361 , -0.128022 , -0.164327 ) +colvars: ( 0.240987 , -0.181025 , -0.261818 ) +colvars: ( 0.401435 , -0.143347 , -0.116702 ) +colvars: ( 0.479399 , -0.21904 , -0.172803 ) +colvars: ( 0.611748 , -0.222018 , -0.0989759 ) +colvars: ( 0.431028 , -0.223196 , -0.20685 ) +colvars: ( 0.436525 , -0.291273 , -0.295315 ) +colvars: ( 0.381357 , -0.149578 , -0.136904 ) +colvars: ( 0.325998 , -0.142976 , -0.160569 ) +colvars: ( 0.308862 , -0.0560768 , -0.0535979 ) +colvars: ( 0.201602 , -0.151402 , -0.24508 ) +colvars: ( 0.176661 , -0.193256 , -0.316125 ) +colvars: ( -0.000579805 , -0.196827 , -0.425176 ) +colvars: ( -0.0923356 , -0.214357 , -0.502753 ) +colvars: ( 0.101114 , -0.247189 , -0.433201 ) +colvars: ( 0.11942 , -0.11064 , -0.23851 ) +colvars: ( -0.000918935 , -0.114676 , -0.314722 ) +colvars: ( -0.0905301 , -0.0337725 , -0.258451 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.89206 , 0.545836 , 1.50063 ) +colvars: ( 4.19494 , 0.468054 , 1.28679 ) +colvars: ( 4.19494 , 0.468054 , 1.28679 ) +colvars: ( 5.58778 , 0.623462 , 1.71405 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.61923 , -0.0805709 , -0.380173 ) +colvars: ( -0.556302 , -0.16267 , -0.350836 ) +colvars: ( -0.508054 , -0.140927 , -0.293375 ) +colvars: ( -0.51556 , -0.190112 , -0.321226 ) +colvars: ( -0.50597 , -0.1319 , -0.287552 ) +colvars: ( -0.489423 , -0.281339 , -0.332629 ) +colvars: ( -0.455043 , -0.321477 , -0.314653 ) +colvars: ( -0.432118 , -0.427804 , -0.33552 ) +colvars: ( -0.392323 , -0.286673 , -0.237256 ) +colvars: ( -0.386991 , -0.261726 , -0.221596 ) +colvars: ( -0.344169 , -0.28116 , -0.186589 ) +colvars: ( -0.284159 , -0.244825 , -0.111283 ) +colvars: ( -0.236734 , -0.259645 , -0.0697447 ) +colvars: ( -0.304572 , -0.14262 , -0.0895949 ) +colvars: ( -0.272931 , -0.113792 , -0.0458956 ) +colvars: ( -0.360178 , -0.0855932 , -0.121927 ) +colvars: ( -0.38777 , 0.0117489 , -0.109461 ) +colvars: ( -0.439582 , 0.0591317 , -0.141962 ) +colvars: ( -0.424073 , 0.0266292 , -0.139798 ) +colvars: ( -0.412699 , 0.082763 , -0.10519 ) +colvars: ( -0.466974 , -0.0267763 , -0.20496 ) +colvars: ( -0.499834 , -0.0282228 , -0.238578 ) +colvars: ( -0.548776 , -0.092846 , -0.314443 ) +colvars: ( -0.446417 , -0.058181 , -0.19727 ) +colvars: ( -0.452775 , -0.0145841 , -0.185658 ) +colvars: ( -0.390753 , -0.131915 , -0.171778 ) +colvars: ( -0.332063 , -0.163149 , -0.125697 ) +colvars: ( -0.281219 , -0.252558 , -0.111522 ) +colvars: ( -0.291737 , -0.0911599 , -0.0554493 ) +colvars: ( -0.277684 , -0.0728513 , -0.0337679 ) +colvars: ( -0.273629 , -0.0466957 , -0.0188936 ) +colvars: ( -0.239295 , 0.027221 , 0.0461291 ) +colvars: ( -0.219871 , 0.0534014 , 0.0764588 ) +colvars: ( -0.283572 , 0.113214 , 0.0371428 ) +colvars: ( -0.256779 , 0.154433 , 0.0810857 ) +colvars: ( -0.353225 , 0.141288 , -0.0212597 ) +colvars: ( -0.40213 , 0.21684 , -0.0392086 ) +colvars: ( -0.473974 , 0.239455 , -0.102066 ) +colvars: ( -0.41189 , 0.197126 , -0.0571564 ) +colvars: ( -0.416332 , 0.257307 , -0.0367715 ) +colvars: ( -0.414866 , 0.111382 , -0.0955503 ) +colvars: ( -0.420153 , 0.0814335 , -0.113229 ) +colvars: ( -0.440355 , -0.0109082 , -0.171659 ) +colvars: ( -0.352761 , 0.0700109 , -0.0502238 ) +colvars: ( -0.35523 , 0.0959901 , -0.0419782 ) +colvars: ( -0.192764 , 0.101927 , 0.123735 ) +colvars: ( -0.142835 , 0.103572 , 0.174587 ) +colvars: ( -0.221038 , 0.17369 , 0.124953 ) +colvars: ( -0.290551 , 0.0295241 , -0.00442667 ) +colvars: ( -0.223244 , 0.0157899 , 0.0575392 ) +colvars: ( -0.169117 , -0.0666042 , 0.0779103 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 14. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 14. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atoms_new_colvar_forces = { ( -4.61450602640700e+00 , -4.31676671528701e-01 , -1.25080020984094e+00 ), ( -3.97510716789020e+00 , -3.64817999724983e-01 , -9.82709320886759e-01 ), ( -4.04759222147279e+00 , -3.91018565422788e-01 , -1.01801876556222e+00 ), ( -5.44284249213996e+00 , -5.54760749370383e-01 , -1.50829039988538e+00 ), ( 2.52718512476039e-01 , 1.17880134339312e-01 , 3.42947612228118e-01 ), ( 4.97792183217986e+00 , 6.09287478385831e-01 , 1.81105109336112e+00 ), ( 4.20656257158341e+00 , 5.05849087254249e-01 , 1.57080852302660e+00 ), ( -4.30961886988918e-02 , 2.90701294203428e-02 , 3.48952279642574e-01 ), ( 4.18718659982550e+00 , 4.96285825796295e-01 , 1.54016151029299e+00 ), ( 5.54998211663514e+00 , 6.35249374838715e-01 , 1.90651372157920e+00 ), ( 1.14439721104215e-02 , 3.89474388950308e-02 , 2.94013247420377e-01 ), ( -2.33043535206590e-05 , 3.25440834054942e-02 , 2.69714613993296e-01 ), ( 2.07206469285749e-02 , 4.66430442639520e-02 , 3.34513106278825e-01 ), ( 4.27649656650401e-02 , 3.66516084532864e-02 , 1.96440421996249e-01 ), ( 1.51505234874290e-02 , 2.23502413638598e-02 , 1.47195309119272e-01 ), ( 1.11225470706758e-01 , 5.61813219637322e-02 , 1.86569185231302e-01 ), ( 1.57000249590496e-01 , 6.18447669604415e-02 , 1.18697289349362e-01 ), ( 2.36270351339931e-01 , 8.77236833964157e-02 , 1.34325378589763e-01 ), ( 1.28728160579330e-01 , 4.50467234393944e-02 , 5.04143418874738e-02 ), ( 1.24200576225722e-01 , 3.61535273370629e-02 , -1.19188382213505e-02 ), ( 1.06363656214637e-01 , 3.96803352031447e-02 , 6.20370267648966e-02 ), ( 7.13181889830789e-02 , 2.22647003640655e-02 , 5.62373875832980e-03 ), ( 5.87608872439214e-02 , 2.24213311806150e-02 , 3.84139966468095e-02 ), ( -9.86194847365840e-04 , -2.75534766873105e-03 , -2.03571868396717e-02 ), ( -1.44554464500086e-02 , -1.50156162722387e-02 , -8.81647134780060e-02 ), ( -4.81467006225004e-02 , -1.05289818277412e-02 , 3.35052098907826e-02 ), ( -1.15260808893536e-01 , -3.27446961034470e-02 , 1.77439571372890e-02 ), ( -1.56639945765975e-01 , -3.61181651663380e-02 , 9.35664818984968e-02 ), ( -1.03005895219810e-01 , -3.45452566823875e-02 , -2.79093368579001e-02 ), ( -1.38921916680910e-01 , -5.21909275820709e-02 , -8.40454132348312e-02 ), ( -5.03464794637534e-02 , -1.59472851414498e-02 , -5.87334630048160e-03 ), ( -2.97284772667758e-02 , -1.46357287018351e-02 , -4.67138061700371e-02 ), ( 2.60238542554710e-02 , 7.88257179222090e-03 , 4.88175185451301e-05 ), ( 1.78925796517954e-03 , -1.48079508047937e-02 , -1.27184088935109e-01 ), ( -1.57924347793951e-02 , -2.65920248764480e-02 , -1.80732343935604e-01 ), ( 4.82095954510571e-02 , -2.05854545221507e-03 , -1.37961606606668e-01 ), ( 7.72690086426210e-02 , -2.20002645233214e-03 , -2.12011950998016e-01 ), ( 1.37773726264281e-01 , 1.74369239463660e-02 , -2.01042331311657e-01 ), ( 1.91378798360463e-02 , -2.60697326981438e-02 , -2.64006370760446e-01 ), ( 2.01931304241948e-02 , -3.39666890545063e-02 , -3.32086015852685e-01 ), ( -3.35084346251156e-02 , -3.81963108192040e-02 , -2.32454068643556e-01 ), ( -9.41550647483956e-02 , -6.15420054768978e-02 , -2.73797973221259e-01 ), ( -1.31493369474420e-01 , -6.69849192020118e-02 , -2.25256601586974e-01 ), ( -1.51159216019756e-01 , -8.13910821533683e-02 , -2.95304308607336e-01 ), ( -1.78568999425414e-01 , -9.72662760378736e-02 , -3.58103215110623e-01 ), ( -1.93343679105279e-01 , -9.48997421716479e-02 , -3.01441021178621e-01 ), ( -2.35170551634876e-01 , -1.10784866676663e-01 , -3.28165619370478e-01 ), ( -1.19923703529548e-01 , -7.34991426099793e-02 , -3.08248179504989e-01 ), ( -1.71131416290035e-01 , -8.11159771046006e-02 , -2.42936577336104e-01 ), ( -2.24162693429279e-01 , -9.88863405666131e-02 , -2.57182521268237e-01 ), ( -2.59646905379640e-01 , -1.00376708649434e-01 , -1.80540731105742e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 14, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 15 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 15, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 15, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 15, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 15, atoms_positions[size = 51] = { ( 8.31202261101125e+00 , 4.23796498118627e-02 , -7.64220071348988e-01 ), ( 6.97868795425818e+00 , -5.46103079445024e-01 , -6.11435181462593e-01 ), ( 6.17174118946339e+00 , -3.33624037573884e-01 , 7.01441582404698e-01 ), ( 4.97558495509138e+00 , -1.82211620719155e-01 , 7.07821553822601e-01 ), ( 7.05477187719790e+00 , -2.03976160973846e+00 , -9.56752700471823e-01 ), ( 6.88995159388955e+00 , -2.63751198225184e-01 , 1.87304167781028e+00 ), ( 6.18671941704904e+00 , -1.31467336757217e-01 , 3.19002055929260e+00 ), ( 7.08962428732410e+00 , -3.51139370372955e-01 , 4.28715408570870e+00 ), ( 5.29213514706219e+00 , 1.10887550309795e+00 , 3.33280986530589e+00 ), ( 4.14322790696180e+00 , 1.03784659138943e+00 , 3.66143109773539e+00 ), ( 5.86102669669466e+00 , 2.24684402162226e+00 , 2.99776379726542e+00 ), ( 5.22909465861429e+00 , 3.58804430388609e+00 , 2.90863920936324e+00 ), ( 6.32898758184422e+00 , 4.51551188683693e+00 , 2.41149544875236e+00 ), ( 3.90514082551049e+00 , 3.73248991539767e+00 , 2.03805080994276e+00 ), ( 2.81539843557420e+00 , 4.14385283470926e+00 , 2.51154985284035e+00 ), ( 3.90424485220926e+00 , 3.24189820908485e+00 , 7.37657034667304e-01 ), ( 2.65545318874566e+00 , 3.04132589384411e+00 , -1.08710069237004e-01 ), ( 3.03368637956660e+00 , 2.72184315385574e+00 , -1.53962636118920e+00 ), ( 1.57965283747802e+00 , 2.19656656186226e+00 , 4.97311505574982e-01 ), ( 4.13704665071233e-01 , 2.53301138784715e+00 , 5.25520790241601e-01 ), ( 2.00634706157258e+00 , 1.01093312800957e+00 , 1.07906058097648e+00 ), ( 1.18099612919785e+00 , 9.45069292926887e-02 , 1.69232947207939e+00 ), ( 2.02880908859515e+00 , -1.12733354866967e+00 , 2.00573693563177e+00 ), ( 5.53894018990116e-01 , 6.08271704663100e-01 , 2.92842622488218e+00 ), ( -6.33073749600056e-01 , 3.50415897877268e-01 , 3.16724657244207e+00 ), ( 1.32663479222770e+00 , 1.34467036890182e+00 , 3.82049540489378e+00 ), ( 8.56929113872508e-01 , 1.95946974867600e+00 , 5.02993732399448e+00 ), ( 2.03892826349660e+00 , 2.64115851607595e+00 , 5.64942613997402e+00 ), ( -3.43447816689619e-01 , 2.91645304024642e+00 , 4.97050972356219e+00 ), ( -1.15335724926495e+00 , 3.05500913433501e+00 , 5.90018402580842e+00 ), ( -4.84149940425839e-01 , 3.59060643176087e+00 , 3.84752616033055e+00 ), ( -1.50369609083765e+00 , 4.54805191745859e+00 , 3.49535023676454e+00 ), ( -7.13307749595086e-01 , 5.40474157759740e+00 , 2.44968592586854e+00 ), ( -2.77242957381128e+00 , 3.87392695363197e+00 , 2.91283382403749e+00 ), ( -3.82493765258508e+00 , 4.47946797763180e+00 , 2.82246734035799e+00 ), ( -2.60763007564851e+00 , 2.65976302871916e+00 , 2.43695328704627e+00 ), ( -3.74756066920069e+00 , 1.84164211135460e+00 , 2.01154163700279e+00 ), ( -3.40875828845985e+00 , 8.75983615192798e-01 , 9.08924061424964e-01 ), ( -4.31570991431919e+00 , 1.06528805904774e+00 , 3.23819136175682e+00 ), ( -5.51905109064995e+00 , 8.54387005753863e-01 , 3.32885063175874e+00 ), ( -3.39788230390646e+00 , 6.75555119521035e-01 , 4.16653064719874e+00 ), ( -3.74080565954384e+00 , 3.74836151898684e-02 , 5.45082325228767e+00 ), ( -2.38334247335428e+00 , -3.19005874588463e-01 , 6.17202715964624e+00 ), ( -4.47084459574025e+00 , 1.00206439945020e+00 , 6.44123375865510e+00 ), ( -5.34097893028944e+00 , 6.06062255611571e-01 , 7.20688505094935e+00 ), ( -6.24187316663723e+00 , 3.57950307162747e+00 , 6.71477529448104e+00 ), ( -6.93765081932641e+00 , 4.29702260556012e+00 , 7.45153130375767e+00 ), ( -6.75092365959200e+00 , 3.19937371474768e+00 , 5.51985142036843e+00 ), ( -4.12772439963364e+00 , 2.27139866060630e+00 , 6.44936894039559e+00 ), ( -4.83332103117952e+00 , 3.19117184751636e+00 , 7.22081853615269e+00 ), ( -4.10481403887107e+00 , 4.58650030551778e+00 , 7.29458450809990e+00 ) } +colvars: Step 15, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_ids[size = 0] = +colvars: Step 15, atom_groups_refcount[size = 0] = +colvars: Step 15, atom_groups_masses[size = 0] = +colvars: Step 15, atom_groups_charges[size = 0] = +colvars: Step 15, atom_groups_coms[size = 0] = +colvars: Step 15, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 15, volmaps_ids[size = 0] = +colvars: Step 15, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 15 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.13381355030095e-01 , 3.42072155991049e-03 , 9.49621200786667e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.13381355030095e-01 , 3.42072155991049e-03 , 9.49621200786667e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.7856 , 1.88339 , -15.0888 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.7856 , 1.88339 , -15.0888 ) to colvar "one". +colvars: Adding total bias energy: 44.8059 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.7856 , 1.88339 , -15.0888 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.89693 , -0.54314 , -1.49067 ) +colvars: ( -4.19912 , -0.465743 , -1.27825 ) +colvars: ( -4.19912 , -0.465743 , -1.27825 ) +colvars: ( -5.59335 , -0.620383 , -1.70266 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.896062 , 0.19488 , 0.627909 ) +colvars: ( 0.77563 , 0.265958 , 0.652727 ) +colvars: ( 0.760162 , 0.258914 , 0.634186 ) +colvars: ( 0.662675 , 0.267095 , 0.587964 ) +colvars: ( 0.650697 , 0.200562 , 0.491542 ) +colvars: ( 0.575271 , 0.344628 , 0.64084 ) +colvars: ( 0.466927 , 0.358998 , 0.596562 ) +colvars: ( 0.389476 , 0.456497 , 0.682104 ) +colvars: ( 0.384924 , 0.314619 , 0.488809 ) +colvars: ( 0.349661 , 0.273193 , 0.412456 ) +colvars: ( 0.35591 , 0.319854 , 0.478815 ) +colvars: ( 0.284496 , 0.277115 , 0.37948 ) +colvars: ( 0.257749 , 0.306063 , 0.402676 ) +colvars: ( 0.34755 , 0.179104 , 0.284801 ) +colvars: ( 0.288408 , 0.135947 , 0.192106 ) +colvars: ( 0.471359 , 0.141714 , 0.307225 ) +colvars: ( 0.544565 , 0.0501234 , 0.22713 ) +colvars: ( 0.675349 , 0.0287385 , 0.275152 ) +colvars: ( 0.552693 , 0.0184069 , 0.189287 ) +colvars: ( 0.536818 , -0.0466096 , 0.0926157 ) +colvars: ( 0.573292 , 0.0663963 , 0.265854 ) +colvars: ( 0.571227 , 0.0503754 , 0.243116 ) +colvars: ( 0.607636 , 0.115115 , 0.351467 ) +colvars: ( 0.445781 , 0.0552093 , 0.175989 ) +colvars: ( 0.438724 , -0.000654933 , 0.0967894 ) +colvars: ( 0.343133 , 0.121088 , 0.204259 ) +colvars: ( 0.217586 , 0.130009 , 0.142564 ) +colvars: ( 0.125515 , 0.215967 , 0.20402 ) +colvars: ( 0.189491 , 0.0562604 , 0.0269888 ) +colvars: ( 0.139661 , 0.0202625 , -0.0506217 ) +colvars: ( 0.223861 , 0.0304813 , 0.0125235 ) +colvars: ( 0.210088 , -0.0420717 , -0.0930394 ) +colvars: ( 0.24622 , -0.0456473 , -0.0766386 ) +colvars: ( 0.285768 , -0.128173 , -0.164308 ) +colvars: ( 0.241472 , -0.181187 , -0.261532 ) +colvars: ( 0.401657 , -0.143431 , -0.116795 ) +colvars: ( 0.479513 , -0.219066 , -0.172724 ) +colvars: ( 0.611624 , -0.22196 , -0.0990785 ) +colvars: ( 0.431351 , -0.22331 , -0.206691 ) +colvars: ( 0.436852 , -0.291369 , -0.294906 ) +colvars: ( 0.38186 , -0.14979 , -0.136957 ) +colvars: ( 0.326718 , -0.14328 , -0.160573 ) +colvars: ( 0.3097 , -0.0564607 , -0.0539117 ) +colvars: ( 0.202547 , -0.151783 , -0.244871 ) +colvars: ( 0.17771 , -0.193668 , -0.315723 ) +colvars: ( 0.000566621 , -0.197244 , -0.42449 ) +colvars: ( -0.0910223 , -0.214828 , -0.501867 ) +colvars: ( 0.101994 , -0.247486 , -0.432468 ) +colvars: ( 0.120448 , -0.111055 , -0.238332 ) +colvars: ( 0.000320215 , -0.115163 , -0.314353 ) +colvars: ( -0.0891587 , -0.0343271 , -0.258257 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.89693 , 0.54314 , 1.49067 ) +colvars: ( 4.19912 , 0.465743 , 1.27825 ) +colvars: ( 4.19912 , 0.465743 , 1.27825 ) +colvars: ( 5.59335 , 0.620383 , 1.70266 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.618496 , -0.0806149 , -0.378058 ) +colvars: ( -0.555788 , -0.162705 , -0.348536 ) +colvars: ( -0.50734 , -0.140971 , -0.291022 ) +colvars: ( -0.515355 , -0.190103 , -0.319095 ) +colvars: ( -0.505768 , -0.13186 , -0.285729 ) +colvars: ( -0.489488 , -0.281326 , -0.330296 ) +colvars: ( -0.455431 , -0.321425 , -0.312435 ) +colvars: ( -0.432747 , -0.427762 , -0.332992 ) +colvars: ( -0.392748 , -0.286584 , -0.235282 ) +colvars: ( -0.387554 , -0.261602 , -0.219884 ) +colvars: ( -0.34446 , -0.281078 , -0.184541 ) +colvars: ( -0.284452 , -0.244711 , -0.109453 ) +colvars: ( -0.236886 , -0.259549 , -0.0677292 ) +colvars: ( -0.304679 , -0.142491 , -0.0881057 ) +colvars: ( -0.273141 , -0.113625 , -0.0446677 ) +colvars: ( -0.360008 , -0.0854921 , -0.120443 ) +colvars: ( -0.387406 , 0.0118607 , -0.108282 ) +colvars: ( -0.438886 , 0.0592028 , -0.140688 ) +colvars: ( -0.423876 , 0.0267656 , -0.138834 ) +colvars: ( -0.412513 , 0.082931 , -0.104531 ) +colvars: ( -0.466922 , -0.0266532 , -0.203837 ) +colvars: ( -0.499978 , -0.0280777 , -0.237616 ) +colvars: ( -0.549023 , -0.0927275 , -0.313221 ) +colvars: ( -0.446858 , -0.0579919 , -0.19646 ) +colvars: ( -0.453286 , -0.0143645 , -0.185134 ) +colvars: ( -0.391369 , -0.131721 , -0.170781 ) +colvars: ( -0.332947 , -0.162915 , -0.12482 ) +colvars: ( -0.282256 , -0.252332 , -0.110354 ) +colvars: ( -0.292527 , -0.0908966 , -0.0548743 ) +colvars: ( -0.278633 , -0.0725512 , -0.0334434 ) +colvars: ( -0.274153 , -0.0464481 , -0.0183049 ) +colvars: ( -0.23969 , 0.0274924 , 0.0464418 ) +colvars: ( -0.219982 , 0.0536461 , 0.0768936 ) +colvars: ( -0.283855 , 0.1135 , 0.0371394 ) +colvars: ( -0.257123 , 0.154754 , 0.0808005 ) +colvars: ( -0.353349 , 0.141547 , -0.0212231 ) +colvars: ( -0.402159 , 0.217108 , -0.039447 ) +colvars: ( -0.473778 , 0.239682 , -0.102174 ) +colvars: ( -0.412205 , 0.197427 , -0.0575574 ) +colvars: ( -0.416646 , 0.257635 , -0.0374789 ) +colvars: ( -0.415434 , 0.11168 , -0.0957474 ) +colvars: ( -0.421015 , 0.0817616 , -0.113546 ) +colvars: ( -0.441413 , -0.010599 , -0.171675 ) +colvars: ( -0.353835 , 0.070382 , -0.0507148 ) +colvars: ( -0.356437 , 0.0963937 , -0.0427266 ) +colvars: ( -0.193897 , 0.10236 , 0.122945 ) +colvars: ( -0.144124 , 0.104041 , 0.173619 ) +colvars: ( -0.221847 , 0.1741 , 0.124114 ) +colvars: ( -0.291665 , 0.0298963 , -0.00477766 ) +colvars: ( -0.224551 , 0.0162011 , 0.057044 ) +colvars: ( -0.170545 , -0.0662015 , 0.0776982 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 15. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 15. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atoms_new_colvar_forces = { ( -4.61936778687056e+00 , -4.28875636713662e-01 , -1.24081622411012e+00 ), ( -3.97927752576044e+00 , -3.62490025082989e-01 , -9.74055099879345e-01 ), ( -4.05179905979518e+00 , -3.88751327715992e-01 , -1.00937787142554e+00 ), ( -5.44842004583146e+00 , -5.51681403457618e-01 , -1.49684846013888e+00 ), ( 2.52821496214122e-01 , 1.17943316152049e-01 , 3.43164616568188e-01 ), ( 4.98271733248943e+00 , 6.06442794201924e-01 , 1.80121182861804e+00 ), ( 4.21061603961148e+00 , 5.03315796242880e-01 , 1.56237371200815e+00 ), ( -4.32710129312120e-02 , 2.87355680351474e-02 , 3.49112196479845e-01 ), ( 4.19129571918370e+00 , 4.93777804565713e-01 , 1.53177353365320e+00 ), ( 5.55545587967625e+00 , 6.31974408426609e-01 , 1.89523312767131e+00 ), ( 1.14506186431756e-02 , 3.87761552168734e-02 , 2.94273707334107e-01 ), ( 4.47403535131508e-05 , 3.24038890923857e-02 , 2.70027462202968e-01 ), ( 2.08632792242771e-02 , 4.65134994254886e-02 , 3.34946572921082e-01 ), ( 4.28713634419879e-02 , 3.66136569733684e-02 , 1.96694969207058e-01 ), ( 1.52672190829746e-02 , 2.23220680487652e-02 , 1.47438481940793e-01 ), ( 1.11351342254400e-01 , 5.62214403208874e-02 , 1.86781868289036e-01 ), ( 1.57158812685396e-01 , 6.19840632516422e-02 , 1.18848149279894e-01 ), ( 2.36463080192088e-01 , 8.79413782569101e-02 , 1.34464225633902e-01 ), ( 1.28816645976026e-01 , 4.51725228088821e-02 , 5.04521585599663e-02 ), ( 1.24305385881526e-01 , 3.63213320186521e-02 , -1.19157963869323e-02 ), ( 1.06370910416383e-01 , 3.97430970902821e-02 , 6.20166558677490e-02 ), ( 7.12495144637919e-02 , 2.22977053019278e-02 , 5.50002839875133e-03 ), ( 5.86131152589200e-02 , 2.23880094676876e-02 , 3.82455591518973e-02 ), ( -1.07704656601298e-03 , -2.78261183358337e-03 , -2.04708797724387e-02 ), ( -1.45618160768809e-02 , -1.50194445426009e-02 , -8.83448048199977e-02 ), ( -4.82362131464319e-02 , -1.06332435126323e-02 , 3.34779953099402e-02 ), ( -1.15361008057320e-01 , -3.29058859531983e-02 , 1.77439890509237e-02 ), ( -1.56740321099998e-01 , -3.63654446716120e-02 , 9.36664496342354e-02 ), ( -1.03036083099045e-01 , -3.46362317737734e-02 , -2.78854511395982e-02 ), ( -1.38972489535878e-01 , -5.22887107320162e-02 , -8.40650628899017e-02 ), ( -5.02920638383860e-02 , -1.59668314607233e-02 , -5.78142132838359e-03 ), ( -2.96014978638097e-02 , -1.45792306693401e-02 , -4.65975861319859e-02 ), ( 2.62376192155431e-02 , 7.99876823009550e-03 , 2.55030979381593e-04 ), ( 1.91266694880055e-03 , -1.46732001437521e-02 , -1.27168189169222e-01 ), ( -1.56515108032224e-02 , -2.64323801435717e-02 , -1.80731878028861e-01 ), ( 4.83081575192512e-02 , -1.88468610713632e-03 , -1.38018070881387e-01 ), ( 7.73544978807220e-02 , -1.95832211906594e-03 , -2.12171150083733e-01 ), ( 1.37846408225428e-01 , 1.77223172321023e-02 , -2.01252771691206e-01 ), ( 1.91459825565006e-02 , -2.58825952833994e-02 , -2.64248404027074e-01 ), ( 2.02061702671993e-02 , -3.37336648216094e-02 , -3.32384401030002e-01 ), ( -3.35737155292727e-02 , -3.81094310150237e-02 , -2.32704434239873e-01 ), ( -9.42968709869637e-02 , -6.15183467315491e-02 , -2.74118782184220e-01 ), ( -1.31712528632276e-01 , -6.70597105056869e-02 , -2.25586794937362e-01 ), ( -1.51287838040672e-01 , -8.14010829483994e-02 , -2.95585625795411e-01 ), ( -1.78726480391682e-01 , -9.72746618564433e-02 , -3.58449667649919e-01 ), ( -1.93330816872829e-01 , -9.48840436070342e-02 , -3.01544761332582e-01 ), ( -2.35145990876308e-01 , -1.10786116175523e-01 , -3.28248003595132e-01 ), ( -1.19852575288214e-01 , -7.33859881344482e-02 , -3.08353821134834e-01 ), ( -1.71216704970340e-01 , -8.11587345035392e-02 , -2.43109562889482e-01 ), ( -2.24230906343134e-01 , -9.89619596618653e-02 , -2.57308526737973e-01 ), ( -2.59704088455363e-01 , -1.00528638482483e-01 , -1.80558815329004e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 15, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 16 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 16, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 16, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 16, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 16, atoms_positions[size = 51] = { ( 8.30584559981966e+00 , 4.18920549749206e-02 , -7.62827408931917e-01 ), ( 6.97262709713975e+00 , -5.47679445776029e-01 , -6.05379216725242e-01 ), ( 6.16442418297579e+00 , -3.42831690267079e-01 , 7.05931054367244e-01 ), ( 4.97232239227887e+00 , -1.78455396513559e-01 , 7.11230999580600e-01 ), ( 7.05471751299227e+00 , -2.04221082906437e+00 , -9.51795507911699e-01 ), ( 6.88578088427731e+00 , -2.63182714075398e-01 , 1.87940202984847e+00 ), ( 6.18614345503480e+00 , -1.36473813325527e-01 , 3.19564118935261e+00 ), ( 7.08484621753552e+00 , -3.53106619971983e-01 , 4.29079136214221e+00 ), ( 5.29603872645111e+00 , 1.10689714471731e+00 , 3.33681046754548e+00 ), ( 4.14768145433506e+00 , 1.03511929553146e+00 , 3.66687942828962e+00 ), ( 5.85714968570103e+00 , 2.24693035412113e+00 , 2.99689244175829e+00 ), ( 5.23297324872810e+00 , 3.58605603227763e+00 , 2.91238409842110e+00 ), ( 6.32721524124312e+00 , 4.51094539045354e+00 , 2.40314480031856e+00 ), ( 3.90154546852211e+00 , 3.72839311188602e+00 , 2.03999828208399e+00 ), ( 2.80849424265705e+00 , 4.14770271386909e+00 , 2.50712703510101e+00 ), ( 3.91341734146436e+00 , 3.24221542915919e+00 , 7.35649238406860e-01 ), ( 2.65347398432954e+00 , 3.03056273185891e+00 , -1.08515797703818e-01 ), ( 3.03560344150804e+00 , 2.72018000543168e+00 , -1.53188357851366e+00 ), ( 1.58478245190695e+00 , 2.19680139496657e+00 , 4.84857448280314e-01 ), ( 4.05794748764460e-01 , 2.54310721789363e+00 , 5.22821481379191e-01 ), ( 2.01446392954469e+00 , 1.01872007024961e+00 , 1.07966365627172e+00 ), ( 1.17915363246752e+00 , 1.01958011700901e-01 , 1.69272268033936e+00 ), ( 2.03131320678593e+00 , -1.12186760591478e+00 , 2.00555250086458e+00 ), ( 5.55592531194352e-01 , 6.08183415383067e-01 , 2.92855945885333e+00 ), ( -6.26628569428618e-01 , 3.49842512123108e-01 , 3.16581279764676e+00 ), ( 1.32585687459329e+00 , 1.34529651624049e+00 , 3.81290372877736e+00 ), ( 8.54391449652899e-01 , 1.96425722534732e+00 , 5.02806857936199e+00 ), ( 2.04534224079621e+00 , 2.64985450952519e+00 , 5.65529063448693e+00 ), ( -3.41096704626099e-01 , 2.91631272770942e+00 , 4.96913317798965e+00 ), ( -1.15045517335613e+00 , 3.05689153647007e+00 , 5.89811906253420e+00 ), ( -4.90079775575702e-01 , 3.57766943315727e+00 , 3.84829906622339e+00 ), ( -1.50764355151631e+00 , 4.54710277212402e+00 , 3.48510009579148e+00 ), ( -7.09277419933967e-01 , 5.40675475620672e+00 , 2.45329350157170e+00 ), ( -2.77189891941281e+00 , 3.87423545331641e+00 , 2.91026949655478e+00 ), ( -3.82290568167701e+00 , 4.48571771041692e+00 , 2.82046138947987e+00 ), ( -2.60994695095092e+00 , 2.66578909698494e+00 , 2.43019103733966e+00 ), ( -3.75350896178922e+00 , 1.83058251763696e+00 , 2.00706483018988e+00 ), ( -3.40531891511751e+00 , 8.80191524655614e-01 , 9.01240964699100e-01 ), ( -4.32035334073315e+00 , 1.06609845153730e+00 , 3.23257900543483e+00 ), ( -5.51434680845415e+00 , 8.47387690179261e-01 , 3.32846100676540e+00 ), ( -3.39045698875149e+00 , 6.78587857596137e-01 , 4.17564412594035e+00 ), ( -3.73232648521104e+00 , 3.60304998623892e-02 , 5.44499178317187e+00 ), ( -2.38438798972812e+00 , -3.16150344974704e-01 , 6.17296653876527e+00 ), ( -4.46889966652845e+00 , 1.00211281854870e+00 , 6.44231557083538e+00 ), ( -5.34487080038993e+00 , 6.04639147144351e-01 , 7.20969187830549e+00 ), ( -6.23694677428182e+00 , 3.58394366005188e+00 , 6.71779129577674e+00 ), ( -6.94267244320899e+00 , 4.29762860792866e+00 , 7.45679689719063e+00 ), ( -6.75169210203605e+00 , 3.19653741058694e+00 , 5.51757902146330e+00 ), ( -4.12950759068337e+00 , 2.26487192367640e+00 , 6.44115742181759e+00 ), ( -4.82630490172218e+00 , 3.19133533958257e+00 , 7.22420135575370e+00 ), ( -4.10514951256287e+00 , 4.58788744247899e+00 , 7.29320145958151e+00 ) } +colvars: Step 16, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_ids[size = 0] = +colvars: Step 16, atom_groups_refcount[size = 0] = +colvars: Step 16, atom_groups_masses[size = 0] = +colvars: Step 16, atom_groups_charges[size = 0] = +colvars: Step 16, atom_groups_coms[size = 0] = +colvars: Step 16, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 16, volmaps_ids[size = 0] = +colvars: Step 16, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 16 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.11271197951965e-01 , 2.91633047576440e-03 , 9.50316650565539e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.11271197951965e-01 , 2.91633047576440e-03 , 9.50316650565539e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.7434 , 1.89347 , -15.1027 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.7434 , 1.89347 , -15.1027 ) to colvar "one". +colvars: Adding total bias energy: 44.7201 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.7434 , 1.89347 , -15.1027 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.90144 , -0.540656 , -1.48135 ) +colvars: ( -4.20298 , -0.463612 , -1.27026 ) +colvars: ( -4.20298 , -0.463612 , -1.27026 ) +colvars: ( -5.59849 , -0.617545 , -1.69202 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.895334 , 0.19502 , 0.625909 ) +colvars: ( 0.775113 , 0.266007 , 0.650628 ) +colvars: ( 0.759544 , 0.259012 , 0.632133 ) +colvars: ( 0.662425 , 0.267048 , 0.586015 ) +colvars: ( 0.650467 , 0.200528 , 0.489858 ) +colvars: ( 0.575234 , 0.344484 , 0.638723 ) +colvars: ( 0.467159 , 0.358752 , 0.59454 ) +colvars: ( 0.389894 , 0.456157 , 0.679825 ) +colvars: ( 0.385248 , 0.314359 , 0.487064 ) +colvars: ( 0.350098 , 0.272903 , 0.410914 ) +colvars: ( 0.356179 , 0.319621 , 0.477089 ) +colvars: ( 0.284828 , 0.276879 , 0.378011 ) +colvars: ( 0.258016 , 0.30585 , 0.401134 ) +colvars: ( 0.347739 , 0.178947 , 0.28361 ) +colvars: ( 0.288709 , 0.135763 , 0.191158 ) +colvars: ( 0.471297 , 0.141654 , 0.306004 ) +colvars: ( 0.544346 , 0.0501441 , 0.22615 ) +colvars: ( 0.674839 , 0.0288683 , 0.274073 ) +colvars: ( 0.552568 , 0.0183948 , 0.188415 ) +colvars: ( 0.536722 , -0.046613 , 0.0920087 ) +colvars: ( 0.573228 , 0.0663415 , 0.264776 ) +colvars: ( 0.571279 , 0.0502753 , 0.242103 ) +colvars: ( 0.60771 , 0.114982 , 0.350163 ) +colvars: ( 0.446102 , 0.0550132 , 0.175129 ) +colvars: ( 0.439099 , -0.000857086 , 0.0961485 ) +colvars: ( 0.343627 , 0.120816 , 0.203294 ) +colvars: ( 0.218331 , 0.129648 , 0.141738 ) +colvars: ( 0.126408 , 0.215534 , 0.202999 ) +colvars: ( 0.190214 , 0.055934 , 0.0264756 ) +colvars: ( 0.140519 , 0.0198964 , -0.0509319 ) +colvars: ( 0.224407 , 0.0302324 , 0.0120582 ) +colvars: ( 0.210581 , -0.0422751 , -0.0932161 ) +colvars: ( 0.246522 , -0.0457739 , -0.0768527 ) +colvars: ( 0.28615 , -0.128317 , -0.164266 ) +colvars: ( 0.24193 , -0.181342 , -0.261233 ) +colvars: ( 0.401858 , -0.143513 , -0.116855 ) +colvars: ( 0.479609 , -0.219094 , -0.172608 ) +colvars: ( 0.611487 , -0.221909 , -0.0991328 ) +colvars: ( 0.431649 , -0.223415 , -0.206492 ) +colvars: ( 0.437155 , -0.291459 , -0.29446 ) +colvars: ( 0.382333 , -0.149983 , -0.136964 ) +colvars: ( 0.327402 , -0.143556 , -0.160527 ) +colvars: ( 0.310499 , -0.0568076 , -0.0541659 ) +colvars: ( 0.203452 , -0.152131 , -0.244624 ) +colvars: ( 0.178717 , -0.194045 , -0.315285 ) +colvars: ( 0.00167065 , -0.197631 , -0.423798 ) +colvars: ( -0.0897546 , -0.215265 , -0.500984 ) +colvars: ( 0.102838 , -0.247765 , -0.431729 ) +colvars: ( 0.121435 , -0.111436 , -0.238125 ) +colvars: ( 0.00151303 , -0.115612 , -0.313966 ) +colvars: ( -0.0878372 , -0.0348387 , -0.25805 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.90144 , 0.540656 , 1.48135 ) +colvars: ( 4.20298 , 0.463612 , 1.27026 ) +colvars: ( 4.20298 , 0.463612 , 1.27026 ) +colvars: ( 5.59849 , 0.617545 , 1.69202 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.61783 , -0.0806685 , -0.37611 ) +colvars: ( -0.555318 , -0.162767 , -0.346399 ) +colvars: ( -0.50667 , -0.141033 , -0.288821 ) +colvars: ( -0.515173 , -0.190132 , -0.317114 ) +colvars: ( -0.505587 , -0.131847 , -0.284037 ) +colvars: ( -0.489558 , -0.281373 , -0.32812 ) +colvars: ( -0.455804 , -0.321446 , -0.310364 ) +colvars: ( -0.433344 , -0.427816 , -0.330625 ) +colvars: ( -0.393144 , -0.28656 , -0.233427 ) +colvars: ( -0.388083 , -0.261541 , -0.218278 ) +colvars: ( -0.344718 , -0.281056 , -0.182601 ) +colvars: ( -0.2847 , -0.244648 , -0.107704 ) +colvars: ( -0.236989 , -0.259502 , -0.0657893 ) +colvars: ( -0.304754 , -0.142389 , -0.0866822 ) +colvars: ( -0.27331 , -0.113481 , -0.0434853 ) +colvars: ( -0.35983 , -0.0854043 , -0.119035 ) +colvars: ( -0.387049 , 0.0119807 , -0.107167 ) +colvars: ( -0.438221 , 0.0592963 , -0.139493 ) +colvars: ( -0.423686 , 0.0269086 , -0.137937 ) +colvars: ( -0.412333 , 0.0831164 , -0.10392 ) +colvars: ( -0.466878 , -0.0265381 , -0.202801 ) +colvars: ( -0.500129 , -0.0279457 , -0.236745 ) +colvars: ( -0.549281 , -0.0926381 , -0.312118 ) +colvars: ( -0.447283 , -0.0578258 , -0.195723 ) +colvars: ( -0.45378 , -0.0141613 , -0.184672 ) +colvars: ( -0.391951 , -0.131566 , -0.169855 ) +colvars: ( -0.333773 , -0.16273 , -0.123997 ) +colvars: ( -0.283216 , -0.252173 , -0.109242 ) +colvars: ( -0.293256 , -0.0906646 , -0.0543248 ) +colvars: ( -0.279511 , -0.0722817 , -0.0331302 ) +colvars: ( -0.274622 , -0.0462174 , -0.0177337 ) +colvars: ( -0.24003 , 0.0277647 , 0.0467622 ) +colvars: ( -0.220048 , 0.0539029 , 0.0773391 ) +colvars: ( -0.284099 , 0.113803 , 0.03715 ) +colvars: ( -0.25742 , 0.155101 , 0.08055 ) +colvars: ( -0.353455 , 0.141829 , -0.0211905 ) +colvars: ( -0.402184 , 0.217416 , -0.0396867 ) +colvars: ( -0.473602 , 0.239956 , -0.102306 ) +colvars: ( -0.412505 , 0.197757 , -0.0579583 ) +colvars: ( -0.416947 , 0.258005 , -0.0381715 ) +colvars: ( -0.415976 , 0.111986 , -0.0959595 ) +colvars: ( -0.421839 , 0.0820857 , -0.113878 ) +colvars: ( -0.442428 , -0.0103161 , -0.17173 ) +colvars: ( -0.354849 , 0.0707449 , -0.0511966 ) +colvars: ( -0.357579 , 0.0967915 , -0.0434553 ) +colvars: ( -0.194937 , 0.102795 , 0.122221 ) +colvars: ( -0.145302 , 0.104512 , 0.172736 ) +colvars: ( -0.222582 , 0.174532 , 0.123341 ) +colvars: ( -0.292705 , 0.0302538 , -0.00511103 ) +colvars: ( -0.225763 , 0.0165932 , 0.0565887 ) +colvars: ( -0.171861 , -0.0658343 , 0.0775239 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 16. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 16. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atoms_new_colvar_forces = { ( -4.62393221994104e+00 , -4.26304109748047e-01 , -1.23155000779684e+00 ), ( -3.98318603531314e+00 , -3.60372108360054e-01 , -9.66028370108865e-01 ), ( -4.05572906156253e+00 , -3.86695296424297e-01 , -1.00135532784653e+00 ), ( -5.45361353122923e+00 , -5.48863813909308e-01 , -1.48619709209284e+00 ), ( 2.52873349102304e-01 , 1.17979161073234e-01 , 3.43312429647552e-01 ), ( 4.98711309987895e+00 , 6.03766465373158e-01 , 1.79195207617560e+00 ), ( 4.21433667248663e+00 , 5.00917723629509e-01 , 1.55443256372642e+00 ), ( -4.34509018936229e-02 , 2.83409155196254e-02 , 3.49199878225349e-01 ), ( 4.19508480578038e+00 , 4.91411459582331e-01 , 1.52389360384485e+00 ), ( 5.56050830394954e+00 , 6.28906469020644e-01 , 1.88465503116507e+00 ), ( 1.14609845957472e-02 , 3.85658689595760e-02 , 2.94488073046964e-01 ), ( 1.27972527221687e-04 , 3.22310406436168e-02 , 2.70307449217059e-01 ), ( 2.10269967585273e-02 , 4.63479945043058e-02 , 3.35344556452762e-01 ), ( 4.29845307156735e-02 , 3.65575299112754e-02 , 1.96928091449742e-01 ), ( 1.53990706991032e-02 , 2.22815859547440e-02 , 1.47672467222464e-01 ), ( 1.11466818929663e-01 , 5.62494583844813e-02 , 1.86969220263956e-01 ), ( 1.57297015412835e-01 , 6.21248231237574e-02 , 1.18983177604912e-01 ), ( 2.36617773495052e-01 , 8.81645796904891e-02 , 1.34580054820728e-01 ), ( 1.28881605333126e-01 , 4.53034398687004e-02 , 5.04787839400021e-02 ), ( 1.24388989691166e-01 , 3.65034654339361e-02 , -1.19115824517484e-02 ), ( 1.06349848594728e-01 , 3.98034081902991e-02 , 6.19751654442269e-02 ), ( 7.11507274984183e-02 , 2.23295978975600e-02 , 5.35801563736707e-03 ), ( 5.84283560220867e-02 , 2.23437665274223e-02 , 3.80447398278145e-02 ), ( -1.18086227742220e-03 , -2.81254785985447e-03 , -2.05933119714489e-02 ), ( -1.46808640692542e-02 , -1.50183451313337e-02 , -8.85235865653149e-02 ), ( -4.83238099615155e-02 , -1.07498888367066e-02 , 3.34393788547477e-02 ), ( -1.15441803819559e-01 , -3.30814562972608e-02 , 1.77415080275554e-02 ), ( -1.56807837943647e-01 , -3.66395915031185e-02 , 9.37569562921980e-02 ), ( -1.03041454392351e-01 , -3.47305835195608e-02 , -2.78491686386393e-02 ), ( -1.38991943713039e-01 , -5.23853203067249e-02 , -8.40620945991603e-02 ), ( -5.02155919001466e-02 , -1.59849815189438e-02 , -5.67549560984493e-03 ), ( -2.94489968667291e-02 , -1.45103988130709e-02 , -4.64538439984492e-02 ), ( 2.64740740958471e-02 , 8.12899888277881e-03 , 4.86459219254942e-04 ), ( 2.05035652520458e-03 , -1.45137341331953e-02 , -1.27116438945519e-01 ), ( -1.54898780905774e-02 , -2.62406155173920e-02 , -1.80682876297122e-01 ), ( 4.84039048901975e-02 , -1.68369371236871e-03 , -1.38045731313653e-01 ), ( 7.74254302074487e-02 , -1.67866867920424e-03 , -2.12295182255925e-01 ), ( 1.37885532338481e-01 , 1.80465692151712e-02 , -2.01438523605025e-01 ), ( 1.91442638224501e-02 , -2.56580641944545e-02 , -2.64450629657562e-01 ), ( 2.02083750589916e-02 , -3.34536379663548e-02 , -3.32631882603284e-01 ), ( -3.36433698722798e-02 , -3.79965538351294e-02 , -2.32923431372171e-01 ), ( -9.44372493111604e-02 , -6.14707751958226e-02 , -2.74404826691171e-01 ), ( -1.31929428397296e-01 , -6.71237319317913e-02 , -2.25895616606678e-01 ), ( -1.51397203547389e-01 , -8.13864419500957e-02 , -2.95820424585032e-01 ), ( -1.78862185823288e-01 , -9.72530075209848e-02 , -3.58740462775067e-01 ), ( -1.93266703998240e-01 , -9.48366795602419e-02 , -3.01577382798790e-01 ), ( -2.35057038029502e-01 , -1.10753556421043e-01 , -3.28248678270264e-01 ), ( -1.19743248264548e-01 , -7.32329493047166e-02 , -3.08388176355380e-01 ), ( -1.71269786765332e-01 , -8.11824467058980e-02 , -2.43236089767739e-01 ), ( -2.24249528089155e-01 , -9.90183537439328e-02 , -2.57377396881962e-01 ), ( -2.59698323337768e-01 , -1.00672968785710e-01 , -1.80526047644573e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 16, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 17 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 17, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 17, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 17, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 17, atoms_positions[size = 51] = { ( 8.30014175749540e+00 , 4.14209336321197e-02 , -7.61076479752835e-01 ), ( 6.96510579831744e+00 , -5.48867673275960e-01 , -5.98745578066627e-01 ), ( 6.15938433081102e+00 , -3.51865155810142e-01 , 7.10959937129136e-01 ), ( 4.96814369829621e+00 , -1.74599055654912e-01 , 7.14405530876505e-01 ), ( 7.05408190991051e+00 , -2.04462705476435e+00 , -9.47086827310487e-01 ), ( 6.88091650377089e+00 , -2.62817011227806e-01 , 1.88604566025066e+00 ), ( 6.18480477574462e+00 , -1.42066901477744e-01 , 3.19873946451125e+00 ), ( 7.08149559817778e+00 , -3.54482354608875e-01 , 4.29542762480813e+00 ), ( 5.30104254983498e+00 , 1.10445470535622e+00 , 3.34071996229546e+00 ), ( 4.15143839661535e+00 , 1.03247761763336e+00 , 3.67272010695036e+00 ), ( 5.85323568922793e+00 , 2.24790632228913e+00 , 2.99560209916197e+00 ), ( 5.23618370718149e+00 , 3.58403251276659e+00 , 2.91569931192652e+00 ), ( 6.32567170250395e+00 , 4.50737419565728e+00 , 2.39424603863690e+00 ), ( 3.89715551171003e+00 , 3.72365196675080e+00 , 2.04164791600279e+00 ), ( 2.80268853248701e+00 , 4.15138165055561e+00 , 2.50252266455473e+00 ), ( 3.92169594309874e+00 , 3.24225447989746e+00 , 7.34057635628520e-01 ), ( 2.65289180099164e+00 , 3.02148462948114e+00 , -1.07929070913402e-01 ), ( 3.03852321246946e+00 , 2.71763698861064e+00 , -1.52536700526375e+00 ), ( 1.58985441651868e+00 , 2.19523956422429e+00 , 4.73259858316049e-01 ), ( 3.97932369926968e-01 , 2.55316545017503e+00 , 5.19991029316518e-01 ), ( 2.02279620946447e+00 , 1.02897519386683e+00 , 1.07894198045913e+00 ), ( 1.17672175709072e+00 , 1.07868540491865e-01 , 1.69345045832561e+00 ), ( 2.03396198359163e+00 , -1.11666031273628e+00 , 2.00593010227910e+00 ), ( 5.57165429018075e-01 , 6.08512629021110e-01 , 2.93037236873306e+00 ), ( -6.20129990467547e-01 , 3.49518171000439e-01 , 3.16445900786119e+00 ), ( 1.32439666649378e+00 , 1.34553301855622e+00 , 3.80421179966588e+00 ), ( 8.51427613206044e-01 , 1.96865383405773e+00 , 5.02675980213683e+00 ), ( 2.05301471733063e+00 , 2.65904315802423e+00 , 5.66163036121760e+00 ), ( -3.39220706008036e-01 , 2.91610450769908e+00 , 4.96817542695472e+00 ), ( -1.14734730315266e+00 , 3.05856795143061e+00 , 5.89578123130764e+00 ), ( -4.95755321705192e-01 , 3.56540563470383e+00 , 3.84877399242367e+00 ), ( -1.51129798305328e+00 , 4.54595447511705e+00 , 3.47450439012542e+00 ), ( -7.05768396183657e-01 , 5.40875014273645e+00 , 2.45650999812695e+00 ), ( -2.77014863891599e+00 , 3.87590513998068e+00 , 2.90736321587238e+00 ), ( -3.82120833571270e+00 , 4.49192703814357e+00 , 2.81867411885874e+00 ), ( -2.61276063570700e+00 , 2.67035471524129e+00 , 2.42320099140277e+00 ), ( -3.75910904387670e+00 , 1.82091769837248e+00 , 2.00348296427044e+00 ), ( -3.40146962560496e+00 , 8.83369634242150e-01 , 8.93971629103607e-01 ), ( -4.32377740955311e+00 , 1.06721184527503e+00 , 3.22672314401887e+00 ), ( -5.50993764092784e+00 , 8.40320182188524e-01 , 3.32834082542474e+00 ), ( -3.38367687218931e+00 , 6.81582725519902e-01 , 4.18453821945106e+00 ), ( -3.72390265898211e+00 , 3.63543918288892e-02 , 5.44008888275078e+00 ), ( -2.38577336322952e+00 , -3.14731306612742e-01 , 6.17325615932580e+00 ), ( -4.46685846755194e+00 , 1.00074373587177e+00 , 6.44268001437340e+00 ), ( -5.34874107970129e+00 , 6.03083005153393e-01 , 7.21231651517560e+00 ), ( -6.23394045531279e+00 , 3.58885199384197e+00 , 6.72131981410933e+00 ), ( -6.94750461378181e+00 , 4.29803921723237e+00 , 7.46191661025079e+00 ), ( -6.75132061314708e+00 , 3.19332815548683e+00 , 5.51501496038582e+00 ), ( -4.13044393384095e+00 , 2.25884438608562e+00 , 6.43280193532708e+00 ), ( -4.82027285112013e+00 , 3.19298004975302e+00 , 7.22815140325672e+00 ), ( -4.10447055911947e+00 , 4.58725873797147e+00 , 7.29113600902870e+00 ) } +colvars: Step 17, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_ids[size = 0] = +colvars: Step 17, atom_groups_refcount[size = 0] = +colvars: Step 17, atom_groups_masses[size = 0] = +colvars: Step 17, atom_groups_charges[size = 0] = +colvars: Step 17, atom_groups_coms[size = 0] = +colvars: Step 17, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 17, volmaps_ids[size = 0] = +colvars: Step 17, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 17 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.09319308134653e-01 , 2.30226602992589e-03 , 9.50955448581177e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.09319308134653e-01 , 2.30226602992589e-03 , 9.50955448581177e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.7044 , 1.90575 , -15.1155 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.7044 , 1.90575 , -15.1155 ) to colvar "one". +colvars: Adding total bias energy: 44.6413 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.7044 , 1.90575 , -15.1155 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.90552 , -0.538416 , -1.47279 ) +colvars: ( -4.20649 , -0.461692 , -1.26292 ) +colvars: ( -4.20649 , -0.461692 , -1.26292 ) +colvars: ( -5.60316 , -0.614987 , -1.68225 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.894611 , 0.195151 , 0.624031 ) +colvars: ( 0.774592 , 0.266058 , 0.648644 ) +colvars: ( 0.758926 , 0.259102 , 0.630183 ) +colvars: ( 0.662161 , 0.267013 , 0.584175 ) +colvars: ( 0.650223 , 0.200501 , 0.488274 ) +colvars: ( 0.575175 , 0.344362 , 0.636717 ) +colvars: ( 0.46736 , 0.35854 , 0.592624 ) +colvars: ( 0.390272 , 0.455863 , 0.677658 ) +colvars: ( 0.385538 , 0.314132 , 0.485408 ) +colvars: ( 0.350497 , 0.272647 , 0.409457 ) +colvars: ( 0.356416 , 0.319415 , 0.475443 ) +colvars: ( 0.285127 , 0.276667 , 0.376604 ) +colvars: ( 0.258254 , 0.305657 , 0.399647 ) +colvars: ( 0.347901 , 0.178802 , 0.282476 ) +colvars: ( 0.28898 , 0.135594 , 0.190255 ) +colvars: ( 0.471217 , 0.141597 , 0.304847 ) +colvars: ( 0.544116 , 0.0501577 , 0.22523 ) +colvars: ( 0.674329 , 0.0289792 , 0.273061 ) +colvars: ( 0.552429 , 0.0183811 , 0.187609 ) +colvars: ( 0.53661 , -0.0466204 , 0.0914579 ) +colvars: ( 0.573146 , 0.0662933 , 0.263778 ) +colvars: ( 0.571309 , 0.0501891 , 0.241174 ) +colvars: ( 0.607759 , 0.11487 , 0.348961 ) +colvars: ( 0.446392 , 0.0548408 , 0.174345 ) +colvars: ( 0.43944 , -0.00103527 , 0.0955791 ) +colvars: ( 0.344082 , 0.120576 , 0.2024 ) +colvars: ( 0.219029 , 0.129327 , 0.140973 ) +colvars: ( 0.127248 , 0.215148 , 0.202037 ) +colvars: ( 0.190892 , 0.0556403 , 0.0260067 ) +colvars: ( 0.141328 , 0.0195668 , -0.0512037 ) +colvars: ( 0.224915 , 0.030005 , 0.0116299 ) +colvars: ( 0.211039 , -0.0424656 , -0.0933706 ) +colvars: ( 0.246797 , -0.0458984 , -0.0770501 ) +colvars: ( 0.286501 , -0.128455 , -0.164202 ) +colvars: ( 0.242356 , -0.181491 , -0.260921 ) +colvars: ( 0.402035 , -0.143593 , -0.11688 ) +colvars: ( 0.479684 , -0.219126 , -0.172455 ) +colvars: ( 0.611338 , -0.221869 , -0.0991352 ) +colvars: ( 0.43192 , -0.223515 , -0.206253 ) +colvars: ( 0.43743 , -0.291545 , -0.29398 ) +colvars: ( 0.382771 , -0.150157 , -0.136921 ) +colvars: ( 0.328043 , -0.143803 , -0.160429 ) +colvars: ( 0.311248 , -0.0571134 , -0.0543544 ) +colvars: ( 0.204306 , -0.152444 , -0.244339 ) +colvars: ( 0.17967 , -0.194382 , -0.314812 ) +colvars: ( 0.00271907 , -0.197987 , -0.423107 ) +colvars: ( -0.088548 , -0.215667 , -0.500114 ) +colvars: ( 0.103637 , -0.248025 , -0.43099 ) +colvars: ( 0.122369 , -0.11178 , -0.237889 ) +colvars: ( 0.00264585 , -0.116017 , -0.313564 ) +colvars: ( -0.0865806 , -0.0353011 , -0.257831 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.90552 , 0.538416 , 1.47279 ) +colvars: ( 4.20649 , 0.461692 , 1.26292 ) +colvars: ( 4.20649 , 0.461692 , 1.26292 ) +colvars: ( 5.60316 , 0.614987 , 1.68225 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.617237 , -0.0807303 , -0.374353 ) +colvars: ( -0.554897 , -0.162858 , -0.344449 ) +colvars: ( -0.506049 , -0.141113 , -0.286791 ) +colvars: ( -0.515016 , -0.1902 , -0.315303 ) +colvars: ( -0.505431 , -0.131861 , -0.282494 ) +colvars: ( -0.489635 , -0.281484 , -0.326122 ) +colvars: ( -0.456159 , -0.321546 , -0.30846 ) +colvars: ( -0.433907 , -0.427976 , -0.32844 ) +colvars: ( -0.393509 , -0.286606 , -0.231707 ) +colvars: ( -0.388571 , -0.261549 , -0.216792 ) +colvars: ( -0.34494 , -0.281098 , -0.180784 ) +colvars: ( -0.2849 , -0.24464 , -0.106048 ) +colvars: ( -0.237041 , -0.259509 , -0.0639373 ) +colvars: ( -0.304795 , -0.142318 , -0.0853353 ) +colvars: ( -0.273433 , -0.113364 , -0.0423571 ) +colvars: ( -0.359643 , -0.0853307 , -0.117715 ) +colvars: ( -0.386699 , 0.0121101 , -0.106128 ) +colvars: ( -0.437592 , 0.059415 , -0.138388 ) +colvars: ( -0.423504 , 0.0270588 , -0.137115 ) +colvars: ( -0.412158 , 0.0833205 , -0.103365 ) +colvars: ( -0.466844 , -0.0264316 , -0.201865 ) +colvars: ( -0.500287 , -0.0278286 , -0.235977 ) +colvars: ( -0.549552 , -0.092581 , -0.31115 ) +colvars: ( -0.447689 , -0.0576861 , -0.19507 ) +colvars: ( -0.454253 , -0.0139774 , -0.184281 ) +colvars: ( -0.392492 , -0.131455 , -0.16901 ) +colvars: ( -0.334533 , -0.162599 , -0.123235 ) +colvars: ( -0.284091 , -0.252089 , -0.108198 ) +colvars: ( -0.293915 , -0.0904689 , -0.0538069 ) +colvars: ( -0.28031 , -0.0720481 , -0.0328328 ) +colvars: ( -0.275032 , -0.0460069 , -0.0171853 ) +colvars: ( -0.240311 , 0.0280361 , 0.0470878 ) +colvars: ( -0.220064 , 0.0541718 , 0.0777931 ) +colvars: ( -0.284299 , 0.114125 , 0.0371728 ) +colvars: ( -0.257664 , 0.155473 , 0.0803347 ) +colvars: ( -0.353538 , 0.142137 , -0.0211656 ) +colvars: ( -0.402203 , 0.217765 , -0.0399309 ) +colvars: ( -0.473447 , 0.240278 , -0.102466 ) +colvars: ( -0.412788 , 0.198118 , -0.0583619 ) +colvars: ( -0.417232 , 0.258417 , -0.0388506 ) +colvars: ( -0.416489 , 0.112299 , -0.0961911 ) +colvars: ( -0.422621 , 0.0824026 , -0.114228 ) +colvars: ( -0.443394 , -0.0100647 , -0.17183 ) +colvars: ( -0.355796 , 0.0710954 , -0.0516714 ) +colvars: ( -0.358649 , 0.0971788 , -0.044165 ) +colvars: ( -0.195873 , 0.103228 , 0.121567 ) +colvars: ( -0.146359 , 0.104978 , 0.171945 ) +colvars: ( -0.223235 , 0.174984 , 0.122637 ) +colvars: ( -0.293662 , 0.0305917 , -0.00542789 ) +colvars: ( -0.226867 , 0.0169606 , 0.0561745 ) +colvars: ( -0.173052 , -0.0655097 , 0.0773882 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 17. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 17. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atoms_new_colvar_forces = { ( -4.62815055561045e+00 , -4.23995474056573e-01 , -1.22311616501379e+00 ), ( -3.98679069559760e+00 , -3.58492590906031e-01 , -9.58726707117377e-01 ), ( -4.05934086166424e+00 , -3.84879073764890e-01 , -9.94048635242549e-01 ), ( -5.45836875016544e+00 , -5.46346704818888e-01 , -1.47646699315704e+00 ), ( 2.52877053876661e-01 , 1.17989351327774e-01 , 3.43392302604611e-01 ), ( 4.99106492956269e+00 , 6.01294492452920e-01 , 1.78338870866727e+00 ), ( 4.21768619258938e+00 , 4.98685681530818e-01 , 1.54708569213552e+00 ), ( -4.36349218542222e-02 , 2.78872965849131e-02 , 3.49217919851065e-01 ), ( 4.19851532526447e+00 , 4.89217470186831e-01 , 1.51662220660519e+00 ), ( 5.56508736105459e+00 , 6.26085860745317e-01 , 1.87491240442127e+00 ), ( 1.14761685523073e-02 , 3.83176410846751e-02 , 2.94658316670772e-01 ), ( 2.27311673549169e-04 , 3.20265038522220e-02 , 2.70556427835990e-01 ), ( 2.12130772158747e-02 , 4.61477749858128e-02 , 3.35709262009671e-01 ), ( 4.31054331259390e-02 , 3.64840174182485e-02 , 1.97140949175543e-01 ), ( 1.55466729079566e-02 , 2.22293637359794e-02 , 1.47898206938958e-01 ), ( 1.11573320369336e-01 , 5.62662571760795e-02 , 1.87132033920166e-01 ), ( 1.57416364867810e-01 , 6.22677753523262e-02 , 1.19102499061421e-01 ), ( 2.36736555308689e-01 , 8.83942194578691e-02 , 1.34672750830872e-01 ), ( 1.28924120467800e-01 , 4.54398987681336e-02 , 5.04939991814637e-02 ), ( 1.24452217835664e-01 , 3.67001262824173e-02 , -1.19068248412217e-02 ), ( 1.06301448613530e-01 , 3.98616790001095e-02 , 6.19125172956823e-02 ), ( 7.10223742608336e-02 , 2.23605128215839e-02 , 5.19743014273452e-03 ), ( 5.82071950869493e-02 , 2.22888161008216e-02 , 3.78115516688273e-02 ), ( -1.29770098089821e-03 , -2.84524603756130e-03 , -2.07246157958354e-02 ), ( -1.48129777873950e-02 , -1.50126748989254e-02 , -8.87015980687740e-02 ), ( -4.84097029276451e-02 , -1.08789016345353e-02 , 3.33898046253918e-02 ), ( -1.15503942874981e-01 , -3.32715684439314e-02 , 1.77371433366362e-02 ), ( -1.56843277971266e-01 , -3.69405728415567e-02 , 9.38393334526097e-02 ), ( -1.03022840015482e-01 , -3.48285999653236e-02 , -2.78002302319697e-02 ), ( -1.38981558459396e-01 , -5.24813106230892e-02 , -8.40364777156737e-02 ), ( -5.01174570159802e-02 , -1.60018360314190e-02 , -5.55539161786267e-03 ), ( -2.92713756063540e-02 , -1.44294281775459e-02 , -4.62827759124423e-02 ), ( 2.67333624896054e-02 , 8.27334936254839e-03 , 7.42980987567671e-04 ), ( 2.20187413035811e-03 , -1.43299766622657e-02 , -1.27029725469207e-01 ), ( -1.53083045192691e-02 , -2.60173723692135e-02 , -1.80586518115724e-01 ), ( 4.84966864707551e-02 , -1.45595191817147e-03 , -1.38045751109204e-01 ), ( 7.74816097863003e-02 , -1.36166205491367e-03 , -2.12385846533022e-01 ), ( 1.37891378301253e-01 , 1.84092284257072e-02 , -2.01601574458287e-01 ), ( 1.91319457446069e-02 , -2.53970370368797e-02 , -2.64614947504997e-01 ), ( 2.01987378424113e-02 , -3.31277439678343e-02 , -3.32830833499215e-01 ), ( -3.37184298029777e-02 , -3.78585727143166e-02 , -2.33112510165987e-01 ), ( -9.45777953167765e-02 , -6.14004526724902e-02 , -2.74657573486360e-01 ), ( -1.32145748965112e-01 , -6.71780544534610e-02 , -2.26184033479536e-01 ), ( -1.51489395053466e-01 , -8.13484963423917e-02 , -2.96010071115899e-01 ), ( -1.78978606748064e-01 , -9.72029263997774e-02 , -3.58977277777855e-01 ), ( -1.93153776379780e-01 , -9.47590584128483e-02 , -3.01540114875522e-01 ), ( -2.34906524564462e-01 , -1.10688762799213e-01 , -3.28168874229867e-01 ), ( -1.19597666023818e-01 , -7.30413168729495e-02 , -3.08352844175269e-01 ), ( -1.71292715350085e-01 , -8.11882935299329e-02 , -2.43317078256175e-01 ), ( -2.24221046364581e-01 , -9.90568445452535e-02 , -2.57389918940128e-01 ), ( -2.59632089779584e-01 , -1.00810811700924e-01 , -1.80442533512445e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 17, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 18 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 18, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 18, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 18, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 18, atoms_positions[size = 51] = { ( 8.29492152155911e+00 , 4.10024056305554e-02 , -7.59019667114383e-01 ), ( 6.95618155035659e+00 , -5.49833619361815e-01 , -5.91623253556879e-01 ), ( 6.15659892821855e+00 , -3.60531379712544e-01 , 7.16586949149385e-01 ), ( 4.96307247456961e+00 , -1.70696146174729e-01 , 7.17351902015087e-01 ), ( 7.05280967742796e+00 , -2.04696348665916e+00 , -9.42573254324749e-01 ), ( 6.87542220778904e+00 , -2.62710186718871e-01 , 1.89300813102855e+00 ), ( 6.18260834605906e+00 , -1.48157496608870e-01 , 3.19940156458429e+00 ), ( 7.07963398728163e+00 , -3.55228365303318e-01 , 4.30095170934118e+00 ), ( 5.30685666094591e+00 , 1.10160129721062e+00 , 3.34453180267969e+00 ), ( 4.15455369109859e+00 , 1.02991906392327e+00 , 3.67895321427891e+00 ), ( 5.84944342689905e+00 , 2.24949092199651e+00 , 2.99399791380715e+00 ), ( 5.23835844225534e+00 , 3.58204670292676e+00 , 2.91840033581230e+00 ), ( 6.32437832438070e+00 , 4.50466681167845e+00 , 2.38491279094262e+00 ), ( 3.89221877193473e+00 , 3.71835966899616e+00 , 2.04295099665439e+00 ), ( 2.79801904872082e+00 , 4.15482742037216e+00 , 2.49773994541295e+00 ), ( 3.92880130252089e+00 , 3.24189250822501e+00 , 7.32819184438415e-01 ), ( 2.65405535884173e+00 , 3.01431699509412e+00 , -1.06941989163933e-01 ), ( 3.04243371748930e+00 , 2.71422805612423e+00 , -1.52032791683391e+00 ), ( 1.59411926756975e+00 , 2.19214687403451e+00 , 4.62787625886367e-01 ), ( 3.90604897647063e-01 , 2.56299942017237e+00 , 5.16970677862218e-01 ), ( 2.03119076698977e+00 , 1.04139606573325e+00 , 1.07692525488152e+00 ), ( 1.17400121263943e+00 , 1.12193966005497e-01 , 1.69452603466745e+00 ), ( 2.03679213424400e+00 , -1.11178217044486e+00 , 2.00689466057382e+00 ), ( 5.58724204903462e-01 , 6.09266033385929e-01 , 2.93359437401471e+00 ), ( -6.13747703330975e-01 , 3.49405809176778e-01 , 3.16324925195188e+00 ), ( 1.32232324727817e+00 , 1.34555114489065e+00 , 3.79478096702290e+00 ), ( 8.48308168825283e-01 , 1.97259021903522e+00 , 5.02593907633248e+00 ), ( 2.06158253431628e+00 , 2.66855924761502e+00 , 5.66831477006168e+00 ), ( -3.37929735335485e-01 , 2.91578888090203e+00 , 4.96768359448415e+00 ), ( -1.14405270425054e+00 , 3.06004939013347e+00 , 5.89322661576763e+00 ), ( -5.01234152634331e-01 , 3.55410676952643e+00 , 3.84872885656980e+00 ), ( -1.51441323034894e+00 , 4.54437249663840e+00 , 3.46392939262252e+00 ), ( -7.02913269087333e-01 , 5.41070128543474e+00 , 2.45932269473302e+00 ), ( -2.76742081648498e+00 , 3.87903079094641e+00 , 2.90396643486297e+00 ), ( -3.81978812863135e+00 , 4.49805218747342e+00 , 2.81711356351771e+00 ), ( -2.61619616729560e+00 , 2.67319283641547e+00 , 2.41603045036765e+00 ), ( -3.76421874631865e+00 , 1.81305869882987e+00 , 2.00085114262667e+00 ), ( -3.39733086851704e+00 , 8.85493386658980e-01 , 8.87088549541825e-01 ), ( -4.32548524241508e+00 , 1.06838804267476e+00 , 3.22110038486433e+00 ), ( -5.50601091655025e+00 , 8.33186724849965e-01 , 3.32846497103526e+00 ), ( -3.37774616414948e+00 , 6.84675166407712e-01 , 4.19260529643886e+00 ), ( -3.71576174878836e+00 , 3.83323758973222e-02 , 5.43648659170493e+00 ), ( -2.38733434575455e+00 , -3.14579981967497e-01 , 6.17288950008614e+00 ), ( -4.46487998291990e+00 , 9.97762808571827e-01 , 6.44233038019791e+00 ), ( -5.35244342243093e+00 , 6.01457615387527e-01 , 7.21465836873856e+00 ), ( -6.23311164917986e+00 , 3.59417372126332e+00 , 6.72526640259087e+00 ), ( -6.95204434573434e+00 , 4.29820420496905e+00 , 7.46681012789176e+00 ), ( -6.74956380232919e+00 , 3.18981640634602e+00 , 5.51239575556105e+00 ), ( -4.13057047178864e+00 , 2.25360069240219e+00 , 6.42460267132524e+00 ), ( -4.81532476982100e+00 , 3.19612160868296e+00 , 7.23253448093177e+00 ), ( -4.10260344332175e+00 , 4.58477295425590e+00 , 7.28859187637104e+00 ) } +colvars: Step 18, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_ids[size = 0] = +colvars: Step 18, atom_groups_refcount[size = 0] = +colvars: Step 18, atom_groups_masses[size = 0] = +colvars: Step 18, atom_groups_charges[size = 0] = +colvars: Step 18, atom_groups_coms[size = 0] = +colvars: Step 18, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 18, volmaps_ids[size = 0] = +colvars: Step 18, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 18 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.07543552262695e-01 , 1.57772719634005e-03 , 9.51532697409047e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.07543552262695e-01 , 1.57772719634005e-03 , 9.51532697409047e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.6689 , 1.92025 , -15.1271 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.6689 , 1.92025 , -15.1271 ) to colvar "one". +colvars: Adding total bias energy: 44.5703 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.6689 , 1.92025 , -15.1271 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.90917 , -0.53644 , -1.46508 ) +colvars: ( -4.20961 , -0.459997 , -1.2563 ) +colvars: ( -4.20961 , -0.459997 , -1.2563 ) +colvars: ( -5.60733 , -0.61273 , -1.67343 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.8939 , 0.195273 , 0.62229 ) +colvars: ( 0.774075 , 0.266109 , 0.646792 ) +colvars: ( 0.758316 , 0.259184 , 0.628354 ) +colvars: ( 0.661889 , 0.266989 , 0.582458 ) +colvars: ( 0.649971 , 0.200483 , 0.486803 ) +colvars: ( 0.575098 , 0.344265 , 0.634839 ) +colvars: ( 0.467529 , 0.358366 , 0.590832 ) +colvars: ( 0.390611 , 0.45562 , 0.675622 ) +colvars: ( 0.385794 , 0.31394 , 0.483856 ) +colvars: ( 0.350857 , 0.272431 , 0.408097 ) +colvars: ( 0.356622 , 0.319239 , 0.473889 ) +colvars: ( 0.285393 , 0.276481 , 0.375272 ) +colvars: ( 0.258461 , 0.305484 , 0.398227 ) +colvars: ( 0.348037 , 0.178673 , 0.281409 ) +colvars: ( 0.28922 , 0.13544 , 0.189407 ) +colvars: ( 0.471121 , 0.141544 , 0.303763 ) +colvars: ( 0.543878 , 0.0501641 , 0.224378 ) +colvars: ( 0.673824 , 0.0290706 , 0.272125 ) +colvars: ( 0.552277 , 0.018366 , 0.186874 ) +colvars: ( 0.536486 , -0.0466322 , 0.0909679 ) +colvars: ( 0.573048 , 0.0662525 , 0.262867 ) +colvars: ( 0.571318 , 0.0501177 , 0.240339 ) +colvars: ( 0.607786 , 0.114781 , 0.347871 ) +colvars: ( 0.446648 , 0.0546935 , 0.173643 ) +colvars: ( 0.439746 , -0.00118822 , 0.0950862 ) +colvars: ( 0.344496 , 0.12037 , 0.201585 ) +colvars: ( 0.219674 , 0.129049 , 0.140274 ) +colvars: ( 0.128029 , 0.214814 , 0.201142 ) +colvars: ( 0.19152 , 0.0553815 , 0.0255864 ) +colvars: ( 0.142081 , 0.0192761 , -0.0514344 ) +colvars: ( 0.225381 , 0.0298007 , 0.0112426 ) +colvars: ( 0.211459 , -0.0426421 , -0.093501 ) +colvars: ( 0.247042 , -0.0460203 , -0.0772285 ) +colvars: ( 0.286819 , -0.128586 , -0.164116 ) +colvars: ( 0.242746 , -0.181634 , -0.2606 ) +colvars: ( 0.402186 , -0.143671 , -0.116869 ) +colvars: ( 0.479739 , -0.219163 , -0.172265 ) +colvars: ( 0.611178 , -0.22184 , -0.0990857 ) +colvars: ( 0.43216 , -0.223608 , -0.205975 ) +colvars: ( 0.437676 , -0.291627 , -0.293469 ) +colvars: ( 0.38317 , -0.150312 , -0.13683 ) +colvars: ( 0.328636 , -0.144018 , -0.16028 ) +colvars: ( 0.311943 , -0.057376 , -0.0544758 ) +colvars: ( 0.205103 , -0.152719 , -0.244018 ) +colvars: ( 0.18056 , -0.194679 , -0.314308 ) +colvars: ( 0.00370186 , -0.198308 , -0.422421 ) +colvars: ( -0.0874139 , -0.216031 , -0.499261 ) +colvars: ( 0.104382 , -0.248265 , -0.430257 ) +colvars: ( 0.123241 , -0.112085 , -0.237626 ) +colvars: ( 0.00370811 , -0.116378 , -0.313151 ) +colvars: ( -0.0854004 , -0.0357115 , -0.257601 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.90917 , 0.53644 , 1.46508 ) +colvars: ( 4.20961 , 0.459997 , 1.2563 ) +colvars: ( 4.20961 , 0.459997 , 1.2563 ) +colvars: ( 5.60733 , 0.61273 , 1.67343 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.616722 , -0.0807982 , -0.372798 ) +colvars: ( -0.554528 , -0.162976 , -0.342697 ) +colvars: ( -0.505478 , -0.141207 , -0.284944 ) +colvars: ( -0.514886 , -0.190308 , -0.313672 ) +colvars: ( -0.505299 , -0.131902 , -0.28111 ) +colvars: ( -0.489717 , -0.281659 , -0.324314 ) +colvars: ( -0.456497 , -0.321727 , -0.306733 ) +colvars: ( -0.434433 , -0.428244 , -0.326449 ) +colvars: ( -0.393839 , -0.286725 , -0.230132 ) +colvars: ( -0.389018 , -0.261627 , -0.215436 ) +colvars: ( -0.345125 , -0.281206 , -0.179099 ) +colvars: ( -0.285049 , -0.244689 , -0.104492 ) +colvars: ( -0.237039 , -0.25957 , -0.0621805 ) +colvars: ( -0.304801 , -0.142279 , -0.0840717 ) +colvars: ( -0.273509 , -0.113274 , -0.0412886 ) +colvars: ( -0.359448 , -0.0852709 , -0.11649 ) +colvars: ( -0.386358 , 0.0122499 , -0.10517 ) +colvars: ( -0.437 , 0.0595613 , -0.137381 ) +colvars: ( -0.42333 , 0.0272166 , -0.136376 ) +colvars: ( -0.411988 , 0.083544 , -0.10287 ) +colvars: ( -0.46682 , -0.0263338 , -0.201037 ) +colvars: ( -0.500452 , -0.0277269 , -0.23532 ) +colvars: ( -0.549835 , -0.0925569 , -0.310325 ) +colvars: ( -0.448075 , -0.0575743 , -0.194509 ) +colvars: ( -0.454704 , -0.0138146 , -0.183967 ) +colvars: ( -0.392991 , -0.13139 , -0.168255 ) +colvars: ( -0.335224 , -0.162526 , -0.122542 ) +colvars: ( -0.284879 , -0.252083 , -0.107226 ) +colvars: ( -0.294502 , -0.0903123 , -0.0533253 ) +colvars: ( -0.281025 , -0.0718538 , -0.0325549 ) +colvars: ( -0.27538 , -0.0458184 , -0.0166637 ) +colvars: ( -0.240528 , 0.0283054 , 0.0474158 ) +colvars: ( -0.220027 , 0.0544522 , 0.0782529 ) +colvars: ( -0.284452 , 0.114463 , 0.0372056 ) +colvars: ( -0.257853 , 0.15587 , 0.0801535 ) +colvars: ( -0.353599 , 0.142469 , -0.0211515 ) +colvars: ( -0.402215 , 0.218155 , -0.0401827 ) +colvars: ( -0.473312 , 0.24065 , -0.10266 ) +colvars: ( -0.413051 , 0.198507 , -0.0587711 ) +colvars: ( -0.417499 , 0.25887 , -0.0395181 ) +colvars: ( -0.41697 , 0.112615 , -0.0964458 ) +colvars: ( -0.423357 , 0.0827095 , -0.114601 ) +colvars: ( -0.444308 , -0.00984817 , -0.17198 ) +colvars: ( -0.356671 , 0.07143 , -0.0521415 ) +colvars: ( -0.35964 , 0.0975518 , -0.0448576 ) +colvars: ( -0.196699 , 0.103655 , 0.120983 ) +colvars: ( -0.147286 , 0.105437 , 0.171247 ) +colvars: ( -0.223801 , 0.175452 , 0.122003 ) +colvars: ( -0.29453 , 0.0309065 , -0.00573036 ) +colvars: ( -0.227859 , 0.017299 , 0.0558005 ) +colvars: ( -0.174111 , -0.0652325 , 0.07729 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 18. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 18. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atoms_new_colvar_forces = { ( -4.63199186926414e+00 , -4.21965218396545e-01 , -1.21558574633418e+00 ), ( -3.99006508628367e+00 , -3.56864437027678e-01 , -9.52209324073797e-01 ), ( -4.06260952482650e+00 , -3.83316071324867e-01 , -9.87517423191293e-01 ), ( -5.46265396933560e+00 , -5.44148820171854e-01 , -1.46774025745692e+00 ), ( 2.52838450519886e-01 , 1.17976408809654e-01 , 3.43409753316738e-01 ), ( 4.99455074893902e+00 , 5.99046314440739e-01 , 1.77560204659984e+00 ), ( 4.22064457405113e+00 , 4.96636169794268e-01 , 1.54040251442313e+00 ), ( -4.38227043909202e-02 , 2.73760811980873e-02 , 3.49172967335116e-01 ), ( 4.20156671415350e+00 , 4.87212114671244e-01 , 1.51002822680228e+00 ), ( 5.56916470083263e+00 , 6.23533520962560e-01 , 1.86609441161746e+00 ), ( 1.14972342676729e-02 , 3.80328002454685e-02 , 2.94789823873343e-01 ), ( 3.43451000375694e-04 , 3.17914452486105e-02 , 2.70779342072598e-01 ), ( 2.14227181961660e-02 , 4.59143646767022e-02 , 3.36046732369687e-01 ), ( 4.32353490996562e-02 , 3.63941370787423e-02 , 1.97336988514932e-01 ), ( 1.57106058911772e-02 , 2.21660889396837e-02 , 1.48118317334512e-01 ), ( 1.11673421408274e-01 , 5.62730903723445e-02 , 1.87273358297197e-01 ), ( 1.57520102373723e-01 , 6.24140613543656e-02 , 1.19207758041775e-01 ), ( 2.36824231820393e-01 , 8.86318286882992e-02 , 1.34743992062622e-01 ), ( 1.28946764504298e-01 , 4.55826367881988e-02 , 5.04983062515025e-02 ), ( 1.24497354942834e-01 , 3.69117589338607e-02 , -1.19021651496601e-02 ), ( 1.06227975373663e-01 , 3.99186171610424e-02 , 6.18295321419749e-02 ), ( 7.08659593229584e-02 , 2.23907783048436e-02 , 5.01819221063698e-03 ), ( 5.79510803244978e-02 , 2.22235891960562e-02 , 3.75465936627963e-02 ), ( -1.42753015197761e-03 , -2.88078605485102e-03 , -2.08651223555693e-02 ), ( -1.49585663463941e-02 , -1.50028625361222e-02 , -8.88803735389048e-02 ), ( -4.84946350473997e-02 , -1.10203210850865e-02 , 3.33300764096249e-02 ), ( -1.15549522598168e-01 , -3.34766052013843e-02 , 1.77316149988748e-02 ), ( -1.56849335140040e-01 , -3.72686111642727e-02 , 9.39158243774778e-02 ), ( -1.02982312572491e-01 , -3.49308227331173e-02 , -2.77388268008082e-02 ), ( -1.38944250648061e-01 , -5.25776131427206e-02 , -8.39893211297022e-02 ), ( -4.99987340279306e-02 , -1.60176358727117e-02 , -5.42109089872812e-03 ), ( -2.90695086701666e-02 , -1.43366633820372e-02 , -4.60852118931290e-02 ), ( 2.70157370241507e-02 , 8.43189607754159e-03 , 1.02442138214723e-03 ), ( 2.36673869014287e-03 , -1.41224930282780e-02 , -1.26910456329147e-01 ), ( -1.51077929558593e-02 , -2.57635245274974e-02 , -1.80446153831180e-01 ), ( 4.85869347753608e-02 , -1.20187823586984e-03 , -1.38020865097516e-01 ), ( 7.75238442668547e-02 , -1.00792117951987e-03 , -2.12447325162941e-01 ), ( 1.37865992739589e-01 , 1.88099748420454e-02 , -2.01746080504194e-01 ), ( 1.91086354015031e-02 , -2.51005877528302e-02 , -2.64746288558128e-01 ), ( 2.01766844828190e-02 , -3.27573501001041e-02 , -3.32987445882389e-01 ), ( -3.38001451271146e-02 , -3.76966301635223e-02 , -2.33275827648116e-01 ), ( -9.47209793171819e-02 , -6.13089407095653e-02 , -2.74881724704049e-01 ), ( -1.32364462259639e-01 , -6.72241704556363e-02 , -2.26455704643539e-01 ), ( -1.51568083687360e-01 , -8.12891381825588e-02 , -2.96159498581740e-01 ), ( -1.79080099878639e-01 , -9.71266931889652e-02 , -3.59166108508444e-01 ), ( -1.92996725924340e-01 , -9.46532932510188e-02 , -3.01437941426688e-01 ), ( -2.34700057458484e-01 , -1.10594138940201e-01 , -3.28013947671509e-01 ), ( -1.19419164758656e-01 , -7.28129396647109e-02 , -3.08253181647993e-01 ), ( -1.71289457234405e-01 , -8.11780271490729e-02 , -2.43356455227854e-01 ), ( -2.24150534071262e-01 , -9.90794672795882e-02 , -2.57350130661441e-01 ), ( -2.59510952425891e-01 , -1.00944015882171e-01 , -1.80310795186701e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 18, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 19 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 19, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 19, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 19, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 19, atoms_positions[size = 51] = { ( 8.29016568556080e+00 , 4.06698503088023e-02 , -7.56709873943808e-01 ), ( 6.94599735216919e+00 , -5.50749837223836e-01 , -5.84155006258614e-01 ), ( 6.15580748001842e+00 , -3.68606829803745e-01 , 7.22837908152150e-01 ), ( 4.95723322053989e+00 , -1.66817333386827e-01 , 7.20083807400076e-01 ), ( 7.05086328351688e+00 , -2.04918183568107e+00 , -9.38184814770755e-01 ), ( 6.86940055722009e+00 , -2.62917482731473e-01 , 1.90028356504105e+00 ), ( 6.17947606996176e+00 , -1.54655252538254e-01 , 3.19785930273638e+00 ), ( 7.07927530556238e+00 , -3.55345958464858e-01 , 4.30722872042406e+00 ), ( 5.31311935542799e+00 , 1.09841937380163e+00 , 3.34822921101458e+00 ), ( 4.15713014090365e+00 , 1.02743973859713e+00 , 3.68556971830120e+00 ), ( 5.84591971680664e+00 , 2.25139529107553e+00 , 2.99218364269678e+00 ), ( 5.23918055313769e+00 , 3.58015005617468e+00 , 2.92033481435295e+00 ), ( 6.32331086605058e+00 , 4.50264880133564e+00 , 2.37526441506070e+00 ), ( 3.88701121106020e+00 , 3.71260739307479e+00 , 2.04386771633033e+00 ), ( 2.79448765359408e+00 , 4.15798984046697e+00 , 2.49279276475371e+00 ), ( 3.93450135362444e+00 , 3.24102272227666e+00 , 7.31874880796859e-01 ), ( 2.65719957690435e+00 , 3.00921494798025e+00 , -1.05547997265674e-01 ), ( 3.04727261327806e+00 , 2.71000869800488e+00 , -1.51691695139718e+00 ), ( 1.59692527577294e+00 , 2.18794488778601e+00 , 4.53626036616700e-01 ), ( 3.84266461533483e-01 , 2.57240994422366e+00 , 5.13706922516542e-01 ), ( 2.03949616752687e+00 , 1.05549421048506e+00 , 1.07375909314133e+00 ), ( 1.17132402764887e+00 , 1.15024769904997e-01 , 1.69589156927417e+00 ), ( 2.03984308916360e+00 , -1.10731133916195e+00 , 2.00844855140052e+00 ), ( 5.60352100194501e-01 , 6.10391271265693e-01 , 2.93787520299176e+00 ), ( -6.07650884272349e-01 , 3.49472309543588e-01 , 3.16225774381691e+00 ), ( 1.31972169446706e+00 , 1.34555701252330e+00 , 3.78503503912101e+00 ), ( 8.45312959777899e-01 , 1.97599832312103e+00 , 5.02552145167832e+00 ), ( 2.07062385644138e+00 , 2.67821594555621e+00 , 5.67519151395927e+00 ), ( -3.37294919573754e-01 , 2.91533326166685e+00 , 4.96765032089662e+00 ), ( -1.14061183342495e+00 , 3.06135069610087e+00 , 5.89053374083556e+00 ), ( -5.06564556008585e-01 , 3.54401302021891e+00 , 3.84796570257251e+00 ), ( -1.51673772132311e+00 , 4.54216454055818e+00 , 3.45374233777667e+00 ), ( -7.00831591912167e-01 , 5.41258555929861e+00 , 2.46174052642702e+00 ), ( -2.76400858138880e+00 , 3.88360415598215e+00 , 2.89991349394933e+00 ), ( -3.81857294493020e+00 , 4.50405658125091e+00 , 2.81578739240627e+00 ), ( -2.62033145837470e+00 , 2.67416887011665e+00 , 2.40875873374679e+00 ), ( -3.76876185319620e+00 , 1.80728258250921e+00 , 1.99916822343542e+00 ), ( -3.39303477301733e+00 , 8.86584790958229e-01 , 8.80525528609449e-01 ), ( -4.32513260189623e+00 , 1.06939488468089e+00 , 3.21616052977844e+00 ), ( -5.50268179432501e+00 , 8.25997951798771e-01 , 3.32880254088488e+00 ), ( -3.37283314174368e+00 , 6.87984528108069e-01 , 4.19931112945264e+00 ), ( -3.70810082719424e+00 , 4.17326140614362e-02 , 5.43447083064241e+00 ), ( -2.38890674390546e+00 , -3.15458062771559e-01 , 6.17186901939838e+00 ), ( -4.46312730645682e+00 , 9.93104584934617e-01 , 6.44131280303784e+00 ), ( -5.35584048260438e+00 , 5.99806496682841e-01 , 7.21661752816569e+00 ), ( -6.23456552528205e+00 , 3.59979020155176e+00 , 6.72948111301887e+00 ), ( -6.95624590919136e+00 , 4.29811286783759e+00 , 7.47143281594149e+00 ), ( -6.74626091907508e+00 , 3.18609816515879e+00 , 5.50997186268318e+00 ), ( -4.12995356453422e+00 , 2.24935615826763e+00 , 6.41684281705873e+00 ), ( -4.81151193535090e+00 , 3.20071974677728e+00 , 7.23716453085567e+00 ), ( -4.09944363849299e+00 , 4.58072674342841e+00 , 7.28577850117491e+00 ) } +colvars: Step 19, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_ids[size = 0] = +colvars: Step 19, atom_groups_refcount[size = 0] = +colvars: Step 19, atom_groups_masses[size = 0] = +colvars: Step 19, atom_groups_charges[size = 0] = +colvars: Step 19, atom_groups_coms[size = 0] = +colvars: Step 19, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 19, volmaps_ids[size = 0] = +colvars: Step 19, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 19 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.05951823016640e-01 , 7.43277606547324e-04 , 9.52046705540854e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.05951823016640e-01 , 7.43277606547324e-04 , 9.52046705540854e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.637 , 1.93693 , -15.1373 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.637 , 1.93693 , -15.1373 ) to colvar "one". +colvars: Adding total bias energy: 44.5074 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.637 , 1.93693 , -15.1373 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.91237 , -0.534728 , -1.45823 ) +colvars: ( -4.21236 , -0.458529 , -1.25043 ) +colvars: ( -4.21236 , -0.458529 , -1.25043 ) +colvars: ( -5.61098 , -0.610774 , -1.66561 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.893209 , 0.195386 , 0.620693 ) +colvars: ( 0.773567 , 0.266161 , 0.645082 ) +colvars: ( 0.757723 , 0.259258 , 0.626656 ) +colvars: ( 0.661613 , 0.266978 , 0.580875 ) +colvars: ( 0.649714 , 0.200474 , 0.485452 ) +colvars: ( 0.575004 , 0.344193 , 0.633099 ) +colvars: ( 0.467669 , 0.358228 , 0.589172 ) +colvars: ( 0.390909 , 0.455426 , 0.673728 ) +colvars: ( 0.386015 , 0.313783 , 0.482417 ) +colvars: ( 0.351178 , 0.272252 , 0.406842 ) +colvars: ( 0.356799 , 0.319091 , 0.47244 ) +colvars: ( 0.285626 , 0.27632 , 0.374024 ) +colvars: ( 0.258641 , 0.305333 , 0.396887 ) +colvars: ( 0.348148 , 0.178559 , 0.280415 ) +colvars: ( 0.28943 , 0.135304 , 0.188619 ) +colvars: ( 0.471015 , 0.141495 , 0.30276 ) +colvars: ( 0.543638 , 0.050164 , 0.223599 ) +colvars: ( 0.673331 , 0.0291432 , 0.27127 ) +colvars: ( 0.552116 , 0.0183499 , 0.186215 ) +colvars: ( 0.536351 , -0.0466477 , 0.0905406 ) +colvars: ( 0.572936 , 0.066219 , 0.262047 ) +colvars: ( 0.571306 , 0.0500609 , 0.239598 ) +colvars: ( 0.60779 , 0.114714 , 0.346896 ) +colvars: ( 0.44687 , 0.0545709 , 0.173025 ) +colvars: ( 0.440015 , -0.00131615 , 0.0946694 ) +colvars: ( 0.344868 , 0.120196 , 0.200851 ) +colvars: ( 0.220265 , 0.128813 , 0.139645 ) +colvars: ( 0.128747 , 0.214531 , 0.200319 ) +colvars: ( 0.192095 , 0.0551573 , 0.0252167 ) +colvars: ( 0.142773 , 0.0190241 , -0.0516236 ) +colvars: ( 0.225804 , 0.0296196 , 0.0108987 ) +colvars: ( 0.211839 , -0.0428041 , -0.093606 ) +colvars: ( 0.247259 , -0.0461388 , -0.0773854 ) +colvars: ( 0.287103 , -0.128709 , -0.164008 ) +colvars: ( 0.243098 , -0.18177 , -0.26027 ) +colvars: ( 0.402312 , -0.143747 , -0.116824 ) +colvars: ( 0.479773 , -0.219203 , -0.172041 ) +colvars: ( 0.611009 , -0.221822 , -0.0989879 ) +colvars: ( 0.432369 , -0.223694 , -0.205663 ) +colvars: ( 0.437889 , -0.291706 , -0.292934 ) +colvars: ( 0.383527 , -0.150447 , -0.136694 ) +colvars: ( 0.329175 , -0.144203 , -0.160085 ) +colvars: ( 0.312579 , -0.0575961 , -0.0545338 ) +colvars: ( 0.205835 , -0.152957 , -0.243667 ) +colvars: ( 0.181381 , -0.194935 , -0.313781 ) +colvars: ( 0.00461293 , -0.198596 , -0.421745 ) +colvars: ( -0.0863596 , -0.216357 , -0.498433 ) +colvars: ( 0.105069 , -0.248485 , -0.429535 ) +colvars: ( 0.124046 , -0.11235 , -0.237339 ) +colvars: ( 0.004693 , -0.116695 , -0.312729 ) +colvars: ( -0.0843039 , -0.0360702 , -0.257362 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.91237 , 0.534728 , 1.45823 ) +colvars: ( 4.21236 , 0.458529 , 1.25043 ) +colvars: ( 4.21236 , 0.458529 , 1.25043 ) +colvars: ( 5.61098 , 0.610774 , 1.66561 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.616281 , -0.0808693 , -0.371446 ) +colvars: ( -0.554208 , -0.163117 , -0.341145 ) +colvars: ( -0.504957 , -0.141314 , -0.283282 ) +colvars: ( -0.514782 , -0.190453 , -0.312224 ) +colvars: ( -0.505192 , -0.131969 , -0.279887 ) +colvars: ( -0.489805 , -0.281897 , -0.322697 ) +colvars: ( -0.456816 , -0.321986 , -0.305186 ) +colvars: ( -0.434924 , -0.428618 , -0.324653 ) +colvars: ( -0.394137 , -0.286915 , -0.228703 ) +colvars: ( -0.389424 , -0.261776 , -0.214211 ) +colvars: ( -0.345273 , -0.281379 , -0.177549 ) +colvars: ( -0.285149 , -0.244794 , -0.10304 ) +colvars: ( -0.236984 , -0.259684 , -0.0605206 ) +colvars: ( -0.304772 , -0.14227 , -0.0828934 ) +colvars: ( -0.273538 , -0.113211 , -0.0402819 ) +colvars: ( -0.359244 , -0.0852239 , -0.115362 ) +colvars: ( -0.386025 , 0.0124012 , -0.104297 ) +colvars: ( -0.436444 , 0.0597364 , -0.136473 ) +colvars: ( -0.423163 , 0.0273829 , -0.135722 ) +colvars: ( -0.411823 , 0.0837869 , -0.102439 ) +colvars: ( -0.466804 , -0.0262438 , -0.20032 ) +colvars: ( -0.500623 , -0.02764 , -0.234778 ) +colvars: ( -0.550128 , -0.092565 , -0.309646 ) +colvars: ( -0.44844 , -0.0574902 , -0.194041 ) +colvars: ( -0.455133 , -0.0136732 , -0.183732 ) +colvars: ( -0.393448 , -0.131371 , -0.16759 ) +colvars: ( -0.335847 , -0.162511 , -0.12192 ) +colvars: ( -0.285578 , -0.252156 , -0.10633 ) +colvars: ( -0.295018 , -0.0901954 , -0.0528822 ) +colvars: ( -0.281658 , -0.0716997 , -0.0322992 ) +colvars: ( -0.275665 , -0.0456524 , -0.0161714 ) +colvars: ( -0.240684 , 0.0285716 , 0.0477436 ) +colvars: ( -0.219937 , 0.0547437 , 0.0787162 ) +colvars: ( -0.284558 , 0.114817 , 0.0372456 ) +colvars: ( -0.257987 , 0.15629 , 0.0800034 ) +colvars: ( -0.353636 , 0.142825 , -0.021151 ) +colvars: ( -0.402219 , 0.218585 , -0.0404446 ) +colvars: ( -0.473196 , 0.241071 , -0.10289 ) +colvars: ( -0.413294 , 0.198924 , -0.0591888 ) +colvars: ( -0.417747 , 0.259362 , -0.040177 ) +colvars: ( -0.417417 , 0.112935 , -0.0967264 ) +colvars: ( -0.424045 , 0.0830049 , -0.115 ) +colvars: ( -0.445169 , -0.00966785 , -0.172183 ) +colvars: ( -0.357473 , 0.0717467 , -0.05261 ) +colvars: ( -0.360553 , 0.0979081 , -0.0455363 ) +colvars: ( -0.197415 , 0.104074 , 0.120466 ) +colvars: ( -0.148086 , 0.105884 , 0.17064 ) +colvars: ( -0.224281 , 0.175935 , 0.121437 ) +colvars: ( -0.295311 , 0.0311961 , -0.00602135 ) +colvars: ( -0.228738 , 0.0176059 , 0.0554637 ) +colvars: ( -0.175039 , -0.0650049 , 0.0772264 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 19. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 19. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atoms_new_colvar_forces = { ( -4.63544419501644e+00 , -4.20210469307563e-01 , -1.20898324434841e+00 ), ( -3.99299929210782e+00 , -3.55484946274648e-01 , -9.46494606331090e-01 ), ( -4.06552732790182e+00 , -3.82004235259854e-01 , -9.81780927731090e-01 ), ( -5.46646077617497e+00 , -5.42268393306697e-01 , -1.46004673915677e+00 ), ( 2.52765676023864e-01 , 1.17943473821310e-01 , 3.43374038057664e-01 ), ( 4.99757064299401e+00 , 5.97023835288657e-01 , 1.76863174513226e+00 ), ( 4.22321014388509e+00 , 4.94770460584830e-01 , 1.53441767442586e+00 ), ( -4.40146132019498e-02 , 2.68083709672712e-02 , 3.49075063476128e-01 ), ( 4.20423660521184e+00 , 4.85396409558875e-01 , 1.50414549465258e+00 ), ( 5.57273604367227e+00 , 6.21250028134693e-01 , 1.85824202630381e+00 ), ( 1.15251448703177e-02 , 3.77126122577807e-02 , 2.94890992779568e-01 ), ( 4.76902213796149e-04 , 3.15269557008686e-02 , 2.70983941329410e-01 ), ( 2.16571142784051e-02 , 4.56492628647812e-02 , 3.36366548282541e-01 ), ( 4.33758665823508e-02 , 3.62889824542237e-02 , 1.97521770142452e-01 ), ( 1.58915225452573e-02 , 2.20924654085242e-02 , 1.48337017459659e-01 ), ( 1.11770702205321e-01 , 5.62714872358337e-02 , 1.87398314401606e-01 ), ( 1.57612989988102e-01 , 6.25652553499279e-02 , 1.19302032624286e-01 ), ( 2.36887918663062e-01 , 8.88795957536135e-02 , 1.34797126490583e-01 ), ( 1.28953381376549e-01 , 4.57327536623671e-02 , 5.04928714782447e-02 ), ( 1.24527961342896e-01 , 3.71391809380055e-02 , -1.18982067115387e-02 ), ( 1.06132711925979e-01 , 3.99752107865736e-02 , 6.17277360600108e-02 ), ( 7.06836776109986e-02 , 2.24209086479583e-02 , 4.82027046087513e-03 ), ( 5.76619801736108e-02 , 2.21486419863283e-02 , 3.72507779259702e-02 ), ( -1.57033537758844e-03 , -2.91926072372384e-03 , -2.10154422166415e-02 ), ( -1.51181454784769e-02 , -1.49893684729367e-02 , -8.90624391297327e-02 ), ( -4.85798776472883e-02 , -1.11743496473575e-02 , 3.32612396381922e-02 ), ( -1.15581829917278e-01 , -3.36972984351649e-02 , 1.77256734256328e-02 ), ( -1.56830362014264e-01 , -3.76244193630479e-02 , 9.39894503345342e-02 ), ( -1.02922960304374e-01 , -3.50380799375384e-02 , -2.76655221950742e-02 ), ( -1.38884275259951e-01 , -5.26755323611779e-02 , -8.39227179726776e-02 ), ( -4.98609822060870e-02 , -1.60327515367708e-02 , -5.27262388788827e-03 ), ( -2.88445005473107e-02 , -1.42324936551007e-02 , -4.58623778592838e-02 ), ( 2.73217648587229e-02 , 8.60482871675118e-03 , 1.33078963528227e-03 ), ( 2.54461228523750e-03 , -1.38917787217629e-02 , -1.26762239167059e-01 ), ( -1.48893347255525e-02 , -2.54799046904008e-02 , -1.80266877552548e-01 ), ( 4.86756905373570e-02 , -9.21690811915205e-04 , -1.37975108490852e-01 ), ( 7.75538908664742e-02 , -6.17762008428668e-04 , -2.12485848399988e-01 ), ( 1.37812964599545e-01 , 1.92489557605193e-02 , -2.01878106175641e-01 ), ( 1.90743275152562e-02 , -2.47696484195315e-02 , -2.64852259364505e-01 ), ( 2.01420904417423e-02 , -3.23436555785761e-02 , -3.33111277628311e-01 ), ( -3.38899456892007e-02 , -3.75118991156526e-02 , -2.33419984883303e-01 ), ( -9.48700463302962e-02 , -6.11980027987171e-02 , -2.75084946294434e-01 ), ( -1.32589743279693e-01 , -6.72639097669000e-02 , -2.26716841639927e-01 ), ( -1.51638265224316e-01 , -8.12106124351630e-02 , -2.96276848845635e-01 ), ( -1.79172581375629e-01 , -9.70269974915623e-02 , -3.59316840047847e-01 ), ( -1.92801949632925e-01 , -9.45219403171258e-02 , -3.01279033292902e-01 ), ( -2.34445343723124e-01 , -1.10472638436355e-01 , -3.27792731520741e-01 ), ( -1.19212032757414e-01 , -7.25498898294642e-02 , -3.08097710642036e-01 ), ( -1.71265530471300e-01 , -8.11538179058320e-02 , -2.43360800467069e-01 ), ( -2.24045130281263e-01 , -9.90888167582585e-02 , -2.57264887939209e-01 ), ( -2.59342950021729e-01 , -1.01075112512468e-01 , -1.80135404624953e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 19, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 20 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 20, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 20, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 8.28582291037697e+00 , 4.04506123830901e-02 , -7.54196570963580e-01 ), ( 6.93477801011369e+00 , -5.51786262542508e-01 , -5.76525850220028e-01 ), ( 6.15654135511678e+00 , -3.75844216369432e-01 , 7.29702736243887e-01 ), ( 4.95083684588076e+00 , -1.63049873260700e-01 , 7.22622667146212e-01 ), ( 7.04822840425256e+00 , -2.05125822808654e+00 , -9.33838802325873e-01 ), ( 6.86298879544170e+00 , -2.63492033772352e-01 , 1.90782093039187e+00 ), ( 6.17535476862579e+00 , -1.61467873005207e-01 , 3.19447807763223e+00 ), ( 7.08038697584318e+00 , -3.54878074422017e-01 , 4.31410976849832e+00 ), ( 5.31942679106160e+00 , 1.09501065270932e+00 , 3.35178346295725e+00 ), ( 4.15930443602701e+00 , 1.02503542539263e+00 , 3.69255428523693e+00 ), ( 5.84279477371476e+00 , 2.25334627387652e+00 , 2.99025393459074e+00 ), ( 5.23840438125392e+00 , 3.57836450753976e+00 , 2.92139319672716e+00 ), ( 6.32240747113683e+00 , 4.50111704883458e+00 , 2.36542025527039e+00 ), ( 3.88181028160009e+00 , 3.70648484501399e+00 , 2.04436620458568e+00 ), ( 2.79206714766409e+00 , 4.16082999865321e+00 , 2.48770343635868e+00 ), ( 3.93862881447229e+00 , 3.23956170779748e+00 , 7.31179710249667e-01 ), ( 2.66241903927475e+00 , 3.00625645576357e+00 , -1.03744703501063e-01 ), ( 3.05292822088169e+00 , 2.70506278162700e+00 , -1.51518325748210e+00 ), ( 1.59778880440673e+00 , 2.18316923674870e+00 , 4.45871092830035e-01 ), ( 3.79300149359787e-01 , 2.58119961872434e+00 , 5.10156322737722e-01 ), ( 2.04754425768075e+00 , 1.07062955324807e+00 , 1.06969022583418e+00 ), ( 1.16903854050100e+00 , 1.16571453589181e-01 , 1.69741818249094e+00 ), ( 2.04314486967146e+00 , -1.10332707217033e+00 , 2.01056812233467e+00 ), ( 5.62094900755023e-01 , 6.11786092234871e-01 , 2.94281295395090e+00 ), ( -6.01998257745626e-01 , 3.49689451878813e-01 , 3.16156299845539e+00 ), ( 1.31668822516108e+00 , 1.34577563521962e+00 , 3.77543109832579e+00 ), ( 8.42716504335045e-01 , 1.97881846216304e+00 , 5.02541834392960e+00 ), ( 2.07967786415177e+00 , 2.68782307153212e+00 , 5.68209741884907e+00 ), ( -3.37344843382937e-01 , 2.91471449609425e+00 , 4.96800851820805e+00 ), ( -1.13708588001649e+00 , 3.06248956541986e+00 , 5.88780199616476e+00 ), ( -5.11775330469444e-01 , 3.53529724018143e+00 , 3.84632332050881e+00 ), ( -1.51803710380555e+00 , 4.53919531397891e+00 , 3.44428420949964e+00 ), ( -6.99624398507824e-01 , 5.41439381873403e+00 , 2.46379309418166e+00 ), ( -2.76022882703025e+00 , 3.88950508193880e+00 , 2.89503343674671e+00 ), ( -3.81748583539279e+00 , 4.50991617428220e+00 , 2.81470056115434e+00 ), ( -2.62519097171536e+00 , 2.67328985787292e+00 , 2.40149432612104e+00 ), ( -3.77272853459107e+00 , 1.80371700509528e+00 , 1.99837671356181e+00 ), ( -3.38871455409835e+00 , 8.86717902389388e-01 , 8.74187404183740e-01 ), ( -4.32255998423662e+00 , 1.07002307118320e+00 , 3.21229150831233e+00 ), ( -5.49998182564857e+00 , 8.18774137488647e-01 , 3.32931951742222e+00 ), ( -3.36904919026829e+00 , 6.91596678914569e-01 , 4.20423547278276e+00 ), ( -3.70107974783840e+00 , 4.62390697929325e-02 , 5.43421582390532e+00 ), ( -2.39033524019067e+00 , -3.17074981101270e-01 , 6.17020508472989e+00 ), ( -4.46175815649799e+00 , 9.86843632633000e-01 , 6.43971260203245e+00 ), ( -5.35881205025882e+00 , 5.98149506814076e-01 , 7.21810107144495e+00 ), ( -6.23824517782367e+00 , 3.60552411038818e+00 , 6.73377298524042e+00 ), ( -6.96012228941194e+00 , 4.29779275147404e+00 , 7.47577581613682e+00 ), ( -6.74134298930255e+00 , 3.18228858940767e+00 , 5.50798663651289e+00 ), ( -4.12867862719011e+00 , 2.24624582899316e+00 , 6.40977342732153e+00 ), ( -4.80883733708504e+00 , 3.20667234951756e+00 , 7.24182070504870e+00 ), ( -4.09497949178953e+00 , 4.57553386748493e+00 , 7.28289299072206e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +colvars: Step 20, atom_groups_refcount[size = 0] = +colvars: Step 20, atom_groups_masses[size = 0] = +colvars: Step 20, atom_groups_charges[size = 0] = +colvars: Step 20, atom_groups_coms[size = 0] = +colvars: Step 20, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_ids[size = 0] = +colvars: Step 20, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 20 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.6088 , 1.95578 , -15.1464 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.6088 , 1.95578 , -15.1464 ) to colvar "one". +colvars: Adding total bias energy: 44.4525 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.6088 , 1.95578 , -15.1464 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.91515 , -0.533261 , -1.45224 ) +colvars: ( -4.21474 , -0.457271 , -1.24529 ) +colvars: ( -4.21474 , -0.457271 , -1.24529 ) +colvars: ( -5.61415 , -0.609098 , -1.65877 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.892544 , 0.19549 , 0.619241 ) +colvars: ( 0.773074 , 0.266213 , 0.643516 ) +colvars: ( 0.757152 , 0.259324 , 0.625094 ) +colvars: ( 0.661335 , 0.266975 , 0.579425 ) +colvars: ( 0.649454 , 0.200472 , 0.484222 ) +colvars: ( 0.574898 , 0.344142 , 0.631501 ) +colvars: ( 0.46778 , 0.358122 , 0.587647 ) +colvars: ( 0.391169 , 0.455275 , 0.67198 ) +colvars: ( 0.386205 , 0.313656 , 0.481093 ) +colvars: ( 0.351459 , 0.272107 , 0.405694 ) +colvars: ( 0.356948 , 0.318969 , 0.471099 ) +colvars: ( 0.285831 , 0.276183 , 0.372867 ) +colvars: ( 0.258798 , 0.3052 , 0.395635 ) +colvars: ( 0.348239 , 0.178457 , 0.2795 ) +colvars: ( 0.289613 , 0.135181 , 0.187896 ) +colvars: ( 0.470901 , 0.14145 , 0.301842 ) +colvars: ( 0.543399 , 0.0501585 , 0.222894 ) +colvars: ( 0.672857 , 0.0291993 , 0.270498 ) +colvars: ( 0.551951 , 0.0183336 , 0.18563 ) +colvars: ( 0.536209 , -0.0466654 , 0.0901744 ) +colvars: ( 0.572815 , 0.0661925 , 0.261317 ) +colvars: ( 0.571276 , 0.0500177 , 0.238949 ) +colvars: ( 0.607772 , 0.114667 , 0.346033 ) +colvars: ( 0.447058 , 0.0544713 , 0.172488 ) +colvars: ( 0.440246 , -0.00142063 , 0.0943242 ) +colvars: ( 0.345197 , 0.120053 , 0.200198 ) +colvars: ( 0.220799 , 0.128616 , 0.139087 ) +colvars: ( 0.129402 , 0.214294 , 0.19957 ) +colvars: ( 0.192616 , 0.0549651 , 0.0248969 ) +colvars: ( 0.143405 , 0.018808 , -0.0517726 ) +colvars: ( 0.226186 , 0.0294603 , 0.0105991 ) +colvars: ( 0.212182 , -0.0429517 , -0.0936848 ) +colvars: ( 0.247451 , -0.0462529 , -0.0775182 ) +colvars: ( 0.287355 , -0.128824 , -0.16388 ) +colvars: ( 0.243414 , -0.181898 , -0.259935 ) +colvars: ( 0.402414 , -0.143819 , -0.116748 ) +colvars: ( 0.479789 , -0.219244 , -0.17179 ) +colvars: ( 0.610834 , -0.221812 , -0.0988481 ) +colvars: ( 0.432546 , -0.223771 , -0.205325 ) +colvars: ( 0.438072 , -0.291778 , -0.292383 ) +colvars: ( 0.383843 , -0.150562 , -0.136519 ) +colvars: ( 0.329659 , -0.144357 , -0.159851 ) +colvars: ( 0.313151 , -0.0577764 , -0.0545361 ) +colvars: ( 0.206501 , -0.15316 , -0.243293 ) +colvars: ( 0.182128 , -0.195153 , -0.313237 ) +colvars: ( 0.00545045 , -0.19885 , -0.421084 ) +colvars: ( -0.0853872 , -0.216646 , -0.497632 ) +colvars: ( 0.105698 , -0.248684 , -0.428829 ) +colvars: ( 0.124781 , -0.112578 , -0.237034 ) +colvars: ( 0.00559788 , -0.116969 , -0.312302 ) +colvars: ( -0.0832935 , -0.0363805 , -0.257115 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.91515 , 0.533261 , 1.45224 ) +colvars: ( 4.21474 , 0.457271 , 1.24529 ) +colvars: ( 4.21474 , 0.457271 , 1.24529 ) +colvars: ( 5.61415 , 0.609098 , 1.65877 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.615911 , -0.0809403 , -0.370289 ) +colvars: ( -0.553936 , -0.163279 , -0.339783 ) +colvars: ( -0.504483 , -0.14143 , -0.281796 ) +colvars: ( -0.514701 , -0.190631 , -0.31095 ) +colvars: ( -0.505106 , -0.132058 , -0.278819 ) +colvars: ( -0.489899 , -0.282191 , -0.321263 ) +colvars: ( -0.457119 , -0.322318 , -0.303811 ) +colvars: ( -0.435381 , -0.42909 , -0.323043 ) +colvars: ( -0.394403 , -0.287171 , -0.227415 ) +colvars: ( -0.389791 , -0.261989 , -0.213114 ) +colvars: ( -0.345387 , -0.281611 , -0.176126 ) +colvars: ( -0.285203 , -0.244949 , -0.101686 ) +colvars: ( -0.23688 , -0.259846 , -0.058954 ) +colvars: ( -0.30471 , -0.142288 , -0.0817978 ) +colvars: ( -0.273523 , -0.113172 , -0.0393358 ) +colvars: ( -0.359032 , -0.0851872 , -0.114328 ) +colvars: ( -0.385698 , 0.0125647 , -0.103504 ) +colvars: ( -0.43592 , 0.0599408 , -0.135661 ) +colvars: ( -0.423002 , 0.0275581 , -0.13515 ) +colvars: ( -0.411661 , 0.0840489 , -0.10207 ) +colvars: ( -0.466795 , -0.0261598 , -0.199708 ) +colvars: ( -0.500798 , -0.0275661 , -0.234345 ) +colvars: ( -0.55043 , -0.0926022 , -0.309107 ) +colvars: ( -0.448784 , -0.057432 , -0.193664 ) +colvars: ( -0.455539 , -0.013552 , -0.183575 ) +colvars: ( -0.393864 , -0.131394 , -0.167013 ) +colvars: ( -0.336404 , -0.16255 , -0.121366 ) +colvars: ( -0.286194 , -0.252303 , -0.105507 ) +colvars: ( -0.295464 , -0.0901165 , -0.0524782 ) +colvars: ( -0.282212 , -0.0715846 , -0.032067 ) +colvars: ( -0.275892 , -0.045508 , -0.0157091 ) +colvars: ( -0.240779 , 0.0288343 , 0.048069 ) +colvars: ( -0.219798 , 0.0550453 , 0.0791805 ) +colvars: ( -0.284619 , 0.115186 , 0.0372899 ) +colvars: ( -0.258068 , 0.156731 , 0.0798802 ) +colvars: ( -0.35365 , 0.143204 , -0.0211658 ) +colvars: ( -0.402215 , 0.219052 , -0.0407192 ) +colvars: ( -0.473097 , 0.241538 , -0.103157 ) +colvars: ( -0.413517 , 0.199366 , -0.0596175 ) +colvars: ( -0.417976 , 0.25989 , -0.0408311 ) +colvars: ( -0.417832 , 0.113257 , -0.0970347 ) +colvars: ( -0.424688 , 0.0832879 , -0.115426 ) +colvars: ( -0.445978 , -0.00952294 , -0.17244 ) +colvars: ( -0.358207 , 0.0720446 , -0.0530801 ) +colvars: ( -0.361391 , 0.0982463 , -0.0462049 ) +colvars: ( -0.198027 , 0.104482 , 0.120009 ) +colvars: ( -0.148764 , 0.106318 , 0.170115 ) +colvars: ( -0.224679 , 0.176429 , 0.120931 ) +colvars: ( -0.296008 , 0.0314599 , -0.00630443 ) +colvars: ( -0.229511 , 0.0178807 , 0.0551591 ) +colvars: ( -0.175844 , -0.0648266 , 0.0771928 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 20. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -4.63851454459905e+00 , -4.18710833064850e-01 , -1.20328608426652e+00 ), ( -3.99559989640659e+00 , -3.54336474175720e-01 , -9.41559888235754e-01 ), ( -4.06810357739189e+00 , -3.80926713958037e-01 , -9.76817699772113e-01 ), ( -5.46980368326514e+00 , -5.40683985020084e-01 , -1.45336332622448e+00 ), ( 2.52668502795200e-01 , 1.17894094436429e-01 , 3.43297404486922e-01 ), ( 5.00014590643842e+00 , 5.95211961482009e-01 , 1.76247508244524e+00 ), ( 4.22539890920215e+00 , 4.93075099844339e-01 , 1.52912952520700e+00 ), ( -4.42117205218343e-02 , 2.61849910581687e-02 , 3.48936847549760e-01 ), ( 4.20654020656410e+00 , 4.83756625787825e-01 , 1.49897132736399e+00 ), ( 5.57582044888118e+00 , 6.19216324851961e-01 , 1.85134641932113e+00 ), ( 1.15606722969959e-02 , 3.73582371308533e-02 , 2.94972551667663e-01 ), ( 6.27937109112076e-04 , 3.12340160260255e-02 , 2.71180143655928e-01 ), ( 2.19173365638969e-02 , 4.53538862226682e-02 , 3.36681036424671e-01 ), ( 4.35287412741041e-02 , 3.61696681282234e-02 , 1.97702509024789e-01 ), ( 1.60900816481230e-02 , 2.20091820921404e-02 , 1.48559775115973e-01 ), ( 1.11869449595165e-01 , 5.62631531725342e-02 , 1.87513672922987e-01 ), ( 1.57700920362817e-01 , 6.27232419132576e-02 , 1.19389577713856e-01 ), ( 2.36936463271923e-01 , 8.91401887092676e-02 , 1.34836894262539e-01 ), ( 1.28948776005967e-01 , 4.58916180710906e-02 , 5.04794295830226e-02 ), ( 1.24548587393342e-01 , 3.73834994690693e-02 , -1.18954687815839e-02 ), ( 1.06019698806145e-01 , 4.00326507775761e-02 , 6.16092423921068e-02 ), ( 7.04782471949013e-02 , 2.24515586964271e-02 , 4.60369604053695e-03 ), ( 5.73422381960390e-02 , 2.20646170469042e-02 , 3.69252747449674e-02 ), ( -1.72611395560524e-03 , -2.96077010773500e-03 , -2.11764063442688e-02 ), ( -1.52922851265740e-02 , -1.49726615376669e-02 , -8.92510974662055e-02 ), ( -4.86671260953066e-02 , -1.13413226333090e-02 , 3.31845028045236e-02 ), ( -1.15605077666369e-01 , -3.39346522378186e-02 , 1.77200417262677e-02 ), ( -1.56792026456609e-01 , -3.80091057503520e-02 , 9.40637658323593e-02 ), ( -1.02848641736711e-01 , -3.51514140984507e-02 , -2.75812107087965e-02 ), ( -1.38806884416938e-01 , -5.27766427227216e-02 , -8.38395789565467e-02 ), ( -4.97061267723764e-02 , -1.60476509528009e-02 , -5.11007628540459e-03 ), ( -2.85976059219338e-02 , -1.41173315546320e-02 , -4.56158111816652e-02 ), ( 2.76522679529432e-02 , 8.79242656069489e-03 , 1.66225761229807e-03 ), ( 2.73532411285460e-03 , -1.36382491455301e-02 , -1.26589601375052e-01 ), ( -1.46538330736033e-02 , -2.51672766893284e-02 , -1.80055129011821e-01 ), ( 4.87645210478707e-02 , -6.15426656884632e-04 , -1.37913496336073e-01 ), ( 7.75743232463488e-02 , -1.91225606735068e-04 , -2.12509192428131e-01 ), ( 1.37737148977943e-01 , 1.97267169501107e-02 , -2.02005130353156e-01 ), ( 1.90294174661668e-02 , -2.44049904625063e-02 , -2.64942523670217e-01 ), ( 2.00953061744231e-02 , -3.18876654614701e-02 , -3.33214475874042e-01 ), ( -3.39893131361256e-02 , -3.73055310094134e-02 , -2.33553485918890e-01 ), ( -9.50287381727212e-02 , -6.10695052311506e-02 , -2.75277236233374e-01 ), ( -1.32826616258851e-01 , -6.72993193787387e-02 , -2.26975689078502e-01 ), ( -1.51705844975594e-01 , -8.11153781239003e-02 , -2.96372806931386e-01 ), ( -1.79263034470665e-01 , -9.69067785137090e-02 , -3.59442438261914e-01 ), ( -1.92577034615937e-01 , -9.43678359874191e-02 , -3.01074097881565e-01 ), ( -2.34151572355940e-01 , -1.10327571437585e-01 , -3.27516835071365e-01 ), ( -1.18981164358574e-01 , -7.22543491267554e-02 , -3.07897440415716e-01 ), ( -1.71227554375326e-01 , -8.11181099169558e-02 , -2.43338813862098e-01 ), ( -2.23913463549683e-01 , -9.90878668961794e-02 , -2.57143314677739e-01 ), ( -2.59137952902184e-01 , -1.01207120969136e-01 , -1.79922622294137e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Saving collective variables state to "test.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped new file mode 100644 index 000000000..39c658b7f --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,17 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x ( -0.3045417105333 , -0.00019915241487762 , 0.95249897999093 ) +} + +restraint { + configuration { + step 20 + name harmonic1 + } +} + diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj new file mode 100644 index 000000000..e14fbd39b --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one + 0 ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ) ( 2.63141320070998e+01 , 1.79666571613238e+00 , -1.49056671814885e+01 ) + 1 ( -3.39359239792396e-01 , 6.97253156444326e-03 , 9.40631006384071e-01 ) ( 2.63051862548186e+01 , 1.81234951460820e+00 , -1.49090198358873e+01 ) + 2 ( -3.38680441300733e-01 , 6.30491679893380e-03 , 9.40880336017551e-01 ) ( 2.62916102849853e+01 , 1.82570180991839e+00 , -1.49140064285569e+01 ) + 3 ( -3.37759603496395e-01 , 5.75914840711148e-03 , 9.41214790818537e-01 ) ( 2.62731935288986e+01 , 1.83661717775484e+00 , -1.49206955245766e+01 ) + 4 ( -3.36592560477046e-01 , 5.33466425476265e-03 , 9.41635274184647e-01 ) ( 2.62498526685116e+01 , 1.84510686080181e+00 , -1.49291051918988e+01 ) + 5 ( -3.35182699996778e-01 , 5.02452781962055e-03 , 9.42139751705160e-01 ) ( 2.62216554589062e+01 , 1.85130958950466e+00 , -1.49391947423091e+01 ) + 6 ( -3.33541437426750e-01 , 4.81523415673580e-03 , 9.42723142306008e-01 ) ( 2.61888302075057e+01 , 1.85549546276235e+00 , -1.49508625543260e+01 ) + 7 ( -3.31688046920632e-01 , 4.68707413595258e-03 , 9.43377480580293e-01 ) ( 2.61517623973833e+01 , 1.85805866317801e+00 , -1.49639493198117e+01 ) + 8 ( -3.29649003636170e-01 , 4.61519105247550e-03 , 9.44092280666053e-01 ) ( 2.61109815316941e+01 , 1.85949632484756e+00 , -1.49782453215269e+01 ) + 9 ( -3.27457007407554e-01 , 4.57131359996204e-03 , 9.44855021361299e-01 ) ( 2.60671416071217e+01 , 1.86037387389783e+00 , -1.49935001354318e+01 ) + 10 ( -3.25149814022648e-01 , 4.52596031009924e-03 , 9.45651687527870e-01 ) ( 2.60209977394236e+01 , 1.86128093969508e+00 , -1.50094334587633e+01 ) + 11 ( -3.22768924320888e-01 , 4.45076971931406e-03 , 9.46467332844427e-01 ) ( 2.59733799453884e+01 , 1.86278475151079e+00 , -1.50257463650944e+01 ) + 12 ( -3.20358118183599e-01 , 4.32056543368708e-03 , 9.47286656101624e-01 ) ( 2.59251638226427e+01 , 1.86538883722332e+00 , -1.50421328302383e+01 ) + 13 ( -3.17961771860725e-01 , 4.11480979755661e-03 , 9.48094604971212e-01 ) ( 2.58772368961852e+01 , 1.86950394994593e+00 , -1.50582918076301e+01 ) + 14 ( -3.15622953688594e-01 , 3.81824775894985e-03 , 9.48877005775216e-01 ) ( 2.58304605327425e+01 , 1.87543519071807e+00 , -1.50739398237102e+01 ) + 15 ( -3.13381355030095e-01 , 3.42072155991049e-03 , 9.49621200786667e-01 ) ( 2.57856285595726e+01 , 1.88338571469886e+00 , -1.50888237239392e+01 ) + 16 ( -3.11271197951965e-01 , 2.91633047576440e-03 , 9.50316650565539e-01 ) ( 2.57434254180100e+01 , 1.89347353638178e+00 , -1.51027327195166e+01 ) + 17 ( -3.09319308134653e-01 , 2.30226602992589e-03 , 9.50955448581177e-01 ) ( 2.57043876216637e+01 , 1.90575482529855e+00 , -1.51155086798294e+01 ) + 18 ( -3.07543552262695e-01 , 1.57772719634005e-03 , 9.51532697409047e-01 ) ( 2.56688725042246e+01 , 1.92024560197027e+00 , -1.51270536563868e+01 ) + 19 ( -3.05951823016640e-01 , 7.43277606547324e-04 , 9.52046705540854e-01 ) ( 2.56370379193035e+01 , 1.93693459376612e+00 , -1.51373338190230e+01 ) + 20 ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ) ( 2.56088356696367e+01 , 1.95578319419462e+00 , -1.51463793080245e+01 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..ddc57f269 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out @@ -0,0 +1,6309 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Called colvarcript::init_commands() +colvars: Defined command "cv_addenergy", with help string: +colvars: Add an energy to the MD engine (no effect in VMD) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: E : float - Amount of energy to add +colvars: Defined command "cv_bias", with help string: +colvars: Prefix for bias-specific commands +colvars: Defined command "cv_colvar", with help string: +colvars: Prefix for colvar-specific commands +colvars: Defined command "cv_config", with help string: +colvars: Read configuration from the given string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf : string - Configuration string +colvars: Defined command "cv_configfile", with help string: +colvars: Read configuration from a file +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf_file : string - Path to configuration file +colvars: Defined command "cv_delete", with help string: +colvars: Delete this Colvars module instance (VMD only) +colvars: Defined command "cv_featurereport", with help string: +colvars: Return a summary of Colvars features used so far and their citations +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: report : string - Feature report and citations +colvars: +colvars: Defined command "cv_frame", with help string: +colvars: Get or set current frame number (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: frame : integer - Frame number (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: frame : integer - Frame number +colvars: +colvars: Defined command "cv_getatomappliedforces", with help string: +colvars: Get the list of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic forces +colvars: +colvars: Defined command "cv_getatomappliedforcesmax", with help string: +colvars: Get the maximum norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesmaxid", with help string: +colvars: Get the atom ID with the largest applied force +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: id : int - ID of the atom with the maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesrms", with help string: +colvars: Get the root-mean-square norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - RMS atomic force +colvars: +colvars: Defined command "cv_resetatomappliedforces", with help string: +colvars: Reset forces applied by Colvars to atoms +colvars: Defined command "cv_getatomids", with help string: +colvars: Get the list of indices of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "cv_getatomcharges", with help string: +colvars: Get the list of charges of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: charges : array of floats - Atomic charges +colvars: +colvars: Defined command "cv_getatommasses", with help string: +colvars: Get the list of masses of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: masses : array of floats - Atomic masses +colvars: +colvars: Defined command "cv_getatompositions", with help string: +colvars: Get the list of cached positions of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: positions : array of arrays of floats - Atomic positions +colvars: +colvars: Defined command "cv_getatomtotalforces", with help string: +colvars: Get the list of cached total forces of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic total foces +colvars: +colvars: Defined command "cv_getconfig", with help string: +colvars: Get the module's configuration string read so far +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "cv_getenergy", with help string: +colvars: Get the current Colvars energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Amount of energy (internal units) +colvars: +colvars: Defined command "cv_getnumactiveatomgroups", with help string: +colvars: Get the number of atom groups that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atom groups +colvars: +colvars: Defined command "cv_getnumactiveatoms", with help string: +colvars: Get the number of atoms that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getnumatoms", with help string: +colvars: Get the number of requested atoms, including those not in use now +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getstepabsolute", with help string: +colvars: Get the current step number of the simulation (including restarts) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Absolute step number +colvars: +colvars: Defined command "cv_getsteprelative", with help string: +colvars: Get the current step number from the start of this job +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Relative step number +colvars: +colvars: Defined command "cv_help", with help string: +colvars: Get the help string of the Colvars scripting interface +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "cv_languageversion", with help string: +colvars: Get the C++ language version number +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - C++ language version +colvars: +colvars: Defined command "cv_list", with help string: +colvars: Return a list of all variables or biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: param : string - "colvars" or "biases"; default is "colvars" (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of elements +colvars: +colvars: Defined command "cv_listcommands", with help string: +colvars: Get the list of script functions, prefixed with "cv_", "colvar_" or "bias_" +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of commands +colvars: +colvars: Defined command "cv_listindexfiles", with help string: +colvars: Get a list of the index files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of index file names +colvars: +colvars: Defined command "cv_listinputfiles", with help string: +colvars: Get a list of all input/configuration files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of file names +colvars: +colvars: Defined command "cv_load", with help string: +colvars: Load data from a state file into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Path to existing state file or input prefix +colvars: Defined command "cv_loadfromstring", with help string: +colvars: Load state data from a string into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "cv_molid", with help string: +colvars: Get or set the molecule ID on which Colvars is defined (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: molid : integer - New molecule ID; -1 means undefined (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: molid : integer - Current molecule ID +colvars: +colvars: Defined command "cv_printframe", with help string: +colvars: Return the values that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: values : string - The values +colvars: +colvars: Defined command "cv_printframelabels", with help string: +colvars: Return the labels that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Labels : string - The labels +colvars: +colvars: Defined command "cv_reset", with help string: +colvars: Delete all internal configuration +colvars: Defined command "cv_resetindexgroups", with help string: +colvars: Clear the index groups loaded so far, allowing to replace them +colvars: Defined command "cv_save", with help string: +colvars: Change the prefix of all output files and save them +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Output prefix with trailing ".colvars.state" gets removed) +colvars: Defined command "cv_savetostring", with help string: +colvars: Write the Colvars state to a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The saved state +colvars: +colvars: Defined command "cv_targettemperature", with help string: +colvars: Get/set target temperature, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: T : float - New target temperature in K (internal use) (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: T : float - Current target temperature in K +colvars: +colvars: Defined command "cv_timestep", with help string: +colvars: Get/set integration timestep, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: dt : float - New integration timestep in MD engine units (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: dt : float - Current integration timestep in MD engine units +colvars: +colvars: Defined command "cv_units", with help string: +colvars: Get or set the current Colvars unit system +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: units : string - The new unit system (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: units : string - The current unit system +colvars: +colvars: Defined command "cv_update", with help string: +colvars: Recalculate colvars and biases +colvars: Defined command "cv_version", with help string: +colvars: Get the Colvars Module version string +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - Colvars version +colvars: +colvars: Defined command "colvar_addforce", with help string: +colvars: Apply the given force onto this colvar (no effects outside run) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: force : float or array - Applied force; must match colvar dimensionality +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float or array - Applied force; matches colvar dimensionality +colvars: +colvars: Defined command "colvar_communicateforces", with help string: +colvars: Communicate bias forces from this colvar to atoms +colvars: Defined command "colvar_cvcflags", with help string: +colvars: Enable or disable individual components by setting their active flags +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: flags : integer array - Zero/nonzero value disables/enables the CVC +colvars: Defined command "colvar_delete", with help string: +colvars: Delete this colvar, along with all biases that depend on it +colvars: Defined command "colvar_get", with help string: +colvars: Get the value of the given feature for this colvar +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "colvar_getappliedforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Applied force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_resetbiasforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: Defined command "colvar_getatomgroups", with help string: +colvars: Return the atom indices used by this colvar as a list of lists +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: groups : array of arrays of ints - Atom indices +colvars: +colvars: Defined command "colvar_getatomids", with help string: +colvars: Return the list of atom indices used by this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "colvar_getconfig", with help string: +colvars: Return the configuration string of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "colvar_getgradients", with help string: +colvars: Return the atomic gradients of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: gradients : array of arrays of floats - Atomic gradients +colvars: +colvars: Defined command "colvar_gettotalforce", with help string: +colvars: Return the sum of internal and external forces to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Total force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_getvolmapids", with help string: +colvars: Return the list of volumetric map indices used by this colvar +colvars: Defined command "colvar_help", with help string: +colvars: Get a help summary or the help string of one colvar subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "colvar_modifycvcs", with help string: +colvars: Modify configuration of individual components by passing string arguments +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: confs : sequence of strings - New configurations; empty strings are skipped +colvars: Defined command "colvar_run_ave", with help string: +colvars: Get the current running average of the value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Averaged value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_set", with help string: +colvars: Set the given feature of this colvar to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "colvar_state", with help string: +colvars: Print a string representation of the feature state of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The feature state +colvars: +colvars: Defined command "colvar_type", with help string: +colvars: Get the type description of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type description +colvars: +colvars: Defined command "colvar_update", with help string: +colvars: Recompute this colvar and return its up-to-date value +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_value", with help string: +colvars: Get the current value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_width", with help string: +colvars: Get the width of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: width : float - Value of the width +colvars: +colvars: Defined command "bias_bin", with help string: +colvars: Get the current grid bin index (flattened if more than 1d) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: bin : integer - Bin index +colvars: +colvars: Defined command "bias_bincount", with help string: +colvars: Get the number of samples at the given grid bin (1D ABF only for now) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: index : integer - Grid index; defaults to current bin (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: samples : integer - Number of samples +colvars: +colvars: Defined command "bias_local_sample_count", with help string: +colvars: Get the number of samples around the current binsamples : integer - Number of samples +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: radius : integer - Sum over radius bins around current bin (optional) +colvars: Defined command "bias_binnum", with help string: +colvars: Get the total number of grid points of this bias (1D ABF only for now) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Bins : integer - Number of grid points +colvars: +colvars: Defined command "bias_delete", with help string: +colvars: Delete this bias +colvars: Defined command "bias_energy", with help string: +colvars: Get the current energy of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Defined command "bias_get", with help string: +colvars: Get the value of the given feature for this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "bias_getconfig", with help string: +colvars: Return the configuration string of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "bias_help", with help string: +colvars: Get a help summary or the help string of one bias subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "bias_load", with help string: +colvars: Load data into this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Read from a file with this name or prefix +colvars: Defined command "bias_loadfromstring", with help string: +colvars: Load state data into this bias from a string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "bias_save", with help string: +colvars: Save data from this bias into a file with the given prefix +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Prefix for the state file of this bias +colvars: Defined command "bias_savetostring", with help string: +colvars: Save data from this bias into a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The bias state +colvars: +colvars: Defined command "bias_set", with help string: +colvars: Set the given feature of this bias to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "bias_share", with help string: +colvars: Share bias information with other replicas (multiple-walker scheme) +colvars: Defined command "bias_state", with help string: +colvars: Print a string representation of the feature state of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - String representation of the bias features +colvars: +colvars: Defined command "bias_type", with help string: +colvars: Print the type of this bias object +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type of this bias object (e.g. metadynamics) +colvars: +colvars: Defined command "bias_update", with help string: +colvars: Recompute this bias and return its up-to-date energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Called script run with 3 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: configfile +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: test.in +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: Executing script function "cv_configfile" +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: Looking for the keyword "logLevel" and its value. +colvars: Keyword "logLevel" not found. +colvars: Looking for the keyword "units" and its value. +colvars: Keyword "units" not found. +colvars: # units = "" [default] +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword value = "index.ndx". +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword "indexFile" not found. +colvars: Looking for the keyword "smp" and its value. +colvars: Keyword "smp" not found. +colvars: # smp = on [default] +colvars: Looking for the keyword "analysis" and its value. +colvars: Keyword "analysis" not found. +colvars: Looking for the keyword "debugGradientsStepSize" and its value. +colvars: Keyword "debugGradientsStepSize" not found. +colvars: Looking for the keyword "monitorEigenvalueCrossing" and its value. +colvars: Keyword "monitorEigenvalueCrossing" not found. +colvars: Looking for the keyword "eigenvalueCrossingThreshold" and its value. +colvars: Keyword "eigenvalueCrossingThreshold" not found. +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword value = "1". +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword "colvarsTrajFrequency" not found. +colvars: # colvarsTrajFrequency = 1 +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword value = "10". +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword "colvarsRestartFrequency" not found. +colvars: # colvarsRestartFrequency = 10 +colvars: Looking for the keyword "scriptedColvarForces" and its value. +colvars: Keyword "scriptedColvarForces" not found. +colvars: # scriptedColvarForces = off [default] +colvars: Looking for the keyword "scriptingAfterBiases" and its value. +colvars: Keyword "scriptingAfterBiases" not found. +colvars: # scriptingAfterBiases = off [default] +colvars: Looking for the keyword "sourceTclFile" and its value. +colvars: Keyword "sourceTclFile" not found. +colvars: # sourceTclFile = "" [default] +colvars: Initializing the collective variables. +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "one" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword value = " +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Initializing a new "distanceDir" component, with configuration: +colvars: +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: unnamed cvc of type "distance" enabling "defined_lower_boundary" +colvars: DEPS: feature "defined_lower_boundary" in unnamed cvc of type "distance" enabled, ref_count = 1. +colvars: DEPS: unnamed cvc of type "distance" enabling "function_of_centers_of_mass" +colvars: DEPS: feature "function_of_centers_of_mass" in unnamed cvc of type "distance" enabled, ref_count = 1. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "function_of_centers_of_mass" +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "distanceDir" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "group1" and its value. +colvars: Keyword value = " +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" +colvars: scalable_calculation_of_centers_of_mass requires exclude explicit_gradient +colvars: scalable_calculation_of_centers_of_mass requires self scalable_calculation +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation" +colvars: scalable_calculation requires exclude explicit_gradient +colvars: DEPS: feature "scalable_calculation" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. +colvars: scalable_calculation_of_centers_of_mass requires self function_of_centers_of_mass +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "function_of_centers_of_mass" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "scalable_calculation_of_centers_of_mass" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. +colvars: Initializing atom group "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group group1 +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group group1 +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = on +colvars: DEPS: atom group group1 enabling "center_to_reference" +colvars: DEPS: feature "center_to_reference" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group group1 +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = on +colvars: DEPS: atom group group1 enabling "rotate_to_origin" +colvars: DEPS: feature "rotate_to_origin" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group1" +colvars: Adding atom 1 for collective variables calculation. +colvars: Adding atom 4 for collective variables calculation. +colvars: Adding atom 10 for collective variables calculation. +colvars: Adding atom 11 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "refPositionsGroup" and its value. +colvars: Keyword "refPositionsGroup" not found. +colvars: Looking for the keyword "fittingGroup" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Within atom group "group1": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Adding atom 6 for collective variables calculation. +colvars: Adding atom 12 for collective variables calculation. +colvars: Adding atom 14 for collective variables calculation. +colvars: Adding atom 16 for collective variables calculation. +colvars: Adding atom 20 for collective variables calculation. +colvars: Adding atom 21 for collective variables calculation. +colvars: Adding atom 22 for collective variables calculation. +colvars: Adding atom 24 for collective variables calculation. +colvars: Adding atom 26 for collective variables calculation. +colvars: Adding atom 30 for collective variables calculation. +colvars: Adding atom 31 for collective variables calculation. +colvars: Adding atom 32 for collective variables calculation. +colvars: Adding atom 34 for collective variables calculation. +colvars: Adding atom 36 for collective variables calculation. +colvars: Adding atom 40 for collective variables calculation. +colvars: Adding atom 41 for collective variables calculation. +colvars: Adding atom 42 for collective variables calculation. +colvars: Adding atom 44 for collective variables calculation. +colvars: Adding atom 46 for collective variables calculation. +colvars: Adding atom 50 for collective variables calculation. +colvars: Adding atom 51 for collective variables calculation. +colvars: Adding atom 52 for collective variables calculation. +colvars: Adding atom 54 for collective variables calculation. +colvars: Adding atom 56 for collective variables calculation. +colvars: Adding atom 60 for collective variables calculation. +colvars: Adding atom 61 for collective variables calculation. +colvars: Adding atom 62 for collective variables calculation. +colvars: Adding atom 64 for collective variables calculation. +colvars: Adding atom 66 for collective variables calculation. +colvars: Adding atom 70 for collective variables calculation. +colvars: Adding atom 71 for collective variables calculation. +colvars: Adding atom 72 for collective variables calculation. +colvars: Adding atom 74 for collective variables calculation. +colvars: Adding atom 76 for collective variables calculation. +colvars: Adding atom 80 for collective variables calculation. +colvars: Adding atom 81 for collective variables calculation. +colvars: Adding atom 82 for collective variables calculation. +colvars: Adding atom 84 for collective variables calculation. +colvars: Adding atom 86 for collective variables calculation. +colvars: Adding atom 90 for collective variables calculation. +colvars: Adding atom 91 for collective variables calculation. +colvars: Adding atom 92 for collective variables calculation. +colvars: Adding atom 93 for collective variables calculation. +colvars: Adding atom 94 for collective variables calculation. +colvars: Adding atom 97 for collective variables calculation. +colvars: Adding atom 99 for collective variables calculation. +colvars: Adding atom 101 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group group1 enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. +colvars: Warning: atom group "group1" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group group1 enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group group1 enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group group1 enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group group1 enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "group1". +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. +colvars: Configuration string for "group1": " +colvars: +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "group2" and its value. +colvars: Keyword value = " +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" +colvars: Initializing atom group "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group group2 +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group group2 +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = on +colvars: DEPS: atom group group2 enabling "center_to_reference" +colvars: DEPS: feature "center_to_reference" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group group2 +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = on +colvars: DEPS: atom group group2 enabling "rotate_to_origin" +colvars: DEPS: feature "rotate_to_origin" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group2" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "refPositionsGroup" and its value. +colvars: Keyword "refPositionsGroup" not found. +colvars: Looking for the keyword "fittingGroup" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Within atom group "group2": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group group2 enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: atom group "group2" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group group2 enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group group2 enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group group2 enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "group2". +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" +colvars: Configuration string for "group2": " +colvars: +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "oneSiteSystemForce" and its value. +colvars: Keyword "oneSiteSystemForce" not found. +colvars: # oneSiteSystemForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Looking for the keyword "oneSiteTotalForce" and its value. +colvars: Keyword "oneSiteTotalForce" not found. +colvars: # oneSiteTotalForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Configuration string for "distanceDir": " +colvars: +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: Initializing the collective variables biases. +colvars: Looking for the keyword "abf" and its value. +colvars: Keyword "abf" not found. +colvars: Looking for the keyword "abmd" and its value. +colvars: Keyword "abmd" not found. +colvars: Looking for the keyword "ALB" and its value. +colvars: Keyword "ALB" not found. +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword value = " +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "harmonic1" [default] +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword "colvars" not found. +colvars: # colvars = { one } +colvars: Applying this bias to collective variable "one". +colvars: Looking for the keyword "stepZeroData" and its value. +colvars: Keyword "stepZeroData" not found. +colvars: # stepZeroData = off [default] +colvars: DEPS: disabling feature "step_zero_data" in bias harmonic1 +colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword "outputEnergy" not found. +colvars: # outputEnergy = off [default] +colvars: Looking for the keyword "outputFreq" and its value. +colvars: Keyword "outputFreq" not found. +colvars: # outputFreq = 10 [default] +colvars: Looking for the keyword "bypassExtendedLagrangian" and its value. +colvars: Keyword "bypassExtendedLagrangian" not found. +colvars: DEPS: disabling feature "bypass_extended_Lagrangian_coordinates" in bias harmonic1 +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "scaledBiasingForce" and its value. +colvars: Keyword "scaledBiasingForce" not found. +colvars: DEPS: disabling feature "scale_biasing_force" in bias harmonic1 +colvars: DEPS: bias harmonic1 enabling "active" +colvars: DEPS: colvar one testing "active" +colvars: DEPS: re-enabling children's active +colvars: DEPS: colvar one enabling "active" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in bias harmonic1 enabled, ref_count = 1. +colvars: Features of "bias harmonic1" (refcount) +colvars: - ON active +colvars: - awake +colvars: - step_zero_data +colvars: - apply_force +colvars: - bypass_extended_Lagrangian_coordinates +colvars: - obtain_total_force +colvars: - output_accumulated_work +colvars: - history_dependent +colvars: - time_dependent +colvars: - require_scalar_variables +colvars: - calculate_a_PMF +colvars: - calculate_TI_samples +colvars: - write_TI_samples_ +colvars: - write_TI_PMF +colvars: - scale_biasing_force +colvars: - Bias on extended-Lagrangian variables +colvars: * child 1 +colvars: Features of "colvar one" (refcount) +colvars: - ON active (1) +colvars: - awake +colvars: - gradient +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - total_force +colvars: - total_force_calculation +colvars: - subtract_applied_force_from_total_force +colvars: - Jacobian_derivative +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - output_total_force +colvars: - lower_boundary +colvars: - upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - scalar +colvars: - ON linear (1) +colvars: - ON homogeneous +colvars: - multiple_timestep +colvars: * child 1 +colvars: Features of "cvc "distanceDir0001" of type "distanceDir"" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - ON defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON explicit_atom_groups +colvars: - gradient +colvars: - explicit_gradient +colvars: - inverse_gradient +colvars: - Jacobian_derivative +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - ON function_of_centers_of_mass (1) +colvars: - ON scalable_calculation (1) +colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids +colvars: * child 1 +colvars: Features of "atom group group1" (refcount) +colvars: - active +colvars: - ON center_to_reference +colvars: - center_to_origin +colvars: - ON rotate_to_origin +colvars: - ON fitting_group +colvars: - ON explicit_atom_gradient (1) +colvars: - ON fit_gradients +colvars: - atomic_forces +colvars: - scalable_group +colvars: - scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: * child 2 +colvars: Features of "atom group group2" (refcount) +colvars: - active +colvars: - ON center_to_reference +colvars: - center_to_origin +colvars: - ON rotate_to_origin +colvars: - ON fitting_group +colvars: - ON explicit_atom_gradient (1) +colvars: - ON fit_gradients +colvars: - atomic_forces +colvars: - scalable_group +colvars: - scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: DEPS: bias harmonic1 enabling "apply_force" +colvars: DEPS: colvar one enabling "gradient" +colvars: DEPS: cvc "distanceDir0001" of type "distanceDir" enabling "gradient" +colvars: DEPS: feature "gradient" in cvc "distanceDir0001" of type "distanceDir" enabled, ref_count = 1. +colvars: DEPS: feature "gradient" in colvar one enabled, ref_count = 1. +colvars: DEPS: feature "apply_force" in bias harmonic1 enabled, ref_count = 1. +colvars: Looking for the keyword "writeTISamples" and its value. +colvars: Keyword "writeTISamples" not found. +colvars: # writeTISamples = off [default] +colvars: DEPS: disabling feature "write_TI_samples_" in bias harmonic1 +colvars: Looking for the keyword "writeTIPMF" and its value. +colvars: Keyword "writeTIPMF" not found. +colvars: # writeTIPMF = off [default] +colvars: DEPS: disabling feature "write_TI_PMF" in bias harmonic1 +colvars: Initializing a new restraint bias. +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword value = "(1.0, 0.1, 0.2)". +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword "centers" not found. +colvars: # centers = { ( 0.9759 , 0.09759 , 0.19518 ) } +colvars: colvarbias_restraint: parsing initial centers, i = 0. +colvars: colvarbias_restraint: parsing target centers. +colvars: Looking for the keyword "targetCenters" and its value. +colvars: Keyword "targetCenters" not found. +colvars: # targetCenters = { ( 0.9759 , 0.09759 , 0.19518 ) } [default] +colvars: Looking for the keyword "outputCenters" and its value. +colvars: Keyword "outputCenters" not found. +colvars: # outputCenters = off [default] +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword value = "10.0". +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword "forceConstant" not found. +colvars: # forceConstant = 10 +colvars: Looking for the keyword "decoupling" and its value. +colvars: Keyword "decoupling" not found. +colvars: # decoupling = off [default] +colvars: Looking for the keyword "targetForceConstant" and its value. +colvars: Keyword "targetForceConstant" not found. +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 40 according to the specified width (0.5). +colvars: Configuration string for "harmonic": " +colvars: +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: ". +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword "harmonic" not found. +colvars: Looking for the keyword "harmonicWalls" and its value. +colvars: Keyword "harmonicWalls" not found. +colvars: Looking for the keyword "histogram" and its value. +colvars: Keyword "histogram" not found. +colvars: Looking for the keyword "histogramRestraint" and its value. +colvars: Keyword "histogramRestraint" not found. +colvars: Looking for the keyword "linear" and its value. +colvars: Keyword "linear" not found. +colvars: Looking for the keyword "metadynamics" and its value. +colvars: Keyword "metadynamics" not found. +colvars: Looking for the keyword "reweightaMD" and its value. +colvars: Keyword "reweightaMD" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: Configuration string for "colvarmodule": " +colvars: colvarsTrajFrequency 1 +colvars: colvarsRestartFrequency 10 +colvars: indexFile index.ndx +colvars: colvar { +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: - distanceDir colvar component (derived from distance): +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Called script run with 3 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "load" +colvars: load +colvars: Using simple-cast script::obj_to_str(): result = "test.colvars.state" +colvars: test.colvars.state +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "load" +colvars: Executing script function "cv_load" +colvars: Using simple-cast script::obj_to_str(): result = "test.colvars.state" +colvars: ---------------------------------------------------------------------- +colvars: Loading state from text file "test.colvars.state". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Looking for the keyword "version" and its value. +colvars: Keyword value = "2024-06-04". +colvars: Looking for the keyword "version" and its value. +colvars: Keyword "version" not found. +colvars: Looking for the keyword "units" and its value. +colvars: Keyword "units" not found. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( -0.3045417105333 , -0.00019915241487762 , 0.95249897999093 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "one" from value: ( -0.304542 , -0.000199152 , 0.952499 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "harmonic1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Restarted harmonic bias "harmonic1" with step number 20. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 20 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 20, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 20, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 8.28582291037697e+00 , 4.04506123830901e-02 , -7.54196570963580e-01 ), ( 6.93477801011369e+00 , -5.51786262542508e-01 , -5.76525850220028e-01 ), ( 6.15654135511678e+00 , -3.75844216369432e-01 , 7.29702736243887e-01 ), ( 4.95083684588076e+00 , -1.63049873260700e-01 , 7.22622667146212e-01 ), ( 7.04822840425256e+00 , -2.05125822808654e+00 , -9.33838802325873e-01 ), ( 6.86298879544170e+00 , -2.63492033772352e-01 , 1.90782093039187e+00 ), ( 6.17535476862579e+00 , -1.61467873005207e-01 , 3.19447807763223e+00 ), ( 7.08038697584318e+00 , -3.54878074422017e-01 , 4.31410976849832e+00 ), ( 5.31942679106160e+00 , 1.09501065270932e+00 , 3.35178346295725e+00 ), ( 4.15930443602701e+00 , 1.02503542539263e+00 , 3.69255428523693e+00 ), ( 5.84279477371476e+00 , 2.25334627387652e+00 , 2.99025393459074e+00 ), ( 5.23840438125392e+00 , 3.57836450753976e+00 , 2.92139319672716e+00 ), ( 6.32240747113683e+00 , 4.50111704883458e+00 , 2.36542025527039e+00 ), ( 3.88181028160009e+00 , 3.70648484501399e+00 , 2.04436620458568e+00 ), ( 2.79206714766409e+00 , 4.16082999865321e+00 , 2.48770343635868e+00 ), ( 3.93862881447229e+00 , 3.23956170779748e+00 , 7.31179710249667e-01 ), ( 2.66241903927475e+00 , 3.00625645576357e+00 , -1.03744703501063e-01 ), ( 3.05292822088169e+00 , 2.70506278162700e+00 , -1.51518325748210e+00 ), ( 1.59778880440673e+00 , 2.18316923674870e+00 , 4.45871092830035e-01 ), ( 3.79300149359787e-01 , 2.58119961872434e+00 , 5.10156322737722e-01 ), ( 2.04754425768075e+00 , 1.07062955324807e+00 , 1.06969022583418e+00 ), ( 1.16903854050100e+00 , 1.16571453589181e-01 , 1.69741818249094e+00 ), ( 2.04314486967146e+00 , -1.10332707217033e+00 , 2.01056812233467e+00 ), ( 5.62094900755023e-01 , 6.11786092234871e-01 , 2.94281295395090e+00 ), ( -6.01998257745626e-01 , 3.49689451878813e-01 , 3.16156299845539e+00 ), ( 1.31668822516108e+00 , 1.34577563521962e+00 , 3.77543109832579e+00 ), ( 8.42716504335045e-01 , 1.97881846216304e+00 , 5.02541834392960e+00 ), ( 2.07967786415177e+00 , 2.68782307153212e+00 , 5.68209741884907e+00 ), ( -3.37344843382937e-01 , 2.91471449609425e+00 , 4.96800851820805e+00 ), ( -1.13708588001649e+00 , 3.06248956541986e+00 , 5.88780199616476e+00 ), ( -5.11775330469444e-01 , 3.53529724018143e+00 , 3.84632332050881e+00 ), ( -1.51803710380555e+00 , 4.53919531397891e+00 , 3.44428420949964e+00 ), ( -6.99624398507824e-01 , 5.41439381873403e+00 , 2.46379309418166e+00 ), ( -2.76022882703025e+00 , 3.88950508193880e+00 , 2.89503343674671e+00 ), ( -3.81748583539279e+00 , 4.50991617428220e+00 , 2.81470056115434e+00 ), ( -2.62519097171536e+00 , 2.67328985787292e+00 , 2.40149432612104e+00 ), ( -3.77272853459107e+00 , 1.80371700509528e+00 , 1.99837671356181e+00 ), ( -3.38871455409835e+00 , 8.86717902389388e-01 , 8.74187404183740e-01 ), ( -4.32255998423662e+00 , 1.07002307118320e+00 , 3.21229150831233e+00 ), ( -5.49998182564857e+00 , 8.18774137488647e-01 , 3.32931951742222e+00 ), ( -3.36904919026829e+00 , 6.91596678914569e-01 , 4.20423547278276e+00 ), ( -3.70107974783840e+00 , 4.62390697929325e-02 , 5.43421582390532e+00 ), ( -2.39033524019067e+00 , -3.17074981101270e-01 , 6.17020508472989e+00 ), ( -4.46175815649799e+00 , 9.86843632633000e-01 , 6.43971260203245e+00 ), ( -5.35881205025882e+00 , 5.98149506814076e-01 , 7.21810107144495e+00 ), ( -6.23824517782367e+00 , 3.60552411038818e+00 , 6.73377298524042e+00 ), ( -6.96012228941194e+00 , 4.29779275147404e+00 , 7.47577581613682e+00 ), ( -6.74134298930255e+00 , 3.18228858940767e+00 , 5.50798663651289e+00 ), ( -4.12867862719011e+00 , 2.24624582899316e+00 , 6.40977342732153e+00 ), ( -4.80883733708504e+00 , 3.20667234951756e+00 , 7.24182070504870e+00 ), ( -4.09497949178953e+00 , 4.57553386748493e+00 , 7.28289299072206e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +colvars: Step 20, atom_groups_refcount[size = 0] = +colvars: Step 20, atom_groups_masses[size = 0] = +colvars: Step 20, atom_groups_charges[size = 0] = +colvars: Step 20, atom_groups_coms[size = 0] = +colvars: Step 20, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_ids[size = 0] = +colvars: Step 20, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 20 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.6088 , 1.95578 , -15.1464 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.6088 , 1.95578 , -15.1464 ) to colvar "one". +colvars: Adding total bias energy: 44.4525 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.6088 , 1.95578 , -15.1464 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.91515 , -0.533261 , -1.45224 ) +colvars: ( -4.21474 , -0.457271 , -1.24529 ) +colvars: ( -4.21474 , -0.457271 , -1.24529 ) +colvars: ( -5.61415 , -0.609098 , -1.65877 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.892544 , 0.19549 , 0.619241 ) +colvars: ( 0.773074 , 0.266213 , 0.643516 ) +colvars: ( 0.757152 , 0.259324 , 0.625094 ) +colvars: ( 0.661335 , 0.266975 , 0.579425 ) +colvars: ( 0.649454 , 0.200472 , 0.484222 ) +colvars: ( 0.574898 , 0.344142 , 0.631501 ) +colvars: ( 0.46778 , 0.358122 , 0.587647 ) +colvars: ( 0.391169 , 0.455275 , 0.67198 ) +colvars: ( 0.386205 , 0.313656 , 0.481093 ) +colvars: ( 0.351459 , 0.272107 , 0.405694 ) +colvars: ( 0.356948 , 0.318969 , 0.471099 ) +colvars: ( 0.285831 , 0.276183 , 0.372867 ) +colvars: ( 0.258798 , 0.3052 , 0.395635 ) +colvars: ( 0.348239 , 0.178457 , 0.2795 ) +colvars: ( 0.289613 , 0.135181 , 0.187896 ) +colvars: ( 0.470901 , 0.14145 , 0.301842 ) +colvars: ( 0.543399 , 0.0501585 , 0.222894 ) +colvars: ( 0.672857 , 0.0291993 , 0.270498 ) +colvars: ( 0.551951 , 0.0183336 , 0.18563 ) +colvars: ( 0.536209 , -0.0466654 , 0.0901744 ) +colvars: ( 0.572815 , 0.0661925 , 0.261317 ) +colvars: ( 0.571276 , 0.0500177 , 0.238949 ) +colvars: ( 0.607772 , 0.114667 , 0.346033 ) +colvars: ( 0.447058 , 0.0544713 , 0.172488 ) +colvars: ( 0.440246 , -0.00142063 , 0.0943242 ) +colvars: ( 0.345197 , 0.120053 , 0.200198 ) +colvars: ( 0.220799 , 0.128616 , 0.139087 ) +colvars: ( 0.129402 , 0.214294 , 0.19957 ) +colvars: ( 0.192616 , 0.0549651 , 0.0248969 ) +colvars: ( 0.143405 , 0.018808 , -0.0517726 ) +colvars: ( 0.226186 , 0.0294603 , 0.0105991 ) +colvars: ( 0.212182 , -0.0429517 , -0.0936848 ) +colvars: ( 0.247451 , -0.0462529 , -0.0775182 ) +colvars: ( 0.287355 , -0.128824 , -0.16388 ) +colvars: ( 0.243414 , -0.181898 , -0.259935 ) +colvars: ( 0.402414 , -0.143819 , -0.116748 ) +colvars: ( 0.479789 , -0.219244 , -0.17179 ) +colvars: ( 0.610834 , -0.221812 , -0.0988481 ) +colvars: ( 0.432546 , -0.223771 , -0.205325 ) +colvars: ( 0.438072 , -0.291778 , -0.292383 ) +colvars: ( 0.383843 , -0.150562 , -0.136519 ) +colvars: ( 0.329659 , -0.144357 , -0.159851 ) +colvars: ( 0.313151 , -0.0577764 , -0.0545361 ) +colvars: ( 0.206501 , -0.15316 , -0.243293 ) +colvars: ( 0.182128 , -0.195153 , -0.313237 ) +colvars: ( 0.00545045 , -0.19885 , -0.421084 ) +colvars: ( -0.0853872 , -0.216646 , -0.497632 ) +colvars: ( 0.105698 , -0.248684 , -0.428829 ) +colvars: ( 0.124781 , -0.112578 , -0.237034 ) +colvars: ( 0.00559788 , -0.116969 , -0.312302 ) +colvars: ( -0.0832935 , -0.0363805 , -0.257115 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.91515 , 0.533261 , 1.45224 ) +colvars: ( 4.21474 , 0.457271 , 1.24529 ) +colvars: ( 4.21474 , 0.457271 , 1.24529 ) +colvars: ( 5.61415 , 0.609098 , 1.65877 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.615911 , -0.0809403 , -0.370289 ) +colvars: ( -0.553936 , -0.163279 , -0.339783 ) +colvars: ( -0.504483 , -0.14143 , -0.281796 ) +colvars: ( -0.514701 , -0.190631 , -0.31095 ) +colvars: ( -0.505106 , -0.132058 , -0.278819 ) +colvars: ( -0.489899 , -0.282191 , -0.321263 ) +colvars: ( -0.457119 , -0.322318 , -0.303811 ) +colvars: ( -0.435381 , -0.42909 , -0.323043 ) +colvars: ( -0.394403 , -0.287171 , -0.227415 ) +colvars: ( -0.389791 , -0.261989 , -0.213114 ) +colvars: ( -0.345387 , -0.281611 , -0.176126 ) +colvars: ( -0.285203 , -0.244949 , -0.101686 ) +colvars: ( -0.23688 , -0.259846 , -0.058954 ) +colvars: ( -0.30471 , -0.142288 , -0.0817978 ) +colvars: ( -0.273523 , -0.113172 , -0.0393358 ) +colvars: ( -0.359032 , -0.0851872 , -0.114328 ) +colvars: ( -0.385698 , 0.0125647 , -0.103504 ) +colvars: ( -0.43592 , 0.0599408 , -0.135661 ) +colvars: ( -0.423002 , 0.0275581 , -0.13515 ) +colvars: ( -0.411661 , 0.0840489 , -0.10207 ) +colvars: ( -0.466795 , -0.0261598 , -0.199708 ) +colvars: ( -0.500798 , -0.0275661 , -0.234345 ) +colvars: ( -0.55043 , -0.0926022 , -0.309107 ) +colvars: ( -0.448784 , -0.057432 , -0.193664 ) +colvars: ( -0.455539 , -0.013552 , -0.183575 ) +colvars: ( -0.393864 , -0.131394 , -0.167013 ) +colvars: ( -0.336404 , -0.16255 , -0.121366 ) +colvars: ( -0.286194 , -0.252303 , -0.105507 ) +colvars: ( -0.295464 , -0.0901165 , -0.0524782 ) +colvars: ( -0.282212 , -0.0715846 , -0.032067 ) +colvars: ( -0.275892 , -0.045508 , -0.0157091 ) +colvars: ( -0.240779 , 0.0288343 , 0.048069 ) +colvars: ( -0.219798 , 0.0550453 , 0.0791805 ) +colvars: ( -0.284619 , 0.115186 , 0.0372899 ) +colvars: ( -0.258068 , 0.156731 , 0.0798802 ) +colvars: ( -0.35365 , 0.143204 , -0.0211658 ) +colvars: ( -0.402215 , 0.219052 , -0.0407192 ) +colvars: ( -0.473097 , 0.241538 , -0.103157 ) +colvars: ( -0.413517 , 0.199366 , -0.0596175 ) +colvars: ( -0.417976 , 0.25989 , -0.0408311 ) +colvars: ( -0.417832 , 0.113257 , -0.0970347 ) +colvars: ( -0.424688 , 0.0832879 , -0.115426 ) +colvars: ( -0.445978 , -0.00952294 , -0.17244 ) +colvars: ( -0.358207 , 0.0720446 , -0.0530801 ) +colvars: ( -0.361391 , 0.0982463 , -0.0462049 ) +colvars: ( -0.198027 , 0.104482 , 0.120009 ) +colvars: ( -0.148764 , 0.106318 , 0.170115 ) +colvars: ( -0.224679 , 0.176429 , 0.120931 ) +colvars: ( -0.296008 , 0.0314599 , -0.00630443 ) +colvars: ( -0.229511 , 0.0178807 , 0.0551591 ) +colvars: ( -0.175844 , -0.0648266 , 0.0771928 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 20. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -4.63851454459905e+00 , -4.18710833064850e-01 , -1.20328608426652e+00 ), ( -3.99559989640659e+00 , -3.54336474175720e-01 , -9.41559888235754e-01 ), ( -4.06810357739189e+00 , -3.80926713958037e-01 , -9.76817699772113e-01 ), ( -5.46980368326514e+00 , -5.40683985020084e-01 , -1.45336332622448e+00 ), ( 2.52668502795200e-01 , 1.17894094436429e-01 , 3.43297404486922e-01 ), ( 5.00014590643842e+00 , 5.95211961482009e-01 , 1.76247508244524e+00 ), ( 4.22539890920215e+00 , 4.93075099844339e-01 , 1.52912952520700e+00 ), ( -4.42117205218343e-02 , 2.61849910581687e-02 , 3.48936847549760e-01 ), ( 4.20654020656410e+00 , 4.83756625787825e-01 , 1.49897132736399e+00 ), ( 5.57582044888118e+00 , 6.19216324851961e-01 , 1.85134641932113e+00 ), ( 1.15606722969959e-02 , 3.73582371308533e-02 , 2.94972551667663e-01 ), ( 6.27937109112076e-04 , 3.12340160260255e-02 , 2.71180143655928e-01 ), ( 2.19173365638969e-02 , 4.53538862226682e-02 , 3.36681036424671e-01 ), ( 4.35287412741041e-02 , 3.61696681282234e-02 , 1.97702509024789e-01 ), ( 1.60900816481230e-02 , 2.20091820921404e-02 , 1.48559775115973e-01 ), ( 1.11869449595165e-01 , 5.62631531725342e-02 , 1.87513672922987e-01 ), ( 1.57700920362817e-01 , 6.27232419132576e-02 , 1.19389577713856e-01 ), ( 2.36936463271923e-01 , 8.91401887092676e-02 , 1.34836894262539e-01 ), ( 1.28948776005967e-01 , 4.58916180710906e-02 , 5.04794295830226e-02 ), ( 1.24548587393342e-01 , 3.73834994690693e-02 , -1.18954687815839e-02 ), ( 1.06019698806145e-01 , 4.00326507775761e-02 , 6.16092423921068e-02 ), ( 7.04782471949013e-02 , 2.24515586964271e-02 , 4.60369604053695e-03 ), ( 5.73422381960390e-02 , 2.20646170469042e-02 , 3.69252747449674e-02 ), ( -1.72611395560524e-03 , -2.96077010773500e-03 , -2.11764063442688e-02 ), ( -1.52922851265740e-02 , -1.49726615376669e-02 , -8.92510974662055e-02 ), ( -4.86671260953066e-02 , -1.13413226333090e-02 , 3.31845028045236e-02 ), ( -1.15605077666369e-01 , -3.39346522378186e-02 , 1.77200417262677e-02 ), ( -1.56792026456609e-01 , -3.80091057503520e-02 , 9.40637658323593e-02 ), ( -1.02848641736711e-01 , -3.51514140984507e-02 , -2.75812107087965e-02 ), ( -1.38806884416938e-01 , -5.27766427227216e-02 , -8.38395789565467e-02 ), ( -4.97061267723764e-02 , -1.60476509528009e-02 , -5.11007628540459e-03 ), ( -2.85976059219338e-02 , -1.41173315546320e-02 , -4.56158111816652e-02 ), ( 2.76522679529432e-02 , 8.79242656069489e-03 , 1.66225761229807e-03 ), ( 2.73532411285460e-03 , -1.36382491455301e-02 , -1.26589601375052e-01 ), ( -1.46538330736033e-02 , -2.51672766893284e-02 , -1.80055129011821e-01 ), ( 4.87645210478707e-02 , -6.15426656884632e-04 , -1.37913496336073e-01 ), ( 7.75743232463488e-02 , -1.91225606735068e-04 , -2.12509192428131e-01 ), ( 1.37737148977943e-01 , 1.97267169501107e-02 , -2.02005130353156e-01 ), ( 1.90294174661668e-02 , -2.44049904625063e-02 , -2.64942523670217e-01 ), ( 2.00953061744231e-02 , -3.18876654614701e-02 , -3.33214475874042e-01 ), ( -3.39893131361256e-02 , -3.73055310094134e-02 , -2.33553485918890e-01 ), ( -9.50287381727212e-02 , -6.10695052311506e-02 , -2.75277236233374e-01 ), ( -1.32826616258851e-01 , -6.72993193787387e-02 , -2.26975689078502e-01 ), ( -1.51705844975594e-01 , -8.11153781239003e-02 , -2.96372806931386e-01 ), ( -1.79263034470665e-01 , -9.69067785137090e-02 , -3.59442438261914e-01 ), ( -1.92577034615937e-01 , -9.43678359874191e-02 , -3.01074097881565e-01 ), ( -2.34151572355940e-01 , -1.10327571437585e-01 , -3.27516835071365e-01 ), ( -1.18981164358574e-01 , -7.22543491267554e-02 , -3.07897440415716e-01 ), ( -1.71227554375326e-01 , -8.11181099169558e-02 , -2.43338813862098e-01 ), ( -2.23913463549683e-01 , -9.90878668961794e-02 , -2.57143314677739e-01 ), ( -2.59137952902184e-01 , -1.01207120969136e-01 , -1.79922622294137e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 21 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 21, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 21, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 21, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 21, atoms_positions[size = 51] = { ( 8.28180982144064e+00 , 4.03632117943420e-02 , -7.51522305517076e-01 ), ( 6.92282117186149e+00 , -5.53103008339236e-01 , -5.68946668768409e-01 ), ( 6.15817431676409e+00 , -3.81985768262077e-01 , 7.37133684205432e-01 ), ( 4.94415676071348e+00 , -1.59493575190565e-01 , 7.24998098558174e-01 ), ( 7.04491903435971e+00 , -2.05318729196479e+00 , -9.29444265677132e-01 ), ( 6.85635102170978e+00 , -2.64482457244509e-01 , 1.91552478321154e+00 ), ( 6.17022515682612e+00 , -1.68498720978849e-01 , 3.18973647048402e+00 ), ( 7.08289173522581e+00 , -3.53907252918931e-01 , 4.32144017771733e+00 ), ( 5.32536611283806e+00 , 1.09148571415860e+00 , 3.35515329207102e+00 ), ( 4.16123089994812e+00 , 1.02270267230411e+00 , 3.69988826087271e+00 ), ( 5.84018046278717e+00 , 2.25510641156531e+00 , 2.98828769631725e+00 ), ( 5.23587224285778e+00 , 3.57667790378110e+00 , 2.92151344030494e+00 ), ( 6.32158086117518e+00 , 4.49985476177825e+00 , 2.35550053278041e+00 ), ( 3.87686982786362e+00 , 3.70008117015323e+00 , 2.04442214020625e+00 ), ( 2.79070884592407e+00 , 4.16331882660186e+00 , 2.48250033805889e+00 ), ( 3.94109497487038e+00 , 3.23745357393277e+00 , 7.30710158843963e-01 ), ( 2.66965416281210e+00 , 3.00544044719939e+00 , -1.01536762164985e-01 ), ( 3.05924471963822e+00 , 2.69949617675075e+00 , -1.51507639779084e+00 ), ( 1.59644807437693e+00 , 2.17841754594632e+00 , 4.39530279055366e-01 ), ( 3.75987150484748e-01 , 2.58918817813005e+00 , 5.06290010091292e-01 ), ( 2.05513241559826e+00 , 1.08606036188264e+00 , 1.06504176262207e+00 ), ( 1.16749512571148e+00 , 1.17140689118167e-01 , 1.69891782543129e+00 ), ( 2.04670833917162e+00 , -1.09990016597589e+00 , 2.01320056995010e+00 ), ( 5.63957095834067e-01 , 6.13312886215627e-01 , 2.94798433857395e+00 ), ( -5.96929929647838e-01 , 3.50034068222415e-01 , 3.16124199273713e+00 ), ( 1.31332645357206e+00 , 1.34643286624227e+00 , 3.76642698902620e+00 ), ( 8.40773797302887e-01 , 1.98100698226988e+00 , 5.02554690429120e+00 ), ( 2.08826803285072e+00 , 2.69720522357921e+00 , 5.68886943540120e+00 ), ( -3.38064874142760e-01 , 2.91392015283261e+00 , 4.96863248251904e+00 ), ( -1.13355401890519e+00 , 3.06348555057185e+00 , 5.88514771970272e+00 ), ( -5.16867469126270e-01 , 3.52805375720305e+00 , 3.84368677302349e+00 ), ( -1.51811690408844e+00 , 4.53539704647674e+00 , 3.43584551271010e+00 ), ( -6.99370800306209e-01 , 5.41613700843609e+00 , 2.46552934668629e+00 ), ( -2.75639412467584e+00 , 3.89650316598925e+00 , 2.88916479315839e+00 ), ( -3.81645391301319e+00 , 4.51562346198390e+00 , 2.81385309793028e+00 ), ( -2.63074454584207e+00 , 2.67070215903842e+00 , 2.39436849186767e+00 ), ( -3.77616839293599e+00 , 1.80233294721421e+00 , 1.99836789333910e+00 ), ( -3.38449240191245e+00 , 8.86020902736430e-01 , 8.67964646598369e-01 ), ( -4.31780739760532e+00 , 1.07009890178842e+00 , 3.20979010835984e+00 ), ( -5.49785604495399e+00 , 8.11545411383148e-01 , 3.32998166249016e+00 ), ( -3.36643319479492e+00 , 6.95550042589655e-01 , 4.20710184038517e+00 ), ( -3.69481482827732e+00 , 5.14816562374844e-02 , 5.43576555656035e+00 ), ( -2.39148179599744e+00 , -3.19110327206271e-01 , 6.16791671623623e+00 ), ( -4.46091515849428e+00 , 9.79194091149395e-01 , 6.43764801078358e+00 ), ( -5.36126211530540e+00 , 5.96481497769695e-01 , 7.21902898040563e+00 ), ( -6.24393584634194e+00 , 3.61115232827763e+00 , 6.73793062424253e+00 ), ( -6.96374054841084e+00 , 4.29730433911356e+00 , 7.47986193898876e+00 ), ( -6.73483228541235e+00 , 3.17851373057506e+00 , 5.50665660752860e+00 ), ( -4.12684263466858e+00 , 2.24431932714025e+00 , 6.40360191191022e+00 ), ( -4.80725733449393e+00 , 3.21381335861946e+00 , 7.24626740560762e+00 ), ( -4.08929591791521e+00 , 4.56969008482376e+00 , 7.28010753422389e+00 ) } +colvars: Step 21, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_ids[size = 0] = +colvars: Step 21, atom_groups_refcount[size = 0] = +colvars: Step 21, atom_groups_masses[size = 0] = +colvars: Step 21, atom_groups_charges[size = 0] = +colvars: Step 21, atom_groups_coms[size = 0] = +colvars: Step 21, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 21, volmaps_ids[size = 0] = +colvars: Step 21, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 21 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.03300920671651e-01 , -1.24565183823531e-03 , 9.52894012926530e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.03300920671651e-01 , -1.24565183823531e-03 , 9.52894012926530e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.584 , 1.97671 , -15.1543 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.584 , 1.97671 , -15.1543 ) to colvar "one". +colvars: Adding total bias energy: 44.4051 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.584 , 1.97671 , -15.1543 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.91753 , -0.532009 , -1.44704 ) +colvars: ( -4.21678 , -0.456197 , -1.24084 ) +colvars: ( -4.21678 , -0.456197 , -1.24084 ) +colvars: ( -5.61688 , -0.607668 , -1.65283 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.891906 , 0.195586 , 0.617925 ) +colvars: ( 0.772598 , 0.266263 , 0.642089 ) +colvars: ( 0.756608 , 0.259381 , 0.623664 ) +colvars: ( 0.66106 , 0.266979 , 0.578105 ) +colvars: ( 0.649197 , 0.200475 , 0.483109 ) +colvars: ( 0.574782 , 0.344106 , 0.63004 ) +colvars: ( 0.467865 , 0.358038 , 0.586254 ) +colvars: ( 0.391392 , 0.455155 , 0.670375 ) +colvars: ( 0.386367 , 0.313552 , 0.479882 ) +colvars: ( 0.351705 , 0.271987 , 0.404649 ) +colvars: ( 0.357075 , 0.318864 , 0.469867 ) +colvars: ( 0.286012 , 0.276062 , 0.371802 ) +colvars: ( 0.258937 , 0.305079 , 0.394476 ) +colvars: ( 0.348314 , 0.178367 , 0.278665 ) +colvars: ( 0.289775 , 0.135071 , 0.187238 ) +colvars: ( 0.470785 , 0.141408 , 0.301007 ) +colvars: ( 0.543166 , 0.0501492 , 0.222262 ) +colvars: ( 0.672405 , 0.0292428 , 0.269806 ) +colvars: ( 0.551783 , 0.018318 , 0.185115 ) +colvars: ( 0.536065 , -0.0466832 , 0.089865 ) +colvars: ( 0.572685 , 0.0661722 , 0.260671 ) +colvars: ( 0.571228 , 0.0499863 , 0.238383 ) +colvars: ( 0.607733 , 0.114636 , 0.345269 ) +colvars: ( 0.447214 , 0.054391 , 0.172023 ) +colvars: ( 0.440442 , -0.00150451 , 0.0940415 ) +colvars: ( 0.345486 , 0.119934 , 0.19962 ) +colvars: ( 0.22128 , 0.12845 , 0.138593 ) +colvars: ( 0.129997 , 0.214092 , 0.198894 ) +colvars: ( 0.193087 , 0.0548001 , 0.0246244 ) +colvars: ( 0.143977 , 0.0186226 , -0.051885 ) +colvars: ( 0.226529 , 0.0293201 , 0.0103425 ) +colvars: ( 0.212492 , -0.0430854 , -0.0937372 ) +colvars: ( 0.247623 , -0.0463613 , -0.0776246 ) +colvars: ( 0.287579 , -0.128929 , -0.163733 ) +colvars: ( 0.243698 , -0.182016 , -0.259597 ) +colvars: ( 0.402497 , -0.143885 , -0.116644 ) +colvars: ( 0.47979 , -0.219282 , -0.171518 ) +colvars: ( 0.610655 , -0.221803 , -0.0986752 ) +colvars: ( 0.432694 , -0.223837 , -0.204969 ) +colvars: ( 0.438223 , -0.29184 , -0.291827 ) +colvars: ( 0.384118 , -0.150658 , -0.136315 ) +colvars: ( 0.330088 , -0.144484 , -0.15959 ) +colvars: ( 0.31366 , -0.0579219 , -0.0544944 ) +colvars: ( 0.2071 , -0.15333 , -0.242905 ) +colvars: ( 0.182803 , -0.195335 , -0.31269 ) +colvars: ( 0.00621687 , -0.199073 , -0.42044 ) +colvars: ( -0.0844942 , -0.2169 , -0.496861 ) +colvars: ( 0.106271 , -0.248861 , -0.428141 ) +colvars: ( 0.125447 , -0.112773 , -0.236717 ) +colvars: ( 0.0064244 , -0.117204 , -0.311877 ) +colvars: ( -0.082367 , -0.0366491 , -0.256863 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.91753 , 0.532009 , 1.44704 ) +colvars: ( 4.21678 , 0.456197 , 1.24084 ) +colvars: ( 4.21678 , 0.456197 , 1.24084 ) +colvars: ( 5.61688 , 0.607668 , 1.65283 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.615602 , -0.0810076 , -0.369309 ) +colvars: ( -0.553704 , -0.163454 , -0.338593 ) +colvars: ( -0.50405 , -0.141549 , -0.28047 ) +colvars: ( -0.514641 , -0.190835 , -0.309834 ) +colvars: ( -0.505038 , -0.132164 , -0.277892 ) +colvars: ( -0.489997 , -0.282534 , -0.319994 ) +colvars: ( -0.457405 , -0.322712 , -0.302592 ) +colvars: ( -0.435808 , -0.429648 , -0.321602 ) +colvars: ( -0.394641 , -0.287483 , -0.226254 ) +colvars: ( -0.390123 , -0.262259 , -0.212131 ) +colvars: ( -0.34547 , -0.281893 , -0.174821 ) +colvars: ( -0.285215 , -0.245148 , -0.100423 ) +colvars: ( -0.236733 , -0.260049 , -0.0574722 ) +colvars: ( -0.304618 , -0.142329 , -0.0807779 ) +colvars: ( -0.273469 , -0.113154 , -0.0384457 ) +colvars: ( -0.358811 , -0.0851582 , -0.11338 ) +colvars: ( -0.385376 , 0.0127408 , -0.102787 ) +colvars: ( -0.435425 , 0.0601736 , -0.134937 ) +colvars: ( -0.422845 , 0.0277427 , -0.134655 ) +colvars: ( -0.411501 , 0.0843291 , -0.101759 ) +colvars: ( -0.466792 , -0.02608 , -0.199194 ) +colvars: ( -0.500975 , -0.0275029 , -0.234014 ) +colvars: ( -0.550739 , -0.0926642 , -0.308698 ) +colvars: ( -0.449109 , -0.0573964 , -0.193372 ) +colvars: ( -0.455923 , -0.0134487 , -0.183492 ) +colvars: ( -0.394244 , -0.131456 , -0.166519 ) +colvars: ( -0.336904 , -0.162639 , -0.120878 ) +colvars: ( -0.286737 , -0.252516 , -0.104752 ) +colvars: ( -0.29585 , -0.090072 , -0.0521115 ) +colvars: ( -0.282695 , -0.0715052 , -0.0318585 ) +colvars: ( -0.276066 , -0.0453829 , -0.0152762 ) +colvars: ( -0.240822 , 0.0290937 , 0.0483898 ) +colvars: ( -0.219615 , 0.0553562 , 0.0796435 ) +colvars: ( -0.28464 , 0.115567 , 0.0373355 ) +colvars: ( -0.258101 , 0.15719 , 0.0797783 ) +colvars: ( -0.353642 , 0.143602 , -0.0211973 ) +colvars: ( -0.402202 , 0.219553 , -0.041008 ) +colvars: ( -0.47301 , 0.242047 , -0.10346 ) +colvars: ( -0.41372 , 0.19983 , -0.0600593 ) +colvars: ( -0.418186 , 0.26045 , -0.0414842 ) +colvars: ( -0.418217 , 0.113579 , -0.0973709 ) +colvars: ( -0.425289 , 0.0835588 , -0.11588 ) +colvars: ( -0.44674 , -0.00941062 , -0.172747 ) +colvars: ( -0.358877 , 0.0723239 , -0.0535549 ) +colvars: ( -0.362162 , 0.0985662 , -0.0468683 ) +colvars: ( -0.198547 , 0.104879 , 0.119604 ) +colvars: ( -0.149335 , 0.106738 , 0.169661 ) +colvars: ( -0.225003 , 0.176932 , 0.120476 ) +colvars: ( -0.29663 , 0.0316992 , -0.00658352 ) +colvars: ( -0.230189 , 0.0181247 , 0.0548804 ) +colvars: ( -0.17654 , -0.0646942 , 0.0771833 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 21. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 21. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atoms_new_colvar_forces = { ( -4.64122776904015e+00 , -4.17430462035631e-01 , -1.19842694137483e+00 ), ( -3.99788899167886e+00 , -3.53388097492481e-01 , -9.37343738530352e-01 ), ( -4.07036342226094e+00 , -3.80053411283391e-01 , -9.72567817047775e-01 ), ( -5.47271843477268e+00 , -5.39356608605815e-01 , -1.44761651153678e+00 ), ( 2.52557618430625e-01 , 1.17832033814582e-01 , 3.43194187277646e-01 ), ( 5.00231710964028e+00 , 5.93580565697120e-01 , 1.75708806280753e+00 ), ( 4.22724308789953e+00 , 4.91523742388943e-01 , 1.52450102653856e+00 ), ( -4.44156059175932e-02 , 2.55069516317784e-02 , 3.48772662262247e-01 ), ( 4.20850881223129e+00 , 4.82266099920002e-01 , 1.49446742226968e+00 ), ( 5.57845842449923e+00 , 6.17396054603903e-01 , 1.84535056502956e+00 ), ( 1.16042863660146e-02 , 3.69709529684829e-02 , 2.95046652017487e-01 ), ( 7.96432107015188e-04 , 3.09136859029808e-02 , 2.71379106274306e-01 ), ( 2.22040284266436e-02 , 4.50297362282180e-02 , 3.37004061353848e-01 ), ( 4.36956298307483e-02 , 3.60373642448502e-02 , 1.97887370271810e-01 ), ( 1.63067370046763e-02 , 2.19169468887107e-02 , 1.48792708452083e-01 ), ( 1.11974233351976e-01 , 5.62498704593333e-02 , 1.87627235244391e-01 ), ( 1.57790381080519e-01 , 6.28899649707613e-02 , 1.19475425943700e-01 ), ( 2.36979706130974e-01 , 8.94163656617664e-02 , 1.34869027391466e-01 ), ( 1.28938337913741e-01 , 4.60606453470170e-02 , 5.04601588302178e-02 ), ( 1.24564403423756e-01 , 3.76458353164540e-02 , -1.18943459271851e-02 ), ( 1.05893496825123e-01 , 4.00922005344408e-02 , 6.14766757574045e-02 ), ( 7.02528486399241e-02 , 2.24834468030063e-02 , 4.36872407426400e-03 ), ( 5.69946237581154e-02 , 2.19722584686867e-02 , 3.65716659864114e-02 ), ( -1.89475792886762e-03 , -3.00538690278939e-03 , -2.13488795274948e-02 ), ( -1.54814285062692e-02 , -1.49532101107763e-02 , -8.94500255718244e-02 ), ( -4.87583053309668e-02 , -1.15215500406721e-02 , 3.31011992449969e-02 ), ( -1.15624059454000e-01 , -3.41896795614565e-02 , 1.77153613311154e-02 ), ( -1.56740904653225e-01 , -3.84237775734388e-02 , 9.41425203159714e-02 ), ( -1.02763736823437e-01 , -3.52719162074792e-02 , -2.74871114356013e-02 ), ( -1.38717967225407e-01 , -5.28825983432749e-02 , -8.37434673842979e-02 ), ( -4.95364227181623e-02 , -1.60628499684035e-02 , -4.93370527315155e-03 ), ( -2.83303107873536e-02 , -1.39916722755991e-02 , -4.53474253713426e-02 ), ( 2.80080137569232e-02 , 8.99489712055920e-03 , 2.01889728907423e-03 ), ( 2.93875292420265e-03 , -1.33624173413813e-02 , -1.26397763016215e-01 ), ( -1.44021922603752e-02 , -2.48265383234662e-02 , -1.79818345390667e-01 ), ( 4.88553431363245e-02 , -2.83192569295265e-04 , -1.37841673828266e-01 ), ( 7.75883326310623e-02 , 2.71567253110505e-04 , -2.12526047690265e-01 ), ( 1.37644360337415e-01 , 2.02437628589764e-02 , -2.02135359298212e-01 ), ( 1.89747254421979e-02 , -2.40074827799895e-02 , -2.65027972415543e-01 ), ( 2.00371917930195e-02 , -3.13905103999074e-02 , -3.33310741492471e-01 ), ( -3.40995722470154e-02 , -3.70787587257643e-02 , -2.33685967415618e-01 ), ( -9.52008606975520e-02 , -6.09254108785846e-02 , -2.75469993003236e-01 ), ( -1.33080367679862e-01 , -6.73325112630011e-02 , -2.27241681799490e-01 ), ( -1.51777101665849e-01 , -8.10060318373823e-02 , -2.96459688598563e-01 ), ( -1.79358866936844e-01 , -9.67691394141569e-02 , -3.59557835653087e-01 ), ( -1.92330306847282e-01 , -9.41940326348025e-02 , -3.00835691903202e-01 ), ( -2.33828886709127e-01 , -1.10162499250053e-01 , -3.27199939583203e-01 ), ( -1.18731823077427e-01 , -7.19287057155311e-02 , -3.07665152024204e-01 ), ( -1.71182740158695e-01 , -8.10734910111616e-02 , -2.43300648476592e-01 ), ( -2.23765053760146e-01 , -9.90797730868727e-02 , -2.56996178086910e-01 ), ( -2.58907028443240e-01 , -1.01343233451123e-01 , -1.79680067307387e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 21, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 22 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 22, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 22, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 22, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 22, atoms_positions[size = 51] = { ( 8.27801368548645e+00 , 4.04154521083087e-02 , -7.48719982598039e-01 ), ( 6.91048178254831e+00 , -5.54844282628265e-01 , -5.61634053620293e-01 ), ( 6.15998899334806e+00 , -3.86782407248557e-01 , 7.45045201710521e-01 ), ( 4.93749817908694e+00 , -1.56253382351994e-01 , 7.27247784002906e-01 ), ( 7.04098154871646e+00 , -2.05498381202224e+00 , -9.24907126413291e-01 ), ( 6.84966641870068e+00 , -2.65929151842961e-01 , 1.92326030422572e+00 ), ( 6.16411047750865e+00 , -1.75644521264806e-01 , 3.18419807209405e+00 ), ( 7.08666977735157e+00 , -3.52549395488943e-01 , 4.32906605591399e+00 ), ( 5.33054928299867e+00 , 1.08795425891365e+00 , 3.35828589703570e+00 ), ( 4.16306444568256e+00 , 1.02043984362175e+00 , 3.70755243742096e+00 ), ( 5.83816978757841e+00 , 2.25648918402764e+00 , 2.98634353700412e+00 ), ( 5.23152682468208e+00 , 3.57504348819360e+00 , 2.92067986950805e+00 ), ( 6.32073118016360e+00 , 4.49864518648533e+00 , 2.34563264114075e+00 ), ( 3.87239920163604e+00 , 3.69348580097200e+00 , 2.04401894200599e+00 ), ( 2.79034998960965e+00 , 4.16543533240563e+00 , 2.47721565504201e+00 ), ( 3.94189801034716e+00 , 3.23467094726968e+00 , 7.30468754417991e-01 ), ( 2.67869166196476e+00 , 3.00668951225046e+00 , -9.89393079298166e-02 ), ( 3.06603237459020e+00 , 2.69343802200018e+00 , -1.51644963865935e+00 ), ( 1.59289453841614e+00 , 2.17429256358265e+00 , 4.34530642985326e-01 ), ( 3.74485678271048e-01 , 2.59622737458133e+00 , 5.02096956065577e-01 ), ( 2.06201476025277e+00 , 1.10100531237450e+00 , 1.06018100447220e+00 ), ( 1.16703150703526e+00 , 1.17105031827408e-01 , 1.70016527342674e+00 ), ( 2.05051994686606e+00 , -1.09708230155034e+00 , 2.01626231749083e+00 ), ( 5.65903621217232e-01 , 6.14817009609931e-01 , 2.95297475259653e+00 ), ( -5.92561426515437e-01 , 3.50487432559455e-01 , 3.16136472744381e+00 ), ( 1.30974532827807e+00 , 1.34773684194957e+00 , 3.75844830461877e+00 ), ( 8.39707064595765e-01 , 1.98254371176299e+00 , 5.02583861033260e+00 ), ( 2.09592827731066e+00 , 2.70621573826577e+00 , 5.69535413725560e+00 ), ( -3.39399534006099e-01 , 2.91294858047198e+00 , 4.96934567299248e+00 ), ( -1.13010863238801e+00 , 3.06435911406876e+00 , 5.88269806602876e+00 ), ( -5.21808874577016e-01 , 3.52229240623140e+00 , 3.83999327035536e+00 ), ( -1.51684318188244e+00 , 4.53077501028791e+00 , 3.42864730545594e+00 ), ( -7.00125566595635e-01 , 5.41784807086397e+00 , 2.46701516327173e+00 ), ( -2.75278692152346e+00 , 3.90427029165478e+00 , 2.88217147780035e+00 ), ( -3.81541548100356e+00 , 4.52118941609546e+00 , 2.81323829061783e+00 ), ( -2.63691140783605e+00 , 2.66667837316107e+00 , 2.38752564076698e+00 ), ( -3.77917708262115e+00 , 1.80294678257828e+00 , 1.99899140484426e+00 ), ( -3.38046820857936e+00 , 8.84672501592023e-01 , 8.61750110511929e-01 ), ( -4.31111065580452e+00 , 1.06949443621696e+00 , 3.20884013303441e+00 ), ( -5.49616869540039e+00 , 8.04350552343177e-01 , 3.33075762198025e+00 ), ( -3.36494439475654e+00 , 6.99826790509561e-01 , 4.20779518487570e+00 ), ( -3.68937388538685e+00 , 5.70683934546486e-02 , 5.43902454796261e+00 ), ( -2.39223176981692e+00 , -3.21238995641683e-01 , 6.16503443092707e+00 ), ( -4.46071627154088e+00 , 9.70497508552942e-01 , 6.43526153201309e+00 ), ( -5.36312442796754e+00 , 5.94773058318206e-01 , 7.21933927948785e+00 ), ( -6.25128250148289e+00 , 3.61642458062405e+00 , 6.74174670270379e+00 ), ( -6.96721167211321e+00 , 4.29673229531940e+00 , 7.48373785142574e+00 ), ( -6.72683623372741e+00 , 3.17490139551974e+00 , 5.50615470481645e+00 ), ( -4.12455101670872e+00 , 2.24354090977720e+00 , 6.39848415514813e+00 ), ( -4.80668381925186e+00 , 3.22191549136373e+00 , 7.25027330885431e+00 ), ( -4.08255995005786e+00 , 4.56373205282011e+00 , 7.27756286077104e+00 ) } +colvars: Step 22, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_ids[size = 0] = +colvars: Step 22, atom_groups_refcount[size = 0] = +colvars: Step 22, atom_groups_masses[size = 0] = +colvars: Step 22, atom_groups_charges[size = 0] = +colvars: Step 22, atom_groups_coms[size = 0] = +colvars: Step 22, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 22, volmaps_ids[size = 0] = +colvars: Step 22, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 22 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.02208395802458e-01 , -2.38936177499928e-03 , 9.53238887402740e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.02208395802458e-01 , -2.38936177499928e-03 , 9.53238887402740e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.5622 , 1.99959 , -15.1612 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.5622 , 1.99959 , -15.1612 ) to colvar "one". +colvars: Adding total bias energy: 44.3642 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.5622 , 1.99959 , -15.1612 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.91958 , -0.530926 , -1.44255 ) +colvars: ( -4.21854 , -0.455269 , -1.23699 ) +colvars: ( -4.21854 , -0.455269 , -1.23699 ) +colvars: ( -5.61922 , -0.606431 , -1.6477 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.891298 , 0.195673 , 0.616732 ) +colvars: ( 0.772142 , 0.266308 , 0.640787 ) +colvars: ( 0.756094 , 0.259429 , 0.622359 ) +colvars: ( 0.66079 , 0.266983 , 0.576903 ) +colvars: ( 0.648943 , 0.200479 , 0.482099 ) +colvars: ( 0.574658 , 0.344074 , 0.628704 ) +colvars: ( 0.467927 , 0.357967 , 0.58498 ) +colvars: ( 0.391581 , 0.455051 , 0.668902 ) +colvars: ( 0.386503 , 0.31346 , 0.478778 ) +colvars: ( 0.351918 , 0.271883 , 0.403698 ) +colvars: ( 0.357184 , 0.318769 , 0.46874 ) +colvars: ( 0.286175 , 0.27595 , 0.370829 ) +colvars: ( 0.259067 , 0.304963 , 0.393412 ) +colvars: ( 0.348379 , 0.178282 , 0.277908 ) +colvars: ( 0.289922 , 0.134969 , 0.186646 ) +colvars: ( 0.470672 , 0.141367 , 0.300252 ) +colvars: ( 0.542945 , 0.0501378 , 0.2217 ) +colvars: ( 0.671979 , 0.0292779 , 0.269189 ) +colvars: ( 0.551617 , 0.0183043 , 0.184664 ) +colvars: ( 0.535921 , -0.0466986 , 0.0896053 ) +colvars: ( 0.572551 , 0.0661567 , 0.260098 ) +colvars: ( 0.571165 , 0.0499642 , 0.237887 ) +colvars: ( 0.607674 , 0.114617 , 0.344591 ) +colvars: ( 0.447341 , 0.0543257 , 0.171619 ) +colvars: ( 0.440603 , -0.00157168 , 0.093809 ) +colvars: ( 0.345737 , 0.119833 , 0.199108 ) +colvars: ( 0.221711 , 0.128306 , 0.138157 ) +colvars: ( 0.130535 , 0.213916 , 0.198285 ) +colvars: ( 0.193512 , 0.0546557 , 0.0243941 ) +colvars: ( 0.144496 , 0.0184613 , -0.0519658 ) +colvars: ( 0.22684 , 0.0291951 , 0.0101261 ) +colvars: ( 0.212775 , -0.0432064 , -0.0937638 ) +colvars: ( 0.247784 , -0.0464628 , -0.0777029 ) +colvars: ( 0.28778 , -0.129023 , -0.163572 ) +colvars: ( 0.243957 , -0.182121 , -0.259256 ) +colvars: ( 0.402565 , -0.143942 , -0.11652 ) +colvars: ( 0.479778 , -0.219312 , -0.171233 ) +colvars: ( 0.610473 , -0.221791 , -0.09848 ) +colvars: ( 0.432816 , -0.22389 , -0.204604 ) +colvars: ( 0.438348 , -0.291888 , -0.291274 ) +colvars: ( 0.384354 , -0.150735 , -0.136093 ) +colvars: ( 0.330464 , -0.144587 , -0.159315 ) +colvars: ( 0.314107 , -0.0580393 , -0.0544232 ) +colvars: ( 0.207637 , -0.153472 , -0.242513 ) +colvars: ( 0.183407 , -0.195486 , -0.312148 ) +colvars: ( 0.00691859 , -0.199267 , -0.419816 ) +colvars: ( -0.0836733 , -0.217123 , -0.49612 ) +colvars: ( 0.106795 , -0.249015 , -0.427476 ) +colvars: ( 0.126051 , -0.112939 , -0.236394 ) +colvars: ( 0.00717829 , -0.117409 , -0.311455 ) +colvars: ( -0.0815173 , -0.0368843 , -0.256607 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.91958 , 0.530926 , 1.44255 ) +colvars: ( 4.21854 , 0.455269 , 1.23699 ) +colvars: ( 4.21854 , 0.455269 , 1.23699 ) +colvars: ( 5.61922 , 0.606431 , 1.6477 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.615342 , -0.081068 , -0.368479 ) +colvars: ( -0.553505 , -0.163637 , -0.33755 ) +colvars: ( -0.50365 , -0.141668 , -0.279279 ) +colvars: ( -0.514596 , -0.191058 , -0.308853 ) +colvars: ( -0.504985 , -0.132281 , -0.277084 ) +colvars: ( -0.490097 , -0.282912 , -0.318866 ) +colvars: ( -0.457678 , -0.323156 , -0.301505 ) +colvars: ( -0.436209 , -0.430275 , -0.320304 ) +colvars: ( -0.394855 , -0.28784 , -0.225202 ) +colvars: ( -0.390426 , -0.262575 , -0.211248 ) +colvars: ( -0.345528 , -0.282217 , -0.173614 ) +colvars: ( -0.285194 , -0.245382 , -0.0992369 ) +colvars: ( -0.23655 , -0.260285 , -0.0560627 ) +colvars: ( -0.304502 , -0.142388 , -0.0798233 ) +colvars: ( -0.273381 , -0.113153 , -0.0376045 ) +colvars: ( -0.358583 , -0.0851334 , -0.112505 ) +colvars: ( -0.385057 , 0.0129294 , -0.102135 ) +colvars: ( -0.434952 , 0.0604325 , -0.134289 ) +colvars: ( -0.42269 , 0.0279367 , -0.134226 ) +colvars: ( -0.41134 , 0.0846256 , -0.1015 ) +colvars: ( -0.466792 , -0.0260017 , -0.198765 ) +colvars: ( -0.501154 , -0.027447 , -0.233771 ) +colvars: ( -0.551051 , -0.0927449 , -0.308398 ) +colvars: ( -0.449417 , -0.0573788 , -0.193153 ) +colvars: ( -0.456289 , -0.0133598 , -0.183472 ) +colvars: ( -0.394593 , -0.131548 , -0.166095 ) +colvars: ( -0.337355 , -0.162769 , -0.120445 ) +colvars: ( -0.287219 , -0.252785 , -0.104056 ) +colvars: ( -0.296185 , -0.0900562 , -0.0517789 ) +colvars: ( -0.283119 , -0.0714562 , -0.0316726 ) +colvars: ( -0.276195 , -0.0452739 , -0.0148702 ) +colvars: ( -0.24082 , 0.0293502 , 0.0487042 ) +colvars: ( -0.219394 , 0.055675 , 0.0801032 ) +colvars: ( -0.284625 , 0.115958 , 0.0373792 ) +colvars: ( -0.258092 , 0.157662 , 0.0796913 ) +colvars: ( -0.353614 , 0.144017 , -0.0212458 ) +colvars: ( -0.402179 , 0.220082 , -0.0413122 ) +colvars: ( -0.472932 , 0.242591 , -0.103797 ) +colvars: ( -0.413904 , 0.200311 , -0.0605158 ) +colvars: ( -0.418379 , 0.261034 , -0.0421404 ) +colvars: ( -0.418576 , 0.113902 , -0.097734 ) +colvars: ( -0.425854 , 0.0838187 , -0.11636 ) +colvars: ( -0.447463 , -0.00932624 , -0.173101 ) +colvars: ( -0.359495 , 0.0725864 , -0.0540374 ) +colvars: ( -0.362874 , 0.098869 , -0.0475311 ) +colvars: ( -0.198989 , 0.105264 , 0.119238 ) +colvars: ( -0.149815 , 0.107142 , 0.169263 ) +colvars: ( -0.225264 , 0.177439 , 0.120061 ) +colvars: ( -0.297189 , 0.0319164 , -0.00686269 ) +colvars: ( -0.230788 , 0.018341 , 0.05462 ) +colvars: ( -0.177144 , -0.0646021 , 0.077191 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 22. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 22. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atoms_new_colvar_forces = { ( -4.64362435756377e+00 , -4.16321194704651e-01 , -1.19429889473242e+00 ), ( -3.99990228228794e+00 , -3.52598135092567e-01 , -9.33750729130365e-01 ), ( -4.07234574656897e+00 , -3.79343361453849e-01 , -9.68937574346586e-01 ), ( -5.47525911635614e+00 , -5.38233018229667e-01 , -1.44268823995777e+00 ), ( 2.52443878974175e-01 , 1.17761098390893e-01 , 3.43079799840084e-01 ), ( 5.00414122367090e+00 , 5.92087663798134e-01 , 1.75238933474071e+00 ), ( 4.22878886327925e+00 , 4.90080094159747e-01 , 1.52046305842616e+00 ), ( -4.46280359178790e-02 , 2.47762004595115e-02 , 3.48597602711519e-01 ), ( 4.21018749106888e+00 , 4.80888127688503e-01 , 1.49056312857843e+00 ), ( 5.58070893782491e+00 , 6.15739269805591e-01 , 1.84015406971542e+00 ), ( 1.16560390185008e-02 , 3.65525467641691e-02 , 2.95125823351423e-01 ), ( 9.81659743208296e-04 , 3.05674320767270e-02 , 2.71592117412813e-01 ), ( 2.25169962255657e-02 , 4.46787080637800e-02 , 3.37349563480097e-01 ), ( 4.38777508747790e-02 , 3.58933885204249e-02 , 1.98084615347076e-01 ), ( 1.65414412495288e-02 , 2.18165616472960e-02 , 1.49041838759211e-01 ), ( 1.12089410180446e-01 , 5.62334033509360e-02 , 1.87747091678590e-01 ), ( 1.57887832402783e-01 , 6.30671026451442e-02 , 1.19564898123775e-01 ), ( 2.37027646426410e-01 , 8.97104619239126e-02 , 1.34899768599632e-01 ), ( 1.28927625299104e-01 , 4.62409997861884e-02 , 5.04375352603180e-02 ), ( 1.24580777446472e-01 , 3.79269316016676e-02 , -1.18950734070895e-02 ), ( 1.05758966362700e-01 , 4.01550369258798e-02 , 6.13331183007590e-02 ), ( 7.00111307789357e-02 , 2.25172608486911e-02 , 4.11608199695629e-03 ), ( 5.66225054757612e-02 , 2.18724627965876e-02 , 3.61922221764853e-02 ), ( -2.07586912512614e-03 , -3.05310394112909e-03 , -2.15334968345647e-02 ), ( -1.56856338671580e-02 , -1.49314828907843e-02 , -8.96627593190330e-02 ), ( -4.88553187575593e-02 , -1.17150805661757e-02 , 3.30127740516600e-02 ), ( -1.15643753911786e-01 , -3.44630269244757e-02 , 1.77121421923910e-02 ), ( -1.56684032691026e-01 , -3.88689624831749e-02 , 9.42292664262888e-02 ), ( -1.02672896972464e-01 , -3.54005052022133e-02 , -2.73847821124761e-02 ), ( -1.38623680370081e-01 , -5.29948936680882e-02 , -8.36384310820289e-02 ), ( -4.93544699417768e-02 , -1.60788539367000e-02 , -4.74412059617574e-03 ), ( -2.80445145685205e-02 , -1.38562043370483e-02 , -4.50596633993366e-02 ), ( 2.83892512819499e-02 , 9.21212993929264e-03 , 2.40027252997335e-03 ), ( 3.15461838966752e-03 , -1.30651888932173e-02 , -1.26192440651879e-01 ), ( -1.41355141392519e-02 , -2.44590685877909e-02 , -1.79564641180884e-01 ), ( 4.89501835535262e-02 , 7.44406614283932e-05 , -1.37765548961327e-01 ), ( 7.75994828162370e-02 , 7.69860807433909e-04 , -2.12545309095866e-01 ), ( 1.37541041867537e-01 , 2.07998907278499e-02 , -2.02276924639687e-01 ), ( 1.89115205871051e-02 , -2.35785218526706e-02 , -2.65119764355857e-01 ), ( 1.99691487776887e-02 , -3.08539813306087e-02 , -3.33414135038022e-01 ), ( -3.42216386398688e-02 , -3.68330974030720e-02 , -2.33827287304473e-01 ), ( -9.53897625555590e-02 , -6.07678345582899e-02 , -2.75674898888469e-01 ), ( -1.33355821119989e-01 , -6.73654953556458e-02 , -2.27524402127826e-01 ), ( -1.51858084555335e-01 , -8.08852759274181e-02 , -2.96550372965769e-01 ), ( -1.79467185481772e-01 , -9.66173181891047e-02 , -3.59678625643018e-01 ), ( -1.92070427972810e-01 , -9.40038035575220e-02 , -3.00577504538688e-01 ), ( -2.33487922282650e-01 , -1.09981192810187e-01 , -3.26857082818203e-01 ), ( -1.18469480902050e-01 , -7.15757868124807e-02 , -3.07414654052692e-01 ), ( -1.71138351879817e-01 , -8.10225781627923e-02 , -2.43257156571619e-01 ), ( -2.23609708137560e-01 , -9.90676724726366e-02 , -2.56835211377563e-01 ), ( -2.58661817009153e-01 , -1.01486434045830e-01 , -1.79416398570087e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 22, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 23 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 23, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 23, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 23, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 23, atoms_positions[size = 51] = { ( 8.27429746962521e+00 , 4.06036157509702e-02 , -7.45811221333781e-01 ), ( 6.89814895970433e+00 , -5.57132158139863e-01 , -5.54788356134842e-01 ), ( 6.16125272567578e+00 , -3.90016952341577e-01 , 7.53315803491462e-01 ), ( 4.93116392242098e+00 , -1.53429427840197e-01 , 7.29416490736373e-01 ), ( 7.03649688185551e+00 , -2.05668176170026e+00 , -9.20135873083620e-01 ), ( 6.84311409611181e+00 , -2.67859649183596e-01 , 1.93086202222441e+00 ), ( 6.15708313102884e+00 , -1.82794871701656e-01 , 3.17847681418513e+00 ), ( 7.09156141113962e+00 , -3.50944028932900e-01 , 4.33683961026652e+00 ), ( 5.33464473956692e+00 , 1.08451682096381e+00 , 3.36111981091096e+00 ), ( 4.16494434116522e+00 , 1.01824808487741e+00 , 3.71552930081859e+00 ), ( 5.83683575193611e+00 , 2.25736920570107e+00 , 2.98445776181100e+00 ), ( 5.22541833598088e+00 , 3.57338366341035e+00 , 2.91891741946717e+00 ), ( 6.31975668496333e+00 , 4.49728306687404e+00 , 2.33595952085990e+00 ), ( 3.86854834426804e+00 , 3.68678879862976e+00 , 2.04314849685128e+00 ), ( 2.79092021797047e+00 , 4.16716484800730e+00 , 2.47188339052941e+00 ), ( 3.94112456132453e+00 , 3.23121327161743e+00 , 7.30485435503054e-01 ), ( 2.68917923481445e+00 , 3.00985703632277e+00 , -9.59822598095681e-02 ), ( 3.07308339945478e+00 , 2.68704707092774e+00 , -1.51906596728011e+00 ), ( 1.58737847579211e+00 , 2.17134676522185e+00 , 4.30734536433780e-01 ), ( 3.74821443213923e-01 , 2.60221365390555e+00 , 4.97585218223441e-01 ), ( 2.06790892817259e+00 , 1.11471083676162e+00 , 1.05548307716818e+00 ), ( 1.16795595293091e+00 , 1.16868356395829e-01 , 1.70092692741333e+00 ), ( 2.05454167484371e+00 , -1.09489668855112e+00 , 2.01963989919140e+00 ), ( 5.67866725486009e-01 , 6.16146933472038e-01 , 2.95740603646982e+00 ), ( -5.88980055708600e-01 , 3.51033993940136e-01 , 3.16198944729408e+00 ), ( 1.30605835604312e+00 , 1.34986049662244e+00 , 3.75185787266952e+00 ), ( 8.39694040643978e-01 , 1.98343834749641e+00 , 5.02624629998882e+00 ), ( 2.10223057455384e+00 , 2.71474388011875e+00 , 5.70141476330299e+00 ), ( -3.41257639357982e-01 , 2.91180788190043e+00 , 4.96993475672268e+00 ), ( -1.12684878864093e+00 , 3.06513076193413e+00 , 5.88058299115213e+00 ), ( -5.26532904763311e-01 , 3.51793805397593e+00 , 3.83523410140131e+00 ), ( -1.51415914887447e+00 , 4.52540752968940e+00 , 3.42282884797735e+00 ), ( -7.01916490147006e-01 , 5.41957919293459e+00 , 2.46832911241757e+00 ), ( -2.74963874236576e+00 , 3.91240327457789e+00 , 2.87395787177507e+00 ), ( -3.81432478709398e+00 , 4.52664284036742e+00 , 2.81284146638220e+00 ), ( -2.64356861389524e+00 , 2.66159465661507e+00 , 2.38111124489002e+00 ), ( -3.78187860183613e+00 , 1.80523304800468e+00 , 2.00006801750482e+00 ), ( -3.37671144410218e+00 , 8.82891697112618e-01 , 8.55454353608698e-01 ), ( -4.30287987719178e+00 , 1.06813451849581e+00 , 3.20949923764685e+00 ), ( -5.49471689898236e+00 , 7.97234279198013e-01 , 3.33162209619445e+00 ), ( -3.36446502722670e+00 , 7.04350371015529e-01 , 4.20636710688359e+00 ), ( -3.68477391160051e+00 , 6.26164951003031e-02 , 5.44375977334306e+00 ), ( -2.39249633019791e+00 , -3.23155733881825e-01 , 6.16160494964322e+00 ), ( -4.46124577897500e+00 , 9.61199961240979e-01 , 6.43270939921157e+00 ), ( -5.36436620737384e+00 , 5.92973254830113e-01 , 7.21899210478604e+00 ), ( -6.25981886385414e+00 , 3.62108568985818e+00 , 6.74504377670797e+00 ), ( -6.97067612820316e+00 , 4.29617417823745e+00 , 7.48746343048008e+00 ), ( -6.71753772535898e+00 , 3.17157222271881e+00 , 5.50659759266702e+00 ), ( -4.12191899872338e+00 , 2.24379465112528e+00 , 6.39452046099481e+00 ), ( -4.80698644005936e+00 , 3.23069779342996e+00 , 7.25362618631062e+00 ), ( -4.07499670009177e+00 , 4.55819783133641e+00 , 7.27536757501923e+00 ) } +colvars: Step 23, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_ids[size = 0] = +colvars: Step 23, atom_groups_refcount[size = 0] = +colvars: Step 23, atom_groups_masses[size = 0] = +colvars: Step 23, atom_groups_charges[size = 0] = +colvars: Step 23, atom_groups_coms[size = 0] = +colvars: Step 23, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 23, volmaps_ids[size = 0] = +colvars: Step 23, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 23 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.01235983053210e-01 , -3.61953298784803e-03 , 9.53542752840645e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.01235983053210e-01 , -3.61953298784803e-03 , 9.53542752840645e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.5427 , 2.02419 , -15.1673 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.5427 , 2.02419 , -15.1673 ) to colvar "one". +colvars: Adding total bias energy: 44.3287 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.5427 , 2.02419 , -15.1673 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.92136 , -0.529959 , -1.43864 ) +colvars: ( -4.22006 , -0.45444 , -1.23363 ) +colvars: ( -4.22006 , -0.45444 , -1.23363 ) +colvars: ( -5.62125 , -0.605327 , -1.64323 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.890716 , 0.195751 , 0.615641 ) +colvars: ( 0.771705 , 0.266344 , 0.639594 ) +colvars: ( 0.75561 , 0.259466 , 0.621163 ) +colvars: ( 0.660525 , 0.266983 , 0.575802 ) +colvars: ( 0.648693 , 0.200481 , 0.481178 ) +colvars: ( 0.574528 , 0.344039 , 0.627476 ) +colvars: ( 0.46797 , 0.357895 , 0.583809 ) +colvars: ( 0.391741 , 0.454946 , 0.667544 ) +colvars: ( 0.386619 , 0.313369 , 0.477765 ) +colvars: ( 0.352104 , 0.271783 , 0.40283 ) +colvars: ( 0.357281 , 0.318673 , 0.467708 ) +colvars: ( 0.286328 , 0.275838 , 0.369941 ) +colvars: ( 0.259195 , 0.304846 , 0.39244 ) +colvars: ( 0.348441 , 0.178198 , 0.277222 ) +colvars: ( 0.290061 , 0.134871 , 0.186115 ) +colvars: ( 0.470567 , 0.141325 , 0.29957 ) +colvars: ( 0.542738 , 0.0501261 , 0.221198 ) +colvars: ( 0.671582 , 0.0293096 , 0.268637 ) +colvars: ( 0.551456 , 0.0182934 , 0.184265 ) +colvars: ( 0.535781 , -0.0467091 , 0.0893861 ) +colvars: ( 0.572413 , 0.0661445 , 0.259585 ) +colvars: ( 0.571088 , 0.0499483 , 0.237445 ) +colvars: ( 0.607595 , 0.114604 , 0.343977 ) +colvars: ( 0.447441 , 0.0542698 , 0.171263 ) +colvars: ( 0.440734 , -0.00162684 , 0.0936123 ) +colvars: ( 0.345957 , 0.119742 , 0.198649 ) +colvars: ( 0.222099 , 0.128175 , 0.13777 ) +colvars: ( 0.131027 , 0.213751 , 0.197734 ) +colvars: ( 0.193899 , 0.0545245 , 0.0241991 ) +colvars: ( 0.144969 , 0.0183161 , -0.0520214 ) +colvars: ( 0.227127 , 0.0290807 , 0.00994534 ) +colvars: ( 0.21304 , -0.0433161 , -0.0937664 ) +colvars: ( 0.24794 , -0.0465565 , -0.0777525 ) +colvars: ( 0.287966 , -0.129104 , -0.163398 ) +colvars: ( 0.244197 , -0.182211 , -0.258915 ) +colvars: ( 0.402621 , -0.143988 , -0.11638 ) +colvars: ( 0.479757 , -0.21933 , -0.170943 ) +colvars: ( 0.610292 , -0.221769 , -0.0982739 ) +colvars: ( 0.432914 , -0.223926 , -0.204241 ) +colvars: ( 0.438448 , -0.291918 , -0.290735 ) +colvars: ( 0.384556 , -0.150796 , -0.135865 ) +colvars: ( 0.330792 , -0.144668 , -0.159037 ) +colvars: ( 0.314496 , -0.0581364 , -0.0543378 ) +colvars: ( 0.208117 , -0.15359 , -0.242127 ) +colvars: ( 0.183948 , -0.195611 , -0.311622 ) +colvars: ( 0.00756533 , -0.199437 , -0.419212 ) +colvars: ( -0.0829134 , -0.217319 , -0.495407 ) +colvars: ( 0.107278 , -0.249147 , -0.426832 ) +colvars: ( 0.126598 , -0.113083 , -0.236073 ) +colvars: ( 0.00786893 , -0.117588 , -0.311042 ) +colvars: ( -0.080734 , -0.0370963 , -0.256349 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.92136 , 0.529959 , 1.43864 ) +colvars: ( 4.22006 , 0.45444 , 1.23363 ) +colvars: ( 4.22006 , 0.45444 , 1.23363 ) +colvars: ( 5.62125 , 0.605327 , 1.64323 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.615116 , -0.0811182 , -0.367766 ) +colvars: ( -0.553328 , -0.163822 , -0.336621 ) +colvars: ( -0.503272 , -0.141781 , -0.278193 ) +colvars: ( -0.514562 , -0.191291 , -0.307976 ) +colvars: ( -0.50494 , -0.132404 , -0.27637 ) +colvars: ( -0.490199 , -0.283315 , -0.317847 ) +colvars: ( -0.45794 , -0.323634 , -0.300521 ) +colvars: ( -0.436592 , -0.43095 , -0.319117 ) +colvars: ( -0.39505 , -0.288229 , -0.224236 ) +colvars: ( -0.390705 , -0.262923 , -0.210442 ) +colvars: ( -0.345565 , -0.282568 , -0.172486 ) +colvars: ( -0.285146 , -0.245641 , -0.0981115 ) +colvars: ( -0.23634 , -0.260542 , -0.05471 ) +colvars: ( -0.304365 , -0.142459 , -0.0789207 ) +colvars: ( -0.273267 , -0.113162 , -0.036803 ) +colvars: ( -0.358348 , -0.0851094 , -0.111689 ) +colvars: ( -0.384739 , 0.0131297 , -0.101534 ) +colvars: ( -0.434493 , 0.0607143 , -0.133702 ) +colvars: ( -0.422534 , 0.0281399 , -0.133851 ) +colvars: ( -0.411178 , 0.0849359 , -0.101284 ) +colvars: ( -0.466792 , -0.0259224 , -0.198403 ) +colvars: ( -0.50133 , -0.0273947 , -0.233597 ) +colvars: ( -0.551365 , -0.0928377 , -0.308187 ) +colvars: ( -0.449709 , -0.0573736 , -0.192993 ) +colvars: ( -0.456638 , -0.0132811 , -0.183504 ) +colvars: ( -0.394917 , -0.131663 , -0.165728 ) +colvars: ( -0.337768 , -0.162929 , -0.120059 ) +colvars: ( -0.287655 , -0.253095 , -0.103407 ) +colvars: ( -0.29648 , -0.0900622 , -0.0514752 ) +colvars: ( -0.283499 , -0.0714308 , -0.0315074 ) +colvars: ( -0.27629 , -0.0451769 , -0.0144878 ) +colvars: ( -0.240783 , 0.0296042 , 0.0490107 ) +colvars: ( -0.219144 , 0.056 , 0.0805576 ) +colvars: ( -0.284583 , 0.116356 , 0.0374181 ) +colvars: ( -0.258052 , 0.158144 , 0.0796121 ) +colvars: ( -0.35357 , 0.144444 , -0.0213105 ) +colvars: ( -0.402146 , 0.220631 , -0.0416319 ) +colvars: ( -0.472858 , 0.243162 , -0.104163 ) +colvars: ( -0.414073 , 0.200805 , -0.0609873 ) +colvars: ( -0.418555 , 0.261637 , -0.0428032 ) +colvars: ( -0.418912 , 0.114225 , -0.0981215 ) +colvars: ( -0.42639 , 0.0840693 , -0.116866 ) +colvars: ( -0.448153 , -0.00926365 , -0.173495 ) +colvars: ( -0.360071 , 0.0728344 , -0.0545299 ) +colvars: ( -0.363542 , 0.0991567 , -0.0481978 ) +colvars: ( -0.199371 , 0.105637 , 0.118898 ) +colvars: ( -0.150226 , 0.107532 , 0.168903 ) +colvars: ( -0.225477 , 0.177948 , 0.119672 ) +colvars: ( -0.297699 , 0.0321153 , -0.00714581 ) +colvars: ( -0.231326 , 0.0185339 , 0.0543697 ) +colvars: ( -0.17768 , -0.0645428 , 0.0772082 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 23. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 23. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atoms_new_colvar_forces = { ( -4.64575743161289e+00 , -4.15326505613297e-01 , -1.19076296803634e+00 ), ( -4.00168649092185e+00 , -3.51917355348099e-01 , -9.30658258525421e-01 ), ( -4.07410036359722e+00 , -3.78747790308645e-01 , -9.65806221149623e-01 ), ( -5.47749434496204e+00 , -5.37249924020170e-01 , -1.43842446864572e+00 ), ( 2.52337569752722e-01 , 1.17684984808824e-01 , 3.42969682070111e-01 ), ( 5.00568797229590e+00 , 5.90683442199245e-01 , 1.74826643842408e+00 ), ( 4.23009348282879e+00 , 4.88701588795172e-01 , 1.51691973520631e+00 ), ( -4.48506074491610e-02 , 2.39964121041804e-02 , 3.48426543992292e-01 ), ( 4.21163211404291e+00 , 4.79579587722694e-01 , 1.48716072007476e+00 ), ( 5.58264553620788e+00 , 6.14187100999375e-01 , 1.83562067933871e+00 ), ( 1.17154659552674e-02 , 3.61057291843637e-02 , 2.95221900517982e-01 ), ( 1.18209149819765e-03 , 3.01974765346887e-02 , 2.71829459849482e-01 ), ( 2.28548090668328e-02 , 4.43034216412574e-02 , 3.37730058256575e-01 ), ( 4.40755488767677e-02 , 3.57393096815321e-02 , 1.98301723434123e-01 ), ( 1.67933492779154e-02 , 2.17090047723988e-02 , 1.49312323153462e-01 ), ( 1.12218626939172e-01 , 5.62154114348050e-02 , 1.87880852793175e-01 ), ( 1.57999076492278e-01 , 6.32557423895876e-02 , 1.19663089947760e-01 ), ( 2.37089595724080e-01 , 9.00238756066837e-02 , 1.34935360934111e-01 ), ( 1.28921942478751e-01 , 4.64332948188317e-02 , 5.04141739618137e-02 ), ( 1.24602841198467e-01 , 3.82267546652744e-02 , -1.18977005562169e-02 ), ( 1.05621047589969e-01 , 4.02220936174156e-02 , 6.11820468842756e-02 ), ( 6.97572206409900e-02 , 2.25535655601284e-02 , 3.84721902750745e-03 ), ( 5.62300373090633e-02 , 2.17663372155614e-02 , 3.57901822997330e-02 ), ( -2.26856832183570e-03 , -3.10378001723801e-03 , -2.17303933299124e-02 ), ( -1.59043130583791e-02 , -1.49079527395067e-02 , -8.98921637339600e-02 ), ( -4.89597869999016e-02 , -1.19214583726327e-02 , 3.29207740570250e-02 ), ( -1.15668917471507e-01 , -3.47545911866313e-02 , 1.77107199605389e-02 ), ( -1.56628441055632e-01 , -3.93440147550789e-02 , 9.43269694789447e-02 ), ( -1.02580792170127e-01 , -3.55377061897655e-02 , -2.72761258967842e-02 ), ( -1.38530076890726e-01 , -5.31146259469866e-02 , -8.35288200314778e-02 ), ( -4.91632319023408e-02 , -1.60961005962525e-02 , -4.54246659236648e-03 ), ( -2.77427244171411e-02 , -1.37119281359061e-02 , -4.47556526852855e-02 ), ( 2.87952298701709e-02 , 9.44344188904662e-03 , 2.80501871740882e-03 ), ( 3.38225490613692e-03 , -1.27481720264506e-02 , -1.25979646178916e-01 ), ( -1.38553165859354e-02 , -2.40670947864300e-02 , -1.79302478598568e-01 ), ( 4.90509220560931e-02 , 4.56027763740180e-04 , -1.37690919185591e-01 ), ( 7.76114436868072e-02 , 1.30168634415467e-03 , -2.12575353587131e-01 ), ( 1.37433913707760e-01 , 2.13935019699319e-02 , -2.02437070743730e-01 ), ( 1.88415277808113e-02 , -2.31204846158066e-02 , -2.65228343518005e-01 ), ( 1.98931297036014e-02 , -3.02810928129784e-02 , -3.33537853596992e-01 ), ( -3.43557749957396e-02 , -3.65705614186257e-02 , -2.33986587762447e-01 ), ( -9.55978177063489e-02 , -6.05991137373955e-02 , -2.75902768015860e-01 ), ( -1.33656605971950e-01 , -6.74000200873311e-02 , -2.27832501128480e-01 ), ( -1.51954015420723e-01 , -8.07559029622601e-02 , -2.96657197009173e-01 ), ( -1.79594076018584e-01 , -9.64546783264336e-02 , -3.59819710675989e-01 ), ( -1.91806007504498e-01 , -9.38006688845488e-02 , -3.00313608283580e-01 ), ( -2.33139361551305e-01 , -1.09787613794228e-01 , -3.26503908255684e-01 ), ( -1.18199679569238e-01 , -7.11991167996441e-02 , -3.07160010584178e-01 ), ( -1.71101171967787e-01 , -8.09679159362541e-02 , -2.43219104040647e-01 ), ( -2.23456922888711e-01 , -9.90544977745803e-02 , -2.56672402983881e-01 ), ( -2.58413908875762e-01 , -1.01639124525717e-01 , -1.79140969048224e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 23, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 24 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 24, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 24, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 24, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 24, atoms_positions[size = 51] = { ( 8.27050693486260e+00 , 4.09127624982683e-02 , -7.42806090655381e-01 ), ( 6.88621568670105e+00 , -5.60059310726248e-01 , -5.48572870137821e-01 ), ( 6.16129515518780e+00 , -3.91528458308412e-01 , 7.61792087129228e-01 ), ( 4.92542029440314e+00 , -1.51106013324024e-01 , 7.31554147396332e-01 ), ( 7.03158015113448e+00 , -2.05833099972738e+00 , -9.15047607445865e-01 ), ( 6.83685602186459e+00 , -2.70283755271464e-01 , 1.93814536333249e+00 ), ( 6.14926766592578e+00 , -1.89834653758469e-01 , 3.17319789943851e+00 ), ( 7.09737077078941e+00 , -3.49242475123280e-01 , 4.34462371079293e+00 ), ( 5.33740413028451e+00 , 1.08125850749346e+00 , 3.36358957320595e+00 ), ( 4.16698029952191e+00 , 1.01613213148207e+00 , 3.72380456879332e+00 ), ( 5.83622822234833e+00 , 2.25768751732082e+00 , 2.98264484758702e+00 ), ( 5.21770525001130e+00 , 3.57159769982799e+00 , 2.91628322785553e+00 ), ( 6.31856084523342e+00 , 4.49558404118750e+00 , 2.32664546080003e+00 ), ( 3.86540003615781e+00 , 3.68008032912721e+00 , 2.04181222945337e+00 ), ( 2.79234653437798e+00 , 4.16849762794638e+00 , 2.46653775960343e+00 ), ( 3.93894407351176e+00 , 3.22710308982714e+00 , 7.30815791996592e-01 ), ( 2.70065275513418e+00 , 3.01473889718690e+00 , -9.27152726836277e-02 ), ( 3.08019268103090e+00 , 2.68051811103968e+00 , -1.52260975474361e+00 ), ( 1.58038830167703e+00 , 2.17003449741302e+00 , 4.27962272263170e-01 ), ( 3.76890274720497e-01 , 2.60709693889937e+00 , 4.92780740745977e-01 ), ( 2.07252038371650e+00 , 1.12651473936430e+00 , 1.05129402273852e+00 ), ( 1.17052731382972e+00 , 1.16829247964910e-01 , 1.70099197039943e+00 ), ( 2.05871543839403e+00 , -1.09333228271432e+00 , 2.02319394446356e+00 ), ( 5.69756880392859e-01 , 6.17173953491876e-01 , 2.96096018787920e+00 ), ( -5.86243433177253e-01 , 3.51659672810033e-01 , 3.16315867736680e+00 ), ( 1.30238298539933e+00 , 1.35292658013224e+00 , 3.74693045288870e+00 ), ( 8.40858366637640e-01 , 1.98373489008161e+00 , 5.02674892399775e+00 ), ( 2.10681210803961e+00 , 2.72271512704815e+00 , 5.70693551908920e+00 ), ( -3.43519716856437e-01 , 2.91051405358141e+00 , 4.97016881234955e+00 ), ( -1.12387250168073e+00 , 3.06582026354575e+00 , 5.87892589210738e+00 ), ( -5.30941070523270e-01 , 3.51483565419997e+00 , 3.82945260072042e+00 ), ( -1.51009601578230e+00 , 4.51944029487591e+00 , 3.41844225089706e+00 ), ( -7.04741000935523e-01 , 5.42139590392118e+00 , 2.46955612833754e+00 ), ( -2.74711625974549e+00 , 3.92045483929236e+00 , 2.86448152596536e+00 ), ( -3.81315408423867e+00 , 4.53202703049446e+00 , 2.81263944285830e+00 ), ( -2.65056261819155e+00 , 2.65589992586603e+00 , 2.37525860555684e+00 ), ( -3.78440623690736e+00 , 1.80874861947133e+00 , 2.00140403543296e+00 ), ( -3.37325789577578e+00 , 8.80921883554445e-01 , 8.49016180122185e-01 ), ( -4.29366231321076e+00 , 1.06600016042967e+00 , 3.21169541573497e+00 ), ( -5.49325096069121e+00 , 7.90243302203479e-01 , 3.33255878205230e+00 ), ( -3.36481210388283e+00 , 7.08989670222816e-01 , 4.20302865597447e+00 ), ( -3.68098259644715e+00 , 6.77797847171094e-02 , 5.44961457973166e+00 ), ( -2.39221081333703e+00 , -3.24595516895883e-01 , 6.15769699700810e+00 ), ( -4.46254628074192e+00 , 9.51820412579295e-01 , 6.43014976591291e+00 ), ( -5.36498975547215e+00 , 5.91014109823318e-01 , 7.21797246583130e+00 ), ( -6.26900483511788e+00 , 3.62489895007615e+00 , 6.74769857767828e+00 ), ( -6.97428682336797e+00 , 4.29572777976654e+00 , 7.49109946089408e+00 ), ( -6.70718335849590e+00 , 3.16863207438861e+00 , 5.50803787349925e+00 ), ( -4.11907560491057e+00 , 2.24489507816142e+00 , 6.39175562171674e+00 ), ( -4.80799524228886e+00 , 3.23983746770053e+00 , 7.25614184578735e+00 ), ( -4.06686554058490e+00 , 4.55359210114628e+00 , 7.27360166871903e+00 ) } +colvars: Step 24, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_ids[size = 0] = +colvars: Step 24, atom_groups_refcount[size = 0] = +colvars: Step 24, atom_groups_masses[size = 0] = +colvars: Step 24, atom_groups_charges[size = 0] = +colvars: Step 24, atom_groups_coms[size = 0] = +colvars: Step 24, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 24, volmaps_ids[size = 0] = +colvars: Step 24, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 24 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.00350438745275e-01 , -4.92097847437880e-03 , 9.53816228587234e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.00350438745275e-01 , -4.92097847437880e-03 , 9.53816228587234e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.525 , 2.05022 , -15.1727 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.525 , 2.05022 , -15.1727 ) to colvar "one". +colvars: Adding total bias energy: 44.2971 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.525 , 2.05022 , -15.1727 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.92294 , -0.529051 , -1.43515 ) +colvars: ( -4.22142 , -0.453661 , -1.23064 ) +colvars: ( -4.22142 , -0.453661 , -1.23064 ) +colvars: ( -5.62305 , -0.60429 , -1.63925 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.890158 , 0.195821 , 0.614626 ) +colvars: ( 0.771286 , 0.26637 , 0.638486 ) +colvars: ( 0.755155 , 0.259493 , 0.620056 ) +colvars: ( 0.660266 , 0.266973 , 0.574779 ) +colvars: ( 0.648449 , 0.200476 , 0.480325 ) +colvars: ( 0.574395 , 0.343992 , 0.626335 ) +colvars: ( 0.467996 , 0.357811 , 0.58272 ) +colvars: ( 0.391877 , 0.454825 , 0.666279 ) +colvars: ( 0.38672 , 0.313268 , 0.476828 ) +colvars: ( 0.352268 , 0.271676 , 0.402028 ) +colvars: ( 0.357371 , 0.318567 , 0.466756 ) +colvars: ( 0.286477 , 0.275719 , 0.369128 ) +colvars: ( 0.259328 , 0.304718 , 0.391552 ) +colvars: ( 0.348504 , 0.178111 , 0.2766 ) +colvars: ( 0.290197 , 0.134772 , 0.185638 ) +colvars: ( 0.470472 , 0.14128 , 0.29895 ) +colvars: ( 0.542547 , 0.0501158 , 0.220746 ) +colvars: ( 0.671214 , 0.0293426 , 0.268139 ) +colvars: ( 0.551302 , 0.018286 , 0.183907 ) +colvars: ( 0.535647 , -0.0467126 , 0.0891965 ) +colvars: ( 0.572275 , 0.0661336 , 0.259116 ) +colvars: ( 0.570999 , 0.0499352 , 0.237038 ) +colvars: ( 0.607498 , 0.11459 , 0.343406 ) +colvars: ( 0.447519 , 0.0542176 , 0.170937 ) +colvars: ( 0.440839 , -0.00167516 , 0.0934357 ) +colvars: ( 0.346151 , 0.119651 , 0.19823 ) +colvars: ( 0.222452 , 0.128045 , 0.137418 ) +colvars: ( 0.13148 , 0.213583 , 0.197232 ) +colvars: ( 0.194257 , 0.0543986 , 0.0240312 ) +colvars: ( 0.145406 , 0.0181787 , -0.0520592 ) +colvars: ( 0.227396 , 0.0289722 , 0.00979407 ) +colvars: ( 0.213295 , -0.0434165 , -0.0937475 ) +colvars: ( 0.248099 , -0.0466416 , -0.0777743 ) +colvars: ( 0.288142 , -0.129171 , -0.163215 ) +colvars: ( 0.244426 , -0.182285 , -0.258574 ) +colvars: ( 0.402672 , -0.144021 , -0.116233 ) +colvars: ( 0.479732 , -0.21933 , -0.170657 ) +colvars: ( 0.610112 , -0.22173 , -0.0980683 ) +colvars: ( 0.432995 , -0.223944 , -0.203889 ) +colvars: ( 0.438529 , -0.291926 , -0.290218 ) +colvars: ( 0.384729 , -0.150841 , -0.135642 ) +colvars: ( 0.331077 , -0.144735 , -0.15877 ) +colvars: ( 0.314835 , -0.0582218 , -0.0542539 ) +colvars: ( 0.208549 , -0.153692 , -0.241757 ) +colvars: ( 0.184434 , -0.195717 , -0.311122 ) +colvars: ( 0.00816947 , -0.199587 , -0.418628 ) +colvars: ( -0.0822007 , -0.217494 , -0.494719 ) +colvars: ( 0.10773 , -0.249258 , -0.426209 ) +colvars: ( 0.127099 , -0.113212 , -0.23576 ) +colvars: ( 0.00850869 , -0.117752 , -0.31064 ) +colvars: ( -0.080003 , -0.0372957 , -0.25609 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.92294 , 0.529051 , 1.43515 ) +colvars: ( 4.22142 , 0.453661 , 1.23064 ) +colvars: ( 4.22142 , 0.453661 , 1.23064 ) +colvars: ( 5.62305 , 0.60429 , 1.63925 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.614908 , -0.0811558 , -0.367132 ) +colvars: ( -0.553162 , -0.164001 , -0.335769 ) +colvars: ( -0.502907 , -0.141886 , -0.277178 ) +colvars: ( -0.514532 , -0.191526 , -0.307171 ) +colvars: ( -0.504899 , -0.132525 , -0.27572 ) +colvars: ( -0.490299 , -0.283728 , -0.316903 ) +colvars: ( -0.458193 , -0.324129 , -0.299607 ) +colvars: ( -0.436961 , -0.431652 , -0.318006 ) +colvars: ( -0.395233 , -0.288635 , -0.223328 ) +colvars: ( -0.390969 , -0.263289 , -0.209691 ) +colvars: ( -0.34559 , -0.282933 , -0.171411 ) +colvars: ( -0.285081 , -0.245912 , -0.0970286 ) +colvars: ( -0.236114 , -0.260811 , -0.0533969 ) +colvars: ( -0.304216 , -0.142534 , -0.0780551 ) +colvars: ( -0.273137 , -0.113177 , -0.0360307 ) +colvars: ( -0.358108 , -0.0850827 , -0.110915 ) +colvars: ( -0.384419 , 0.0133403 , -0.100971 ) +colvars: ( -0.434041 , 0.0610141 , -0.133157 ) +colvars: ( -0.422376 , 0.0283513 , -0.133514 ) +colvars: ( -0.411012 , 0.0852568 , -0.101099 ) +colvars: ( -0.46679 , -0.0258397 , -0.198088 ) +colvars: ( -0.501503 , -0.0273424 , -0.233474 ) +colvars: ( -0.551676 , -0.0929349 , -0.308036 ) +colvars: ( -0.44999 , -0.0573747 , -0.192876 ) +colvars: ( -0.456975 , -0.0132079 , -0.183576 ) +colvars: ( -0.395224 , -0.13179 , -0.165403 ) +colvars: ( -0.338156 , -0.163108 , -0.119707 ) +colvars: ( -0.288061 , -0.25343 , -0.102794 ) +colvars: ( -0.296749 , -0.0900821 , -0.0511945 ) +colvars: ( -0.283848 , -0.071421 , -0.0313599 ) +colvars: ( -0.276362 , -0.0450871 , -0.0141246 ) +colvars: ( -0.240723 , 0.0298563 , 0.0493082 ) +colvars: ( -0.218875 , 0.056329 , 0.0810049 ) +colvars: ( -0.284522 , 0.116757 , 0.0374498 ) +colvars: ( -0.25799 , 0.158631 , 0.0795338 ) +colvars: ( -0.353513 , 0.14488 , -0.0213902 ) +colvars: ( -0.402104 , 0.221194 , -0.041966 ) +colvars: ( -0.472782 , 0.243751 , -0.104553 ) +colvars: ( -0.414228 , 0.201307 , -0.0614735 ) +colvars: ( -0.418718 , 0.26225 , -0.0434751 ) +colvars: ( -0.419231 , 0.114547 , -0.0985298 ) +colvars: ( -0.426903 , 0.0843128 , -0.117393 ) +colvars: ( -0.44882 , -0.00921564 , -0.173919 ) +colvars: ( -0.360618 , 0.0730712 , -0.0550341 ) +colvars: ( -0.364178 , 0.099432 , -0.0488725 ) +colvars: ( -0.199715 , 0.105999 , 0.118571 ) +colvars: ( -0.150593 , 0.107908 , 0.168564 ) +colvars: ( -0.225658 , 0.178455 , 0.119295 ) +colvars: ( -0.298176 , 0.0323002 , -0.00743635 ) +colvars: ( -0.231824 , 0.0187091 , 0.054121 ) +colvars: ( -0.178171 , -0.0645071 , 0.077227 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 24. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 24. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atoms_new_colvar_forces = { ( -4.64768925340399e+00 , -4.14385897830330e-01 , -1.18765726324132e+00 ), ( -4.00329633385016e+00 , -3.51292610341177e-01 , -9.27924699615057e-01 ), ( -4.07568479174637e+00 , -3.78213636415218e-01 , -9.63034016470924e-01 ), ( -5.47950289858256e+00 , -5.36338777500186e-01 , -1.43464549015554e+00 ), ( 2.52247728100370e-01 , 1.17607144837762e-01 , 3.42878285760502e-01 ), ( 5.00703567367485e+00 , 5.89314673083556e-01 , 1.74458359343299e+00 ), ( 4.23122189922366e+00 , 4.87343341846568e-01 , 1.51375504692721e+00 ), ( -4.50844355471096e-02 , 2.31735662897316e-02 , 3.48273210603471e-01 ), ( 4.21290595488496e+00 , 4.78294858967199e-01 , 1.48414202929429e+00 ), ( 5.58435188446993e+00 , 6.12676862849093e-01 , 1.83158756566952e+00 ), ( 1.17815309183518e-02 , 3.56344350859484e-02 , 2.95345052165564e-01 ), ( 1.39527720639177e-03 , 2.98070494706035e-02 , 2.72099411002732e-01 ), ( 2.32145233122851e-02 , 4.39074599414199e-02 , 3.38155328130077e-01 ), ( 4.42884388578303e-02 , 3.55770183824760e-02 , 1.98544622085880e-01 ), ( 1.70606064798460e-02 , 2.15954895259924e-02 , 1.49607801367326e-01 ), ( 1.12364402327663e-01 , 5.61973759167895e-02 , 1.88034958832262e-01 ), ( 1.58128706307591e-01 , 6.34561297058981e-02 , 1.19774406274265e-01 ), ( 2.37173419024315e-01 , 9.03566710502176e-02 , 1.34981565454175e-01 ), ( 1.28925952277339e-01 , 4.66373627711320e-02 , 5.03926675630357e-02 ), ( 1.24635092654600e-01 , 3.85441920074173e-02 , -1.19020764141277e-02 ), ( 1.05484534568384e-01 , 4.02939372512230e-02 , 6.10272351547240e-02 ), ( 6.94956820275506e-02 , 2.25927287032315e-02 , 3.56447470925120e-03 ), ( 5.58222546537899e-02 , 2.16552368518423e-02 , 3.53699234236275e-02 ), ( -2.47135925810860e-03 , -3.15710012834207e-03 , -2.19389956134244e-02 ), ( -1.61360408849052e-02 , -1.48830978119519e-02 , -9.01399907045330e-02 ), ( -4.90728248685874e-02 , -1.21395414838307e-02 , 3.28268230544758e-02 ), ( -1.15703711744919e-01 , -3.50632298865104e-02 , 1.77112250988428e-02 ), ( -1.56580705937949e-01 , -3.98466686837114e-02 , 9.44376794295900e-02 ), ( -1.02491861011419e-01 , -3.56834795290565e-02 , -2.71633668503098e-02 ), ( -1.38442750990986e-01 , -5.32423094681212e-02 , -8.34190841660912e-02 ), ( -4.89660148765012e-02 , -1.61149140274058e-02 , -4.33054415288853e-03 ), ( -2.74281777646190e-02 , -1.35602397762497e-02 , -4.44392822423457e-02 ), ( 2.92238361493918e-02 , 9.68738890265097e-03 , 3.23053726750785e-03 ), ( 3.62043830759501e-03 , -1.24139036315880e-02 , -1.25765456593385e-01 ), ( -1.35636932780754e-02 , -2.36539584331770e-02 , -1.79040307025521e-01 ), ( 4.91590633679874e-02 , 8.58945727306770e-04 , -1.37623114702033e-01 ), ( 7.76277306438035e-02 , 1.86343451800031e-03 , -2.12623385200723e-01 ), ( 1.37329610487336e-01 , 2.20210884399716e-02 , -2.02621448432406e-01 ), ( 1.87668989808830e-02 , -2.26370595571488e-02 , -2.65362555955722e-01 ), ( 1.98116057162201e-02 , -2.96764945622195e-02 , -3.33693128572212e-01 ), ( -3.45014111337715e-02 , -3.62938188514576e-02 , -2.34171460541389e-01 ), ( -9.58260107055832e-02 , -6.04218507684637e-02 , -2.76162522816596e-01 ), ( -1.33984559994027e-01 , -6.74374435503455e-02 , -2.28172756594489e-01 ), ( -1.52068778590725e-01 , -8.06207699928350e-02 , -2.96790945140726e-01 ), ( -1.79743992424764e-01 , -9.62846849475359e-02 , -3.59994069271663e-01 ), ( -1.91545215140248e-01 , -9.35883964956654e-02 , -3.00057696700772e-01 ), ( -2.32793478473568e-01 , -1.09585879117182e-01 , -3.26155879383167e-01 ), ( -1.17927872493770e-01 , -7.08030939809125e-02 , -3.06914765472131e-01 ), ( -1.71077019077921e-01 , -8.09118864898879e-02 , -2.43196423576792e-01 ), ( -2.23315319914395e-01 , -9.90428208980078e-02 , -2.56519288543278e-01 ), ( -2.58174232927881e-01 , -1.01802827967514e-01 , -1.78863428551754e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 24, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 25 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 25, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 25, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 25, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 25, atoms_positions[size = 51] = { ( 8.26647924113907e+00 , 4.13179421244837e-02 , -7.39704319030450e-01 ), ( 6.87504378717396e+00 , -5.63680794226234e-01 , -5.43097344800070e-01 ), ( 6.15957936861644e+00 , -3.91234137028024e-01 , 7.70294817300408e-01 ), ( 4.92046658609037e+00 , -1.49341302318207e-01 , 7.33713088607941e-01 ), ( 7.02637738568081e+00 , -2.05999234530478e+00 , -9.09574040424618e-01 ), ( 6.83102022020697e+00 , -2.73189407059131e-01 , 1.94492006868935e+00 ), ( 6.14083899143568e+00 , -1.96649410894756e-01 , 3.16895711496001e+00 ), ( 7.10387128111467e+00 , -3.47595762084743e-01 , 4.35229617187487e+00 ), ( 5.33868170818087e+00 , 1.07824508398872e+00 , 3.36563180334843e+00 ), ( 4.16924218668598e+00 , 1.01410089115945e+00 , 3.73236796230498e+00 ), ( 5.83636834616802e+00 , 2.25745208996869e+00 , 2.98089997359473e+00 ), ( 5.20864757810393e+00 , 3.56957245844521e+00 , 2.91285775636473e+00 ), ( 6.31705620144432e+00 , 4.49339279089957e+00 , 2.31787522863057e+00 ), ( 3.86296977967216e+00 , 3.67344909542297e+00 , 2.04002226175517e+00 ), ( 2.79455645455796e+00 , 4.16942805909256e+00 , 2.46121204790199e+00 ), ( 3.93559624390625e+00 , 3.22238101929181e+00 , 7.31536372169389e-01 ), ( 2.71257288372061e+00 , 3.02108978381586e+00 , -8.92124402548022e-02 ), ( 3.08718036466247e+00 , 2.67408286573452e+00 , -1.52670658557882e+00 ), ( 1.57260597604337e+00 , 2.17067653702486e+00 , 4.26019628236451e-01 ), ( 3.80472307064121e-01 , 2.61088420554297e+00 , 4.87723705084447e-01 ), ( 2.07558023753614e+00 , 1.13589788556777e+00 , 1.04789679267253e+00 ), ( 1.17493250223783e+00 , 1.17344948434977e-01 , 1.70020104547663e+00 ), ( 2.06297012787758e+00 , -1.09234301309062e+00 , 2.02676626443017e+00 ), ( 5.71476168770821e-01 , 6.17809229056732e-01 , 2.96339779042952e+00 ), ( -5.84379828605167e-01 , 3.52350045985900e-01 , 3.16489618716293e+00 ), ( 1.29883879500052e+00 , 1.35699639850161e+00 , 3.74383470095006e+00 ), ( 8.43262697449691e-01 , 1.98351330129065e+00 , 5.02735344011084e+00 ), ( 2.10939969981363e+00 , 2.73008646872006e+00 , 5.71182363896326e+00 ), ( -3.46047044646963e-01 , 2.90908857240431e+00 , 4.96982194901969e+00 ), ( -1.12126849545417e+00 , 3.06644595133659e+00 , 5.87783361124985e+00 ), ( -5.34909653132848e-01 , 3.51276060146897e+00 , 3.82273837551560e+00 ), ( -1.50477688260082e+00 , 4.51307521955318e+00 , 3.41545366482764e+00 ), ( -7.08562451968667e-01 , 5.42337020236753e+00 , 2.47077946899051e+00 ), ( -2.74531503184144e+00 , 3.92797028087999e+00 , 2.85376251607557e+00 ), ( -3.81189297077074e+00 , 4.53739408044238e+00 , 2.81260060017561e+00 ), ( -2.65772243228862e+00 , 2.65007890944884e+00 , 2.37007604687258e+00 ), ( -3.78688535884526e+00 , 1.81296755538521e+00 , 2.00280574981871e+00 ), ( -3.37011105180502e+00 , 8.79011922787073e-01 , 8.42406291768775e-01 ), ( -4.28409289745128e+00 , 1.06312784605231e+00 , 3.21523361808659e+00 ), ( -5.49149943216895e+00 , 7.83421661368256e-01 , 3.33356267635616e+00 ), ( -3.36575603084633e+00 , 7.13569148392799e-01 , 4.19813108139739e+00 ), ( -3.67792446450366e+00 , 7.22702883285445e-02 , 5.45613409071240e+00 ), ( -2.39132996350769e+00 , -3.25346984705185e-01 , 6.15340691029519e+00 ), ( -4.46461207121171e+00 , 9.42912929193460e-01 , 6.42773040028982e+00 ), ( -5.36503185174231e+00 , 5.88816414161381e-01 , 7.21629148964332e+00 ), ( -6.27826863574096e+00 , 3.62766812535031e+00 , 6.74966196335481e+00 ), ( -6.97819138625597e+00 , 4.29547838009075e+00 , 7.49469506730733e+00 ), ( -6.69607027180097e+00 , 3.16616660359056e+00 , 5.51046162579048e+00 ), ( -4.11616753887897e+00 , 2.24660348701733e+00 , 6.39018318393223e+00 ), ( -4.80950490461211e+00 , 3.24898521176349e+00 , 7.25766730504329e+00 ), ( -4.05844207046985e+00 , 4.55035542879320e+00 , 7.27232106602667e+00 ) } +colvars: Step 25, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_ids[size = 0] = +colvars: Step 25, atom_groups_refcount[size = 0] = +colvars: Step 25, atom_groups_masses[size = 0] = +colvars: Step 25, atom_groups_charges[size = 0] = +colvars: Step 25, atom_groups_coms[size = 0] = +colvars: Step 25, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 25, volmaps_ids[size = 0] = +colvars: Step 25, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 25 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.99515551202827e-01 , -6.27415312265916e-03 , 9.54070788563543e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.99515551202827e-01 , -6.27415312265916e-03 , 9.54070788563543e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.5083 , 2.07728 , -15.1778 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.5083 , 2.07728 , -15.1778 ) to colvar "one". +colvars: Adding total bias energy: 44.2678 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.5083 , 2.07728 , -15.1778 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.9244 , -0.528143 , -1.43193 ) +colvars: ( -4.22267 , -0.452883 , -1.22788 ) +colvars: ( -4.22267 , -0.452883 , -1.22788 ) +colvars: ( -5.62472 , -0.603253 , -1.63557 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.889617 , 0.195883 , 0.613661 ) +colvars: ( 0.77088 , 0.266382 , 0.637437 ) +colvars: ( 0.754725 , 0.259507 , 0.619017 ) +colvars: ( 0.660013 , 0.266948 , 0.573812 ) +colvars: ( 0.648211 , 0.200461 , 0.479519 ) +colvars: ( 0.574259 , 0.343922 , 0.625255 ) +colvars: ( 0.46801 , 0.357704 , 0.58169 ) +colvars: ( 0.391993 , 0.454672 , 0.665082 ) +colvars: ( 0.386811 , 0.313148 , 0.475947 ) +colvars: ( 0.352417 , 0.271551 , 0.401272 ) +colvars: ( 0.35746 , 0.318442 , 0.465868 ) +colvars: ( 0.286628 , 0.275584 , 0.368377 ) +colvars: ( 0.259472 , 0.304574 , 0.390738 ) +colvars: ( 0.348575 , 0.178016 , 0.276028 ) +colvars: ( 0.290339 , 0.134668 , 0.185206 ) +colvars: ( 0.47039 , 0.141231 , 0.298377 ) +colvars: ( 0.542375 , 0.0501084 , 0.220332 ) +colvars: ( 0.670873 , 0.029381 , 0.26768 ) +colvars: ( 0.551157 , 0.0182826 , 0.183575 ) +colvars: ( 0.535521 , -0.0467075 , 0.0890249 ) +colvars: ( 0.572137 , 0.0661222 , 0.258673 ) +colvars: ( 0.570901 , 0.0499213 , 0.236649 ) +colvars: ( 0.607386 , 0.11457 , 0.342855 ) +colvars: ( 0.447581 , 0.0541633 , 0.170626 ) +colvars: ( 0.440923 , -0.00172194 , 0.0932634 ) +colvars: ( 0.346326 , 0.119553 , 0.197834 ) +colvars: ( 0.22278 , 0.127907 , 0.137089 ) +colvars: ( 0.131907 , 0.213401 , 0.196764 ) +colvars: ( 0.194595 , 0.0542703 , 0.0238812 ) +colvars: ( 0.145818 , 0.0180409 , -0.052087 ) +colvars: ( 0.227657 , 0.0288647 , 0.00966498 ) +colvars: ( 0.213547 , -0.0435099 , -0.093711 ) +colvars: ( 0.248268 , -0.0467178 , -0.0777705 ) +colvars: ( 0.288318 , -0.129226 , -0.163028 ) +colvars: ( 0.244652 , -0.182341 , -0.258236 ) +colvars: ( 0.402723 , -0.144039 , -0.116084 ) +colvars: ( 0.479706 , -0.219311 , -0.170382 ) +colvars: ( 0.609935 , -0.221671 , -0.0978739 ) +colvars: ( 0.433063 , -0.223944 , -0.203556 ) +colvars: ( 0.438597 , -0.291911 , -0.28973 ) +colvars: ( 0.384881 , -0.150874 , -0.135433 ) +colvars: ( 0.33133 , -0.144791 , -0.158525 ) +colvars: ( 0.315133 , -0.0583043 , -0.054186 ) +colvars: ( 0.208944 , -0.153783 , -0.24141 ) +colvars: ( 0.184878 , -0.195809 , -0.310654 ) +colvars: ( 0.00874516 , -0.199722 , -0.418064 ) +colvars: ( -0.0815191 , -0.217652 , -0.494053 ) +colvars: ( 0.108164 , -0.249349 , -0.425607 ) +colvars: ( 0.127567 , -0.113333 , -0.23546 ) +colvars: ( 0.00911224 , -0.117907 , -0.310252 ) +colvars: ( -0.0793083 , -0.0374929 , -0.255833 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.9244 , 0.528143 , 1.43193 ) +colvars: ( 4.22267 , 0.452883 , 1.22788 ) +colvars: ( 4.22267 , 0.452883 , 1.22788 ) +colvars: ( 5.62472 , 0.603253 , 1.63557 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.614702 , -0.0811791 , -0.366537 ) +colvars: ( -0.552998 , -0.164169 , -0.334955 ) +colvars: ( -0.502544 , -0.141977 , -0.276198 ) +colvars: ( -0.514499 , -0.191753 , -0.306402 ) +colvars: ( -0.504855 , -0.132639 , -0.275104 ) +colvars: ( -0.490395 , -0.284137 , -0.315995 ) +colvars: ( -0.458441 , -0.324625 , -0.29873 ) +colvars: ( -0.437323 , -0.432356 , -0.316933 ) +colvars: ( -0.395409 , -0.289041 , -0.222451 ) +colvars: ( -0.391225 , -0.263657 , -0.208968 ) +colvars: ( -0.345608 , -0.283298 , -0.170365 ) +colvars: ( -0.28501 , -0.246183 , -0.0959695 ) +colvars: ( -0.235881 , -0.261079 , -0.052106 ) +colvars: ( -0.30406 , -0.142608 , -0.077211 ) +colvars: ( -0.272999 , -0.113191 , -0.0352764 ) +colvars: ( -0.357863 , -0.0850504 , -0.110163 ) +colvars: ( -0.384095 , 0.0135592 , -0.10043 ) +colvars: ( -0.433588 , 0.0613264 , -0.132636 ) +colvars: ( -0.422214 , 0.0285695 , -0.1332 ) +colvars: ( -0.41084 , 0.0855844 , -0.100933 ) +colvars: ( -0.466783 , -0.0257515 , -0.1978 ) +colvars: ( -0.50167 , -0.0272864 , -0.233378 ) +colvars: ( -0.551981 , -0.0930292 , -0.307918 ) +colvars: ( -0.450263 , -0.0573759 , -0.192784 ) +colvars: ( -0.457302 , -0.0131355 , -0.18367 ) +colvars: ( -0.395521 , -0.13192 , -0.165102 ) +colvars: ( -0.338532 , -0.163294 , -0.119376 ) +colvars: ( -0.288454 , -0.253773 , -0.102202 ) +colvars: ( -0.297005 , -0.0901074 , -0.0509301 ) +colvars: ( -0.284184 , -0.0714187 , -0.0312266 ) +colvars: ( -0.276424 , -0.0450001 , -0.0137758 ) +colvars: ( -0.240652 , 0.0301069 , 0.0495958 ) +colvars: ( -0.218597 , 0.0566595 , 0.0814434 ) +colvars: ( -0.28445 , 0.11716 , 0.0374722 ) +colvars: ( -0.257916 , 0.159117 , 0.0794494 ) +colvars: ( -0.353447 , 0.145318 , -0.0214825 ) +colvars: ( -0.402054 , 0.221761 , -0.0423129 ) +colvars: ( -0.4727 , 0.244348 , -0.10496 ) +colvars: ( -0.414372 , 0.20181 , -0.0619728 ) +colvars: ( -0.418869 , 0.262864 , -0.044158 ) +colvars: ( -0.419538 , 0.114868 , -0.0989539 ) +colvars: ( -0.427404 , 0.0845517 , -0.117936 ) +colvars: ( -0.449473 , -0.00917436 , -0.174363 ) +colvars: ( -0.361149 , 0.0733003 , -0.0555504 ) +colvars: ( -0.364797 , 0.0996983 , -0.0495581 ) +colvars: ( -0.200041 , 0.106351 , 0.118241 ) +colvars: ( -0.150941 , 0.108272 , 0.168226 ) +colvars: ( -0.225823 , 0.178956 , 0.118916 ) +colvars: ( -0.298637 , 0.0324764 , -0.00773716 ) +colvars: ( -0.232304 , 0.0188726 , 0.053866 ) +colvars: ( -0.178644 , -0.0644851 , 0.0772396 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 25. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 25. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atoms_new_colvar_forces = { ( -4.64948756095428e+00 , -4.13439291828986e-01 , -1.18480670773194e+00 ), ( -4.00479132833903e+00 , -3.50670548975840e-01 , -9.25397990014676e-01 ), ( -4.07716089475674e+00 , -3.77687205838323e-01 , -9.60470723093749e-01 ), ( -5.48136916192064e+00 , -5.35430659330811e-01 , -1.43115688287139e+00 ), ( 2.52181597677831e-01 , 1.17530671406522e-01 , 3.42818191943839e-01 ), ( 5.00826689944451e+00 , 5.87929015984952e-01 , 1.74119012383961e+00 ), ( 4.23224320958635e+00 , 4.85961914117738e-01 , 1.51084005862460e+00 ), ( -4.53299383844284e-02 , 2.23161598796638e-02 , 3.48149373987012e-01 ), ( 4.21407614077276e+00 , 4.76989575965902e-01 , 1.48137569047540e+00 ), ( 5.58591707834861e+00 , 6.11147024926502e-01 , 1.82787533870091e+00 ), ( 1.18526327959609e-02 , 3.51439238842934e-02 , 2.95503028926826e-01 ), ( 1.61784480253113e-03 , 2.94004757606297e-02 , 2.72407516963776e-01 ), ( 2.35916107228643e-02 , 4.34954443323341e-02 , 3.38631494050623e-01 ), ( 4.45146884578941e-02 , 3.54087394106518e-02 , 1.98817135463419e-01 ), ( 1.73402789090328e-02 , 2.14774790721180e-02 , 1.49929958572946e-01 ), ( 1.12527853010140e-01 , 5.61805438401422e-02 , 1.88214155803622e-01 ), ( 1.58279710995860e-01 , 6.36675388980660e-02 , 1.19902201345429e-01 ), ( 2.37284957302291e-01 , 9.07073783884466e-02 , 1.35043258219505e-01 ), ( 1.28943366503910e-01 , 4.68521409286993e-02 , 5.03754339000972e-02 ), ( 1.24681081122516e-01 , 3.88769146776185e-02 , -1.19078528749632e-02 ), ( 1.05353852889349e-01 , 4.03706967490713e-02 , 6.08726120436782e-02 ), ( 6.92313967924517e-02 , 2.26348775035257e-02 , 3.27111647088477e-03 ), ( 5.54050234091135e-02 , 2.15407634451548e-02 , 3.49369558101449e-02 ), ( -2.68208617801030e-03 , -3.21256072460118e-03 , -2.21579198649446e-02 ), ( -1.63784846723828e-02 , -1.48573971962397e-02 , -9.04065980312773e-02 ), ( -4.91948928862027e-02 , -1.23674258014483e-02 , 3.27325763051586e-02 ), ( -1.15751409118683e-01 , -3.53866302937504e-02 , 1.77135703708122e-02 ), ( -1.56546557813829e-01 , -4.03728427141371e-02 , 9.45623168355812e-02 ), ( -1.02410080676360e-01 , -3.58371346035933e-02 , -2.70489822126664e-02 ), ( -1.38366528627789e-01 , -5.33777745801066e-02 , -8.33135581479110e-02 ), ( -4.87663871659194e-02 , -1.61354760258328e-02 , -4.11083565946385e-03 ), ( -2.71048443349625e-02 , -1.34029532189842e-02 , -4.41151594302592e-02 ), ( 2.96714380911476e-02 , 9.94169242311833e-03 , 3.67288250589587e-03 ), ( 3.86730902926330e-03 , -1.20659286276481e-02 , -1.25555757218082e-01 ), ( -1.32633676730242e-02 , -2.32242038655585e-02 , -1.78786182691266e-01 ), ( 4.92755720308022e-02 , 1.27927584963763e-03 , -1.37566691360937e-01 ), ( 7.76514750872815e-02 , 2.44968703026865e-03 , -2.12694926057886e-01 ), ( 1.37234330427815e-01 , 2.26770186745583e-02 , -2.02833615040340e-01 ), ( 1.86901376560987e-02 , -2.21333657959578e-02 , -2.65528976674672e-01 ), ( 1.97274783911037e-02 , -2.90466185365198e-02 , -3.33888381374860e-01 ), ( -3.46570693524684e-02 , -3.60062352467616e-02 , -2.34387324194230e-01 ), ( -9.60737018977827e-02 , -6.02389013742452e-02 , -2.76460435338491e-01 ), ( -1.34339372973070e-01 , -6.74786525812855e-02 , -2.28549402827962e-01 ), ( -1.52204573620836e-01 , -8.04827487455011e-02 , -2.96960054084250e-01 ), ( -1.79919344719066e-01 , -9.61108481712673e-02 , -3.60211790051426e-01 ), ( -1.91295411010890e-01 , -9.33709515315276e-02 , -2.99822360065218e-01 ), ( -2.32459688418046e-01 , -1.09380186994132e-01 , -3.25827501792330e-01 ), ( -1.17659239403470e-01 , -7.03930204690202e-02 , -3.06691218416824e-01 ), ( -1.71070372517956e-01 , -8.08566327727080e-02 , -2.43197581056251e-01 ), ( -2.23192168145597e-01 , -9.90347394586472e-02 , -2.56386300745341e-01 ), ( -2.57952498696039e-01 , -1.01978017846182e-01 , -1.78593282236159e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 25, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 26 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 26, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 26, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 26, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 26, atoms_positions[size = 51] = { ( 8.26205239752480e+00 , 4.17861095508959e-02 , -7.36497976160026e-01 ), ( 6.86492861219213e+00 , -5.68006057331467e-01 , -5.38408245729133e-01 ), ( 6.15575880373052e+00 , -3.89145198560351e-01 , 7.78626756454447e-01 ), ( 4.91641141657925e+00 , -1.48159488662435e-01 , 7.35944748484878e-01 ), ( 7.02105945376621e+00 , -2.06173192940476e+00 , -9.03666871821229e-01 ), ( 6.82568670419811e+00 , -2.76540136320467e-01 , 1.95100449392704e+00 ), ( 6.13201574755223e+00 , -2.03132769618362e-01 , 3.16628161151743e+00 ), ( 7.11081336669961e+00 , -3.46144117825693e-01 , 4.35975397553465e+00 ), ( 5.33844452189291e+00 , 1.07552146128050e+00 , 3.36719199102191e+00 ), ( 4.17175427628001e+00 , 1.01216774981376e+00 , 3.74121326351912e+00 ), ( 5.83724125006816e+00 , 2.25673342517408e+00 , 2.97920302646140e+00 ), ( 5.19859217756977e+00 , 3.56719475753549e+00 , 2.90873731308147e+00 ), ( 6.31516624242152e+00 , 4.49059059497252e+00 , 2.30984432201073e+00 ), ( 3.86121298874540e+00 , 3.66697976162258e+00 , 2.03780240984338e+00 ), ( 2.79747927766635e+00 , 4.16995460021236e+00 , 2.45593795652224e+00 ), ( 3.93137273749838e+00 , 3.21710006063874e+00 , 7.32737347216327e-01 ), ( 2.72436717702653e+00 , 3.02864357442996e+00 , -8.55753859222168e-02 ), ( 3.09391136477563e+00 , 2.66800126019767e+00 , -1.53095148108278e+00 ), ( 1.56484332658655e+00 , 2.17344006797225e+00 , 4.24726928436034e-01 ), ( 3.85256113664264e-01 , 2.61363713558315e+00 , 4.82462912434993e-01 ), ( 2.07688786596953e+00 , 1.14251941696581e+00 , 1.04548290902294e+00 ), ( 1.18126391324449e+00 , 1.18698867350510e-01 , 1.69846823698885e+00 ), ( 2.06722914051942e+00 , -1.09185219296440e+00 , 2.03018947728645e+00 ), ( 5.72932284036482e-01 , 6.18016252148053e-01 , 2.96457033899761e+00 ), ( -5.83389856128054e-01 , 3.53088781229802e-01 , 3.16720495991994e+00 ), ( 1.29554352042694e+00 , 1.36206327507269e+00 , 3.74262366623888e+00 ), ( 8.46905018374119e-01 , 1.98288773896191e+00 , 5.02809351234227e+00 ), ( 2.10982943699306e+00 , 2.73683957529722e+00 , 5.71601040168050e+00 ), ( -3.48691564249082e-01 , 2.90755570990568e+00 , 4.96869716000486e+00 ), ( -1.11910830076749e+00 , 3.06702408721855e+00 , 5.87738662576611e+00 ), ( -5.38299507738895e-01 , 3.51143389068214e+00 , 3.81521826160860e+00 ), ( -1.49841316651143e+00 , 4.50655457331812e+00 , 3.41374998518704e+00 ), ( -7.13307173668709e-01 , 5.42557465211419e+00 , 2.47207181043199e+00 ), ( -2.74426074560518e+00 , 3.93452643364649e+00 , 2.84188904337389e+00 ), ( -3.81054527032278e+00 , 4.54279757655199e+00 , 2.81268540552791e+00 ), ( -2.66487287946726e+00 , 2.64461164051670e+00 , 2.36563604672446e+00 ), ( -3.78942071808140e+00 , 1.81732420609061e+00 , 2.00409239548599e+00 ), ( -3.36724691286651e+00 , 8.77397578921159e-01 , 8.35624170805012e-01 ), ( -4.27483687507342e+00 , 1.05960458804490e+00 , 3.21981228547757e+00 ), ( -5.48919671412730e+00 , 7.76806002655777e-01 , 3.33464133071916e+00 ), ( -3.36704285696833e+00 , 7.17883542668495e-01 , 4.19213543387207e+00 ), ( -3.67549156336728e+00 , 7.58723829031180e-02 , 5.46280014150180e+00 ), ( -2.38982180673833e+00 , -3.25257752944606e-01 , 6.14886247459941e+00 ), ( -4.46738429536682e+00 , 9.35025765420735e-01 , 6.42557686319628e+00 ), ( -5.36456091151722e+00 , 5.86296350961117e-01 , 7.21398596315178e+00 ), ( -6.28704969800571e+00 , 3.62925592625597e+00 , 6.75097197160871e+00 ), ( -6.98251566748287e+00 , 4.29548720179496e+00 , 7.49827636498684e+00 ), ( -6.68453148675172e+00 , 3.16423838127918e+00 , 5.51379138521932e+00 ), ( -4.11335977853752e+00 , 2.24864953726479e+00 , 6.38975320399807e+00 ), ( -4.81128217109908e+00 , 3.25778323522353e+00 , 7.25807991639679e+00 ), ( -4.05000539885017e+00 , 4.54883688938649e+00 , 7.27155992532855e+00 ) } +colvars: Step 26, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_ids[size = 0] = +colvars: Step 26, atom_groups_refcount[size = 0] = +colvars: Step 26, atom_groups_masses[size = 0] = +colvars: Step 26, atom_groups_charges[size = 0] = +colvars: Step 26, atom_groups_coms[size = 0] = +colvars: Step 26, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 26, volmaps_ids[size = 0] = +colvars: Step 26, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 26 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.98694198360127e-01 , -7.65591975074812e-03 , 9.54318166419759e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.98694198360127e-01 , -7.65591975074812e-03 , 9.54318166419759e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.4919 , 2.10492 , -15.1828 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.4919 , 2.10492 , -15.1828 ) to colvar "one". +colvars: Adding total bias energy: 44.2392 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.4919 , 2.10492 , -15.1828 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.92583 , -0.527182 , -1.42881 ) +colvars: ( -4.2239 , -0.452058 , -1.2252 ) +colvars: ( -4.2239 , -0.452058 , -1.2252 ) +colvars: ( -5.62635 , -0.602155 , -1.63201 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.889087 , 0.195938 , 0.612717 ) +colvars: ( 0.770486 , 0.266378 , 0.63642 ) +colvars: ( 0.754315 , 0.259511 , 0.618018 ) +colvars: ( 0.659764 , 0.266905 , 0.572873 ) +colvars: ( 0.647976 , 0.200434 , 0.478735 ) +colvars: ( 0.574123 , 0.343825 , 0.624209 ) +colvars: ( 0.468016 , 0.357563 , 0.580691 ) +colvars: ( 0.392098 , 0.454475 , 0.663925 ) +colvars: ( 0.386898 , 0.312998 , 0.475099 ) +colvars: ( 0.352559 , 0.271399 , 0.400542 ) +colvars: ( 0.357553 , 0.318289 , 0.465023 ) +colvars: ( 0.286786 , 0.275426 , 0.367672 ) +colvars: ( 0.259632 , 0.304408 , 0.389981 ) +colvars: ( 0.348656 , 0.17791 , 0.275493 ) +colvars: ( 0.29049 , 0.134555 , 0.184808 ) +colvars: ( 0.470323 , 0.141176 , 0.297838 ) +colvars: ( 0.54222 , 0.0501049 , 0.219942 ) +colvars: ( 0.670554 , 0.0294286 , 0.267244 ) +colvars: ( 0.551021 , 0.0182833 , 0.183256 ) +colvars: ( 0.535405 , -0.0466926 , 0.0888594 ) +colvars: ( 0.572001 , 0.0661081 , 0.258239 ) +colvars: ( 0.570798 , 0.0499032 , 0.236258 ) +colvars: ( 0.607261 , 0.114538 , 0.342301 ) +colvars: ( 0.447632 , 0.0541017 , 0.170314 ) +colvars: ( 0.440994 , -0.0017723 , 0.0930806 ) +colvars: ( 0.346489 , 0.119441 , 0.197447 ) +colvars: ( 0.223094 , 0.127751 , 0.13677 ) +colvars: ( 0.13232 , 0.213192 , 0.196318 ) +colvars: ( 0.194925 , 0.0541326 , 0.0237394 ) +colvars: ( 0.146217 , 0.017895 , -0.0521127 ) +colvars: ( 0.227918 , 0.0287535 , 0.0095499 ) +colvars: ( 0.213806 , -0.0435984 , -0.0936612 ) +colvars: ( 0.248453 , -0.046785 , -0.0777447 ) +colvars: ( 0.288498 , -0.129267 , -0.16284 ) +colvars: ( 0.244884 , -0.182381 , -0.2579 ) +colvars: ( 0.402778 , -0.144041 , -0.115941 ) +colvars: ( 0.479682 , -0.21927 , -0.170124 ) +colvars: ( 0.609761 , -0.221588 , -0.0977 ) +colvars: ( 0.433124 , -0.223924 , -0.203249 ) +colvars: ( 0.438657 , -0.291871 , -0.289276 ) +colvars: ( 0.38502 , -0.150898 , -0.135249 ) +colvars: ( 0.33156 , -0.144842 , -0.158311 ) +colvars: ( 0.315403 , -0.0583922 , -0.0541465 ) +colvars: ( 0.209316 , -0.15387 , -0.241091 ) +colvars: ( 0.185294 , -0.195896 , -0.310223 ) +colvars: ( 0.00930755 , -0.199847 , -0.417515 ) +colvars: ( -0.0808517 , -0.2178 , -0.493403 ) +colvars: ( 0.108592 , -0.249422 , -0.425022 ) +colvars: ( 0.128015 , -0.113453 , -0.235179 ) +colvars: ( 0.00969566 , -0.118063 , -0.309879 ) +colvars: ( -0.0786325 , -0.0376979 , -0.255578 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.92583 , 0.527182 , 1.42881 ) +colvars: ( 4.2239 , 0.452058 , 1.2252 ) +colvars: ( 4.2239 , 0.452058 , 1.2252 ) +colvars: ( 5.62635 , 0.602155 , 1.63201 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.614481 , -0.0811872 , -0.365942 ) +colvars: ( -0.552822 , -0.164321 , -0.334141 ) +colvars: ( -0.502171 , -0.142052 , -0.275219 ) +colvars: ( -0.514459 , -0.191964 , -0.305634 ) +colvars: ( -0.504803 , -0.13274 , -0.27449 ) +colvars: ( -0.490486 , -0.284528 , -0.315089 ) +colvars: ( -0.458685 , -0.325103 , -0.297854 ) +colvars: ( -0.437685 , -0.43304 , -0.315861 ) +colvars: ( -0.395584 , -0.289433 , -0.221578 ) +colvars: ( -0.391479 , -0.264013 , -0.20825 ) +colvars: ( -0.345626 , -0.283649 , -0.169322 ) +colvars: ( -0.284941 , -0.246443 , -0.0949155 ) +colvars: ( -0.235652 , -0.261335 , -0.0508202 ) +colvars: ( -0.303904 , -0.142673 , -0.0763727 ) +colvars: ( -0.272862 , -0.113199 , -0.0345293 ) +colvars: ( -0.357615 , -0.0850101 , -0.109417 ) +colvars: ( -0.383766 , 0.0137834 , -0.0998939 ) +colvars: ( -0.433126 , 0.0616444 , -0.13212 ) +colvars: ( -0.422044 , 0.0287924 , -0.132891 ) +colvars: ( -0.410661 , 0.0859141 , -0.100774 ) +colvars: ( -0.466768 , -0.0256561 , -0.197517 ) +colvars: ( -0.501828 , -0.0272233 , -0.233287 ) +colvars: ( -0.552277 , -0.0931133 , -0.307804 ) +colvars: ( -0.45053 , -0.0573711 , -0.192699 ) +colvars: ( -0.457622 , -0.013059 , -0.183771 ) +colvars: ( -0.395815 , -0.132043 , -0.164807 ) +colvars: ( -0.338909 , -0.163472 , -0.119052 ) +colvars: ( -0.288851 , -0.254109 , -0.101618 ) +colvars: ( -0.297263 , -0.09013 , -0.050675 ) +colvars: ( -0.284522 , -0.0714151 , -0.0311036 ) +colvars: ( -0.276486 , -0.0449113 , -0.0134363 ) +colvars: ( -0.240583 , 0.0303561 , 0.0498728 ) +colvars: ( -0.21832 , 0.0569883 , 0.0818716 ) +colvars: ( -0.284377 , 0.117558 , 0.0374836 ) +colvars: ( -0.257841 , 0.159597 , 0.0793528 ) +colvars: ( -0.353377 , 0.145753 , -0.0215846 ) +colvars: ( -0.401997 , 0.222323 , -0.0426698 ) +colvars: ( -0.472607 , 0.244942 , -0.105375 ) +colvars: ( -0.41451 , 0.202309 , -0.0624825 ) +colvars: ( -0.419013 , 0.263471 , -0.0448523 ) +colvars: ( -0.41984 , 0.115186 , -0.0993879 ) +colvars: ( -0.427899 , 0.0847884 , -0.118489 ) +colvars: ( -0.450121 , -0.00913185 , -0.174817 ) +colvars: ( -0.361678 , 0.0735255 , -0.0560788 ) +colvars: ( -0.365414 , 0.0999592 , -0.0502564 ) +colvars: ( -0.20037 , 0.106694 , 0.117897 ) +colvars: ( -0.151294 , 0.108625 , 0.167871 ) +colvars: ( -0.22599 , 0.179447 , 0.118522 ) +colvars: ( -0.299099 , 0.0326491 , -0.0080503 ) +colvars: ( -0.232789 , 0.0190311 , 0.0535972 ) +colvars: ( -0.179124 , -0.0644662 , 0.0772385 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 26. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 26. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atoms_new_colvar_forces = { ( -4.65122199350796e+00 , -4.12430965680350e-01 , -1.18203244769683e+00 ), ( -4.00623265903138e+00 , -3.50001036904643e-01 , -9.22923807473896e-01 ), ( -4.07859163157510e+00 , -3.77117596485990e-01 , -9.57963690131977e-01 ), ( -5.48317872546510e+00 , -5.34460776572132e-01 , -1.42775999062148e+00 ), ( 2.52144283009204e-01 , 1.17458214311684e-01 , 3.42799443021439e-01 ), ( 5.00946428913979e+00 , 5.86478754543285e-01 , 1.73792866801520e+00 ), ( 4.23322716506996e+00 , 4.84518484815516e-01 , 1.50803994180249e+00 ), ( -4.55867378539800e-02 , 2.14350083430519e-02 , 3.48064264481249e-01 ), ( 4.21521022765265e+00 , 4.75623826234595e-01 , 1.47872426506244e+00 ), ( 5.58743109026427e+00 , 6.09541528637903e-01 , 1.82429777907329e+00 ), ( 1.19266878857350e-02 , 3.46406576125291e-02 , 2.95700715890141e-01 ), ( 1.84563761051221e-03 , 2.89830771059171e-02 , 2.72756226117522e-01 ), ( 2.39801225301171e-02 , 4.30729307354178e-02 , 3.39160576960902e-01 ), ( 4.47514645752732e-02 , 3.52369807367713e-02 , 1.99120714153984e-01 ), ( 1.76284474102675e-02 , 2.13566551455872e-02 , 1.50278358166791e-01 ), ( 1.12708605603493e-01 , 5.61658959697750e-02 , 1.88421193981063e-01 ), ( 1.58453289204960e-01 , 6.38882845716083e-02 , 1.20048559639609e-01 ), ( 2.37427701748859e-01 , 9.10730182385947e-02 , 1.35124140860172e-01 ), ( 1.28976749968850e-01 , 4.70756905526893e-02 , 5.03645831077629e-02 ), ( 1.24743209605684e-01 , 3.92214262823626e-02 , -1.19145108360773e-02 ), ( 1.05232862567391e-01 , 4.04520538596028e-02 , 6.07220837311741e-02 ), ( 6.89693730247213e-02 , 2.26798892246959e-02 , 2.97123231983654e-03 ), ( 5.49848351625235e-02 , 2.14247203736171e-02 , 3.44977316927867e-02 ), ( -2.89799710172167e-03 , -3.26948391773036e-03 , -2.23849922959762e-02 ), ( -1.66284727461301e-02 , -1.48313220428684e-02 , -9.06908655913465e-02 ), ( -4.93257420058050e-02 , -1.26024886413324e-02 , 3.26396593706691e-02 ), ( -1.15814208905717e-01 , -3.57213584700012e-02 , 1.77174633909183e-02 ), ( -1.56530584531230e-01 , -4.09167267399266e-02 , 9.47006059954786e-02 ), ( -1.02338779740558e-01 , -3.59973401670387e-02 , -2.69355915416408e-02 ), ( -1.38305237479625e-01 , -5.35201643464268e-02 , -8.32162477592325e-02 ), ( -4.85680405386822e-02 , -1.61578171552481e-02 , -3.88642298419647e-03 ), ( -2.67772984944918e-02 , -1.32422528386300e-02 , -4.37884424156643e-02 ), ( 3.01329675171860e-02 , 1.02032965942717e-02 , 4.12686185508110e-03 ), ( 4.12040337949232e-03 , -1.17087146451299e-02 , -1.25355981658625e-01 ), ( -1.29576321734095e-02 , -2.27834682403991e-02 , -1.78547403469024e-01 ), ( 4.94007865482561e-02 , 1.71189403955313e-03 , -1.37525207437093e-01 ), ( 7.76852434754888e-02 , 3.05333934288804e-03 , -2.12793513649491e-01 ), ( 1.37153522977005e-01 , 2.33536613497733e-02 , -2.03074806101602e-01 ), ( 1.86139721968092e-02 , -2.16158358743594e-02 , -2.65731524349282e-01 ), ( 1.96439304720072e-02 , -2.83995313437912e-02 , -3.34128733916946e-01 ), ( -3.48204166235399e-02 , -3.57117957159627e-02 , -2.34637084053992e-01 ), ( -9.63386157300486e-02 , -6.00533069326539e-02 , -2.76799718063321e-01 ), ( -1.34718529429084e-01 , -6.75240404033961e-02 , -2.28963807315661e-01 ), ( -1.52361782945018e-01 , -8.03446535693402e-02 , -2.97170116172539e-01 ), ( -1.80120349475619e-01 , -9.59366354408885e-02 , -3.60479474228422e-01 ), ( -1.91062836148284e-01 , -9.31523923260678e-02 , -2.99618463388877e-01 ), ( -2.32146152594691e-01 , -1.09174704521400e-01 , -3.25531619386484e-01 ), ( -1.17398495923477e-01 , -6.99749701730693e-02 , -3.06499820913342e-01 ), ( -1.71084152004181e-01 , -8.08040007777962e-02 , -2.43229116074439e-01 ), ( -2.23093045962109e-01 , -9.90318162507992e-02 , -2.56282234357960e-01 ), ( -2.57756750613568e-01 , -1.02164092444319e-01 , -1.78339434804573e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 26, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 27 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 27, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 27, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 27, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 27, atoms_positions[size = 51] = { ( 8.25707472183859e+00 , 4.22785545844635e-02 , -7.33175419821030e-01 ), ( 6.85606891564990e+00 , -5.72993184382743e-01 , -5.34486564205437e-01 ), ( 6.14971346582996e+00 , -3.85373599008369e-01 , 7.86581713390112e-01 ), ( 4.91325846372904e+00 , -1.47546829791428e-01 , 7.38296205810287e-01 ), ( 7.01581372425447e+00 , -2.06361573840916e+00 , -8.97301976640849e-01 ), ( 6.82087835887150e+00 , -2.80274776070182e-01 , 1.95623975081528e+00 ), ( 6.12304983126280e+00 , -2.09194224725478e-01 , 3.16559515508167e+00 ), ( 7.11793439373644e+00 , -3.45009299620143e-01 , 4.36691734274913e+00 ), ( 5.33677230759923e+00 , 1.07311241893511e+00 , 3.36823126876214e+00 ), ( 4.17449455394443e+00 , 1.01035056432143e+00 , 3.75033775452345e+00 ), ( 5.83878873373422e+00 , 2.25565506890960e+00 , 2.97752353818648e+00 ), ( 5.18795047354684e+00 , 3.56436390710717e+00 , 2.90402910828106e+00 ), ( 6.31282670043946e+00 , 4.48710215388794e+00 , 2.30274091881490e+00 ), ( 3.86003843099403e+00 , 3.66074961395375e+00 , 2.03518881628772e+00 ), ( 2.80104566768147e+00 , 4.17008041424924e+00 , 2.45074539172103e+00 ), ( 3.92659499658068e+00 , 3.21131980145144e+00 , 7.34512932575729e-01 ), ( 2.73547363376623e+00 , 3.03713617549576e+00 , -8.19334207195935e-02 ), ( 3.10030640312578e+00 , 2.66254209841518e+00 , -1.53494248536318e+00 ), ( 1.55796569836131e+00 , 2.17833489691590e+00 , 4.23945681356006e-01 ), ( 3.90870358978620e-01 , 2.61546398796180e+00 , 4.77049062459298e-01 ), ( 2.07634801048823e+00 , 1.14623546721613e+00 , 1.04413182538187e+00 ), ( 1.18950058561543e+00 , 1.21074670819899e-01 , 1.69579367795851e+00 ), ( 2.07141663863220e+00 , -1.09176100201853e+00 , 2.03329812501245e+00 ), ( 5.74051227837035e-01 , 6.17817431639855e-01 , 2.96442611850330e+00 ), ( -5.83248988561473e-01 , 3.53856649208231e-01 , 3.17006622801460e+00 ), ( 1.29260676386410e+00 , 1.36805146008650e+00 , 3.74323432458433e+00 ), ( 8.51718493279761e-01 , 1.98200105562231e+00 , 5.02902499753843e+00 ), ( 2.10805989657198e+00 , 2.74297448255918e+00 , 5.71945263723591e+00 ), ( -3.51305830993778e-01 , 2.90593982582615e+00 , 4.96664900296609e+00 ), ( -1.11743950864434e+00 , 3.06756828414869e+00 , 5.87763028936677e+00 ), ( -5.40967944065125e-01 , 3.51054118367759e+00 , 3.80704470696793e+00 ), ( -1.49129375088998e+00 , 4.50014160905025e+00 , 3.41314980510574e+00 ), ( -7.18863436720035e-01 , 5.42807854382700e+00 , 2.47348661014230e+00 ), ( -2.74391701810042e+00 , 3.93976915318521e+00 , 2.82901925908208e+00 ), ( -3.80912399494000e+00 , 4.54828466459966e+00 , 2.81284716313668e+00 ), ( -2.67184672670405e+00 , 2.63993264062169e+00 , 2.36196741368408e+00 ), ( -3.79208950657429e+00 , 1.82126070497219e+00 , 2.00510634091807e+00 ), ( -3.36462056606770e+00 , 8.76286310715767e-01 , 8.28690483062027e-01 ), ( -4.26652954382035e+00 , 1.05555900505266e+00 , 3.22504867431751e+00 ), ( -5.48611075001312e+00 , 7.70421404314483e-01 , 3.33581476316994e+00 ), ( -3.36841678980655e+00 , 7.21715307195188e-01 , 4.18557284378883e+00 ), ( -3.67355759015422e+00 , 7.84487286731862e-02 , 5.46907258756486e+00 ), ( -2.38766192379755e+00 , -3.24232250810556e-01 , 6.14422340041738e+00 ), ( -4.47074852197242e+00 , 9.28660456885802e-01 , 6.42378233765041e+00 ), ( -5.36367199328626e+00 , 5.83372383130967e-01 , 7.21111603369968e+00 ), ( -6.29483858506010e+00 , 3.62959734156973e+00 , 6.75175798337722e+00 ), ( -6.98735006179341e+00 , 4.29578222764064e+00 , 7.50183775606877e+00 ), ( -6.67291941140437e+00 , 3.16288637103370e+00 , 5.51789416999225e+00 ), ( -4.11083041741113e+00 , 2.25075669738573e+00 , 6.39038185059985e+00 ), ( -4.81307774675290e+00 , 3.26588499697105e+00 , 7.25728511232413e+00 ), ( -4.04182732129257e+00 , 4.54927180676174e+00 , 7.27132923334030e+00 ) } +colvars: Step 27, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_ids[size = 0] = +colvars: Step 27, atom_groups_refcount[size = 0] = +colvars: Step 27, atom_groups_masses[size = 0] = +colvars: Step 27, atom_groups_charges[size = 0] = +colvars: Step 27, atom_groups_coms[size = 0] = +colvars: Step 27, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 27, volmaps_ids[size = 0] = +colvars: Step 27, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 27 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.97850201345680e-01 , -9.04087721924012e-03 , 9.54569808917841e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.97850201345680e-01 , -9.04087721924012e-03 , 9.54569808917841e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.475 , 2.13262 , -15.1878 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.475 , 2.13262 , -15.1878 ) to colvar "one". +colvars: Adding total bias energy: 44.2097 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.475 , 2.13262 , -15.1878 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.92729 , -0.526119 , -1.42562 ) +colvars: ( -4.22515 , -0.451147 , -1.22247 ) +colvars: ( -4.22515 , -0.451147 , -1.22247 ) +colvars: ( -5.62802 , -0.60094 , -1.62836 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.888561 , 0.195986 , 0.611767 ) +colvars: ( 0.770096 , 0.266359 , 0.635406 ) +colvars: ( 0.753917 , 0.259503 , 0.617035 ) +colvars: ( 0.659517 , 0.26684 , 0.571938 ) +colvars: ( 0.647745 , 0.200392 , 0.47795 ) +colvars: ( 0.573986 , 0.343694 , 0.62317 ) +colvars: ( 0.468019 , 0.357382 , 0.579698 ) +colvars: ( 0.392197 , 0.454225 , 0.662779 ) +colvars: ( 0.386986 , 0.312814 , 0.474263 ) +colvars: ( 0.352698 , 0.271214 , 0.399819 ) +colvars: ( 0.357652 , 0.318105 , 0.4642 ) +colvars: ( 0.286957 , 0.275242 , 0.366994 ) +colvars: ( 0.25981 , 0.304216 , 0.389264 ) +colvars: ( 0.34875 , 0.177789 , 0.27498 ) +colvars: ( 0.290655 , 0.134431 , 0.18443 ) +colvars: ( 0.47027 , 0.141114 , 0.297315 ) +colvars: ( 0.54208 , 0.0501064 , 0.219562 ) +colvars: ( 0.670252 , 0.0294884 , 0.266815 ) +colvars: ( 0.550894 , 0.0182879 , 0.182934 ) +colvars: ( 0.535298 , -0.0466676 , 0.0886882 ) +colvars: ( 0.571868 , 0.06609 , 0.257797 ) +colvars: ( 0.57069 , 0.0498781 , 0.235848 ) +colvars: ( 0.607128 , 0.11449 , 0.341724 ) +colvars: ( 0.447678 , 0.054028 , 0.169984 ) +colvars: ( 0.441058 , -0.00183084 , 0.0928738 ) +colvars: ( 0.34665 , 0.119308 , 0.197051 ) +colvars: ( 0.223405 , 0.12757 , 0.136446 ) +colvars: ( 0.132731 , 0.212948 , 0.195879 ) +colvars: ( 0.195255 , 0.0539795 , 0.0235963 ) +colvars: ( 0.146615 , 0.0177343 , -0.0521439 ) +colvars: ( 0.228187 , 0.0286348 , 0.00944027 ) +colvars: ( 0.214077 , -0.0436845 , -0.0936034 ) +colvars: ( 0.248658 , -0.0468437 , -0.0777018 ) +colvars: ( 0.288689 , -0.129297 , -0.162654 ) +colvars: ( 0.245127 , -0.182404 , -0.257569 ) +colvars: ( 0.402841 , -0.144029 , -0.115808 ) +colvars: ( 0.479665 , -0.219206 , -0.169887 ) +colvars: ( 0.609592 , -0.22148 , -0.0975542 ) +colvars: ( 0.433185 , -0.223888 , -0.202972 ) +colvars: ( 0.438717 , -0.291807 , -0.288858 ) +colvars: ( 0.385153 , -0.150917 , -0.135096 ) +colvars: ( 0.33178 , -0.144893 , -0.158134 ) +colvars: ( 0.315656 , -0.0584931 , -0.0541457 ) +colvars: ( 0.209679 , -0.15396 , -0.240806 ) +colvars: ( 0.185698 , -0.195983 , -0.309832 ) +colvars: ( 0.00987202 , -0.199967 , -0.41698 ) +colvars: ( -0.0801811 , -0.217945 , -0.492763 ) +colvars: ( 0.109025 , -0.24948 , -0.424452 ) +colvars: ( 0.128458 , -0.113579 , -0.234918 ) +colvars: ( 0.0102756 , -0.118226 , -0.309522 ) +colvars: ( -0.077958 , -0.0379191 , -0.255327 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.92729 , 0.526119 , 1.42562 ) +colvars: ( 4.22515 , 0.451147 , 1.22247 ) +colvars: ( 4.22515 , 0.451147 , 1.22247 ) +colvars: ( 5.62802 , 0.60094 , 1.62836 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.614232 , -0.0811803 , -0.365307 ) +colvars: ( -0.552626 , -0.164452 , -0.33329 ) +colvars: ( -0.501779 , -0.142111 , -0.274206 ) +colvars: ( -0.514405 , -0.192153 , -0.304834 ) +colvars: ( -0.504737 , -0.132823 , -0.273847 ) +colvars: ( -0.490569 , -0.284889 , -0.314148 ) +colvars: ( -0.458928 , -0.325547 , -0.296947 ) +colvars: ( -0.43805 , -0.433682 , -0.314755 ) +colvars: ( -0.395763 , -0.289796 , -0.220681 ) +colvars: ( -0.39174 , -0.264341 , -0.207512 ) +colvars: ( -0.345651 , -0.283973 , -0.16826 ) +colvars: ( -0.284883 , -0.246681 , -0.0938493 ) +colvars: ( -0.235437 , -0.26157 , -0.0495239 ) +colvars: ( -0.303755 , -0.142724 , -0.0755256 ) +colvars: ( -0.272735 , -0.113196 , -0.033779 ) +colvars: ( -0.357365 , -0.0849601 , -0.108658 ) +colvars: ( -0.383431 , 0.0140095 , -0.0993481 ) +colvars: ( -0.432649 , 0.061961 , -0.131589 ) +colvars: ( -0.421867 , 0.0290174 , -0.132572 ) +colvars: ( -0.410475 , 0.0862409 , -0.10061 ) +colvars: ( -0.466744 , -0.0255527 , -0.197217 ) +colvars: ( -0.501976 , -0.0271507 , -0.233178 ) +colvars: ( -0.552559 , -0.0931808 , -0.307665 ) +colvars: ( -0.450794 , -0.057355 , -0.192601 ) +colvars: ( -0.45794 , -0.0129745 , -0.183864 ) +colvars: ( -0.396114 , -0.13215 , -0.164502 ) +colvars: ( -0.339298 , -0.163633 , -0.118724 ) +colvars: ( -0.289267 , -0.25442 , -0.101028 ) +colvars: ( -0.297536 , -0.0901417 , -0.0504221 ) +colvars: ( -0.284876 , -0.0714023 , -0.0309867 ) +colvars: ( -0.276561 , -0.0448166 , -0.0131011 ) +colvars: ( -0.240528 , 0.0306039 , 0.0501388 ) +colvars: ( -0.218056 , 0.0573122 , 0.0822881 ) +colvars: ( -0.284312 , 0.117949 , 0.037483 ) +colvars: ( -0.257777 , 0.160066 , 0.0792386 ) +colvars: ( -0.353307 , 0.14618 , -0.0216932 ) +colvars: ( -0.401934 , 0.222872 , -0.0430332 ) +colvars: ( -0.4725 , 0.245521 , -0.10579 ) +colvars: ( -0.414644 , 0.202796 , -0.0629994 ) +colvars: ( -0.419153 , 0.264063 , -0.0455574 ) +colvars: ( -0.420141 , 0.115502 , -0.0998255 ) +colvars: ( -0.428397 , 0.0850252 , -0.119046 ) +colvars: ( -0.450773 , -0.00908048 , -0.175269 ) +colvars: ( -0.362218 , 0.0737505 , -0.0566178 ) +colvars: ( -0.366043 , 0.100218 , -0.0509683 ) +colvars: ( -0.200724 , 0.107031 , 0.117525 ) +colvars: ( -0.151678 , 0.108971 , 0.167484 ) +colvars: ( -0.226175 , 0.179925 , 0.118103 ) +colvars: ( -0.299578 , 0.0328233 , -0.008377 ) +colvars: ( -0.233297 , 0.0191909 , 0.0533083 ) +colvars: ( -0.179635 , -0.0644404 , 0.0772172 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 27. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 27. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atoms_new_colvar_forces = { ( -4.65296081977426e+00 , -4.11312705557336e-01 , -1.17916008772739e+00 ), ( -4.00768029090664e+00 , -3.49239975194913e-01 , -9.20352639313350e-01 ), ( -4.08003811411862e+00 , -3.76459577667287e-01 , -9.55364839374468e-01 ), ( -5.48501441621184e+00 , -5.33372168442400e-01 , -1.42426104389976e+00 ), ( 2.52138641933223e-01 , 1.17391937735812e-01 , 3.42829134871724e-01 ), ( 5.01070682101693e+00 , 5.84923668710267e-01 , 1.73464248142854e+00 ), ( 4.23424100363589e+00 , 4.82981191763409e-01 , 1.50522024816815e+00 ), ( -4.58536623926896e-02 , 2.05427050707424e-02 , 3.48024251207226e-01 ), ( 4.21637313973278e+00 , 4.74164541274561e-01 , 1.47605064479100e+00 ), ( 5.58898066213222e+00 , 6.07813101360608e-01 , 1.82067046887196e+00 ), ( 1.20012843991646e-02 , 3.41319982543776e-02 , 2.95940013966073e-01 ), ( 2.07397374634494e-03 , 2.85609252921863e-02 , 2.73144892550298e-01 ), ( 2.43730655906460e-02 , 4.26461642087121e-02 , 3.39740554537315e-01 ), ( 4.49950340960591e-02 , 3.50644361442745e-02 , 1.99454449928156e-01 ), ( 1.79204477193564e-02 , 2.12348526140277e-02 , 1.50650538172148e-01 ), ( 1.12904897239592e-01 , 5.61541437196705e-02 , 1.88656757453513e-01 ), ( 1.58648879535336e-01 , 6.41158613298745e-02 , 1.20214221008044e-01 ), ( 2.37602741866410e-01 , 9.14493290622493e-02 , 1.35226574661627e-01 ), ( 1.29027453197392e-01 , 4.73053343221808e-02 , 5.03618105822811e-02 ), ( 1.24822666774852e-01 , 3.95732743818971e-02 , -1.19214115296327e-02 ), ( 1.05124709295540e-01 , 4.05372902357212e-02 , 6.05793376808745e-02 ), ( 6.87145083550892e-02 , 2.27274122019718e-02 , 2.66950114117548e-03 ), ( 5.45684863152882e-02 , 2.13090318935963e-02 , 3.40593050796351e-02 ), ( -3.11589770804638e-03 , -3.32705763392897e-03 , -2.26173778145858e-02 ), ( -1.68821862929575e-02 , -1.48053264855598e-02 , -9.09902991383552e-02 ), ( -4.94644486604823e-02 , -1.28415349537229e-02 , 3.25496031065721e-02 ), ( -1.15893175122578e-01 , -3.60630646757415e-02 , 1.77224473323606e-02 ), ( -1.56536050944452e-01 , -4.14711124683289e-02 , 9.48511588781837e-02 ), ( -1.02280512861679e-01 , -3.61622204374825e-02 , -2.68258140137797e-02 ), ( -1.38261579627269e-01 , -5.36680204526655e-02 , -8.31306352208558e-02 ), ( -4.83746147798912e-02 , -1.61818255316141e-02 , -3.66081561889643e-03 ), ( -2.64504892957892e-02 , -1.30805877873015e-02 , -4.34645786850419e-02 ), ( 3.06022118555119e-02 , 1.04685390390452e-02 , 4.58631529407322e-03 ), ( 4.37677488117461e-03 , -1.13474290652661e-02 , -1.25170880444443e-01 ), ( -1.26501967680394e-02 , -2.23382067824819e-02 , -1.78330200676609e-01 ), ( 4.95344100922709e-02 , 2.15073650728362e-03 , -1.37501106295696e-01 ), ( 7.77309124365870e-02 , 3.66596779577744e-03 , -2.12920626180573e-01 ), ( 1.37091638773848e-01 , 2.40417941483328e-02 , -2.03343988863783e-01 ), ( 1.85411855798203e-02 , -2.10919042222366e-02 , -2.65971384318865e-01 ), ( 1.95642232487680e-02 , -2.77445444453748e-02 , -3.34415900716037e-01 ), ( -3.49884372076176e-02 , -3.54149312666511e-02 , -2.34921087245561e-01 ), ( -9.66170468589573e-02 , -5.98681899508674e-02 , -2.77180474857296e-01 ), ( -1.35117541849459e-01 , -6.75735453120726e-02 , -2.29414492495197e-01 ), ( -1.52539064568009e-01 , -8.02091633733153e-02 , -2.97423703707888e-01 ), ( -1.80345153304820e-01 , -9.57653730012568e-02 , -3.60800033095277e-01 ), ( -1.90852406581196e-01 , -9.29367337701306e-02 , -2.99454680761945e-01 ), ( -2.31859491857151e-01 , -1.08973437221603e-01 , -3.25278848708273e-01 ), ( -1.17149733614289e-01 , -6.95555299430406e-02 , -3.06348746628624e-01 ), ( -1.71119675535397e-01 , -8.07555096423477e-02 , -2.43295385378938e-01 ), ( -2.23021682685284e-01 , -9.90350769743407e-02 , -2.56213866725295e-01 ), ( -2.57593083922671e-01 , -1.02359484807312e-01 , -1.78109761274513e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 27, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 28 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 28, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 28, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 28, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 28, atoms_positions[size = 51] = { ( 8.25141340854426e+00 , 4.27536282804912e-02 , -7.29725994031609e-01 ), ( 6.84854699653572e+00 , -5.78547352399702e-01 , -5.31252244068400e-01 ), ( 6.14156144486969e+00 , -3.80128091238656e-01 , 7.93954175858301e-01 ), ( 4.91090319376561e+00 , -1.47452241413164e-01 , 7.40807027092780e-01 ), ( 7.01083426050679e+00 , -2.06570502831762e+00 , -8.90481937115680e-01 ), ( 6.81655824705060e+00 , -2.84309611543218e-01 , 1.96050257029610e+00 ), ( 6.11421396110600e+00 , -2.14765450508097e-01 , 3.16719043487638e+00 ), ( 7.12497025687971e+00 , -3.44290203456815e-01 , 4.37373323952401e+00 ), ( 5.33384700079385e+00 , 1.07102518527734e+00 , 3.36873249068690e+00 ), ( 4.17739900898167e+00 , 1.00867135062195e+00 , 3.75974114323684e+00 ), ( 5.84090449077922e+00 , 2.25437915242626e+00 , 2.97582603771991e+00 ), ( 5.17716996576211e+00 , 3.56100320466418e+00 , 2.89884898440734e+00 ), ( 6.30998720471564e+00 , 4.48290067080877e+00 , 2.29672269161662e+00 ), ( 3.85932624226183e+00 , 3.65482484265207e+00 , 2.03223007067337e+00 ), ( 2.80518594525855e+00 , 4.16981451965320e+00 , 2.44566261000768e+00 ), ( 3.92159037766972e+00 , 3.20510104452146e+00 , 7.36950134680403e-01 ), ( 2.74538211176792e+00 , 3.04632820041106e+00 , -7.84400041895933e-02 ), ( 3.10634109201099e+00 , 2.65795581205966e+00 , -1.53831388862997e+00 ), ( 1.55281004852930e+00 , 2.18522467602309e+00 , 4.23598740903130e-01 ), ( 3.96919996569759e-01 , 2.61650672876596e+00 , 4.71528067747315e-01 ), ( 2.07399362523043e+00 , 1.14710419105956e+00 , 1.04379963922736e+00 ), ( 1.19949703016448e+00 , 1.24539394452611e-01 , 1.69226605133456e+00 ), ( 2.07546170430011e+00 , -1.09195909223405e+00 , 2.03594002120556e+00 ), ( 5.74786986110250e-01 , 6.17294307072151e-01 , 2.96300966829902e+00 ), ( -5.83910403574269e-01 , 3.54631339281729e-01 , 3.17343959820756e+00 ), ( 1.29012230674650e+00 , 1.37482080659538e+00 , 3.74549593994039e+00 ), ( 8.57574906695895e-01 , 1.98101570800191e+00 , 5.03021857247255e+00 ), ( 2.10417777431513e+00 , 2.74850558933916e+00 , 5.72213587654337e+00 ), ( -3.53752140166753e-01 , 2.90426287217386e+00 , 4.96360272743720e+00 ), ( -1.11628089028881e+00 , 3.06808899351948e+00 , 5.87856796744518e+00 ), ( -5.42781412788149e-01 , 3.50975443616853e+00 , 3.79838250670944e+00 ), ( -1.48376766275157e+00 , 4.49409930721731e+00 , 3.41341740585530e+00 ), ( -7.25083029546796e-01 , 5.43094619757340e+00 , 2.47505103414817e+00 ), ( -2.74419821951965e+00 , 3.94344555631195e+00 , 2.81537941094484e+00 ), ( -3.80764518051608e+00 , 4.55388854735453e+00 , 2.81303279853192e+00 ), ( -2.67849491347269e+00 , 2.63639349089204e+00 , 2.35905104810708e+00 ), ( -3.79493973802081e+00 , 1.82427408223173e+00 , 2.00571974234432e+00 ), ( -3.36217318157316e+00 , 8.75847101644811e-01 , 8.21638446381836e-01 ), ( -4.25971851468650e+00 , 1.05114915890384e+00 , 3.23051094510326e+00 ), ( -5.48206829895481e+00 , 7.64278204292921e-01 , 3.33711393630714e+00 ), ( -3.36963992716763e+00 , 7.24852928217748e-01 , 4.17899837112041e+00 ), ( -3.67199351459272e+00 , 7.99383341296954e-02 , 5.47443312913220e+00 ), ( -2.38482928791074e+00 , -3.22224431186230e-01 , 6.13967727718150e+00 ), ( -4.47453583041730e+00 , 9.24233948201306e-01 , 6.42240033392267e+00 ), ( -5.36247984538019e+00 , 5.79971900486630e-01 , 7.20776101314810e+00 ), ( -6.30121080914747e+00 , 3.62870685334762e+00 , 6.75223485354252e+00 ), ( -6.99273978261157e+00 , 4.29635231725488e+00 , 7.50533706521696e+00 ), ( -6.66158733267067e+00 , 3.16212698083009e+00 , 5.52259367060144e+00 ), ( -4.10875929173951e+00 , 2.25266922278055e+00 , 6.39196066096449e+00 ), ( -4.81464283416042e+00 , 3.27297540982399e+00 , 7.25521556339087e+00 ), ( -4.03416089454241e+00 , 4.55176819897888e+00 , 7.27161276872507e+00 ) } +colvars: Step 28, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_ids[size = 0] = +colvars: Step 28, atom_groups_refcount[size = 0] = +colvars: Step 28, atom_groups_masses[size = 0] = +colvars: Step 28, atom_groups_charges[size = 0] = +colvars: Step 28, atom_groups_coms[size = 0] = +colvars: Step 28, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 28, volmaps_ids[size = 0] = +colvars: Step 28, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 28 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.96949879926448e-01 , -1.04029858363134e-02 , 9.54836397870000e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.96949879926448e-01 , -1.04029858363134e-02 , 9.54836397870000e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.457 , 2.15986 , -15.1931 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.457 , 2.15986 , -15.1931 ) to colvar "one". +colvars: Adding total bias energy: 44.1777 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.457 , 2.15986 , -15.1931 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.92886 , -0.524915 , -1.42221 ) +colvars: ( -4.2265 , -0.450114 , -1.21955 ) +colvars: ( -4.2265 , -0.450114 , -1.21955 ) +colvars: ( -5.62981 , -0.599565 , -1.62447 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.888032 , 0.196029 , 0.610784 ) +colvars: ( 0.769705 , 0.266323 , 0.634369 ) +colvars: ( 0.753524 , 0.259486 , 0.61604 ) +colvars: ( 0.65927 , 0.266753 , 0.57098 ) +colvars: ( 0.647515 , 0.200333 , 0.477142 ) +colvars: ( 0.573849 , 0.343527 , 0.622111 ) +colvars: ( 0.468022 , 0.357157 , 0.578685 ) +colvars: ( 0.392296 , 0.453916 , 0.661616 ) +colvars: ( 0.387079 , 0.31259 , 0.473415 ) +colvars: ( 0.352842 , 0.27099 , 0.39908 ) +colvars: ( 0.357762 , 0.317885 , 0.463377 ) +colvars: ( 0.287142 , 0.275029 , 0.366325 ) +colvars: ( 0.260008 , 0.303996 , 0.388569 ) +colvars: ( 0.34886 , 0.177651 , 0.274472 ) +colvars: ( 0.290837 , 0.134293 , 0.184058 ) +colvars: ( 0.470229 , 0.141045 , 0.296791 ) +colvars: ( 0.541952 , 0.0501137 , 0.219177 ) +colvars: ( 0.669961 , 0.0295627 , 0.266379 ) +colvars: ( 0.550776 , 0.0182965 , 0.182597 ) +colvars: ( 0.5352 , -0.0466322 , 0.0885004 ) +colvars: ( 0.571739 , 0.0660664 , 0.25733 ) +colvars: ( 0.570582 , 0.0498437 , 0.235403 ) +colvars: ( 0.606988 , 0.114422 , 0.341103 ) +colvars: ( 0.447725 , 0.0539386 , 0.169623 ) +colvars: ( 0.441123 , -0.00190145 , 0.0926315 ) +colvars: ( 0.346815 , 0.119151 , 0.196634 ) +colvars: ( 0.223722 , 0.127358 , 0.136106 ) +colvars: ( 0.133151 , 0.212663 , 0.195432 ) +colvars: ( 0.195597 , 0.053806 , 0.0234426 ) +colvars: ( 0.147024 , 0.0175533 , -0.0521877 ) +colvars: ( 0.22847 , 0.0285052 , 0.00932752 ) +colvars: ( 0.214367 , -0.0437703 , -0.0935429 ) +colvars: ( 0.248884 , -0.0468944 , -0.0776473 ) +colvars: ( 0.288896 , -0.129316 , -0.162474 ) +colvars: ( 0.245388 , -0.182412 , -0.257242 ) +colvars: ( 0.402916 , -0.144003 , -0.115691 ) +colvars: ( 0.479656 , -0.219119 , -0.169676 ) +colvars: ( 0.609427 , -0.221345 , -0.0974421 ) +colvars: ( 0.433252 , -0.223835 , -0.202728 ) +colvars: ( 0.438783 , -0.291721 , -0.288477 ) +colvars: ( 0.38529 , -0.150933 , -0.134978 ) +colvars: ( 0.332 , -0.144951 , -0.158 ) +colvars: ( 0.315906 , -0.0586135 , -0.054191 ) +colvars: ( 0.210046 , -0.154058 , -0.240555 ) +colvars: ( 0.186105 , -0.196079 , -0.30948 ) +colvars: ( 0.0104534 , -0.200089 , -0.416454 ) +colvars: ( -0.0794907 , -0.218091 , -0.492128 ) +colvars: ( 0.109476 , -0.249528 , -0.423891 ) +colvars: ( 0.12891 , -0.113716 , -0.234681 ) +colvars: ( 0.0108686 , -0.118403 , -0.30918 ) +colvars: ( -0.0772672 , -0.0381642 , -0.255081 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.92886 , 0.524915 , 1.42221 ) +colvars: ( 4.2265 , 0.450114 , 1.21955 ) +colvars: ( 4.2265 , 0.450114 , 1.21955 ) +colvars: ( 5.62981 , 0.599565 , 1.62447 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.61394 , -0.08116 , -0.364598 ) +colvars: ( -0.5524 , -0.16456 , -0.332368 ) +colvars: ( -0.501359 , -0.142153 , -0.273129 ) +colvars: ( -0.514332 , -0.192314 , -0.303969 ) +colvars: ( -0.504653 , -0.132886 , -0.273149 ) +colvars: ( -0.490642 , -0.285209 , -0.313141 ) +colvars: ( -0.459171 , -0.325945 , -0.29598 ) +colvars: ( -0.438424 , -0.434263 , -0.313583 ) +colvars: ( -0.39595 , -0.290117 , -0.219738 ) +colvars: ( -0.392011 , -0.26463 , -0.206734 ) +colvars: ( -0.345688 , -0.284259 , -0.167157 ) +colvars: ( -0.284844 , -0.246888 , -0.0927553 ) +colvars: ( -0.235245 , -0.261775 , -0.0482031 ) +colvars: ( -0.303619 , -0.142757 , -0.0746565 ) +colvars: ( -0.272626 , -0.113179 , -0.0330162 ) +colvars: ( -0.357116 , -0.0848995 , -0.107872 ) +colvars: ( -0.383087 , 0.0142335 , -0.0987784 ) +colvars: ( -0.432152 , 0.0622684 , -0.131027 ) +colvars: ( -0.42168 , 0.0292414 , -0.132228 ) +colvars: ( -0.410281 , 0.0865596 , -0.100428 ) +colvars: ( -0.466708 , -0.025441 , -0.196882 ) +colvars: ( -0.502111 , -0.0270668 , -0.233032 ) +colvars: ( -0.552826 , -0.0932266 , -0.307474 ) +colvars: ( -0.451058 , -0.057323 , -0.192474 ) +colvars: ( -0.458258 , -0.0128784 , -0.183933 ) +colvars: ( -0.396424 , -0.132232 , -0.16417 ) +colvars: ( -0.33971 , -0.163765 , -0.118378 ) +colvars: ( -0.289716 , -0.254691 , -0.100421 ) +colvars: ( -0.297834 , -0.0901355 , -0.0501647 ) +colvars: ( -0.285261 , -0.0713728 , -0.0308719 ) +colvars: ( -0.27666 , -0.0447125 , -0.0127652 ) +colvars: ( -0.240496 , 0.0308498 , 0.0503938 ) +colvars: ( -0.217812 , 0.0576278 , 0.0826918 ) +colvars: ( -0.284263 , 0.118328 , 0.0374699 ) +colvars: ( -0.257733 , 0.160517 , 0.0791024 ) +colvars: ( -0.35324 , 0.146593 , -0.0218048 ) +colvars: ( -0.401866 , 0.223398 , -0.0433994 ) +colvars: ( -0.472375 , 0.246076 , -0.106196 ) +colvars: ( -0.414778 , 0.203266 , -0.0635194 ) +colvars: ( -0.419291 , 0.26463 , -0.0462717 ) +colvars: ( -0.420448 , 0.115812 , -0.10026 ) +colvars: ( -0.428904 , 0.0852642 , -0.1196 ) +colvars: ( -0.451436 , -0.00901328 , -0.175706 ) +colvars: ( -0.36278 , 0.0739788 , -0.0571654 ) +colvars: ( -0.366695 , 0.100478 , -0.0516932 ) +colvars: ( -0.201121 , 0.107362 , 0.117117 ) +colvars: ( -0.152114 , 0.109311 , 0.167051 ) +colvars: ( -0.226392 , 0.180386 , 0.117647 ) +colvars: ( -0.300087 , 0.0330038 , -0.00871765 ) +colvars: ( -0.233849 , 0.0193583 , 0.0529941 ) +colvars: ( -0.180198 , -0.0643977 , 0.07717 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 28. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 28. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atoms_new_colvar_forces = { ( -4.65476812955759e+00 , -4.10045996947463e-01 , -1.17602627053731e+00 ), ( -4.00919047605904e+00 , -3.48351339099113e-01 , -9.17545331736287e-01 ), ( -4.08155711778757e+00 , -3.75675728317876e-01 , -9.52536146563627e-01 ), ( -5.48695296182584e+00 , -5.32118393030834e-01 , -1.42047838166992e+00 ), ( 2.52165400875046e-01 , 1.17333527735657e-01 , 3.42911262032302e-01 ), ( 5.01206675503852e+00 , 5.83232939253654e-01 , 1.73118138788782e+00 ), ( 4.23534680006229e+00 , 4.81326584524782e-01 , 1.50225204283461e+00 ), ( -4.61288191429134e-02 , 1.96528860056323e-02 , 3.48032787079061e-01 ), ( 4.21762464441680e+00 , 4.72587014941585e-01 , 1.47322332645969e+00 ), ( 5.59064587845707e+00 , 6.05925444067054e-01 , 1.81681779345799e+00 ), ( 1.20738874940310e-02 , 3.36258089171626e-02 , 2.96220005207911e-01 ), ( 2.29798203928566e-03 , 2.81405175212899e-02 , 2.73570080702721e-01 ), ( 2.47629158927604e-02 , 4.22217640943423e-02 , 3.40365812986325e-01 ), ( 4.52410721441125e-02 , 3.48938705627658e-02 , 1.99815318408579e-01 ), ( 1.82112042517809e-02 , 2.11139811399131e-02 , 1.51042308591674e-01 ), ( 1.13113824739186e-01 , 5.61457566187413e-02 , 1.88919585237016e-01 ), ( 1.58864369542766e-01 , 6.43471729409368e-02 , 1.20398624464579e-01 ), ( 2.37808950079305e-01 , 9.18311328291469e-02 , 1.35351524138479e-01 ), ( 1.29095661454724e-01 , 4.75378728697175e-02 , 5.03683180846414e-02 ), ( 1.24919473592923e-01 , 3.99273648323862e-02 , -1.19278687483283e-02 ), ( 1.05031737468460e-01 , 4.06253752835865e-02 , 6.04476526193786e-02 ), ( 6.84713480458817e-02 , 2.27769076335840e-02 , 2.37089042450869e-03 ), ( 5.41627061514108e-02 , 2.11956434725954e-02 , 3.36289132160833e-02 ), ( -3.33235988143127e-03 , -3.38439301768139e-03 , -2.28517792585316e-02 ), ( -1.71354304230992e-02 , -1.47798435189928e-02 , -9.13012720837809e-02 ), ( -4.96095178023854e-02 , -1.30810065829210e-02 , 3.24637873151127e-02 ), ( -1.15988281381791e-01 , -3.64067874593997e-02 , 1.77279658818581e-02 ), ( -1.56564834085649e-01 , -4.20278731472885e-02 , 9.50116798854930e-02 ), ( -1.02237003830339e-01 , -3.63295082040771e-02 , -2.67221132056988e-02 ), ( -1.38237108558767e-01 , -5.38194321132817e-02 , -8.30595184101709e-02 ), ( -4.81895154744584e-02 , -1.62072680224376e-02 , -3.43772607775143e-03 ), ( -2.61294590358489e-02 , -1.29205333531506e-02 , -4.31490010360505e-02 ), ( 3.10722386606848e-02 , 1.07333928007365e-02 , 5.04450116982869e-03 ), ( 4.63316821339083e-03 , -1.09876373558418e-02 , -1.25004344944768e-01 ), ( -1.23449908203879e-02 , -2.18953257600948e-02 , -1.78139518761754e-01 ), ( 4.96755595934390e-02 , 2.58916802575213e-03 , -1.37495704434840e-01 ), ( 7.77895977856998e-02 , 4.27833880291345e-03 , -2.13075808840435e-01 ), ( 1.37051955652804e-01 , 2.47311820808655e-02 , -2.03638146602475e-01 ), ( 1.84744211386928e-02 , -2.05695887295308e-02 , -2.66247194822574e-01 ), ( 1.94914637038850e-02 , -2.70916913745008e-02 , -3.34748408375694e-01 ), ( -3.51576903850040e-02 , -3.51202989156158e-02 , -2.35237322598323e-01 ), ( -9.69042283388186e-02 , -5.96866435063923e-02 , -2.77599946885010e-01 ), ( -1.35530400030107e-01 , -6.76267423189185e-02 , -2.29897428265782e-01 ), ( -1.52733628638114e-01 , -8.00787590584912e-02 , -2.97720470395002e-01 ), ( -1.80590177992081e-01 , -9.56001638513193e-02 , -3.61172824965231e-01 ), ( -1.90667631628592e-01 , -9.27278108950850e-02 , -2.99337209654511e-01 ), ( -2.31604641098833e-01 , -1.08780110183448e-01 , -3.25077189622499e-01 ), ( -1.16916318483069e-01 , -6.91414811356912e-02 , -3.06243655941052e-01 ), ( -1.71176778451799e-01 , -8.07123558763408e-02 , -2.43398496883655e-01 ), ( -2.22979978003921e-01 , -9.90450628986568e-02 , -2.56185743873434e-01 ), ( -2.57465537777492e-01 , -1.02561872280358e-01 , -1.77910742891168e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 28, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 29 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 29, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 29, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 29, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 29, atoms_positions[size = 51] = { ( 8.24496138808168e+00 , 4.31696617009711e-02 , -7.26144896093100e-01 ), ( 6.84232247426870e+00 , -5.84524722450423e-01 , -5.28573266826814e-01 ), ( 6.13164468639699e+00 , -3.73699905659251e-01 , 8.00548954494365e-01 ), ( 4.90914110199627e+00 , -1.47792375751190e-01 , 7.43506777214514e-01 ), ( 7.00631140322438e+00 , -2.06805294892657e+00 , -8.83236646834291e-01 ), ( 6.81263376358257e+00 , -2.88542671960002e-01 , 1.96371574058638e+00 ), ( 6.10578932678212e+00 , -2.19803667256985e-01 , 3.17121049962957e+00 ), ( 7.13166755204546e+00 , -3.44061232085154e-01 , 4.38017766658372e+00 ), ( 5.32993294139157e+00 , 1.06925331121861e+00 , 3.36870511542620e+00 ), ( 4.18037027744364e+00 , 1.00715570332890e+00 , 3.76942404051173e+00 ), ( 5.84343425506103e+00 , 2.25308779944875e+00 , 2.97407534749559e+00 ), ( 5.16670178200228e+00 , 3.55706968834576e+00 , 2.89332095680574e+00 ), ( 6.30661364560706e+00 , 4.47800974454676e+00 , 2.29189326246384e+00 ), ( 3.85894836095718e+00 , 3.64925687156038e+00 , 2.02898673489838e+00 ), ( 2.80982764874967e+00 , 4.16917318049284e+00 , 2.44071659063784e+00 ), ( 3.91666894951431e+00 , 3.19850135757316e+00 , 7.40116628974484e-01 ), ( 2.75367085851993e+00 , 3.05602432092180e+00 , -7.52655643942308e-02 ), ( 3.11203335116034e+00 , 2.65444460648948e+00 , -1.54076284315453e+00 ), ( 1.55010470025782e+00 , 2.19385032442025e+00 , 4.23680650168264e-01 ), ( 4.03023766497359e-01 , 2.61692523559002e+00 , 4.65935578917440e-01 ), ( 2.06998946133020e+00 , 1.14537990473560e+00 , 1.04431888027783e+00 ), ( 1.21098258133945e+00 , 1.29037058993668e-01 , 1.68805594186284e+00 ), ( 2.07930062216384e+00 , -1.09233521711463e+00 , 2.03798648300783e+00 ), ( 5.75126953005429e-01 , 6.16581675883185e-01 , 2.96045522085957e+00 ), ( -5.85307758248492e-01 , 3.55388145161849e-01 , 3.17726424655820e+00 ), ( 1.28816079063222e+00 , 1.38217698582714e+00 , 3.74914636804183e+00 ), ( 8.64291464259602e-01 , 1.98010175305726e+00 , 5.03175022927395e+00 ), ( 2.09839475624342e+00 , 2.75346067402022e+00 , 5.72407913019983e+00 ), ( -3.55909994471641e-01 , 2.90254232076419e+00 , 4.95956773823758e+00 ), ( -1.11561987567268e+00 , 3.06859309354974e+00 , 5.88015681122639e+00 ), ( -5.43627798137215e-01 , 3.50875435559019e+00 , 3.78939503753594e+00 ), ( -1.47622161559560e+00 , 4.48866909636002e+00 , 3.41427878800857e+00 ), ( -7.31785633997068e-01 , 5.43423662577483e+00 , 2.47676181149411e+00 ), ( -2.74498543237162e+00 , 3.94542770599967e+00 , 2.80125835034849e+00 ), ( -3.80612156567671e+00 , 4.55962236672602e+00 , 2.81318360675681e+00 ), ( -2.68469459647624e+00 , 2.63423255024100e+00 , 2.35681928446616e+00 ), ( -3.79799201892991e+00 , 1.82595810604839e+00 , 2.00583757586995e+00 ), ( -3.35983872216255e+00 , 8.76205411708678e-01 , 8.14507318830490e-01 ), ( -4.25481381552370e+00 , 1.04654833296319e+00 , 3.23575420221390e+00 ), ( -5.47697540325327e+00 , 7.58370076846867e-01 , 3.33857794941254e+00 ), ( -3.37050768005777e+00 , 7.27108621774589e-01 , 4.17294251406612e+00 ), ( -3.67068236925121e+00 , 8.03484199349822e-02 , 5.47842770098067e+00 ), ( -2.38130405574370e+00 , -3.19228682540857e-01 , 6.13543053245953e+00 ), ( -4.47852896853978e+00 , 9.22046457306445e-01 , 6.42144130767386e+00 ), ( -5.36111030389346e+00 , 5.76037218940877e-01 , 7.20401337907534e+00 ), ( -6.30585224909303e+00 , 3.62667918534697e+00 , 6.75268695987722e+00 ), ( -6.99867967050315e+00 , 4.29714524440254e+00 , 7.50869529813025e+00 ), ( -6.65086956854691e+00 , 3.16195575138039e+00 , 5.52768532598170e+00 ), ( -4.10731209823951e+00 , 2.25417776325648e+00 , 6.39436352277790e+00 ), ( -4.81574900061354e+00 , 3.27878997363146e+00 , 7.25183376897882e+00 ), ( -4.02722822094389e+00 , 4.55630501417280e+00 , 7.27236308788831e+00 ) } +colvars: Step 29, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_ids[size = 0] = +colvars: Step 29, atom_groups_refcount[size = 0] = +colvars: Step 29, atom_groups_masses[size = 0] = +colvars: Step 29, atom_groups_charges[size = 0] = +colvars: Step 29, atom_groups_coms[size = 0] = +colvars: Step 29, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 29, volmaps_ids[size = 0] = +colvars: Step 29, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 29 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.95963250214387e-01 , -1.17171742424022e-02 , 9.55127458693503e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.95963250214387e-01 , -1.17171742424022e-02 , 9.55127458693503e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.4373 , 2.18614 , -15.1989 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.4373 , 2.18614 , -15.1989 ) to colvar "one". +colvars: Adding total bias energy: 44.1421 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.4373 , 2.18614 , -15.1989 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.9306 , -0.523543 , -1.41844 ) +colvars: ( -4.22799 , -0.448938 , -1.21631 ) +colvars: ( -4.22799 , -0.448938 , -1.21631 ) +colvars: ( -5.6318 , -0.597998 , -1.62016 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.887491 , 0.196068 , 0.609742 ) +colvars: ( 0.769309 , 0.266273 , 0.633282 ) +colvars: ( 0.753128 , 0.259462 , 0.615007 ) +colvars: ( 0.659022 , 0.266643 , 0.569974 ) +colvars: ( 0.647285 , 0.200259 , 0.476289 ) +colvars: ( 0.573713 , 0.343324 , 0.621005 ) +colvars: ( 0.468029 , 0.356885 , 0.577627 ) +colvars: ( 0.392401 , 0.453544 , 0.660409 ) +colvars: ( 0.387181 , 0.312325 , 0.472534 ) +colvars: ( 0.352997 , 0.270725 , 0.398308 ) +colvars: ( 0.357885 , 0.317629 , 0.462531 ) +colvars: ( 0.287345 , 0.274784 , 0.365646 ) +colvars: ( 0.260226 , 0.303748 , 0.387874 ) +colvars: ( 0.348985 , 0.177497 , 0.273952 ) +colvars: ( 0.291038 , 0.13414 , 0.183681 ) +colvars: ( 0.4702 , 0.140969 , 0.29625 ) +colvars: ( 0.541833 , 0.0501276 , 0.218772 ) +colvars: ( 0.669674 , 0.0296538 , 0.265918 ) +colvars: ( 0.550664 , 0.0183091 , 0.18223 ) +colvars: ( 0.535111 , -0.0465865 , 0.088286 ) +colvars: ( 0.571614 , 0.0660369 , 0.256824 ) +colvars: ( 0.570477 , 0.0497983 , 0.23491 ) +colvars: ( 0.606848 , 0.114333 , 0.340423 ) +colvars: ( 0.44778 , 0.0538309 , 0.169219 ) +colvars: ( 0.441195 , -0.00198709 , 0.0923439 ) +colvars: ( 0.346991 , 0.118965 , 0.196181 ) +colvars: ( 0.224057 , 0.127112 , 0.135738 ) +colvars: ( 0.133593 , 0.212332 , 0.194964 ) +colvars: ( 0.195959 , 0.0536085 , 0.0232699 ) +colvars: ( 0.147456 , 0.0173478 , -0.0522501 ) +colvars: ( 0.228774 , 0.0283622 , 0.00920348 ) +colvars: ( 0.214679 , -0.0438579 , -0.0934848 ) +colvars: ( 0.249134 , -0.0469379 , -0.0775872 ) +colvars: ( 0.289123 , -0.129327 , -0.162304 ) +colvars: ( 0.245672 , -0.182408 , -0.25692 ) +colvars: ( 0.403005 , -0.143965 , -0.115594 ) +colvars: ( 0.479657 , -0.219012 , -0.169493 ) +colvars: ( 0.609267 , -0.221184 , -0.0973677 ) +colvars: ( 0.43333 , -0.22377 , -0.202517 ) +colvars: ( 0.438859 , -0.291615 , -0.288129 ) +colvars: ( 0.385438 , -0.15095 , -0.134898 ) +colvars: ( 0.332232 , -0.145019 , -0.157909 ) +colvars: ( 0.316167 , -0.0587586 , -0.0542876 ) +colvars: ( 0.210431 , -0.154169 , -0.240339 ) +colvars: ( 0.186531 , -0.196187 , -0.309164 ) +colvars: ( 0.0110653 , -0.200218 , -0.415933 ) +colvars: ( -0.0787655 , -0.218245 , -0.49149 ) +colvars: ( 0.109954 , -0.249569 , -0.423334 ) +colvars: ( 0.129385 , -0.11387 , -0.234467 ) +colvars: ( 0.0114899 , -0.118601 , -0.308851 ) +colvars: ( -0.076544 , -0.0384391 , -0.25484 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.9306 , 0.523543 , 1.41844 ) +colvars: ( 4.22799 , 0.448938 , 1.21631 ) +colvars: ( 4.22799 , 0.448938 , 1.21631 ) +colvars: ( 5.6318 , 0.597998 , 1.62016 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.613596 , -0.0811287 , -0.363784 ) +colvars: ( -0.552137 , -0.164644 , -0.331345 ) +colvars: ( -0.500905 , -0.142178 , -0.271961 ) +colvars: ( -0.514235 , -0.192443 , -0.303014 ) +colvars: ( -0.504547 , -0.132926 , -0.272372 ) +colvars: ( -0.490703 , -0.28548 , -0.312041 ) +colvars: ( -0.459416 , -0.326283 , -0.294925 ) +colvars: ( -0.43881 , -0.434764 , -0.312318 ) +colvars: ( -0.39615 , -0.290387 , -0.218727 ) +colvars: ( -0.3923 , -0.264869 , -0.205894 ) +colvars: ( -0.345742 , -0.284499 , -0.165994 ) +colvars: ( -0.284832 , -0.247055 , -0.09162 ) +colvars: ( -0.235083 , -0.261941 , -0.0468463 ) +colvars: ( -0.3035 , -0.142769 , -0.0737538 ) +colvars: ( -0.272543 , -0.113144 , -0.0322326 ) +colvars: ( -0.356868 , -0.0848283 , -0.107043 ) +colvars: ( -0.382736 , 0.0144512 , -0.0981723 ) +colvars: ( -0.43163 , 0.062559 , -0.130419 ) +colvars: ( -0.421483 , 0.0294607 , -0.131845 ) +colvars: ( -0.410078 , 0.0868648 , -0.100219 ) +colvars: ( -0.466658 , -0.0253218 , -0.196494 ) +colvars: ( -0.502233 , -0.0269706 , -0.232829 ) +colvars: ( -0.553074 , -0.0932467 , -0.307209 ) +colvars: ( -0.451324 , -0.0572715 , -0.192303 ) +colvars: ( -0.458579 , -0.0127682 , -0.183963 ) +colvars: ( -0.39675 , -0.132282 , -0.163797 ) +colvars: ( -0.340155 , -0.163859 , -0.118004 ) +colvars: ( -0.29021 , -0.25491 , -0.0997851 ) +colvars: ( -0.298168 , -0.0901052 , -0.0498965 ) +colvars: ( -0.285688 , -0.07132 , -0.0307548 ) +colvars: ( -0.27679 , -0.044596 , -0.0124243 ) +colvars: ( -0.240498 , 0.0310932 , 0.050638 ) +colvars: ( -0.217599 , 0.0579317 , 0.0830817 ) +colvars: ( -0.284237 , 0.118692 , 0.0374444 ) +colvars: ( -0.257718 , 0.160946 , 0.0789408 ) +colvars: ( -0.353182 , 0.146985 , -0.0219155 ) +colvars: ( -0.401796 , 0.223893 , -0.0437641 ) +colvars: ( -0.472231 , 0.246595 , -0.106585 ) +colvars: ( -0.414915 , 0.203713 , -0.0640381 ) +colvars: ( -0.419431 , 0.265164 , -0.0469928 ) +colvars: ( -0.420763 , 0.116117 , -0.100684 ) +colvars: ( -0.429427 , 0.0855069 , -0.120144 ) +colvars: ( -0.452117 , -0.00892433 , -0.176119 ) +colvars: ( -0.363373 , 0.0742132 , -0.0577187 ) +colvars: ( -0.367382 , 0.100743 , -0.0524296 ) +colvars: ( -0.201576 , 0.107689 , 0.116663 ) +colvars: ( -0.152619 , 0.109647 , 0.166558 ) +colvars: ( -0.226654 , 0.180829 , 0.117147 ) +colvars: ( -0.300639 , 0.033195 , -0.00907176 ) +colvars: ( -0.234458 , 0.0195389 , 0.0526508 ) +colvars: ( -0.180832 , -0.0643294 , 0.0770926 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 29. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 29. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atoms_new_colvar_forces = { ( -4.65670159896063e+00 , -4.08603245295588e-01 , -1.17248338832359e+00 ), ( -4.01081376059348e+00 , -3.47308389336129e-01 , -9.14376974525829e-01 ), ( -4.08319913905012e+00 , -3.74737763463260e-01 , -9.49353477771137e-01 ), ( -5.48906241479621e+00 , -5.30665138777830e-01 , -1.41624757619421e+00 ), ( 2.52223437262611e-01 , 1.17284250024612e-01 , 3.43046777243059e-01 ), ( 5.01360736918691e+00 , 5.81386139237082e-01 , 1.72740619230722e+00 ), ( 4.23659945449720e+00 , 4.79540278728374e-01 , 1.49901573079741e+00 ), ( -4.64097000039294e-02 , 1.87794700133804e-02 , 3.48090574780212e-01 ), ( 4.21901745949712e+00 , 4.70875623332618e-01 , 1.47012036760910e+00 ), ( 5.59249756172167e+00 , 6.03854352079664e-01 , 1.81257809150848e+00 ), ( 1.21420596463037e-02 , 3.31300536477400e-02 , 2.96537315922656e-01 ), ( 2.51295238291405e-03 , 2.77284524975311e-02 , 2.74026059475105e-01 ), ( 2.51421681268256e-02 , 4.18064178338594e-02 , 3.41027837901573e-01 ), ( 4.54850116818478e-02 , 3.47280177999697e-02 , 2.00198561189227e-01 ), ( 1.84955889131971e-02 , 2.09959552992393e-02 , 1.51448159221894e-01 ), ( 1.13331676742972e-01 , 5.61410166432581e-02 , 1.89206719646637e-01 ), ( 1.59096415911424e-01 , 6.45788001457709e-02 , 1.20600031918681e-01 ), ( 2.38043327640614e-01 , 9.22127564609505e-02 , 1.35498585969918e-01 ), ( 1.29180529304181e-01 , 4.77698309462621e-02 , 5.03847641696983e-02 ), ( 1.25032612853243e-01 , 4.02783067915264e-02 , -1.19332314880314e-02 ), ( 1.04955467542364e-01 , 4.07150739558410e-02 , 6.03297392363021e-02 ), ( 6.82438775493076e-02 , 2.28277004719674e-02 , 2.08034221619557e-03 ), ( 5.37738046835708e-02 , 2.10864232617241e-02 , 3.32135610827194e-02 ), ( -3.54394089022969e-03 , -3.44058762846728e-03 , -2.30846602652034e-02 ), ( -1.73839271660975e-02 , -1.47552893298079e-02 , -9.16193368580235e-02 ), ( -4.97590224128163e-02 , -1.33172069675699e-02 , 3.23834025334986e-02 ), ( -1.16098532855008e-01 , -3.67472864829769e-02 , 1.77334420465540e-02 ), ( -1.56617457444929e-01 , -4.25784809673612e-02 , 9.51792402380099e-02 ), ( -1.02209152476269e-01 , -3.64967191819821e-02 , -2.66266524781619e-02 ), ( -1.38232294586396e-01 , -5.39722136465613e-02 , -8.30048967703130e-02 ), ( -4.80157555533287e-02 , -1.62338174601158e-02 , -3.22083761748142e-03 ), ( -2.58190670978757e-02 , -1.27646491473488e-02 , -4.28468377510776e-02 ), ( 3.15358576418900e-02 , 1.09937270877574e-02 , 5.49450268599003e-03 ), ( 4.88620365064174e-03 , -1.06349913601279e-02 , -1.24859303680468e-01 ), ( -1.20459642122228e-02 , -2.14618069143226e-02 , -1.77978899604409e-01 ), ( 4.98228494490220e-02 , 3.02036764157301e-03 , -1.37509267139386e-01 ), ( 7.78616316904814e-02 , 4.88094120234234e-03 , -2.13256942338586e-01 ), ( 1.37036486962564e-01 , 2.54111895390794e-02 , -2.03952705998990e-01 ), ( 1.84159931481138e-02 , -2.00570645719621e-02 , -2.66555412586245e-01 ), ( 1.94283757548011e-02 , -2.64511957672210e-02 , -3.35122039918450e-01 ), ( -3.53246008274327e-02 , -3.48325692850346e-02 , -2.35581780810036e-01 ), ( -9.71947768698217e-02 , -5.95116441472318e-02 , -2.78052948298791e-01 ), ( -1.35950125977703e-01 , -6.76829710476064e-02 , -2.30406485867260e-01 ), ( -1.52941623455422e-01 , -7.99556941520047e-02 , -2.98057449210995e-01 ), ( -1.80850595746373e-01 , -9.54438451521055e-02 , -3.61594031021475e-01 ), ( -1.90510651540727e-01 , -9.25291744751124e-02 , -2.99269665468407e-01 ), ( -2.31384846837763e-01 , -1.08598088089967e-01 , -3.24931828297016e-01 ), ( -1.16700860208935e-01 , -6.87394953148224e-02 , -3.06187647134030e-01 ), ( -1.71254047595557e-01 , -8.06754525103905e-02 , -2.43538397776284e-01 ), ( -2.22968165961279e-01 , -9.90619272759284e-02 , -2.56200122489818e-01 ), ( -2.57376150321236e-01 , -1.02768436893290e-01 , -1.77747202016434e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 29, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 30 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 30, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 30, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 30, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 30, atoms_positions[size = 51] = { ( 8.23764193151924e+00 , 4.34878621784569e-02 , -7.22437387351404e-01 ), ( 6.83724067727916e+00 , -5.90741777013381e-01 , -5.26277494276041e-01 ), ( 6.12049077818646e+00 , -3.66440296478970e-01 , 8.06190454945147e-01 ), ( 4.90768664730820e+00 , -1.48460272081974e-01 , 7.46413529312125e-01 ), ( 7.00242145471206e+00 , -2.07070238324471e+00 , -8.75621911133484e-01 ), ( 6.80896701816145e+00 , -2.92859449865948e-01 , 1.96585507175947e+00 ), ( 6.09805478625004e+00 , -2.24291356172958e-01 , 3.17764083144861e+00 ), ( 7.13779513547567e+00 , -3.44372284591930e-01 , 4.38625597261496e+00 ), ( 5.32534991678670e+00 , 1.06778123422510e+00 , 3.36818872219414e+00 ), ( 4.18328955469913e+00 , 1.00583200263353e+00 , 3.77938602514822e+00 ), ( 5.84618264800347e+00 , 2.25196209074770e+00 , 2.97224130362163e+00 ), ( 5.15696718996734e+00 , 3.55256190620906e+00 , 2.88757690727946e+00 ), ( 6.30269107155688e+00 , 4.47250092280947e+00 , 2.28828329070379e+00 ), ( 3.85878899047357e+00 , 3.64407916479059e+00 , 2.02553026289166e+00 ), ( 2.81489301642761e+00 , 4.16818120475770e+00 , 2.43593349206520e+00 ), ( 3.91210307526539e+00 , 3.19157198544600e+00 , 7.44048834694064e-01 ), ( 2.76003615434961e+00 , 3.06608629331018e+00 , -7.25874883058444e-02 ), ( 3.11742337169011e+00 , 2.65213617856577e+00 , -1.54206552610553e+00 ), ( 1.55039770860550e+00 , 2.20386198781653e+00 , 4.24256136232630e-01 ), ( 4.08849667016392e-01 , 2.61688082708039e+00 , 4.60293697403412e-01 ), ( 2.06461603838958e+00 , 1.14149691206851e+00 , 1.04541097965762e+00 ), ( 1.22357232347860e+00 , 1.34393220866268e-01 , 1.68340199992315e+00 ), ( 2.08287824275055e+00 , -1.09278633478080e+00 , 2.03934021088462e+00 ), ( 5.75092496965859e-01 , 6.15856553332651e-01 , 2.95697480938450e+00 ), ( -5.87357636235547e-01 , 3.56101442773918e-01 , 3.18146113194469e+00 ), ( 1.28676477647157e+00 , 1.38988639904308e+00 , 3.75385474851258e+00 ), ( 8.71640430576094e-01 , 1.97942310063133e+00 , 5.03369067882944e+00 ), ( 2.09103448113220e+00 , 2.75788254961826e+00 , 5.72533971686084e+00 ), ( -3.57681243375300e-01 , 2.90078969757531e+00 , 4.95464372313808e+00 ), ( -1.11541264578088e+00 , 3.06908366402439e+00 , 5.88230677576328e+00 ), ( -5.43427370177526e-01 , 3.50725177810262e+00 , 3.78023131228879e+00 ), ( -1.46905417259948e+00 , 4.48405143604890e+00 , 3.41543895300378e+00 ), ( -7.38765937891440e-01 , 5.43800335188954e+00 , 2.47858519576284e+00 ), ( -2.74614344700853e+00 , 3.94572527756033e+00 , 2.78699832532386e+00 ), ( -3.80455714654773e+00 , 4.56547520913436e+00 , 2.81323605280181e+00 ), ( -2.69035509257330e+00 , 2.63355514221594e+00 , 2.35515850510570e+00 ), ( -3.80124210147649e+00 , 1.82603550884334e+00 , 2.00539763392691e+00 ), ( -3.35755012040177e+00 , 8.77442195063242e-01 , 8.07339675899194e-01 ), ( -4.25205059122558e+00 , 1.04193013701143e+00 , 3.24035718745224e+00 ), ( -5.47083100450072e+00 , 7.52673426353046e-01 , 3.34025030578420e+00 ), ( -3.37085931211436e+00 , 7.28334365476863e-01 , 4.16786494900867e+00 ), ( -3.66953107693088e+00 , 7.97427501274149e-02 , 5.48070385346425e+00 ), ( -2.37706726794794e+00 , -3.15272299660837e-01 , 6.13169480962639e+00 ), ( -4.48247484924873e+00 , 9.22257244466278e-01 , 6.42087370465327e+00 ), ( -5.35969050463327e+00 , 5.71530653848507e-01 , 7.19997128922252e+00 ), ( -6.30857477849050e+00 , 3.62368382711476e+00 , 6.75344333301841e+00 ), ( -7.00511359239387e+00 , 4.29806989977957e+00 , 7.51180125044996e+00 ), ( -6.64106161108270e+00 , 3.16234887923283e+00 , 5.53295301740457e+00 ), ( -4.10662351090596e+00 , 2.25514070803843e+00 , 6.39745035366231e+00 ), ( -4.81620877959101e+00 , 3.28313127591232e+00 , 7.24713868314063e+00 ), ( -4.02120918464972e+00 , 4.56274305514335e+00 , 7.27350034759277e+00 ) } +colvars: Step 30, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_ids[size = 0] = +colvars: Step 30, atom_groups_refcount[size = 0] = +colvars: Step 30, atom_groups_masses[size = 0] = +colvars: Step 30, atom_groups_charges[size = 0] = +colvars: Step 30, atom_groups_coms[size = 0] = +colvars: Step 30, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 30, volmaps_ids[size = 0] = +colvars: Step 30, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 30 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.94864820949374e-01 , -1.29606427096605e-02 , 9.55451076249876e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.94864820949374e-01 , -1.29606427096605e-02 , 9.55451076249876e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.4153 , 2.21101 , -15.2054 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.4153 , 2.21101 , -15.2054 ) to colvar "one". +colvars: Adding total bias energy: 44.1015 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.4153 , 2.21101 , -15.2054 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.93255 , -0.521985 , -1.41418 ) +colvars: ( -4.22966 , -0.447602 , -1.21266 ) +colvars: ( -4.22966 , -0.447602 , -1.21266 ) +colvars: ( -5.63404 , -0.596219 , -1.6153 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.886932 , 0.196107 , 0.608619 ) +colvars: ( 0.768901 , 0.26621 , 0.63212 ) +colvars: ( 0.752721 , 0.259434 , 0.613913 ) +colvars: ( 0.65877 , 0.266512 , 0.5689 ) +colvars: ( 0.647051 , 0.20017 , 0.475371 ) +colvars: ( 0.573578 , 0.343084 , 0.619829 ) +colvars: ( 0.468045 , 0.356567 , 0.576502 ) +colvars: ( 0.392518 , 0.45311 , 0.659131 ) +colvars: ( 0.387297 , 0.312018 , 0.471599 ) +colvars: ( 0.353168 , 0.270417 , 0.397482 ) +colvars: ( 0.358021 , 0.317335 , 0.461643 ) +colvars: ( 0.287566 , 0.274508 , 0.364938 ) +colvars: ( 0.260463 , 0.303472 , 0.38716 ) +colvars: ( 0.349126 , 0.177326 , 0.273406 ) +colvars: ( 0.291259 , 0.133972 , 0.183283 ) +colvars: ( 0.470178 , 0.140887 , 0.295676 ) +colvars: ( 0.541718 , 0.0501492 , 0.218335 ) +colvars: ( 0.669382 , 0.0297634 , 0.265418 ) +colvars: ( 0.550556 , 0.018326 , 0.181823 ) +colvars: ( 0.535027 , -0.0465307 , 0.088036 ) +colvars: ( 0.571492 , 0.0660015 , 0.256265 ) +colvars: ( 0.570375 , 0.0497414 , 0.234355 ) +colvars: ( 0.606709 , 0.114222 , 0.339668 ) +colvars: ( 0.447847 , 0.0537034 , 0.168761 ) +colvars: ( 0.44128 , -0.00208979 , 0.0920032 ) +colvars: ( 0.347186 , 0.11875 , 0.195681 ) +colvars: ( 0.224417 , 0.126828 , 0.13533 ) +colvars: ( 0.134065 , 0.211952 , 0.194462 ) +colvars: ( 0.196348 , 0.0533846 , 0.0230707 ) +colvars: ( 0.147919 , 0.0171144 , -0.0523364 ) +colvars: ( 0.229103 , 0.028204 , 0.00906062 ) +colvars: ( 0.215019 , -0.043949 , -0.0934342 ) +colvars: ( 0.249408 , -0.0469752 , -0.0775274 ) +colvars: ( 0.289373 , -0.129331 , -0.162144 ) +colvars: ( 0.245982 , -0.182393 , -0.256602 ) +colvars: ( 0.40311 , -0.143915 , -0.115519 ) +colvars: ( 0.479671 , -0.218884 , -0.169338 ) +colvars: ( 0.609111 , -0.220998 , -0.0973333 ) +colvars: ( 0.433424 , -0.223693 , -0.20234 ) +colvars: ( 0.438952 , -0.291493 , -0.287813 ) +colvars: ( 0.385605 , -0.150971 , -0.134859 ) +colvars: ( 0.332487 , -0.1451 , -0.157863 ) +colvars: ( 0.316452 , -0.0589326 , -0.0544384 ) +colvars: ( 0.210846 , -0.154298 , -0.240155 ) +colvars: ( 0.186989 , -0.196314 , -0.308882 ) +colvars: ( 0.0117196 , -0.200357 , -0.415411 ) +colvars: ( -0.0779919 , -0.218412 , -0.490842 ) +colvars: ( 0.110468 , -0.249607 , -0.422778 ) +colvars: ( 0.129894 , -0.114046 , -0.234275 ) +colvars: ( 0.0121534 , -0.118823 , -0.308533 ) +colvars: ( -0.0757742 , -0.0387487 , -0.254604 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.93255 , 0.521985 , 1.41418 ) +colvars: ( 4.22966 , 0.447602 , 1.21266 ) +colvars: ( 4.22966 , 0.447602 , 1.21266 ) +colvars: ( 5.63404 , 0.596219 , 1.6153 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.613189 , -0.0810902 , -0.362837 ) +colvars: ( -0.55183 , -0.164703 , -0.330196 ) +colvars: ( -0.500411 , -0.142189 , -0.270679 ) +colvars: ( -0.514113 , -0.192538 , -0.301946 ) +colvars: ( -0.504416 , -0.132943 , -0.271493 ) +colvars: ( -0.490751 , -0.285696 , -0.310822 ) +colvars: ( -0.459664 , -0.326552 , -0.293761 ) +colvars: ( -0.439211 , -0.435174 , -0.310935 ) +colvars: ( -0.396365 , -0.290596 , -0.21763 ) +colvars: ( -0.392608 , -0.265048 , -0.204978 ) +colvars: ( -0.345817 , -0.284683 , -0.164757 ) +colvars: ( -0.284851 , -0.247177 , -0.0904324 ) +colvars: ( -0.234959 , -0.262065 , -0.0454442 ) +colvars: ( -0.303403 , -0.142757 , -0.072808 ) +colvars: ( -0.27249 , -0.11309 , -0.0314217 ) +colvars: ( -0.356624 , -0.0847472 , -0.106162 ) +colvars: ( -0.382377 , 0.014658 , -0.0975193 ) +colvars: ( -0.431081 , 0.062825 , -0.129752 ) +colvars: ( -0.421276 , 0.0296717 , -0.131412 ) +colvars: ( -0.409867 , 0.0871514 , -0.099973 ) +colvars: ( -0.466595 , -0.0251964 , -0.196037 ) +colvars: ( -0.50234 , -0.0268624 , -0.232553 ) +colvars: ( -0.553302 , -0.0932388 , -0.306848 ) +colvars: ( -0.451595 , -0.0571982 , -0.192073 ) +colvars: ( -0.458904 , -0.0126423 , -0.183943 ) +colvars: ( -0.397096 , -0.132296 , -0.163371 ) +colvars: ( -0.340639 , -0.163907 , -0.117592 ) +colvars: ( -0.290758 , -0.255066 , -0.0991117 ) +colvars: ( -0.298545 , -0.0900459 , -0.0496119 ) +colvars: ( -0.286166 , -0.0712385 , -0.0306315 ) +colvars: ( -0.276959 , -0.0444651 , -0.0120742 ) +colvars: ( -0.240542 , 0.0313336 , 0.0508715 ) +colvars: ( -0.217422 , 0.0582208 , 0.0834569 ) +colvars: ( -0.284241 , 0.119036 , 0.0374067 ) +colvars: ( -0.257738 , 0.161349 , 0.0787514 ) +colvars: ( -0.353136 , 0.147353 , -0.0220217 ) +colvars: ( -0.401725 , 0.224349 , -0.0441229 ) +colvars: ( -0.472065 , 0.247069 , -0.106949 ) +colvars: ( -0.415057 , 0.204131 , -0.0645506 ) +colvars: ( -0.419575 , 0.26566 , -0.0477175 ) +colvars: ( -0.421091 , 0.116415 , -0.10109 ) +colvars: ( -0.42997 , 0.0857542 , -0.120669 ) +colvars: ( -0.452821 , -0.0088089 , -0.176496 ) +colvars: ( -0.364005 , 0.0744563 , -0.0582742 ) +colvars: ( -0.36811 , 0.101015 , -0.053175 ) +colvars: ( -0.202102 , 0.108013 , 0.116158 ) +colvars: ( -0.15321 , 0.109981 , 0.165997 ) +colvars: ( -0.226973 , 0.181251 , 0.116596 ) +colvars: ( -0.301243 , 0.0334005 , -0.00943806 ) +colvars: ( -0.235138 , 0.0197377 , 0.0522761 ) +colvars: ( -0.181551 , -0.0642274 , 0.0769818 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 30. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 30. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atoms_new_colvar_forces = { ( -4.65881091939876e+00 , -4.06968120314540e-01 , -1.16840238818501e+00 ), ( -4.01259358032102e+00 , -3.46094103673623e-01 , -9.10739126726648e-01 ), ( -4.08500707211808e+00 , -3.73627074879122e-01 , -9.45708790057030e-01 ), ( -5.49140042669050e+00 , -5.28990826826190e-01 , -1.41142445350943e+00 ), ( 2.52310153882297e-01 , 1.17245050973893e-01 , 3.43233812656448e-01 ), ( 5.01538155268732e+00 , 5.79373455956572e-01 , 1.72319150686184e+00 ), ( 4.23804539388424e+00 , 4.77616972499955e-01 , 1.49540352721395e+00 ), ( -4.66932933661841e-02 , 1.79360249762789e-02 , 3.48195888080529e-01 ), ( 4.22059604661739e+00 , 4.69023894582741e-01 , 1.46663195302982e+00 ), ( 5.59459557872950e+00 , 6.01587933622038e-01 , 1.80780689775655e+00 ), ( 1.22036576053411e-02 , 3.26524769744383e-02 , 2.96886579167257e-01 ), ( 2.71463857431481e-03 , 2.73311738642717e-02 , 2.74505365585359e-01 ), ( 2.55038209539085e-02 , 4.14066479723788e-02 , 3.41715979929007e-01 ), ( 4.57223673038846e-02 , 3.45695136287414e-02 , 2.00598114581399e-01 ), ( 1.87687384216944e-02 , 2.08826494366835e-02 , 1.51861686024796e-01 ), ( 1.13554277538003e-01 , 5.61400918390356e-02 , 1.89513813429391e-01 ), ( 1.59340801145138e-01 , 6.48072574791715e-02 , 1.20815692473921e-01 ), ( 2.38301424210039e-01 , 9.25884298643695e-02 , 1.35666078056799e-01 ), ( 1.29280362701120e-01 , 4.79976864448071e-02 , 5.04112447680767e-02 ), ( 1.25160204334001e-01 , 4.06207218780376e-02 , -1.19369634997108e-02 ), ( 1.04896631401357e-01 , 4.08050540322550e-02 , 6.02276324059099e-02 ), ( 6.80353805583742e-02 , 2.28790287623235e-02 , 1.80250378573932e-03 ), ( 5.34073998551376e-02 , 2.09830827474990e-02 , 3.28196814256284e-02 ), ( -3.74737265029546e-03 , -3.49478322671525e-03 , -2.33124478720126e-02 ), ( -1.76235755051978e-02 , -1.47320771849530e-02 , -9.19395380793947e-02 ), ( -4.99107481254734e-02 , -1.35464979593908e-02 , 3.23094349505738e-02 ), ( -1.16222130293656e-01 , -3.70793398559244e-02 , 1.77383571994701e-02 ), ( -1.56693200381850e-01 , -4.31144610918196e-02 , 9.53505650187003e-02 ), ( -1.02197093582566e-01 , -3.66613140666613e-02 , -2.65411825785693e-02 ), ( -1.38246652814804e-01 , -5.41240772698316e-02 , -8.29679131441682e-02 ), ( -4.78558447552094e-02 , -1.62610800080856e-02 , -3.01360594317225e-03 ), ( -2.55237677150758e-02 , -1.26153609324877e-02 , -4.25626857807359e-02 ), ( 3.19860317098683e-02 , 1.12455380919655e-02 , 5.92957814641218e-03 ), ( 5.13253613542508e-03 , -1.02949683798535e-02 , -1.24737697548967e-01 ), ( -1.17569251341706e-02 , -2.10443969816043e-02 , -1.77850474287525e-01 ), ( 4.99744876498038e-02 , 3.43765614314540e-03 , -1.37541144724287e-01 ), ( 7.79465816443118e-02 , 5.46443654812256e-03 , -2.13460583700742e-01 ), ( 1.37045972366390e-01 , 2.60713052287931e-02 , -2.04282010464686e-01 ), ( 1.83677323443324e-02 , -1.95623160281763e-02 , -2.66890762743745e-01 ), ( 1.93771121279581e-02 , -2.58330372192186e-02 , -3.35530387264055e-01 ), ( -3.54857268323370e-02 , -3.45562660806737e-02 , -2.35948882720711e-01 ), ( -9.74831256497132e-02 , -5.93460093254548e-02 , -2.78532379609905e-01 ), ( -1.36369320069997e-01 , -6.77414792650407e-02 , -2.30933941610206e-01 ), ( -1.53158546674371e-01 , -7.98420084693437e-02 , -2.98429456801982e-01 ), ( -1.81120831575947e-01 , -9.52989983892606e-02 , -3.62057158421327e-01 ), ( -1.90382370507147e-01 , -9.23440416893015e-02 , -2.99253140362582e-01 ), ( -2.31201787327718e-01 , -1.08430352512025e-01 , -3.24845129873043e-01 ), ( -1.16505248632433e-01 , -6.83559056895193e-02 , -3.06181368845499e-01 ), ( -1.71349111804265e-01 , -8.06454986331246e-02 , -2.43713070981057e-01 ), ( -2.22985072315737e-01 , -9.90855597099133e-02 , -2.56257046623407e-01 ), ( -2.57325140138640e-01 , -1.02976127885664e-01 , -1.77622160587966e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 30, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 31 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 31, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 31, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 31, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 31, atoms_positions[size = 51] = { ( 8.22941084026228e+00 , 4.36749769543978e-02 , -7.18621583689367e-01 ), ( 6.83305420288219e+00 , -5.96988975407460e-01 , -5.24166185980071e-01 ), ( 6.10875524310126e+00 , -3.58733500923816e-01 , 8.10731339652800e-01 ), ( 4.90620094583905e+00 , -1.49336137565181e-01 , 7.49533505038693e-01 ), ( 6.99931696608724e+00 , -2.07368476449803e+00 , -8.67716105921819e-01 ), ( 6.80539003638100e+00 , -2.97139186636095e-01 , 1.96695212025050e+00 ), ( 6.09127797716714e+00 , -2.28232556248832e-01 , 3.18631289136950e+00 ), ( 7.14315406746370e+00 , -3.45249092142572e-01 , 4.39200054025935e+00 ), ( 5.32044209121276e+00 , 1.06658887182539e+00 , 3.36725510049905e+00 ), ( 4.18603037560149e+00 , 1.00473045623169e+00 , 3.78962333808555e+00 ), ( 5.84892705851717e+00 , 2.25116097769853e+00 , 2.97030239169369e+00 ), ( 5.14832632924866e+00 , 3.54752561087709e+00 , 2.88175441289174e+00 ), ( 6.29822649453593e+00 , 4.46648668649917e+00 , 2.28584013479202e+00 ), ( 3.85876266979869e+00 , 3.63930487835275e+00 , 2.02194135992216e+00 ), ( 2.82029704916939e+00 , 4.16687282796321e+00 , 2.43133907059033e+00 ), ( 3.90811144966727e+00 , 3.18435644065381e+00 , 7.48741431967163e-01 ), ( 2.76431355179194e+00 , 3.07643748956219e+00 , -7.05785399871600e-02 ), ( 3.12255235446029e+00 , 2.65106606563690e+00 , -1.54208321619305e+00 ), ( 1.55400022995286e+00 , 2.21485573332563e+00 , 4.25446502440629e-01 ), ( 4.14145201665343e-01 , 2.61652135448712e+00 , 4.54610465312730e-01 ), ( 2.05823839185384e+00 , 1.13604124284228e+00 , 1.04671185348618e+00 ), ( 1.23678874253541e+00 , 1.40330017506145e-01 , 1.67859216312030e+00 ), ( 2.08614956330000e+00 , -1.09322444702513e+00 , 2.03993981786123e+00 ), ( 5.74734786829843e-01 , 6.15323230609918e-01 , 2.95284198190612e+00 ), ( -5.89961581429437e-01 , 3.56746753170733e-01 , 3.18593612454118e+00 ), ( 1.28594774705375e+00 , 1.39769439973023e+00 , 3.75924844058372e+00 ), ( 8.79360863105517e-01 , 1.97912354248784e+00 , 5.03609488066649e+00 ), ( 2.08250915154670e+00 , 2.76183205204844e+00 , 5.72601543567959e+00 ), ( -3.58992529289012e-01 , 2.89900987599641e+00 , 4.94901836297140e+00 ), ( -1.11558684442524e+00 , 3.06956005806150e+00 , 5.88488327078344e+00 ), ( -5.42141757288871e-01 , 3.50500614815991e+00 , 3.77101523755500e+00 ), ( -1.46264856467718e+00 , 4.48038996091603e+00 , 3.41659970972265e+00 ), ( -7.45803378814604e-01 , 5.44229325687175e+00 , 2.48046156663435e+00 ), ( -2.74753671508654e+00 , 3.94448582899662e+00 , 2.77298201048496e+00 ), ( -3.80294354604345e+00 , 4.57141070604620e+00 , 2.81312284409483e+00 ), ( -2.69542189659159e+00 , 2.63432658681899e+00 , 2.35391468138239e+00 ), ( -3.80466204071939e+00 , 1.82437737008172e+00 , 2.00436847669041e+00 ), ( -3.35524475150449e+00 , 8.79595506689076e-01 , 8.00182337387689e-01 ), ( -4.25146804812157e+00 , 1.03745427117025e+00 , 3.24395614338712e+00 ), ( -5.46373221310415e+00 , 7.47148061980620e-01 , 3.34217475200824e+00 ), ( -3.37058427268309e+00 , 7.28435592423857e-01 , 4.16411508250186e+00 ), ( -3.66847776419296e+00 , 7.82294633074592e-02 , 5.48104017014891e+00 ), ( -2.37210241559387e+00 , -3.10411740259109e-01 , 6.12867005167131e+00 ), ( -4.48610335711135e+00 , 9.24869842126096e-01 , 6.42062931423176e+00 ), ( -5.35833854877040e+00 , 5.66438513069246e-01 , 7.19573018552646e+00 ), ( -6.30932159115756e+00 , 3.61995396072790e+00 , 6.75484613630149e+00 ), ( -7.01193811435146e+00 , 4.29900249317163e+00 , 7.51452057012353e+00 ), ( -6.63240230872822e+00 , 3.16326438018767e+00 , 5.53818626220439e+00 ), ( -4.10678338443630e+00 , 2.25549878696156e+00 , 6.40106808876789e+00 ), ( -4.81589387776778e+00 , 3.28588167151493e+00 , 7.24117541390520e+00 ), ( -4.01623305667354e+00 , 4.57084667656110e+00 , 7.27491591648259e+00 ) } +colvars: Step 31, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_ids[size = 0] = +colvars: Step 31, atom_groups_refcount[size = 0] = +colvars: Step 31, atom_groups_masses[size = 0] = +colvars: Step 31, atom_groups_charges[size = 0] = +colvars: Step 31, atom_groups_coms[size = 0] = +colvars: Step 31, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 31, volmaps_ids[size = 0] = +colvars: Step 31, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 31 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.93633996751009e-01 , -1.41137029745784e-02 , 9.55813726277445e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.93633996751009e-01 , -1.41137029745784e-02 , 9.55813726277445e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.3907 , 2.23407 , -15.2127 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.3907 , 2.23407 , -15.2127 ) to colvar "one". +colvars: Adding total bias energy: 44.0552 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.3907 , 2.23407 , -15.2127 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.93477 , -0.520235 , -1.40933 ) +colvars: ( -4.23157 , -0.446101 , -1.2085 ) +colvars: ( -4.23157 , -0.446101 , -1.2085 ) +colvars: ( -5.63657 , -0.59422 , -1.60976 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.886349 , 0.196149 , 0.607395 ) +colvars: ( 0.768477 , 0.266139 , 0.630863 ) +colvars: ( 0.752296 , 0.259407 , 0.612734 ) +colvars: ( 0.658511 , 0.266364 , 0.567736 ) +colvars: ( 0.646813 , 0.200069 , 0.474371 ) +colvars: ( 0.573444 , 0.342812 , 0.61856 ) +colvars: ( 0.468071 , 0.356205 , 0.575288 ) +colvars: ( 0.392652 , 0.452617 , 0.65776 ) +colvars: ( 0.387428 , 0.311671 , 0.470592 ) +colvars: ( 0.35336 , 0.270069 , 0.396589 ) +colvars: ( 0.358173 , 0.317008 , 0.460693 ) +colvars: ( 0.287807 , 0.274203 , 0.364183 ) +colvars: ( 0.260719 , 0.30317 , 0.386408 ) +colvars: ( 0.349281 , 0.17714 , 0.272819 ) +colvars: ( 0.291499 , 0.13379 , 0.182854 ) +colvars: ( 0.470162 , 0.140801 , 0.295053 ) +colvars: ( 0.541603 , 0.0501797 , 0.217853 ) +colvars: ( 0.66908 , 0.0298935 , 0.264867 ) +colvars: ( 0.550452 , 0.0183477 , 0.181365 ) +colvars: ( 0.534949 , -0.0464645 , 0.087743 ) +colvars: ( 0.571373 , 0.0659609 , 0.255641 ) +colvars: ( 0.570281 , 0.0496732 , 0.23373 ) +colvars: ( 0.606576 , 0.114089 , 0.338826 ) +colvars: ( 0.447932 , 0.0535557 , 0.168241 ) +colvars: ( 0.441385 , -0.00221057 , 0.0916032 ) +colvars: ( 0.347404 , 0.118504 , 0.195123 ) +colvars: ( 0.224811 , 0.126505 , 0.134875 ) +colvars: ( 0.134576 , 0.211522 , 0.193915 ) +colvars: ( 0.196773 , 0.0531328 , 0.0228387 ) +colvars: ( 0.148422 , 0.0168513 , -0.0524507 ) +colvars: ( 0.229462 , 0.0280296 , 0.00889228 ) +colvars: ( 0.215387 , -0.044045 , -0.0933953 ) +colvars: ( 0.249705 , -0.0470071 , -0.0774734 ) +colvars: ( 0.289648 , -0.12933 , -0.161998 ) +colvars: ( 0.24632 , -0.182371 , -0.256288 ) +colvars: ( 0.403232 , -0.143856 , -0.11547 ) +colvars: ( 0.479698 , -0.21874 , -0.169211 ) +colvars: ( 0.608958 , -0.220789 , -0.0973402 ) +colvars: ( 0.433538 , -0.223609 , -0.202194 ) +colvars: ( 0.439065 , -0.291356 , -0.287524 ) +colvars: ( 0.385796 , -0.150999 , -0.134859 ) +colvars: ( 0.332773 , -0.145199 , -0.15786 ) +colvars: ( 0.316771 , -0.059138 , -0.0546447 ) +colvars: ( 0.211303 , -0.154449 , -0.240002 ) +colvars: ( 0.187493 , -0.196463 , -0.308628 ) +colvars: ( 0.0124262 , -0.200513 , -0.414884 ) +colvars: ( -0.077159 , -0.218597 , -0.490178 ) +colvars: ( 0.111025 , -0.249646 , -0.422215 ) +colvars: ( 0.130449 , -0.114246 , -0.234104 ) +colvars: ( 0.0128707 , -0.119075 , -0.308223 ) +colvars: ( -0.0749454 , -0.0390967 , -0.254372 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.93477 , 0.520235 , 1.40933 ) +colvars: ( 4.23157 , 0.446101 , 1.2085 ) +colvars: ( 4.23157 , 0.446101 , 1.2085 ) +colvars: ( 5.63657 , 0.59422 , 1.60976 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.612714 , -0.0810492 , -0.361736 ) +colvars: ( -0.551476 , -0.164739 , -0.328901 ) +colvars: ( -0.499874 , -0.14219 , -0.269266 ) +colvars: ( -0.513961 , -0.192597 , -0.300744 ) +colvars: ( -0.504259 , -0.132936 , -0.270497 ) +colvars: ( -0.490784 , -0.285851 , -0.309466 ) +colvars: ( -0.459915 , -0.326746 , -0.29247 ) +colvars: ( -0.439628 , -0.435481 , -0.309415 ) +colvars: ( -0.396598 , -0.290738 , -0.216433 ) +colvars: ( -0.39294 , -0.265163 , -0.203971 ) +colvars: ( -0.345916 , -0.284807 , -0.163432 ) +colvars: ( -0.284907 , -0.247248 , -0.0891838 ) +colvars: ( -0.234877 , -0.262141 , -0.0439898 ) +colvars: ( -0.303332 , -0.142719 , -0.0718115 ) +colvars: ( -0.272473 , -0.113014 , -0.0305779 ) +colvars: ( -0.356384 , -0.0846576 , -0.105218 ) +colvars: ( -0.38201 , 0.0148495 , -0.0968107 ) +colvars: ( -0.430502 , 0.0630591 , -0.129016 ) +colvars: ( -0.421059 , 0.0298703 , -0.130918 ) +colvars: ( -0.409649 , 0.087414 , -0.0996817 ) +colvars: ( -0.466518 , -0.0250669 , -0.195499 ) +colvars: ( -0.502432 , -0.0267431 , -0.232189 ) +colvars: ( -0.553507 , -0.0932021 , -0.306374 ) +colvars: ( -0.451871 , -0.0571019 , -0.191773 ) +colvars: ( -0.459236 , -0.0125001 , -0.18386 ) +colvars: ( -0.397466 , -0.132269 , -0.162881 ) +colvars: ( -0.341167 , -0.163903 , -0.117133 ) +colvars: ( -0.291366 , -0.25515 , -0.0983926 ) +colvars: ( -0.298973 , -0.0899536 , -0.0493056 ) +colvars: ( -0.286701 , -0.0711241 , -0.0304981 ) +colvars: ( -0.277174 , -0.0443182 , -0.0117114 ) +colvars: ( -0.240635 , 0.0315701 , 0.0510948 ) +colvars: ( -0.217289 , 0.0584922 , 0.0838168 ) +colvars: ( -0.284279 , 0.119358 , 0.0373577 ) +colvars: ( -0.257801 , 0.161721 , 0.0785326 ) +colvars: ( -0.353104 , 0.147691 , -0.0221197 ) +colvars: ( -0.401655 , 0.224759 , -0.0444717 ) +colvars: ( -0.471878 , 0.24749 , -0.10728 ) +colvars: ( -0.415207 , 0.204516 , -0.0650523 ) +colvars: ( -0.419726 , 0.26611 , -0.0484419 ) +colvars: ( -0.421434 , 0.116703 , -0.101473 ) +colvars: ( -0.430537 , 0.0860067 , -0.121169 ) +colvars: ( -0.453551 , -0.00866356 , -0.176826 ) +colvars: ( -0.364682 , 0.0747098 , -0.0588278 ) +colvars: ( -0.368888 , 0.101295 , -0.0539257 ) +colvars: ( -0.202709 , 0.108337 , 0.115597 ) +colvars: ( -0.153897 , 0.110317 , 0.165361 ) +colvars: ( -0.227356 , 0.181649 , 0.115992 ) +colvars: ( -0.301908 , 0.0336233 , -0.00981448 ) +colvars: ( -0.235899 , 0.0199591 , 0.0518689 ) +colvars: ( -0.182366 , -0.0640851 , 0.0768356 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 31. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 31. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atoms_new_colvar_forces = { ( -4.66113688161655e+00 , -4.05135184602716e-01 , -1.16367389088499e+00 ), ( -4.01456544465088e+00 , -3.44700949904404e-01 , -9.06540597900646e-01 ), ( -4.08701549031908e+00 , -3.72334593613221e-01 , -9.41510912939705e-01 ), ( -5.49401334502561e+00 , -5.27086362162900e-01 , -1.40588628005506e+00 ), ( 2.52421883872536e-01 , 1.17216689223596e-01 , 3.43468021005117e-01 ), ( 5.01743120489049e+00 , 5.77195319297558e-01 , 1.71842718291959e+00 ), ( 4.23972195655386e+00 , 4.75559997317382e-01 , 1.49132072934045e+00 ), ( -4.69761885536258e-02 , 1.71353376620547e-02 , 3.48344991781273e-01 ), ( 4.22239605110036e+00 , 4.67034094164927e-01 , 1.46266171952488e+00 ), ( 5.59698801797817e+00 , 5.99126131386157e-01 , 1.80237850317957e+00 ), ( 1.22569785677200e-02 , 3.22004023080397e-02 , 2.97260925795616e-01 ), ( 2.89947393451162e-03 , 2.69548120952914e-02 , 2.74999354104193e-01 ), ( 2.58417341654628e-02 , 4.10286803199074e-02 , 3.42418185431564e-01 ), ( 4.59489894821550e-02 , 3.44208720431577e-02 , 2.01007023311371e-01 ), ( 1.90262889382226e-02 , 2.07758823646663e-02 , 1.52275976849330e-01 ), ( 1.13777293155053e-01 , 5.61431198344201e-02 , 1.89835449907698e-01 ), ( 1.59592774129915e-01 , 6.50292072234674e-02 , 1.21042022707783e-01 ), ( 2.38577766740824e-01 , 9.29526113299943e-02 , 1.35851173213925e-01 ), ( 1.29392819497884e-01 , 4.82180540366782e-02 , 5.04473049042816e-02 ), ( 1.25299698040462e-01 , 4.09494793887644e-02 , -1.19387084039878e-02 ), ( 1.04855255729952e-01 , 4.08939797955200e-02 , 6.01426459633320e-02 ), ( 6.78483766348649e-02 , 2.29300856713723e-02 , 1.54153626017012e-03 ), ( 5.30682546953771e-02 , 2.08871268240285e-02 , 3.24529105020316e-02 ), ( -3.93969744826089e-03 , -3.54621076703741e-03 , -2.35316890863778e-02 ), ( -1.78506448584630e-02 , -1.47106388087243e-02 , -9.22566850467691e-02 ), ( -5.00623230433725e-02 , -1.37654444146957e-02 , 3.22426742561518e-02 ), ( -1.16356650433801e-01 , -3.73979693387564e-02 , 1.77423188685170e-02 ), ( -1.56790262395194e-01 , -4.36277265470911e-02 , 9.55222918925579e-02 ), ( -1.02200295341637e-01 , -3.68208284205977e-02 , -2.64669747004680e-02 ), ( -1.38278910459662e-01 , -5.42727798771095e-02 , -8.29488556952516e-02 ), ( -4.77117382083829e-02 , -1.62886195485267e-02 , -2.81911927980735e-03 ), ( -2.52474673249706e-02 , -1.24748809918986e-02 , -4.23004726359222e-02 ), ( 3.24161849539219e-02 , 1.14851209317580e-02 , 6.34341234101454e-03 ), ( 5.36897028621786e-03 , -9.97269336708345e-03 , -1.24640530757740e-01 ), ( -1.14814323175646e-02 , -2.06494007483504e-02 , -1.77755054636872e-01 ), ( 5.01283712737642e-02 , 3.83472494588458e-03 , -1.37589945559419e-01 ), ( 7.80433069604085e-02 , 6.01997205558669e-03 , -2.13682326641160e-01 ), ( 1.37079947324538e-01 , 2.67015156433917e-02 , -2.04619770554298e-01 ), ( 1.83308867736479e-02 , -1.90929088493055e-02 , -2.67246705008063e-01 ), ( 1.93391319359338e-02 , -2.52466680488760e-02 , -3.35965427889963e-01 ), ( -3.56379696936009e-02 , -3.42956768451885e-02 , -2.36331912240935e-01 ), ( -9.77638844851895e-02 , -5.91924040976156e-02 , -2.79029743364876e-01 ), ( -1.36780622728546e-01 , -6.78015637844769e-02 , -2.31470958944401e-01 ), ( -1.53379621117242e-01 , -7.97395827371071e-02 , -2.98829541778815e-01 ), ( -1.81395019090666e-01 , -9.51680105579518e-02 , -3.62553593115967e-01 ), ( -1.90282656778418e-01 , -9.21753079908156e-02 , -2.99286406032441e-01 ), ( -2.31055786305619e-01 , -1.08279539418096e-01 , -3.24816807636920e-01 ), ( -1.16330744662527e-01 , -6.79965825131494e-02 , -3.06223265951223e-01 ), ( -1.71458942561447e-01 , -8.06230705850004e-02 , -2.43918805502511e-01 ), ( -2.23028420531419e-01 , -9.91157231288625e-02 , -2.56354539021633e-01 ), ( -2.57311177664526e-01 , -1.03181894194047e-01 , -1.77536832794198e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 31, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 32 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 32, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 32, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 32, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 32, atoms_positions[size = 51] = { ( 8.22025644610011e+00 , 4.37055216046504e-02 , -7.14729272559206e-01 ), ( 6.82945426398495e+00 , -6.03046869416644e-01 , -5.22029034574170e-01 ), ( 6.09715063681014e+00 , -3.50969027036988e-01 , 8.14060420824796e-01 ), ( 4.90432535135465e+00 , -1.50298573950058e-01 , 7.52861782547554e-01 ), ( 6.99711789817992e+00 , -2.07701949038308e+00 , -8.59615092260211e-01 ), ( 6.80172294492906e+00 , -3.01261013154195e-01 , 1.96709235130160e+00 ), ( 6.08570759058685e+00 , -2.31646840319499e-01 , 3.19691902165685e+00 ), ( 7.14758531481322e+00 , -3.46692917288126e-01 , 4.39746558807305e+00 ), ( 5.31554628571039e+00 , 1.06565571809091e+00 , 3.36600902078069e+00 ), ( 4.18847267881250e+00 , 1.00388202075946e+00 , 3.80012630742550e+00 ), ( 5.85143706628531e+00 , 2.25080272687727e+00 , 2.96824791658596e+00 ), ( 5.14105246611948e+00 , 3.54205701785969e+00 , 2.87599097505194e+00 ), ( 6.29325062239867e+00 , 4.46010982708403e+00 , 2.28442810266564e+00 ), ( 3.85882774184686e+00 , 3.63492568223562e+00 , 2.01830788491864e+00 ), ( 2.82594672314431e+00 , 4.16529189701689e+00 , 2.42695896512935e+00 ), ( 3.90484865349249e+00 , 3.17689088390449e+00 , 7.54139586863759e-01 ), ( 2.76648942503954e+00 , 3.08705804793703e+00 , -6.93950152739506e-02 ), ( 3.12744558504317e+00 , 2.65117133289642e+00 , -1.54076214646921e+00 ), ( 1.56095038348625e+00 , 2.22641149158040e+00 , 4.27405594623885e-01 ), ( 4.18759538363859e-01 , 2.61596969517098e+00 , 4.48882249112137e-01 ), ( 2.05126769093368e+00 , 1.12970817680754e+00 , 1.04780851641551e+00 ), ( 1.25009173358664e+00 , 1.46490578823352e-01 , 1.67394197125757e+00 ), ( 2.08908230800507e+00 , -1.09358117505684e+00 , 2.03976049277909e+00 ), ( 5.74126662252645e-01 , 6.15195831391415e-01 , 2.94837225818096e+00 ), ( -5.93007809274588e-01 , 3.57303106276294e-01 , 3.19058391237586e+00 ), ( 1.28569765285871e+00 , 1.40534509336286e+00 , 3.76494171092987e+00 ), ( 8.87171580784718e-01 , 1.97931419064781e+00 , 5.03899291928245e+00 ), ( 2.07328712171941e+00 , 2.76539047549728e+00 , 5.72624147199300e+00 ), ( -3.59795059105076e-01 , 2.89720122350267e+00 , 4.94295627919127e+00 ), ( -1.11604658839503e+00 , 3.07001831801347e+00 , 5.88771348640713e+00 ), ( -5.39780564301514e-01 , 3.50183967049821e+00 , 3.76183834391896e+00 ), ( -1.45734630089973e+00 , 4.47776051640672e+00 , 3.41747718600615e+00 ), ( -7.52674298789564e-01 , 5.44714386066550e+00 , 2.48231410243051e+00 ), ( -2.74904247712941e+00 , 3.94198243376910e+00 , 2.75961592016998e+00 ), ( -3.80125888774024e+00 , 4.57736842353900e+00 , 2.81277453690773e+00 ), ( -2.69987873691698e+00 , 2.63637905734000e+00 , 2.35290162243892e+00 ), ( -3.80819914573231e+00 , 1.82100792831724e+00 , 2.00274632498308e+00 ), ( -3.35286891891693e+00 , 8.82663495728610e-01 , 7.93089446633534e-01 ), ( -4.25290670435825e+00 , 1.03325407596833e+00 , 3.24627259364973e+00 ), ( -5.45587046822941e+00 , 7.41739074756565e-01 , 3.34439122005340e+00 ), ( -3.36962569338273e+00 , 7.27381920070494e-01 , 4.16190335803550e+00 ), ( -3.66749372898384e+00 , 7.59509805069767e-02 , 5.47936541279648e+00 ), ( -2.36639900794246e+00 , -3.04732995730435e-01 , 6.12652629112228e+00 ), ( -4.48915051854569e+00 , 9.29727693847123e-01 , 6.42061214899054e+00 ), ( -5.35715343423749e+00 , 5.60773925730106e-01 , 7.19137430986862e+00 ), ( -6.30816257618388e+00 , 3.61577064167445e+00 , 6.75721558358170e+00 ), ( -7.01900994077516e+00 , 4.29979617627293e+00 , 7.51670827752640e+00 ), ( -6.62506000808668e+00 , 3.16464319275810e+00 , 5.54319705967107e+00 ), ( -4.10782923883749e+00 , 2.25528114373913e+00 , 6.40505076511689e+00 ), ( -4.81474827357504e+00 , 3.28701158886541e+00 , 7.23404586108623e+00 ), ( -4.01237364420152e+00 , 4.58031152041965e+00 , 7.27648138133984e+00 ) } +colvars: Step 32, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_ids[size = 0] = +colvars: Step 32, atom_groups_refcount[size = 0] = +colvars: Step 32, atom_groups_masses[size = 0] = +colvars: Step 32, atom_groups_charges[size = 0] = +colvars: Step 32, atom_groups_coms[size = 0] = +colvars: Step 32, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 32, volmaps_ids[size = 0] = +colvars: Step 32, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 32 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.92255140925596e-01 , -1.51601432225139e-02 , 9.56220216613324e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.92255140925596e-01 , -1.51601432225139e-02 , 9.56220216613324e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.3631 , 2.255 , -15.2208 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.3631 , 2.255 , -15.2208 ) to colvar "one". +colvars: Adding total bias energy: 44.0022 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.3631 , 2.255 , -15.2208 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.93728 , -0.518296 , -1.4038 ) +colvars: ( -4.23372 , -0.444438 , -1.20375 ) +colvars: ( -4.23372 , -0.444438 , -1.20375 ) +colvars: ( -5.63943 , -0.592005 , -1.60344 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.885736 , 0.196198 , 0.606052 ) +colvars: ( 0.768032 , 0.266064 , 0.62949 ) +colvars: ( 0.751846 , 0.259383 , 0.611451 ) +colvars: ( 0.658245 , 0.266201 , 0.566465 ) +colvars: ( 0.646569 , 0.199959 , 0.473274 ) +colvars: ( 0.573312 , 0.342511 , 0.61718 ) +colvars: ( 0.468111 , 0.355803 , 0.573967 ) +colvars: ( 0.392808 , 0.452068 , 0.656276 ) +colvars: ( 0.387578 , 0.311287 , 0.469496 ) +colvars: ( 0.353575 , 0.269683 , 0.395612 ) +colvars: ( 0.358341 , 0.316649 , 0.459664 ) +colvars: ( 0.288067 , 0.273871 , 0.363366 ) +colvars: ( 0.260991 , 0.302845 , 0.3856 ) +colvars: ( 0.349451 , 0.17694 , 0.272176 ) +colvars: ( 0.291759 , 0.133594 , 0.182381 ) +colvars: ( 0.470148 , 0.140712 , 0.29437 ) +colvars: ( 0.541484 , 0.0502205 , 0.217315 ) +colvars: ( 0.668761 , 0.0300459 , 0.264253 ) +colvars: ( 0.550347 , 0.0183755 , 0.180848 ) +colvars: ( 0.534872 , -0.0463878 , 0.0874003 ) +colvars: ( 0.571257 , 0.0659168 , 0.254944 ) +colvars: ( 0.570194 , 0.0495949 , 0.233026 ) +colvars: ( 0.60645 , 0.113937 , 0.337888 ) +colvars: ( 0.448036 , 0.0533883 , 0.167652 ) +colvars: ( 0.441513 , -0.00234953 , 0.0911393 ) +colvars: ( 0.34765 , 0.118229 , 0.1945 ) +colvars: ( 0.225245 , 0.126145 , 0.134365 ) +colvars: ( 0.135133 , 0.211045 , 0.193312 ) +colvars: ( 0.197237 , 0.0528526 , 0.0225684 ) +colvars: ( 0.148971 , 0.0165572 , -0.0525963 ) +colvars: ( 0.229852 , 0.0278384 , 0.00869276 ) +colvars: ( 0.215786 , -0.0441471 , -0.093372 ) +colvars: ( 0.250024 , -0.0470344 , -0.0774303 ) +colvars: ( 0.289948 , -0.129327 , -0.161866 ) +colvars: ( 0.246688 , -0.182343 , -0.255976 ) +colvars: ( 0.403372 , -0.143789 , -0.115447 ) +colvars: ( 0.479737 , -0.218579 , -0.169111 ) +colvars: ( 0.608807 , -0.220557 , -0.0973883 ) +colvars: ( 0.433673 , -0.223519 , -0.202078 ) +colvars: ( 0.439201 , -0.291209 , -0.287256 ) +colvars: ( 0.386017 , -0.151035 , -0.134897 ) +colvars: ( 0.333099 , -0.145317 , -0.157898 ) +colvars: ( 0.317133 , -0.0593765 , -0.0549063 ) +colvars: ( 0.211809 , -0.154625 , -0.239875 ) +colvars: ( 0.18805 , -0.196639 , -0.308396 ) +colvars: ( 0.0131927 , -0.200687 , -0.414345 ) +colvars: ( -0.0762583 , -0.218804 , -0.489491 ) +colvars: ( 0.111631 , -0.24969 , -0.42164 ) +colvars: ( 0.131056 , -0.114474 , -0.233952 ) +colvars: ( 0.013651 , -0.119359 , -0.307918 ) +colvars: ( -0.0740482 , -0.0394861 , -0.254144 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.93728 , 0.518296 , 1.4038 ) +colvars: ( 4.23372 , 0.444438 , 1.20375 ) +colvars: ( 4.23372 , 0.444438 , 1.20375 ) +colvars: ( 5.63943 , 0.592005 , 1.60344 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.612168 , -0.081011 , -0.360463 ) +colvars: ( -0.551073 , -0.164756 , -0.327442 ) +colvars: ( -0.499291 , -0.142183 , -0.267708 ) +colvars: ( -0.51378 , -0.192622 , -0.299395 ) +colvars: ( -0.504073 , -0.132909 , -0.269369 ) +colvars: ( -0.490803 , -0.285945 , -0.307958 ) +colvars: ( -0.46017 , -0.326861 , -0.291036 ) +colvars: ( -0.440063 , -0.435679 , -0.307743 ) +colvars: ( -0.39685 , -0.290809 , -0.215124 ) +colvars: ( -0.393296 , -0.265208 , -0.202862 ) +colvars: ( -0.34604 , -0.284868 , -0.162011 ) +colvars: ( -0.285003 , -0.247266 , -0.0878676 ) +colvars: ( -0.23484 , -0.262166 , -0.0424783 ) +colvars: ( -0.30329 , -0.142656 , -0.0707586 ) +colvars: ( -0.272495 , -0.112917 , -0.0296973 ) +colvars: ( -0.356151 , -0.0845614 , -0.104204 ) +colvars: ( -0.381637 , 0.0150211 , -0.0960399 ) +colvars: ( -0.429894 , 0.0632544 , -0.128202 ) +colvars: ( -0.420832 , 0.0300523 , -0.130356 ) +colvars: ( -0.409424 , 0.0876477 , -0.0993387 ) +colvars: ( -0.466427 , -0.0249362 , -0.194869 ) +colvars: ( -0.502509 , -0.0266149 , -0.231725 ) +colvars: ( -0.55369 , -0.0931371 , -0.30577 ) +colvars: ( -0.452155 , -0.0569825 , -0.191391 ) +colvars: ( -0.459575 , -0.0123419 , -0.183705 ) +colvars: ( -0.397862 , -0.1322 , -0.162317 ) +colvars: ( -0.341744 , -0.163844 , -0.11662 ) +colvars: ( -0.292039 , -0.255156 , -0.0976213 ) +colvars: ( -0.299454 , -0.0898256 , -0.0489732 ) +colvars: ( -0.287298 , -0.0709734 , -0.0303509 ) +colvars: ( -0.277437 , -0.0441544 , -0.0113328 ) +colvars: ( -0.240779 , 0.0318019 , 0.0513086 ) +colvars: ( -0.217203 , 0.0587436 , 0.0841605 ) +colvars: ( -0.284356 , 0.119654 , 0.0372984 ) +colvars: ( -0.257911 , 0.16206 , 0.0782838 ) +colvars: ( -0.35309 , 0.147995 , -0.0222064 ) +colvars: ( -0.401587 , 0.225118 , -0.0448062 ) +colvars: ( -0.47167 , 0.24785 , -0.107571 ) +colvars: ( -0.415367 , 0.204863 , -0.065538 ) +colvars: ( -0.419885 , 0.266508 , -0.0491619 ) +colvars: ( -0.421796 , 0.116981 , -0.101826 ) +colvars: ( -0.431131 , 0.0862639 , -0.121637 ) +colvars: ( -0.45431 , -0.00848623 , -0.177102 ) +colvars: ( -0.365409 , 0.0749749 , -0.0593749 ) +colvars: ( -0.369718 , 0.101586 , -0.0546776 ) +colvars: ( -0.203403 , 0.108662 , 0.114978 ) +colvars: ( -0.154688 , 0.110656 , 0.164646 ) +colvars: ( -0.227809 , 0.182023 , 0.11533 ) +colvars: ( -0.302637 , 0.0338655 , -0.0101983 ) +colvars: ( -0.236746 , 0.0202066 , 0.0514294 ) +colvars: ( -0.183284 , -0.0638968 , 0.0766535 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 32. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 32. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atoms_new_colvar_forces = { ( -4.66371102591230e+00 , -4.03108964363214e-01 , -1.15820798596336e+00 ), ( -4.01675663350797e+00 , -3.43130137810241e-01 , -9.01707106066292e-01 ), ( -4.08925044966919e+00 , -3.70860108725764e-01 , -9.36685231752763e-01 ), ( -5.49693601592321e+00 , -5.24954207557312e-01 , -1.39953153167732e+00 ), ( 2.52554295812457e-01 , 1.17199880609433e-01 , 3.43743015528026e-01 ), ( 5.01978731179025e+00 , 5.74861572024135e-01 , 1.71301867903129e+00 ), ( 4.24165735603726e+00 , 4.73380521419315e-01 , 1.48668606921446e+00 ), ( -4.72546736643991e-02 , 1.63891815790046e-02 , 3.48532627110861e-01 ), ( 4.22444428474445e+00 , 4.64916443920783e-01 , 1.45812711877909e+00 ), ( 5.59971110612098e+00 , 5.96479709432429e-01 , 1.79618621805133e+00 ), ( 1.23008468655991e-02 , 3.17806401081756e-02 , 2.97652475730474e-01 ), ( 3.06469063464188e-03 , 2.66051153802273e-02 , 2.75498708322126e-01 ), ( 2.61508432088345e-02 , 4.06783998890108e-02 , 3.43121657631734e-01 ), ( 4.61612378118703e-02 , 3.42844957475941e-02 , 2.01417820198638e-01 ), ( 1.92645195514352e-02 , 2.06774247491469e-02 , 1.52683940566499e-01 ), ( 1.13996482945326e-01 , 5.61502908543405e-02 , 1.90165461674944e-01 ), ( 1.59847355211528e-01 , 6.52416205323519e-02 , 1.21274797105210e-01 ), ( 2.38866271080539e-01 , 9.33002275995184e-02 , 1.36050074004627e-01 ), ( 1.29515114960020e-01 , 4.84278175314965e-02 , 5.04919822170475e-02 ), ( 1.25448073601597e-01 , 4.12598532743568e-02 , -1.19383341771881e-02 ), ( 1.04830783767252e-01 , 4.09805880377966e-02 , 6.00753899202985e-02 ), ( 6.76846351085205e-02 , 2.29800541197846e-02 , 1.30100616918369e-03 ), ( 5.27602235630881e-02 , 2.07998341590421e-02 , 3.21179821468798e-02 ), ( -4.11834679177236e-03 , -3.59422003470590e-03 , -2.37391576435703e-02 ), ( -1.80618954532191e-02 , -1.46914480780025e-02 , -9.25655735811133e-02 ), ( -5.02113274078761e-02 , -1.39709047056644e-02 , 3.21837401792543e-02 ), ( -1.16499231796863e-01 , -3.76985895625691e-02 , 1.77451109272561e-02 ), ( -1.56905970204270e-01 , -4.41107915627325e-02 , 9.56911853435947e-02 ), ( -1.02217688175030e-01 , -3.69729669167259e-02 , -2.64048015758559e-02 ), ( -1.38327199632664e-01 , -5.44162375232505e-02 , -8.29472186361900e-02 ), ( -4.75848419275651e-02 , -1.63159791008098e-02 , -2.64002023231284e-03 ), ( -2.49934619343552e-02 , -1.23451677871875e-02 , -4.20634066880590e-02 ), ( 3.28203992193124e-02 , 1.17091776468809e-02 , 6.73026623476447e-03 ), ( 5.59253081824335e-03 , -9.67284311954994e-03 , -1.24567987384370e-01 ), ( -1.12227400726866e-02 , -2.02825749746560e-02 , -1.77692310560003e-01 ), ( 5.02821784521819e-02 , 4.20576744836687e-03 , -1.37653731562304e-01 ), ( 7.81500500880993e-02 , 6.53935916657833e-03 , -2.13917157994911e-01 ), ( 1.37136884228048e-01 , 2.72925288160855e-02 , -2.04959465287842e-01 ), ( 1.83060832079743e-02 , -1.86558758877152e-02 , -2.67615889250135e-01 ), ( 1.93151507462338e-02 , -2.47008717780605e-02 , -3.36418092191162e-01 ), ( -3.57787137323783e-02 , -3.40548260393282e-02 , -2.36723431730402e-01 ), ( -9.80321088681891e-02 , -5.90533841039637e-02 , -2.79535637804341e-01 ), ( -1.37177069516403e-01 , -6.78626948157561e-02 , -2.32008029886811e-01 ), ( -1.53600112564750e-01 , -7.96502197231649e-02 , -2.99249454025762e-01 ), ( -1.81667382585330e-01 , -9.50531689033827e-02 , -3.63073174329622e-01 ), ( -1.90210588269541e-01 , -9.20256077497498e-02 , -2.99366242248604e-01 ), ( -2.30946095334873e-01 , -1.08148023110278e-01 , -3.24844250519836e-01 ), ( -1.16178110918724e-01 , -6.76669024793121e-02 , -3.06309936976110e-01 ), ( -1.71580143375189e-01 , -8.06087224475810e-02 , -2.44150524929662e-01 ), ( -2.23095161228034e-01 , -9.91521899124832e-02 , -2.56488893382598e-01 ), ( -2.57331721108966e-01 , -1.03382875272694e-01 , -1.77490748029093e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 32, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 33 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 33, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 33, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 33, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 33, atoms_positions[size = 51] = { ( 8.21019791909521e+00 , 4.35633802325072e-02 , -7.10804529210888e-01 ), ( 6.82610715402917e+00 , -6.08702601628082e-01 , -5.19660907800472e-01 ), ( 6.08636982847500e+00 , -3.43516541447193e-01 , 8.16109789822522e-01 ), ( 4.90171740614450e+00 , -1.51234661265515e-01 , 7.56383814582825e-01 ), ( 6.99590387864465e+00 , -2.08071358662901e+00 , -8.51425606012143e-01 ), ( 6.79779319273434e+00 , -3.05109564227999e-01 , 1.96640893949061e+00 ), ( 6.08156543438362e+00 , -2.34562584634943e-01 , 3.20903737278150e+00 ), ( 7.15097502010524e+00 , -3.48679337406306e-01 , 4.40271942538223e+00 ), ( 5.31096306737649e+00 , 1.06496399948851e+00 , 3.36458768786987e+00 ), ( 4.19051563911193e+00 , 1.00331723044316e+00 , 3.81087672380921e+00 ), ( 5.85349645287331e+00 , 2.25095102916827e+00 , 2.96607854054684e+00 ), ( 5.13531478217963e+00 , 3.53630270778699e+00 , 2.87041395678720e+00 ), ( 6.28781736907147e+00 , 4.45353109012302e+00 , 2.28383910326184e+00 ), ( 3.85899355872802e+00 , 3.63091209857713e+00 , 2.01472246475161e+00 ), ( 2.83174176427113e+00 , 4.16349116383337e+00 , 2.42281879466273e+00 ), ( 3.90240065601318e+00 , 3.16920614770501e+00 , 7.60134964710312e-01 ), ( 2.76670172157189e+00 , 3.09797126086086e+00 , -6.91656707907341e-02 ), ( 3.13210313366296e+00 , 2.65229591985997e+00 , -1.53813174351084e+00 ), ( 1.57100155371032e+00 , 2.23812901945626e+00 , 4.30288626030736e-01 ), ( 4.22655310526989e-01 , 2.61531683195227e+00 , 4.43098682874497e-01 ), ( 2.04412513050292e+00 , 1.12324601649572e+00 , 1.04828171708230e+00 ), ( 1.26291367643280e+00 , 1.52471038482506e-01 , 1.66977158914457e+00 ), ( 2.09166067237580e+00 , -1.09381048195222e+00 , 2.03881102148452e+00 ), ( 5.73351864534817e-01 , 6.15679762509812e-01 , 2.94390160366273e+00 ), ( -5.96372825253587e-01 , 3.57755428110507e-01 , 3.19529252919828e+00 ), ( 1.28598432385745e+00 , 1.41260095346227e+00 , 3.77056370833815e+00 ), ( 8.94784505225517e-01 , 1.98006379732528e+00 , 5.04238327326131e+00 ), ( 2.06385512913826e+00 , 2.76865949475112e+00 , 5.72618092003640e+00 ), ( -3.60062097218326e-01 , 2.89535661157304e+00 , 4.93677968134798e+00 ), ( -1.11667932050255e+00 , 3.07045197048428e+00 , 5.89059613594728e+00 ), ( -5.36405371385116e-01 , 3.49764622877992e+00 , 3.75275692967691e+00 ), ( -1.45342361975039e+00 , 4.47616593488856e+00 , 3.41781805826289e+00 ), ( -7.59165807068616e-01 , 5.45257919281522e+00 , 2.48405980664348e+00 ), ( -2.75055981152918e+00 , 3.93858955483025e+00 , 2.74731074556576e+00 ), ( -3.79946948160685e+00 , 4.58326796810441e+00 , 2.81212187429832e+00 ), ( -2.70374724078334e+00 , 2.63943159515823e+00 , 2.35191174282680e+00 ), ( -3.81177363832016e+00 , 1.81609485447502e+00 , 2.00055152302758e+00 ), ( -3.35038102202661e+00 , 8.86608142278450e-01 , 7.86125718186561e-01 ), ( -4.25602419354840e+00 , 1.02942668200217e+00 , 3.24713244968131e+00 ), ( -5.44751868472733e+00 , 7.36379853289974e-01 , 3.34693232400797e+00 ), ( -3.36798237884827e+00 , 7.25213959190701e-01 , 4.16128616031333e+00 ), ( -3.66657995644053e+00 , 7.30773804175590e-02 , 5.47576568491923e+00 ), ( -2.35995830595435e+00 , -2.98354522442641e-01 , 6.12538658020151e+00 ), ( -4.49138257388260e+00 , 9.36520548828004e-01 , 6.42070963892303e+00 ), ( -5.35620617875941e+00 , 5.54578423938489e-01 , 7.18696910577752e+00 ), ( -6.30528090797248e+00 , 3.61144313631416e+00 , 6.76081477239903e+00 ), ( -7.02615654732738e+00 , 4.30029315541803e+00 , 7.51822328567389e+00 ), ( -6.61912434425324e+00 , 3.16641104306728e+00 , 5.54783557432400e+00 ), ( -4.10974603712149e+00 , 2.25460191083565e+00 , 6.40922090787994e+00 ), ( -4.81279459463440e+00 , 3.28658348388144e+00 , 7.22591772667137e+00 ), ( -4.00964714373989e+00 , 4.59079164212638e+00 , 7.27806214886563e+00 ) } +colvars: Step 33, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_ids[size = 0] = +colvars: Step 33, atom_groups_refcount[size = 0] = +colvars: Step 33, atom_groups_masses[size = 0] = +colvars: Step 33, atom_groups_charges[size = 0] = +colvars: Step 33, atom_groups_coms[size = 0] = +colvars: Step 33, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 33, volmaps_ids[size = 0] = +colvars: Step 33, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 33 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.90717372797486e-01 , -1.60872298396465e-02 , 9.56673721908266e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.90717372797486e-01 , -1.60872298396465e-02 , 9.56673721908266e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.3323 , 2.27354 , -15.2299 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.3323 , 2.27354 , -15.2299 ) to colvar "one". +colvars: Adding total bias energy: 43.9423 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.3323 , 2.27354 , -15.2299 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.9401 , -0.51618 , -1.3975 ) +colvars: ( -4.23613 , -0.442624 , -1.19836 ) +colvars: ( -4.23613 , -0.442624 , -1.19836 ) +colvars: ( -5.64265 , -0.589588 , -1.59624 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.885089 , 0.196259 , 0.604573 ) +colvars: ( 0.767564 , 0.26599 , 0.627986 ) +colvars: ( 0.751366 , 0.25937 , 0.610046 ) +colvars: ( 0.65797 , 0.266029 , 0.56507 ) +colvars: ( 0.646317 , 0.199844 , 0.472066 ) +colvars: ( 0.573181 , 0.342187 , 0.615672 ) +colvars: ( 0.468168 , 0.355366 , 0.572524 ) +colvars: ( 0.392989 , 0.451471 , 0.65466 ) +colvars: ( 0.38775 , 0.310871 , 0.468298 ) +colvars: ( 0.353818 , 0.269261 , 0.39454 ) +colvars: ( 0.358527 , 0.316263 , 0.45854 ) +colvars: ( 0.288348 , 0.273516 , 0.362473 ) +colvars: ( 0.261279 , 0.302501 , 0.38472 ) +colvars: ( 0.349634 , 0.17673 , 0.271468 ) +colvars: ( 0.292039 , 0.133387 , 0.181856 ) +colvars: ( 0.470134 , 0.140623 , 0.293614 ) +colvars: ( 0.541358 , 0.0502734 , 0.216711 ) +colvars: ( 0.668418 , 0.0302226 , 0.263564 ) +colvars: ( 0.550242 , 0.0184106 , 0.180264 ) +colvars: ( 0.534796 , -0.0463002 , 0.0870028 ) +colvars: ( 0.571143 , 0.0658711 , 0.254165 ) +colvars: ( 0.570116 , 0.0495085 , 0.232237 ) +colvars: ( 0.606336 , 0.113768 , 0.336845 ) +colvars: ( 0.448164 , 0.0532028 , 0.166989 ) +colvars: ( 0.441668 , -0.00250595 , 0.0906084 ) +colvars: ( 0.347928 , 0.117927 , 0.193805 ) +colvars: ( 0.225723 , 0.125748 , 0.133794 ) +colvars: ( 0.135742 , 0.210521 , 0.192647 ) +colvars: ( 0.197744 , 0.0525445 , 0.0222558 ) +colvars: ( 0.149572 , 0.0162317 , -0.0527755 ) +colvars: ( 0.230276 , 0.0276308 , 0.00845728 ) +colvars: ( 0.216215 , -0.0442562 , -0.0933674 ) +colvars: ( 0.250362 , -0.047058 , -0.0774025 ) +colvars: ( 0.290275 , -0.129322 , -0.161749 ) +colvars: ( 0.247086 , -0.182312 , -0.255666 ) +colvars: ( 0.403528 , -0.143715 , -0.115452 ) +colvars: ( 0.479789 , -0.218404 , -0.169037 ) +colvars: ( 0.608656 , -0.220305 , -0.0974772 ) +colvars: ( 0.433833 , -0.223425 , -0.201987 ) +colvars: ( 0.439361 , -0.291054 , -0.287006 ) +colvars: ( 0.386271 , -0.151082 , -0.134973 ) +colvars: ( 0.333469 , -0.145456 , -0.157974 ) +colvars: ( 0.317546 , -0.0596485 , -0.055222 ) +colvars: ( 0.212371 , -0.154828 , -0.239769 ) +colvars: ( 0.18867 , -0.196844 , -0.308179 ) +colvars: ( 0.0140244 , -0.200885 , -0.413789 ) +colvars: ( -0.0752839 , -0.219039 , -0.488773 ) +colvars: ( 0.112288 , -0.249744 , -0.421048 ) +colvars: ( 0.131724 , -0.114732 , -0.233816 ) +colvars: ( 0.0145014 , -0.119678 , -0.307614 ) +colvars: ( -0.0730751 , -0.0399188 , -0.253918 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.9401 , 0.51618 , 1.3975 ) +colvars: ( 4.23613 , 0.442624 , 1.19836 ) +colvars: ( 4.23613 , 0.442624 , 1.19836 ) +colvars: ( 5.64265 , 0.589588 , 1.59624 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.611548 , -0.0809819 , -0.359006 ) +colvars: ( -0.550619 , -0.164757 , -0.32581 ) +colvars: ( -0.498663 , -0.142175 , -0.265995 ) +colvars: ( -0.513568 , -0.192616 , -0.297887 ) +colvars: ( -0.503859 , -0.132863 , -0.268099 ) +colvars: ( -0.490807 , -0.285977 , -0.306285 ) +colvars: ( -0.460428 , -0.326894 , -0.289449 ) +colvars: ( -0.440514 , -0.435763 , -0.305907 ) +colvars: ( -0.397122 , -0.290808 , -0.213694 ) +colvars: ( -0.393679 , -0.265181 , -0.201644 ) +colvars: ( -0.346192 , -0.284864 , -0.160487 ) +colvars: ( -0.28514 , -0.247228 , -0.0864795 ) +colvars: ( -0.234852 , -0.26214 , -0.0409069 ) +colvars: ( -0.303278 , -0.142567 , -0.0696452 ) +colvars: ( -0.272558 , -0.112798 , -0.028777 ) +colvars: ( -0.355926 , -0.084461 , -0.103116 ) +colvars: ( -0.381258 , 0.0151685 , -0.0952021 ) +colvars: ( -0.429258 , 0.0634042 , -0.127306 ) +colvars: ( -0.420598 , 0.0302137 , -0.12972 ) +colvars: ( -0.409194 , 0.0878478 , -0.0989387 ) +colvars: ( -0.466321 , -0.0248074 , -0.194139 ) +colvars: ( -0.502571 , -0.0264804 , -0.231153 ) +colvars: ( -0.55385 , -0.0930458 , -0.305027 ) +colvars: ( -0.452446 , -0.0568411 , -0.190921 ) +colvars: ( -0.459923 , -0.0121691 , -0.18347 ) +colvars: ( -0.398284 , -0.132087 , -0.161672 ) +colvars: ( -0.34237 , -0.163725 , -0.116047 ) +colvars: ( -0.292779 , -0.255078 , -0.0967922 ) +colvars: ( -0.299992 , -0.0896601 , -0.0486108 ) +colvars: ( -0.287961 , -0.0707844 , -0.0301863 ) +colvars: ( -0.277752 , -0.0439735 , -0.0109358 ) +colvars: ( -0.240979 , 0.0320283 , 0.0515134 ) +colvars: ( -0.217169 , 0.0589729 , 0.0844876 ) +colvars: ( -0.284474 , 0.119922 , 0.0372298 ) +colvars: ( -0.25807 , 0.162363 , 0.078005 ) +colvars: ( -0.353094 , 0.148261 , -0.0222785 ) +colvars: ( -0.401524 , 0.225419 , -0.0451226 ) +colvars: ( -0.471441 , 0.248141 , -0.107817 ) +colvars: ( -0.415539 , 0.205167 , -0.0660031 ) +colvars: ( -0.420056 , 0.266851 , -0.0498733 ) +colvars: ( -0.422177 , 0.117244 , -0.102143 ) +colvars: ( -0.431752 , 0.086525 , -0.122066 ) +colvars: ( -0.455098 , -0.00827615 , -0.177313 ) +colvars: ( -0.366186 , 0.075252 , -0.0599107 ) +colvars: ( -0.370603 , 0.101888 , -0.0554258 ) +colvars: ( -0.204189 , 0.108988 , 0.114301 ) +colvars: ( -0.155587 , 0.111001 , 0.16385 ) +colvars: ( -0.228336 , 0.182372 , 0.114611 ) +colvars: ( -0.303433 , 0.0341286 , -0.0105864 ) +colvars: ( -0.237683 , 0.0204831 , 0.0509591 ) +colvars: ( -0.184308 , -0.0636578 , 0.0764359 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 33. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 33. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atoms_new_colvar_forces = { ( -4.66655574300186e+00 , -4.00902551228220e-01 , -1.15193312667992e+00 ), ( -4.01918630331649e+00 , -3.41390444913296e-01 , -8.96180175342897e-01 ), ( -4.09172970574186e+00 , -3.69211140349797e-01 , -9.31172632754234e-01 ), ( -5.50019213997382e+00 , -5.22606887274410e-01 , -1.39227871176518e+00 ), ( 2.52702783917087e-01 , 1.17195426405282e-01 , 3.44050889792059e-01 ), ( 5.02247053472502e+00 , 5.72390204245951e-01 , 1.70688672720813e+00 ), ( 4.24387108384171e+00 , 4.71096411775340e-01 , 1.48143145527619e+00 ), ( -4.75248358392963e-02 , 1.57082050546262e-02 , 3.48752533987886e-01 ), ( 4.22675912127380e+00 , 4.62687987289125e-01 , 1.45295913779938e+00 ), ( 5.60278969040657e+00 , 5.93668745614696e-01 , 1.78914176923980e+00 ), ( 1.23346479196570e-02 , 3.13994536011904e-02 , 2.98052823653341e-01 ), ( 3.20835919647033e-03 , 2.62874237462203e-02 , 2.75993914291455e-01 ), ( 2.64272565295787e-02 , 4.03613431814258e-02 , 3.43813461473831e-01 ), ( 4.63560867491589e-02 , 3.41626951824440e-02 , 2.01822879649986e-01 ), ( 1.94804224645847e-02 , 2.05890100582586e-02 , 1.53078593040516e-01 ), ( 1.14207902246984e-01 , 5.61619147734442e-02 , 1.90497251216933e-01 ), ( 1.60099607314098e-01 , 6.54418893589465e-02 , 1.21509353208883e-01 ), ( 2.39160631010491e-01 , 9.36268397490796e-02 , 1.36258229385052e-01 ), ( 1.29644226518945e-01 , 4.86242203272269e-02 , 5.05438805427701e-02 ), ( 1.25602041419272e-01 , 4.15476220209901e-02 , -1.19359545640073e-02 ), ( 1.04822221961650e-01 , 4.10637469228252e-02 , 6.00258382021666e-02 ), ( 6.75452449747612e-02 , 2.30281370618511e-02 , 1.08384131479711e-03 ), ( 5.24862788586783e-02 , 2.07222593548226e-02 , 3.18187102291569e-02 ), ( -4.28117649710569e-03 , -3.63829511389917e-03 , -2.39319243863618e-02 ), ( -1.82546405832218e-02 , -1.46750380924692e-02 , -9.28611702470923e-02 ), ( -5.03553875248300e-02 , -1.41600832214690e-02 , 3.21331187282011e-02 ), ( -1.16646762040843e-01 , -3.79771022679259e-02 , 1.77467233426216e-02 ), ( -1.57037015614155e-01 , -4.45569027199628e-02 , 9.58543067398101e-02 ), ( -1.02247813282843e-01 , -3.71156695591439e-02 , -2.63549592165182e-02 ), ( -1.38389263824373e-01 , -5.45526099222540e-02 , -8.29618124420032e-02 ), ( -4.74760601312511e-02 , -1.63427007569159e-02 , -2.47847536744859e-03 ), ( -2.47644333951621e-02 , -1.22279128492849e-02 , -4.18539922142991e-02 ), ( 3.31935253179527e-02 , 1.19148753588699e-02 , 7.08505482883817e-03 ), ( 5.80050214181399e-03 , -9.39960248250518e-03 , -1.24519592442528e-01 ), ( -1.09837786282649e-02 , -1.99490843643051e-02 , -1.77661006407395e-01 ), ( 5.04334597901761e-02 , 4.54554852983705e-03 , -1.37730223819585e-01 ), ( 7.82645576028812e-02 , 7.01516940411967e-03 , -2.14159801717374e-01 ), ( 1.37214389368312e-01 , 2.78359038733265e-02 , -2.05294694805041e-01 ), ( 1.82933405891691e-02 , -1.82576651770395e-02 , -2.67990596393569e-01 ), ( 1.93051533878304e-02 , -2.42036996894018e-02 , -3.36878815523230e-01 ), ( -3.59059070395407e-02 , -3.38374749886532e-02 , -2.37115681710708e-01 ), ( -9.82834906838154e-02 , -5.89314424008209e-02 , -2.80040234577893e-01 ), ( -1.37552356276809e-01 , -6.79246083473129e-02 , -2.32535390494389e-01 ), ( -1.53815592270519e-01 , -7.95757209751634e-02 , -2.99680132312586e-01 ), ( -1.81932549662521e-01 , -9.49567513149216e-02 , -3.63604788171385e-01 ), ( -1.90164720332336e-01 , -9.18973887196884e-02 , -2.99487861935775e-01 ), ( -2.30871214150350e-01 , -1.08038010646822e-01 , -3.24922972744714e-01 ), ( -1.16047761909081e-01 , -6.73717649025961e-02 , -3.06436572939371e-01 ), ( -1.71709220190476e-01 , -8.06030743773704e-02 , -2.44402163509378e-01 ), ( -2.23181807344551e-01 , -9.91948579420006e-02 , -2.56655048131742e-01 ), ( -2.57383390271271e-01 , -1.03576548292250e-01 , -1.77481980535176e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 33, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 34 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 34, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 34, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 34, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 34, atoms_positions[size = 51] = { ( 8.19928248168927e+00 , 4.32426689753966e-02 , -7.06900358608923e-01 ), ( 6.82269070189451e+00 , -6.13764926659809e-01 , -5.16880035718534e-01 ), ( 6.07701132309998e+00 , -3.36705544159249e-01 , 8.16861088770233e-01 ), ( 4.89808556299347e+00 , -1.52047783855024e-01 , 7.60077270528482e-01 ), ( 6.99570786501574e+00 , -2.08476137883713e+00 , -8.43257407036207e-01 ), ( 6.79345392752965e+00 , -3.08580009346970e-01 , 1.96507289322943e+00 ), ( 6.07903706363312e+00 , -2.37011156592875e-01 , 3.22216430071421e+00 ), ( 7.15325739125771e+00 , -3.51156564941396e-01 , 4.40783514370672e+00 ), ( 5.30693357635731e+00 , 1.06450062938171e+00 , 3.36315875996404e+00 ), ( 4.19208799221550e+00 , 1.00306496304032e+00 , 3.82184551922138e+00 ), ( 5.85492400911472e+00 , 2.25160696744740e+00 , 2.96380532347502e+00 ), ( 5.13117200184208e+00 , 3.53045480547987e+00 , 2.86512724648861e+00 ), ( 6.28200019777729e+00 , 4.44691711279416e+00 , 2.28381154465095e+00 ), ( 3.85932041175221e+00 , 3.62721564676007e+00 , 2.01127992536186e+00 ), ( 2.83757715452672e+00 , 4.16153060129455e+00 , 2.41894403045113e+00 ), ( 3.90078613714491e+00 , 3.16133099871682e+00 , 7.66566242117880e-01 ), ( 2.76522915842112e+00 , 3.10922334815726e+00 , -6.99820658943434e-02 ), ( 3.13649903500476e+00 , 2.65420589741729e+00 , -1.53430359023798e+00 ), ( 1.58363709122344e+00 , 2.24965893509786e+00 , 4.34218323836917e-01 ), ( 4.25908640926286e-01 , 2.61461992610346e+00 , 4.37249439916099e-01 ), ( 2.03721554601976e+00 , 1.11739097228770e+00 , 1.04774787933842e+00 ), ( 1.27469598890323e+00 , 1.57857677434009e-01 , 1.66638272373459e+00 ), ( 2.09388972574858e+00 , -1.09389004942111e+00 , 2.03712822296875e+00 ), ( 5.72493319881723e-01 , 6.16953391732061e-01 , 2.93976427211256e+00 ), ( -5.99923271234357e-01 , 3.58096679238054e-01 , 3.19994832001263e+00 ), ( 1.28676895845726e+00 , 1.41926069400591e+00 , 3.77578364299027e+00 ), ( 9.01917625907552e-01 , 1.98139301607146e+00 , 5.04622921438861e+00 ), ( 2.05468060339195e+00 , 2.77175716623085e+00 , 5.72600999785528e+00 ), ( -3.59784887976669e-01 , 2.89346526189633e+00 , 4.93084205638007e+00 ), ( -1.11736388386602e+00 , 3.07085315791936e+00 , 5.89331397417883e+00 ), ( -5.32130846876883e-01 , 3.49239472997256e+00 , 3.74379401902314e+00 ), ( -1.45107255452032e+00 , 4.47553686818780e+00 , 3.41741341749673e+00 ), ( -7.65090001147442e-01 , 5.45860499633047e+00 , 2.48562051225388e+00 ), ( -2.75201405685088e+00 , 3.93474907322799e+00 , 2.73645960600855e+00 ), ( -3.79753418105992e+00 , 4.58901549333180e+00 , 2.81109890187318e+00 ), ( -2.70708351781196e+00 , 2.64312098712079e+00 , 2.35072894724435e+00 ), ( -3.81527726316310e+00 , 1.80992686265173e+00 , 1.99782470976297e+00 ), ( -3.34775320239414e+00 , 8.91359605135749e-01 , 7.79368123263810e-01 ), ( -4.26032807276174e+00 , 1.02602624411697e+00 , 3.24647485168588e+00 ), ( -5.43901038056310e+00 , 7.30996178392527e-01 , 3.34982070449990e+00 ), ( -3.36570977315917e+00 , 7.22044864349293e-01 , 4.16216573739025e+00 ), ( -3.66575877559271e+00 , 6.98030386715717e-02 , 5.47047854661170e+00 ), ( -2.35280113648233e+00 , -2.91430069069599e-01 , 6.12531361013041e+00 ), ( -4.49261716443863e+00 , 9.44801538298533e-01 , 6.42080466597303e+00 ), ( -5.35553307291137e+00 , 5.47922125948171e-01 , 7.18255546743241e+00 ), ( -6.30095269654030e+00 , 3.60728638503266e+00 , 6.76581792426097e+00 ), ( -7.03318933709519e+00 , 4.30033811984162e+00 , 7.51894318036934e+00 ), ( -6.61460457490353e+00 , 3.16848186313731e+00 , 5.55200359987311e+00 ), ( -4.11247216608464e+00 , 2.25364742528459e+00 , 6.41339366894072e+00 ), ( -4.81013341147260e+00 , 3.28475172278346e+00 , 7.21702956500683e+00 ), ( -4.00801121720644e+00 , 4.60191943380506e+00 , 7.27953341872253e+00 ) } +colvars: Step 34, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_ids[size = 0] = +colvars: Step 34, atom_groups_refcount[size = 0] = +colvars: Step 34, atom_groups_masses[size = 0] = +colvars: Step 34, atom_groups_charges[size = 0] = +colvars: Step 34, atom_groups_coms[size = 0] = +colvars: Step 34, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 34, volmaps_ids[size = 0] = +colvars: Step 34, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 34 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.89014188887543e-01 , -1.68855035770422e-02 , 9.57175886862297e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.89014188887543e-01 , -1.68855035770422e-02 , 9.57175886862297e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.2983 , 2.28951 , -15.2399 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.2983 , 2.28951 , -15.2399 ) to colvar "one". +colvars: Adding total bias energy: 43.875 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.2983 , 2.28951 , -15.2399 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.94323 , -0.513907 , -1.39039 ) +colvars: ( -4.23882 , -0.440675 , -1.19226 ) +colvars: ( -4.23882 , -0.440675 , -1.19226 ) +colvars: ( -5.64623 , -0.586992 , -1.58812 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.884406 , 0.196339 , 0.602947 ) +colvars: ( 0.767071 , 0.265925 , 0.626335 ) +colvars: ( 0.750853 , 0.259373 , 0.608503 ) +colvars: ( 0.657684 , 0.265854 , 0.56354 ) +colvars: ( 0.646057 , 0.199729 , 0.470735 ) +colvars: ( 0.573052 , 0.341848 , 0.614021 ) +colvars: ( 0.468243 , 0.354901 , 0.570946 ) +colvars: ( 0.3932 , 0.450833 , 0.652897 ) +colvars: ( 0.387943 , 0.310429 , 0.466984 ) +colvars: ( 0.354091 , 0.268811 , 0.393363 ) +colvars: ( 0.358729 , 0.315856 , 0.457308 ) +colvars: ( 0.288649 , 0.273142 , 0.361492 ) +colvars: ( 0.261582 , 0.302142 , 0.383755 ) +colvars: ( 0.349829 , 0.176511 , 0.270683 ) +colvars: ( 0.292336 , 0.13317 , 0.181269 ) +colvars: ( 0.470119 , 0.140537 , 0.292775 ) +colvars: ( 0.541221 , 0.0503403 , 0.216035 ) +colvars: ( 0.668048 , 0.0304258 , 0.262794 ) +colvars: ( 0.550133 , 0.0184546 , 0.179607 ) +colvars: ( 0.534719 , -0.0462008 , 0.0865461 ) +colvars: ( 0.571031 , 0.0658266 , 0.253297 ) +colvars: ( 0.570048 , 0.0494165 , 0.231356 ) +colvars: ( 0.606234 , 0.113586 , 0.335691 ) +colvars: ( 0.448318 , 0.0530013 , 0.166247 ) +colvars: ( 0.441852 , -0.00267842 , 0.0900083 ) +colvars: ( 0.34824 , 0.1176 , 0.193031 ) +colvars: ( 0.22625 , 0.125317 , 0.133156 ) +colvars: ( 0.136407 , 0.209954 , 0.19191 ) +colvars: ( 0.198298 , 0.0522093 , 0.0218975 ) +colvars: ( 0.150226 , 0.0158754 , -0.0529897 ) +colvars: ( 0.230735 , 0.0274071 , 0.00818198 ) +colvars: ( 0.216675 , -0.0443729 , -0.0933839 ) +colvars: ( 0.250718 , -0.0470786 , -0.0773939 ) +colvars: ( 0.290626 , -0.129317 , -0.161648 ) +colvars: ( 0.247514 , -0.182281 , -0.255356 ) +colvars: ( 0.4037 , -0.143636 , -0.115483 ) +colvars: ( 0.479852 , -0.218218 , -0.168988 ) +colvars: ( 0.608503 , -0.220033 , -0.0976057 ) +colvars: ( 0.434016 , -0.223329 , -0.20192 ) +colvars: ( 0.439546 , -0.290895 , -0.286766 ) +colvars: ( 0.38656 , -0.151139 , -0.135083 ) +colvars: ( 0.333887 , -0.145618 , -0.158084 ) +colvars: ( 0.318015 , -0.0599536 , -0.0555897 ) +colvars: ( 0.212993 , -0.155059 , -0.239682 ) +colvars: ( 0.189357 , -0.197081 , -0.307972 ) +colvars: ( 0.0149245 , -0.20111 , -0.413211 ) +colvars: ( -0.0742322 , -0.219305 , -0.488019 ) +colvars: ( 0.112999 , -0.24981 , -0.420432 ) +colvars: ( 0.132454 , -0.11502 , -0.233692 ) +colvars: ( 0.0154263 , -0.120034 , -0.307307 ) +colvars: ( -0.0720213 , -0.0403961 , -0.253691 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.94323 , 0.513907 , 1.39039 ) +colvars: ( 4.23882 , 0.440675 , 1.19226 ) +colvars: ( 4.23882 , 0.440675 , 1.19226 ) +colvars: ( 5.64623 , 0.586992 , 1.58812 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.610856 , -0.0809681 , -0.357355 ) +colvars: ( -0.550115 , -0.164746 , -0.323994 ) +colvars: ( -0.49799 , -0.142168 , -0.26412 ) +colvars: ( -0.513325 , -0.192581 , -0.296212 ) +colvars: ( -0.503618 , -0.132802 , -0.266681 ) +colvars: ( -0.490795 , -0.285949 , -0.304441 ) +colvars: ( -0.460691 , -0.326845 , -0.287701 ) +colvars: ( -0.440982 , -0.435731 , -0.303899 ) +colvars: ( -0.397415 , -0.290733 , -0.212138 ) +colvars: ( -0.394087 , -0.265082 , -0.200309 ) +colvars: ( -0.346371 , -0.284794 , -0.158854 ) +colvars: ( -0.285319 , -0.247135 , -0.0850164 ) +colvars: ( -0.234913 , -0.26206 , -0.0392741 ) +colvars: ( -0.303298 , -0.142453 , -0.0684687 ) +colvars: ( -0.272665 , -0.112658 , -0.0278152 ) +colvars: ( -0.355711 , -0.0843587 , -0.101951 ) +colvars: ( -0.380876 , 0.0152876 , -0.0942942 ) +colvars: ( -0.428594 , 0.0635029 , -0.126323 ) +colvars: ( -0.420355 , 0.0303503 , -0.129006 ) +colvars: ( -0.40896 , 0.0880099 , -0.098478 ) +colvars: ( -0.466202 , -0.0246841 , -0.193303 ) +colvars: ( -0.502618 , -0.0263429 , -0.230464 ) +colvars: ( -0.553985 , -0.0929311 , -0.304133 ) +colvars: ( -0.452744 , -0.0566793 , -0.190354 ) +colvars: ( -0.460279 , -0.0119836 , -0.183147 ) +colvars: ( -0.398733 , -0.13193 , -0.16094 ) +colvars: ( -0.343046 , -0.163547 , -0.115409 ) +colvars: ( -0.293586 , -0.254914 , -0.0959012 ) +colvars: ( -0.300587 , -0.0894564 , -0.0482148 ) +colvars: ( -0.288689 , -0.0705557 , -0.0300012 ) +colvars: ( -0.278121 , -0.0437755 , -0.0105182 ) +colvars: ( -0.241237 , 0.0322484 , 0.0517098 ) +colvars: ( -0.217187 , 0.0591784 , 0.0847973 ) +colvars: ( -0.284635 , 0.12016 , 0.0371532 ) +colvars: ( -0.258281 , 0.162628 , 0.0776964 ) +colvars: ( -0.35312 , 0.148485 , -0.0223336 ) +colvars: ( -0.401467 , 0.225659 , -0.0454175 ) +colvars: ( -0.471194 , 0.248357 , -0.108014 ) +colvars: ( -0.415724 , 0.205425 , -0.0664434 ) +colvars: ( -0.420237 , 0.267132 , -0.0505718 ) +colvars: ( -0.422578 , 0.117492 , -0.102418 ) +colvars: ( -0.432402 , 0.0867885 , -0.12245 ) +colvars: ( -0.455916 , -0.00803373 , -0.177454 ) +colvars: ( -0.367015 , 0.0755409 , -0.0604303 ) +colvars: ( -0.371543 , 0.1022 , -0.0561652 ) +colvars: ( -0.205068 , 0.109317 , 0.113565 ) +colvars: ( -0.156597 , 0.111353 , 0.162972 ) +colvars: ( -0.228938 , 0.182695 , 0.113835 ) +colvars: ( -0.304297 , 0.0344133 , -0.0109753 ) +colvars: ( -0.238711 , 0.0207904 , 0.0504598 ) +colvars: ( -0.185441 , -0.0633648 , 0.0761839 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 34. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 34. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atoms_new_colvar_forces = { ( -4.66968467730647e+00 , -3.98535764896394e-01 , -1.14479461041868e+00 ), ( -4.02186586847765e+00 , -3.39496664546440e-01 , -8.89915685724953e-01 ), ( -4.09446320674110e+00 , -3.67401420752595e-01 , -9.24928118480411e-01 ), ( -5.50379499139976e+00 , -5.20064962826203e-01 , -1.38406475081348e+00 ), ( 2.52862835477283e-01 , 1.17204291123779e-01 , 3.44382801753356e-01 ), ( 5.02549211289822e+00 , 5.69805601309177e-01 , 1.69996671677032e+00 ), ( 4.24637458075738e+00 , 4.68730693662607e-01 , 1.47550146077075e+00 ), ( -4.77826762691794e-02 , 1.51018406915943e-02 , 3.48997985736102e-01 ), ( 4.22935114677442e+00 , 4.60371048307047e-01 , 1.44710174918278e+00 ), ( 5.60623807569989e+00 , 5.90720588683336e-01 , 1.78117433018362e+00 ), ( 1.23583210274947e-02 , 3.10625175598719e-02 , 2.98453522761200e-01 ), ( 3.32937256284721e-03 , 2.60066305896624e-02 , 2.76475718081853e-01 ), ( 2.66682738421338e-02 , 4.00826650770476e-02 , 3.44481103295033e-01 ), ( 4.65311855232145e-02 , 3.40576859424195e-02 , 2.02214762867393e-01 ), ( 1.96717261233661e-02 , 2.05123269665865e-02 , 1.53453323880322e-01 ), ( 1.14408069799234e-01 , 5.61784555554073e-02 , 1.90824123900925e-01 ), ( 1.60344882671914e-01 , 6.56278969761322e-02 , 1.21740820184294e-01 ), ( 2.39454688381125e-01 , 9.39287530714586e-02 , 1.36470596032705e-01 ), ( 1.29777095602017e-01 , 4.88049277296106e-02 , 5.06012713544814e-02 ), ( 1.25758244751251e-01 , 4.18091399735610e-02 , -1.19319263436668e-02 ), ( 1.04828297798102e-01 , 4.11424993347926e-02 , 5.99934316120360e-02 ), ( 6.74307158151144e-02 , 2.30735869252806e-02 , 8.92324837849123e-04 ), ( 5.22485813188008e-02 , 2.06552450324260e-02 , 3.15580193981421e-02 ), ( -4.42647633581983e-03 , -3.67805829784899e-03 , -2.41074103710462e-02 ), ( -1.84267726514626e-02 , -1.46620019873643e-02 , -9.31387800215068e-02 ), ( -5.04922619256448e-02 , -1.43305662789096e-02 , 3.20911979132146e-02 ), ( -1.16796066394915e-01 , -3.82299637879766e-02 , 1.77473599654943e-02 ), ( -1.57179713700557e-01 , -4.49601392162065e-02 , 9.60091466302025e-02 ), ( -1.02288980792726e-01 , -3.72471605576334e-02 , -2.63173188765250e-02 ), ( -1.38462668260544e-01 , -5.46803596104781e-02 , -8.29909122011471e-02 ), ( -4.73858656743748e-02 , -1.63683457195723e-02 , -2.33617285988538e-03 ), ( -2.45624769203801e-02 , -1.21245386428889e-02 , -4.16740783774202e-02 ), ( 3.35312460520490e-02 , 1.20998749539420e-02 , 7.40339352567526e-03 ), ( 5.99045553348876e-03 , -9.15663385549989e-03 , -1.24494393770357e-01 ), ( -1.07671472680909e-02 , -1.96534698778889e-02 , -1.77659266847587e-01 ), ( 5.05797346371175e-02 , 4.84945799729997e-03 , -1.37817007716939e-01 ), ( 7.83842258201953e-02 , 7.44081322069479e-03 , -2.14405048442866e-01 ), ( 1.37309438586973e-01 , 2.83241572130489e-02 , -2.05619494926364e-01 ), ( 1.82921229476102e-02 , -1.79040872757231e-02 , -2.68363169853558e-01 ), ( 1.93084549023900e-02 , -2.37624063076849e-02 , -3.37338080264935e-01 ), ( -3.60180996619245e-02 , -3.36471058673632e-02 , -2.37500976269758e-01 ), ( -9.85144937590744e-02 , -5.88290225385445e-02 , -2.80533758359584e-01 ), ( -1.37901044314944e-01 , -6.79873512947285e-02 , -2.33043437489882e-01 ), ( -1.54022156249555e-01 , -7.95179237640221e-02 , -3.00112216125075e-01 ), ( -1.82185810088524e-01 , -9.48810688857158e-02 , -3.64136988654834e-01 ), ( -1.90143353503948e-01 , -9.17929585012935e-02 , -2.99645402220216e-01 ), ( -2.30829218684587e-01 , -1.07951603903597e-01 , -3.25047146027383e-01 ), ( -1.15939912742137e-01 , -6.71155963308890e-02 , -3.06597447195414e-01 ), ( -1.71842830975162e-01 , -8.06068647110167e-02 , -2.44667082588142e-01 ), ( -2.23284761602432e-01 , -9.92438254814662e-02 , -2.56847022337407e-01 ), ( -2.57462353602662e-01 , -1.03760832180838e-01 , -1.77507457058724e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 34, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 35 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 35, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 35, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 35, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 35, atoms_positions[size = 51] = { ( 8.18758198097177e+00 , 4.27478682525558e-02 , -7.03073864718682e-01 ), ( 6.81892603616415e+00 , -6.18076415183793e-01 , -5.13546428131625e-01 ), ( 6.06951427437994e+00 , -3.30810763696199e-01 , 8.16350677814167e-01 ), ( 4.89321910407625e+00 , -1.52662587114762e-01 , 7.63913756830912e-01 ), ( 6.99651171726648e+00 , -2.08914407394131e+00 , -8.35214586840129e-01 ), ( 6.78859984438564e+00 , -3.11582634416293e-01 , 1.96328053406074e+00 ), ( 6.07826062298173e+00 , -2.39023088884221e-01 , 3.23575089194013e+00 ), ( 7.15441537341716e+00 , -3.54044338483169e-01 , 4.41288117313694e+00 ), ( 5.30362416804953e+00 , 1.06425780254130e+00 , 3.36191654236819e+00 ), ( 4.19315491042160e+00 , 1.00315119612648e+00 , 3.83299120788568e+00 ), ( 5.85558945301547e+00 , 2.25270701717089e+00 , 2.96144771599686e+00 ), ( 5.12857791808631e+00 , 3.52474021572560e+00 , 2.86019759651651e+00 ), ( 6.27588499529192e+00 , 4.44043001841798e+00 , 2.28405402729534e+00 ), ( 3.85991209859930e+00 , 3.62377298029292e+00 , 2.00807455715279e+00 ), ( 2.84334728192445e+00 , 4.15947479199413e+00 , 2.41535962459290e+00 ), ( 3.89996305372963e+00 , 3.15329603214102e+00 , 7.73224350753064e-01 ), ( 2.76246883684866e+00 , 3.12085996583065e+00 , -7.18906541142714e-02 ), ( 3.14058835980832e+00 , 2.65661167071910e+00 , -1.52946994391430e+00 ), ( 1.59811093466795e+00 , 2.26072624846230e+00 , 4.39253167874339e-01 ), ( 4.28697049253433e-01 , 2.61390503461078e+00 , 4.31331776322257e-01 ), ( 2.03091355842757e+00 , 1.11280160418402e+00 , 1.04589431623526e+00 ), ( 1.28492381556108e+00 , 1.62266000909496e-01 , 1.66403632346912e+00 ), ( 2.09579951205790e+00 , -1.09382170507587e+00 , 2.03477050502121e+00 ), ( 5.71622244880999e-01 , 6.19151258205981e-01 , 2.93627140596799e+00 ), ( -6.03518368501017e-01 , 3.58329528393548e-01 , 3.20444114748897e+00 ), ( 1.28801333045379e+00 , 1.42517414274212e+00 , 3.78033168563557e+00 ), ( 9.08307043256981e-01 , 1.98327309741441e+00 , 5.05045869603861e+00 ), ( 2.04617960728112e+00 , 2.77480964603669e+00 , 5.72590075891612e+00 ), ( -3.58967862256763e-01 , 2.89151536062043e+00 , 4.92549707964069e+00 ), ( -1.11797911682967e+00 , 3.07121399168678e+00 , 5.89564811768541e+00 ), ( -5.27122678693306e-01 , 3.48612701333263e+00 , 3.73494587033308e+00 ), ( -1.45038797102721e+00 , 4.47573847155800e+00 , 3.41610927692764e+00 ), ( -7.70296733412233e-01 , 5.46520426033772e+00 , 2.48693167492189e+00 ), ( -2.75335684941670e+00 , 3.93092928480662e+00 , 2.72741557414028e+00 ), ( -3.79541083274844e+00 , 4.59451203402486e+00 , 2.80964670439779e+00 ), ( -2.70997109251309e+00 , 2.64703993841399e+00 , 2.34914280380566e+00 ), ( -3.81857542077355e+00 , 1.80288221679954e+00 , 1.99462250318659e+00 ), ( -3.34497155680255e+00 , 8.96821350508929e-01 , 7.72904907828611e-01 ), ( -4.26522253219310e+00 , 1.02306043001778e+00 , 3.24435040202505e+00 ), ( -5.43071260761457e+00 , 7.25511300010191e-01 , 3.35306729611027e+00 ), ( -3.36291898738489e+00 , 7.18055332355550e-01 , 4.16430494982979e+00 ), ( -3.66506207886651e+00 , 6.63448298643537e-02 , 5.46387395862483e+00 ), ( -2.34497695303459e+00 , -2.84148804099343e-01 , 6.12630206690102e+00 ), ( -4.49273886878980e+00 , 9.54014263844208e-01 , 6.42078726816540e+00 ), ( -5.35513187654054e+00 , 5.40902278628718e-01 , 7.17814661148211e+00 ), ( -6.29552184861197e+00 , 3.60359691419288e+00 , 6.77228531577779e+00 ), ( -7.03991858334833e+00 , 4.29979172811510e+00 , 7.51877764950065e+00 ), ( -6.61143450534926e+00 , 3.17076314448908e+00 , 5.55566431774449e+00 ), ( -4.11590920405686e+00 , 2.25265547618249e+00 , 6.41738370151145e+00 ), ( -4.80693600371367e+00 , 3.28175856712602e+00 , 7.20769015248805e+00 ), ( -4.00736480079121e+00 , 4.61331469004481e+00 , 7.28079518983349e+00 ) } +colvars: Step 35, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_ids[size = 0] = +colvars: Step 35, atom_groups_refcount[size = 0] = +colvars: Step 35, atom_groups_masses[size = 0] = +colvars: Step 35, atom_groups_charges[size = 0] = +colvars: Step 35, atom_groups_coms[size = 0] = +colvars: Step 35, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 35, volmaps_ids[size = 0] = +colvars: Step 35, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 35 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.87142969394406e-01 , -1.75485194704134e-02 , 9.57726978105848e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.87142969394406e-01 , -1.75485194704134e-02 , 9.57726978105848e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.2609 , 2.30277 , -15.2509 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.2609 , 2.30277 , -15.2509 ) to colvar "one". +colvars: Adding total bias energy: 43.8002 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.2609 , 2.30277 , -15.2509 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.94669 , -0.5115 , -1.38241 ) +colvars: ( -4.24179 , -0.438611 , -1.18542 ) +colvars: ( -4.24179 , -0.438611 , -1.18542 ) +colvars: ( -5.65019 , -0.584243 , -1.57901 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.883684 , 0.196443 , 0.601163 ) +colvars: ( 0.766551 , 0.265873 , 0.624526 ) +colvars: ( 0.750303 , 0.259397 , 0.60681 ) +colvars: ( 0.657389 , 0.265683 , 0.561863 ) +colvars: ( 0.645787 , 0.199619 , 0.469274 ) +colvars: ( 0.572927 , 0.341499 , 0.612216 ) +colvars: ( 0.468338 , 0.354415 , 0.569221 ) +colvars: ( 0.393442 , 0.450162 , 0.650976 ) +colvars: ( 0.388161 , 0.309966 , 0.465545 ) +colvars: ( 0.354395 , 0.268335 , 0.392073 ) +colvars: ( 0.35895 , 0.315433 , 0.455957 ) +colvars: ( 0.288969 , 0.272753 , 0.360412 ) +colvars: ( 0.261897 , 0.301774 , 0.382692 ) +colvars: ( 0.350034 , 0.176287 , 0.269814 ) +colvars: ( 0.292651 , 0.132946 , 0.180613 ) +colvars: ( 0.470099 , 0.140458 , 0.291845 ) +colvars: ( 0.54107 , 0.0504231 , 0.215278 ) +colvars: ( 0.667647 , 0.0306573 , 0.261934 ) +colvars: ( 0.550018 , 0.0185095 , 0.178871 ) +colvars: ( 0.534637 , -0.046089 , 0.086027 ) +colvars: ( 0.570919 , 0.065786 , 0.252334 ) +colvars: ( 0.569991 , 0.0493217 , 0.230381 ) +colvars: ( 0.606145 , 0.113396 , 0.334422 ) +colvars: ( 0.448497 , 0.0527864 , 0.165423 ) +colvars: ( 0.442067 , -0.00286504 , 0.0893378 ) +colvars: ( 0.348588 , 0.117251 , 0.192175 ) +colvars: ( 0.226827 , 0.124855 , 0.132449 ) +colvars: ( 0.13713 , 0.209348 , 0.191098 ) +colvars: ( 0.198899 , 0.0518486 , 0.0214911 ) +colvars: ( 0.150937 , 0.0154889 , -0.0532398 ) +colvars: ( 0.231228 , 0.0271684 , 0.00786386 ) +colvars: ( 0.217163 , -0.0444977 , -0.0934235 ) +colvars: ( 0.251089 , -0.0470969 , -0.0774078 ) +colvars: ( 0.291001 , -0.129314 , -0.161561 ) +colvars: ( 0.247969 , -0.182252 , -0.255044 ) +colvars: ( 0.403886 , -0.143552 , -0.115542 ) +colvars: ( 0.479923 , -0.218021 , -0.16896 ) +colvars: ( 0.608347 , -0.219743 , -0.0977721 ) +colvars: ( 0.434223 , -0.223233 , -0.201871 ) +colvars: ( 0.439755 , -0.290733 , -0.286533 ) +colvars: ( 0.386884 , -0.151207 , -0.135224 ) +colvars: ( 0.334356 , -0.145801 , -0.158223 ) +colvars: ( 0.318543 , -0.0602908 , -0.0560066 ) +colvars: ( 0.213679 , -0.155319 , -0.239607 ) +colvars: ( 0.190115 , -0.19735 , -0.307768 ) +colvars: ( 0.0158941 , -0.201365 , -0.412605 ) +colvars: ( -0.0731018 , -0.219605 , -0.487222 ) +colvars: ( 0.113762 , -0.249894 , -0.419789 ) +colvars: ( 0.133251 , -0.115341 , -0.233577 ) +colvars: ( 0.0164282 , -0.120429 , -0.306993 ) +colvars: ( -0.0708842 , -0.0409186 , -0.253463 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.94669 , 0.5115 , 1.38241 ) +colvars: ( 4.24179 , 0.438611 , 1.18542 ) +colvars: ( 4.24179 , 0.438611 , 1.18542 ) +colvars: ( 5.65019 , 0.584243 , 1.57901 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.610093 , -0.0809758 , -0.355505 ) +colvars: ( -0.549561 , -0.164729 , -0.321991 ) +colvars: ( -0.497273 , -0.142169 , -0.26208 ) +colvars: ( -0.513053 , -0.19252 , -0.294366 ) +colvars: ( -0.503349 , -0.132731 , -0.265108 ) +colvars: ( -0.490767 , -0.285863 , -0.302419 ) +colvars: ( -0.460956 , -0.326717 , -0.285785 ) +colvars: ( -0.441466 , -0.435584 , -0.301713 ) +colvars: ( -0.397727 , -0.290586 , -0.210451 ) +colvars: ( -0.394521 , -0.264911 , -0.198853 ) +colvars: ( -0.346578 , -0.284658 , -0.15711 ) +colvars: ( -0.285542 , -0.246986 , -0.0834765 ) +colvars: ( -0.235025 , -0.261927 , -0.0375793 ) +colvars: ( -0.30335 , -0.142316 , -0.0672275 ) +colvars: ( -0.272814 , -0.112497 , -0.0268108 ) +colvars: ( -0.355505 , -0.084257 , -0.100705 ) +colvars: ( -0.380491 , 0.015375 , -0.0933141 ) +colvars: ( -0.427904 , 0.0635458 , -0.125252 ) +colvars: ( -0.420107 , 0.0304586 , -0.128209 ) +colvars: ( -0.408723 , 0.0881304 , -0.0979538 ) +colvars: ( -0.466071 , -0.0245699 , -0.192357 ) +colvars: ( -0.50265 , -0.026206 , -0.229653 ) +colvars: ( -0.554097 , -0.0927967 , -0.303084 ) +colvars: ( -0.45305 , -0.0564996 , -0.189687 ) +colvars: ( -0.460644 , -0.0117879 , -0.182732 ) +colvars: ( -0.399208 , -0.131731 , -0.160116 ) +colvars: ( -0.343772 , -0.163309 , -0.114702 ) +colvars: ( -0.29446 , -0.254664 , -0.0949447 ) +colvars: ( -0.301238 , -0.0892146 , -0.0477825 ) +colvars: ( -0.289482 , -0.0702872 , -0.0297926 ) +colvars: ( -0.278542 , -0.043561 , -0.0100782 ) +colvars: ( -0.241552 , 0.0324615 , 0.0518986 ) +colvars: ( -0.217259 , 0.0593593 , 0.0850894 ) +colvars: ( -0.28484 , 0.120367 , 0.0370699 ) +colvars: ( -0.258544 , 0.162852 , 0.077359 ) +colvars: ( -0.353167 , 0.148665 , -0.0223693 ) +colvars: ( -0.401417 , 0.225832 , -0.0456881 ) +colvars: ( -0.470928 , 0.248494 , -0.108157 ) +colvars: ( -0.415921 , 0.205633 , -0.066855 ) +colvars: ( -0.420431 , 0.26735 , -0.0512539 ) +colvars: ( -0.422999 , 0.117721 , -0.102648 ) +colvars: ( -0.433079 , 0.0870524 , -0.122784 ) +colvars: ( -0.456762 , -0.00776047 , -0.177517 ) +colvars: ( -0.367895 , 0.0758405 , -0.0609292 ) +colvars: ( -0.372538 , 0.102522 , -0.056891 ) +colvars: ( -0.206039 , 0.109651 , 0.112772 ) +colvars: ( -0.157716 , 0.111714 , 0.162012 ) +colvars: ( -0.229616 , 0.182991 , 0.113002 ) +colvars: ( -0.305229 , 0.0347197 , -0.0113617 ) +colvars: ( -0.239829 , 0.0211296 , 0.0499341 ) +colvars: ( -0.186681 , -0.0630155 , 0.0758994 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 35. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 35. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atoms_new_colvar_forces = { ( -4.67310333701294e+00 , -3.96032869940031e-01 , -1.13675305028486e+00 ), ( -4.02479957028831e+00 , -3.37467689934347e-01 , -8.82882424665855e-01 ), ( -4.09745376704392e+00 , -3.65449000257380e-01 , -9.17919437563292e-01 ), ( -5.50774836181518e+00 , -5.17354476923141e-01 , -1.37484342627038e+00 ), ( 2.53030350518999e-01 , 1.17227596444910e-01 , 3.44729588176145e-01 ), ( 5.02885491171662e+00 , 5.67136221560684e-01 , 1.69220810896820e+00 ), ( 4.24917203563580e+00 , 4.66309522141449e-01 , 1.46885282471950e+00 ), ( -4.80242524581079e-02 , 1.45781511894730e-02 , 3.49262293185711e-01 ), ( 4.23222393718410e+00 , 4.57991206770844e-01 , 1.44051137186065e+00 ), ( 5.61006104746842e+00 , 5.87667202087456e-01 , 1.77222956826844e+00 ), ( 1.23723178987559e-02 , 3.07748147024519e-02 , 2.98846552446167e-01 ), ( 3.42739432270961e-03 , 2.57670842615945e-02 , 2.76935566089332e-01 ), ( 2.68723556617763e-02 , 3.98470279859051e-02 , 3.45113093705503e-01 ), ( 4.66848876722257e-02 , 3.39715386165191e-02 , 2.02586559466735e-01 ), ( 1.98368929854562e-02 , 2.04489747721448e-02 , 1.53802157009476e-01 ), ( 1.14594104233756e-01 , 5.62005173865854e-02 , 1.91139632044393e-01 ), ( 1.60579043884203e-01 , 6.57980516184638e-02 , 1.21964372100301e-01 ), ( 2.39742772996248e-01 , 9.42030829912775e-02 , 1.36681939673041e-01 ), ( 1.29910816783726e-01 , 4.89680709008115e-02 , 5.06622184299092e-02 ), ( 1.25913455107463e-01 , 4.20414027096970e-02 , -1.19268204007757e-02 ), ( 1.04847609558364e-01 , 4.12160899635881e-02 , 5.99771987505697e-02 ), ( 6.73410827361106e-02 , 2.31157352696927e-02 , 7.28103622259585e-04 ), ( 5.20485563198561e-02 , 2.05994314268606e-02 , 3.13379855807844e-02 ), ( -4.55297079334849e-03 , -3.71326528800056e-03 , -2.42634388459483e-02 ), ( -1.85767713735709e-02 , -1.46529696763599e-02 , -9.33942113425376e-02 ), ( -5.06199247262318e-02 , -1.44803594209622e-02 , 3.20582915336324e-02 ), ( -1.16944090443793e-01 , -3.84542482717961e-02 , 1.77474215944577e-02 ), ( -1.57330263863535e-01 , -4.53155236639219e-02 , 9.61537190643975e-02 ), ( -1.02339422117264e-01 , -3.73659870840615e-02 , -2.62913984055313e-02 ), ( -1.38544996413361e-01 , -5.47982872395032e-02 , -8.30324292047760e-02 ), ( -4.73143735272678e-02 , -1.63925143830818e-02 , -2.21433014419287e-03 ), ( -2.43891322746087e-02 , -1.20361919765720e-02 , -4.15249114609246e-02 ), ( 3.38301237189134e-02 , 1.22623486766634e-02 , 7.68164970826732e-03 ), ( 6.16028199457325e-03 , -8.94702602556456e-03 , -1.24491135655574e-01 ), ( -1.05750968292833e-02 , -1.93995854997111e-02 , -1.77684834745378e-01 ), ( 5.07185958852135e-02 , 5.11358691736646e-03 , -1.37911719580562e-01 ), ( 7.85062642577156e-02 , 7.81065713001006e-03 , -2.14648055937921e-01 ), ( 1.37418630195967e-01 , 2.87509036442712e-02 , -2.05928610860533e-01 ), ( 1.83014219457107e-02 , -1.76002080764069e-02 , -2.68726426506252e-01 ), ( 1.93237985701823e-02 , -2.33833163173352e-02 , -3.37786932931459e-01 ), ( -3.61144502819910e-02 , -3.34868527864934e-02 , -2.37872090743582e-01 ), ( -9.87224474023593e-02 , -5.87484647035892e-02 , -2.81006968561271e-01 ), ( -1.38218723413092e-01 , -6.80512651421760e-02 , -2.33523157650282e-01 ), ( -1.54216600811588e-01 , -7.94786656696858e-02 , -3.00536569962526e-01 ), ( -1.82423321499678e-01 , -9.48284207823263e-02 , -3.64658632862215e-01 ), ( -1.90144766825209e-01 , -9.17144630820363e-02 , -2.99832436309255e-01 ), ( -2.30818052273284e-01 , -1.07890787533157e-01 , -3.25210159533535e-01 ), ( -1.15854697122805e-01 , -6.69022906216085e-02 , -3.06786410634412e-01 ), ( -1.71978000601565e-01 , -8.06209422725339e-02 , -2.44938506930591e-01 ), ( -2.23400608647969e-01 , -9.92994026605735e-02 , -2.57058381513554e-01 ), ( -2.57564689392599e-01 , -1.03934143936365e-01 , -1.77563306489887e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 35, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 36 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 36, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 36, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 36, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 36, atoms_positions[size = 51] = { ( 8.17518917512548e+00 , 4.20932162402850e-02 , -6.99380683784479e-01 ), ( 6.81460123882792e+00 , -6.21522171600354e-01 , -5.09578424489461e-01 ), ( 6.06410997214541e+00 , -3.26043161463894e-01 , 8.14673069718519e-01 ), ( 4.88701023537668e+00 , -1.53027098069873e-01 , 7.67860023067761e-01 ), ( 6.99824440044699e+00 , -2.09382931386667e+00 , -8.27386655102873e-01 ), ( 6.78317908220918e+00 , -3.14047143732065e-01 , 1.96123951362137e+00 ), ( 6.07931470397312e+00 , -2.40626383838944e-01 , 3.24924024298311e+00 ), ( 7.15447925384046e+00 , -3.57234629211548e-01 , 4.41791319142681e+00 ), ( 5.30111987545515e+00 , 1.06423224442739e+00 , 3.36107596992258e+00 ), ( 4.19372091455259e+00 , 1.00359783505039e+00 , 3.84425956338652e+00 ), ( 5.85542179024010e+00 , 2.25412648552387e+00 , 2.95903112006657e+00 ), ( 5.12739809162237e+00 , 3.51940370590129e+00 , 2.85564495005150e+00 ), ( 6.26956012748138e+00 , 4.43421892228316e+00 , 2.28426989991293e+00 ), ( 3.86090195107428e+00 , 3.62051193243425e+00 , 2.00519708133362e+00 ), ( 2.84895138029515e+00 , 4.15738956160830e+00 , 2.41208938018834e+00 ), ( 3.89983954776634e+00 , 3.14513750676237e+00 , 7.79862184348236e-01 ), ( 2.75890327575505e+00 , 3.13290364879249e+00 , -7.48869054177583e-02 ), ( 3.14432045991482e+00 , 2.65919342218048e+00 , -1.52389762352200e+00 ), ( 1.61351123419885e+00 , 2.27114458901352e+00 , 4.45361991052464e-01 ), ( 4.31276139932799e-01 , 2.61317351245067e+00 , 4.25357566582053e-01 ), ( 2.02555983656296e+00 , 1.11000187885621e+00 , 1.04250449293346e+00 ), ( 1.29315621293675e+00 , 1.65377976174572e-01 , 1.66293187119804e+00 ), ( 2.09744766219105e+00 , -1.09363106718668e+00 , 2.03181238049657e+00 ), ( 5.70789693138863e-01 , 6.22350067753368e-01 , 2.93369174430324e+00 ), ( -6.07013237367369e-01 , 3.58467436784136e-01 , 3.20866962649618e+00 ), ( 1.28968641523697e+00 , 1.43025310862581e+00 , 3.78401468528374e+00 ), ( 9.13717777439262e-01 , 1.98562890454697e+00 , 5.05496771534087e+00 ), ( 2.03869413228311e+00 , 2.77793948732377e+00 , 5.72600455843582e+00 ), ( -3.57624002886876e-01 , 2.88949728773538e+00 , 4.92106557794947e+00 ), ( -1.11841225104512e+00 , 3.07152796678649e+00 , 5.89739292844448e+00 ), ( -5.21592068985012e-01 , 3.47895078341291e+00 , 3.72619207610853e+00 ), ( -1.45136143851699e+00 , 4.47658226302127e+00 , 3.41381303059645e+00 ), ( -7.74683171499790e-01 , 5.47233397985892e+00 , 2.48794766162271e+00 ), ( -2.75456271630087e+00 , 3.92758039691698e+00 , 2.72047005088196e+00 ), ( -3.79306389594734e+00 , 4.59966286284149e+00 , 2.80771741377871e+00 ), ( -2.71251020359701e+00 , 2.65077831472665e+00 , 2.34696276135925e+00 ), ( -3.82151457473994e+00 , 1.79539277372270e+00 , 1.99101247269911e+00 ), ( -3.34203536663097e+00 , 9.02876114262936e-01 , 7.66831669818640e-01 ), ( -4.27006467355301e+00 , 1.02049005288999e+00 , 3.24090970652971e+00 ), ( -5.42299517375100e+00 , 7.19851795765019e-01 , 3.35667038536792e+00 ), ( -3.35977181021253e+00 , 7.13481608601062e-01 , 4.16735503723690e+00 ), ( -3.66451828935214e+00 , 6.29393383345861e-02 , 5.45642322517551e+00 ), ( -2.33657262210542e+00 , -2.76730996101650e-01 , 6.12827789323743e+00 ), ( -4.49170751016758e+00 , 9.63528712671481e-01 , 6.42056484459742e+00 ), ( -5.35496151743373e+00 , 5.33639852320449e-01 , 7.17372801345931e+00 ), ( -6.28937224752982e+00 , 3.60062919018572e+00 , 6.78014779680789e+00 ), ( -7.04616889789833e+00 , 4.29854293934481e+00 , 7.51767903209868e+00 ), ( -6.60948320503296e+00 , 3.17316282929707e+00 , 5.55884665002323e+00 ), ( -4.11993287885638e+00 , 2.25188914754568e+00 , 6.42101339223344e+00 ), ( -4.80343157933424e+00 , 3.27792611513744e+00 , 7.19827113426333e+00 ), ( -4.00755025383473e+00 , 4.62458441110233e+00 , 7.28178260714863e+00 ) } +colvars: Step 36, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_ids[size = 0] = +colvars: Step 36, atom_groups_refcount[size = 0] = +colvars: Step 36, atom_groups_masses[size = 0] = +colvars: Step 36, atom_groups_charges[size = 0] = +colvars: Step 36, atom_groups_coms[size = 0] = +colvars: Step 36, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 36, volmaps_ids[size = 0] = +colvars: Step 36, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 36 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.85104418391494e-01 , -1.80726295704393e-02 , 9.58326066990801e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.85104418391494e-01 , -1.80726295704393e-02 , 9.58326066990801e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.2201 , 2.31325 , -15.2629 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.2201 , 2.31325 , -15.2629 ) to colvar "one". +colvars: Adding total bias energy: 43.718 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.2201 , 2.31325 , -15.2629 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.95047 , -0.508986 , -1.37354 ) +colvars: ( -4.24503 , -0.436455 , -1.17781 ) +colvars: ( -4.24503 , -0.436455 , -1.17781 ) +colvars: ( -5.6545 , -0.581371 , -1.56888 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.882922 , 0.196576 , 0.599212 ) +colvars: ( 0.766003 , 0.265841 , 0.622549 ) +colvars: ( 0.749716 , 0.259448 , 0.604956 ) +colvars: ( 0.657083 , 0.26552 , 0.560031 ) +colvars: ( 0.645508 , 0.199519 , 0.467674 ) +colvars: ( 0.572806 , 0.341148 , 0.610248 ) +colvars: ( 0.468455 , 0.353916 , 0.567341 ) +colvars: ( 0.393719 , 0.449467 , 0.648885 ) +colvars: ( 0.388403 , 0.309488 , 0.463973 ) +colvars: ( 0.354732 , 0.267841 , 0.390662 ) +colvars: ( 0.359189 , 0.315 , 0.454478 ) +colvars: ( 0.289308 , 0.272355 , 0.359225 ) +colvars: ( 0.262225 , 0.301399 , 0.381522 ) +colvars: ( 0.35025 , 0.176062 , 0.268853 ) +colvars: ( 0.292982 , 0.132718 , 0.179883 ) +colvars: ( 0.470073 , 0.140387 , 0.290816 ) +colvars: ( 0.540903 , 0.0505233 , 0.214436 ) +colvars: ( 0.667212 , 0.0309185 , 0.260978 ) +colvars: ( 0.549896 , 0.0185767 , 0.178054 ) +colvars: ( 0.534549 , -0.0459643 , 0.085443 ) +colvars: ( 0.570807 , 0.0657522 , 0.251273 ) +colvars: ( 0.569944 , 0.0492273 , 0.22931 ) +colvars: ( 0.606072 , 0.113202 , 0.333033 ) +colvars: ( 0.448704 , 0.052561 , 0.164517 ) +colvars: ( 0.442313 , -0.00306365 , 0.0885969 ) +colvars: ( 0.348973 , 0.116884 , 0.191233 ) +colvars: ( 0.227457 , 0.124365 , 0.13167 ) +colvars: ( 0.137913 , 0.208707 , 0.190207 ) +colvars: ( 0.199548 , 0.0514644 , 0.0210352 ) +colvars: ( 0.151705 , 0.0150739 , -0.053526 ) +colvars: ( 0.231754 , 0.0269159 , 0.00750072 ) +colvars: ( 0.21768 , -0.0446308 , -0.0934876 ) +colvars: ( 0.251472 , -0.0471137 , -0.0774467 ) +colvars: ( 0.291397 , -0.129313 , -0.161489 ) +colvars: ( 0.248449 , -0.182227 , -0.254729 ) +colvars: ( 0.404084 , -0.143464 , -0.115628 ) +colvars: ( 0.480002 , -0.217816 , -0.168952 ) +colvars: ( 0.608185 , -0.219437 , -0.0979746 ) +colvars: ( 0.434452 , -0.223139 , -0.201839 ) +colvars: ( 0.439987 , -0.290572 , -0.286301 ) +colvars: ( 0.387245 , -0.151288 , -0.135394 ) +colvars: ( 0.334877 , -0.146006 , -0.158389 ) +colvars: ( 0.319132 , -0.0606583 , -0.0564695 ) +colvars: ( 0.214428 , -0.155609 , -0.239541 ) +colvars: ( 0.190943 , -0.197653 , -0.30756 ) +colvars: ( 0.0169329 , -0.201652 , -0.411967 ) +colvars: ( -0.0718932 , -0.219942 , -0.486378 ) +colvars: ( 0.114576 , -0.249996 , -0.419112 ) +colvars: ( 0.134113 , -0.115693 , -0.233467 ) +colvars: ( 0.0175077 , -0.120863 , -0.306667 ) +colvars: ( -0.0696627 , -0.0414862 , -0.25323 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.95047 , 0.508986 , 1.37354 ) +colvars: ( 4.24503 , 0.436455 , 1.17781 ) +colvars: ( 4.24503 , 0.436455 , 1.17781 ) +colvars: ( 5.6545 , 0.581371 , 1.56888 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.60926 , -0.0810102 , -0.353452 ) +colvars: ( -0.548959 , -0.16471 , -0.319797 ) +colvars: ( -0.496515 , -0.142181 , -0.259874 ) +colvars: ( -0.512751 , -0.192439 , -0.292345 ) +colvars: ( -0.503054 , -0.132652 , -0.263378 ) +colvars: ( -0.490725 , -0.285723 , -0.300217 ) +colvars: ( -0.461223 , -0.326511 , -0.2837 ) +colvars: ( -0.441965 , -0.435324 , -0.299346 ) +colvars: ( -0.398058 , -0.290369 , -0.208629 ) +colvars: ( -0.39498 , -0.264671 , -0.197273 ) +colvars: ( -0.346812 , -0.284459 , -0.155254 ) +colvars: ( -0.285806 , -0.246782 , -0.0818589 ) +colvars: ( -0.235185 , -0.261741 , -0.0358225 ) +colvars: ( -0.303433 , -0.142156 , -0.0659207 ) +colvars: ( -0.273007 , -0.112317 , -0.0257631 ) +colvars: ( -0.355309 , -0.0841582 , -0.0993785 ) +colvars: ( -0.380105 , 0.015428 , -0.0922609 ) +colvars: ( -0.427192 , 0.0635293 , -0.12409 ) +colvars: ( -0.419853 , 0.0305356 , -0.127329 ) +colvars: ( -0.408485 , 0.0882064 , -0.0973644 ) +colvars: ( -0.465928 , -0.0244682 , -0.191297 ) +colvars: ( -0.502668 , -0.0260733 , -0.228717 ) +colvars: ( -0.554185 , -0.0926464 , -0.301873 ) +colvars: ( -0.453364 , -0.0563048 , -0.188915 ) +colvars: ( -0.461016 , -0.0115849 , -0.182221 ) +colvars: ( -0.39971 , -0.131492 , -0.159199 ) +colvars: ( -0.344545 , -0.163013 , -0.113923 ) +colvars: ( -0.295398 , -0.254326 , -0.0939201 ) +colvars: ( -0.301945 , -0.0889354 , -0.0473117 ) +colvars: ( -0.290339 , -0.0699795 , -0.0295581 ) +colvars: ( -0.279015 , -0.0433307 , -0.00961442 ) +colvars: ( -0.241925 , 0.0326671 , 0.0520805 ) +colvars: ( -0.217385 , 0.0595147 , 0.0853637 ) +colvars: ( -0.285089 , 0.12054 , 0.0369808 ) +colvars: ( -0.258859 , 0.163036 , 0.0769935 ) +colvars: ( -0.353236 , 0.148799 , -0.0223841 ) +colvars: ( -0.401374 , 0.225937 , -0.0459323 ) +colvars: ( -0.470646 , 0.248548 , -0.108243 ) +colvars: ( -0.416132 , 0.205789 , -0.0672352 ) +colvars: ( -0.420638 , 0.2675 , -0.0519165 ) +colvars: ( -0.423439 , 0.117928 , -0.102828 ) +colvars: ( -0.433783 , 0.0873143 , -0.123063 ) +colvars: ( -0.457634 , -0.00745866 , -0.177497 ) +colvars: ( -0.368824 , 0.0761496 , -0.0614039 ) +colvars: ( -0.373585 , 0.102852 , -0.0575993 ) +colvars: ( -0.2071 , 0.109988 , 0.111925 ) +colvars: ( -0.158943 , 0.112085 , 0.160972 ) +colvars: ( -0.230369 , 0.183261 , 0.112115 ) +colvars: ( -0.306226 , 0.035047 , -0.0117425 ) +colvars: ( -0.241034 , 0.0215009 , 0.0493846 ) +colvars: ( -0.188024 , -0.0626092 , 0.0755846 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 36. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 36. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atoms_new_colvar_forces = { ( -4.67680981299801e+00 , -3.93419916334486e-01 , -1.12778318560016e+00 ), ( -4.02798514651675e+00 , -3.35324300766826e-01 , -8.75060941564380e-01 ), ( -4.10069782795079e+00 , -3.63374047640199e-01 , -9.10126025505338e-01 ), ( -5.51204759434347e+00 , -5.14503949669059e-01 , -1.36458418189624e+00 ), ( 2.53201889104779e-01 , 1.17266526636215e-01 , 3.45082379454502e-01 ), ( 5.03255445975864e+00 , 5.64411751762652e-01 , 1.68357415874436e+00 ), ( 4.25226117945735e+00 , 4.63859699208330e-01 , 1.46145420076683e+00 ), ( -4.82458599130015e-02 , 1.41435778571937e-02 , 3.49539244433002e-01 ), ( 4.23537483968622e+00 , 4.55574827155590e-01 , 1.43315658751557e+00 ), ( 5.61425492030036e+00 , 5.84541952670831e-01 , 1.76226904624533e+00 ), ( 1.23775269804394e-02 , 3.05404514231495e-02 , 2.99224754699200e-01 ), ( 3.50277966765278e-03 , 2.55724155068570e-02 , 2.77366022666686e-01 ), ( 2.70390582350280e-02 , 3.96583996008955e-02 , 3.45699491308639e-01 ), ( 4.68162565367057e-02 , 3.39060756844611e-02 , 2.02932223767680e-01 ), ( 1.99751033407011e-02 , 2.04003788145163e-02 , 1.54120009683309e-01 ), ( 1.14763828025389e-01 , 5.62287821693943e-02 , 1.91437924425326e-01 ), ( 1.60798654370062e-01 , 6.59512912585725e-02 , 1.22175503058931e-01 ), ( 2.40019999516228e-01 , 9.44477896663818e-02 , 1.36887169004425e-01 ), ( 1.30042805383875e-01 , 4.91122799905491e-02 , 5.07247209508654e-02 ), ( 1.26064754385581e-01 , 4.22421186779151e-02 , -1.19213659144137e-02 ), ( 1.04878753326529e-01 , 4.12839777406290e-02 , 5.99758822557784e-02 ), ( 6.72759970684957e-02 , 2.31540224131994e-02 , 5.92195849687366e-04 ), ( 5.18869509811863e-02 , 2.05552565174021e-02 , 3.11598614291391e-02 ), ( -4.65982110295154e-03 , -3.74379495012654e-03 , -2.43982955194266e-02 ), ( -1.87037042917493e-02 , -1.46485608145348e-02 , -9.36239450211399e-02 ), ( -5.07366490487596e-02 , -1.46079351699329e-02 , 3.20346436320663e-02 ), ( -1.17088071469363e-01 , -3.86477185652305e-02 , 1.77474629975729e-02 ), ( -1.57485001610508e-01 , -4.56191623608826e-02 , 9.62866167913694e-02 ), ( -1.02397424798874e-01 , -3.74710527330217e-02 , -2.62764450692238e-02 ), ( -1.38634018126673e-01 , -5.49055469670486e-02 , -8.30840938867525e-02 ), ( -4.72614037490586e-02 , -1.64148658586030e-02 , -2.11370006647546e-03 ), ( -2.42454000906378e-02 , -1.19637250350060e-02 , -4.14071703745038e-02 ), ( 3.40876523484299e-02 , 1.24009986279386e-02 , 7.91702180405973e-03 ), ( 6.30824401740210e-03 , -8.77320775895118e-03 , -1.24508403625052e-01 ), ( -1.04094839494642e-02 , -1.91904853948852e-02 , -1.77735294023034e-01 ), ( 5.08478268221022e-02 , 5.33484317368221e-03 , -1.38012201110185e-01 ), ( 7.86278744573657e-02 , 8.12020109017481e-03 , -2.14884607329695e-01 ), ( 1.37538442333592e-01 , 2.91110561140189e-02 , -2.06217724862702e-01 ), ( 1.83198662480812e-02 , -1.73501684897990e-02 , -2.69074034768406e-01 ), ( 1.93494883849533e-02 , -2.30715995812671e-02 , -3.38217460007524e-01 ), ( -3.61947045778886e-02 , -3.33593697512488e-02 , -2.38222634245323e-01 ), ( -9.89056009258076e-02 , -5.86918788434534e-02 , -2.81451636606534e-01 ), ( -1.38502138712054e-01 , -6.81169108964202e-02 , -2.33966571218231e-01 ), ( -1.54396547496042e-01 , -7.94596715048706e-02 , -3.00944805405404e-01 ), ( -1.82642254530010e-01 , -9.48009548315469e-02 , -3.65159513066281e-01 ), ( -1.90167387725943e-01 , -9.16637867674694e-02 , -3.00042470677464e-01 ), ( -2.30835743628847e-01 , -1.07857331891220e-01 , -3.25405165291124e-01 ), ( -1.15792229930688e-01 , -6.67350667777830e-02 , -3.06997356751722e-01 ), ( -1.72112286169905e-01 , -8.06461958226265e-02 , -2.45209961894309e-01 ), ( -2.23526347308519e-01 , -9.93620573571558e-02 , -2.57282706431221e-01 ), ( -2.57686689771386e-01 , -1.04095411226895e-01 , -1.77645223752059e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 36, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 37 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 37, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 37, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 37, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 37, atoms_positions[size = 51] = { ( 8.16221384686843e+00 , 4.13014786872230e-02 , -6.95869465127482e-01 ), ( 6.80958518252857e+00 , -6.24035047837337e-01 , -5.04964972430719e-01 ), ( 6.06079494684484e+00 , -3.22545667083951e-01 , 8.11981869964738e-01 ), ( 4.87946608224906e+00 , -1.53112496283750e-01 , 7.71878512263832e-01 ), ( 7.00078352714887e+00 , -2.09877085823173e+00 , -8.19840147577199e-01 ), ( 6.77720007689676e+00 , -3.15926781875816e-01 , 1.95915457666183e+00 ), ( 6.08220694026630e+00 , -2.41846162620031e-01 , 3.26210281971864e+00 ), ( 7.15352338552264e+00 , -3.60595148601759e-01 , 4.42296851794176e+00 ), ( 5.29942667186752e+00 , 1.06442318130758e+00 , 3.36086393669537e+00 ), ( 4.19382876288619e+00 , 1.00442170620445e+00 , 3.85558490510857e+00 ), ( 5.85440905365025e+00 , 2.25568752711447e+00 , 2.95658460900511e+00 ), ( 5.12743496896675e+00 , 3.51468625382453e+00 , 2.85144103841877e+00 ), ( 6.26310532944841e+00 , 4.42841268469618e+00 , 2.28417907685263e+00 ), ( 3.86243396392037e+00 , 3.61735898954025e+00 , 2.00273107308675e+00 ), ( 2.85429970161286e+00 , 4.15533815267892e+00 , 2.40915508884607e+00 ), ( 3.90028805200589e+00 , 3.13690048343511e+00 , 7.86208055968976e-01 ), ( 2.75505920966684e+00 , 3.14533620009754e+00 , -7.89119396031499e-02 ), ( 3.14765550464798e+00 , 2.66162645196632e+00 , -1.51791246315896e+00 ), ( 1.62884174060956e+00 , 2.28082042718727e+00 , 4.52408139830500e-01 ), ( 4.33947229136713e-01 , 2.61241076171236e+00 , 4.19358483211939e-01 ), ( 2.02146154905566e+00 , 1.10933944749563e+00 , 1.03747347142710e+00 ), ( 1.29905019023886e+00 , 1.66973494111863e-01 , 1.66318925038576e+00 ), ( 2.09891934597921e+00 , -1.09336629375871e+00 , 2.02834132117978e+00 ), ( 5.70021758784393e-01 , 6.26558661209594e-01 , 2.93223567614384e+00 ), ( -6.10263237510015e-01 , 3.58535047388056e-01 , 3.21254611976693e+00 ), ( 1.29176679194291e+00 , 1.43447739519174e+00 , 3.78672618261532e+00 ), ( 9.17953237815866e-01 , 1.98834562347871e+00 , 5.05962679594164e+00 ), ( 2.03247948558527e+00 , 2.78125232226779e+00 , 5.72643872335939e+00 ), ( -3.55771138815002e-01 , 2.88740730470469e+00 , 4.91780379415905e+00 ), ( -1.11856643667602e+00 , 3.07179125326318e+00 , 5.89837009466563e+00 ), ( -5.15786722327386e-01 , 3.47102828849230e+00 , 3.71750773797147e+00 ), ( -1.45388225734082e+00 , 4.47784206387289e+00 , 3.41049560690259e+00 ), ( -7.78199021904833e-01 , 5.47992384229274e+00 , 2.48864337010154e+00 ), ( -2.75562363679492e+00 , 3.92509055318619e+00 , 2.71583357918873e+00 ), ( -3.79047210252953e+00 , 4.60438687176698e+00 , 2.80527800043448e+00 ), ( -2.71480438238707e+00 , 2.65396324850562e+00 , 2.34403103673808e+00 ), ( -3.82393508277507e+00 , 1.78790832685572e+00 , 1.98706744895440e+00 ), ( -3.33895603665298e+00 , 9.09392570698246e-01 , 7.61244875945969e-01 ), ( -4.27422515739842e+00 , 1.01823156606361e+00 , 3.23638416754381e+00 ), ( -5.41619906673795e+00 , 7.13953851763116e-01 , 3.36061517707978e+00 ), ( -3.35646940904617e+00 , 7.08597569109325e-01 , 4.17089315247876e+00 ), ( -3.66414071394427e+00 , 5.98366873055360e-02 , 5.44865864809506e+00 ), ( -2.32771899477028e+00 , -2.69418780756333e-01 , 6.13110451020095e+00 ), ( -4.48955885516758e+00 , 9.72684049461152e-01 , 6.42006993069601e+00 ), ( -5.35494548616549e+00 , 5.26273943951513e-01 , 7.16926044539897e+00 ), ( -6.28289914525333e+00 , 3.59857504559191e+00 , 6.78920310227812e+00 ), ( -7.05179379342705e+00 , 4.29651912581031e+00 , 7.51564897131421e+00 ), ( -6.60857004327578e+00 , 3.17559654682944e+00 , 5.56164275402900e+00 ), ( -4.12440330771683e+00 , 2.25160864170603e+00 , 6.42412050527497e+00 ), ( -4.79989001669577e+00 , 3.27364371953981e+00 , 7.18919260728866e+00 ), ( -4.00836098535606e+00 , 4.63532012837581e+00 , 7.28246892452509e+00 ) } +colvars: Step 37, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_ids[size = 0] = +colvars: Step 37, atom_groups_refcount[size = 0] = +colvars: Step 37, atom_groups_masses[size = 0] = +colvars: Step 37, atom_groups_charges[size = 0] = +colvars: Step 37, atom_groups_coms[size = 0] = +colvars: Step 37, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 37, volmaps_ids[size = 0] = +colvars: Step 37, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 37 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.82901971968914e-01 , -1.84568715824041e-02 , 9.58971229050950e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.82901971968914e-01 , -1.84568715824041e-02 , 9.58971229050950e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.176 , 2.32094 , -15.2758 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.176 , 2.32094 , -15.2758 ) to colvar "one". +colvars: Adding total bias energy: 43.6285 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.176 , 2.32094 , -15.2758 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.95456 , -0.506389 , -1.36376 ) +colvars: ( -4.24853 , -0.434229 , -1.16943 ) +colvars: ( -4.24853 , -0.434229 , -1.16943 ) +colvars: ( -5.65917 , -0.578405 , -1.55771 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.882121 , 0.196743 , 0.597088 ) +colvars: ( 0.765428 , 0.265834 , 0.620398 ) +colvars: ( 0.749091 , 0.25953 , 0.602934 ) +colvars: ( 0.656767 , 0.265371 , 0.558038 ) +colvars: ( 0.645219 , 0.199433 , 0.465931 ) +colvars: ( 0.57269 , 0.340802 , 0.60811 ) +colvars: ( 0.468596 , 0.353409 , 0.565301 ) +colvars: ( 0.394033 , 0.448757 , 0.646619 ) +colvars: ( 0.388672 , 0.309002 , 0.462263 ) +colvars: ( 0.355103 , 0.267334 , 0.389127 ) +colvars: ( 0.359447 , 0.314561 , 0.452866 ) +colvars: ( 0.289667 , 0.27195 , 0.357924 ) +colvars: ( 0.262563 , 0.301023 , 0.380236 ) +colvars: ( 0.350473 , 0.175838 , 0.267795 ) +colvars: ( 0.293327 , 0.132487 , 0.179074 ) +colvars: ( 0.47004 , 0.140328 , 0.289685 ) +colvars: ( 0.540719 , 0.0506422 , 0.213505 ) +colvars: ( 0.666739 , 0.0312103 , 0.259921 ) +colvars: ( 0.549766 , 0.0186575 , 0.177152 ) +colvars: ( 0.534454 , -0.0458261 , 0.0847927 ) +colvars: ( 0.570694 , 0.0657274 , 0.250112 ) +colvars: ( 0.569906 , 0.0491358 , 0.22814 ) +colvars: ( 0.606014 , 0.113007 , 0.331525 ) +colvars: ( 0.448938 , 0.0523278 , 0.163526 ) +colvars: ( 0.442589 , -0.00327204 , 0.0877863 ) +colvars: ( 0.349394 , 0.116503 , 0.190205 ) +colvars: ( 0.228138 , 0.12385 , 0.130818 ) +colvars: ( 0.138757 , 0.208035 , 0.189233 ) +colvars: ( 0.200243 , 0.0510586 , 0.0205292 ) +colvars: ( 0.152529 , 0.014632 , -0.0538477 ) +colvars: ( 0.232313 , 0.0266506 , 0.00709116 ) +colvars: ( 0.218221 , -0.0447724 , -0.0935773 ) +colvars: ( 0.251866 , -0.0471296 , -0.077513 ) +colvars: ( 0.291813 , -0.129316 , -0.161432 ) +colvars: ( 0.248953 , -0.182208 , -0.254409 ) +colvars: ( 0.404292 , -0.143374 , -0.11574 ) +colvars: ( 0.480085 , -0.217605 , -0.168962 ) +colvars: ( 0.608014 , -0.219115 , -0.0982113 ) +colvars: ( 0.434702 , -0.223048 , -0.201819 ) +colvars: ( 0.44024 , -0.290413 , -0.286065 ) +colvars: ( 0.387639 , -0.15138 , -0.13559 ) +colvars: ( 0.335449 , -0.146233 , -0.158577 ) +colvars: ( 0.319783 , -0.0610538 , -0.0569749 ) +colvars: ( 0.21524 , -0.155929 , -0.239478 ) +colvars: ( 0.191842 , -0.19799 , -0.307344 ) +colvars: ( 0.0180391 , -0.201971 , -0.411294 ) +colvars: ( -0.0706082 , -0.220319 , -0.485481 ) +colvars: ( 0.11544 , -0.25012 , -0.418399 ) +colvars: ( 0.135042 , -0.116077 , -0.23336 ) +colvars: ( 0.018664 , -0.121336 , -0.306328 ) +colvars: ( -0.0683577 , -0.042098 , -0.25299 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.95456 , 0.506389 , 1.36376 ) +colvars: ( 4.24853 , 0.434229 , 1.16943 ) +colvars: ( 4.24853 , 0.434229 , 1.16943 ) +colvars: ( 5.65917 , 0.578405 , 1.55771 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.60836 , -0.0810755 , -0.351197 ) +colvars: ( -0.548311 , -0.164692 , -0.317412 ) +colvars: ( -0.495716 , -0.142208 , -0.257501 ) +colvars: ( -0.512422 , -0.192339 , -0.290148 ) +colvars: ( -0.502733 , -0.132569 , -0.26149 ) +colvars: ( -0.490667 , -0.285531 , -0.297832 ) +colvars: ( -0.461493 , -0.326232 , -0.281443 ) +colvars: ( -0.442477 , -0.434954 , -0.296796 ) +colvars: ( -0.398407 , -0.290084 , -0.206673 ) +colvars: ( -0.395461 , -0.264363 , -0.195569 ) +colvars: ( -0.347071 , -0.284199 , -0.153284 ) +colvars: ( -0.28611 , -0.246525 , -0.0801632 ) +colvars: ( -0.235394 , -0.261503 , -0.0340038 ) +colvars: ( -0.303548 , -0.141975 , -0.0645481 ) +colvars: ( -0.273241 , -0.112119 , -0.0246715 ) +colvars: ( -0.355125 , -0.0840638 , -0.0979711 ) +colvars: ( -0.379718 , 0.0154449 , -0.0911346 ) +colvars: ( -0.426457 , 0.0634514 , -0.12284 ) +colvars: ( -0.419595 , 0.0305793 , -0.126365 ) +colvars: ( -0.408244 , 0.0882359 , -0.0967091 ) +colvars: ( -0.465773 , -0.0243815 , -0.190124 ) +colvars: ( -0.502671 , -0.0259478 , -0.227655 ) +colvars: ( -0.55425 , -0.0924842 , -0.3005 ) +colvars: ( -0.453684 , -0.0560974 , -0.188037 ) +colvars: ( -0.461396 , -0.0113773 , -0.181612 ) +colvars: ( -0.400235 , -0.131215 , -0.158185 ) +colvars: ( -0.345364 , -0.162659 , -0.11307 ) +colvars: ( -0.296397 , -0.253904 , -0.0928257 ) +colvars: ( -0.302705 , -0.0886203 , -0.0468007 ) +colvars: ( -0.291257 , -0.0696336 , -0.0292959 ) +colvars: ( -0.279539 , -0.0430858 , -0.00912572 ) +colvars: ( -0.242353 , 0.0328647 , 0.0522563 ) +colvars: ( -0.217563 , 0.0596447 , 0.0856206 ) +colvars: ( -0.285379 , 0.12068 , 0.0368871 ) +colvars: ( -0.259225 , 0.163179 , 0.076601 ) +colvars: ( -0.353327 , 0.148886 , -0.022377 ) +colvars: ( -0.401339 , 0.225971 , -0.0461488 ) +colvars: ( -0.470349 , 0.248516 , -0.108272 ) +colvars: ( -0.416356 , 0.205891 , -0.0675823 ) +colvars: ( -0.420856 , 0.267582 , -0.0525578 ) +colvars: ( -0.423898 , 0.118113 , -0.102957 ) +colvars: ( -0.434512 , 0.087572 , -0.123284 ) +colvars: ( -0.458533 , -0.00713113 , -0.177392 ) +colvars: ( -0.369801 , 0.0764664 , -0.0618515 ) +colvars: ( -0.374683 , 0.103189 , -0.0582871 ) +colvars: ( -0.208249 , 0.110329 , 0.111024 ) +colvars: ( -0.160272 , 0.112466 , 0.159855 ) +colvars: ( -0.231193 , 0.183504 , 0.111175 ) +colvars: ( -0.307286 , 0.035394 , -0.0121154 ) +colvars: ( -0.242324 , 0.0219036 , 0.0488137 ) +colvars: ( -0.189467 , -0.0621461 , 0.0752416 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 37. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 37. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atoms_new_colvar_forces = { ( -4.68079553249617e+00 , -3.90721895618969e-01 , -1.11787324656340e+00 ), ( -4.03141453603078e+00 , -3.33086813782210e-01 , -8.66442892955978e-01 ), ( -4.10418623448907e+00 , -3.61196511182811e-01 , -9.01538438505066e-01 ), ( -5.51668060541587e+00 , -5.11541154617190e-01 , -1.35327157498399e+00 ), ( 2.53374825165688e-01 , 1.17322169448769e-01 , 3.45433181799156e-01 ), ( 5.03657985327035e+00 , 5.61659960641624e-01 , 1.67404209341983e+00 ), ( 4.25563397348131e+00 , 4.61405922504199e-01 , 1.45328628285756e+00 ), ( -4.84442616610080e-02 , 1.38025975533743e-02 , 3.49823453963319e-01 ), ( 4.23879566335603e+00 , 4.53146327700456e-01 , 1.42501824867508e+00 ), ( 5.61880848900630e+00 , 5.81376086152293e-01 , 1.75127016885759e+00 ), ( 1.23751629209414e-02 , 3.03624050329420e-02 , 2.99582223305569e-01 ), ( 3.55647451650315e-03 , 2.54253041427815e-02 , 2.77761155557903e-01 ), ( 2.71689427313820e-02 , 3.95197786985720e-02 , 3.46232417577520e-01 ), ( 4.69250501267432e-02 , 3.38627285580941e-02 , 2.03246898926615e-01 ), ( 2.00862325737857e-02 , 2.03676767578085e-02 , 1.54402948805392e-01 ), ( 1.14915835889301e-01 , 5.62639135599647e-02 , 1.91714090264702e-01 ), ( 1.61001132407563e-01 , 6.60870744671900e-02 , 1.22370314969212e-01 ), ( 2.40282509037127e-01 , 9.46617001859483e-02 , 1.37081687589387e-01 ), ( 1.30170935491765e-01 , 4.92367151919846e-02 , 5.07868671384857e-02 ), ( 1.26209697484766e-01 , 4.24097939166141e-02 , -1.19163708031666e-02 ), ( 1.04920415505240e-01 , 4.13458390222983e-02 , 5.99880583284731e-02 ), ( 6.72347892241592e-02 , 2.31880262838069e-02 , 4.84986555042671e-04 ), ( 5.17638537920039e-02 , 2.05229437716475e-02 , 3.10240696105379e-02 ), ( -4.74663551212839e-03 , -3.76963808851908e-03 , -2.45108020970518e-02 ), ( -1.88072262373017e-02 , -1.46493220805063e-02 , -9.38253083188769e-02 ), ( -5.08410918623465e-02 , -1.47122946893009e-02 , 3.20204100219570e-02 ), ( -1.17225692763493e-01 , -3.88089109282382e-02 , 1.77481262564441e-02 ), ( -1.57640630657621e-01 , -4.58684192517203e-02 , 9.64070293321571e-02 ), ( -1.02461440260749e-01 , -3.75616505670021e-02 , -2.62715214286438e-02 ), ( -1.38727817224171e-01 , -5.50016507571514e-02 , -8.31436370117906e-02 ), ( -4.72265238926294e-02 , -1.64351362572042e-02 , -2.03456716462021e-03 ), ( -2.41317300224776e-02 , -1.19076615469125e-02 , -4.13209718239030e-02 ), ( 3.43023282685017e-02 , 1.25150853629424e-02 , 8.10765798596971e-03 ), ( 6.43305557384805e-03 , -8.63682620381885e-03 , -1.24544725572984e-01 ), ( -1.02716843777416e-02 , -1.90282633652653e-02 , -1.77808237161421e-01 ), ( 5.09655320331248e-02 , 5.51110593631737e-03 , -1.38116611939811e-01 ), ( 7.87464417376239e-02 , 8.36631309864255e-03 , -2.15111316988457e-01 ), ( 1.37665484322824e-01 , 2.94010824133421e-02 , -2.06483634438232e-01 ), ( 1.83458559865556e-02 , -1.71569406424844e-02 , -2.69400847097267e-01 ), ( 1.93835544705327e-02 , -2.28309663692608e-02 , -3.38623206007411e-01 ), ( -3.62591465777498e-02 , -3.32666481258157e-02 , -2.38547396361860e-01 ), ( -9.90631394023752e-02 , -5.86609636197708e-02 , -2.81861005796358e-01 ), ( -1.38749283366791e-01 , -6.81849563023802e-02 , -2.34367180870072e-01 ), ( -1.54560510038397e-01 , -7.94623831678002e-02 , -3.01329780997028e-01 ), ( -1.82840869088693e-01 , -9.48004587363242e-02 , -3.65630962124531e-01 ), ( -1.90209875224079e-01 , -9.16423897349099e-02 , -3.00269394055042e-01 ), ( -2.30880522584762e-01 , -1.07852628794259e-01 , -3.25625569717512e-01 ), ( -1.15752595115674e-01 , -6.66162568833465e-02 , -3.07224625198104e-01 ), ( -1.72243879691875e-01 , -8.06834379363101e-02 , -2.45475689578199e-01 ), ( -2.23659542413118e-01 , -9.94323139694904e-02 , -2.57514036532548e-01 ), ( -2.57825081966900e-01 , -1.04244057182641e-01 , -1.77748819704570e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 37, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 38 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 38, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 38, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 38, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 38, atoms_positions[size = 51] = { ( 8.14877873702211e+00 , 4.04022721702150e-02 , -6.92577086270675e-01 ), ( 6.80383152526671e+00 , -6.25597810854992e-01 , -4.99771627510369e-01 ), ( 6.05932862659391e+00 , -3.20392500925269e-01 , 8.08487337579745e-01 ), ( 4.87070927794586e+00 , -1.52911259798077e-01 , 7.75927389735424e-01 ), ( 7.00396081156044e+00 , -2.10390864650469e+00 , -8.12611727360559e-01 ), ( 6.77073270899749e+00 , -3.17202239475859e-01 , 1.95721416087662e+00 ), ( 6.08686545431381e+00 , -2.42704371492925e-01 , 3.27386819011241e+00 ), ( 7.15166129400360e+00 , -3.63976099229150e-01 , 4.42806348262264e+00 ), ( 5.29848152657454e+00 , 1.06482932961643e+00 , 3.36150801488537e+00 ), ( 4.19355467261569e+00 , 1.00563379356190e+00 , 3.86689314972318e+00 ), ( 5.85259008782183e+00 , 2.25717099327585e+00 , 2.95413915945799e+00 ), ( 5.12845700669889e+00 , 3.51080158512586e+00 , 2.84751873236696e+00 ), ( 6.25658169578520e+00 , 4.42311314391522e+00 , 2.28353460841378e+00 ), ( 3.86464129015471e+00 , 3.61424732694166e+00 , 2.00074863629636e+00 ), ( 2.85931974231682e+00 , 4.15337731964328e+00 , 2.40657553175952e+00 ), ( 3.90116127535849e+00 , 3.12864077430610e+00 , 7.91981858618513e-01 ), ( 2.75146176774071e+00 , 3.15808893346107e+00 , -8.38524301874596e-02 ), ( 3.15058020779582e+00 , 2.66360425680610e+00 , -1.51187231648151e+00 ), ( 1.64311380419904e+00 , 2.28974777568346e+00 , 4.60145209510769e-01 ), ( 4.37019188271778e-01 , 2.61159587015864e+00 , 4.13388133914335e-01 ), ( 2.01889031571544e+00 , 1.11096194922320e+00 , 1.03081568585815e+00 ), ( 1.30237801467038e+00 , 1.66952552639638e-01 , 1.66483452152124e+00 ), ( 2.10032363952688e+00 , -1.09309550185934e+00 , 2.02445737458888e+00 ), ( 5.69319084217896e-01 , 6.31712977451387e-01 , 2.93204363618353e+00 ), ( -6.13129327738737e-01 , 3.58567830265565e-01 , 3.21600122017048e+00 ), ( 1.29424026004458e+00 , 1.43789524187990e+00 , 3.78845033901546e+00 ), ( 9.20863346462551e-01 , 1.99127820048878e+00 , 5.06428998086043e+00 ), ( 2.02769970654205e+00 , 2.78482427262160e+00 , 5.72727759600340e+00 ), ( -3.53429738457185e-01 , 2.88525141896991e+00 , 4.91587622733329e+00 ), ( -1.11836681366995e+00 , 3.07200369822809e+00 , 5.89844056717887e+00 ), ( -5.09978582591622e-01 , 3.46256168935760e+00 , 3.70887589967705e+00 ), ( -1.45774543366842e+00 , 4.47927258473410e+00 , 3.40618952998717e+00 ), ( -7.80847160084358e-01 , 5.48787734405077e+00 , 2.48901293264984e+00 ), ( -2.75654315918850e+00 , 3.92374661648390e+00 , 2.71362055129860e+00 ), ( -3.78763499735523e+00 , 4.60862489696840e+00 , 2.80231332205132e+00 ), ( -2.71694603742992e+00 , 2.65629449817826e+00 , 2.34023304844123e+00 ), ( -3.82568791162424e+00 , 1.78086501651260e+00 , 1.98285962576433e+00 ), ( -3.33575644565417e+00 , 9.16232299352979e-01 , 7.56233762708860e-01 ), ( -4.27714753389729e+00 , 1.01616214271383e+00 , 3.23106157672000e+00 ), ( -5.41060709338710e+00 , 7.07769419654237e-01 , 3.36487357914603e+00 ), ( -3.35323357058458e+00 , 7.03693457278879e-01 , 4.17446542367788e+00 ), ( -3.66391973477359e+00 , 5.72897449881609e-02 , 5.44112795976568e+00 ), ( -2.31859332615496e+00 , -2.62462774180647e-01 , 6.13459495972546e+00 ), ( -4.48639827864321e+00 , 9.80835634045819e-01 , 6.41926482609842e+00 ), ( -5.35497870111677e+00 , 5.18953963119411e-01 , 7.16468574383976e+00 ), ( -6.27648156798849e+00 , 3.59754886587097e+00 , 6.79912500299058e+00 ), ( -7.05668789292172e+00 , 4.29369310510554e+00 , 7.51274068172582e+00 ), ( -6.60848210980863e+00 , 3.17799348101263e+00 , 5.56419804658952e+00 ), ( -4.12917365884651e+00 , 2.25204464458803e+00 , 6.42656371846837e+00 ), ( -4.79660124309934e+00 , 3.26935026374641e+00 , 7.18090217513124e+00 ), ( -4.00955688686220e+00 , 4.64510175581389e+00 , 7.28286043509099e+00 ) } +colvars: Step 38, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_ids[size = 0] = +colvars: Step 38, atom_groups_refcount[size = 0] = +colvars: Step 38, atom_groups_masses[size = 0] = +colvars: Step 38, atom_groups_charges[size = 0] = +colvars: Step 38, atom_groups_coms[size = 0] = +colvars: Step 38, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 38, volmaps_ids[size = 0] = +colvars: Step 38, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 38 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.80541218552965e-01 , -1.87029804430822e-02 , 9.59659743458776e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.80541218552965e-01 , -1.87029804430822e-02 , 9.59659743458776e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.1288 , 2.32586 , -15.2896 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.1288 , 2.32586 , -15.2896 ) to colvar "one". +colvars: Adding total bias energy: 43.532 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.1288 , 2.32586 , -15.2896 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.95893 , -0.503731 , -1.35307 ) +colvars: ( -4.25228 , -0.431949 , -1.16026 ) +colvars: ( -4.25228 , -0.431949 , -1.16026 ) +colvars: ( -5.66416 , -0.575369 , -1.5455 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.881279 , 0.196945 , 0.594789 ) +colvars: ( 0.764825 , 0.265855 , 0.618068 ) +colvars: ( 0.748426 , 0.259646 , 0.600738 ) +colvars: ( 0.656441 , 0.26524 , 0.55588 ) +colvars: ( 0.64492 , 0.199364 , 0.464042 ) +colvars: ( 0.57258 , 0.340464 , 0.605798 ) +colvars: ( 0.468759 , 0.3529 , 0.563096 ) +colvars: ( 0.394384 , 0.448036 , 0.644174 ) +colvars: ( 0.388965 , 0.30851 , 0.460412 ) +colvars: ( 0.355507 , 0.266817 , 0.387465 ) +colvars: ( 0.359722 , 0.314122 , 0.451115 ) +colvars: ( 0.290043 , 0.271543 , 0.356506 ) +colvars: ( 0.262912 , 0.300648 , 0.37883 ) +colvars: ( 0.350704 , 0.175617 , 0.266637 ) +colvars: ( 0.293686 , 0.132255 , 0.178184 ) +colvars: ( 0.469999 , 0.140281 , 0.288448 ) +colvars: ( 0.540515 , 0.0507802 , 0.212481 ) +colvars: ( 0.666228 , 0.0315327 , 0.258762 ) +colvars: ( 0.549625 , 0.0187526 , 0.176165 ) +colvars: ( 0.534349 , -0.0456746 , 0.0840755 ) +colvars: ( 0.570579 , 0.0657134 , 0.24885 ) +colvars: ( 0.569878 , 0.0490494 , 0.226872 ) +colvars: ( 0.605971 , 0.112816 , 0.329896 ) +colvars: ( 0.449197 , 0.0520892 , 0.162452 ) +colvars: ( 0.442895 , -0.00348821 , 0.0869073 ) +colvars: ( 0.349852 , 0.11611 , 0.18909 ) +colvars: ( 0.228871 , 0.123314 , 0.129893 ) +colvars: ( 0.139661 , 0.207337 , 0.188175 ) +colvars: ( 0.200985 , 0.0506334 , 0.019973 ) +colvars: ( 0.153407 , 0.0141651 , -0.0542042 ) +colvars: ( 0.232902 , 0.026374 , 0.00663461 ) +colvars: ( 0.218786 , -0.0449223 , -0.0936928 ) +colvars: ( 0.252266 , -0.0471453 , -0.0776079 ) +colvars: ( 0.292245 , -0.129324 , -0.161388 ) +colvars: ( 0.249476 , -0.182196 , -0.254084 ) +colvars: ( 0.404508 , -0.143283 , -0.115876 ) +colvars: ( 0.480171 , -0.217388 , -0.168988 ) +colvars: ( 0.607833 , -0.21878 , -0.0984801 ) +colvars: ( 0.43497 , -0.22296 , -0.201808 ) +colvars: ( 0.44051 , -0.290257 , -0.285822 ) +colvars: ( 0.388067 , -0.151483 , -0.135808 ) +colvars: ( 0.33607 , -0.14648 , -0.158782 ) +colvars: ( 0.320495 , -0.0614751 , -0.057519 ) +colvars: ( 0.216114 , -0.156277 , -0.239415 ) +colvars: ( 0.19281 , -0.198359 , -0.307114 ) +colvars: ( 0.0192098 , -0.202324 , -0.410581 ) +colvars: ( -0.0692499 , -0.220735 , -0.484529 ) +colvars: ( 0.11635 , -0.250268 , -0.417647 ) +colvars: ( 0.136034 , -0.116492 , -0.233252 ) +colvars: ( 0.0198949 , -0.121847 , -0.305971 ) +colvars: ( -0.066971 , -0.0427524 , -0.252743 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.95893 , 0.503731 , 1.35307 ) +colvars: ( 4.25228 , 0.431949 , 1.16026 ) +colvars: ( 4.25228 , 0.431949 , 1.16026 ) +colvars: ( 5.66416 , 0.575369 , 1.5455 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.607396 , -0.0811741 , -0.34874 ) +colvars: ( -0.547618 , -0.164679 , -0.314838 ) +colvars: ( -0.494879 , -0.14225 , -0.254962 ) +colvars: ( -0.512065 , -0.192224 , -0.287777 ) +colvars: ( -0.502387 , -0.132485 , -0.259446 ) +colvars: ( -0.490595 , -0.285292 , -0.295268 ) +colvars: ( -0.461763 , -0.325881 , -0.279015 ) +colvars: ( -0.443001 , -0.434479 , -0.294063 ) +colvars: ( -0.398773 , -0.289734 , -0.204583 ) +colvars: ( -0.395964 , -0.26399 , -0.19374 ) +colvars: ( -0.347355 , -0.283879 , -0.1512 ) +colvars: ( -0.286453 , -0.246216 , -0.0783894 ) +colvars: ( -0.235648 , -0.261215 , -0.0321233 ) +colvars: ( -0.303693 , -0.141774 , -0.0631096 ) +colvars: ( -0.273515 , -0.111903 , -0.0235359 ) +colvars: ( -0.35495 , -0.0839748 , -0.0964831 ) +colvars: ( -0.37933 , 0.0154252 , -0.0899356 ) +colvars: ( -0.425701 , 0.0633118 , -0.121501 ) +colvars: ( -0.419331 , 0.0305885 , -0.125318 ) +colvars: ( -0.408002 , 0.0882184 , -0.0959881 ) +colvars: ( -0.465607 , -0.0243118 , -0.188837 ) +colvars: ( -0.502661 , -0.0258319 , -0.226466 ) +colvars: ( -0.554292 , -0.0923131 , -0.298966 ) +colvars: ( -0.454011 , -0.0558801 , -0.187053 ) +colvars: ( -0.461783 , -0.0111675 , -0.180904 ) +colvars: ( -0.400784 , -0.130903 , -0.157075 ) +colvars: ( -0.346226 , -0.162251 , -0.112143 ) +colvars: ( -0.297455 , -0.253399 , -0.0916607 ) +colvars: ( -0.303515 , -0.0882709 , -0.0462486 ) +colvars: ( -0.292232 , -0.0692515 , -0.0290047 ) +colvars: ( -0.280111 , -0.0428271 , -0.00861134 ) +colvars: ( -0.242834 , 0.0330542 , 0.052427 ) +colvars: ( -0.217792 , 0.0597498 , 0.0858607 ) +colvars: ( -0.285711 , 0.120785 , 0.0367894 ) +colvars: ( -0.259639 , 0.163282 , 0.0761827 ) +colvars: ( -0.353438 , 0.148924 , -0.0223474 ) +colvars: ( -0.401311 , 0.225935 , -0.0463374 ) +colvars: ( -0.470036 , 0.248399 , -0.108244 ) +colvars: ( -0.416592 , 0.205938 , -0.0678955 ) +colvars: ( -0.421087 , 0.267594 , -0.0531771 ) +colvars: ( -0.424375 , 0.118273 , -0.103034 ) +colvars: ( -0.435265 , 0.0878232 , -0.123448 ) +colvars: ( -0.459454 , -0.00678093 , -0.177201 ) +colvars: ( -0.370822 , 0.0767889 , -0.0622706 ) +colvars: ( -0.375828 , 0.103531 , -0.0589526 ) +colvars: ( -0.209481 , 0.110673 , 0.110073 ) +colvars: ( -0.161701 , 0.112857 , 0.158663 ) +colvars: ( -0.232086 , 0.183721 , 0.110183 ) +colvars: ( -0.308406 , 0.0357591 , -0.0124788 ) +colvars: ( -0.243693 , 0.0223364 , 0.0482234 ) +colvars: ( -0.191006 , -0.0616276 , 0.0748727 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 38. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 38. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atoms_new_colvar_forces = { ( -4.68504596593723e+00 , -3.87960044554837e-01 , -1.10702493925305e+00 ), ( -4.03507454616897e+00 , -3.30772868806218e-01 , -8.57030935206698e-01 ), ( -4.10790495556206e+00 , -3.58933917415277e-01 , -8.92158331179923e-01 ), ( -5.52162879898756e+00 , -5.08490065370030e-01 , -1.34090541382355e+00 ), ( 2.53547409807237e-01 , 1.17395343649830e-01 , 3.45775403176845e-01 ), ( 5.04091444867002e+00 , 5.58903662245786e-01 , 1.66360378252024e+00 ), ( 4.25927712420322e+00 , 4.58968120362369e-01 , 1.44434234185778e+00 ), ( -4.86169599682644e-02 , 1.35573361755443e-02 , 3.50110621415940e-01 ), ( 4.24247321253911e+00 , 4.50725540939055e-01 , 1.41609001358819e+00 ), ( 5.62370379124786e+00 , 5.78195336211898e-01 , 1.73922672541253e+00 ), ( 1.23666273463987e-02 , 3.02422454952214e-02 , 2.99914640683939e-01 ), ( 3.58989977694230e-03 , 2.53272254604359e-02 , 2.78116884271365e-01 ), ( 2.72634678160686e-02 , 3.94329001137475e-02 , 3.46706534634495e-01 ), ( 4.70116903514599e-02 , 3.38423850950537e-02 , 2.03527221670406e-01 ), ( 2.01708266466297e-02 , 2.03515991148052e-02 , 1.54648439753815e-01 ), ( 1.15049531051039e-01 , 5.63064566006523e-02 , 1.91964485654303e-01 ), ( 1.61184870150210e-01 , 6.62053769391688e-02 , 1.22545803357855e-01 ), ( 2.40527655710593e-01 , 9.48445406100823e-02 , 1.37261743010277e-01 ), ( 1.30293647844552e-01 , 4.93411042457558e-02 , 5.08469877054185e-02 ), ( 1.26346453868404e-01 , 4.25438295628965e-02 , -1.19126281563288e-02 ), ( 1.04971429695855e-01 , 4.14015704463733e-02 , 6.00122413028724e-02 ), ( 6.72165009221579e-02 , 2.32174900127881e-02 , 4.06207199910719e-04 ), ( 5.16786736507181e-02 , 2.05024805236968e-02 , 3.09301614310952e-02 ), ( -4.81348973304196e-03 , -3.79088971167800e-03 , -2.46004014656881e-02 ), ( -1.88875810881352e-02 , -1.46556633711438e-02 , -9.39966504518929e-02 ), ( -5.09323798536477e-02 , -1.47930398366066e-02 , 3.20156209176616e-02 ), ( -1.17355219398364e-01 , -3.89372323921185e-02 , 1.77500594058494e-02 ), ( -1.57794431188953e-01 , -4.60621112272657e-02 , 9.65147346148430e-02 ), ( -1.02530163051209e-01 , -3.76375000794702e-02 , -2.62755864450294e-02 ), ( -1.38824877862961e-01 , -5.50864743684770e-02 , -8.32089577353211e-02 ), ( -4.72090688131942e-02 , -1.64531555692097e-02 , -1.97673131999296e-03 ), ( -2.40479788659493e-02 , -1.18681527321205e-02 , -4.12658442023945e-02 ), ( 3.44737419770871e-02 , 1.26044700774544e-02 , 8.25280977670068e-03 ), ( 6.53398962619500e-03 , -8.53860662145461e-03 , -1.24598629209296e-01 ), ( -1.01624664771037e-02 , -1.89138686042996e-02 , -1.77901375590074e-01 ), ( 5.10702798626905e-02 , 5.64140043345243e-03 , -1.38223502965335e-01 ), ( 7.88597348547954e-02 , 8.54749130007304e-03 , -2.15325787422210e-01 ), ( 1.37796735547282e-01 , 2.96192904115347e-02 , -2.06724388549256e-01 ), ( 1.83777162934834e-02 , -1.70220590215046e-02 , -2.69703184484445e-01 ), ( 1.94239440017776e-02 , -2.26633310832260e-02 , -3.38999530485407e-01 ), ( -3.63085283047891e-02 , -3.32098185281161e-02 , -2.38842661451588e-01 ), ( -9.91951666535170e-02 , -5.86568132718223e-02 , -2.82230221411499e-01 ), ( -1.38959462318140e-01 , -6.82560615145092e-02 , -2.34720410979020e-01 ), ( -1.54707908207242e-01 , -7.94877772935072e-02 , -3.01686063575200e-01 ), ( -1.83018527797304e-01 , -9.48281363681882e-02 , -3.66066412603138e-01 ), ( -1.90271117983092e-01 , -9.16511265324128e-02 , -3.00507860855284e-01 ), ( -2.30950834508462e-01 , -1.07877507039663e-01 , -3.25865450825500e-01 ), ( -1.15735761416530e-01 , -6.65470676589007e-02 , -3.07463332151836e-01 ), ( -1.72371650621547e-01 , -8.07332797727855e-02 , -2.45731027583700e-01 ), ( -2.23798397383055e-01 , -9.95106432150125e-02 , -2.57747268007509e-01 ), ( -2.57977165311456e-01 , -1.04379984067821e-01 , -1.77869935972177e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 38, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 39 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 39, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 39, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 39, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 39, atoms_positions[size = 51] = { ( 8.13501525759879e+00 , 3.94301437201377e-02 , -6.89525118168788e-01 ), ( 6.79737406289504e+00 , -6.26242921438514e-01 , -4.94139159645281e-01 ), ( 6.05925587723481e+00 , -3.19591065981759e-01 , 8.04449984366639e-01 ), ( 4.86096696215647e+00 , -1.52434410451711e-01 , 7.79960468702964e-01 ), ( 7.00757152055447e+00 , -2.10916947785025e+00 , -8.05703765902434e-01 ), ( 6.76390357467338e+00 , -3.17885143998751e-01 , 1.95557875649197e+00 ), ( 6.09313497227905e+00 , -2.43218284076312e-01 , 3.28415217784596e+00 ), ( 7.14903957909723e+00 , -3.67219896303452e-01 , 4.43319355840772e+00 ), ( 5.29816852780219e+00 , 1.06544532202552e+00 , 3.36322307375322e+00 ), ( 4.19300058306129e+00 , 1.00723876295409e+00 , 3.87810648871806e+00 ), ( 5.85004057706449e+00 , 2.25833157077558e+00 , 2.95172641623963e+00 ), ( 5.13022679803697e+00 , 3.50791439777201e+00 , 2.84379152633758e+00 ), ( 6.25002502961042e+00 , 4.41838871842487e+00 , 2.28213293111414e+00 ), ( 3.86762467160158e+00 , 3.61112430358377e+00 , 1.99930532274789e+00 ), ( 2.86396181294268e+00 , 4.15155375400149e+00 , 2.40436550760949e+00 ), ( 3.90230863312830e+00 , 3.12042543592870e+00 , 7.96912654362322e-01 ), ( 2.74858853518684e+00 , 3.17104178934016e+00 , -8.95446414171198e-02 ), ( 3.15311824947009e+00 , 2.66485814787895e+00 , -1.50613180371636e+00 ), ( 1.65544040594615e+00 , 2.29799485442806e+00 , 4.68225471915235e-01 ), ( 4.40768580680346e-01 , 2.61071078748745e+00 , 4.07520387417323e-01 ), ( 2.01807257960741e+00 , 1.11481109030766e+00 , 1.02266699128096e+00 ), ( 1.30303799677655e+00 , 1.65345710704498e-01 , 1.66779133679323e+00 ), ( 2.10178587628848e+00 , -1.09290224130655e+00 , 2.02027483147359e+00 ), ( 5.68660695442402e-01 , 6.37676733633720e-01 , 2.93317950514362e+00 ), ( -6.15484185506568e-01 , 3.58610951757020e-01 , 3.21898741594644e+00 ), ( 1.29709335507056e+00 , 1.44061775520531e+00 , 3.78925943748216e+00 ), ( 9.22351265956098e-01 , 1.99426240830054e+00 , 5.06880552607546e+00 ), ( 2.02442768164686e+00 , 2.78869245086042e+00 , 5.72854810117999e+00 ), ( -3.50622535899037e-01 , 2.88304906050733e+00 , 4.91533596090805e+00 ), ( -1.11776468139881e+00 , 3.07216942105024e+00 , 5.89751320452373e+00 ), ( -5.04448951998347e-01 , 3.45377628926940e+00 , 3.70029845630575e+00 ), ( -1.46266588566389e+00 , 4.48062897336731e+00 , 3.40098346263665e+00 ), ( -7.82680278322045e-01 , 5.49607569209838e+00 , 2.48906666761961e+00 ), ( -2.75733130889330e+00 , 3.92370376616143e+00 , 2.71383902844605e+00 ), ( -3.78457733504229e+00 , 4.61234595519783e+00 , 2.79882796855850e+00 ), ( -2.71900328656696e+00 , 2.65757234810844e+00 , 2.33550480644871e+00 ), ( -3.82665257343246e+00 , 1.77465978260212e+00 , 1.97845524345337e+00 ), ( -3.33247112892680e+00 , 9.23256509077847e-01 , 7.51871898070328e-01 ), ( -4.27840057343480e+00 , 1.01412722932380e+00 , 3.22525925468793e+00 ), ( -5.40641953384532e+00 , 7.01271558429892e-01 , 3.36940403470712e+00 ), ( -3.35028167834817e+00 , 6.99054643628883e-01 , 4.17763098059498e+00 ), ( -3.66382024617179e+00 , 5.55391358636345e-02 , 5.43434836263815e+00 ), ( -2.30941607457838e+00 , -2.56106232906855e-01 , 6.13852807308339e+00 ), ( -4.48238857897561e+00 , 9.87402879999148e-01 , 6.41814265630123e+00 ), ( -5.35493720737201e+00 , 5.11829946319280e-01 , 7.15993460884329e+00 ), ( -6.27045762569907e+00 , 3.59758060766193e+00 , 6.80948482476097e+00 ), ( -7.06079560794194e+00 , 4.29008647703466e+00 , 7.50905685615827e+00 ), ( -6.60899199977438e+00 , 3.18029928965737e+00 , 5.56669433576142e+00 ), ( -4.13409708582981e+00 , 2.25337631161557e+00 , 6.42822554641307e+00 ), ( -4.79385256846801e+00 , 3.26551090628151e+00 , 7.17384911190218e+00 ), ( -4.01088640611851e+00 , 4.65351479489929e+00 , 7.28298517741049e+00 ) } +colvars: Step 39, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_ids[size = 0] = +colvars: Step 39, atom_groups_refcount[size = 0] = +colvars: Step 39, atom_groups_masses[size = 0] = +colvars: Step 39, atom_groups_charges[size = 0] = +colvars: Step 39, atom_groups_coms[size = 0] = +colvars: Step 39, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 39, volmaps_ids[size = 0] = +colvars: Step 39, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 39 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.78029409440391e-01 , -1.88154958979349e-02 , 9.60388267629474e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.78029409440391e-01 , -1.88154958979349e-02 , 9.60388267629474e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.0786 , 2.32811 , -15.3042 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.0786 , 2.32811 , -15.3042 ) to colvar "one". +colvars: Adding total bias energy: 43.4287 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.0786 , 2.32811 , -15.3042 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.96357 , -0.501028 , -1.34148 ) +colvars: ( -4.25626 , -0.429631 , -1.15032 ) +colvars: ( -4.25626 , -0.429631 , -1.15032 ) +colvars: ( -5.66946 , -0.572281 , -1.53226 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.880397 , 0.197185 , 0.592315 ) +colvars: ( 0.764194 , 0.265906 , 0.61556 ) +colvars: ( 0.747723 , 0.259796 , 0.598367 ) +colvars: ( 0.656105 , 0.265128 , 0.553558 ) +colvars: ( 0.644611 , 0.199313 , 0.462008 ) +colvars: ( 0.572474 , 0.340138 , 0.603312 ) +colvars: ( 0.468947 , 0.352393 , 0.560728 ) +colvars: ( 0.394772 , 0.447311 , 0.641549 ) +colvars: ( 0.389284 , 0.308017 , 0.458419 ) +colvars: ( 0.355944 , 0.266293 , 0.385677 ) +colvars: ( 0.360015 , 0.313683 , 0.449225 ) +colvars: ( 0.290437 , 0.271136 , 0.354969 ) +colvars: ( 0.26327 , 0.300275 , 0.377301 ) +colvars: ( 0.350942 , 0.1754 , 0.265378 ) +colvars: ( 0.294056 , 0.132023 , 0.177212 ) +colvars: ( 0.469949 , 0.140248 , 0.287103 ) +colvars: ( 0.54029 , 0.0509371 , 0.211365 ) +colvars: ( 0.665678 , 0.0318848 , 0.2575 ) +colvars: ( 0.549473 , 0.0188622 , 0.175092 ) +colvars: ( 0.534232 , -0.0455099 , 0.083292 ) +colvars: ( 0.570461 , 0.065711 , 0.247486 ) +colvars: ( 0.569857 , 0.0489694 , 0.225508 ) +colvars: ( 0.605942 , 0.112629 , 0.328149 ) +colvars: ( 0.449481 , 0.051847 , 0.161297 ) +colvars: ( 0.443229 , -0.00371055 , 0.0859621 ) +colvars: ( 0.350344 , 0.115707 , 0.187889 ) +colvars: ( 0.229653 , 0.122759 , 0.128895 ) +colvars: ( 0.140623 , 0.206615 , 0.187035 ) +colvars: ( 0.20177 , 0.0501904 , 0.0193677 ) +colvars: ( 0.154338 , 0.0136751 , -0.0545941 ) +colvars: ( 0.23352 , 0.0260869 , 0.00613145 ) +colvars: ( 0.219372 , -0.0450804 , -0.0938341 ) +colvars: ( 0.252671 , -0.0471612 , -0.0777321 ) +colvars: ( 0.292691 , -0.129336 , -0.161357 ) +colvars: ( 0.250017 , -0.182191 , -0.253752 ) +colvars: ( 0.404729 , -0.143189 , -0.116036 ) +colvars: ( 0.480255 , -0.217166 , -0.169028 ) +colvars: ( 0.607638 , -0.218431 , -0.098779 ) +colvars: ( 0.435253 , -0.222876 , -0.201804 ) +colvars: ( 0.440796 , -0.290106 , -0.285569 ) +colvars: ( 0.388524 , -0.151596 , -0.136047 ) +colvars: ( 0.336737 , -0.146746 , -0.159003 ) +colvars: ( 0.321265 , -0.0619198 , -0.0580986 ) +colvars: ( 0.217046 , -0.156651 , -0.239349 ) +colvars: ( 0.193843 , -0.19876 , -0.306866 ) +colvars: ( 0.0204417 , -0.202711 , -0.409826 ) +colvars: ( -0.067822 , -0.22119 , -0.483519 ) +colvars: ( 0.117303 , -0.250438 , -0.416852 ) +colvars: ( 0.137087 , -0.116936 , -0.233141 ) +colvars: ( 0.0211973 , -0.122395 , -0.305594 ) +colvars: ( -0.0655056 , -0.0434473 , -0.252485 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.96357 , 0.501028 , 1.34148 ) +colvars: ( 4.25626 , 0.429631 , 1.15032 ) +colvars: ( 4.25626 , 0.429631 , 1.15032 ) +colvars: ( 5.66946 , 0.572281 , 1.53226 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.606369 , -0.0813065 , -0.346087 ) +colvars: ( -0.546882 , -0.16467 , -0.312079 ) +colvars: ( -0.494004 , -0.142309 , -0.252263 ) +colvars: ( -0.511681 , -0.192096 , -0.285236 ) +colvars: ( -0.502018 , -0.132401 , -0.257249 ) +colvars: ( -0.490507 , -0.285008 , -0.292527 ) +colvars: ( -0.462034 , -0.325465 , -0.276419 ) +colvars: ( -0.443535 , -0.433903 , -0.291151 ) +colvars: ( -0.399154 , -0.289323 , -0.20236 ) +colvars: ( -0.396488 , -0.263557 , -0.191787 ) +colvars: ( -0.347662 , -0.283503 , -0.149005 ) +colvars: ( -0.286832 , -0.245857 , -0.0765381 ) +colvars: ( -0.235945 , -0.260877 , -0.0301812 ) +colvars: ( -0.303865 , -0.141555 , -0.061606 ) +colvars: ( -0.273826 , -0.11167 , -0.0223563 ) +colvars: ( -0.354783 , -0.0838916 , -0.0949159 ) +colvars: ( -0.37894 , 0.0153696 , -0.0886653 ) +colvars: ( -0.424924 , 0.0631122 , -0.120075 ) +colvars: ( -0.419063 , 0.0305636 , -0.124188 ) +colvars: ( -0.407758 , 0.0881545 , -0.0952028 ) +colvars: ( -0.46543 , -0.0242597 , -0.187439 ) +colvars: ( -0.502637 , -0.025727 , -0.225153 ) +colvars: ( -0.554312 , -0.0921356 , -0.297272 ) +colvars: ( -0.454342 , -0.0556548 , -0.185964 ) +colvars: ( -0.462175 , -0.0109573 , -0.1801 ) +colvars: ( -0.401354 , -0.130558 , -0.155869 ) +colvars: ( -0.347128 , -0.161792 , -0.111142 ) +colvars: ( -0.298568 , -0.252815 , -0.0904252 ) +colvars: ( -0.304373 , -0.0878892 , -0.0456553 ) +colvars: ( -0.293262 , -0.0688353 , -0.0286842 ) +colvars: ( -0.280728 , -0.0425557 , -0.00807094 ) +colvars: ( -0.243365 , 0.0332355 , 0.0525935 ) +colvars: ( -0.218068 , 0.0598309 , 0.0860851 ) +colvars: ( -0.28608 , 0.120858 , 0.0366886 ) +colvars: ( -0.260099 , 0.163344 , 0.0757397 ) +colvars: ( -0.353568 , 0.148915 , -0.0222955 ) +colvars: ( -0.401289 , 0.22583 , -0.0464984 ) +colvars: ( -0.469708 , 0.248197 , -0.10816 ) +colvars: ( -0.416839 , 0.20593 , -0.0681754 ) +colvars: ( -0.421327 , 0.267538 , -0.0537746 ) +colvars: ( -0.424868 , 0.118407 , -0.10306 ) +colvars: ( -0.43604 , 0.0880662 , -0.123554 ) +colvars: ( -0.460398 , -0.00641104 , -0.176925 ) +colvars: ( -0.371885 , 0.0771152 , -0.0626612 ) +colvars: ( -0.377019 , 0.103875 , -0.0595956 ) +colvars: ( -0.210792 , 0.11102 , 0.109073 ) +colvars: ( -0.163223 , 0.113258 , 0.157399 ) +colvars: ( -0.233044 , 0.183911 , 0.109143 ) +colvars: ( -0.309582 , 0.0361404 , -0.0128318 ) +colvars: ( -0.245139 , 0.0227973 , 0.0476154 ) +colvars: ( -0.192635 , -0.0610563 , 0.0744798 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 39. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 39. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atoms_new_colvar_forces = { ( -4.68954119047701e+00 , -3.85149724894070e-01 , -1.09525402232860e+00 ), ( -4.03894739503836e+00 , -3.28395697579528e-01 , -8.46839141921896e-01 ), ( -4.11183566162515e+00 , -3.56599657591745e-01 , -8.81998947583959e-01 ), ( -5.52686777124093e+00 , -5.05368468946877e-01 , -1.32750154128391e+00 ), ( 2.53718766023828e-01 , 1.17486469897245e-01 , 3.46104292120658e-01 ), ( 5.04553629527217e+00 , 5.56158317413406e-01 , 1.65226684793111e+00 ), ( 4.26317238704944e+00 , 4.56559334622244e-01 , 1.43462913794130e+00 ), ( -4.87624794298556e-02 , 1.34072186325228e-02 , 3.50397711199689e-01 ), ( 4.24638961908121e+00 , 4.48325620682142e-01 , 1.40637926803101e+00 ), ( 5.62891661354505e+00 , 5.75017243947897e-01 , 1.72614998039327e+00 ), ( 1.23533589188348e-02 , 3.01798934975890e-02 , 3.00219552681599e-01 ), ( 3.60483316666277e-03 , 2.52782325660993e-02 , 2.78431275904403e-01 ), ( 2.73248780575444e-02 , 3.93979863742646e-02 , 3.47119459388892e-01 ), ( 4.70772234125372e-02 , 3.38452650549425e-02 , 2.03771588358902e-01 ), ( 2.02300781732224e-02 , 2.03523723913996e-02 , 1.54855569729158e-01 ), ( 1.15165136335723e-01 , 5.63567640425060e-02 , 1.92187018719023e-01 ), ( 1.61349319706483e-01 , 6.63067071145899e-02 , 1.22700114093274e-01 ), ( 2.40754141612545e-01 , 9.49969894515954e-02 , 1.37424738931895e-01 ), ( 1.30410028913662e-01 , 4.94257881605713e-02 , 5.09037929291311e-02 ), ( 1.26473924482915e-01 , 4.26446206098426e-02 , -1.19108247164042e-02 ), ( 1.05030804314861e-01 , 4.14512984492250e-02 , 6.00469667202549e-02 ), ( 6.72198933172334e-02 , 2.32423466184547e-02 , 3.54904215881441e-04 ), ( 5.16300913153956e-02 , 2.04935944620715e-02 , 3.08767541824016e-02 ), ( -4.86095333326475e-03 , -3.80774743249413e-03 , -2.46672436484585e-02 ), ( -1.89456051778193e-02 , -1.46678089418535e-02 , -9.41375044331503e-02 ), ( -5.10101901904896e-02 , -1.48504441014234e-02 , 3.20201355732448e-02 ), ( -1.17475611531463e-01 , -3.90330585698587e-02 , 1.77538354151428e-02 ), ( -1.57944436853938e-01 , -4.62006940530025e-02 , 9.66100785696662e-02 ), ( -1.02602584369978e-01 , -3.76987875748095e-02 , -2.62875637930174e-02 ), ( -1.38924135643100e-01 , -5.51602740603401e-02 , -8.32782652662297e-02 ), ( -4.72081429702560e-02 , -1.64688624861600e-02 , -1.93948289092324e-03 ), ( -2.39933500713810e-02 , -1.18449335598510e-02 , -4.12406820793752e-02 ), ( 3.46026790678287e-02 , 1.26696650526816e-02 , 8.35299547683815e-03 ), ( 6.61099790286646e-03 , -8.47822285746856e-03 , -1.24668666134085e-01 ), ( -1.00818450242713e-02 , -1.88469378746466e-02 , -1.78012603048105e-01 ), ( 5.11612433368664e-02 , 5.72605910654783e-03 , -1.38331859343317e-01 ), ( 7.89660975446043e-02 , 8.66410248820965e-03 , -2.15526723541092e-01 ), ( 1.37929758977092e-01 , 2.97660898000908e-02 , -2.06939389288260e-01 ), ( 1.84138537434986e-02 , -1.69453840340082e-02 , -2.69979066918451e-01 ), ( 1.94687170202535e-02 , -2.25685165960764e-02 , -3.39343896595633e-01 ), ( -3.63439889633463e-02 , -3.31889835654128e-02 , -2.39106475208884e-01 ), ( -9.93026663182876e-02 , -5.86797627539019e-02 , -2.82556703646834e-01 ), ( -1.39133331405120e-01 , -6.83307997173733e-02 , -2.35024001069001e-01 ), ( -1.54839043094663e-01 , -7.95362226189403e-02 , -3.02010322409087e-01 ), ( -1.83175664045330e-01 , -9.48844323358188e-02 , -3.66461874899253e-01 ), ( -1.90350171977169e-01 , -9.16900988761847e-02 , -3.00753594623707e-01 ), ( -2.31045281665251e-01 , -1.07932084547541e-01 , -3.26119885692409e-01 ), ( -1.15741452536877e-01 , -6.65273756963924e-02 , -3.07709622182550e-01 ), ( -1.72495142798950e-01 , -8.07960371360381e-02 , -2.45972727412390e-01 ), ( -2.23941765568113e-01 , -9.95973836571451e-02 , -2.57978483112888e-01 ), ( -2.58140878941947e-01 , -1.04503578377180e-01 , -1.78004903434872e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 39, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 40 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } +colvars: Step 40, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 40, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 40, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 40, atoms_positions[size = 51] = { ( 8.12105901178684e+00 , 3.84226283907114e-02 , -6.86717885048334e-01 ), ( 6.79031524301517e+00 , -6.26050504072990e-01 , -4.88274685603578e-01 ), ( 6.05995211580310e+00 , -3.20085794055288e-01 , 8.00170068632393e-01 ), ( 4.85054921410866e+00 , -1.51708376423104e-01 , 7.83927579783448e-01 ), ( 7.01138742580607e+00 , -2.11446858072754e+00 , -7.99083136874665e-01 ), ( 6.75688571289485e+00 , -3.18020767235407e-01 , 1.95437180756530e+00 ), ( 6.10077878305847e+00 , -2.43397095496519e-01 , 3.29267868076293e+00 ), ( 7.14583106110183e+00 , -3.70172886093937e-01 , 4.43833555648328e+00 ), ( 5.29833883198606e+00 , 1.06625811215479e+00 , 3.36619681421965e+00 ), ( 4.19228440064791e+00 , 1.00923478775605e+00 , 3.88914924887784e+00 ), ( 5.84685642653782e+00 , 2.25891568630460e+00 , 2.94937774317570e+00 ), ( 5.13252402954428e+00 , 3.50612309515531e+00 , 2.84017930938219e+00 ), ( 6.24344427519495e+00 , 4.41426944231342e+00 , 2.27981822599335e+00 ), ( 3.87143338382539e+00 , 3.60795730140310e+00 , 1.99843462826635e+00 ), ( 2.86820328051534e+00 , 4.14990122379047e+00 , 2.40253508354811e+00 ), ( 3.90359165474461e+00 , 3.11233173226373e+00 , 8.00756320838139e-01 ), ( 2.74682823285188e+00 , 3.18403024342829e+00 , -9.57831846352821e-02 ), ( 3.15533221828101e+00 , 2.66517251318307e+00 , -1.50100632762412e+00 ), ( 1.66512306771901e+00 , 2.30568485079699e+00 , 4.76221142802963e-01 ), ( 4.45402504043012e-01 , 2.60974796336796e+00 , 4.01843763817422e-01 ), ( 2.01917037167459e+00 , 1.12063296128010e+00 , 1.01328106062490e+00 ), ( 1.30105928161206e+00 , 1.62311836724961e-01 , 1.67187984927862e+00 ), ( 2.10343630165357e+00 , -1.09287845043043e+00 , 2.01592429128284e+00 ), ( 5.68011572073184e-01 , 6.44248180171018e-01 , 2.93562930904170e+00 ), ( -6.17218642168799e-01 , 3.58717315596372e-01 , 3.22148163939923e+00 ), ( 1.30030456484385e+00 , 1.44280744325559e+00 , 3.78930477101615e+00 ), ( 9.22378520478911e-01 , 1.99712651411855e+00 , 5.07302735114155e+00 ), ( 2.02264712416081e+00 , 2.79285061496176e+00 , 5.73022970446251e+00 ), ( -3.47376027355219e-01 , 2.88083606144856e+00 , 4.91611465581226e+00 ), ( -1.11673949208574e+00 , 3.07229694576606e+00 , 5.89554932337739e+00 ), ( -4.99471962080539e-01 , 3.44490303313808e+00 , 3.69180412368484e+00 ), ( -1.46829772733846e+00 , 4.48168554569302e+00 , 3.39501400705136e+00 ), ( -7.83794803040324e-01 , 5.50438459908698e+00 , 2.48882738957871e+00 ), ( -2.75800104042783e+00 , 3.92496746891646e+00 , 2.71638667872342e+00 ), ( -3.78135058786988e+00 , 4.61555058188124e+00 , 2.79484660644305e+00 ), ( -2.72101007952248e+00 , 2.65771618414932e+00 , 2.32983712611732e+00 ), ( -3.82675332822892e+00 , 1.76963084128839e+00 , 1.97391075134387e+00 ), ( -3.32914723792086e+00 , 9.30331970886669e-01 , 7.48209808092791e-01 ), ( -4.27771848726241e+00 , 1.01195061406328e+00 , 3.21929726464452e+00 ), ( -5.40373708027661e+00 , 6.94458199866029e-01 , 3.37415144200379e+00 ), ( -3.34779907680153e+00 , 6.94943417684864e-01 , 4.18000273089232e+00 ), ( -3.66378416447534e+00 , 5.47958850223550e-02 , 5.42876490230581e+00 ), ( -2.30044147106763e+00 , -2.50568962720670e-01 , 6.14266632592068e+00 ), ( -4.47773362413644e+00 , 9.91914202203342e-01 , 6.41672486665103e+00 ), ( -5.35468974719743e+00 , 5.05041768878412e-01 , 7.15493552115057e+00 ), ( -6.26510458721272e+00 , 3.59861756350138e+00 , 6.81978333230359e+00 ), ( -7.06411553698509e+00 , 4.28576896347840e+00 , 7.50474367817482e+00 ), ( -6.60987420839401e+00 , 3.18247523255589e+00 , 5.56932785453876e+00 ), ( -4.13903219713242e+00 , 2.25571592522886e+00 , 6.42901319882496e+00 ), ( -4.79190564018779e+00 , 3.26258861232214e+00 , 7.16845632251530e+00 ), ( -4.01210959687813e+00 , 4.66018193684896e+00 , 7.28287892592627e+00 ) } +colvars: Step 40, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_ids[size = 0] = +colvars: Step 40, atom_groups_refcount[size = 0] = +colvars: Step 40, atom_groups_masses[size = 0] = +colvars: Step 40, atom_groups_charges[size = 0] = +colvars: Step 40, atom_groups_coms[size = 0] = +colvars: Step 40, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 40, volmaps_ids[size = 0] = +colvars: Step 40, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 40 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.75375163222155e-01 , -1.88018998907846e-02 , 9.61152957671602e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.75375163222155e-01 , -1.88018998907846e-02 , 9.61152957671602e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 25.0255 , 2.32784 , -15.3195 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 25.0255 , 2.32784 , -15.3195 ) to colvar "one". +colvars: Adding total bias energy: 43.319 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 25.0255 , 2.32784 , -15.3195 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -4.96845 , -0.498288 , -1.32901 ) +colvars: ( -4.26044 , -0.427282 , -1.13963 ) +colvars: ( -4.26044 , -0.427282 , -1.13963 ) +colvars: ( -5.67503 , -0.569152 , -1.51802 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.879475 , 0.19746 , 0.589668 ) +colvars: ( 0.763537 , 0.265986 , 0.612876 ) +colvars: ( 0.746982 , 0.259979 , 0.595824 ) +colvars: ( 0.655758 , 0.265036 , 0.551074 ) +colvars: ( 0.64429 , 0.199281 , 0.45983 ) +colvars: ( 0.572374 , 0.339824 , 0.600655 ) +colvars: ( 0.469157 , 0.351888 , 0.558199 ) +colvars: ( 0.395198 , 0.446581 , 0.638748 ) +colvars: ( 0.389628 , 0.307523 , 0.456287 ) +colvars: ( 0.356411 , 0.265765 , 0.383765 ) +colvars: ( 0.360325 , 0.313246 , 0.447198 ) +colvars: ( 0.290847 , 0.270728 , 0.353316 ) +colvars: ( 0.263638 , 0.299906 , 0.37565 ) +colvars: ( 0.351185 , 0.175187 , 0.264019 ) +colvars: ( 0.294437 , 0.131791 , 0.176159 ) +colvars: ( 0.469888 , 0.140228 , 0.285653 ) +colvars: ( 0.540044 , 0.0511119 , 0.210158 ) +colvars: ( 0.665088 , 0.0322651 , 0.256135 ) +colvars: ( 0.549308 , 0.0189857 , 0.173935 ) +colvars: ( 0.534103 , -0.0453327 , 0.0824438 ) +colvars: ( 0.570338 , 0.0657203 , 0.246025 ) +colvars: ( 0.569843 , 0.0488962 , 0.22405 ) +colvars: ( 0.605925 , 0.112449 , 0.326288 ) +colvars: ( 0.449787 , 0.0516022 , 0.160062 ) +colvars: ( 0.443589 , -0.00393792 , 0.0849533 ) +colvars: ( 0.350868 , 0.115297 , 0.186605 ) +colvars: ( 0.230482 , 0.122188 , 0.127828 ) +colvars: ( 0.141642 , 0.205871 , 0.185814 ) +colvars: ( 0.202596 , 0.0497313 , 0.0187152 ) +colvars: ( 0.155318 , 0.0131637 , -0.0550156 ) +colvars: ( 0.234164 , 0.0257902 , 0.00558312 ) +colvars: ( 0.219976 , -0.0452463 , -0.0940002 ) +colvars: ( 0.25308 , -0.0471777 , -0.0778849 ) +colvars: ( 0.293149 , -0.129353 , -0.161338 ) +colvars: ( 0.250572 , -0.182194 , -0.253413 ) +colvars: ( 0.404953 , -0.143094 , -0.116219 ) +colvars: ( 0.480337 , -0.21694 , -0.169081 ) +colvars: ( 0.607428 , -0.21807 , -0.0991062 ) +colvars: ( 0.435549 , -0.222795 , -0.201805 ) +colvars: ( 0.441093 , -0.289959 , -0.285304 ) +colvars: ( 0.389008 , -0.151718 , -0.136303 ) +colvars: ( 0.337447 , -0.147029 , -0.159235 ) +colvars: ( 0.322088 , -0.0623854 , -0.0587106 ) +colvars: ( 0.218032 , -0.157051 , -0.239277 ) +colvars: ( 0.194937 , -0.199189 , -0.306599 ) +colvars: ( 0.0217305 , -0.203128 , -0.40903 ) +colvars: ( -0.0663289 , -0.221682 , -0.482451 ) +colvars: ( 0.118294 , -0.25063 , -0.416016 ) +colvars: ( 0.138196 , -0.117408 , -0.233025 ) +colvars: ( 0.0225668 , -0.122976 , -0.305196 ) +colvars: ( -0.0639655 , -0.0441802 , -0.252215 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 4.96845 , 0.498288 , 1.32901 ) +colvars: ( 4.26044 , 0.427282 , 1.13963 ) +colvars: ( 4.26044 , 0.427282 , 1.13963 ) +colvars: ( 5.67503 , 0.569152 , 1.51802 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( -0.605283 , -0.0814713 , -0.343245 ) +colvars: ( -0.546104 , -0.164667 , -0.30914 ) +colvars: ( -0.493093 , -0.142383 , -0.249407 ) +colvars: ( -0.511271 , -0.191956 , -0.28253 ) +colvars: ( -0.501624 , -0.132316 , -0.254904 ) +colvars: ( -0.490404 , -0.284682 , -0.289614 ) +colvars: ( -0.462304 , -0.324985 , -0.273661 ) +colvars: ( -0.444078 , -0.433233 , -0.288065 ) +colvars: ( -0.399548 , -0.288853 , -0.200008 ) +colvars: ( -0.397029 , -0.263067 , -0.189715 ) +colvars: ( -0.347989 , -0.283073 , -0.146701 ) +colvars: ( -0.287244 , -0.245451 , -0.0746108 ) +colvars: ( -0.236282 , -0.260492 , -0.028178 ) +colvars: ( -0.304062 , -0.141317 , -0.0600384 ) +colvars: ( -0.274171 , -0.111421 , -0.0211333 ) +colvars: ( -0.354625 , -0.0838134 , -0.0932714 ) +colvars: ( -0.378549 , 0.0152802 , -0.0873257 ) +colvars: ( -0.424126 , 0.0628556 , -0.118566 ) +colvars: ( -0.418788 , 0.0305061 , -0.122979 ) +colvars: ( -0.407511 , 0.0880463 , -0.0943553 ) +colvars: ( -0.465241 , -0.0242249 , -0.185934 ) +colvars: ( -0.502599 , -0.0256335 , -0.22372 ) +colvars: ( -0.554309 , -0.0919531 , -0.295426 ) +colvars: ( -0.454677 , -0.0554227 , -0.184774 ) +colvars: ( -0.462572 , -0.0107479 , -0.179202 ) +colvars: ( -0.401943 , -0.130182 , -0.154572 ) +colvars: ( -0.348068 , -0.161285 , -0.110068 ) +colvars: ( -0.299731 , -0.252158 , -0.0891205 ) +colvars: ( -0.305274 , -0.0874775 , -0.0450216 ) +colvars: ( -0.294343 , -0.0683874 , -0.0283346 ) +colvars: ( -0.281387 , -0.0422725 , -0.0075047 ) +colvars: ( -0.243943 , 0.033409 , 0.0527565 ) +colvars: ( -0.218389 , 0.0598896 , 0.0862951 ) +colvars: ( -0.286484 , 0.120899 , 0.0365849 ) +colvars: ( -0.260601 , 0.163369 , 0.075273 ) +colvars: ( -0.353715 , 0.148861 , -0.022222 ) +colvars: ( -0.401272 , 0.225658 , -0.0466333 ) +colvars: ( -0.469366 , 0.247914 , -0.108023 ) +colvars: ( -0.417096 , 0.20587 , -0.0684236 ) +colvars: ( -0.421577 , 0.267415 , -0.0543518 ) +colvars: ( -0.425375 , 0.118515 , -0.103036 ) +colvars: ( -0.436835 , 0.0882998 , -0.123605 ) +colvars: ( -0.461361 , -0.00602419 , -0.176568 ) +colvars: ( -0.372987 , 0.0774436 , -0.0630242 ) +colvars: ( -0.378251 , 0.10422 , -0.0602171 ) +colvars: ( -0.212177 , 0.111369 , 0.108026 ) +colvars: ( -0.164834 , 0.113666 , 0.156066 ) +colvars: ( -0.234063 , 0.184075 , 0.108055 ) +colvars: ( -0.310811 , 0.0365359 , -0.0131747 ) +colvars: ( -0.246656 , 0.0232837 , 0.0469907 ) +colvars: ( -0.194349 , -0.0604355 , 0.0740647 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 40. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 40. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atoms_new_colvar_forces = { ( -4.69425621928030e+00 , -3.82299293531605e-01 , -1.08259138985050e+00 ), ( -4.04301104341328e+00 , -3.25963208101038e-01 , -8.35893878661085e-01 ), ( -4.11595607698720e+00 , -3.54202091663012e-01 , -8.71086049655236e-01 ), ( -5.53236771588536e+00 , -5.02186714644302e-01 , -1.31309315973091e+00 ), ( 2.53888846719415e-01 , 1.17595525457716e-01 , 3.46417250400701e-01 ), ( 5.05041829897174e+00 , 5.53430773090023e-01 , 1.64005611225967e+00 ), ( 4.26729665699043e+00 , 4.54184594630911e-01 , 1.42416813087359e+00 ), ( -4.88806078491699e-02 , 1.33487489633205e-02 , 3.50683065016341e-01 ), ( 4.25052245994865e+00 , 4.45951931194706e-01 , 1.39590834641362e+00 ), ( 5.63441670782379e+00 , 5.71849738829720e-01 , 1.71207020437378e+00 ), ( 1.23366993044769e-02 , 3.01734792405036e-02 , 3.00496560792935e-01 ), ( 3.60330382822177e-03 , 2.52768315020174e-02 , 2.78704756676739e-01 ), ( 2.73561002156189e-02 , 3.94136106638130e-02 , 3.47472063103420e-01 ), ( 4.71232770937250e-02 , 3.38708564598179e-02 , 2.03980348396035e-01 ), ( 2.02658012733531e-02 , 2.03696695196413e-02 , 1.55025212261148e-01 ), ( 1.15263686220147e-01 , 5.64149706436544e-02 , 1.92381357469619e-01 ), ( 1.61495044376692e-01 , 6.63921394750813e-02 , 1.22832733602513e-01 ), ( 2.40962099296910e-01 , 9.51207430915074e-02 , 1.37569466093544e-01 ), ( 1.30519861097751e-01 , 4.94917657810325e-02 , 5.09564742764324e-02 ), ( 1.26591825707300e-01 , 4.27136321467979e-02 , -1.19114698073206e-02 ), ( 1.05097731844517e-01 , 4.14953960140019e-02 , 6.00908493172415e-02 ), ( 6.72434452314901e-02 , 2.32627372292199e-02 , 3.29411571107774e-04 ), ( 5.16160106797033e-02 , 2.04957380611913e-02 , 3.08614760964039e-02 ), ( -4.89011140648138e-03 , -3.82051532300732e-03 , -2.47122525670103e-02 ), ( -1.89827265351792e-02 , -1.46857755478728e-02 , -9.42487078872073e-02 ), ( -5.10748135423793e-02 , -1.48855039510186e-02 , 3.20336041855653e-02 ), ( -1.17586606502013e-01 , -3.90978081951123e-02 , 1.77598887431232e-02 ), ( -1.58089567227928e-01 , -4.62863930833078e-02 , 9.66939541792814e-02 ), ( -1.02678024282419e-01 , -3.77462019687896e-02 , -2.63063912756204e-02 ), ( -1.39025002292574e-01 , -5.52237131152498e-02 , -8.33501808145621e-02 ), ( -4.72226162435921e-02 , -1.64823154225552e-02 , -1.92158104703002e-03 ), ( -2.39663382418125e-02 , -1.18372933854927e-02 , -4.12437048147867e-02 ), ( 3.46912021407856e-02 , 1.27118771004866e-02 , 8.41013004242197e-03 ), ( 6.66481432988858e-03 , -8.45421436963140e-03 , -1.24753419439499e-01 ), ( -1.00289522664995e-02 , -1.88256908193125e-02 , -1.78140029209524e-01 ), ( 5.12383161124934e-02 , 5.76682664923539e-03 , -1.38441123385543e-01 ), ( 7.90646052522583e-02 , 8.71853503463832e-03 , -2.15714006408506e-01 ), ( 1.38062868973438e-01 , 2.98441641896576e-02 , -2.07129458099311e-01 ), ( 1.84528915679896e-02 , -1.69249601769574e-02 , -2.70228373715246e-01 ), ( 1.95162161633862e-02 , -2.25440771252065e-02 , -3.39656071605553e-01 ), ( -3.63669778407855e-02 , -3.32031259312454e-02 , -2.39338835403575e-01 ), ( -9.93874519156564e-02 , -5.87293132402941e-02 , -2.82840417994324e-01 ), ( -1.39272909769278e-01 , -6.84096349353490e-02 , -2.35278296104018e-01 ), ( -1.54955051902739e-01 , -7.96074177852305e-02 , -3.02301613111528e-01 ), ( -1.83313726057656e-01 , -9.49689547058241e-02 , -3.66816281783523e-01 ), ( -1.90446178428819e-01 , -9.17585877080269e-02 , -3.01003597891805e-01 ), ( -2.31162538711229e-01 , -1.08015703657244e-01 , -3.26385175995963e-01 ), ( -1.15769016831794e-01 , -6.65556151205041e-02 , -3.07960838121793e-01 ), ( -1.72614546231601e-01 , -8.08716967814934e-02 , -2.46199182186840e-01 ), ( -2.24089127527084e-01 , -9.96927216164915e-02 , -2.58205183976685e-01 ), ( -2.58314823991350e-01 , -1.04615743063521e-01 , -1.78150725600739e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 40, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Saving collective variables state to "test.restart.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped new file mode 100644 index 000000000..defd4fc4a --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,17 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x ( -0.27537516322216 , -0.018801899890785 , 0.9611529576716 ) +} + +restraint { + configuration { + step 40 + name harmonic1 + } +} + diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj new file mode 100644 index 000000000..dd9505092 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one + 20 ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ) ( 2.56088356696367e+01 , 1.95578319419462e+00 , -1.51463793080245e+01 ) + 21 ( -3.03300920671651e-01 , -1.24565183823531e-03 , 9.52894012926530e-01 ) ( 2.55840198724037e+01 , 1.97671318266177e+00 , -1.51542799667365e+01 ) + 22 ( -3.02208395802458e-01 , -2.38936177499928e-03 , 9.53238887402740e-01 ) ( 2.55621693750198e+01 , 1.99958738139705e+00 , -1.51611774562607e+01 ) + 23 ( -3.01235983053210e-01 , -3.61953298784803e-03 , 9.53542752840645e-01 ) ( 2.55427211200349e+01 , 2.02419080565403e+00 , -1.51672547650188e+01 ) + 24 ( -3.00350438745275e-01 , -4.92097847437880e-03 , 9.53816228587234e-01 ) ( 2.55250102338762e+01 , 2.05021971538464e+00 , -1.51727242799506e+01 ) + 25 ( -2.99515551202827e-01 , -6.27415312265916e-03 , 9.54070788563543e-01 ) ( 2.55083124830272e+01 , 2.07728320835025e+00 , -1.51778154794767e+01 ) + 26 ( -2.98694198360127e-01 , -7.65591975074812e-03 , 9.54318166419759e-01 ) ( 2.54918854261732e+01 , 2.10491854091203e+00 , -1.51827630366011e+01 ) + 27 ( -2.97850201345680e-01 , -9.04087721924012e-03 , 9.54569808917841e-01 ) ( 2.54750054858843e+01 , 2.13261769028187e+00 , -1.51877958865627e+01 ) + 28 ( -2.96949879926448e-01 , -1.04029858363134e-02 , 9.54836397870000e-01 ) ( 2.54569990574996e+01 , 2.15985986262333e+00 , -1.51931276656059e+01 ) + 29 ( -2.95963250214387e-01 , -1.17171742424022e-02 , 9.55127458693503e-01 ) ( 2.54372664632584e+01 , 2.18614363074511e+00 , -1.51989488820759e+01 ) + 30 ( -2.94864820949374e-01 , -1.29606427096605e-02 , 9.55451076249876e-01 ) ( 2.54152978779581e+01 , 2.21101300009028e+00 , -1.52054212332034e+01 ) + 31 ( -2.93633996751009e-01 , -1.41137029745784e-02 , 9.55813726277445e-01 ) ( 2.53906813939908e+01 , 2.23407420538864e+00 , -1.52126742337548e+01 ) + 32 ( -2.92255140925596e-01 , -1.51601432225139e-02 , 9.56220216613324e-01 ) ( 2.53631042774826e+01 , 2.25500301034735e+00 , -1.52208040404724e+01 ) + 33 ( -2.90717372797486e-01 , -1.60872298396465e-02 , 9.56673721908266e-01 ) ( 2.53323489149204e+01 , 2.27354474269000e+00 , -1.52298741463712e+01 ) + 34 ( -2.89014188887543e-01 , -1.68855035770422e-02 , 9.57175886862297e-01 ) ( 2.52982852367215e+01 , 2.28951021743791e+00 , -1.52399174454518e+01 ) + 35 ( -2.87142969394406e-01 , -1.75485194704134e-02 , 9.57726978105848e-01 ) ( 2.52608608468588e+01 , 2.30277053530534e+00 , -1.52509392703228e+01 ) + 36 ( -2.85104418391494e-01 , -1.80726295704393e-02 , 9.58326066990801e-01 ) ( 2.52200898268005e+01 , 2.31325273730585e+00 , -1.52629210480219e+01 ) + 37 ( -2.82901971968914e-01 , -1.84568715824041e-02 , 9.58971229050950e-01 ) ( 2.51760408983489e+01 , 2.32093757754515e+00 , -1.52758242892249e+01 ) + 38 ( -2.80541218552965e-01 , -1.87029804430822e-02 , 9.59659743458776e-01 ) ( 2.51288258300300e+01 , 2.32585975475871e+00 , -1.52895945773814e+01 ) + 39 ( -2.78029409440391e-01 , -1.88154958979349e-02 , 9.60388267629474e-01 ) ( 2.50785896477785e+01 , 2.32811006385576e+00 , -1.53041650607953e+01 ) + 40 ( -2.75375163222155e-01 , -1.88018998907846e-02 , 9.61152957671602e-01 ) ( 2.50255047234138e+01 , 2.32783814371276e+00 , -1.53194588616379e+01 ) diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt new file mode 100644 index 000000000..e1d311c69 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt @@ -0,0 +1,3 @@ +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-06-04. +colvars: Using NAMD interface, version "2023-12-05". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in new file mode 100644 index 000000000..dff68dbf5 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in @@ -0,0 +1,41 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + distanceDir { + group1 { + indexGroup group1 + centerToReference yes + rotateToReference yes + #enableFitGradients no + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + group2 { + indexGroup group2 + centerToReference yes + rotateToReference yes + #enableFitGradients no + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + } +} + +harmonic { + colvars one + centers (1.0, 0.1, 0.2) + forceConstant 10.0 +} diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out new file mode 100644 index 000000000..f146e17b2 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out @@ -0,0 +1,4821 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Called colvarcript::init_commands() +colvars: Defined command "cv_addenergy", with help string: +colvars: Add an energy to the MD engine (no effect in VMD) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: E : float - Amount of energy to add +colvars: Defined command "cv_bias", with help string: +colvars: Prefix for bias-specific commands +colvars: Defined command "cv_colvar", with help string: +colvars: Prefix for colvar-specific commands +colvars: Defined command "cv_config", with help string: +colvars: Read configuration from the given string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf : string - Configuration string +colvars: Defined command "cv_configfile", with help string: +colvars: Read configuration from a file +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf_file : string - Path to configuration file +colvars: Defined command "cv_delete", with help string: +colvars: Delete this Colvars module instance (VMD only) +colvars: Defined command "cv_featurereport", with help string: +colvars: Return a summary of Colvars features used so far and their citations +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: report : string - Feature report and citations +colvars: +colvars: Defined command "cv_frame", with help string: +colvars: Get or set current frame number (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: frame : integer - Frame number (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: frame : integer - Frame number +colvars: +colvars: Defined command "cv_getatomappliedforces", with help string: +colvars: Get the list of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic forces +colvars: +colvars: Defined command "cv_getatomappliedforcesmax", with help string: +colvars: Get the maximum norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesmaxid", with help string: +colvars: Get the atom ID with the largest applied force +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: id : int - ID of the atom with the maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesrms", with help string: +colvars: Get the root-mean-square norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - RMS atomic force +colvars: +colvars: Defined command "cv_resetatomappliedforces", with help string: +colvars: Reset forces applied by Colvars to atoms +colvars: Defined command "cv_getatomids", with help string: +colvars: Get the list of indices of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "cv_getatomcharges", with help string: +colvars: Get the list of charges of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: charges : array of floats - Atomic charges +colvars: +colvars: Defined command "cv_getatommasses", with help string: +colvars: Get the list of masses of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: masses : array of floats - Atomic masses +colvars: +colvars: Defined command "cv_getatompositions", with help string: +colvars: Get the list of cached positions of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: positions : array of arrays of floats - Atomic positions +colvars: +colvars: Defined command "cv_getatomtotalforces", with help string: +colvars: Get the list of cached total forces of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic total foces +colvars: +colvars: Defined command "cv_getconfig", with help string: +colvars: Get the module's configuration string read so far +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "cv_getenergy", with help string: +colvars: Get the current Colvars energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Amount of energy (internal units) +colvars: +colvars: Defined command "cv_getnumactiveatomgroups", with help string: +colvars: Get the number of atom groups that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atom groups +colvars: +colvars: Defined command "cv_getnumactiveatoms", with help string: +colvars: Get the number of atoms that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getnumatoms", with help string: +colvars: Get the number of requested atoms, including those not in use now +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getstepabsolute", with help string: +colvars: Get the current step number of the simulation (including restarts) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Absolute step number +colvars: +colvars: Defined command "cv_getsteprelative", with help string: +colvars: Get the current step number from the start of this job +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Relative step number +colvars: +colvars: Defined command "cv_help", with help string: +colvars: Get the help string of the Colvars scripting interface +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "cv_languageversion", with help string: +colvars: Get the C++ language version number +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - C++ language version +colvars: +colvars: Defined command "cv_list", with help string: +colvars: Return a list of all variables or biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: param : string - "colvars" or "biases"; default is "colvars" (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of elements +colvars: +colvars: Defined command "cv_listcommands", with help string: +colvars: Get the list of script functions, prefixed with "cv_", "colvar_" or "bias_" +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of commands +colvars: +colvars: Defined command "cv_listindexfiles", with help string: +colvars: Get a list of the index files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of index file names +colvars: +colvars: Defined command "cv_listinputfiles", with help string: +colvars: Get a list of all input/configuration files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of file names +colvars: +colvars: Defined command "cv_load", with help string: +colvars: Load data from a state file into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Path to existing state file or input prefix +colvars: Defined command "cv_loadfromstring", with help string: +colvars: Load state data from a string into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "cv_molid", with help string: +colvars: Get or set the molecule ID on which Colvars is defined (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: molid : integer - New molecule ID; -1 means undefined (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: molid : integer - Current molecule ID +colvars: +colvars: Defined command "cv_printframe", with help string: +colvars: Return the values that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: values : string - The values +colvars: +colvars: Defined command "cv_printframelabels", with help string: +colvars: Return the labels that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Labels : string - The labels +colvars: +colvars: Defined command "cv_reset", with help string: +colvars: Delete all internal configuration +colvars: Defined command "cv_resetindexgroups", with help string: +colvars: Clear the index groups loaded so far, allowing to replace them +colvars: Defined command "cv_save", with help string: +colvars: Change the prefix of all output files and save them +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Output prefix with trailing ".colvars.state" gets removed) +colvars: Defined command "cv_savetostring", with help string: +colvars: Write the Colvars state to a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The saved state +colvars: +colvars: Defined command "cv_targettemperature", with help string: +colvars: Get/set target temperature, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: T : float - New target temperature in K (internal use) (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: T : float - Current target temperature in K +colvars: +colvars: Defined command "cv_timestep", with help string: +colvars: Get/set integration timestep, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: dt : float - New integration timestep in MD engine units (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: dt : float - Current integration timestep in MD engine units +colvars: +colvars: Defined command "cv_units", with help string: +colvars: Get or set the current Colvars unit system +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: units : string - The new unit system (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: units : string - The current unit system +colvars: +colvars: Defined command "cv_update", with help string: +colvars: Recalculate colvars and biases +colvars: Defined command "cv_version", with help string: +colvars: Get the Colvars Module version string +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - Colvars version +colvars: +colvars: Defined command "colvar_addforce", with help string: +colvars: Apply the given force onto this colvar (no effects outside run) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: force : float or array - Applied force; must match colvar dimensionality +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float or array - Applied force; matches colvar dimensionality +colvars: +colvars: Defined command "colvar_communicateforces", with help string: +colvars: Communicate bias forces from this colvar to atoms +colvars: Defined command "colvar_cvcflags", with help string: +colvars: Enable or disable individual components by setting their active flags +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: flags : integer array - Zero/nonzero value disables/enables the CVC +colvars: Defined command "colvar_delete", with help string: +colvars: Delete this colvar, along with all biases that depend on it +colvars: Defined command "colvar_get", with help string: +colvars: Get the value of the given feature for this colvar +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "colvar_getappliedforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Applied force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_resetbiasforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: Defined command "colvar_getatomgroups", with help string: +colvars: Return the atom indices used by this colvar as a list of lists +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: groups : array of arrays of ints - Atom indices +colvars: +colvars: Defined command "colvar_getatomids", with help string: +colvars: Return the list of atom indices used by this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "colvar_getconfig", with help string: +colvars: Return the configuration string of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "colvar_getgradients", with help string: +colvars: Return the atomic gradients of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: gradients : array of arrays of floats - Atomic gradients +colvars: +colvars: Defined command "colvar_gettotalforce", with help string: +colvars: Return the sum of internal and external forces to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Total force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_getvolmapids", with help string: +colvars: Return the list of volumetric map indices used by this colvar +colvars: Defined command "colvar_help", with help string: +colvars: Get a help summary or the help string of one colvar subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "colvar_modifycvcs", with help string: +colvars: Modify configuration of individual components by passing string arguments +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: confs : sequence of strings - New configurations; empty strings are skipped +colvars: Defined command "colvar_run_ave", with help string: +colvars: Get the current running average of the value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Averaged value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_set", with help string: +colvars: Set the given feature of this colvar to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "colvar_state", with help string: +colvars: Print a string representation of the feature state of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The feature state +colvars: +colvars: Defined command "colvar_type", with help string: +colvars: Get the type description of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type description +colvars: +colvars: Defined command "colvar_update", with help string: +colvars: Recompute this colvar and return its up-to-date value +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_value", with help string: +colvars: Get the current value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_width", with help string: +colvars: Get the width of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: width : float - Value of the width +colvars: +colvars: Defined command "bias_bin", with help string: +colvars: Get the current grid bin index (flattened if more than 1d) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: bin : integer - Bin index +colvars: +colvars: Defined command "bias_bincount", with help string: +colvars: Get the number of samples at the given grid bin (1D ABF only for now) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: index : integer - Grid index; defaults to current bin (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: samples : integer - Number of samples +colvars: +colvars: Defined command "bias_local_sample_count", with help string: +colvars: Get the number of samples around the current binsamples : integer - Number of samples +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: radius : integer - Sum over radius bins around current bin (optional) +colvars: Defined command "bias_binnum", with help string: +colvars: Get the total number of grid points of this bias (1D ABF only for now) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Bins : integer - Number of grid points +colvars: +colvars: Defined command "bias_delete", with help string: +colvars: Delete this bias +colvars: Defined command "bias_energy", with help string: +colvars: Get the current energy of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Defined command "bias_get", with help string: +colvars: Get the value of the given feature for this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "bias_getconfig", with help string: +colvars: Return the configuration string of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "bias_help", with help string: +colvars: Get a help summary or the help string of one bias subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "bias_load", with help string: +colvars: Load data into this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Read from a file with this name or prefix +colvars: Defined command "bias_loadfromstring", with help string: +colvars: Load state data into this bias from a string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "bias_save", with help string: +colvars: Save data from this bias into a file with the given prefix +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Prefix for the state file of this bias +colvars: Defined command "bias_savetostring", with help string: +colvars: Save data from this bias into a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The bias state +colvars: +colvars: Defined command "bias_set", with help string: +colvars: Set the given feature of this bias to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "bias_share", with help string: +colvars: Share bias information with other replicas (multiple-walker scheme) +colvars: Defined command "bias_state", with help string: +colvars: Print a string representation of the feature state of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - String representation of the bias features +colvars: +colvars: Defined command "bias_type", with help string: +colvars: Print the type of this bias object +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type of this bias object (e.g. metadynamics) +colvars: +colvars: Defined command "bias_update", with help string: +colvars: Recompute this bias and return its up-to-date energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: Called script run with 3 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: configfile +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: test.in +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: Executing script function "cv_configfile" +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: Looking for the keyword "logLevel" and its value. +colvars: Keyword "logLevel" not found. +colvars: Looking for the keyword "units" and its value. +colvars: Keyword "units" not found. +colvars: # units = "" [default] +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword value = "index.ndx". +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword "indexFile" not found. +colvars: Looking for the keyword "smp" and its value. +colvars: Keyword "smp" not found. +colvars: # smp = on [default] +colvars: Looking for the keyword "analysis" and its value. +colvars: Keyword "analysis" not found. +colvars: Looking for the keyword "debugGradientsStepSize" and its value. +colvars: Keyword "debugGradientsStepSize" not found. +colvars: Looking for the keyword "monitorEigenvalueCrossing" and its value. +colvars: Keyword "monitorEigenvalueCrossing" not found. +colvars: Looking for the keyword "eigenvalueCrossingThreshold" and its value. +colvars: Keyword "eigenvalueCrossingThreshold" not found. +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword value = "1". +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword "colvarsTrajFrequency" not found. +colvars: # colvarsTrajFrequency = 1 +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword value = "10". +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword "colvarsRestartFrequency" not found. +colvars: # colvarsRestartFrequency = 10 +colvars: Looking for the keyword "scriptedColvarForces" and its value. +colvars: Keyword "scriptedColvarForces" not found. +colvars: # scriptedColvarForces = off [default] +colvars: Looking for the keyword "scriptingAfterBiases" and its value. +colvars: Keyword "scriptingAfterBiases" not found. +colvars: # scriptingAfterBiases = off [default] +colvars: Looking for the keyword "sourceTclFile" and its value. +colvars: Keyword "sourceTclFile" not found. +colvars: # sourceTclFile = "" [default] +colvars: Initializing the collective variables. +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: orientation { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "one" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: ". +colvars: Initializing a new "orientation" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "orientation" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "orientation" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "orientation" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = on +colvars: DEPS: atom group atoms enabling "center_to_reference" +colvars: DEPS: feature "center_to_reference" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = on +colvars: DEPS: atom group atoms enabling "rotate_to_origin" +colvars: DEPS: feature "rotate_to_origin" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "RMSD_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "RMSD_atoms" +colvars: Adding atom 4 for collective variables calculation. +colvars: Adding atom 14 for collective variables calculation. +colvars: Adding atom 24 for collective variables calculation. +colvars: Adding atom 34 for collective variables calculation. +colvars: Adding atom 44 for collective variables calculation. +colvars: Adding atom 54 for collective variables calculation. +colvars: Adding atom 64 for collective variables calculation. +colvars: Adding atom 74 for collective variables calculation. +colvars: Adding atom 84 for collective variables calculation. +colvars: Adding atom 99 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "refPositionsGroup" and its value. +colvars: Keyword "refPositionsGroup" not found. +colvars: Looking for the keyword "fittingGroup" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Within atom group "atoms": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Adding atom 1 for collective variables calculation. +colvars: Adding atom 6 for collective variables calculation. +colvars: Adding atom 10 for collective variables calculation. +colvars: Adding atom 11 for collective variables calculation. +colvars: Adding atom 12 for collective variables calculation. +colvars: Adding atom 16 for collective variables calculation. +colvars: Adding atom 20 for collective variables calculation. +colvars: Adding atom 21 for collective variables calculation. +colvars: Adding atom 22 for collective variables calculation. +colvars: Adding atom 26 for collective variables calculation. +colvars: Adding atom 30 for collective variables calculation. +colvars: Adding atom 31 for collective variables calculation. +colvars: Adding atom 32 for collective variables calculation. +colvars: Adding atom 36 for collective variables calculation. +colvars: Adding atom 40 for collective variables calculation. +colvars: Adding atom 41 for collective variables calculation. +colvars: Adding atom 42 for collective variables calculation. +colvars: Adding atom 46 for collective variables calculation. +colvars: Adding atom 50 for collective variables calculation. +colvars: Adding atom 51 for collective variables calculation. +colvars: Adding atom 52 for collective variables calculation. +colvars: Adding atom 56 for collective variables calculation. +colvars: Adding atom 60 for collective variables calculation. +colvars: Adding atom 61 for collective variables calculation. +colvars: Adding atom 62 for collective variables calculation. +colvars: Adding atom 66 for collective variables calculation. +colvars: Adding atom 70 for collective variables calculation. +colvars: Adding atom 71 for collective variables calculation. +colvars: Adding atom 72 for collective variables calculation. +colvars: Adding atom 76 for collective variables calculation. +colvars: Adding atom 80 for collective variables calculation. +colvars: Adding atom 81 for collective variables calculation. +colvars: Adding atom 82 for collective variables calculation. +colvars: Adding atom 86 for collective variables calculation. +colvars: Adding atom 90 for collective variables calculation. +colvars: Adding atom 91 for collective variables calculation. +colvars: Adding atom 92 for collective variables calculation. +colvars: Adding atom 93 for collective variables calculation. +colvars: Adding atom 94 for collective variables calculation. +colvars: Adding atom 97 for collective variables calculation. +colvars: Adding atom 101 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group atoms enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. +colvars: Warning: atom group "atoms" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group atoms enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group atoms enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group atoms enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: DEPS: unnamed cvc of type "orientation" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "orientation" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "rmsd_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Looking for the keyword "closestToQuaternion" and its value. +colvars: Keyword "closestToQuaternion" not found. +colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] +colvars: Configuration string for "orientation": " +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: ". +colvars: Done initializing a "orientation" component, named "orientation0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 4-dimensional unit quaternion with 4 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: orientation { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: Initializing the collective variables biases. +colvars: Looking for the keyword "abf" and its value. +colvars: Keyword "abf" not found. +colvars: Looking for the keyword "abmd" and its value. +colvars: Keyword "abmd" not found. +colvars: Looking for the keyword "ALB" and its value. +colvars: Keyword "ALB" not found. +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword value = " +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +colvars: forceConstant 10.0 +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "harmonic1" [default] +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword "colvars" not found. +colvars: # colvars = { one } +colvars: Applying this bias to collective variable "one". +colvars: Looking for the keyword "stepZeroData" and its value. +colvars: Keyword "stepZeroData" not found. +colvars: # stepZeroData = off [default] +colvars: DEPS: disabling feature "step_zero_data" in bias harmonic1 +colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword "outputEnergy" not found. +colvars: # outputEnergy = off [default] +colvars: Looking for the keyword "outputFreq" and its value. +colvars: Keyword "outputFreq" not found. +colvars: # outputFreq = 10 [default] +colvars: Looking for the keyword "bypassExtendedLagrangian" and its value. +colvars: Keyword "bypassExtendedLagrangian" not found. +colvars: DEPS: disabling feature "bypass_extended_Lagrangian_coordinates" in bias harmonic1 +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "scaledBiasingForce" and its value. +colvars: Keyword "scaledBiasingForce" not found. +colvars: DEPS: disabling feature "scale_biasing_force" in bias harmonic1 +colvars: DEPS: bias harmonic1 enabling "active" +colvars: DEPS: colvar one testing "active" +colvars: DEPS: re-enabling children's active +colvars: DEPS: colvar one enabling "active" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in bias harmonic1 enabled, ref_count = 1. +colvars: Features of "bias harmonic1" (refcount) +colvars: - ON active +colvars: - awake +colvars: - step_zero_data +colvars: - apply_force +colvars: - bypass_extended_Lagrangian_coordinates +colvars: - obtain_total_force +colvars: - output_accumulated_work +colvars: - history_dependent +colvars: - time_dependent +colvars: - require_scalar_variables +colvars: - calculate_a_PMF +colvars: - calculate_TI_samples +colvars: - write_TI_samples_ +colvars: - write_TI_PMF +colvars: - scale_biasing_force +colvars: - Bias on extended-Lagrangian variables +colvars: * child 1 +colvars: Features of "colvar one" (refcount) +colvars: - ON active (1) +colvars: - awake +colvars: - gradient +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - total_force +colvars: - total_force_calculation +colvars: - subtract_applied_force_from_total_force +colvars: - Jacobian_derivative +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - output_total_force +colvars: - lower_boundary +colvars: - upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - scalar +colvars: - ON linear (1) +colvars: - ON homogeneous +colvars: - multiple_timestep +colvars: * child 1 +colvars: Features of "cvc "orientation0001" of type "orientation"" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON explicit_atom_groups +colvars: - gradient +colvars: - explicit_gradient +colvars: - inverse_gradient +colvars: - Jacobian_derivative +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - function_of_centers_of_mass +colvars: - scalable_calculation +colvars: - scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids +colvars: * child 1 +colvars: Features of "atom group atoms" (refcount) +colvars: - active +colvars: - ON center_to_reference +colvars: - center_to_origin +colvars: - ON rotate_to_origin +colvars: - ON fitting_group +colvars: - ON explicit_atom_gradient (1) +colvars: - ON fit_gradients +colvars: - atomic_forces +colvars: - scalable_group +colvars: - scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: DEPS: bias harmonic1 enabling "apply_force" +colvars: DEPS: colvar one enabling "gradient" +colvars: DEPS: cvc "orientation0001" of type "orientation" enabling "gradient" +colvars: DEPS: feature "gradient" in cvc "orientation0001" of type "orientation" enabled, ref_count = 1. +colvars: DEPS: feature "gradient" in colvar one enabled, ref_count = 1. +colvars: DEPS: feature "apply_force" in bias harmonic1 enabled, ref_count = 1. +colvars: Looking for the keyword "writeTISamples" and its value. +colvars: Keyword "writeTISamples" not found. +colvars: # writeTISamples = off [default] +colvars: DEPS: disabling feature "write_TI_samples_" in bias harmonic1 +colvars: Looking for the keyword "writeTIPMF" and its value. +colvars: Keyword "writeTIPMF" not found. +colvars: # writeTIPMF = off [default] +colvars: DEPS: disabling feature "write_TI_PMF" in bias harmonic1 +colvars: Initializing a new restraint bias. +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword value = "(0.9, 0.5, 0.5, 0.5)". +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword "centers" not found. +colvars: # centers = { ( 0.720577 , 0.40032 , 0.40032 , 0.40032 ) } +colvars: colvarbias_restraint: parsing initial centers, i = 0. +colvars: colvarbias_restraint: parsing target centers. +colvars: Looking for the keyword "targetCenters" and its value. +colvars: Keyword "targetCenters" not found. +colvars: # targetCenters = { ( 0.720577 , 0.40032 , 0.40032 , 0.40032 ) } [default] +colvars: Looking for the keyword "outputCenters" and its value. +colvars: Keyword "outputCenters" not found. +colvars: # outputCenters = off [default] +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword value = "10.0". +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword "forceConstant" not found. +colvars: # forceConstant = 10 +colvars: Looking for the keyword "decoupling" and its value. +colvars: Keyword "decoupling" not found. +colvars: # decoupling = off [default] +colvars: Looking for the keyword "targetForceConstant" and its value. +colvars: Keyword "targetForceConstant" not found. +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 40 according to the specified width (0.5). +colvars: Configuration string for "harmonic": " +colvars: +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +colvars: forceConstant 10.0 +colvars: ". +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword "harmonic" not found. +colvars: Looking for the keyword "harmonicWalls" and its value. +colvars: Keyword "harmonicWalls" not found. +colvars: Looking for the keyword "histogram" and its value. +colvars: Keyword "histogram" not found. +colvars: Looking for the keyword "histogramRestraint" and its value. +colvars: Keyword "histogramRestraint" not found. +colvars: Looking for the keyword "linear" and its value. +colvars: Keyword "linear" not found. +colvars: Looking for the keyword "metadynamics" and its value. +colvars: Keyword "metadynamics" not found. +colvars: Looking for the keyword "reweightaMD" and its value. +colvars: Keyword "reweightaMD" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: Configuration string for "colvarmodule": " +colvars: colvarsTrajFrequency 1 +colvars: colvarsRestartFrequency 10 +colvars: indexFile index.ndx +colvars: colvar { +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: orientation { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +colvars: forceConstant 10.0 +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 0 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 0, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 0, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 0, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 0, atoms_positions[size = 51] = { ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 ), ( 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 ), ( 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 ), ( 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 ), ( 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 ), ( 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 ), ( -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 ), ( -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 ), ( -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 ), ( -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ), ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 ), ( 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 ), ( 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 ), ( 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ), ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 ), ( 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 ), ( 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 ), ( 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ), ( 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 ), ( 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 ), ( 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 ), ( 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 ), ( 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 ), ( 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 ), ( 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 ), ( 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 ), ( 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 ), ( 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 ), ( 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 ), ( -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 ), ( 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 ), ( 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 ), ( -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 ), ( -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 ), ( -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 ), ( -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 ), ( -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 ), ( -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 ), ( -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 ), ( -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 ), ( -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 ), ( -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 ), ( -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 ), ( -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 ), ( -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 ), ( -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 ), ( -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 ), ( -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 ), ( -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 ), ( -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 ), ( -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) } +colvars: Step 0, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atom_groups_ids[size = 0] = +colvars: Step 0, atom_groups_refcount[size = 0] = +colvars: Step 0, atom_groups_masses[size = 0] = +colvars: Step 0, atom_groups_charges[size = 0] = +colvars: Step 0, atom_groups_coms[size = 0] = +colvars: Step 0, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 0, volmaps_ids[size = 0] = +colvars: Step 0, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 0 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.325899 , 16.9799 , 17.1828 , 18.1199 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.325899 , 16.9799 , 17.1828 , 18.1199 ) to colvar "one". +colvars: Adding total bias energy: 11.4 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.325899 , 16.9799 , 17.1828 , 18.1199 ) +colvars: Applying force on main group : +colvars: ( -0.0914855 , 0.387383 , -0.469189 ) +colvars: ( 0.0144955 , 0.0457765 , -0.305096 ) +colvars: ( -0.045855 , 0.102069 , 0.090945 ) +colvars: ( -0.115898 , 0.302237 , 0.0731432 ) +colvars: ( -0.0220234 , 0.12126 , -0.212113 ) +colvars: ( 0.083554 , -0.219864 , -0.0457459 ) +colvars: ( 0.00831741 , -0.109858 , 0.306951 ) +colvars: ( -0.0487266 , 0.074898 , 0.215487 ) +colvars: ( 0.0806562 , -0.231591 , 0.0243652 ) +colvars: ( 0.136965 , -0.472311 , 0.321252 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242619 , -0.099509 , 0.0941691 ) +colvars: ( 0.0197743 , -0.0822842 , 0.0814769 ) +colvars: ( 0.0264141 , -0.0972948 , 0.0583337 ) +colvars: ( 0.012266 , -0.0562309 , 0.0713109 ) +colvars: ( 0.0124028 , -0.0539034 , 0.0602814 ) +colvars: ( 0.00550365 , -0.0358654 , 0.0745595 ) +colvars: ( -0.00253999 , -0.0091824 , 0.0685833 ) +colvars: ( -0.0085687 , 0.00815418 , 0.0747591 ) +colvars: ( -0.00204345 , -0.00357842 , 0.0399323 ) +colvars: ( -0.00572407 , 0.00898773 , 0.0357709 ) +colvars: ( 0.00280344 , -0.013616 , 0.0193567 ) +colvars: ( 0.00420365 , -0.0109922 , -0.00869314 ) +colvars: ( 0.0092221 , -0.0222623 , -0.0264859 ) +colvars: ( 0.00879317 , -0.0238089 , -0.0149203 ) +colvars: ( 0.00670562 , -0.0134687 , -0.0301396 ) +colvars: ( 0.0150473 , -0.0465248 , -0.00239287 ) +colvars: ( 0.0196808 , -0.0603193 , -0.00525839 ) +colvars: ( 0.0275363 , -0.0878761 , 0.00657333 ) +colvars: ( 0.014216 , -0.0466103 , 0.00836819 ) +colvars: ( 0.0141624 , -0.043593 , -0.00303505 ) +colvars: ( 0.00921987 , -0.0371107 , 0.0329673 ) +colvars: ( 0.00303884 , -0.0213887 , 0.0475137 ) +colvars: ( -0.000963776 , -0.0158643 , 0.0755701 ) +colvars: ( -0.00383069 , 0.00384917 , 0.0326059 ) +colvars: ( -0.00591198 , 0.0109771 , 0.0301642 ) +colvars: ( -0.00728977 , 0.0174875 , 0.0213767 ) +colvars: ( -0.0132238 , 0.040328 , 0.00433919 ) +colvars: ( -0.0161563 , 0.0513986 , -0.00321421 ) +colvars: ( -0.00968017 , 0.035611 , -0.021196 ) +colvars: ( -0.013705 , 0.0498622 , -0.0277874 ) +colvars: ( -0.00191793 , 0.014975 , -0.0358941 ) +colvars: ( 0.0024297 , 0.00727988 , -0.0595869 ) +colvars: ( 0.0106648 , -0.0152502 , -0.0726306 ) +colvars: ( 0.00439025 , -0.000289713 , -0.0538644 ) +colvars: ( 0.00337836 , 0.00667816 , -0.0690684 ) +colvars: ( 0.00708426 , -0.0143615 , -0.0313118 ) +colvars: ( 0.00850087 , -0.0210378 , -0.0223472 ) +colvars: ( 0.0129338 , -0.0408167 , 0.00125159 ) +colvars: ( 0.000421517 , 0.0021478 , -0.0138787 ) +colvars: ( 0.000330987 , 0.00388313 , -0.0196891 ) +colvars: ( -0.00659621 , 0.0206663 , -3.74609e-05 ) +colvars: ( -0.0147858 , 0.044299 , 0.00802262 ) +colvars: ( -0.0206332 , 0.0573694 , 0.0289999 ) +colvars: ( -0.0189787 , 0.0632654 , -0.0153318 ) +colvars: ( -0.0226927 , 0.0752153 , -0.0166095 ) +colvars: ( -0.0167512 , 0.0728367 , -0.0815558 ) +colvars: ( -0.0198067 , 0.0870491 , -0.10014 ) +colvars: ( -0.0085258 , 0.0471754 , -0.0819464 ) +colvars: ( -0.0185683 , 0.0667252 , -0.0343222 ) +colvars: ( -0.0222448 , 0.0840291 , -0.0574973 ) +colvars: ( -0.0242478 , 0.0927893 , -0.0674521 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 0. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 0. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atoms_new_colvar_forces = { ( -7.17112331393693e-02 , 3.05098327565957e-01 , -3.87711644832293e-01 ), ( 1.19555459248557e-02 , 3.65941097357604e-02 , -2.36512628285003e-01 ), ( -4.16513128784966e-02 , 9.10770464245731e-02 , 8.22518324392786e-02 ), ( -9.62168257886831e-02 , 2.41917479955852e-01 , 6.78847980688516e-02 ), ( -1.89845157517858e-02 , 9.98710219002420e-02 , -1.64599111102358e-01 ), ( 7.03301603774896e-02 , -1.79535932890023e-01 , -4.14067432161946e-02 ), ( 1.07471104828031e-02 , -1.02577848089066e-01 , 2.47364312690905e-01 ), ( -4.02256833871764e-02 , 5.38601721942073e-02 , 1.93139708020977e-01 ), ( 6.58704306067279e-02 , -1.87291492706406e-01 , 3.23878619810793e-02 ), ( 1.14720183887631e-01 , -3.88281468777201e-01 , 2.63754453050035e-01 ), ( 2.42618507983615e-02 , -9.95090220875313e-02 , 9.41691127788629e-02 ), ( 2.64140528573990e-02 , -9.72948413283316e-02 , 5.83337189788877e-02 ), ( 1.22660085012390e-02 , -5.62309126513698e-02 , 7.13109049758973e-02 ), ( 1.24027961622539e-02 , -5.39033622796542e-02 , 6.02813703425287e-02 ), ( 5.50365180277709e-03 , -3.58654134074757e-02 , 7.45595484006017e-02 ), ( -8.56869612739025e-03 , 8.15418354809084e-03 , 7.47590614158032e-02 ), ( -2.04345135727017e-03 , -3.57842067967311e-03 , 3.99322594237481e-02 ), ( -5.72407370686545e-03 , 8.98773129963851e-03 , 3.57708956627444e-02 ), ( 2.80344276950839e-03 , -1.36159740030154e-02 , 1.93567445096325e-02 ), ( 9.22210196636199e-03 , -2.22622813867358e-02 , -2.64859467986244e-02 ), ( 8.79316761791039e-03 , -2.38089040285720e-02 , -1.49202518973436e-02 ), ( 6.70562195329319e-03 , -1.34686650666172e-02 , -3.01395709833031e-02 ), ( 1.50473126186007e-02 , -4.65247806418302e-02 , -2.39287487045654e-03 ), ( 2.75363017231425e-02 , -8.78760894143468e-02 , 6.57333075023515e-03 ), ( 1.42160293860021e-02 , -4.66103438169562e-02 , 8.36819326569623e-03 ), ( 1.41623599363496e-02 , -4.35929741103034e-02 , -3.03504901951588e-03 ), ( 9.21986652441758e-03 , -3.71107050197726e-02 , 3.29673234888841e-02 ), ( -9.63775655681931e-04 , -1.58643052576496e-02 , 7.55701254462465e-02 ), ( -3.83069289063363e-03 , 3.84917215687278e-03 , 3.26059455401106e-02 ), ( -5.91198486374499e-03 , 1.09771288603378e-02 , 3.01642040800903e-02 ), ( -7.28976560942452e-03 , 1.74875351287834e-02 , 2.13767345680998e-02 ), ( -1.61562664646153e-02 , 5.13986449348097e-02 , -3.21420801068685e-03 ), ( -9.68017103615191e-03 , 3.56109507442153e-02 , -2.11960333401958e-02 ), ( -1.37049814773182e-02 , 4.98621539927025e-02 , -2.77874076093298e-02 ), ( -1.91792500276001e-03 , 1.49750007080970e-02 , -3.58941052675410e-02 ), ( 1.06647740597758e-02 , -1.52501737314967e-02 , -7.26305692651966e-02 ), ( 4.39025313827158e-03 , -2.89712934588417e-04 , -5.38644244704754e-02 ), ( 3.37835546017515e-03 , 6.67816083650675e-03 , -6.90684195578746e-02 ), ( 7.08425965807474e-03 , -1.43615244078311e-02 , -3.13117755624624e-02 ), ( 1.29337999684502e-02 , -4.08166651615065e-02 , 1.25159424194878e-03 ), ( 4.21517000834667e-04 , 2.14779898690001e-03 , -1.38787149564562e-02 ), ( 3.30986545488312e-04 , 3.88313347866908e-03 , -1.96891054554931e-02 ), ( -6.59621209084941e-03 , 2.06662848702344e-02 , -3.74608751278817e-05 ), ( -2.06331572427302e-02 , 5.73693700933228e-02 , 2.89999395613771e-02 ), ( -1.89787290812637e-02 , 6.32653631722135e-02 , -1.53318322023093e-02 ), ( -2.26926653990437e-02 , 7.52153031654799e-02 , -1.66095079265972e-02 ), ( -1.67511882905597e-02 , 7.28367292485312e-02 , -8.15558389781937e-02 ), ( -1.98067264091487e-02 , 8.70491413541379e-02 , -1.00140043772665e-01 ), ( -8.52580045706230e-03 , 4.71754189750805e-02 , -8.19464349448593e-02 ), ( -1.85683188859792e-02 , 6.67251710260006e-02 , -3.43221673997345e-02 ), ( -2.42477887341905e-02 , 9.27892795207383e-02 , -6.74521030822303e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 0, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 1 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 1, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 1, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 1, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 1, atoms_positions[size = 51] = { ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 ), ( 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 ), ( 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 ), ( 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 ), ( 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 ), ( 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 ), ( -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 ), ( -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 ), ( -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 ), ( -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ), ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 ), ( 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 ), ( 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 ), ( 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 ), ( 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 ), ( 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 ), ( 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 ), ( 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 ), ( 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 ), ( 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 ), ( 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 ), ( 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 ), ( 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 ), ( 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 ), ( 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 ), ( 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 ), ( 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 ), ( 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 ), ( 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 ), ( -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 ), ( 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 ), ( 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 ), ( -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 ), ( -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 ), ( -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 ), ( -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 ), ( -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 ), ( -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 ), ( -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 ), ( -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 ), ( -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 ), ( -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 ), ( -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 ), ( -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 ), ( -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 ), ( -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 ), ( -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 ), ( -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 ), ( -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 ), ( -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 ), ( -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ) } +colvars: Step 1, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atom_groups_ids[size = 0] = +colvars: Step 1, atom_groups_refcount[size = 0] = +colvars: Step 1, atom_groups_masses[size = 0] = +colvars: Step 1, atom_groups_charges[size = 0] = +colvars: Step 1, atom_groups_coms[size = 0] = +colvars: Step 1, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 1, volmaps_ids[size = 0] = +colvars: Step 1, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 1 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.321564 , 16.9819 , 17.1859 , 18.1247 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.321564 , 16.9819 , 17.1859 , 18.1247 ) to colvar "one". +colvars: Adding total bias energy: 11.4044 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.321564 , 16.9819 , 17.1859 , 18.1247 ) +colvars: Applying force on main group : +colvars: ( -0.0912787 , 0.387178 , -0.469438 ) +colvars: ( 0.0145922 , 0.0456048 , -0.305129 ) +colvars: ( -0.0458554 , 0.102118 , 0.0908979 ) +colvars: ( -0.115858 , 0.302319 , 0.0729669 ) +colvars: ( -0.0219428 , 0.121167 , -0.212198 ) +colvars: ( 0.083524 , -0.219922 , -0.0456155 ) +colvars: ( 0.0082118 , -0.109708 , 0.307032 ) +colvars: ( -0.0487751 , 0.0750392 , 0.215444 ) +colvars: ( 0.0805998 , -0.231596 , 0.0244957 ) +colvars: ( 0.136782 , -0.472199 , 0.321545 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242477 , -0.0994947 , 0.0942202 ) +colvars: ( 0.0197636 , -0.0822787 , 0.081522 ) +colvars: ( 0.0264136 , -0.0972997 , 0.0583864 ) +colvars: ( 0.0122549 , -0.0562266 , 0.0713435 ) +colvars: ( 0.0123936 , -0.053898 , 0.0603111 ) +colvars: ( 0.00549001 , -0.0358637 , 0.0745845 ) +colvars: ( -0.00255532 , -0.00918127 , 0.0685958 ) +colvars: ( -0.00858663 , 0.00815197 , 0.0747659 ) +colvars: ( -0.00205062 , -0.00358459 , 0.0399413 ) +colvars: ( -0.00573267 , 0.00898459 , 0.0357727 ) +colvars: ( 0.00280516 , -0.0136319 , 0.0193713 ) +colvars: ( 0.00421382 , -0.0110156 , -0.00868052 ) +colvars: ( 0.00924091 , -0.0222964 , -0.0264666 ) +colvars: ( 0.00880524 , -0.0238285 , -0.0149042 ) +colvars: ( 0.00672045 , -0.0134897 , -0.0301295 ) +colvars: ( 0.0150576 , -0.0465389 , -0.00236712 ) +colvars: ( 0.0196922 , -0.0603288 , -0.00522859 ) +colvars: ( 0.0275473 , -0.0878823 , 0.00661567 ) +colvars: ( 0.0142198 , -0.0466104 , 0.00839006 ) +colvars: ( 0.0141681 , -0.0435921 , -0.00301635 ) +colvars: ( 0.00921461 , -0.0371037 , 0.0329854 ) +colvars: ( 0.0030257 , -0.0213728 , 0.0475234 ) +colvars: ( -0.000986126 , -0.0158418 , 0.0755784 ) +colvars: ( -0.0038424 , 0.0038615 , 0.0326038 ) +colvars: ( -0.00592522 , 0.0109937 , 0.0301569 ) +colvars: ( -0.00729812 , 0.0174917 , 0.0213701 ) +colvars: ( -0.0132295 , 0.0403271 , 0.00432209 ) +colvars: ( -0.0161591 , 0.0513892 , -0.00323396 ) +colvars: ( -0.00967789 , 0.0356052 , -0.0212125 ) +colvars: ( -0.0137034 , 0.0498583 , -0.0278117 ) +colvars: ( -0.00190789 , 0.0149632 , -0.0359009 ) +colvars: ( 0.00244756 , 0.00726349 , -0.0595916 ) +colvars: ( 0.0106906 , -0.015274 , -0.0726241 ) +colvars: ( 0.0044053 , -0.000297824 , -0.0538682 ) +colvars: ( 0.00339644 , 0.00666896 , -0.0690768 ) +colvars: ( 0.00709322 , -0.014361 , -0.0313096 ) +colvars: ( 0.00850598 , -0.0210284 , -0.0223442 ) +colvars: ( 0.0129336 , -0.0407998 , 0.00126359 ) +colvars: ( 0.000419979 , 0.00216349 , -0.0138874 ) +colvars: ( 0.000329655 , 0.0039021 , -0.0197005 ) +colvars: ( -0.00660377 , 0.0206837 , -5.32553e-05 ) +colvars: ( -0.0147996 , 0.0443218 , 0.00799532 ) +colvars: ( -0.0206544 , 0.0573951 , 0.0289684 ) +colvars: ( -0.0189875 , 0.0632816 , -0.0153681 ) +colvars: ( -0.0227038 , 0.0752357 , -0.0166529 ) +colvars: ( -0.0167393 , 0.0728312 , -0.0815967 ) +colvars: ( -0.0197909 , 0.0870392 , -0.100188 ) +colvars: ( -0.00851097 , 0.0471709 , -0.0819763 ) +colvars: ( -0.0185701 , 0.066731 , -0.0343585 ) +colvars: ( -0.0222411 , 0.0840279 , -0.0575417 ) +colvars: ( -0.0242402 , 0.0927787 , -0.0674981 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 1. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 1. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atoms_new_colvar_forces = { ( -7.15151729651260e-02 , 3.04899243481533e-01 , -3.87916030963302e-01 ), ( 1.20368649362899e-02 , 3.64235792090596e-02 , -2.36533693202075e-01 ), ( -4.16415878718478e-02 , 9.11022438626934e-02 , 8.22174068287411e-02 ), ( -9.61659395369152e-02 , 2.41989972764637e-01 , 6.77382993270643e-02 ), ( -1.89170945988754e-02 , 9.97945490695020e-02 , -1.64675032270572e-01 ), ( 7.02945076928405e-02 , -1.79595291976670e-01 , -4.12934261331383e-02 ), ( 1.06593636141036e-02 , -1.02444767354498e-01 , 2.47440239914315e-01 ), ( -4.02691431255613e-02 , 5.40107887471147e-02 , 1.93099494398337e-01 ), ( 6.58001964113642e-02 , -1.87274572435745e-01 , 3.24910083791860e-02 ), ( 1.14541196581312e-01 , -3.88171056981776e-01 , 2.64003649424930e-01 ), ( 2.42477192528996e-02 , -9.94947081114131e-02 , 9.42201611607529e-02 ), ( 2.64136166976736e-02 , -9.72996799526701e-02 , 5.83863996262244e-02 ), ( 1.22548721116594e-02 , -5.62266396301048e-02 , 7.13435168350051e-02 ), ( 1.23936399651521e-02 , -5.38979530864836e-02 , 6.03110988177678e-02 ), ( 5.49001413551297e-03 , -3.58637287706379e-02 , 7.45844785550286e-02 ), ( -8.58662775485298e-03 , 8.15197217862955e-03 , 7.47658701006714e-02 ), ( -2.05061868858449e-03 , -3.58458690191429e-03 , 3.99413123521106e-02 ), ( -5.73267269837427e-03 , 8.98459258558919e-03 , 3.57726717890164e-02 ), ( 2.80515992656613e-03 , -1.36318939949399e-02 , 1.93713053854992e-02 ), ( 9.24091216374164e-03 , -2.22963827594714e-02 , -2.64665663613212e-02 ), ( 8.80524457636114e-03 , -2.38284772346292e-02 , -1.49041760335850e-02 ), ( 6.72044863046050e-03 , -1.34897386302215e-02 , -3.01294931954585e-02 ), ( 1.50576435827247e-02 , -4.65389127767602e-02 , -2.36711837470063e-03 ), ( 2.75472753380666e-02 , -8.78822788846253e-02 , 6.61567117283608e-03 ), ( 1.42197676549019e-02 , -4.66103962861243e-02 , 8.39005985454352e-03 ), ( 1.41681378086040e-02 , -4.35920831820608e-02 , -3.01634853592154e-03 ), ( 9.21461496103597e-03 , -3.71036824034249e-02 , 3.29854494207997e-02 ), ( -9.86126451234636e-04 , -1.58417642622825e-02 , 7.55784048787670e-02 ), ( -3.84239612560993e-03 , 3.86150425286693e-03 , 3.26037689714234e-02 ), ( -5.92521514581768e-03 , 1.09937156748894e-02 , 3.01569322569409e-02 ), ( -7.29812275527947e-03 , 1.74916709978540e-02 , 2.13701287787168e-02 ), ( -1.61590546113848e-02 , 5.13892040394262e-02 , -3.23396497301815e-03 ), ( -9.67788551506929e-03 , 3.56052475625837e-02 , -2.12124757482175e-02 ), ( -1.37034108862765e-02 , 4.98582644999593e-02 , -2.78117321811795e-02 ), ( -1.90789273977489e-03 , 1.49631727913749e-02 , -3.59009302348894e-02 ), ( 1.06906045511525e-02 , -1.52740011368780e-02 , -7.26241198821211e-02 ), ( 4.40529849774725e-03 , -2.97823815696022e-04 , -5.38681586639291e-02 ), ( 3.39643922578235e-03 , 6.66896241573230e-03 , -6.90768027297062e-02 ), ( 7.09321783492851e-03 , -1.43609832339387e-02 , -3.13096039888957e-02 ), ( 1.29336183664370e-02 , -4.07998296242983e-02 , 1.26359385658362e-03 ), ( 4.19979277285392e-04 , 2.16348662453615e-03 , -1.38873734861057e-02 ), ( 3.29655166819156e-04 , 3.90209739378588e-03 , -1.97005199557689e-02 ), ( -6.60377269842420e-03 , 2.06837283573336e-02 , -5.32553285992549e-05 ), ( -2.06544209370330e-02 , 5.73950938853213e-02 , 2.89683973885608e-02 ), ( -1.89875466809821e-02 , 6.32816036261560e-02 , -1.53681222592533e-02 ), ( -2.27038413337324e-02 , 7.52356909090834e-02 , -1.66528519569391e-02 ), ( -1.67393048554064e-02 , 7.28311918128840e-02 , -8.15966907597996e-02 ), ( -1.97909234720973e-02 , 8.70391604498609e-02 , -1.00187941489201e-01 ), ( -8.51097375894001e-03 , 4.71708543895567e-02 , -8.19762682790733e-02 ), ( -1.85700756693449e-02 , 6.67309773118485e-02 , -3.43585040385876e-02 ), ( -2.42401880848779e-02 , 9.27786645334536e-02 , -6.74981184484641e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 1, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 2 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 2, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 2, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 2, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 2, atoms_positions[size = 51] = { ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 ), ( 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 ), ( 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 ), ( 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 ), ( 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 ), ( 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 ), ( -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 ), ( -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 ), ( -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 ), ( -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ), ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 ), ( 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 ), ( 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 ), ( 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 ), ( 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 ), ( 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 ), ( 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 ), ( 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 ), ( 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 ), ( 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 ), ( 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 ), ( 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 ), ( 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 ), ( 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 ), ( 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 ), ( 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 ), ( 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 ), ( 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 ), ( 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 ), ( -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 ), ( 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 ), ( 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 ), ( -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 ), ( -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 ), ( -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 ), ( -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 ), ( -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 ), ( -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 ), ( -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 ), ( -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 ), ( -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 ), ( -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 ), ( -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 ), ( -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 ), ( -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 ), ( -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 ), ( -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 ), ( -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 ), ( -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 ), ( -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 ), ( -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ) } +colvars: Step 2, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atom_groups_ids[size = 0] = +colvars: Step 2, atom_groups_refcount[size = 0] = +colvars: Step 2, atom_groups_masses[size = 0] = +colvars: Step 2, atom_groups_charges[size = 0] = +colvars: Step 2, atom_groups_coms[size = 0] = +colvars: Step 2, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 2, volmaps_ids[size = 0] = +colvars: Step 2, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 2 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.317383 , 16.9856 , 17.1892 , 18.1276 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.317383 , 16.9856 , 17.1892 , 18.1276 ) to colvar "one". +colvars: Adding total bias energy: 11.4086 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.317383 , 16.9856 , 17.1892 , 18.1276 ) +colvars: Applying force on main group : +colvars: ( -0.091124 , 0.386959 , -0.469762 ) +colvars: ( 0.0146691 , 0.0453691 , -0.305174 ) +colvars: ( -0.0458469 , 0.102162 , 0.090916 ) +colvars: ( -0.115827 , 0.302459 , 0.0727965 ) +colvars: ( -0.0218867 , 0.121077 , -0.212343 ) +colvars: ( 0.0835022 , -0.220029 , -0.0454782 ) +colvars: ( 0.00813549 , -0.109536 , 0.307174 ) +colvars: ( -0.048817 , 0.0752539 , 0.215389 ) +colvars: ( 0.0805502 , -0.231606 , 0.0245895 ) +colvars: ( 0.136645 , -0.472109 , 0.321893 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242404 , -0.0994785 , 0.0942791 ) +colvars: ( 0.0197577 , -0.0822678 , 0.0815733 ) +colvars: ( 0.0264151 , -0.0973002 , 0.0584427 ) +colvars: ( 0.012248 , -0.0562158 , 0.0713815 ) +colvars: ( 0.0123883 , -0.0538885 , 0.0603456 ) +colvars: ( 0.00548062 , -0.0358515 , 0.0746148 ) +colvars: ( -0.00256663 , -0.00916782 , 0.0686132 ) +colvars: ( -0.00860057 , 0.0081667 , 0.0747778 ) +colvars: ( -0.00205646 , -0.00358005 , 0.0399526 ) +colvars: ( -0.00573963 , 0.0089911 , 0.0357767 ) +colvars: ( 0.0028055 , -0.0136375 , 0.0193858 ) +colvars: ( 0.0042199 , -0.0110304 , -0.00867064 ) +colvars: ( 0.00925294 , -0.0223213 , -0.0264522 ) +colvars: ( 0.00881337 , -0.0238438 , -0.0148909 ) +colvars: ( 0.0067303 , -0.0135079 , -0.0301235 ) +colvars: ( 0.0150654 , -0.0465513 , -0.00234284 ) +colvars: ( 0.0197014 , -0.0603408 , -0.00520006 ) +colvars: ( 0.0275571 , -0.087893 , 0.00665785 ) +colvars: ( 0.0142236 , -0.0466134 , 0.00841248 ) +colvars: ( 0.0141736 , -0.0435966 , -0.00299782 ) +colvars: ( 0.00921202 , -0.0370972 , 0.0330065 ) +colvars: ( 0.00301748 , -0.0213574 , 0.0475379 ) +colvars: ( -0.00100091 , -0.0158167 , 0.0755941 ) +colvars: ( -0.00385036 , 0.00387472 , 0.032605 ) +colvars: ( -0.00593416 , 0.0110093 , 0.0301533 ) +colvars: ( -0.00730451 , 0.0174998 , 0.0213654 ) +colvars: ( -0.0132348 , 0.0403316 , 0.00430525 ) +colvars: ( -0.0161631 , 0.0513889 , -0.00325476 ) +colvars: ( -0.0096774 , 0.0356017 , -0.0212309 ) +colvars: ( -0.0137036 , 0.0498557 , -0.0278383 ) +colvars: ( -0.00190157 , 0.0149514 , -0.0359114 ) +colvars: ( 0.00245963 , 0.0072439 , -0.0596021 ) +colvars: ( 0.0107086 , -0.0153023 , -0.072625 ) +colvars: ( 0.00441605 , -0.00031281 , -0.0538765 ) +colvars: ( 0.00340925 , 0.00665107 , -0.0690909 ) +colvars: ( 0.00710037 , -0.0143685 , -0.0313096 ) +colvars: ( 0.00851106 , -0.0210302 , -0.022342 ) +colvars: ( 0.0129357 , -0.0407951 , 0.00127717 ) +colvars: ( 0.000420014 , 0.00216889 , -0.0138956 ) +colvars: ( 0.000330068 , 0.00390817 , -0.0197116 ) +colvars: ( -0.00660857 , 0.0206947 , -6.74622e-05 ) +colvars: ( -0.0148093 , 0.0443395 , 0.00797068 ) +colvars: ( -0.0206698 , 0.0574198 , 0.0289413 ) +colvars: ( -0.0189943 , 0.0632932 , -0.015404 ) +colvars: ( -0.0227124 , 0.0752503 , -0.0166955 ) +colvars: ( -0.0167324 , 0.0728193 , -0.0816438 ) +colvars: ( -0.0197817 , 0.0870227 , -0.100244 ) +colvars: ( -0.00850116 , 0.0471568 , -0.0820123 ) +colvars: ( -0.0185724 , 0.0667338 , -0.0343967 ) +colvars: ( -0.0222404 , 0.0840242 , -0.0575902 ) +colvars: ( -0.0242373 , 0.0927691 , -0.0675498 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 2. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 2. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atoms_new_colvar_forces = { ( -7.13662406347475e-02 , 3.04690881238521e-01 , -3.88189014550433e-01 ), ( 1.21024777996464e-02 , 3.62012543772250e-02 , -2.36560385329191e-01 ), ( -4.16270344260805e-02 , 9.11317483620320e-02 , 8.22453445505728e-02 ), ( -9.61258643475432e-02 , 2.42118549983633e-01 , 6.75964639859510e-02 ), ( -1.88692093361642e-02 , 9.97197189297282e-02 , -1.64805343769547e-01 ), ( 7.02674381185762e-02 , -1.79697300167168e-01 , -4.11729051286209e-02 ), ( 1.05951211671063e-02 , -1.02292489843847e-01 , 2.47571722543744e-01 ), ( -4.03059854417923e-02 , 5.42236285493406e-02 , 1.93046549392435e-01 ), ( 6.57408551090289e-02 , -1.87266309856294e-01 , 3.25601520815156e-02 ), ( 1.14404466188646e-01 , -3.88084904837303e-01 , 2.64302707504789e-01 ), ( 2.42403744165811e-02 , -9.94785187554915e-02 , 9.42791291950214e-02 ), ( 2.64150718872813e-02 , -9.73002134525345e-02 , 5.84427219892992e-02 ), ( 1.22480322060636e-02 , -5.62157918593996e-02 , 7.13815477024520e-02 ), ( 1.23883380687533e-02 , -5.38885112017688e-02 , 6.03455655484888e-02 ), ( 5.48062002843824e-03 , -3.58514915394607e-02 , 7.46148407252745e-02 ), ( -8.60056519272734e-03 , 8.16670443437686e-03 , 7.47778066468873e-02 ), ( -2.05645685993396e-03 , -3.58005212530679e-03 , 3.99526483103971e-02 ), ( -5.73963473120446e-03 , 8.99109627006217e-03 , 3.57767175444479e-02 ), ( 2.80549872017285e-03 , -1.36374684939331e-02 , 1.93857966829495e-02 ), ( 9.25294348776421e-03 , -2.23212932966850e-02 , -2.64521663051807e-02 ), ( 8.81336594162522e-03 , -2.38438300993918e-02 , -1.48909470506634e-02 ), ( 6.73030250851154e-03 , -1.35078732001586e-02 , -3.01234731955913e-02 ), ( 1.50653818005725e-02 , -4.65512686167406e-02 , -2.34284311242762e-03 ), ( 2.75570538265062e-02 , -8.78929598017612e-02 , 6.65785423175934e-03 ), ( 1.42236341148245e-02 , -4.66134370995714e-02 , 8.41248205826075e-03 ), ( 1.41735565627240e-02 , -4.35966335485880e-02 , -2.99781666970647e-03 ), ( 9.21202377418917e-03 , -3.70972210496742e-02 , 3.30065277669219e-02 ), ( -1.00090754604269e-03 , -1.58167028261417e-02 , 7.55940860707059e-02 ), ( -3.85036480540487e-03 , 3.87472044758625e-03 , 3.26050293851104e-02 ), ( -5.93416109216629e-03 , 1.10093226221347e-02 , 3.01533130775972e-02 ), ( -7.30451303321866e-03 , 1.74998354864693e-02 , 2.13654311507231e-02 ), ( -1.61630628639610e-02 , 5.13889365763393e-02 , -3.25476401672865e-03 ), ( -9.67740222362291e-03 , 3.56016733585189e-02 , -2.12309147297704e-02 ), ( -1.37036427268514e-02 , 4.98557230830785e-02 , -2.78383479874705e-02 ), ( -1.90156928795647e-03 , 1.49514486553429e-02 , -3.59113664694244e-02 ), ( 1.07086125914830e-02 , -1.53022610381287e-02 , -7.26250027034179e-02 ), ( 4.41605431417831e-03 , -3.12810190896927e-04 , -5.38764592683203e-02 ), ( 3.40925420915234e-03 , 6.65106748886611e-03 , -6.90909274179423e-02 ), ( 7.10036528785388e-03 , -1.43684525078162e-02 , -3.13096231913525e-02 ), ( 1.29357293014539e-02 , -4.07951303363235e-02 , 1.27717136871923e-03 ), ( 4.20013690039623e-04 , 2.16888898682387e-03 , -1.38956021720835e-02 ), ( 3.30067539764028e-04 , 3.90817206331382e-03 , -1.97116211345700e-02 ), ( -6.60857296101589e-03 , 2.06946733874849e-02 , -6.74622074879811e-05 ), ( -2.06697591996960e-02 , 5.74197879098366e-02 , 2.89412848935110e-02 ), ( -1.89943446265396e-02 , 6.32931538792098e-02 , -1.54039897267542e-02 ), ( -2.27123621770474e-02 , 7.52502973237281e-02 , -1.66954809253169e-02 ), ( -1.67323700772781e-02 , 7.28193141294979e-02 , -8.16437923409835e-02 ), ( -1.97816905755823e-02 , 8.70227179902238e-02 , -1.00243802160594e-01 ), ( -8.50116034360863e-03 , 4.71568068651273e-02 , -8.20123108275631e-02 ), ( -1.85724328597233e-02 , 6.67337512843182e-02 , -3.43967090628983e-02 ), ( -2.42373452910282e-02 , 9.27690520615654e-02 , -6.75498229534928e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 2, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 3 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 3, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 3, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 3, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 3, atoms_positions[size = 51] = { ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 ), ( 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 ), ( 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 ), ( 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 ), ( 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 ), ( 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 ), ( -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 ), ( -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 ), ( -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 ), ( -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ), ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 ), ( 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 ), ( 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 ), ( 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 ), ( 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 ), ( 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 ), ( 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 ), ( 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 ), ( 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 ), ( 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 ), ( 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 ), ( 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 ), ( 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 ), ( 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 ), ( 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 ), ( 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 ), ( 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 ), ( 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 ), ( 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 ), ( -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 ), ( 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 ), ( 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 ), ( -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 ), ( -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 ), ( -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 ), ( -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 ), ( -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 ), ( -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 ), ( -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 ), ( -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 ), ( -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 ), ( -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 ), ( -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 ), ( -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 ), ( -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 ), ( -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 ), ( -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 ), ( -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 ), ( -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 ), ( -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 ), ( -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ) } +colvars: Step 3, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atom_groups_ids[size = 0] = +colvars: Step 3, atom_groups_refcount[size = 0] = +colvars: Step 3, atom_groups_masses[size = 0] = +colvars: Step 3, atom_groups_charges[size = 0] = +colvars: Step 3, atom_groups_coms[size = 0] = +colvars: Step 3, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 3, volmaps_ids[size = 0] = +colvars: Step 3, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 3 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.31341 , 16.9909 , 17.1929 , 18.1283 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.31341 , 16.9909 , 17.1929 , 18.1283 ) to colvar "one". +colvars: Adding total bias energy: 11.4128 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.31341 , 16.9909 , 17.1929 , 18.1283 ) +colvars: Applying force on main group : +colvars: ( -0.0910214 , 0.386732 , -0.470161 ) +colvars: ( 0.0147286 , 0.0450715 , -0.305228 ) +colvars: ( -0.0458313 , 0.102201 , 0.0910038 ) +colvars: ( -0.115809 , 0.30266 , 0.0726359 ) +colvars: ( -0.0218546 , 0.120992 , -0.212549 ) +colvars: ( 0.0834914 , -0.220185 , -0.045336 ) +colvars: ( 0.0080871 , -0.109346 , 0.307379 ) +colvars: ( -0.0488551 , 0.0755417 , 0.215322 ) +colvars: ( 0.0805094 , -0.23162 , 0.0246419 ) +colvars: ( 0.136555 , -0.472047 , 0.322292 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.02424 , -0.0994602 , 0.0943451 ) +colvars: ( 0.0197569 , -0.0822515 , 0.0816304 ) +colvars: ( 0.0264188 , -0.097296 , 0.0585027 ) +colvars: ( 0.0122455 , -0.0561986 , 0.0714248 ) +colvars: ( 0.0123869 , -0.0538751 , 0.0603845 ) +colvars: ( 0.00547533 , -0.0358294 , 0.0746508 ) +colvars: ( -0.00257422 , -0.00914307 , 0.068636 ) +colvars: ( -0.00861093 , 0.00819692 , 0.0747956 ) +colvars: ( -0.00206113 , -0.00356557 , 0.0399669 ) +colvars: ( -0.00574519 , 0.00900642 , 0.0357835 ) +colvars: ( 0.00280448 , -0.0136331 , 0.0194012 ) +colvars: ( 0.00422205 , -0.0110366 , -0.00866222 ) +colvars: ( 0.00925853 , -0.0223369 , -0.026441 ) +colvars: ( 0.0088178 , -0.0238547 , -0.0148796 ) +colvars: ( 0.00673546 , -0.0135228 , -0.0301205 ) +colvars: ( 0.0150709 , -0.0465613 , -0.00231954 ) +colvars: ( 0.0197089 , -0.0603544 , -0.00517271 ) +colvars: ( 0.0275662 , -0.0879069 , 0.00669967 ) +colvars: ( 0.0142279 , -0.0466189 , 0.00843518 ) +colvars: ( 0.0141789 , -0.0436058 , -0.00297984 ) +colvars: ( 0.00921216 , -0.0370911 , 0.0330301 ) +colvars: ( 0.00301407 , -0.0213424 , 0.0475563 ) +colvars: ( -0.00100842 , -0.0157897 , 0.0756162 ) +colvars: ( -0.00385481 , 0.00388845 , 0.0326092 ) +colvars: ( -0.00593907 , 0.0110236 , 0.0301526 ) +colvars: ( -0.00730917 , 0.0175115 , 0.0213627 ) +colvars: ( -0.01324 , 0.0403407 , 0.00428905 ) +colvars: ( -0.0161686 , 0.0513969 , -0.00327568 ) +colvars: ( -0.00967884 , 0.0355999 , -0.0212509 ) +colvars: ( -0.0137059 , 0.0498541 , -0.0278668 ) +colvars: ( -0.00189886 , 0.01494 , -0.0359248 ) +colvars: ( 0.00246616 , 0.00722169 , -0.0596176 ) +colvars: ( 0.0107193 , -0.0153339 , -0.0726324 ) +colvars: ( 0.0044228 , -0.000333908 , -0.0538892 ) +colvars: ( 0.00341711 , 0.00662537 , -0.0691106 ) +colvars: ( 0.00710595 , -0.0143832 , -0.0313122 ) +colvars: ( 0.00851636 , -0.0210424 , -0.0223414 ) +colvars: ( 0.0129404 , -0.0408016 , 0.00129102 ) +colvars: ( 0.00042165 , 0.00216453 , -0.0139044 ) +colvars: ( 0.000332266 , 0.00390202 , -0.0197237 ) +colvars: ( -0.00661078 , 0.0206991 , -8.09922e-05 ) +colvars: ( -0.0148152 , 0.0443516 , 0.00794768 ) +colvars: ( -0.0206797 , 0.0574425 , 0.0289176 ) +colvars: ( -0.0189995 , 0.0632996 , -0.0154401 ) +colvars: ( -0.0227187 , 0.0752586 , -0.0167382 ) +colvars: ( -0.0167305 , 0.0728012 , -0.0816968 ) +colvars: ( -0.0197791 , 0.0869999 , -0.100307 ) +colvars: ( -0.00849626 , 0.0471338 , -0.0820545 ) +colvars: ( -0.0185757 , 0.0667331 , -0.0344369 ) +colvars: ( -0.0222427 , 0.0840176 , -0.0576426 ) +colvars: ( -0.0242395 , 0.0927599 , -0.0676063 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 3. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 3. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atoms_new_colvar_forces = { ( -7.12644910002888e-02 , 3.04480391919715e-01 , -3.88530416773670e-01 ), ( 1.21543402350703e-02 , 3.59283757073496e-02 , -2.36592346550597e-01 ), ( -4.16092138833091e-02 , 9.11640888447168e-02 , 8.23416306242972e-02 ), ( -9.61000764313615e-02 , 2.42305695294195e-01 , 6.74632194161953e-02 ), ( -1.88405647185787e-02 , 9.96498172188486e-02 , -1.64992595806876e-01 ), ( 7.02514835169250e-02 , -1.79844182937403e-01 , -4.10469774921604e-02 ), ( 1.05532653731170e-02 , -1.02124362545298e-01 , 2.47761381423188e-01 ), ( -4.03387808327078e-02 , 5.44992483058144e-02 , 1.92980165253870e-01 ), ( 6.56942024572184e-02 , -1.87268005160499e-01 , 3.25895903711645e-02 ), ( 1.14312103245404e-01 , -3.88029814824987e-01 , 2.64649278438540e-01 ), ( 2.42399874948257e-02 , -9.94601615884302e-02 , 9.43450526358905e-02 ), ( 2.64187832067172e-02 , -9.72959614091883e-02 , 5.85026645399138e-02 ), ( 1.22455016217257e-02 , -5.61985927602022e-02 , 7.14248035735868e-02 ), ( 1.23869408467411e-02 , -5.38750852851352e-02 , 6.03844516287721e-02 ), ( 5.47533482913114e-03 , -3.58293646823109e-02 , 7.46507658907643e-02 ), ( -8.61093066863975e-03 , 8.19691911326328e-03 , 7.47955564010663e-02 ), ( -2.06113077404795e-03 , -3.56556978390652e-03 , 3.99668789943306e-02 ), ( -5.74519237302200e-03 , 9.00641804914424e-03 , 3.57835237496780e-02 ), ( 2.80447863484305e-03 , -1.36331338607282e-02 , 1.94012145925844e-02 ), ( 9.25852941616702e-03 , -2.23368932576550e-02 , -2.64410106981663e-02 ), ( 8.81779507607160e-03 , -2.38547195085519e-02 , -1.48796460307627e-02 ), ( 6.73545618225761e-03 , -1.35227630184473e-02 , -3.01205268766796e-02 ), ( 1.50708708581964e-02 , -4.65613398889311e-02 , -2.31954133071604e-03 ), ( 2.75661986728460e-02 , -8.79069437037276e-02 , 6.69966718119029e-03 ), ( 1.42278972265037e-02 , -4.66188536979522e-02 , 8.43518305129557e-03 ), ( 1.41789197697816e-02 , -4.36058466193783e-02 , -2.97984094516618e-03 ), ( 9.21216484792188e-03 , -3.70911405406308e-02 , 3.30300824801763e-02 ), ( -1.00842453813973e-03 , -1.57897001341701e-02 , 7.56161841724666e-02 ), ( -3.85480601482357e-03 , 3.88845033974037e-03 , 3.26092204945920e-02 ), ( -5.93907177018090e-03 , 1.10235923365747e-02 , 3.01526170963657e-02 ), ( -7.30916548846552e-03 , 1.75114619452427e-02 , 2.13626571248804e-02 ), ( -1.61686021542056e-02 , 5.13968697461965e-02 , -3.27568354660324e-03 ), ( -9.67884364851469e-03 , 3.55998969369253e-02 , -2.12508875909159e-02 ), ( -1.37058643655233e-02 , 4.98541172211488e-02 , -2.78668434034106e-02 ), ( -1.89885720037668e-03 , 1.49399596092170e-02 , -3.59248246074874e-02 ), ( 1.07192981146069e-02 , -1.53339454667564e-02 , -7.26323591285075e-02 ), ( 4.42280297726436e-03 , -3.33908263890920e-04 , -5.38891907297017e-02 ), ( 3.41711373116267e-03 , 6.62536545954213e-03 , -6.91106420905072e-02 ), ( 7.10595226173296e-03 , -1.43831502417926e-02 , -3.13121755456011e-02 ), ( 1.29403714170504e-02 , -4.08015816582177e-02 , 1.29101937417115e-03 ), ( 4.21650163844445e-04 , 2.16452996514270e-03 , -1.39044294702790e-02 ), ( 3.32265751315244e-04 , 3.90201987778178e-03 , -1.97236621643520e-02 ), ( -6.61077765359962e-03 , 2.06991412040919e-02 , -8.09922488427135e-05 ), ( -2.06797382433100e-02 , 5.74425477014770e-02 , 2.89176437746283e-02 ), ( -1.89994930796128e-02 , 6.32995810538052e-02 , -1.54400667540050e-02 ), ( -2.27186777545924e-02 , 7.52586020414951e-02 , -1.67382012788684e-02 ), ( -1.67304543184278e-02 , 7.28011998778589e-02 , -8.16968210356079e-02 ), ( -1.97790932339822e-02 , 8.69999150277857e-02 , -1.00307053543935e-01 ), ( -8.49625951876390e-03 , 4.71338235969838e-02 , -8.20544860518998e-02 ), ( -1.85756727929090e-02 , 6.67331167231479e-02 , -3.44368813268715e-02 ), ( -2.42395254710581e-02 , 9.27598757209877e-02 , -6.76063492614180e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 3, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 4 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 4, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 4, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 4, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 4, atoms_positions[size = 51] = { ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 ), ( 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 ), ( 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 ), ( 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 ), ( 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 ), ( 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 ), ( -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 ), ( -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 ), ( -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 ), ( -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ), ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 ), ( 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 ), ( 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 ), ( 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 ), ( 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 ), ( 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 ), ( 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 ), ( 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 ), ( 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 ), ( 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 ), ( 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 ), ( 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 ), ( 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 ), ( 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 ), ( 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 ), ( 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 ), ( 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 ), ( 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 ), ( 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 ), ( -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 ), ( 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 ), ( 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 ), ( -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 ), ( -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 ), ( -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 ), ( -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 ), ( -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 ), ( -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 ), ( -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 ), ( -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 ), ( -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 ), ( -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 ), ( -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 ), ( -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 ), ( -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 ), ( -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 ), ( -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 ), ( -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 ), ( -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 ), ( -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 ), ( -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ) } +colvars: Step 4, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atom_groups_ids[size = 0] = +colvars: Step 4, atom_groups_refcount[size = 0] = +colvars: Step 4, atom_groups_masses[size = 0] = +colvars: Step 4, atom_groups_charges[size = 0] = +colvars: Step 4, atom_groups_coms[size = 0] = +colvars: Step 4, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 4, volmaps_ids[size = 0] = +colvars: Step 4, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 4 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.30965 , 16.9978 , 17.1971 , 18.1267 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.30965 , 16.9978 , 17.1971 , 18.1267 ) to colvar "one". +colvars: Adding total bias energy: 11.4167 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.30965 , 16.9978 , 17.1971 , 18.1267 ) +colvars: Applying force on main group : +colvars: ( -0.0909692 , 0.386505 , -0.470634 ) +colvars: ( 0.0147734 , 0.0447146 , -0.305294 ) +colvars: ( -0.0458102 , 0.102233 , 0.0911652 ) +colvars: ( -0.115806 , 0.302923 , 0.0724881 ) +colvars: ( -0.0218454 , 0.120916 , -0.212817 ) +colvars: ( 0.083494 , -0.220392 , -0.0451908 ) +colvars: ( 0.00806427 , -0.109141 , 0.307649 ) +colvars: ( -0.0488924 , 0.0759017 , 0.215243 ) +colvars: ( 0.0804791 , -0.23164 , 0.0246495 ) +colvars: ( 0.136513 , -0.47202 , 0.32274 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242467 , -0.0994396 , 0.0944171 ) +colvars: ( 0.0197612 , -0.0822299 , 0.0816931 ) +colvars: ( 0.0264252 , -0.0972868 , 0.0585663 ) +colvars: ( 0.0122473 , -0.0561755 , 0.0714732 ) +colvars: ( 0.0123895 , -0.0538579 , 0.0604275 ) +colvars: ( 0.00547399 , -0.0357982 , 0.0746924 ) +colvars: ( -0.00257839 , -0.00910817 , 0.0686644 ) +colvars: ( -0.00861821 , 0.00824101 , 0.0748198 ) +colvars: ( -0.00206482 , -0.00354202 , 0.0399846 ) +colvars: ( -0.00574961 , 0.00902966 , 0.0357936 ) +colvars: ( 0.00280216 , -0.0136195 , 0.0194185 ) +colvars: ( 0.0042205 , -0.0110347 , -0.00865408 ) +colvars: ( 0.00925813 , -0.0223433 , -0.0264315 ) +colvars: ( 0.00881888 , -0.0238611 , -0.0148694 ) +colvars: ( 0.00673627 , -0.0135342 , -0.0301198 ) +colvars: ( 0.0150745 , -0.0465688 , -0.00229675 ) +colvars: ( 0.0197151 , -0.0603688 , -0.00514642 ) +colvars: ( 0.0275754 , -0.0879233 , 0.00674093 ) +colvars: ( 0.0142329 , -0.0466261 , 0.00845792 ) +colvars: ( 0.0141846 , -0.043619 , -0.00296277 ) +colvars: ( 0.0092151 , -0.0370854 , 0.0330557 ) +colvars: ( 0.00301529 , -0.0213282 , 0.0475781 ) +colvars: ( -0.00100909 , -0.0157614 , 0.0756439 ) +colvars: ( -0.00385599 , 0.00390235 , 0.0326159 ) +colvars: ( -0.00594027 , 0.0110362 , 0.0301542 ) +colvars: ( -0.00731235 , 0.017526 , 0.0213618 ) +colvars: ( -0.0132453 , 0.0403538 , 0.00427381 ) +colvars: ( -0.016176 , 0.0514121 , -0.00329589 ) +colvars: ( -0.00968233 , 0.0355997 , -0.021272 ) +colvars: ( -0.0137103 , 0.0498532 , -0.0278969 ) +colvars: ( -0.00189961 , 0.0149289 , -0.0359408 ) +colvars: ( 0.00246753 , 0.00719745 , -0.0596376 ) +colvars: ( 0.0107233 , -0.0153681 , -0.0726455 ) +colvars: ( 0.00442589 , -0.000360306 , -0.0539063 ) +colvars: ( 0.0034204 , 0.00659283 , -0.0691359 ) +colvars: ( 0.00711026 , -0.0144043 , -0.0313176 ) +colvars: ( 0.00852211 , -0.0210639 , -0.0223433 ) +colvars: ( 0.0129478 , -0.0408182 , 0.00130395 ) +colvars: ( 0.000424886 , 0.00215107 , -0.0139148 ) +colvars: ( 0.000336254 , 0.00388448 , -0.0197378 ) +colvars: ( -0.00661062 , 0.0206973 , -9.46778e-05 ) +colvars: ( -0.0148177 , 0.0443581 , 0.00792542 ) +colvars: ( -0.0206851 , 0.0574627 , 0.0288966 ) +colvars: ( -0.0190034 , 0.0633007 , -0.0154769 ) +colvars: ( -0.0227233 , 0.0752604 , -0.0167818 ) +colvars: ( -0.0167336 , 0.0727772 , -0.0817556 ) +colvars: ( -0.0197832 , 0.0869712 , -0.100377 ) +colvars: ( -0.00849614 , 0.0471027 , -0.0821028 ) +colvars: ( -0.0185801 , 0.0667289 , -0.0344791 ) +colvars: ( -0.0222485 , 0.084008 , -0.0576986 ) +colvars: ( -0.024247 , 0.0927508 , -0.067667 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 4. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 4. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atoms_new_colvar_forces = { ( -7.12080210552797e-02 , 3.04274726531718e-01 , -3.88940587640774e-01 ), ( 1.21950269985741e-02 , 3.56064499150579e-02 , -2.36629571966559e-01 ), ( -4.15896800926495e-02 , 9.11984131701159e-02 , 8.25110748151548e-02 ), ( -9.60913610694842e-02 , 2.42553891617927e-01 , 6.73416799725295e-02 ), ( -1.88301065662091e-02 , 9.95877660607348e-02 , -1.65239019876376e-01 ), ( 7.02486546083075e-02 , -1.80038089572669e-01 , -4.09170337765094e-02 ), ( 1.05318019430700e-02 , -1.01943502700610e-01 , 2.48011589427611e-01 ), ( -4.03702441420600e-02 , 5.48377999542595e-02 , 1.92899941686077e-01 ), ( 6.56614060203969e-02 , -1.87281426243981e-01 , 3.25748774948746e-02 ), ( 1.14264326869696e-01 , -3.88012490794451e-01 , 2.65041892347769e-01 ), ( 2.42467051015945e-02 , -9.94396336710934e-02 , 9.44171391294592e-02 ), ( 2.64251678200815e-02 , -9.72867887154741e-02 , 5.85662658018812e-02 ), ( 1.22472752364769e-02 , -5.61754900662332e-02 , 7.14731700813468e-02 ), ( 1.23894843053070e-02 , -5.38579145569750e-02 , 6.04275201891246e-02 ), ( 5.47399239743080e-03 , -3.57982173847452e-02 , 7.46924353005460e-02 ), ( -8.61820629816763e-03 , 8.24101256205583e-03 , 7.48197995077387e-02 ), ( -2.06481714081862e-03 , -3.54201942450395e-03 , 3.99845925012198e-02 ), ( -5.74960578369700e-03 , 9.02966184445511e-03 , 3.57935634859857e-02 ), ( 2.80215815799665e-03 , -1.36194994617910e-02 , 1.94184830640624e-02 ), ( 9.25813419184906e-03 , -2.23432881756588e-02 , -2.64315357010282e-02 ), ( 8.81887984484594e-03 , -2.38610548708190e-02 , -1.48694441646478e-02 ), ( 6.73627359909724e-03 , -1.35342143700938e-02 , -3.01197791283318e-02 ), ( 1.50745344951528e-02 , -4.65688049220078e-02 , -2.29674594399060e-03 ), ( 2.75753596529584e-02 , -8.79232773311727e-02 , 6.74093354014295e-03 ), ( 1.42328598821259e-02 , -4.66261458490982e-02 , 8.45792361108824e-03 ), ( 1.41845692241518e-02 , -4.36190215434519e-02 , -2.96277053426434e-03 ), ( 9.21509811267395e-03 , -3.70853528776646e-02 , 3.30557103690731e-02 ), ( -1.00908817873593e-03 , -1.57613613752127e-02 , 7.56438621946769e-02 ), ( -3.85598849795090e-03 , 3.90235192006697e-03 , 3.26159055815450e-02 ), ( -5.94027352971036e-03 , 1.10362439836852e-02 , 3.01542014974282e-02 ), ( -7.31235222693024e-03 , 1.75260063960574e-02 , 2.13618346567090e-02 ), ( -1.61760008919845e-02 , 5.14120787753115e-02 , -3.29589385739106e-03 ), ( -9.68233173784903e-03 , 3.55996626468111e-02 , -2.12719940992636e-02 ), ( -1.37102747661633e-02 , 4.98531642203748e-02 , -2.78968717294853e-02 ), ( -1.89961262970978e-03 , 1.49288570247522e-02 , -3.59407974062863e-02 ), ( 1.07232945874884e-02 , -1.53680987893684e-02 , -7.26454605633824e-02 ), ( 4.42589088117630e-03 , -3.60305744266164e-04 , -5.39062707052113e-02 ), ( 3.42040381532136e-03 , 6.59283053457814e-03 , -6.91358624396322e-02 ), ( 7.11026470043291e-03 , -1.44042598923488e-02 , -3.13175947834697e-02 ), ( 1.29477734767760e-02 , -4.08181704267577e-02 , 1.30395382414031e-03 ), ( 4.24885994011587e-04 , 2.15107073748631e-03 , -1.39148029314400e-02 ), ( 3.36253599568686e-04 , 3.88447745033494e-03 , -1.97377999334930e-02 ), ( -6.61061592184173e-03 , 2.06973135737414e-02 , -9.46778005412389e-05 ), ( -2.06850655568149e-02 , 5.74627047385668e-02 , 2.88966154320564e-02 ), ( -1.90034487268360e-02 , 6.33007217508657e-02 , -1.54769495934924e-02 ), ( -2.27233448939688e-02 , 7.52604092524772e-02 , -1.67817706510836e-02 ), ( -1.67336131493115e-02 , 7.27772224080956e-02 , -8.17555554242184e-02 ), ( -1.97831682663396e-02 , 8.69711573163882e-02 , -1.00377263119591e-01 ), ( -8.49613558415377e-03 , 4.71026760275649e-02 , -8.21027934280728e-02 ), ( -1.85801247869260e-02 , 6.67289400821420e-02 , -3.44791463843032e-02 ), ( -2.42469940229704e-02 , 9.27508182648225e-02 , -6.76669719294010e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 4, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 5 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 5, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 5, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 5, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 5, atoms_positions[size = 51] = { ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 ), ( 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 ), ( 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 ), ( 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 ), ( 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 ), ( 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 ), ( -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 ), ( -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 ), ( -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 ), ( -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ), ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 ), ( 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 ), ( 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 ), ( 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 ), ( 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 ), ( 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 ), ( 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 ), ( 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 ), ( 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 ), ( 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 ), ( 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 ), ( 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 ), ( 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 ), ( 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 ), ( 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 ), ( 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 ), ( 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 ), ( 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 ), ( 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 ), ( -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 ), ( 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 ), ( 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 ), ( -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 ), ( -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 ), ( -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 ), ( -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 ), ( -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 ), ( -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 ), ( -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 ), ( -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 ), ( -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 ), ( -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 ), ( -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 ), ( -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 ), ( -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 ), ( -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 ), ( -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 ), ( -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 ), ( -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 ), ( -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 ), ( -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ) } +colvars: Step 5, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atom_groups_ids[size = 0] = +colvars: Step 5, atom_groups_refcount[size = 0] = +colvars: Step 5, atom_groups_masses[size = 0] = +colvars: Step 5, atom_groups_charges[size = 0] = +colvars: Step 5, atom_groups_coms[size = 0] = +colvars: Step 5, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 5, volmaps_ids[size = 0] = +colvars: Step 5, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 5 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.306059 , 17.0062 , 17.202 , 18.1229 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.306059 , 17.0062 , 17.202 , 18.1229 ) to colvar "one". +colvars: Adding total bias energy: 11.4206 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.306059 , 17.0062 , 17.202 , 18.1229 ) +colvars: Applying force on main group : +colvars: ( -0.0909638 , 0.386284 , -0.471181 ) +colvars: ( 0.014807 , 0.0443021 , -0.305371 ) +colvars: ( -0.0457855 , 0.10226 , 0.0914018 ) +colvars: ( -0.115822 , 0.303249 , 0.0723549 ) +colvars: ( -0.0218569 , 0.120851 , -0.213149 ) +colvars: ( 0.0835114 , -0.220651 , -0.0450438 ) +colvars: ( 0.0080638 , -0.108924 , 0.307986 ) +colvars: ( -0.0489315 , 0.0763321 , 0.215154 ) +colvars: ( 0.0804605 , -0.231668 , 0.0246104 ) +colvars: ( 0.136517 , -0.472035 , 0.323238 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242606 , -0.0994173 , 0.0944948 ) +colvars: ( 0.0197707 , -0.0822038 , 0.0817612 ) +colvars: ( 0.0264346 , -0.097273 , 0.0586336 ) +colvars: ( 0.0122533 , -0.0561471 , 0.0715266 ) +colvars: ( 0.012396 , -0.0538374 , 0.0604746 ) +colvars: ( 0.00547639 , -0.0357591 , 0.07474 ) +colvars: ( -0.00257952 , -0.00906428 , 0.0686987 ) +colvars: ( -0.00862288 , 0.00829741 , 0.0748511 ) +colvars: ( -0.00206769 , -0.00351031 , 0.0400063 ) +colvars: ( -0.00575313 , 0.00905996 , 0.0358072 ) +colvars: ( 0.00279862 , -0.0135973 , 0.0194383 ) +colvars: ( 0.00421553 , -0.011025 , -0.00864537 ) +colvars: ( 0.00925229 , -0.0223408 , -0.0264226 ) +colvars: ( 0.00881701 , -0.0238629 , -0.0148597 ) +colvars: ( 0.00673317 , -0.0135422 , -0.0301206 ) +colvars: ( 0.0150768 , -0.0465736 , -0.00227413 ) +colvars: ( 0.0197207 , -0.0603837 , -0.00512115 ) +colvars: ( 0.0275852 , -0.0879414 , 0.00678149 ) +colvars: ( 0.0142388 , -0.046635 , 0.00848051 ) +colvars: ( 0.0141908 , -0.0436356 , -0.00294689 ) +colvars: ( 0.00922085 , -0.0370799 , 0.0330831 ) +colvars: ( 0.0030209 , -0.0213149 , 0.0476026 ) +colvars: ( -0.00100338 , -0.0157323 , 0.0756765 ) +colvars: ( -0.00385421 , 0.00391614 , 0.0326248 ) +colvars: ( -0.00593813 , 0.0110471 , 0.0301576 ) +colvars: ( -0.00731435 , 0.017543 , 0.021363 ) +colvars: ( -0.0132512 , 0.0403702 , 0.00425982 ) +colvars: ( -0.0161855 , 0.0514338 , -0.00331475 ) +colvars: ( -0.00968796 , 0.0356008 , -0.0212939 ) +colvars: ( -0.013717 , 0.0498528 , -0.0279282 ) +colvars: ( -0.00190365 , 0.0149183 , -0.0359589 ) +colvars: ( 0.00246414 , 0.00717173 , -0.0596617 ) +colvars: ( 0.0107213 , -0.0154039 , -0.0726638 ) +colvars: ( 0.0044257 , -0.000391221 , -0.0539277 ) +colvars: ( 0.00341955 , 0.00655443 , -0.0691666 ) +colvars: ( 0.00711359 , -0.014431 , -0.0313262 ) +colvars: ( 0.00852855 , -0.0210938 , -0.0223482 ) +colvars: ( 0.0129581 , -0.040844 , 0.00131507 ) +colvars: ( 0.000429688 , 0.00212923 , -0.0139274 ) +colvars: ( 0.000341999 , 0.00385646 , -0.0197549 ) +colvars: ( -0.00660835 , 0.0206895 , -0.000109137 ) +colvars: ( -0.0148174 , 0.044359 , 0.00790321 ) +colvars: ( -0.0206865 , 0.0574799 , 0.0288776 ) +colvars: ( -0.0190067 , 0.0632967 , -0.0155151 ) +colvars: ( -0.0227269 , 0.0752559 , -0.0168267 ) +colvars: ( -0.0167418 , 0.072748 , -0.0818199 ) +colvars: ( -0.0197939 , 0.0869372 , -0.100454 ) +colvars: ( -0.0085006 , 0.0470643 , -0.0821573 ) +colvars: ( -0.0185861 , 0.0667214 , -0.0345236 ) +colvars: ( -0.0222579 , 0.0839955 , -0.057758 ) +colvars: ( -0.0242599 , 0.0927419 , -0.0677312 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 5. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 5. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atoms_new_colvar_forces = { ( -7.11930917715262e-02 , 3.04080402889663e-01 , -3.89420117659556e-01 ), ( 1.22274699460667e-02 , 3.52378104756379e-02 , -2.36672496748529e-01 ), ( -4.15700140483639e-02 , 9.12349296696296e-02 , 8.27563970021866e-02 ), ( -9.61016217912612e-02 , 2.42865160914319e-01 , 6.72337999946861e-02 ), ( -1.88360121209974e-02 , 9.95358134491225e-02 , -1.65545997411328e-01 ), ( 7.02602719142824e-02 , -1.80280636028130e-01 , -4.07839832834661e-02 ), ( 1.05279361141261e-02 , -1.01752713338897e-01 , 2.48323952446562e-01 ), ( -4.04029387005403e-02 , 5.52382955877266e-02 , 1.92806022433958e-01 ), ( 6.56430458681339e-02 , -1.87308994968492e-01 , 3.25135719017205e-02 ), ( 1.14259433857731e-01 , -3.88039115593396e-01 , 2.65479921768059e-01 ), ( 2.42605798564394e-02 , -9.94172883871254e-02 , 9.44948179787660e-02 ), ( 2.64346007973788e-02 , -9.72729724027510e-02 , 5.86335564201711e-02 ), ( 1.22532987785135e-02 , -5.61471444227930e-02 , 7.15265885148806e-02 ), ( 1.23959564254596e-02 , -5.38374384588434e-02 , 6.04746134511424e-02 ), ( 5.47639039529515e-03 , -3.57590564742181e-02 , 7.47400233883485e-02 ), ( -8.62288446849312e-03 , 8.29741139291352e-03 , 7.48511040577863e-02 ), ( -2.06769030098720e-03 , -3.51031338390929e-03 , 4.00062583395601e-02 ), ( -5.75313344233234e-03 , 9.05996009845718e-03 , 3.58072218150797e-02 ), ( 2.79862073872496e-03 , -1.35972818387436e-02 , 1.94383059596313e-02 ), ( 9.25229494769087e-03 , -2.23407885089335e-02 , -2.64225913728223e-02 ), ( 8.81700552361751e-03 , -2.38629084835913e-02 , -1.48597374907990e-02 ), ( 6.73316724776024e-03 , -1.35421597401508e-02 , -3.01205976460819e-02 ), ( 1.50768098167967e-02 , -4.65735796171252e-02 , -2.27412576343031e-03 ), ( 2.75851638634807e-02 , -8.79413881509297e-02 , 6.78148943275173e-03 ), ( 1.42388046236963e-02 , -4.66350043773231e-02 , 8.48051060091069e-03 ), ( 1.41908282837240e-02 , -4.36356336581280e-02 , -2.94688817210362e-03 ), ( 9.22084526028328e-03 , -3.70798975284593e-02 , 3.30831159893830e-02 ), ( -1.00338374270740e-03 , -1.57322786602175e-02 , 7.56765366312058e-02 ), ( -3.85421467521831e-03 , 3.91614128972128e-03 , 3.26247802985022e-02 ), ( -5.93813236113047e-03 , 1.10470979535649e-02 , 3.01576079069810e-02 ), ( -7.31435281678647e-03 , 1.75430114049752e-02 , 2.13630069306248e-02 ), ( -1.61855455840492e-02 , 5.14338186761766e-02 , -3.31475159770605e-03 ), ( -9.68795659419696e-03 , 3.56008411236023e-02 , -2.12939333607702e-02 ), ( -1.37170377970814e-02 , 4.98527717794188e-02 , -2.79281712479423e-02 ), ( -1.90365092081225e-03 , 1.49183129164942e-02 , -3.59589220985608e-02 ), ( 1.07212998249860e-02 , -1.54039102464941e-02 , -7.26638156649286e-02 ), ( 4.42569541964384e-03 , -3.91221119058605e-04 , -5.39276752213949e-02 ), ( 3.41955036969028e-03 , 6.55443034604825e-03 , -6.91665708908388e-02 ), ( 7.11358937522634e-03 , -1.44310237929892e-02 , -3.13261600722330e-02 ), ( 1.29581107015235e-02 , -4.08439956241160e-02 , 1.31506744524187e-03 ), ( 4.29688150890716e-04 , 2.12923211316452e-03 , -1.39274449810552e-02 ), ( 3.41999448111169e-04 , 3.85645860323836e-03 , -1.97549178900757e-02 ), ( -6.60834719336973e-03 , 2.06895144376888e-02 , -1.09137290942866e-04 ), ( -2.06864898021626e-02 , 5.74799121391366e-02 , 2.88775969811894e-02 ), ( -1.90066753015798e-02 , 6.32967248326141e-02 , -1.55150723924351e-02 ), ( -2.27269315783031e-02 , 7.52558980269329e-02 , -1.68267407696857e-02 ), ( -1.67418411274645e-02 , 7.27480314369913e-02 , -8.18198566656224e-02 ), ( -1.97938715038249e-02 , 8.69371697033174e-02 , -1.00454140405606e-01 ), ( -8.50060401083803e-03 , 4.70643098012962e-02 , -8.21572711273281e-02 ), ( -1.85860961724292e-02 , 6.67213789483478e-02 , -3.45235959012453e-02 ), ( -2.42599397228173e-02 , 9.27419047946174e-02 , -6.77311545628400e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 5, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 6 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 6, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 6, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 6, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 6, atoms_positions[size = 51] = { ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 ), ( 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 ), ( 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 ), ( 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 ), ( 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 ), ( 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 ), ( -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 ), ( -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 ), ( -3.77765611267382e+00 , 9.58922869679192e-02 , 5.48159808807106e+00 ), ( -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ), ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 ), ( 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 ), ( 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 ), ( 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 ), ( 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 ), ( 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 ), ( 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 ), ( 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 ), ( 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 ), ( 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 ), ( 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 ), ( 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 ), ( 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 ), ( 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 ), ( 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 ), ( 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 ), ( 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 ), ( 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 ), ( 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 ), ( -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 ), ( 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 ), ( 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 ), ( -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 ), ( -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 ), ( -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 ), ( -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 ), ( -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 ), ( -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 ), ( -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 ), ( -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 ), ( -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 ), ( -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 ), ( -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 ), ( -2.40918974321356e+00 , -3.98829720444864e-01 , 6.14201010890720e+00 ), ( -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 ), ( -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 ), ( -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 ), ( -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 ), ( -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 ), ( -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 ), ( -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ) } +colvars: Step 6, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_ids[size = 0] = +colvars: Step 6, atom_groups_refcount[size = 0] = +colvars: Step 6, atom_groups_masses[size = 0] = +colvars: Step 6, atom_groups_charges[size = 0] = +colvars: Step 6, atom_groups_coms[size = 0] = +colvars: Step 6, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 6, volmaps_ids[size = 0] = +colvars: Step 6, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 6 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.30256 , 17.0161 , 17.2076 , 18.1168 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.30256 , 17.0161 , 17.2076 , 18.1168 ) to colvar "one". +colvars: Adding total bias energy: 11.4245 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.30256 , 17.0161 , 17.2076 , 18.1168 ) +colvars: Applying force on main group : +colvars: ( -0.0909996 , 0.386077 , -0.471804 ) +colvars: ( 0.0148327 , 0.0438389 , -0.305461 ) +colvars: ( -0.0457593 , 0.102283 , 0.0917129 ) +colvars: ( -0.115858 , 0.303639 , 0.0722371 ) +colvars: ( -0.0218863 , 0.120798 , -0.213543 ) +colvars: ( 0.0835446 , -0.220962 , -0.0448955 ) +colvars: ( 0.00808168 , -0.1087 , 0.308388 ) +colvars: ( -0.0489749 , 0.076829 , 0.215056 ) +colvars: ( 0.0804539 , -0.231708 , 0.0245252 ) +colvars: ( 0.136565 , -0.472096 , 0.323784 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242815 , -0.0993938 , 0.0945777 ) +colvars: ( 0.0197853 , -0.0821738 , 0.0818345 ) +colvars: ( 0.0264473 , -0.0972552 , 0.0587045 ) +colvars: ( 0.0122634 , -0.0561144 , 0.071585 ) +colvars: ( 0.0124062 , -0.0538143 , 0.0605256 ) +colvars: ( 0.00548227 , -0.035713 , 0.0747936 ) +colvars: ( -0.00257797 , -0.00901257 , 0.0687391 ) +colvars: ( -0.00862544 , 0.00836465 , 0.0748898 ) +colvars: ( -0.00206992 , -0.00347136 , 0.0400321 ) +colvars: ( -0.00575601 , 0.00909652 , 0.0358247 ) +colvars: ( 0.00279397 , -0.0135673 , 0.0194611 ) +colvars: ( 0.00420746 , -0.0110081 , -0.00863562 ) +colvars: ( 0.00924159 , -0.0223299 , -0.0264136 ) +colvars: ( 0.00881257 , -0.0238605 , -0.0148502 ) +colvars: ( 0.00672658 , -0.0135467 , -0.0301227 ) +colvars: ( 0.0150781 , -0.0465758 , -0.00225154 ) +colvars: ( 0.019726 , -0.060399 , -0.00509691 ) +colvars: ( 0.0275961 , -0.0879611 , 0.00682117 ) +colvars: ( 0.0142459 , -0.0466453 , 0.0085028 ) +colvars: ( 0.0141979 , -0.0436554 , -0.00293238 ) +colvars: ( 0.00922935 , -0.0370749 , 0.0331121 ) +colvars: ( 0.00303061 , -0.0213028 , 0.0476297 ) +colvars: ( -0.000991874 , -0.015703 , 0.0757139 ) +colvars: ( -0.00384981 , 0.00392961 , 0.0326357 ) +colvars: ( -0.00593304 , 0.0110561 , 0.0301626 ) +colvars: ( -0.00731543 , 0.0175621 , 0.0213662 ) +colvars: ( -0.0132578 , 0.0403898 , 0.00424724 ) +colvars: ( -0.0161974 , 0.0514616 , -0.00333187 ) +colvars: ( -0.00969574 , 0.0356034 , -0.0213165 ) +colvars: ( -0.0137262 , 0.0498531 , -0.0279606 ) +colvars: ( -0.00191074 , 0.0149085 , -0.035979 ) +colvars: ( 0.00245645 , 0.00714504 , -0.0596898 ) +colvars: ( 0.010714 , -0.0154408 , -0.0726872 ) +colvars: ( 0.00442261 , -0.000425946 , -0.0539534 ) +colvars: ( 0.00341501 , 0.00651108 , -0.0692028 ) +colvars: ( 0.00711619 , -0.0144628 , -0.031338 ) +colvars: ( 0.00853583 , -0.0211312 , -0.0223566 ) +colvars: ( 0.0129715 , -0.0408783 , 0.00132384 ) +colvars: ( 0.000435991 , 0.00209977 , -0.0139427 ) +colvars: ( 0.000349434 , 0.00381892 , -0.0197755 ) +colvars: ( -0.00660424 , 0.0206762 , -0.000124684 ) +colvars: ( -0.0148148 , 0.0443547 , 0.00788074 ) +colvars: ( -0.0206847 , 0.0574942 , 0.0288603 ) +colvars: ( -0.0190096 , 0.0632881 , -0.0155546 ) +colvars: ( -0.0227299 , 0.0752456 , -0.0168733 ) +colvars: ( -0.016755 , 0.0727145 , -0.0818896 ) +colvars: ( -0.019811 , 0.086899 , -0.100537 ) +colvars: ( -0.00850939 , 0.0470198 , -0.0822179 ) +colvars: ( -0.0185938 , 0.0667109 , -0.0345702 ) +colvars: ( -0.0222711 , 0.0839807 , -0.0578208 ) +colvars: ( -0.0242784 , 0.0927335 , -0.0677985 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 6. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 6. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atoms_new_colvar_forces = { ( -7.12142262303992e-02 , 3.03903301715952e-01 , -3.89969129550351e-01 ), ( 1.22547356452154e-02 , 3.48262951672449e-02 , -2.36721963920782e-01 ), ( -4.15518674361304e-02 , 9.12751560648350e-02 , 8.30772582640576e-02 ), ( -9.61317320933757e-02 , 2.43240346979410e-01 , 6.71401363520435e-02 ), ( -1.88556777097379e-02 , 9.94952870708496e-02 , -1.65913347874103e-01 ), ( 7.02868318338666e-02 , -1.80572282391047e-01 , -4.06482640014998e-02 ), ( 1.05381289914210e-02 , -1.01554511095457e-01 , 2.48698582925828e-01 ), ( -4.04390358015067e-02 , 5.56977300193671e-02 , 1.92699294429561e-01 ), ( 6.56391566883627e-02 , -1.87353793800463e-01 , 3.24058940221479e-02 ), ( 1.14293775414791e-01 , -3.88114795924072e-01 , 2.65963163735460e-01 ), ( 2.42814729749294e-02 , -9.93938454081909e-02 , 9.45777245589051e-02 ), ( 2.64473139563615e-02 , -9.72552236470947e-02 , 5.87044852956407e-02 ), ( 1.22634185313900e-02 , -5.61144142202651e-02 , 7.15849993395887e-02 ), ( 1.24062468740887e-02 , -5.38142909992530e-02 , 6.05256176470266e-02 ), ( 5.48226526174387e-03 , -3.57129885325301e-02 , 7.47936140876123e-02 ), ( -8.62544006295661e-03 , 8.36465137573990e-03 , 7.48898030521818e-02 ), ( -2.06991625388785e-03 , -3.47135619509694e-03 , 4.00321364199732e-02 ), ( -5.75601257738078e-03 , 9.09651790518482e-03 , 3.58247231259840e-02 ), ( 2.79396502781401e-03 , -1.35672817619064e-02 , 1.94610539947598e-02 ), ( 9.24159279432054e-03 , -2.23299181608012e-02 , -2.64135889483069e-02 ), ( 8.81256516211875e-03 , -2.38605293913080e-02 , -1.48502275938890e-02 ), ( 6.72657734904849e-03 , -1.35466756974881e-02 , -3.01226642825190e-02 ), ( 1.50780930352461e-02 , -4.65758441774542e-02 , -2.25154451988601e-03 ), ( 2.75961135614895e-02 , -8.79611454331461e-02 , 6.82117273635850e-03 ), ( 1.42459402549000e-02 , -4.66453423016032e-02 , 8.50280256995158e-03 ), ( 1.41979492402755e-02 , -4.36553747142220e-02 , -2.93238398181345e-03 ), ( 9.22935271210501e-03 , -3.70749488738609e-02 , 3.31121184968349e-02 ), ( -9.91874405938820e-04 , -1.57029967626075e-02 , 7.57139032005495e-02 ), ( -3.84980968726094e-03 , 3.92961372844109e-03 , 3.26356944825281e-02 ), ( -5.93303553292433e-03 , 1.10560962669028e-02 , 3.01626091603370e-02 ), ( -7.31542887547997e-03 , 1.75621364522944e-02 , 2.13662184603644e-02 ), ( -1.61974194508721e-02 , 5.14615739051055e-02 , -3.33186857750587e-03 ), ( -9.69573856621546e-03 , 3.56034451247036e-02 , -2.13165194953996e-02 ), ( -1.37262291647893e-02 , 4.98530577430511e-02 , -2.79605666016103e-02 ), ( -1.91073603828273e-03 , 1.49085110410628e-02 , -3.59790018535196e-02 ), ( 1.07140432385856e-02 , -1.54407701911095e-02 , -7.26871956581507e-02 ), ( 4.42261271019296e-03 , -4.25945906022851e-04 , -5.39534073383785e-02 ), ( 3.41501168760075e-03 , 6.51107644294852e-03 , -6.92027722989708e-02 ), ( 7.11618928681651e-03 , -1.44627849641822e-02 , -3.13380424647115e-02 ), ( 1.29714546559885e-02 , -4.08783185679446e-02 , 1.32383933489511e-03 ), ( 4.35990744562135e-04 , 2.09976734191281e-03 , -1.39427446383950e-02 ), ( 3.49433995726928e-04 , 3.81891985606553e-03 , -1.97754914609517e-02 ), ( -6.60423860307249e-03 , 2.06762093489714e-02 , -1.24683954910893e-04 ), ( -2.06847286332335e-02 , 5.74941934675936e-02 , 2.88603238042472e-02 ), ( -1.90095738981270e-02 , 6.32880734562383e-02 , -1.55546171706953e-02 ), ( -2.27299338339649e-02 , 7.52456489187880e-02 , -1.68733466161828e-02 ), ( -1.67550040694721e-02 , 7.27145435033735e-02 , -8.18896108779006e-02 ), ( -1.98109971023338e-02 , 8.68989856646780e-02 , -1.00537483379429e-01 ), ( -8.50939441170506e-03 , 4.70198123865680e-02 , -8.22179224442125e-02 ), ( -1.85938018440016e-02 , 6.67108998990059e-02 , -3.45702310150741e-02 ), ( -2.42783793459124e-02 , 9.27335282708393e-02 , -6.77985489776879e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 6, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 7 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 7, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 7, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 7, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 7, atoms_positions[size = 51] = { ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 ), ( 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 ), ( 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 ), ( 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 ), ( 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 ), ( 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 ), ( -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 ), ( -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 ), ( -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 ), ( -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ), ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 ), ( 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 ), ( 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 ), ( 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 ), ( 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 ), ( 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 ), ( 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 ), ( 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 ), ( 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 ), ( 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 ), ( 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 ), ( 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 ), ( 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 ), ( 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 ), ( 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 ), ( 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 ), ( 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 ), ( 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 ), ( 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 ), ( -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 ), ( 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 ), ( 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 ), ( -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 ), ( -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 ), ( -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 ), ( -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 ), ( -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 ), ( -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 ), ( -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 ), ( -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 ), ( -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 ), ( -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 ), ( -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 ), ( -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 ), ( -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 ), ( -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 ), ( -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 ), ( -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 ), ( -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 ), ( -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 ), ( -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ) } +colvars: Step 7, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_ids[size = 0] = +colvars: Step 7, atom_groups_refcount[size = 0] = +colvars: Step 7, atom_groups_masses[size = 0] = +colvars: Step 7, atom_groups_charges[size = 0] = +colvars: Step 7, atom_groups_coms[size = 0] = +colvars: Step 7, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 7, volmaps_ids[size = 0] = +colvars: Step 7, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 7 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851382e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851382e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.299051 , 17.0274 , 17.2141 , 18.1088 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.299051 , 17.0274 , 17.2141 , 18.1088 ) to colvar "one". +colvars: Adding total bias energy: 11.4284 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.299051 , 17.0274 , 17.2141 , 18.1088 ) +colvars: Applying force on main group : +colvars: ( -0.0910691 , 0.38589 , -0.472499 ) +colvars: ( 0.014854 , 0.043332 , -0.305565 ) +colvars: ( -0.0457336 , 0.102307 , 0.0920943 ) +colvars: ( -0.115913 , 0.304093 , 0.0721336 ) +colvars: ( -0.0219298 , 0.120758 , -0.213998 ) +colvars: ( 0.0835932 , -0.221324 , -0.0447461 ) +colvars: ( 0.0081132 , -0.108469 , 0.308855 ) +colvars: ( -0.0490242 , 0.0773859 , 0.21495 ) +colvars: ( 0.0804595 , -0.231765 , 0.0243971 ) +colvars: ( 0.13665 , -0.472208 , 0.324378 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.024309 , -0.0993703 , 0.0946656 ) +colvars: ( 0.0198048 , -0.0821413 , 0.0819129 ) +colvars: ( 0.0264633 , -0.0972347 , 0.0587789 ) +colvars: ( 0.0122773 , -0.0560783 , 0.0716483 ) +colvars: ( 0.0124201 , -0.0537893 , 0.0605804 ) +colvars: ( 0.00549126 , -0.0356612 , 0.0748531 ) +colvars: ( -0.00257414 , -0.00895415 , 0.0687856 ) +colvars: ( -0.00862632 , 0.00844138 , 0.0749359 ) +colvars: ( -0.00207165 , -0.00342604 , 0.0400622 ) +colvars: ( -0.00575845 , 0.00913861 , 0.0358461 ) +colvars: ( 0.0027883 , -0.0135304 , 0.0194867 ) +colvars: ( 0.00419665 , -0.0109847 , -0.00862485 ) +colvars: ( 0.00922665 , -0.0223114 , -0.0264045 ) +colvars: ( 0.00880595 , -0.0238544 , -0.0148409 ) +colvars: ( 0.00671697 , -0.013548 , -0.030126 ) +colvars: ( 0.0150787 , -0.046576 , -0.00222908 ) +colvars: ( 0.0197315 , -0.0604148 , -0.00507382 ) +colvars: ( 0.0276085 , -0.0879828 , 0.00685983 ) +colvars: ( 0.0142544 , -0.0466573 , 0.00852471 ) +colvars: ( 0.0142061 , -0.0436781 , -0.00291933 ) +colvars: ( 0.00924046 , -0.0370708 , 0.0331426 ) +colvars: ( 0.003044 , -0.021292 , 0.0476592 ) +colvars: ( -0.000975224 , -0.015674 , 0.0757559 ) +colvars: ( -0.00384312 , 0.00394266 , 0.0326486 ) +colvars: ( -0.00592539 , 0.0110633 , 0.0301692 ) +colvars: ( -0.00731581 , 0.0175832 , 0.0213715 ) +colvars: ( -0.0132652 , 0.0404123 , 0.00423615 ) +colvars: ( -0.0162117 , 0.051495 , -0.00334715 ) +colvars: ( -0.00970559 , 0.0356076 , -0.0213397 ) +colvars: ( -0.0137378 , 0.0498543 , -0.027994 ) +colvars: ( -0.00192056 , 0.0148996 , -0.036001 ) +colvars: ( 0.00244499 , 0.0071178 , -0.0597218 ) +colvars: ( 0.0107023 , -0.0154783 , -0.0727156 ) +colvars: ( 0.00441706 , -0.000463856 , -0.0539834 ) +colvars: ( 0.00340729 , 0.00646361 , -0.0692444 ) +colvars: ( 0.00711829 , -0.014499 , -0.0313533 ) +colvars: ( 0.00854406 , -0.0211756 , -0.0223684 ) +colvars: ( 0.0129877 , -0.0409205 , 0.00133019 ) +colvars: ( 0.00044369 , 0.00206347 , -0.0139607 ) +colvars: ( 0.000358445 , 0.00377287 , -0.0197995 ) +colvars: ( -0.00659855 , 0.020658 , -0.000141289 ) +colvars: ( -0.0148102 , 0.0443458 , 0.00785807 ) +colvars: ( -0.0206804 , 0.0575059 , 0.0288449 ) +colvars: ( -0.0190124 , 0.0632756 , -0.0155955 ) +colvars: ( -0.0227327 , 0.0752306 , -0.0169215 ) +colvars: ( -0.0167728 , 0.0726779 , -0.0819647 ) +colvars: ( -0.0198341 , 0.0868579 , -0.100627 ) +colvars: ( -0.00852211 , 0.0469704 , -0.0822846 ) +colvars: ( -0.0186033 , 0.0666983 , -0.0346189 ) +colvars: ( -0.022288 , 0.0839646 , -0.0578867 ) +colvars: ( -0.0243021 , 0.0927264 , -0.067869 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 7. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 7. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atoms_new_colvar_forces = { ( -7.12643629297238e-02 , 3.03748456819681e-01 , -3.90586407900473e-01 ), ( 1.22798357354463e-02 , 3.43778085240194e-02 , -2.36779111668178e-01 ), ( -4.15369806328073e-02 , 9.13219268139160e-02 , 8.34694649792221e-02 ), ( -9.61814499206716e-02 , 2.43678342667974e-01 , 6.70597490320277e-02 ), ( -1.88857517066456e-02 , 9.94664433603135e-02 , -1.66338638098737e-01 ), ( 7.03279301363652e-02 , -1.80911714089215e-01 , -4.05099162241549e-02 ), ( 1.05581846145116e-02 , -1.01351207901457e-01 , 2.49133378748631e-01 ), ( -4.04801416450276e-02 , 5.62103343343931e-02 , 1.92581516655001e-01 ), ( 6.56492670474172e-02 , -1.87419378224912e-01 , 3.22551691858706e-02 ), ( 1.14361816218885e-01 , -3.88242959643882e-01 , 2.66491224123914e-01 ), ( 2.43089604741000e-02 , -9.93703389638662e-02 , 9.46656398079234e-02 ), ( 2.64633115886798e-02 , -9.72346559646698e-02 , 5.87788599655936e-02 ), ( 1.22773304643787e-02 , -5.60783277865503e-02 , 7.16482732771626e-02 ), ( 1.24200974597789e-02 , -5.37892737835383e-02 , 6.05804114728067e-02 ), ( 5.49126095479498e-03 , -3.56612002445239e-02 , 7.48531138676495e-02 ), ( -8.62632024734143e-03 , 8.44138021182978e-03 , 7.49358821822966e-02 ), ( -2.07165217509811e-03 , -3.42604475726389e-03 , 4.00622073248809e-02 ), ( -5.75844877153946e-03 , 9.13861103854014e-03 , 3.58460704568341e-02 ), ( 2.78830006708309e-03 , -1.35303913001015e-02 , 1.94867025441894e-02 ), ( 9.22664704378498e-03 , -2.23114382528987e-02 , -2.64045420530178e-02 ), ( 8.80594631376906e-03 , -2.38543535758261e-02 , -1.48409418464280e-02 ), ( 6.71696820112536e-03 , -1.35479989898134e-02 , -3.01259814853927e-02 ), ( 1.50787036067345e-02 , -4.65760405505027e-02 , -2.22907699732126e-03 ), ( 2.76085096907280e-02 , -8.79828374284035e-02 , 6.85982871925103e-03 ), ( 1.42543599808695e-02 , -4.66572795962589e-02 , 8.52471407991168e-03 ), ( 1.42060734830385e-02 , -4.36781388833885e-02 , -2.91933397806574e-03 ), ( 9.24045584481542e-03 , -3.70707957299862e-02 , 3.31426363027339e-02 ), ( -9.75223585295903e-04 , -1.56739823609264e-02 , 7.57558939840136e-02 ), ( -3.84312252210567e-03 , 3.94265579472863e-03 , 3.26486365211450e-02 ), ( -5.92538821370363e-03 , 1.10633157410566e-02 , 3.01692052913536e-02 ), ( -7.31580955849081e-03 , 1.75831579539413e-02 , 2.13714897525162e-02 ), ( -1.62116519386518e-02 , 5.14950342863534e-02 , -3.34714876103202e-03 ), ( -9.70559411338392e-03 , 3.56076117306303e-02 , -2.13396788115715e-02 ), ( -1.37377903715564e-02 , 4.98543287436506e-02 , -2.79939571721177e-02 ), ( -1.92056274355791e-03 , 1.48996290499974e-02 , -3.60009908034978e-02 ), ( 1.07022807165507e-02 , -1.54782919591166e-02 , -7.27155880541698e-02 ), ( 4.41705954600045e-03 , -4.63856402268637e-04 , -5.39834426064317e-02 ), ( 3.40728678849276e-03 , 6.46360802827689e-03 , -6.92444234215556e-02 ), ( 7.11828967127039e-03 , -1.44989851915113e-02 , -3.13532550881224e-02 ), ( 1.29877290166139e-02 , -4.09205362039969e-02 , 1.33018961029170e-03 ), ( 4.43689718407329e-04 , 2.06347307826286e-03 , -1.39606995589762e-02 ), ( 3.58444950702431e-04 , 3.77287300218497e-03 , -1.97995143891150e-02 ), ( -6.59855400003896e-03 , 2.06580134531092e-02 , -1.41289081215119e-04 ), ( -2.06804274679637e-02 , 5.75059489194441e-02 , 2.88448741084997e-02 ), ( -1.90124333628416e-02 , 6.32755773639386e-02 , -1.55954735441749e-02 ), ( -2.27327171854041e-02 , 7.52306358455108e-02 , -1.69214580765575e-02 ), ( -1.67727728860836e-02 , 7.26779069784233e-02 , -8.19646548939965e-02 ), ( -1.98340970554791e-02 , 8.68579024560199e-02 , -1.00627094487174e-01 ), ( -8.52210798867692e-03 , 4.69703868264598e-02 , -8.22846297106069e-02 ), ( -1.86033074160002e-02 , 6.66982592868968e-02 , -3.46189230904566e-02 ), ( -2.43020708962544e-02 , 9.27264054753276e-02 , -6.78689601911793e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 7, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 8 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 8, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 8, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 8, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 8, atoms_positions[size = 51] = { ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 ), ( 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 ), ( 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 ), ( 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 ), ( 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 ), ( 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 ), ( -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 ), ( -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 ), ( -3.77960603765112e+00 , 8.28285620991697e-02 , 5.48323895924115e+00 ), ( -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ), ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 ), ( 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 ), ( 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 ), ( 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 ), ( 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 ), ( 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 ), ( 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 ), ( 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 ), ( 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 ), ( 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 ), ( 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 ), ( 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 ), ( 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 ), ( 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 ), ( 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 ), ( 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 ), ( 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 ), ( 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 ), ( 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 ), ( -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 ), ( 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 ), ( 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 ), ( -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 ), ( -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 ), ( -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 ), ( -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 ), ( -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 ), ( -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 ), ( -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 ), ( -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 ), ( -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 ), ( -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 ), ( -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 ), ( -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 ), ( -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 ), ( -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 ), ( -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 ), ( -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 ), ( -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 ), ( -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 ), ( -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ) } +colvars: Step 8, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_ids[size = 0] = +colvars: Step 8, atom_groups_refcount[size = 0] = +colvars: Step 8, atom_groups_masses[size = 0] = +colvars: Step 8, atom_groups_charges[size = 0] = +colvars: Step 8, atom_groups_coms[size = 0] = +colvars: Step 8, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 8, volmaps_ids[size = 0] = +colvars: Step 8, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 8 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.295423 , 17.0401 , 17.2212 , 18.0992 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.295423 , 17.0401 , 17.2212 , 18.0992 ) to colvar "one". +colvars: Adding total bias energy: 11.4325 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.295423 , 17.0401 , 17.2212 , 18.0992 ) +colvars: Applying force on main group : +colvars: ( -0.0911636 , 0.385727 , -0.473265 ) +colvars: ( 0.014874 , 0.0427907 , -0.305683 ) +colvars: ( -0.0457106 , 0.102335 , 0.092538 ) +colvars: ( -0.115987 , 0.304607 , 0.0720423 ) +colvars: ( -0.0219828 , 0.120731 , -0.214508 ) +colvars: ( 0.0836559 , -0.221733 , -0.0445952 ) +colvars: ( 0.00815306 , -0.108235 , 0.309381 ) +colvars: ( -0.0490804 , 0.0779933 , 0.214839 ) +colvars: ( 0.0804766 , -0.231843 , 0.0242323 ) +colvars: ( 0.136765 , -0.472373 , 0.325018 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243423 , -0.099348 , 0.0947584 ) +colvars: ( 0.0198284 , -0.0821074 , 0.081996 ) +colvars: ( 0.0264823 , -0.0972127 , 0.0588563 ) +colvars: ( 0.0122945 , -0.05604 , 0.0717161 ) +colvars: ( 0.0124371 , -0.0537633 , 0.0606388 ) +colvars: ( 0.00550291 , -0.0356049 , 0.0749182 ) +colvars: ( -0.00256845 , -0.00889013 , 0.0688379 ) +colvars: ( -0.00862594 , 0.00852632 , 0.0749889 ) +colvars: ( -0.00207305 , -0.00337529 , 0.0400961 ) +colvars: ( -0.00576061 , 0.00918556 , 0.035871 ) +colvars: ( 0.00278174 , -0.0134876 , 0.0195148 ) +colvars: ( 0.00418349 , -0.0109556 , -0.00861349 ) +colvars: ( 0.00920812 , -0.0222864 , -0.026396 ) +colvars: ( 0.00879753 , -0.023845 , -0.0148322 ) +colvars: ( 0.00670483 , -0.0135465 , -0.0301308 ) +colvars: ( 0.0150789 , -0.0465748 , -0.00220699 ) +colvars: ( 0.0197372 , -0.0604317 , -0.00505201 ) +colvars: ( 0.0276224 , -0.0880071 , 0.00689733 ) +colvars: ( 0.014264 , -0.0466711 , 0.00854622 ) +colvars: ( 0.0142152 , -0.043704 , -0.00290769 ) +colvars: ( 0.00925386 , -0.0370678 , 0.0331747 ) +colvars: ( 0.00306056 , -0.0212828 , 0.0476914 ) +colvars: ( -0.000954217 , -0.0156456 , 0.0758026 ) +colvars: ( -0.00383453 , 0.00395525 , 0.0326637 ) +colvars: ( -0.00591562 , 0.011069 , 0.0301776 ) +colvars: ( -0.00731569 , 0.0176059 , 0.0213788 ) +colvars: ( -0.0132736 , 0.0404377 , 0.00422649 ) +colvars: ( -0.0162281 , 0.051534 , -0.00336079 ) +colvars: ( -0.00971731 , 0.0356136 , -0.0213634 ) +colvars: ( -0.0137515 , 0.049857 , -0.0280283 ) +colvars: ( -0.00193274 , 0.0148918 , -0.036025 ) +colvars: ( 0.00243035 , 0.00709033 , -0.0597577 ) +colvars: ( 0.0106868 , -0.0155163 , -0.0727491 ) +colvars: ( 0.00440948 , -0.000504406 , -0.0540177 ) +colvars: ( 0.00339693 , 0.0064128 , -0.0692914 ) +colvars: ( 0.00712007 , -0.0145391 , -0.0313716 ) +colvars: ( 0.00855323 , -0.0212261 , -0.0223833 ) +colvars: ( 0.0130067 , -0.0409701 , 0.00133448 ) +colvars: ( 0.000452637 , 0.00202122 , -0.0139809 ) +colvars: ( 0.000368871 , 0.00371942 , -0.0198265 ) +colvars: ( -0.00659155 , 0.0206357 , -0.000158597 ) +colvars: ( -0.0148042 , 0.0443333 , 0.00783563 ) +colvars: ( -0.0206741 , 0.0575159 , 0.0288316 ) +colvars: ( -0.0190154 , 0.0632603 , -0.0156372 ) +colvars: ( -0.0227355 , 0.0752122 , -0.0169706 ) +colvars: ( -0.0167946 , 0.0726394 , -0.0820447 ) +colvars: ( -0.0198624 , 0.0868154 , -0.100723 ) +colvars: ( -0.00853819 , 0.0469173 , -0.0823571 ) +colvars: ( -0.0186145 , 0.0666844 , -0.0346694 ) +colvars: ( -0.0223082 , 0.0839483 , -0.0579556 ) +colvars: ( -0.0243305 , 0.0927215 , -0.0679423 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 8. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 8. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atoms_new_colvar_forces = { ( -7.13351423072813e-02 , 3.03619825792168e-01 , -3.91268617939964e-01 ), ( 1.23055499660459e-02 , 3.39005917766654e-02 , -2.36845225742551e-01 ), ( -4.15271491397816e-02 , 9.13791618604164e-02 , 8.39245305411536e-02 ), ( -9.62494045652913e-02 , 2.44175455092806e-01 , 6.69902520302190e-02 ), ( -1.89222535399380e-02 , 9.94484271845722e-02 , -1.66816690819095e-01 ), ( 7.03822543304743e-02 , -1.81295378894829e-01 , -4.03686971085317e-02 ), ( 1.05834154712841e-02 , -1.01144992174696e-01 , 2.49623497290294e-01 ), ( -4.05271851974778e-02 , 5.67671746608100e-02 , 1.92455361027341e-01 ), ( 6.56724380837020e-02 , -1.87509424162519e-01 , 3.20679681604365e-02 ), ( 1.14456342649259e-01 , -3.88424805112912e-01 , 2.67062889902466e-01 ), ( 2.43422720664008e-02 , -9.93480134779912e-02 , 9.47584074895654e-02 ), ( 2.64823207884572e-02 , -9.72127013570269e-02 , 5.88563122381287e-02 ), ( 1.22945465945720e-02 , -5.60400376600130e-02 , 7.17161479237924e-02 ), ( 1.24370696655174e-02 , -5.37633069113443e-02 , 6.06388129855506e-02 ), ( 5.50290662739556e-03 , -3.56049421041010e-02 , 7.49181815458750e-02 ), ( -8.62594279342891e-03 , 8.52631563305037e-03 , 7.49889010438598e-02 ), ( -2.07304727561448e-03 , -3.37528964129998e-03 , 4.00961351411889e-02 ), ( -5.76061164789090e-03 , 9.18555649372059e-03 , 3.58710078036011e-02 ), ( 2.78174471784882e-03 , -1.34876115706387e-02 , 1.95148242584832e-02 ), ( 9.20812060560969e-03 , -2.22863671904897e-02 , -2.63960131935175e-02 ), ( 8.79752854486906e-03 , -2.38450026309958e-02 , -1.48322003035765e-02 ), ( 6.70483229466327e-03 , -1.35465340002202e-02 , -3.01308249087184e-02 ), ( 1.50788672216310e-02 , -4.65748402463062e-02 , -2.20698674250555e-03 ), ( 2.76224099666520e-02 , -8.80070809511392e-02 , 6.89732827922291e-03 ), ( 1.42640174897213e-02 , -4.66710917663395e-02 , 8.54621834415305e-03 ), ( 1.42152092039004e-02 , -4.37039689431695e-02 , -2.90768681103621e-03 ), ( 9.25385553881755e-03 , -3.70677988178844e-02 , 3.31746574587554e-02 ), ( -9.54216635819503e-04 , -1.56455971443211e-02 , 7.58025888278881e-02 ), ( -3.83453115114318e-03 , 3.95524868266385e-03 , 3.26636909607623e-02 ), ( -5.91561681798440e-03 , 1.10689709469262e-02 , 3.01775794099485e-02 ), ( -7.31568557729522e-03 , 1.76059473675832e-02 , 2.13787882331402e-02 ), ( -1.62280883237696e-02 , 5.15340202994481e-02 , -3.36079177638941e-03 ), ( -9.71731425170028e-03 , 3.56135592412924e-02 , -2.13634329163894e-02 ), ( -1.37515004753704e-02 , 4.98570258920335e-02 , -2.80282978586587e-02 ), ( -1.93274202187645e-03 , 1.48918151276390e-02 , -3.60249531028628e-02 ), ( 1.06868010425364e-02 , -1.55163054887531e-02 , -7.27491027760079e-02 ), ( 4.40947940082497e-03 , -5.04406089998529e-04 , -5.40176678525476e-02 ), ( 3.39692613696997e-03 , 6.41279540689519e-03 , -6.92913568633798e-02 ), ( 7.12007193986920e-03 , -1.45391352614655e-02 , -3.13716172491232e-02 ), ( 1.30066812693670e-02 , -4.09701058428207e-02 , 1.33447796586508e-03 ), ( 4.52637477376300e-04 , 2.02121811019220e-03 , -1.39809114433900e-02 ), ( 3.68871321751038e-04 , 3.71941944337004e-03 , -1.98264904541570e-02 ), ( -6.59155139229773e-03 , 2.06356960691847e-02 , -1.58597446801256e-04 ), ( -2.06741434674982e-02 , 5.75159193607012e-02 , 2.88316092525700e-02 ), ( -1.90154049605807e-02 , 6.32603313301188e-02 , -1.56372478319434e-02 ), ( -2.27354870994093e-02 , 7.52121778503086e-02 , -1.69705931059206e-02 ), ( -1.67945805077401e-02 , 7.26394386828972e-02 , -8.20447054617395e-02 ), ( -1.98624280707300e-02 , 8.68154008280787e-02 , -1.00722691225296e-01 ), ( -8.53818784940369e-03 , 4.69173202401636e-02 , -8.23570774196875e-02 ), ( -1.86144965450949e-02 , 6.66844476645428e-02 , -3.46693975793695e-02 ), ( -2.43304588010985e-02 , 9.27214764030263e-02 , -6.79422921811020e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 8, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 9 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 9, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 9, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 9, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 9, atoms_positions[size = 51] = { ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 ), ( 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 ), ( 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 ), ( 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 ), ( 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 ), ( 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 ), ( -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 ), ( -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 ), ( -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 ), ( -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ), ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 ), ( 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 ), ( 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 ), ( 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 ), ( 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 ), ( 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 ), ( 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 ), ( 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 ), ( 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 ), ( 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 ), ( 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 ), ( 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 ), ( 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 ), ( 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 ), ( 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 ), ( 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 ), ( 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 ), ( 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 ), ( 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 ), ( -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 ), ( 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 ), ( 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 ), ( -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 ), ( -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 ), ( -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 ), ( -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 ), ( -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 ), ( -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 ), ( -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 ), ( -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 ), ( -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 ), ( -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 ), ( -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 ), ( -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 ), ( -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 ), ( -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 ), ( -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 ), ( -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 ), ( -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 ), ( -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 ), ( -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ) } +colvars: Step 9, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_ids[size = 0] = +colvars: Step 9, atom_groups_refcount[size = 0] = +colvars: Step 9, atom_groups_masses[size = 0] = +colvars: Step 9, atom_groups_charges[size = 0] = +colvars: Step 9, atom_groups_coms[size = 0] = +colvars: Step 9, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 9, volmaps_ids[size = 0] = +colvars: Step 9, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 9 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.291575 , 17.0541 , 17.2289 , 18.0884 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.291575 , 17.0541 , 17.2289 , 18.0884 ) to colvar "one". +colvars: Adding total bias energy: 11.4369 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.291575 , 17.0541 , 17.2289 , 18.0884 ) +colvars: Applying force on main group : +colvars: ( -0.0912729 , 0.385594 , -0.474093 ) +colvars: ( 0.0148956 , 0.0422267 , -0.305817 ) +colvars: ( -0.0456926 , 0.102373 , 0.093032 ) +colvars: ( -0.116076 , 0.305175 , 0.0719597 ) +colvars: ( -0.0220405 , 0.120715 , -0.215066 ) +colvars: ( 0.0837305 , -0.222184 , -0.0444423 ) +colvars: ( 0.0081957 , -0.108001 , 0.309959 ) +colvars: ( -0.0491436 , 0.0786383 , 0.214725 ) +colvars: ( 0.0805042 , -0.231946 , 0.0240398 ) +colvars: ( 0.1369 , -0.472592 , 0.325703 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243803 , -0.0993282 , 0.0948558 ) +colvars: ( 0.0198555 , -0.0820737 , 0.0820835 ) +colvars: ( 0.0265038 , -0.097191 , 0.0589363 ) +colvars: ( 0.0123144 , -0.0560008 , 0.0717882 ) +colvars: ( 0.0124565 , -0.0537374 , 0.0607005 ) +colvars: ( 0.00551661 , -0.0355455 , 0.0749882 ) +colvars: ( -0.00256136 , -0.00882159 , 0.0688952 ) +colvars: ( -0.00862469 , 0.00861819 , 0.075048 ) +colvars: ( -0.00207424 , -0.00332004 , 0.0401333 ) +colvars: ( -0.00576263 , 0.00923668 , 0.035899 ) +colvars: ( 0.00277443 , -0.0134401 , 0.0195446 ) +colvars: ( 0.00416843 , -0.0109218 , -0.00860234 ) +colvars: ( 0.00918672 , -0.022256 , -0.026389 ) +colvars: ( 0.00878768 , -0.0238333 , -0.0148245 ) +colvars: ( 0.00669069 , -0.0135428 , -0.0301377 ) +colvars: ( 0.0150787 , -0.0465731 , -0.00218568 ) +colvars: ( 0.0197432 , -0.0604503 , -0.00503165 ) +colvars: ( 0.0276376 , -0.0880347 , 0.00693359 ) +colvars: ( 0.0142747 , -0.0466871 , 0.00856735 ) +colvars: ( 0.0142252 , -0.043733 , -0.00289726 ) +colvars: ( 0.00926911 , -0.0370663 , 0.0332082 ) +colvars: ( 0.00307966 , -0.0212752 , 0.0477262 ) +colvars: ( -0.000929764 , -0.0156181 , 0.0758541 ) +colvars: ( -0.00382444 , 0.00396746 , 0.032681 ) +colvars: ( -0.00590417 , 0.0110734 , 0.030188 ) +colvars: ( -0.00731521 , 0.0176304 , 0.021388 ) +colvars: ( -0.0132828 , 0.0404663 , 0.00421809 ) +colvars: ( -0.0162464 , 0.0515784 , -0.00337326 ) +colvars: ( -0.00973056 , 0.0356215 , -0.0213879 ) +colvars: ( -0.013767 , 0.0498617 , -0.0280636 ) +colvars: ( -0.0019468 , 0.0148852 , -0.036051 ) +colvars: ( 0.00241322 , 0.00706286 , -0.0597976 ) +colvars: ( 0.0106684 , -0.0155548 , -0.0727879 ) +colvars: ( 0.00440034 , -0.00054711 , -0.0540558 ) +colvars: ( 0.00338453 , 0.00635935 , -0.0693432 ) +colvars: ( 0.00712167 , -0.0145828 , -0.0313927 ) +colvars: ( 0.00856324 , -0.0212821 , -0.0224007 ) +colvars: ( 0.0130279 , -0.0410265 , 0.00133745 ) +colvars: ( 0.00046264 , 0.00197397 , -0.0140026 ) +colvars: ( 0.0003805 , 0.00365978 , -0.0198555 ) +colvars: ( -0.00658348 , 0.0206102 , -0.000175983 ) +colvars: ( -0.0147969 , 0.0443184 , 0.00781409 ) +colvars: ( -0.0206663 , 0.0575251 , 0.0288211 ) +colvars: ( -0.0190185 , 0.0632436 , -0.0156793 ) +colvars: ( -0.0227383 , 0.0751919 , -0.01702 ) +colvars: ( -0.0168196 , 0.0726005 , -0.0821293 ) +colvars: ( -0.0198949 , 0.086773 , -0.100824 ) +colvars: ( -0.00855692 , 0.0468619 , -0.0824347 ) +colvars: ( -0.0186271 , 0.0666706 , -0.0347212 ) +colvars: ( -0.022331 , 0.083933 , -0.058027 ) +colvars: ( -0.0243627 , 0.0927198 , -0.0680185 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 9. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 9. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atoms_new_colvar_forces = { ( -7.14173720653988e-02 , 3.03520052049550e-01 , -3.92009785651569e-01 ), ( 1.23342420189076e-02 , 3.34051155343946e-02 , -2.36921588255221e-01 ), ( -4.15241266423430e-02 , 9.14514427042298e-02 , 8.44297030591048e-02 ), ( -9.63331533612291e-02 , 2.44725046427125e-01 , 6.69280120891987e-02 ), ( -1.89607984864655e-02 , 9.94393414177422e-02 , -1.67339404363429e-01 ), ( 7.04476436573704e-02 , -1.81717278785775e-01 , -4.02242178643844e-02 ), ( 1.06089134397880e-02 , -1.00937973904036e-01 , 2.50161143716076e-01 ), ( -4.05803503902119e-02 , 5.73562046068344e-02 , 1.92324357692035e-01 ), ( 6.57073059950226e-02 , -1.87627270111012e-01 , 3.18539040038509e-02 ), ( 1.14568853707169e-01 , -3.88658891277373e-01 , 2.67675620853643e-01 ), ( 2.43802816273955e-02 , -9.93281874098511e-02 , 9.48558475196411e-02 ), ( 2.65037845454748e-02 , -9.71909867682365e-02 , 5.89362890305024e-02 ), ( 1.23143907242286e-02 , -5.60007579469611e-02 , 7.17881814673141e-02 ), ( 1.24565401286085e-02 , -5.37373630896944e-02 , 6.07005352450290e-02 ), ( 5.51661482992866e-03 , -3.55455043228472e-02 , 7.49881872869175e-02 ), ( -8.62469301701959e-03 , 8.61819191963210e-03 , 7.50479617281995e-02 ), ( -2.07424105302506e-03 , -3.32003763727391e-03 , 4.01332666040667e-02 ), ( -5.76263256060389e-03 , 9.23667566792743e-03 , 3.58990112766273e-02 ), ( 2.77442962802959e-03 , -1.34400622886135e-02 , 1.95446294702857e-02 ), ( 9.18672312511947e-03 , -2.22559787396961e-02 , -2.63889931974540e-02 ), ( 8.78768419625598e-03 , -2.38332647478740e-02 , -1.48245460439309e-02 ), ( 6.69069192888830e-03 , -1.35428452060799e-02 , -3.01376619569618e-02 ), ( 1.50787137839697e-02 , -4.65730867592132e-02 , -2.18567840461604e-03 ), ( 2.76376217799769e-02 , -8.80346894842445e-02 , 6.93358865624687e-03 ), ( 1.42747227515129e-02 , -4.66871377959406e-02 , 8.56734570785393e-03 ), ( 1.42252270283724e-02 , -4.37329821937682e-02 , -2.89726261151907e-03 ), ( 9.26911427579752e-03 , -3.70663365654842e-02 , 3.32082031893863e-02 ), ( -9.29764348433053e-04 , -1.56180778191128e-02 , 7.58541079446727e-02 ), ( -3.82444347630877e-03 , 3.96746298948432e-03 , 3.26809834852590e-02 ), ( -5.90417007842335e-03 , 1.10734044656187e-02 , 3.01880303085622e-02 ), ( -7.31520771406639e-03 , 1.76304377592534e-02 , 2.13880036242598e-02 ), ( -1.62463832765021e-02 , 5.15783873773705e-02 , -3.37326477439167e-03 ), ( -9.73056072304787e-03 , 3.56215314413404e-02 , -2.13878722217663e-02 ), ( -1.37669713898938e-02 , 4.98616515224360e-02 , -2.80635756631084e-02 ), ( -1.94679852005065e-03 , 1.48851647538967e-02 , -3.60510088394936e-02 ), ( 1.06684267389560e-02 , -1.55548296526290e-02 , -7.27878605475704e-02 ), ( 4.40034243909777e-03 , -5.47109796954654e-04 , -5.40558287094212e-02 ), ( 3.38453211590400e-03 , 6.35935043890287e-03 , -6.93432179144250e-02 ), ( 7.12167142475610e-03 , -1.45827751867512e-02 , -3.13927394832841e-02 ), ( 1.30278759427845e-02 , -4.10264554725312e-02 , 1.33745297410011e-03 ), ( 4.62640012449616e-04 , 1.97396863527872e-03 , -1.40026278660333e-02 ), ( 3.80499989890732e-04 , 3.65978008219712e-03 , -1.98554826335770e-02 ), ( -6.58348401757125e-03 , 2.06101712556980e-02 , -1.75982618459987e-04 ), ( -2.06663438231585e-02 , 5.75251140088467e-02 , 2.88210760175877e-02 ), ( -1.90184995833039e-02 , 6.32436419183766e-02 , -1.56793092131453e-02 ), ( -2.27382858128587e-02 , 7.51918527306527e-02 , -1.70199767768858e-02 ), ( -1.68196160872486e-02 , 7.26005373823680e-02 , -8.21293047577027e-02 ), ( -1.98949441245263e-02 , 8.67730382686525e-02 , -1.00823829224095e-01 ), ( -8.55691582416121e-03 , 4.68619408623113e-02 , -8.24346991593812e-02 ), ( -1.86270664811170e-02 , 6.66706057166005e-02 , -3.47212383429930e-02 ), ( -2.43626649786876e-02 , 9.27197710252338e-02 , -6.80184858556002e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 9, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 10 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 10, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 10, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 10, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 10, atoms_positions[size = 51] = { ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 ), ( 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 ), ( 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 ), ( 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 ), ( 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 ), ( 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 ), ( -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 ), ( -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 ), ( -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 ), ( -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ), ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 ), ( 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 ), ( 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 ), ( 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 ), ( 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 ), ( 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 ), ( 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 ), ( 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 ), ( 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 ), ( 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 ), ( 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 ), ( 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 ), ( 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 ), ( 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 ), ( 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 ), ( 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 ), ( 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 ), ( 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 ), ( 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 ), ( -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 ), ( 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 ), ( 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 ), ( -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 ), ( -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 ), ( -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 ), ( -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 ), ( -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 ), ( -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 ), ( -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 ), ( -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 ), ( -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 ), ( -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 ), ( -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 ), ( -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 ), ( -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 ), ( -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 ), ( -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 ), ( -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 ), ( -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 ), ( -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 ), ( -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ) } +colvars: Step 10, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_ids[size = 0] = +colvars: Step 10, atom_groups_refcount[size = 0] = +colvars: Step 10, atom_groups_masses[size = 0] = +colvars: Step 10, atom_groups_charges[size = 0] = +colvars: Step 10, atom_groups_coms[size = 0] = +colvars: Step 10, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 10, volmaps_ids[size = 0] = +colvars: Step 10, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 10 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.287427 , 17.069 , 17.2369 , 18.0771 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.287427 , 17.069 , 17.2369 , 18.0771 ) to colvar "one". +colvars: Adding total bias energy: 11.4416 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.287427 , 17.069 , 17.2369 , 18.0771 ) +colvars: Applying force on main group : +colvars: ( -0.0913866 , 0.385492 , -0.474976 ) +colvars: ( 0.014921 , 0.0416532 , -0.305966 ) +colvars: ( -0.0456814 , 0.102428 , 0.0935609 ) +colvars: ( -0.116179 , 0.305789 , 0.0718814 ) +colvars: ( -0.0220975 , 0.120706 , -0.21566 ) +colvars: ( 0.0838138 , -0.222667 , -0.0442867 ) +colvars: ( 0.0082356 , -0.107768 , 0.310577 ) +colvars: ( -0.0492129 , 0.0793055 , 0.214612 ) +colvars: ( 0.0805409 , -0.232078 , 0.0238308 ) +colvars: ( 0.137046 , -0.472861 , 0.326426 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0244216 , -0.0993121 , 0.0949577 ) +colvars: ( 0.019885 , -0.0820416 , 0.0821746 ) +colvars: ( 0.0265269 , -0.0971712 , 0.0590181 ) +colvars: ( 0.012336 , -0.0559617 , 0.0718637 ) +colvars: ( 0.0124777 , -0.0537124 , 0.0607652 ) +colvars: ( 0.00553171 , -0.0354842 , 0.0750622 ) +colvars: ( -0.00255336 , -0.00874962 , 0.0689566 ) +colvars: ( -0.00862291 , 0.00871572 , 0.0751117 ) +colvars: ( -0.00207536 , -0.00326128 , 0.0401727 ) +colvars: ( -0.0057646 , 0.00929127 , 0.0359293 ) +colvars: ( 0.0027665 , -0.013389 , 0.019575 ) +colvars: ( 0.00415194 , -0.0108845 , -0.00859243 ) +colvars: ( 0.0091632 , -0.0222218 , -0.0263847 ) +colvars: ( 0.00877678 , -0.0238201 , -0.0148187 ) +colvars: ( 0.00667509 , -0.0135376 , -0.0301471 ) +colvars: ( 0.0150783 , -0.0465717 , -0.00216564 ) +colvars: ( 0.0197494 , -0.0604714 , -0.00501288 ) +colvars: ( 0.0276537 , -0.0880665 , 0.00696858 ) +colvars: ( 0.0142862 , -0.0467058 , 0.00858817 ) +colvars: ( 0.0142359 , -0.0437653 , -0.00288777 ) +colvars: ( 0.00928567 , -0.0370668 , 0.0332433 ) +colvars: ( 0.00310055 , -0.0212694 , 0.047764 ) +colvars: ( -0.000902878 , -0.0155915 , 0.0759105 ) +colvars: ( -0.00381329 , 0.00397944 , 0.0327006 ) +colvars: ( -0.00589151 , 0.0110771 , 0.0302009 ) +colvars: ( -0.00731449 , 0.0176566 , 0.0213989 ) +colvars: ( -0.0132926 , 0.040498 , 0.00421064 ) +colvars: ( -0.016266 , 0.0516279 , -0.00338525 ) +colvars: ( -0.00974488 , 0.0356317 , -0.0214131 ) +colvars: ( -0.0137837 , 0.0498687 , -0.0280998 ) +colvars: ( -0.00196218 , 0.0148797 , -0.0360793 ) +colvars: ( 0.00239432 , 0.00703553 , -0.0598414 ) +colvars: ( 0.010648 , -0.015594 , -0.0728319 ) +colvars: ( 0.00439013 , -0.000591528 , -0.0540975 ) +colvars: ( 0.00337074 , 0.00630394 , -0.0693994 ) +colvars: ( 0.00712318 , -0.0146294 , -0.031416 ) +colvars: ( 0.0085739 , -0.0213428 , -0.0224197 ) +colvars: ( 0.0130507 , -0.0410889 , 0.00134016 ) +colvars: ( 0.000473458 , 0.00192279 , -0.0140248 ) +colvars: ( 0.000393067 , 0.0035953 , -0.0198852 ) +colvars: ( -0.0065746 , 0.0205825 , -0.000192625 ) +colvars: ( -0.0147888 , 0.0443022 , 0.00779432 ) +colvars: ( -0.0206574 , 0.0575347 , 0.0288139 ) +colvars: ( -0.0190216 , 0.0632269 , -0.0157209 ) +colvars: ( -0.022741 , 0.0751714 , -0.0170686 ) +colvars: ( -0.0168469 , 0.0725626 , -0.0822178 ) +colvars: ( -0.0199303 , 0.0867323 , -0.10093 ) +colvars: ( -0.00857744 , 0.0468056 , -0.0825167 ) +colvars: ( -0.0186405 , 0.0666579 , -0.0347739 ) +colvars: ( -0.0223557 , 0.08392 , -0.0581005 ) +colvars: ( -0.0243975 , 0.0927223 , -0.0680975 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 10. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 10. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atoms_new_colvar_forces = { ( -7.15016607715429e-02 , 3.03450248290296e-01 , -3.92801115143173e-01 ), ( 1.23676636514961e-02 , 3.29036024770242e-02 , -2.37009333522469e-01 ), ( -4.15294698469746e-02 , 9.15434694739862e-02 , 8.49684851875916e-02 ), ( -9.64292968119024e-02 , 2.45317517705941e-01 , 6.68684776651641e-02 ), ( -1.89969183888788e-02 , 9.94364123729832e-02 , -1.67895921441165e-01 ), ( 7.05212056674245e-02 , -1.82169054972534e-01 , -4.00760890945774e-02 ), ( 1.06299188456399e-02 , -1.00732179998986e-01 , 2.50735712205887e-01 ), ( -4.06390391411500e-02 , 5.79627727319512e-02 , 1.92192742745201e-01 ), ( 6.57521305972952e-02 , -1.87775429438928e-01 , 3.16250898809562e-02 ), ( 1.14690118965508e-01 , -3.88940933598096e-01 , 2.68325226130177e-01 ), ( 2.44215543618543e-02 , -9.93121128890011e-02 , 9.49576777085679e-02 ), ( 2.65268959319662e-02 , -9.71711911284568e-02 , 5.90180610098199e-02 ), ( 1.23360273326501e-02 , -5.59616922094030e-02 , 7.18637286173737e-02 ), ( 1.24777272206467e-02 , -5.37123954054054e-02 , 6.07651560900780e-02 ), ( 5.53170505664086e-03 , -3.54841808979951e-02 , 7.50622055553943e-02 ), ( -8.62291255185739e-03 , 8.71572042334931e-03 , 7.51117297407181e-02 ), ( -2.07535676767601e-03 , -3.26128095343410e-03 , 4.01726641337359e-02 ), ( -5.76460113859217e-03 , 9.29126628119511e-03 , 3.59293100500467e-02 ), ( 2.76649955079081e-03 , -1.33889700503236e-02 , 1.95750408014193e-02 ), ( 9.16320150588291e-03 , -2.22217657715012e-02 , -2.63847478136887e-02 ), ( 8.77677580102878e-03 , -2.38200554097055e-02 , -1.48186594740397e-02 ), ( 6.67509070954950e-03 , -1.35376306408063e-02 , -3.01470585284635e-02 ), ( 1.50782845708932e-02 , -4.65717205649901e-02 , -2.16564122789621e-03 ), ( 2.76537239190706e-02 , -8.80665291346259e-02 , 6.96858447717809e-03 ), ( 1.42861554171493e-02 , -4.67057844220242e-02 , 8.58817479450385e-03 ), ( 1.42358707997841e-02 , -4.37652957110214e-02 , -2.88776698081043e-03 ), ( 9.28567383034638e-03 , -3.70667515371096e-02 , 3.32432904895662e-02 ), ( -9.02878066972223e-04 , -1.55915280171617e-02 , 7.59105106601409e-02 ), ( -3.81328853416054e-03 , 3.97944496036692e-03 , 3.27006272124910e-02 ), ( -5.89151124666769e-03 , 1.10770632059042e-02 , 3.02008998913624e-02 ), ( -7.31448604032661e-03 , 1.76565883927560e-02 , 2.13989346487279e-02 ), ( -1.62660173524484e-02 , 5.16279375578137e-02 , -3.38524703866288e-03 ), ( -9.74488071294648e-03 , 3.56317430010617e-02 , -2.14131237375987e-02 ), ( -1.37836669147457e-02 , 4.98686933275603e-02 , -2.80997837478720e-02 ), ( -1.96218459227142e-03 , 1.48797039895180e-02 , -3.60792790294987e-02 ), ( 1.06479972601359e-02 , -1.55940292832885e-02 , -7.28318919398760e-02 ), ( 4.39013310678059e-03 , -5.91527552862357e-04 , -5.40974975810518e-02 ), ( 3.37074168129654e-03 , 6.30393571727351e-03 , -6.93994276341061e-02 ), ( 7.12317534535211e-03 , -1.46294393396425e-02 , -3.14160328614953e-02 ), ( 1.30507102522968e-02 , -4.10889103847666e-02 , 1.34016377943249e-03 ), ( 4.73458451596478e-04 , 1.92279396386442e-03 , -1.40248176248883e-02 ), ( 3.93066712348838e-04 , 3.59530102454662e-03 , -1.98852042495396e-02 ), ( -6.57460039163598e-03 , 2.05824681853941e-02 , -1.92624994433728e-04 ), ( -2.06574072402664e-02 , 5.75347116778676e-02 , 2.88139007127607e-02 ), ( -1.90216018460062e-02 , 6.32269308398371e-02 , -1.57208546495785e-02 ), ( -2.27410084662747e-02 , 7.51713819207301e-02 , -1.70686233836183e-02 ), ( -1.68468604051727e-02 , 7.25625867508809e-02 , -8.22177879392403e-02 ), ( -1.99303402800334e-02 , 8.67323329271237e-02 , -1.00929847872743e-01 ), ( -8.57744112834063e-03 , 4.68055646721169e-02 , -8.25166553580956e-02 ), ( -1.86405497075895e-02 , 6.66579250535560e-02 , -3.47739046838852e-02 ), ( -2.43975282009917e-02 , 9.27222723871716e-02 , -6.80974566358273e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 10, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 11 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 11, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 11, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 11, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 11, atoms_positions[size = 51] = { ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 ), ( 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 ), ( 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 ), ( 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 ), ( 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 ), ( 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 ), ( -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 ), ( -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 ), ( -3.76978320280504e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 ), ( -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ), ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 ), ( 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 ), ( 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 ), ( 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 ), ( 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 ), ( 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 ), ( 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 ), ( 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 ), ( 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 ), ( 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 ), ( 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 ), ( 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 ), ( 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 ), ( 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 ), ( 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 ), ( 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 ), ( 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 ), ( 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 ), ( 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 ), ( -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 ), ( 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 ), ( 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 ), ( -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 ), ( -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 ), ( -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 ), ( -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 ), ( -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 ), ( -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 ), ( -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 ), ( -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 ), ( -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 ), ( -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 ), ( -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 ), ( -2.38523274426802e+00 , -3.45124047741376e-01 , 6.16281301316000e+00 ), ( -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 ), ( -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 ), ( -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 ), ( -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 ), ( -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 ), ( -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 ), ( -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ) } +colvars: Step 11, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_ids[size = 0] = +colvars: Step 11, atom_groups_refcount[size = 0] = +colvars: Step 11, atom_groups_masses[size = 0] = +colvars: Step 11, atom_groups_charges[size = 0] = +colvars: Step 11, atom_groups_coms[size = 0] = +colvars: Step 11, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 11, volmaps_ids[size = 0] = +colvars: Step 11, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 11 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.282926 , 17.0847 , 17.245 , 18.0657 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.282926 , 17.0847 , 17.245 , 18.0657 ) to colvar "one". +colvars: Adding total bias energy: 11.4466 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.282926 , 17.0847 , 17.245 , 18.0657 ) +colvars: Applying force on main group : +colvars: ( -0.0914946 , 0.385422 , -0.4759 ) +colvars: ( 0.0149517 , 0.0410846 , -0.30613 ) +colvars: ( -0.0456789 , 0.102505 , 0.0941065 ) +colvars: ( -0.116289 , 0.306436 , 0.0718024 ) +colvars: ( -0.0221489 , 0.120702 , -0.216278 ) +colvars: ( 0.083902 , -0.223173 , -0.0441278 ) +colvars: ( 0.00826781 , -0.107538 , 0.311223 ) +colvars: ( -0.0492868 , 0.0799779 , 0.214504 ) +colvars: ( 0.0805848 , -0.232241 , 0.023618 ) +colvars: ( 0.137192 , -0.473174 , 0.327181 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0244644 , -0.0993009 , 0.0950635 ) +colvars: ( 0.0199155 , -0.0820124 , 0.0822687 ) +colvars: ( 0.0265507 , -0.0971549 , 0.0591007 ) +colvars: ( 0.0123585 , -0.055924 , 0.0719419 ) +colvars: ( 0.0124997 , -0.0536893 , 0.0608321 ) +colvars: ( 0.00554745 , -0.0354222 , 0.075139 ) +colvars: ( -0.00254491 , -0.00867533 , 0.0690209 ) +colvars: ( -0.00862088 , 0.00881758 , 0.0751785 ) +colvars: ( -0.00207649 , -0.00320005 , 0.0402132 ) +colvars: ( -0.00576656 , 0.00934859 , 0.0359609 ) +colvars: ( 0.00275811 , -0.0133356 , 0.0196048 ) +colvars: ( 0.00413455 , -0.010845 , -0.00858494 ) +colvars: ( 0.00913831 , -0.0221854 , -0.0263847 ) +colvars: ( 0.00876515 , -0.0238064 , -0.0148153 ) +colvars: ( 0.00665857 , -0.0135317 , -0.0301596 ) +colvars: ( 0.0150775 , -0.0465717 , -0.0021474 ) +colvars: ( 0.0197555 , -0.0604955 , -0.0049958 ) +colvars: ( 0.0276701 , -0.0881034 , 0.00700234 ) +colvars: ( 0.0142979 , -0.0467273 , 0.00860881 ) +colvars: ( 0.0142468 , -0.043801 , -0.00287882 ) +colvars: ( 0.00930289 , -0.0370693 , 0.0332799 ) +colvars: ( 0.00312243 , -0.0212653 , 0.0478048 ) +colvars: ( -0.000874617 , -0.0155659 , 0.0759717 ) +colvars: ( -0.0038015 , 0.00399139 , 0.0327227 ) +colvars: ( -0.0058781 , 0.0110805 , 0.0302165 ) +colvars: ( -0.00731359 , 0.0176844 , 0.0214113 ) +colvars: ( -0.0133025 , 0.0405329 , 0.00420375 ) +colvars: ( -0.0162863 , 0.0516824 , -0.00339755 ) +colvars: ( -0.00975974 , 0.0356443 , -0.0214393 ) +colvars: ( -0.0138009 , 0.0498786 , -0.0281369 ) +colvars: ( -0.00197831 , 0.0148754 , -0.0361098 ) +colvars: ( 0.00237443 , 0.00700837 , -0.0598889 ) +colvars: ( 0.0106263 , -0.0156342 , -0.0728811 ) +colvars: ( 0.00437932 , -0.000637252 , -0.0541421 ) +colvars: ( 0.00335619 , 0.00624717 , -0.0694592 ) +colvars: ( 0.00712462 , -0.0146786 , -0.0314407 ) +colvars: ( 0.00858493 , -0.0214074 , -0.022439 ) +colvars: ( 0.0130744 , -0.0411567 , 0.00134385 ) +colvars: ( 0.000484816 , 0.00186885 , -0.0140463 ) +colvars: ( 0.000406263 , 0.00352743 , -0.0199141 ) +colvars: ( -0.00656514 , 0.0205537 , -0.000207596 ) +colvars: ( -0.0147799 , 0.0442863 , 0.00777727 ) +colvars: ( -0.0206476 , 0.0575459 , 0.0288107 ) +colvars: ( -0.0190245 , 0.0632116 , -0.015761 ) +colvars: ( -0.0227434 , 0.0751525 , -0.0171154 ) +colvars: ( -0.0168752 , 0.0725269 , -0.0823093 ) +colvars: ( -0.0199671 , 0.0866947 , -0.10104 ) +colvars: ( -0.00859884 , 0.0467494 , -0.0826018 ) +colvars: ( -0.0186544 , 0.0666476 , -0.0348268 ) +colvars: ( -0.0223812 , 0.0839105 , -0.0581756 ) +colvars: ( -0.0244337 , 0.0927298 , -0.068179 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 11. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 11. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atoms_new_colvar_forces = { ( -7.15791435066877e-02 , 3.03409844462010e-01 , -3.93631147743522e-01 ), ( 1.24067694561056e-02 , 3.24092617088106e-02 , -2.37109313249408e-01 ), ( -4.15443493045436e-02 , 9.16594876814856e-02 , 8.55215908680847e-02 ), ( -9.65336402837815e-02 , 2.45940639162059e-01 , 6.68066014202904e-02 ), ( -1.90264360132423e-02 , 9.94362277505718e-02 , -1.68473121692907e-01 ), ( 7.05994752262471e-02 , -1.82640351786385e-01 , -3.99240593208833e-02 ), ( 1.06422393313364e-02 , -1.00529505736157e-01 , 2.51334253191404e-01 ), ( -4.07018668681346e-02 , 5.85704993383106e-02 , 1.92065217655378e-01 ), ( 6.58048500158185e-02 , -1.87955153690664e-01 , 3.13953139770057e-02 ), ( 1.14810836548122e-01 , -3.89263845763161e-01 , 2.69005747608971e-01 ), ( 2.44644420365523e-02 , -9.93008604362819e-02 , 9.50634540303171e-02 ), ( 2.65506639926814e-02 , -9.71549085398045e-02 , 5.91007414354449e-02 ), ( 1.23585185415142e-02 , -5.59239645083762e-02 , 7.19419408988772e-02 ), ( 1.24997439276150e-02 , -5.36892724561221e-02 , 6.08321053385152e-02 ), ( 5.54744932916615e-03 , -3.54222256237558e-02 , 7.51390424022061e-02 ), ( -8.62087934123943e-03 , 8.81757783726286e-03 , 7.51785053849694e-02 ), ( -2.07649081258038e-03 , -3.20004659983506e-03 , 4.02131668863943e-02 ), ( -5.76656001638264e-03 , 9.34859228802996e-03 , 3.59609344382249e-02 ), ( 2.75811391441253e-03 , -1.33356313310753e-02 , 1.96047867239134e-02 ), ( 9.13831399376691e-03 , -2.21853675629404e-02 , -2.63846638597659e-02 ), ( 8.76514693055518e-03 , -2.38063605419795e-02 , -1.48152755324360e-02 ), ( 6.65857259966534e-03 , -1.35316767744980e-02 , -3.01595939520679e-02 ), ( 1.50775434890925e-02 , -4.65716981852416e-02 , -2.14739829676821e-03 ), ( 2.76701085567005e-02 , -8.81033908999233e-02 , 7.00234061373576e-03 ), ( 1.42978914433128e-02 , -4.67273424783863e-02 , 8.60881480028640e-03 ), ( 1.42467794788397e-02 , -4.38009674766436e-02 , -2.87882066252855e-03 ), ( 9.30289142383668e-03 , -3.70693093754741e-02 , 3.32798991260648e-02 ), ( -8.74616788559080e-04 , -1.55659268803168e-02 , 7.59717207069584e-02 ), ( -3.80149697823639e-03 , 3.99139497661138e-03 , 3.27226818702287e-02 ), ( -5.87809955712979e-03 , 1.10804620992655e-02 , 3.02165111697874e-02 ), ( -7.31358799819382e-03 , 1.76843548454293e-02 , 2.14112914406596e-02 ), ( -1.62863320779151e-02 , 5.16823604558912e-02 , -3.39755451020750e-03 ), ( -9.75973706289892e-03 , 3.56443383847642e-02 , -2.14393173203162e-02 ), ( -1.38009410110882e-02 , 4.98785618144178e-02 , -2.81368949956214e-02 ), ( -1.97831014138354e-03 , 1.48753846947268e-02 , -3.61098401943824e-02 ), ( 1.06263319165018e-02 , -1.56341624769058e-02 , -7.28810696503613e-02 ), ( 4.37932488352575e-03 , -6.37252128288116e-04 , -5.41420695521195e-02 ), ( 3.35619138322246e-03 , 6.24716942821833e-03 , -6.94591804691144e-02 ), ( 7.12461969116057e-03 , -1.46786360570569e-02 , -3.14407424751560e-02 ), ( 1.30744491935402e-02 , -4.11566574770348e-02 , 1.34384855831247e-03 ), ( 4.84816048636935e-04 , 1.86884529652321e-03 , -1.40462649459062e-02 ), ( 4.06262902972105e-04 , 3.52742628407919e-03 , -1.99141343288618e-02 ), ( -6.56514050363635e-03 , 2.05536818096240e-02 , -2.07595716940279e-04 ), ( -2.06476219371302e-02 , 5.75459498804657e-02 , 2.88107008122013e-02 ), ( -1.90244943026149e-02 , 6.32116292719994e-02 , -1.57609754741589e-02 ), ( -2.27434304429232e-02 , 7.51525034805505e-02 , -1.71154202691943e-02 ), ( -1.68751559011819e-02 , 7.25268655901674e-02 , -8.23092755311854e-02 ), ( -1.99671400786953e-02 , 8.66946604746156e-02 , -1.01039844952936e-01 ), ( -8.59883664831505e-03 , 4.67494396675215e-02 , -8.26018445395924e-02 ), ( -1.86543551069504e-02 , 6.66475511479637e-02 , -3.48267535670694e-02 ), ( -2.44336835714561e-02 , 9.27298049549328e-02 , -6.81790385548220e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 11, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 12 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 12, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 12, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 12, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 12, atoms_positions[size = 51] = { ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 ), ( 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 ), ( 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 ), ( 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 ), ( 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 ), ( 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 ), ( -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 ), ( -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 ), ( -3.76368207226495e+00 , 5.16946302547613e-02 , 5.47019231775250e+00 ), ( -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ), ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 ), ( 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 ), ( 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 ), ( 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 ), ( 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 ), ( 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 ), ( 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 ), ( 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 ), ( 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 ), ( 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 ), ( 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 ), ( 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 ), ( 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 ), ( 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 ), ( 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 ), ( 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 ), ( 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 ), ( 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 ), ( 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 ), ( -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 ), ( 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 ), ( 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 ), ( -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 ), ( -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 ), ( -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 ), ( -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 ), ( -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 ), ( -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 ), ( -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 ), ( -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 ), ( -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 ), ( -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 ), ( -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 ), ( -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 ), ( -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 ), ( -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 ), ( -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 ), ( -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 ), ( -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 ), ( -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 ), ( -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ) } +colvars: Step 12, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_ids[size = 0] = +colvars: Step 12, atom_groups_refcount[size = 0] = +colvars: Step 12, atom_groups_masses[size = 0] = +colvars: Step 12, atom_groups_charges[size = 0] = +colvars: Step 12, atom_groups_coms[size = 0] = +colvars: Step 12, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 12, volmaps_ids[size = 0] = +colvars: Step 12, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 12 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.278055 , 17.1008 , 17.2528 , 18.055 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.278055 , 17.1008 , 17.2528 , 18.055 ) to colvar "one". +colvars: Adding total bias energy: 11.452 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.278055 , 17.1008 , 17.2528 , 18.055 ) +colvars: Applying force on main group : +colvars: ( -0.091588 , 0.385384 , -0.476851 ) +colvars: ( 0.014988 , 0.0405351 , -0.306308 ) +colvars: ( -0.0456861 , 0.102607 , 0.0946493 ) +colvars: ( -0.116403 , 0.307104 , 0.0717178 ) +colvars: ( -0.0221903 , 0.120698 , -0.216905 ) +colvars: ( 0.083991 , -0.22369 , -0.0439651 ) +colvars: ( 0.00828836 , -0.107313 , 0.311882 ) +colvars: ( -0.0493627 , 0.0806373 , 0.214404 ) +colvars: ( 0.0806337 , -0.232438 , 0.0234152 ) +colvars: ( 0.137329 , -0.473524 , 0.327961 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0245072 , -0.0992953 , 0.0951725 ) +colvars: ( 0.0199458 , -0.0819872 , 0.0823646 ) +colvars: ( 0.026574 , -0.0971435 , 0.0591833 ) +colvars: ( 0.0123809 , -0.0558886 , 0.0720218 ) +colvars: ( 0.0125217 , -0.0536687 , 0.0609007 ) +colvars: ( 0.00556313 , -0.0353608 , 0.0752173 ) +colvars: ( -0.00253642 , -0.00859978 , 0.0690865 ) +colvars: ( -0.00861879 , 0.00892242 , 0.0752463 ) +colvars: ( -0.0020777 , -0.00313737 , 0.0402535 ) +colvars: ( -0.0057685 , 0.00940789 , 0.0359928 ) +colvars: ( 0.00274944 , -0.0132814 , 0.0196325 ) +colvars: ( 0.00411674 , -0.0108046 , -0.00858106 ) +colvars: ( 0.00911279 , -0.0221485 , -0.0263901 ) +colvars: ( 0.00875311 , -0.0237932 , -0.0148151 ) +colvars: ( 0.00664165 , -0.0135258 , -0.0301758 ) +colvars: ( 0.0150764 , -0.0465739 , -0.00213147 ) +colvars: ( 0.0197612 , -0.0605234 , -0.00498048 ) +colvars: ( 0.027686 , -0.0881459 , 0.00703491 ) +colvars: ( 0.0143094 , -0.046752 , 0.00862938 ) +colvars: ( 0.0142575 , -0.04384 , -0.00287 ) +colvars: ( 0.00932009 , -0.0370742 , 0.0333179 ) +colvars: ( 0.00314451 , -0.0212626 , 0.0478486 ) +colvars: ( -0.000846018 , -0.0155412 , 0.0760375 ) +colvars: ( -0.00378948 , 0.00400354 , 0.0327471 ) +colvars: ( -0.00586436 , 0.0110841 , 0.0302351 ) +colvars: ( -0.00731254 , 0.0177137 , 0.0214247 ) +colvars: ( -0.0133124 , 0.0405709 , 0.00419702 ) +colvars: ( -0.0163066 , 0.0517412 , -0.00341105 ) +colvars: ( -0.00977455 , 0.0356594 , -0.0214666 ) +colvars: ( -0.0138181 , 0.0498916 , -0.0281748 ) +colvars: ( -0.00199458 , 0.0148721 , -0.0361427 ) +colvars: ( 0.00235427 , 0.00698136 , -0.0599399 ) +colvars: ( 0.0106042 , -0.0156755 , -0.0729351 ) +colvars: ( 0.00436835 , -0.0006839 , -0.0541888 ) +colvars: ( 0.00334147 , 0.00618963 , -0.0695215 ) +colvars: ( 0.00712599 , -0.0147298 , -0.031466 ) +colvars: ( 0.008596 , -0.0214749 , -0.0224575 ) +colvars: ( 0.0130983 , -0.0412288 , 0.00134981 ) +colvars: ( 0.00049641 , 0.00181331 , -0.0140657 ) +colvars: ( 0.000419748 , 0.00345764 , -0.0199406 ) +colvars: ( -0.00655533 , 0.0205249 , -0.000219935 ) +colvars: ( -0.0147705 , 0.0442718 , 0.00776387 ) +colvars: ( -0.0206372 , 0.05756 , 0.028812 ) +colvars: ( -0.0190269 , 0.0631991 , -0.0157987 ) +colvars: ( -0.0227452 , 0.0751369 , -0.0171592 ) +colvars: ( -0.0169033 , 0.0724945 , -0.0824027 ) +colvars: ( -0.0200038 , 0.0866612 , -0.101153 ) +colvars: ( -0.00862017 , 0.0466947 , -0.0826889 ) +colvars: ( -0.0186678 , 0.0666405 , -0.0348791 ) +colvars: ( -0.0224065 , 0.0839055 , -0.0582514 ) +colvars: ( -0.0244697 , 0.092743 , -0.0682629 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 12. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 12. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atoms_new_colvar_forces = { ( -7.16421680750279e-02 , 3.03396548751539e-01 , -3.94486220717945e-01 ), ( 1.24515909749765e-02 , 3.19353701028632e-02 , -2.37221977925211e-01 ), ( -4.15693683146454e-02 , 9.18027746722944e-02 , 8.60682081256656e-02 ), ( -9.66413963586872e-02 , 2.46580175116835e-01 , 6.67373004675042e-02 ), ( -1.90458239292532e-02 , 9.94350184313190e-02 , -1.69056362419433e-01 ), ( 7.06786042823088e-02 , -1.83119401980232e-01 , -3.97681292658151e-02 ), ( 1.06426346587686e-02 , -1.00331643510678e-01 , 2.51942191228478e-01 ), ( -4.07667108107428e-02 , 5.91623733313463e-02 , 1.91946646728410e-01 ), ( 6.58631416517817e-02 , -1.88166122049303e-01 , 3.11790396547625e-02 ), ( 1.14922285106495e-01 , -3.89618039834855e-01 , 2.69709548896305e-01 ), ( 2.45072064690875e-02 , -9.92952513398520e-02 , 9.51725380397601e-02 ), ( 2.65739974674320e-02 , -9.71435419165180e-02 , 5.91833122237861e-02 ), ( 1.23808965877678e-02 , -5.58885675058319e-02 , 7.20217919193645e-02 ), ( 1.25216656406114e-02 , -5.36687337202716e-02 , 6.09006716071648e-02 ), ( 5.56312902213689e-03 , -3.53608099000057e-02 , 7.52172944233855e-02 ), ( -8.61878532719258e-03 , 8.92242158732669e-03 , 7.52463376805511e-02 ), ( -2.07770157462097e-03 , -3.13736891666858e-03 , 4.02534722876006e-02 ), ( -5.76850016691932e-03 , 9.40789227218322e-03 , 3.59927854806369e-02 ), ( 2.74944431517631e-03 , -1.32813564898526e-02 , 1.96325014128747e-02 ), ( 9.11279236113812e-03 , -2.21484706889497e-02 , -2.63901170934250e-02 ), ( 8.75310807004707e-03 , -2.37931703636637e-02 , -1.48151159553400e-02 ), ( 6.64165272602963e-03 , -1.35258005651302e-02 , -3.01757967596976e-02 ), ( 1.50763901547272e-02 , -4.65739180996560e-02 , -2.13146940458401e-03 ), ( 2.76860357759323e-02 , -8.81459002274344e-02 , 7.03490641253196e-03 ), ( 1.43094379929380e-02 , -4.67520260279631e-02 , 8.62938073013700e-03 ), ( 1.42575165045805e-02 , -4.38399629483993e-02 , -2.87000166804047e-03 ), ( 9.32008697586987e-03 , -3.70741783280618e-02 , 3.33179476827688e-02 ), ( -8.46017739415173e-04 , -1.55411561800035e-02 , 7.60374898142788e-02 ), ( -3.78947514792484e-03 , 4.00354032955485e-03 , 3.27471322944332e-02 ), ( -5.86436487064504e-03 , 1.10841396046405e-02 , 3.02351262515298e-02 ), ( -7.31253639742771e-03 , 1.77136686845677e-02 , 2.14247141411940e-02 ), ( -1.63065776924027e-02 , 5.17412136033583e-02 , -3.41105376001136e-03 ), ( -9.77454806826517e-03 , 3.56593718965960e-02 , -2.14665548734431e-02 ), ( -1.38180877017203e-02 , 4.98915524044661e-02 , -2.81748384597231e-02 ), ( -1.99458201197298e-03 , 1.48720940467247e-02 , -3.61426953349021e-02 ), ( 1.06041811229485e-02 , -1.56755236088371e-02 , -7.29350852936609e-02 ), ( 4.36834845946130e-03 , -6.83900191805435e-04 , -5.41887880626872e-02 ), ( 3.34147327126993e-03 , 6.18962776423781e-03 , -6.95214782203114e-02 ), ( 7.12598681052463e-03 , -1.47298439811097e-02 , -3.14660014810572e-02 ), ( 1.30982744407057e-02 , -4.12287535926886e-02 , 1.34981438346011e-03 ), ( 4.96410404255612e-04 , 1.81331109876103e-03 , -1.40656698696598e-02 ), ( 4.19748344476731e-04 , 3.45764211772422e-03 , -1.99406416982656e-02 ), ( -6.55532830509409e-03 , 2.05249114086253e-02 , -2.19934544421123e-04 ), ( -2.06371808932977e-02 , 5.75600182245067e-02 , 2.88120279806772e-02 ), ( -1.90268865001024e-02 , 6.31990805317706e-02 , -1.57987157085620e-02 ), ( -2.27452399178175e-02 , 7.51368540083220e-02 , -1.71592008838816e-02 ), ( -1.69032961322243e-02 , 7.24944830113589e-02 , -8.24026922858791e-02 ), ( -2.00038076931115e-02 , 8.66611845674294e-02 , -1.01152684539195e-01 ), ( -8.62016999247503e-03 , 4.66946998990970e-02 , -8.26889476000254e-02 ), ( -1.86678199864865e-02 , 6.66405053489124e-02 , -3.48790635755432e-02 ), ( -2.44696659839757e-02 , 9.27429691514109e-02 , -6.82629424665394e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 12, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 13 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 13, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 13, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 13, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 13, atoms_positions[size = 51] = { ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 ), ( 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 ), ( 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 ), ( 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 ), ( 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 ), ( 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 ), ( -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 ), ( -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 ), ( -3.75656449248184e+00 , 4.54305739009394e-02 , 5.46430316905750e+00 ), ( -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ), ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 ), ( 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 ), ( 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 ), ( 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 ), ( 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 ), ( 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 ), ( 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 ), ( 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 ), ( 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 ), ( 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 ), ( 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 ), ( 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 ), ( 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 ), ( 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 ), ( 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 ), ( 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 ), ( 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 ), ( 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 ), ( 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 ), ( -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 ), ( 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 ), ( 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 ), ( -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 ), ( -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 ), ( -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 ), ( -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 ), ( -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 ), ( -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 ), ( -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 ), ( -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 ), ( -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 ), ( -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 ), ( -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 ), ( -2.38255516970056e+00 , -3.29059335914522e-01 , 6.16893615475952e+00 ), ( -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 ), ( -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 ), ( -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 ), ( -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 ), ( -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 ), ( -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 ), ( -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ) } +colvars: Step 13, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_ids[size = 0] = +colvars: Step 13, atom_groups_refcount[size = 0] = +colvars: Step 13, atom_groups_masses[size = 0] = +colvars: Step 13, atom_groups_charges[size = 0] = +colvars: Step 13, atom_groups_coms[size = 0] = +colvars: Step 13, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 13, volmaps_ids[size = 0] = +colvars: Step 13, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 13 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610562e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610562e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.27283 , 17.117 , 17.26 , 18.0454 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.27283 , 17.117 , 17.26 , 18.0454 ) to colvar "one". +colvars: Adding total bias energy: 11.4577 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.27283 , 17.117 , 17.26 , 18.0454 ) +colvars: Applying force on main group : +colvars: ( -0.0916595 , 0.385373 , -0.477812 ) +colvars: ( 0.0150295 , 0.0400184 , -0.306499 ) +colvars: ( -0.0457034 , 0.10274 , 0.0951693 ) +colvars: ( -0.116514 , 0.307776 , 0.0716229 ) +colvars: ( -0.0222185 , 0.12069 , -0.217526 ) +colvars: ( 0.0840762 , -0.224206 , -0.0437986 ) +colvars: ( 0.00829457 , -0.107094 , 0.312538 ) +colvars: ( -0.0494376 , 0.0812664 , 0.214316 ) +colvars: ( 0.0806852 , -0.232666 , 0.0232353 ) +colvars: ( 0.137447 , -0.473898 , 0.328755 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0245481 , -0.0992958 , 0.0952841 ) +colvars: ( 0.0199747 , -0.081967 , 0.0824613 ) +colvars: ( 0.0265958 , -0.0971382 , 0.0592647 ) +colvars: ( 0.0124022 , -0.0558563 , 0.0721021 ) +colvars: ( 0.0125426 , -0.0536514 , 0.06097 ) +colvars: ( 0.00557809 , -0.035301 , 0.0752954 ) +colvars: ( -0.00252824 , -0.00852398 , 0.0691518 ) +colvars: ( -0.00861672 , 0.00902892 , 0.0753132 ) +colvars: ( -0.002079 , -0.00307426 , 0.0402922 ) +colvars: ( -0.00577036 , 0.0094684 , 0.0360237 ) +colvars: ( 0.00274067 , -0.0132274 , 0.0196568 ) +colvars: ( 0.004099 , -0.0107644 , -0.00858193 ) +colvars: ( 0.0090873 , -0.0221127 , -0.0264024 ) +colvars: ( 0.00874092 , -0.0237814 , -0.0148188 ) +colvars: ( 0.00662479 , -0.0135208 , -0.0301961 ) +colvars: ( 0.0150747 , -0.0465792 , -0.00211835 ) +colvars: ( 0.0197662 , -0.0605555 , -0.00496698 ) +colvars: ( 0.0277007 , -0.0881945 , 0.00706632 ) +colvars: ( 0.0143203 , -0.0467799 , 0.00864997 ) +colvars: ( 0.0142676 , -0.0438821 , -0.00286089 ) +colvars: ( 0.00933659 , -0.0370814 , 0.0333573 ) +colvars: ( 0.00316602 , -0.0212612 , 0.0478954 ) +colvars: ( -0.000818031 , -0.015517 , 0.0761074 ) +colvars: ( -0.00377758 , 0.00401611 , 0.0327739 ) +colvars: ( -0.00585068 , 0.0110886 , 0.0302569 ) +colvars: ( -0.00731131 , 0.0177444 , 0.0214388 ) +colvars: ( -0.0133216 , 0.0406119 , 0.00419 ) +colvars: ( -0.016326 , 0.0518039 , -0.00342658 ) +colvars: ( -0.00978873 , 0.0356768 , -0.0214949 ) +colvars: ( -0.0138344 , 0.0499078 , -0.0282135 ) +colvars: ( -0.00201044 , 0.0148697 , -0.0361778 ) +colvars: ( 0.0023345 , 0.00695447 , -0.0599938 ) +colvars: ( 0.0105822 , -0.0157184 , -0.0729935 ) +colvars: ( 0.00435756 , -0.000731103 , -0.0542368 ) +colvars: ( 0.0033271 , 0.00613185 , -0.0695852 ) +colvars: ( 0.00712721 , -0.0147825 , -0.0314909 ) +colvars: ( 0.00860672 , -0.0215446 , -0.0224739 ) +colvars: ( 0.0131213 , -0.0413042 , 0.00135932 ) +colvars: ( 0.000507929 , 0.00175736 , -0.0140817 ) +colvars: ( 0.000433168 , 0.00338741 , -0.0199631 ) +colvars: ( -0.00654536 , 0.0204972 , -0.000228719 ) +colvars: ( -0.0147607 , 0.0442601 , 0.00775503 ) +colvars: ( -0.0206262 , 0.057578 , 0.0288183 ) +colvars: ( -0.0190284 , 0.0631905 , -0.0158331 ) +colvars: ( -0.0227461 , 0.0751259 , -0.0171988 ) +colvars: ( -0.0169301 , 0.0724663 , -0.0824968 ) +colvars: ( -0.0200389 , 0.0866328 , -0.101267 ) +colvars: ( -0.00864057 , 0.0466423 , -0.0827765 ) +colvars: ( -0.0186803 , 0.0666376 , -0.0349301 ) +colvars: ( -0.0224303 , 0.0839057 , -0.0583273 ) +colvars: ( -0.024504 , 0.0927621 , -0.0683487 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 13. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 13. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atoms_new_colvar_forces = { ( -7.16848023051113e-02 , 3.03406467638823e-01 , -3.95351133644467e-01 ), ( 1.25012248682017e-02 , 3.14943727627139e-02 , -2.37347290328934e-01 ), ( -4.16044411846217e-02 , 9.19752550270074e-02 , 8.65873739393493e-02 ), ( -9.67474317693075e-02 , 2.47220693613752e-01 , 6.66558943569052e-02 ), ( -1.90524738522307e-02 , 9.94289567745099e-02 , -1.69630346467483e-01 ), ( 7.07545776624680e-02 , -1.83593734852738e-01 , -3.96086306355424e-02 ), ( 1.06290758170036e-02 , -1.00140025421509e-01 , 2.52544176616428e-01 ), ( -4.08308398476370e-02 , 5.97218751038244e-02 , 1.91841739524069e-01 ), ( 6.59244950506003e-02 , -1.88406306432059e-01 , 3.09903758344904e-02 ), ( 1.15016863749082e-01 , -3.89991960993715e-01 , 2.70427575233416e-01 ), ( 2.45481445884070e-02 , -9.92958410899459e-02 , 9.52840930616265e-02 ), ( 2.65957911792211e-02 , -9.71382388271648e-02 , 5.92646586708680e-02 ), ( 1.24022347475679e-02 , -5.58563360999198e-02 , 7.21021236988898e-02 ), ( 1.25425974982060e-02 , -5.36513706759084e-02 , 6.09700270201490e-02 ), ( 5.57808745511938e-03 , -3.53009942223408e-02 , 7.52954309343477e-02 ), ( -8.61672322330426e-03 , 9.02891576978664e-03 , 7.53131644443017e-02 ), ( -2.07900302590006e-03 , -3.07425778523133e-03 , 4.02922287168525e-02 ), ( -5.77036135321706e-03 , 9.46839655898241e-03 , 3.60237167170881e-02 ), ( 2.74066918054248e-03 , -1.32274107216639e-02 , 1.96568235606399e-02 ), ( 9.08730461783739e-03 , -2.21127046888010e-02 , -2.64023654543353e-02 ), ( 8.74092384788639e-03 , -2.37814157636701e-02 , -1.48188371221037e-02 ), ( 6.62478995543603e-03 , -1.35207891048718e-02 , -3.01961009405069e-02 ), ( 1.50746759309285e-02 , -4.65791626355137e-02 , -2.11834520072257e-03 ), ( 2.77006951945339e-02 , -8.81944669602844e-02 , 7.06632082557573e-03 ), ( 1.43202720040025e-02 , -4.67799343049266e-02 , 8.64996682972771e-03 ), ( 1.42676038711970e-02 , -4.38821442318173e-02 , -2.86089251963269e-03 ), ( 9.33659139362305e-03 , -3.70814288695834e-02 , 3.33572802635675e-02 ), ( -8.18030508691837e-04 , -1.55170421736455e-02 , 7.61073953459294e-02 ), ( -3.77758137799796e-03 , 4.01610561392808e-03 , 3.27738837575518e-02 ), ( -5.85068443666082e-03 , 1.10886119627274e-02 , 3.02569227489172e-02 ), ( -7.31131086834053e-03 , 1.77444252210332e-02 , 2.14388024426093e-02 ), ( -1.63259668292790e-02 , 5.18039334556752e-02 , -3.42657571196879e-03 ), ( -9.78872925192463e-03 , 3.56768071899492e-02 , -2.14948856921123e-02 ), ( -1.38343934007992e-02 , 4.99078327240418e-02 , -2.82134820935630e-02 ), ( -2.01044257050174e-03 , 1.48696753973150e-02 , -3.61777607784963e-02 ), ( 1.05821837722758e-02 , -1.57183863544096e-02 , -7.29934628812077e-02 ), ( 4.35756463209935e-03 , -7.31103056545410e-04 , -5.42367928014887e-02 ), ( 3.32709631940647e-03 , 6.13185076270506e-03 , -6.95851912988013e-02 ), ( 7.12720782650704e-03 , -1.47825181119657e-02 , -3.14908973687674e-02 ), ( 1.31213393285447e-02 , -4.13041633119196e-02 , 1.35932021834392e-03 ), ( 5.07929024846427e-04 , 1.75736416947850e-03 , -1.40817469322971e-02 ), ( 4.33168120790732e-04 , 3.38741176200938e-03 , -1.99631079092444e-02 ), ( -6.54536392556075e-03 , 2.04972001762583e-02 , -2.28718574320056e-04 ), ( -2.06261824379717e-02 , 5.75779688968008e-02 , 2.88183375108143e-02 ), ( -1.90284464589579e-02 , 6.31904647620932e-02 , -1.58331227728328e-02 ), ( -2.27460733223221e-02 , 7.51258762596511e-02 , -1.71988077928391e-02 ), ( -1.69301143808959e-02 , 7.24663474530253e-02 , -8.24968095319391e-02 ), ( -2.00388592213415e-02 , 8.66328293638355e-02 , -1.01267035271360e-01 ), ( -8.64057100669299e-03 , 4.66423398936291e-02 , -8.27764979146890e-02 ), ( -1.86802642125722e-02 , 6.66376349052638e-02 , -3.49300618005685e-02 ), ( -2.45040168644952e-02 , 9.27621234713304e-02 , -6.83487328322347e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 13, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 14 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 14, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 14, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 14, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 14, atoms_positions[size = 51] = { ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 ), ( 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 ), ( 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 ), ( 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 ), ( 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 ), ( 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 ), ( -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 ), ( -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 ), ( -3.74870489789954e+00 , 4.05644189334812e-02 , 5.45803072342270e+00 ), ( -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ), ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 ), ( 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 ), ( 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 ), ( 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 ), ( 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 ), ( 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 ), ( 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 ), ( 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 ), ( 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 ), ( 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 ), ( 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 ), ( 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 ), ( 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 ), ( 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 ), ( 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 ), ( 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 ), ( 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 ), ( 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 ), ( 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 ), ( -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 ), ( 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 ), ( 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 ), ( -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 ), ( -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 ), ( -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 ), ( -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 ), ( -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 ), ( -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 ), ( -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 ), ( -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 ), ( -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 ), ( -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 ), ( -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 ), ( -2.38241107657785e+00 , -3.23121881461260e-01 , 6.17120868209903e+00 ), ( -4.47207562252775e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 ), ( -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 ), ( -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 ), ( -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 ), ( -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 ), ( -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 ), ( -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ) } +colvars: Step 14, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_ids[size = 0] = +colvars: Step 14, atom_groups_refcount[size = 0] = +colvars: Step 14, atom_groups_masses[size = 0] = +colvars: Step 14, atom_groups_charges[size = 0] = +colvars: Step 14, atom_groups_coms[size = 0] = +colvars: Step 14, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 14, volmaps_ids[size = 0] = +colvars: Step 14, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 14 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.267298 , 17.1331 , 17.2664 , 18.0375 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.267298 , 17.1331 , 17.2664 , 18.0375 ) to colvar "one". +colvars: Adding total bias energy: 11.4636 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.267298 , 17.1331 , 17.2664 , 18.0375 ) +colvars: Applying force on main group : +colvars: ( -0.091704 , 0.385387 , -0.478767 ) +colvars: ( 0.0150746 , 0.0395461 , -0.3067 ) +colvars: ( -0.0457305 , 0.102903 , 0.0956478 ) +colvars: ( -0.116616 , 0.308438 , 0.0715138 ) +colvars: ( -0.0222311 , 0.120675 , -0.218125 ) +colvars: ( 0.0841532 , -0.224706 , -0.0436286 ) +colvars: ( 0.00828513 , -0.106883 , 0.313175 ) +colvars: ( -0.0495078 , 0.0818492 , 0.214242 ) +colvars: ( 0.0807368 , -0.232924 , 0.0230906 ) +colvars: ( 0.13754 , -0.474285 , 0.329552 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0245857 , -0.0993029 , 0.0953971 ) +colvars: ( 0.020001 , -0.0819523 , 0.0825574 ) +colvars: ( 0.026615 , -0.0971399 , 0.0593436 ) +colvars: ( 0.0124217 , -0.0558279 , 0.0721817 ) +colvars: ( 0.0125617 , -0.0536376 , 0.0610393 ) +colvars: ( 0.00559176 , -0.0352437 , 0.0753719 ) +colvars: ( -0.00252062 , -0.00844891 , 0.0692154 ) +colvars: ( -0.00861469 , 0.00913574 , 0.075377 ) +colvars: ( -0.00208037 , -0.00301168 , 0.0403281 ) +colvars: ( -0.00577204 , 0.00952933 , 0.0360526 ) +colvars: ( 0.00273197 , -0.013175 , 0.0196765 ) +colvars: ( 0.00408175 , -0.0107258 , -0.00858852 ) +colvars: ( 0.00906243 , -0.0220796 , -0.0264225 ) +colvars: ( 0.00872881 , -0.0237719 , -0.014827 ) +colvars: ( 0.00660837 , -0.0135173 , -0.0302208 ) +colvars: ( 0.0150722 , -0.0465881 , -0.00210846 ) +colvars: ( 0.0197698 , -0.0605919 , -0.00495532 ) +colvars: ( 0.0277133 , -0.0882493 , 0.00709659 ) +colvars: ( 0.0143299 , -0.046811 , 0.00867063 ) +colvars: ( 0.0142766 , -0.0439273 , -0.00285112 ) +colvars: ( 0.00935179 , -0.037091 , 0.0333977 ) +colvars: ( 0.00318628 , -0.0212609 , 0.047945 ) +colvars: ( -0.000791477 , -0.0154934 , 0.0761808 ) +colvars: ( -0.00376611 , 0.00402928 , 0.0328028 ) +colvars: ( -0.00583737 , 0.0110943 , 0.030282 ) +colvars: ( -0.00730986 , 0.0177765 , 0.0214531 ) +colvars: ( -0.0133298 , 0.0406555 , 0.00418232 ) +colvars: ( -0.0163437 , 0.0518698 , -0.00344484 ) +colvars: ( -0.00980173 , 0.0356965 , -0.0215243 ) +colvars: ( -0.0138492 , 0.0499274 , -0.0282526 ) +colvars: ( -0.0020254 , 0.014868 , -0.0362149 ) +colvars: ( 0.00231569 , 0.00692764 , -0.0600501 ) +colvars: ( 0.0105609 , -0.0157629 , -0.0730556 ) +colvars: ( 0.00434725 , -0.00077849 , -0.0542852 ) +colvars: ( 0.00331347 , 0.00607436 , -0.0696491 ) +colvars: ( 0.00712817 , -0.0148361 , -0.0315145 ) +colvars: ( 0.00861671 , -0.0216152 , -0.0224869 ) +colvars: ( 0.0131428 , -0.0413818 , 0.00137347 ) +colvars: ( 0.000519065 , 0.00170212 , -0.0140933 ) +colvars: ( 0.00044617 , 0.00331813 , -0.01998 ) +colvars: ( -0.00653542 , 0.0204715 , -0.000233128 ) +colvars: ( -0.0147505 , 0.0442522 , 0.00775152 ) +colvars: ( -0.0206146 , 0.0576006 , 0.02883 ) +colvars: ( -0.0190288 , 0.0631867 , -0.0158633 ) +colvars: ( -0.0227456 , 0.0751208 , -0.0172332 ) +colvars: ( -0.0169546 , 0.0724432 , -0.0825903 ) +colvars: ( -0.0200709 , 0.0866103 , -0.101381 ) +colvars: ( -0.00865928 , 0.0465932 , -0.082863 ) +colvars: ( -0.018691 , 0.0666396 , -0.034979 ) +colvars: ( -0.0224517 , 0.0839118 , -0.0584022 ) +colvars: ( -0.0245354 , 0.0927874 , -0.0684358 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 14. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 14. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atoms_new_colvar_forces = { ( -7.17030729248560e-02 , 3.03434412847935e-01 , -3.96209881834245e-01 ), ( 1.25539674912846e-02 , 3.10971748466751e-02 , -2.37484688240301e-01 ), ( -4.16487740410050e-02 , 9.21772717626605e-02 , 8.70592462212864e-02 ), ( -9.68465681352754e-02 , 2.47846407485462e-01 , 6.65584771335487e-02 ), ( -1.90448258776952e-02 , 9.94144511414792e-02 , -1.70179970081159e-01 ), ( 7.08234560023367e-02 , -1.84050882202746e-01 , -3.94462726906446e-02 ), ( 1.06008164335397e-02 , -9.99558236220789e-02 , 2.53124929639883e-01 ), ( -4.08911448281357e-02 , 6.02339263019856e-02 , 1.91754774692143e-01 ), ( 6.59863081703112e-02 , -1.88672016902237e-01 , 3.08421610939228e-02 ), ( 1.15088456013817e-01 , -3.90372791027753e-01 , 2.71149704495937e-01 ), ( 2.45856886529822e-02 , -9.93029314643077e-02 , 9.53970980947032e-02 ), ( 2.66150021200131e-02 , -9.71398604141635e-02 , 5.93436150137355e-02 ), ( 1.24217001709229e-02 , -5.58279443000605e-02 , 7.21817026324729e-02 ), ( 1.25617262932672e-02 , -5.36376273244229e-02 , 6.10392612117306e-02 ), ( 5.59176317587433e-03 , -3.52437222501083e-02 , 7.53718830903424e-02 ), ( -8.61469376918818e-03 , 9.13573878138333e-03 , 7.53769537257818e-02 ), ( -2.08036764354213e-03 , -3.01168138675437e-03 , 4.03281283495174e-02 ), ( -5.77204210497506e-03 , 9.52933492292574e-03 , 3.60526155123662e-02 ), ( 2.73196767940917e-03 , -1.31749730390552e-02 , 1.96764929056506e-02 ), ( 9.06243454595903e-03 , -2.20795588291178e-02 , -2.64224504586307e-02 ), ( 8.72881036570474e-03 , -2.37719186216426e-02 , -1.48269814368021e-02 ), ( 6.60837365683509e-03 , -1.35173489297917e-02 , -3.02208077794285e-02 ), ( 1.50722263329384e-02 , -4.65880566497031e-02 , -2.10846056423043e-03 ), ( 2.77132714691932e-02 , -8.82492552943065e-02 , 7.09658509678953e-03 ), ( 1.43298786671376e-02 , -4.68110431832540e-02 , 8.67062510312126e-03 ), ( 1.42765588857720e-02 , -4.39272648779111e-02 , -2.85112288428024e-03 ), ( 9.35178577309466e-03 , -3.70910423075215e-02 , 3.33976601877557e-02 ), ( -7.91476888628795e-04 , -1.54934024438347e-02 , 7.61808486456305e-02 ), ( -3.76611455213548e-03 , 4.02928451363875e-03 , 3.28027615403106e-02 ), ( -5.83737261763688e-03 , 1.10943335602030e-02 , 3.02819747857202e-02 ), ( -7.30985707112402e-03 , 1.77764718021673e-02 , 2.14531452840506e-02 ), ( -1.63437274011271e-02 , 5.18698487860540e-02 , -3.44483737933500e-03 ), ( -9.80172955653648e-03 , 3.56965236015377e-02 , -2.15242878391028e-02 ), ( -1.38491829664301e-02 , 4.99274418679334e-02 , -2.82526227196997e-02 ), ( -2.02539614964378e-03 , 1.48679519023049e-02 , -3.62148591869112e-02 ), ( 1.05608512952179e-02 , -1.57629483249763e-02 , -7.30555800588351e-02 ), ( 4.34725410231148e-03 , -7.78490150777868e-04 , -5.42851718364163e-02 ), ( 3.31346888814621e-03 , 6.07435944700226e-03 , -6.96491258062289e-02 ), ( 7.12817424489928e-03 , -1.48360902169562e-02 , -3.15145377778368e-02 ), ( 1.31428212464034e-02 , -4.13817917713363e-02 , 1.37346881309776e-03 ), ( 5.19064722109662e-04 , 1.70212341462858e-03 , -1.40933202424561e-02 ), ( 4.46170100063446e-04 , 3.31812885537241e-03 , -1.99800460475654e-02 ), ( -6.53542118172565e-03 , 2.04714903649538e-02 , -2.33128257942877e-04 ), ( -2.06146479410913e-02 , 5.76006473823990e-02 , 2.88299600818956e-02 ), ( -1.90288349421177e-02 , 6.31867488549733e-02 , -1.58633007683796e-02 ), ( -2.27455548385216e-02 , 7.51207571365791e-02 , -1.72331583835215e-02 ), ( -1.69545518180851e-02 , 7.24431631875390e-02 , -8.25902995953081e-02 ), ( -2.00709479746416e-02 , 8.66102831783137e-02 , -1.01381424086626e-01 ), ( -8.65927776259551e-03 , 4.65932132315996e-02 , -8.28629606271324e-02 ), ( -1.86910394658317e-02 , 6.66395860461118e-02 , -3.49789572629907e-02 ), ( -2.45353740469984e-02 , 9.27873903110001e-02 , -6.84358195053828e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 14, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 15 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 15, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 15, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 15, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 15, atoms_positions[size = 51] = { ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 ), ( 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 ), ( 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 ), ( 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 ), ( 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 ), ( 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 ), ( -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 ), ( -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 ), ( -3.74037993756623e+00 , 3.73480401968941e-02 , 5.45181495688655e+00 ), ( -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ), ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 ), ( 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 ), ( 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 ), ( 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 ), ( 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 ), ( 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 ), ( 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 ), ( 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 ), ( 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 ), ( 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 ), ( 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 ), ( 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 ), ( 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 ), ( 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 ), ( 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 ), ( 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 ), ( 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 ), ( 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 ), ( 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 ), ( -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 ), ( 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 ), ( 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 ), ( -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 ), ( -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 ), ( -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 ), ( -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 ), ( -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 ), ( -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 ), ( -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 ), ( -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 ), ( -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 ), ( -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 ), ( -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 ), ( -2.38290213212965e+00 , -3.18712087726499e-01 , 6.17288759969147e+00 ), ( -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 ), ( -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 ), ( -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 ), ( -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 ), ( -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 ), ( -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 ), ( -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ) } +colvars: Step 15, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_ids[size = 0] = +colvars: Step 15, atom_groups_refcount[size = 0] = +colvars: Step 15, atom_groups_masses[size = 0] = +colvars: Step 15, atom_groups_charges[size = 0] = +colvars: Step 15, atom_groups_coms[size = 0] = +colvars: Step 15, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 15, volmaps_ids[size = 0] = +colvars: Step 15, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 15 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155576e-02 , 1.18858573400358e-02 , -1.18348863683820e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155576e-02 , 1.18858573400358e-02 , -1.18348863683820e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.261534 , 17.1486 , 17.2715 , 18.0316 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.261534 , 17.1486 , 17.2715 , 18.0316 ) to colvar "one". +colvars: Adding total bias energy: 11.4698 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.261534 , 17.1486 , 17.2715 , 18.0316 ) +colvars: Applying force on main group : +colvars: ( -0.0917185 , 0.385418 , -0.479698 ) +colvars: ( 0.0151213 , 0.0391283 , -0.306909 ) +colvars: ( -0.0457664 , 0.103097 , 0.0960677 ) +colvars: ( -0.116706 , 0.309075 , 0.0713877 ) +colvars: ( -0.0222271 , 0.12065 , -0.218688 ) +colvars: ( 0.0842181 , -0.225181 , -0.0434558 ) +colvars: ( 0.00825998 , -0.106681 , 0.313778 ) +colvars: ( -0.04957 , 0.0823715 , 0.214185 ) +colvars: ( 0.080786 , -0.233207 , 0.0229914 ) +colvars: ( 0.137602 , -0.474671 , 0.33034 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246185 , -0.0993166 , 0.0955104 ) +colvars: ( 0.0200236 , -0.0819437 , 0.0826516 ) +colvars: ( 0.0266307 , -0.097149 , 0.059419 ) +colvars: ( 0.0124386 , -0.0558039 , 0.0722593 ) +colvars: ( 0.0125783 , -0.0536278 , 0.0611074 ) +colvars: ( 0.0056037 , -0.0351898 , 0.0754451 ) +colvars: ( -0.00251373 , -0.00837552 , 0.0692755 ) +colvars: ( -0.00861264 , 0.00924155 , 0.0754358 ) +colvars: ( -0.00208174 , -0.00295058 , 0.04036 ) +colvars: ( -0.00577342 , 0.00958992 , 0.0360785 ) +colvars: ( 0.00272352 , -0.0131251 , 0.0196904 ) +colvars: ( 0.00406539 , -0.0106899 , -0.00860157 ) +colvars: ( 0.00903869 , -0.0220503 , -0.0264511 ) +colvars: ( 0.00871695 , -0.0237654 , -0.0148399 ) +colvars: ( 0.00659273 , -0.0135161 , -0.03025 ) +colvars: ( 0.0150689 , -0.046601 , -0.00210215 ) +colvars: ( 0.0197719 , -0.0606329 , -0.00494554 ) +colvars: ( 0.027723 , -0.0883101 , 0.00712566 ) +colvars: ( 0.0143378 , -0.0468452 , 0.00869135 ) +colvars: ( 0.0142839 , -0.0439749 , -0.0028404 ) +colvars: ( 0.00936512 , -0.0371029 , 0.0334388 ) +colvars: ( 0.0032047 , -0.0212613 , 0.0479969 ) +colvars: ( -0.000767051 , -0.0154701 , 0.0762571 ) +colvars: ( -0.00375532 , 0.00404322 , 0.0328335 ) +colvars: ( -0.00582469 , 0.0111017 , 0.0303102 ) +colvars: ( -0.00730811 , 0.0178096 , 0.0214673 ) +colvars: ( -0.0133365 , 0.0407016 , 0.00417367 ) +colvars: ( -0.0163591 , 0.0519382 , -0.00346638 ) +colvars: ( -0.00981306 , 0.0357183 , -0.0215547 ) +colvars: ( -0.0138619 , 0.0499503 , -0.028292 ) +colvars: ( -0.00203902 , 0.0148667 , -0.0362537 ) +colvars: ( 0.00229829 , 0.00690086 , -0.0601081 ) +colvars: ( 0.0105406 , -0.0158093 , -0.0731207 ) +colvars: ( 0.00433763 , -0.00082566 , -0.054333 ) +colvars: ( 0.00330091 , 0.00601769 , -0.0697121 ) +colvars: ( 0.00712876 , -0.0148899 , -0.0315361 ) +colvars: ( 0.00862556 , -0.021686 , -0.0224956 ) +colvars: ( 0.013162 , -0.0414605 , 0.00139311 ) +colvars: ( 0.000529527 , 0.00164865 , -0.0140994 ) +colvars: ( 0.000458419 , 0.00325111 , -0.0199902 ) +colvars: ( -0.00652566 , 0.0204486 , -0.000232521 ) +colvars: ( -0.01474 , 0.0442489 , 0.00775389 ) +colvars: ( -0.0206026 , 0.0576286 , 0.028847 ) +colvars: ( -0.0190277 , 0.0631887 , -0.0158885 ) +colvars: ( -0.0227433 , 0.0751224 , -0.0172613 ) +colvars: ( -0.0169757 , 0.0724254 , -0.0826818 ) +colvars: ( -0.0200989 , 0.086594 , -0.101494 ) +colvars: ( -0.00867565 , 0.046548 , -0.0829468 ) +colvars: ( -0.0186996 , 0.0666468 , -0.035025 ) +colvars: ( -0.0224698 , 0.083924 , -0.0584754 ) +colvars: ( -0.0245625 , 0.0928186 , -0.0685235 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 15. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 15. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atoms_new_colvar_forces = { ( -7.16949290049834e-02 , 3.03474386830269e-01 , -3.97046304863662e-01 ), ( 1.26075871768278e-02 , 3.07527449828283e-02 , -2.37633102868567e-01 ), ( -4.17009663573045e-02 , 9.24074981387009e-02 , 8.74661003276692e-02 ), ( -9.69339385370995e-02 , 2.48441896040349e-01 , 6.64422051068895e-02 ), ( -1.90223480977663e-02 , 9.93884227003578e-02 , -1.70691018987116e-01 ), ( 7.08816450632660e-02 , -1.84478966273026e-01 , -3.92821711082243e-02 ), ( 1.05582685074796e-02 , -9.97800400249164e-02 , 2.53669949381410e-01 ), ( -4.09444626684394e-02 , 6.06855197421953e-02 , 1.91689409105388e-01 ), ( 6.60460181362832e-02 , -1.88958089484125e-01 , 3.07452614062881e-02 ), ( 1.15132613755772e-01 , -3.90747225325214e-01 , 2.71865086326974e-01 ), ( 2.46184640764127e-02 , -9.93165721706982e-02 , 9.55103597383862e-02 ), ( 2.66307072466724e-02 , -9.71489574950985e-02 , 5.94190206706606e-02 ), ( 1.24385783576097e-02 , -5.58039125261095e-02 , 7.22592691180316e-02 ), ( 1.25783473850690e-02 , -5.36278041390523e-02 , 6.11074116288131e-02 ), ( 5.60369514890443e-03 , -3.51898383705384e-02 , 7.54451200188047e-02 ), ( -8.61263899903100e-03 , 9.24154583271543e-03 , 7.54358198108120e-02 ), ( -2.08174033617832e-03 , -2.95057966487033e-03 , 4.03599892786103e-02 ), ( -5.77342095425320e-03 , 9.58991721603904e-03 , 3.60784709629169e-02 ), ( 2.72351577197190e-03 , -1.31251301023363e-02 , 1.96904464620740e-02 ), ( 9.03869059047242e-03 , -2.20503408746778e-02 , -2.64510800630670e-02 ), ( 8.71694929791339e-03 , -2.37653627920194e-02 , -1.48399149504546e-02 ), ( 6.59273362777683e-03 , -1.35160743118100e-02 , -3.02500320355194e-02 ), ( 1.50688725450407e-02 , -4.66010358784319e-02 , -2.10215211531109e-03 ), ( 2.77230111502822e-02 , -8.83101398980123e-02 , 7.12565967045664e-03 ), ( 1.43377869775359e-02 , -4.68451858579056e-02 , 8.69135479693351e-03 ), ( 1.42839316102877e-02 , -4.39749472823456e-02 , -2.84039866961499e-03 ), ( 9.36512460506414e-03 , -3.71029112834419e-02 , 3.34387634313426e-02 ), ( -7.67051236185161e-04 , -1.54700848230630e-02 , 7.62570819365013e-02 ), ( -3.75532166399210e-03 , 4.04321632367066e-03 , 3.28334978472288e-02 ), ( -5.82469119645842e-03 , 1.11016688047768e-02 , 3.03102195604810e-02 ), ( -7.30810612237384e-03 , 1.78095870567290e-02 , 2.14673383326389e-02 ), ( -1.63591489797325e-02 , 5.19381615875535e-02 , -3.46637651232031e-03 ), ( -9.81305659264498e-03 , 3.57183112578093e-02 , -2.15546526463102e-02 ), ( -1.38618534791799e-02 , 4.99502805211779e-02 , -2.82919814203272e-02 ), ( -2.03901561513156e-03 , 1.48667419014925e-02 , -3.62537044187399e-02 ), ( 1.05405919753518e-02 , -1.58092773650867e-02 , -7.31206596138427e-02 ), ( 4.33763159321967e-03 , -8.25659687975372e-04 , -5.43329959677468e-02 ), ( 3.30091166802390e-03 , 6.01768930062787e-03 , -6.97120700059172e-02 ), ( 7.12876070240522e-03 , -1.48899474877114e-02 , -3.15361024336851e-02 ), ( 1.31619639603794e-02 , -4.14604738001422e-02 , 1.39310822023035e-03 ), ( 5.29527032387887e-04 , 1.64865096373702e-03 , -1.40994166020852e-02 ), ( 4.58418665716039e-04 , 3.25111466051151e-03 , -1.99902166450620e-02 ), ( -6.52565516598719e-03 , 2.04486038718644e-02 , -2.32521360264111e-04 ), ( -2.06025650233246e-02 , 5.76286370246274e-02 , 2.88470449160681e-02 ), ( -1.90277436193707e-02 , 6.31886535767905e-02 , -1.58884792059689e-02 ), ( -2.27433417372783e-02 , 7.51223872874197e-02 , -1.72613295599796e-02 ), ( -1.69756928755969e-02 , 7.24254347727082e-02 , -8.26817853858622e-02 ), ( -2.00989076652020e-02 , 8.65940068037253e-02 , -1.01494282967316e-01 ), ( -8.67565012061669e-03 , 4.65480494214555e-02 , -8.29467996197521e-02 ), ( -1.86995694597294e-02 , 6.66467836543689e-02 , -3.50249837064717e-02 ), ( -2.45625311202662e-02 , 9.28186466441078e-02 , -6.85234543224205e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 15, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 16 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 16, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 16, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 16, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 16, atoms_positions[size = 51] = { ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 ), ( 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 ), ( 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 ), ( 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 ), ( 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 ), ( 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 ), ( -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 ), ( -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 ), ( -3.73185754983895e+00 , 3.59121509335080e-02 , 5.44610695064150e+00 ), ( -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ), ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 ), ( 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 ), ( 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 ), ( 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 ), ( 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 ), ( 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 ), ( 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 ), ( 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 ), ( 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 ), ( 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 ), ( 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 ), ( 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 ), ( 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 ), ( 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 ), ( 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 ), ( 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 ), ( 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 ), ( 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 ), ( 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 ), ( -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 ), ( 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 ), ( 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 ), ( -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 ), ( -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 ), ( -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 ), ( -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 ), ( -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 ), ( -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 ), ( -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 ), ( -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 ), ( -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 ), ( -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 ), ( -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 ), ( -2.38388494433047e+00 , -3.15826223986612e-01 , 6.17394163944166e+00 ), ( -4.46828024629854e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 ), ( -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 ), ( -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 ), ( -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 ), ( -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 ), ( -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 ), ( -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ) } +colvars: Step 16, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_ids[size = 0] = +colvars: Step 16, atom_groups_refcount[size = 0] = +colvars: Step 16, atom_groups_masses[size = 0] = +colvars: Step 16, atom_groups_charges[size = 0] = +colvars: Step 16, atom_groups_coms[size = 0] = +colvars: Step 16, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 16, volmaps_ids[size = 0] = +colvars: Step 16, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 16 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147335e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147335e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.255634 , 17.1633 , 17.2751 , 18.028 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.255634 , 17.1633 , 17.2751 , 18.028 ) to colvar "one". +colvars: Adding total bias energy: 11.476 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.255634 , 17.1633 , 17.2751 , 18.028 ) +colvars: Applying force on main group : +colvars: ( -0.0917017 , 0.385461 , -0.480587 ) +colvars: ( 0.0151674 , 0.0387729 , -0.307122 ) +colvars: ( -0.0458095 , 0.10332 , 0.0964144 ) +colvars: ( -0.116777 , 0.309671 , 0.0712431 ) +colvars: ( -0.0222062 , 0.120611 , -0.219201 ) +colvars: ( 0.0842676 , -0.225617 , -0.0432817 ) +colvars: ( 0.00822 , -0.106488 , 0.314333 ) +colvars: ( -0.0496209 , 0.0828217 , 0.214148 ) +colvars: ( 0.0808304 , -0.233509 , 0.0229457 ) +colvars: ( 0.13763 , -0.475045 , 0.331108 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246453 , -0.0993365 , 0.0956225 ) +colvars: ( 0.0200417 , -0.0819413 , 0.0827426 ) +colvars: ( 0.0266421 , -0.0971657 , 0.0594898 ) +colvars: ( 0.0124523 , -0.0557846 , 0.0723336 ) +colvars: ( 0.0125919 , -0.0536221 , 0.0611735 ) +colvars: ( 0.0056135 , -0.0351401 , 0.0755137 ) +colvars: ( -0.00250772 , -0.0083048 , 0.0693309 ) +colvars: ( -0.0086105 , 0.00934488 , 0.0754881 ) +colvars: ( -0.00208306 , -0.00289191 , 0.0403868 ) +colvars: ( -0.00577439 , 0.00964928 , 0.0361004 ) +colvars: ( 0.00271549 , -0.0130789 , 0.0196979 ) +colvars: ( 0.00405025 , -0.0106575 , -0.00862144 ) +colvars: ( 0.00901655 , -0.0220262 , -0.0264885 ) +colvars: ( 0.00870552 , -0.0237623 , -0.0148577 ) +colvars: ( 0.00657817 , -0.0135174 , -0.0302836 ) +colvars: ( 0.0150645 , -0.0466183 , -0.00209959 ) +colvars: ( 0.019772 , -0.0606781 , -0.00493758 ) +colvars: ( 0.0277293 , -0.0883766 , 0.00715349 ) +colvars: ( 0.0143436 , -0.046882 , 0.00871211 ) +colvars: ( 0.0142893 , -0.0440246 , -0.00282851 ) +colvars: ( 0.00937614 , -0.0371168 , 0.0334802 ) +colvars: ( 0.00322079 , -0.0212621 , 0.0480507 ) +colvars: ( -0.000745361 , -0.015447 , 0.0763351 ) +colvars: ( -0.00374542 , 0.00405797 , 0.0328657 ) +colvars: ( -0.00581288 , 0.0111109 , 0.0303414 ) +colvars: ( -0.007306 , 0.0178434 , 0.021481 ) +colvars: ( -0.0133414 , 0.0407494 , 0.00416382 ) +colvars: ( -0.0163716 , 0.0520079 , -0.0034915 ) +colvars: ( -0.00982229 , 0.0357418 , -0.0215858 ) +colvars: ( -0.0138719 , 0.0499761 , -0.0283312 ) +colvars: ( -0.00205093 , 0.0148659 , -0.0362939 ) +colvars: ( 0.00228272 , 0.00687419 , -0.060167 ) +colvars: ( 0.0105218 , -0.0158573 , -0.0731877 ) +colvars: ( 0.00432888 , -0.000872138 , -0.0543793 ) +colvars: ( 0.0032897 , 0.00596244 , -0.0697728 ) +colvars: ( 0.00712886 , -0.0149434 , -0.0315549 ) +colvars: ( 0.00863295 , -0.0217557 , -0.0224992 ) +colvars: ( 0.0131781 , -0.0415389 , 0.00141874 ) +colvars: ( 0.000539048 , 0.00159799 , -0.0140994 ) +colvars: ( 0.000469602 , 0.00318767 , -0.0199927 ) +colvars: ( -0.00651622 , 0.0204292 , -0.00022652 ) +colvars: ( -0.0147291 , 0.0442508 , 0.00776244 ) +colvars: ( -0.02059 , 0.0576622 , 0.0288695 ) +colvars: ( -0.0190249 , 0.0631966 , -0.0159081 ) +colvars: ( -0.0227392 , 0.0751313 , -0.0172827 ) +colvars: ( -0.0169928 , 0.0724135 , -0.0827699 ) +colvars: ( -0.0201218 , 0.0865842 , -0.101604 ) +colvars: ( -0.00868915 , 0.0465075 , -0.0830265 ) +colvars: ( -0.0187054 , 0.0666594 , -0.0350675 ) +colvars: ( -0.0224837 , 0.0839423 , -0.0585457 ) +colvars: ( -0.0245845 , 0.0928555 , -0.0686107 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 16. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 16. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atoms_new_colvar_forces = { ( -7.16599920626334e-02 , 3.03520189493113e-01 , -3.97844554110196e-01 ), ( 1.26596866495085e-02 , 3.04680490772270e-02 , -2.37791019205751e-01 ), ( -4.17592178733622e-02 , 9.26629575009943e-02 , 8.77929809589357e-02 ), ( -9.70053794347984e-02 , 2.48992623070873e-01 , 6.63054983454753e-02 ), ( -1.89853945294203e-02 , 9.93485496391636e-02 , -1.71150647534301e-01 ), ( 7.09261775017845e-02 , -1.84867108646044e-01 , -3.91178688867081e-02 ), ( 1.05027258080738e-02 , -9.96136798939432e-02 , 2.54166018544938e-01 ), ( -4.09879563722719e-02 , 6.10659904102845e-02 , 1.91648579072606e-01 ), ( 6.61012658667263e-02 , -1.89258161381491e-01 , 3.07081105841715e-02 ), ( 1.15146596997167e-01 , -3.91102227968993e-01 , 2.72562397837632e-01 ), ( 2.46453030855937e-02 , -9.93365220421225e-02 , 9.56225083588144e-02 ), ( 2.66421414788933e-02 , -9.71657300342827e-02 , 5.94897841061073e-02 ), ( 1.24522694746926e-02 , -5.57846102591163e-02 , 7.23335698331391e-02 ), ( 1.25918663087693e-02 , -5.36220502851586e-02 , 6.11734810795629e-02 ), ( 5.61350142569207e-03 , -3.51401203977188e-02 , 7.55136988866750e-02 ), ( -8.61049745184722e-03 , 9.34488100012722e-03 , 7.54880974356862e-02 ), ( -2.08306110857869e-03 , -2.89191085757775e-03 , 4.03868197279044e-02 ), ( -5.77438653909533e-03 , 9.64928220907090e-03 , 3.61004204614304e-02 ), ( 2.71548615893903e-03 , -1.30789072162389e-02 , 1.96979142124408e-02 ), ( 9.01654505317238e-03 , -2.20261826877445e-02 , -2.64884795675305e-02 ), ( 8.70551878740282e-03 , -2.37622854338400e-02 , -1.48577425980512e-02 ), ( 6.57817314530783e-03 , -1.35174371713845e-02 , -3.02836212361381e-02 ), ( 1.50644910475842e-02 , -4.66183167563982e-02 , -2.09959283310227e-03 ), ( 2.77292875578808e-02 , -8.83766259112437e-02 , 7.15349274759623e-03 ), ( 1.43436005142690e-02 , -4.68820099433303e-02 , 8.71210519613895e-03 ), ( 1.42893406669391e-02 , -4.40246300593357e-02 , -2.82851322219024e-03 ), ( 9.37614206359767e-03 , -3.71168203279471e-02 , 3.34801668491546e-02 ), ( -7.45360757258770e-04 , -1.54469884200433e-02 , 7.63350951705038e-02 ), ( -3.74542386156819e-03 , 4.05796942472545e-03 , 3.28656966491896e-02 ), ( -5.81287991845205e-03 , 1.11108772852015e-02 , 3.03413992192289e-02 ), ( -7.30600279987892e-03 , 1.78434469740859e-02 , 2.14809824211243e-02 ), ( -1.63716194505806e-02 , 5.20078778820190e-02 , -3.49150141876508e-03 ), ( -9.82228967181317e-03 , 3.57418436312302e-02 , -2.15857699885616e-02 ), ( -1.38718942693465e-02 , 4.99760774537983e-02 , -2.83312021543967e-02 ), ( -2.05092887520623e-03 , 1.48658588304507e-02 , -3.62938698788685e-02 ), ( 1.05217736834276e-02 , -1.58572613080413e-02 , -7.31877103025308e-02 ), ( 4.32888255023710e-03 , -8.72137630605562e-04 , -5.43793223663522e-02 ), ( 3.28969909537636e-03 , 5.96243711290139e-03 , -6.97728044235884e-02 ), ( 7.12885665987957e-03 , -1.49433842714813e-02 , -3.15548733162422e-02 ), ( 1.31781063569408e-02 , -4.15389021041050e-02 , 1.41874342019564e-03 ), ( 5.39047621159523e-04 , 1.59798991413936e-03 , -1.40993565514254e-02 ), ( 4.69602162734557e-04 , 3.18766520365176e-03 , -1.99927400393244e-02 ), ( -6.51622058373523e-03 , 2.04292485461563e-02 , -2.26519647382126e-04 ), ( -2.05899546307361e-02 , 5.76622094085089e-02 , 2.88694586745091e-02 ), ( -1.90249363443350e-02 , 6.31966262801517e-02 , -1.59081022548893e-02 ), ( -2.27391746568829e-02 , 7.51313288340186e-02 , -1.72826679888529e-02 ), ( -1.69927675860640e-02 , 7.24134595931748e-02 , -8.27698731950902e-02 ), ( -2.01217530075865e-02 , 8.65842216823478e-02 , -1.01603973274608e-01 ), ( -8.68915196928373e-03 , 4.65074767613662e-02 , -8.30265180199556e-02 ), ( -1.87053800613670e-02 , 6.66594018957552e-02 , -3.50674513075242e-02 ), ( -2.45844639056470e-02 , 9.28554718936520e-02 , -6.86107244708341e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 16, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 17 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 17, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 17, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 17, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 17, atoms_positions[size = 51] = { ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 ), ( 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 ), ( 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 ), ( 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 ), ( 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 ), ( 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 ), ( -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 ), ( -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 ), ( -3.72338871222330e+00 , 3.62579539864891e-02 , 5.44133506196972e+00 ), ( -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ), ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 ), ( 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 ), ( 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 ), ( 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 ), ( 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 ), ( 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 ), ( 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 ), ( 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 ), ( 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 ), ( 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 ), ( 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 ), ( 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 ), ( 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 ), ( 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 ), ( 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 ), ( 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 ), ( 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 ), ( 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 ), ( 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 ), ( -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 ), ( 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 ), ( 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 ), ( -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 ), ( -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 ), ( -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 ), ( -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 ), ( -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 ), ( -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 ), ( -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 ), ( -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 ), ( -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 ), ( -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 ), ( -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 ), ( -2.38520263482904e+00 , -3.14375701461254e-01 , 6.17435317935263e+00 ), ( -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 ), ( -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 ), ( -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 ), ( -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 ), ( -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 ), ( -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 ), ( -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ) } +colvars: Step 17, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_ids[size = 0] = +colvars: Step 17, atom_groups_refcount[size = 0] = +colvars: Step 17, atom_groups_masses[size = 0] = +colvars: Step 17, atom_groups_charges[size = 0] = +colvars: Step 17, atom_groups_coms[size = 0] = +colvars: Step 17, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 17, volmaps_ids[size = 0] = +colvars: Step 17, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 17 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652891e-02 , -1.16317231514313e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652891e-02 , -1.16317231514313e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.24972 , 17.1768 , 17.2771 , 18.0268 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.24972 , 17.1768 , 17.2771 , 18.0268 ) to colvar "one". +colvars: Adding total bias energy: 11.4822 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.24972 , 17.1768 , 17.2771 , 18.0268 ) +colvars: Applying force on main group : +colvars: ( -0.0916539 , 0.385511 , -0.481418 ) +colvars: ( 0.0152108 , 0.0384861 , -0.307337 ) +colvars: ( -0.0458583 , 0.103569 , 0.0966761 ) +colvars: ( -0.116828 , 0.310212 , 0.0710794 ) +colvars: ( -0.0221691 , 0.120557 , -0.219653 ) +colvars: ( 0.0842992 , -0.226004 , -0.043108 ) +colvars: ( 0.00816662 , -0.106306 , 0.314827 ) +colvars: ( -0.0496581 , 0.0831902 , 0.214132 ) +colvars: ( 0.0808682 , -0.233823 , 0.0229594 ) +colvars: ( 0.137622 , -0.475392 , 0.331842 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246652 , -0.0993622 , 0.095732 ) +colvars: ( 0.0200547 , -0.081945 , 0.0828289 ) +colvars: ( 0.0266487 , -0.09719 , 0.0595549 ) +colvars: ( 0.0124623 , -0.0557702 , 0.0724034 ) +colvars: ( 0.0126018 , -0.0536203 , 0.0612364 ) +colvars: ( 0.00562084 , -0.0350953 , 0.0755763 ) +colvars: ( -0.00250275 , -0.00823786 , 0.0693803 ) +colvars: ( -0.00860827 , 0.00944407 , 0.0755324 ) +colvars: ( -0.00208429 , -0.00283671 , 0.0404079 ) +colvars: ( -0.00577487 , 0.00970643 , 0.0361178 ) +colvars: ( 0.00270805 , -0.0130373 , 0.0196985 ) +colvars: ( 0.00403671 , -0.0106296 , -0.00864803 ) +colvars: ( 0.00899649 , -0.0220081 , -0.0265342 ) +colvars: ( 0.00869473 , -0.0237631 , -0.0148802 ) +colvars: ( 0.00656501 , -0.0135218 , -0.0303211 ) +colvars: ( 0.015059 , -0.0466399 , -0.00210071 ) +colvars: ( 0.01977 , -0.060727 , -0.00493129 ) +colvars: ( 0.0277317 , -0.0884477 , 0.00718007 ) +colvars: ( 0.014347 , -0.0469209 , 0.00873279 ) +colvars: ( 0.0142925 , -0.0440755 , -0.00281534 ) +colvars: ( 0.00938445 , -0.0371324 , 0.0335213 ) +colvars: ( 0.00323406 , -0.0212632 , 0.0481056 ) +colvars: ( -0.000726988 , -0.0154241 , 0.0764136 ) +colvars: ( -0.00373665 , 0.00407353 , 0.0328988 ) +colvars: ( -0.0058022 , 0.0111221 , 0.030375 ) +colvars: ( -0.00730354 , 0.0178776 , 0.0214937 ) +colvars: ( -0.0133442 , 0.0407982 , 0.00415264 ) +colvars: ( -0.0163807 , 0.0520777 , -0.00352026 ) +colvars: ( -0.00982908 , 0.0357666 , -0.0216173 ) +colvars: ( -0.0138789 , 0.0500043 , -0.0283699 ) +colvars: ( -0.00206079 , 0.0148651 , -0.0363347 ) +colvars: ( 0.00226939 , 0.00684774 , -0.0602258 ) +colvars: ( 0.0105048 , -0.0159066 , -0.0732554 ) +colvars: ( 0.00432121 , -0.000917336 , -0.0544232 ) +colvars: ( 0.00328012 , 0.00590931 , -0.0698301 ) +colvars: ( 0.0071284 , -0.0149955 , -0.0315702 ) +colvars: ( 0.00863861 , -0.0218232 , -0.0224973 ) +colvars: ( 0.0131907 , -0.0416155 , 0.00145046 ) +colvars: ( 0.000547381 , 0.00155123 , -0.0140928 ) +colvars: ( 0.000479435 , 0.00312913 , -0.0199872 ) +colvars: ( -0.0065073 , 0.020414 , -0.0002151 ) +colvars: ( -0.0147181 , 0.0442583 , 0.00777702 ) +colvars: ( -0.0205769 , 0.0577013 , 0.0288967 ) +colvars: ( -0.0190203 , 0.0632108 , -0.0159219 ) +colvars: ( -0.0227329 , 0.0751478 , -0.0172969 ) +colvars: ( -0.0170051 , 0.0724073 , -0.0828532 ) +colvars: ( -0.0201387 , 0.0865809 , -0.101709 ) +colvars: ( -0.00869932 , 0.046472 , -0.0831007 ) +colvars: ( -0.0187081 , 0.0666773 , -0.0351058 ) +colvars: ( -0.0224929 , 0.0839663 , -0.0586123 ) +colvars: ( -0.0246003 , 0.0928971 , -0.0686965 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 17. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 17. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atoms_new_colvar_forces = { ( -7.15991844821387e-02 , 3.03566046493554e-01 , -3.98589394335568e-01 ), ( 1.27080880761104e-02 , 3.02482168390730e-02 , -2.37956547495991e-01 ), ( -4.18215965128955e-02 , 9.29391300559080e-02 , 8.80280661517742e-02 ), ( -9.70578106655439e-02 , 2.49485275638335e-01 , 6.61481548320792e-02 ), ( -1.89349892460271e-02 , 9.92934578601701e-02 , -1.71547671981010e-01 ), ( 7.09549756938869e-02 , -1.85205681928521e-01 , -3.89553397840212e-02 ), ( 1.04360069804476e-02 , -9.94579562621154e-02 , 2.54601524564221e-01 ), ( -4.10194911993123e-02 , 6.13670159681508e-02 , 1.91634456228622e-01 ), ( 6.61500758622970e-02 , -1.89564992241884e-01 , 3.07364530191408e-02 ), ( 1.15129312716163e-01 , -3.91425701068371e-01 , 2.73230025879347e-01 ), ( 2.46652291494805e-02 , -9.93621704587275e-02 , 9.57319835750408e-02 ), ( 2.66487201515362e-02 , -9.71899657435523e-02 , 5.95549496710853e-02 ), ( 1.24622672888664e-02 , -5.57702453559136e-02 , 7.24033746190143e-02 ), ( 1.26017842784006e-02 , -5.36203395040831e-02 , 6.12364446426536e-02 ), ( 5.62084309259653e-03 , -3.50953115725839e-02 , 7.55762909057078e-02 ), ( -8.60826813568425e-03 , 9.44406645854298e-03 , 7.55323767690547e-02 ), ( -2.08429098101708e-03 , -2.83671367062415e-03 , 4.04078631431500e-02 ), ( -5.77487048564608e-03 , 9.70643059913455e-03 , 3.61177754946845e-02 ), ( 2.70805118577230e-03 , -1.30373194634878e-02 , 1.96985074289443e-02 ), ( 8.99648984984500e-03 , -2.20080768587484e-02 , -2.65342276660742e-02 ), ( 8.69473273520900e-03 , -2.37630816502961e-02 , -1.48802114220181e-02 ), ( 6.56501421850286e-03 , -1.35217932541125e-02 , -3.03210592179036e-02 ), ( 1.50590452715200e-02 , -4.66398655552029e-02 , -2.10071241619051e-03 ), ( 2.77316589065012e-02 , -8.84477423995499e-02 , 7.18007358178622e-03 ), ( 1.43470225305447e-02 , -4.69209172028335e-02 , 8.73278967907638e-03 ), ( 1.42925048375785e-02 , -4.40754955097007e-02 , -2.81534258881913e-03 ), ( 9.38444695561450e-03 , -3.71324088332392e-02 , 3.35213337177348e-02 ), ( -7.26987884782412e-04 , -1.54240642662770e-02 , 7.64135749901223e-02 ), ( -3.73665213056787e-03 , 4.07353264834061e-03 , 3.28987833829794e-02 ), ( -5.80219750707640e-03 , 1.11221101587789e-02 , 3.03749870854370e-02 ), ( -7.30353687369275e-03 , 1.78775846305822e-02 , 2.14936665260160e-02 ), ( -1.63806520613838e-02 , 5.20777052185658e-02 , -3.52025758798728e-03 ), ( -9.82908388362489e-03 , 3.57666323257724e-02 , -2.16173158817409e-02 ), ( -1.38788964719874e-02 , 5.00043362505760e-02 , -2.83698539092528e-02 ), ( -2.06079367882705e-03 , 1.48650968594908e-02 , -3.63347462413643e-02 ), ( 1.05048058308129e-02 , -1.59065676245395e-02 , -7.32554311863814e-02 ), ( 4.32121096086670e-03 , -9.17335633906932e-04 , -5.44231732871726e-02 ), ( 3.28011518369856e-03 , 5.90930783998450e-03 , -6.98300821185564e-02 ), ( 7.12840086648953e-03 , -1.49955402368339e-02 , -3.15702448585199e-02 ), ( 1.31906996331723e-02 , -4.16155160943026e-02 , 1.45046337050661e-03 ), ( 5.47380948155791e-04 , 1.55122543651114e-03 , -1.40928369624719e-02 ), ( 4.79435149741417e-04 , 3.12912676270520e-03 , -1.99871975294202e-02 ), ( -6.50729574857995e-03 , 2.04140395217321e-02 , -2.15099640596013e-04 ), ( -2.05769479255007e-02 , 5.77012793802570e-02 , 2.88966554445180e-02 ), ( -1.90202892635905e-02 , 6.32108127600351e-02 , -1.59219288397588e-02 ), ( -2.27329271959792e-02 , 7.51477831841043e-02 , -1.72969138581540e-02 ), ( -1.70051329242468e-02 , 7.24073007431202e-02 , -8.28531707934524e-02 ), ( -2.01386533689387e-02 , 8.65808706267130e-02 , -1.01708791742204e-01 ), ( -8.69931533541390e-03 , 4.64720375584738e-02 , -8.31006752311498e-02 ), ( -1.87081206453085e-02 , 6.66773226446364e-02 , -3.51058027924910e-02 ), ( -2.46003337460445e-02 , 9.28970579261590e-02 , -6.86965453344270e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 17, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 18 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 18, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 18, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 18, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 18, atoms_positions[size = 51] = { ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 ), ( 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 ), ( 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 ), ( 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 ), ( 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 ), ( 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 ), ( -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 ), ( -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 ), ( -3.71520050105914e+00 , 3.82616194620359e-02 , 5.43787192954506e+00 ), ( -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ), ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 ), ( 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 ), ( 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 ), ( 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 ), ( 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 ), ( 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 ), ( 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 ), ( 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 ), ( 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 ), ( 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 ), ( 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 ), ( 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 ), ( 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 ), ( 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 ), ( 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 ), ( 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 ), ( 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 ), ( 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 ), ( 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 ), ( -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 ), ( 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 ), ( 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 ), ( -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 ), ( -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 ), ( -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 ), ( -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 ), ( -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 ), ( -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 ), ( -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 ), ( -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 ), ( -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 ), ( -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 ), ( -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 ), ( -2.38669067542351e+00 , -3.14191400105748e-01 , 6.17411576908559e+00 ), ( -4.46409638252639e+00 , 9.98162053848096e-01 , 6.44369645585639e+00 ), ( -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 ), ( -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 ), ( -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 ), ( -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 ), ( -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 ), ( -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ) } +colvars: Step 18, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_ids[size = 0] = +colvars: Step 18, atom_groups_refcount[size = 0] = +colvars: Step 18, atom_groups_masses[size = 0] = +colvars: Step 18, atom_groups_charges[size = 0] = +colvars: Step 18, atom_groups_coms[size = 0] = +colvars: Step 18, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 18, volmaps_ids[size = 0] = +colvars: Step 18, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 18 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.243937 , 17.1889 , 17.2775 , 18.0283 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.243937 , 17.1889 , 17.2775 , 18.0283 ) to colvar "one". +colvars: Adding total bias energy: 11.4881 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.243937 , 17.1889 , 17.2775 , 18.0283 ) +colvars: Applying force on main group : +colvars: ( -0.0915762 , 0.385562 , -0.482176 ) +colvars: ( 0.0152502 , 0.0382727 , -0.30755 ) +colvars: ( -0.0459114 , 0.103837 , 0.0968436 ) +colvars: ( -0.116855 , 0.310687 , 0.0708977 ) +colvars: ( -0.0221167 , 0.120487 , -0.220033 ) +colvars: ( 0.0843119 , -0.226333 , -0.042937 ) +colvars: ( 0.00810137 , -0.106136 , 0.31525 ) +colvars: ( -0.0496803 , 0.0834693 , 0.214138 ) +colvars: ( 0.0808983 , -0.234142 , 0.0230362 ) +colvars: ( 0.137578 , -0.475702 , 0.33253 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246774 , -0.0993925 , 0.095837 ) +colvars: ( 0.0200619 , -0.0819545 , 0.0829092 ) +colvars: ( 0.0266501 , -0.097221 , 0.0596138 ) +colvars: ( 0.0124681 , -0.0557608 , 0.0724675 ) +colvars: ( 0.0126077 , -0.0536224 , 0.0612953 ) +colvars: ( 0.00562539 , -0.0350561 , 0.0756317 ) +colvars: ( -0.00249902 , -0.00817592 , 0.0694225 ) +colvars: ( -0.00860607 , 0.00953712 , 0.0755675 ) +colvars: ( -0.00208543 , -0.00278615 , 0.0404226 ) +colvars: ( -0.00577488 , 0.00976017 , 0.03613 ) +colvars: ( 0.00270139 , -0.0130014 , 0.0196923 ) +colvars: ( 0.00402512 , -0.0106071 , -0.00868066 ) +colvars: ( 0.00897909 , -0.0219969 , -0.0265871 ) +colvars: ( 0.00868487 , -0.023768 , -0.0149066 ) +colvars: ( 0.00655364 , -0.0135294 , -0.0303614 ) +colvars: ( 0.0150526 , -0.0466654 , -0.00210513 ) +colvars: ( 0.0197658 , -0.0607786 , -0.00492634 ) +colvars: ( 0.0277299 , -0.088522 , 0.00720549 ) +colvars: ( 0.0143479 , -0.046961 , 0.00875331 ) +colvars: ( 0.0142933 , -0.0441264 , -0.00280083 ) +colvars: ( 0.00938972 , -0.0371491 , 0.0335616 ) +colvars: ( 0.00324408 , -0.021264 , 0.0481603 ) +colvars: ( -0.000712546 , -0.0154013 , 0.0764908 ) +colvars: ( -0.00372928 , 0.00408981 , 0.032932 ) +colvars: ( -0.00579296 , 0.0111354 , 0.0304101 ) +colvars: ( -0.00730077 , 0.0179114 , 0.0215049 ) +colvars: ( -0.0133449 , 0.040847 , 0.00414004 ) +colvars: ( -0.0163859 , 0.052146 , -0.00355241 ) +colvars: ( -0.00983317 , 0.035792 , -0.0216488 ) +colvars: ( -0.0138826 , 0.0500343 , -0.0284074 ) +colvars: ( -0.00206827 , 0.0148642 , -0.0363755 ) +colvars: ( 0.00225872 , 0.00682171 , -0.060283 ) +colvars: ( 0.0104902 , -0.0159566 , -0.0733221 ) +colvars: ( 0.00431488 , -0.000960525 , -0.0544635 ) +colvars: ( 0.0032725 , 0.00585914 , -0.0698826 ) +colvars: ( 0.00712741 , -0.0150454 , -0.0315817 ) +colvars: ( 0.00864236 , -0.0218868 , -0.0224897 ) +colvars: ( 0.0131993 , -0.0416884 , 0.00148789 ) +colvars: ( 0.000554304 , 0.00150954 , -0.01408 ) +colvars: ( 0.00048766 , 0.00307696 , -0.0199737 ) +colvars: ( -0.0064991 , 0.0204035 , -0.000198666 ) +colvars: ( -0.0147073 , 0.0442715 , 0.00779696 ) +colvars: ( -0.0205639 , 0.0577454 , 0.0289276 ) +colvars: ( -0.0190138 , 0.063231 , -0.0159301 ) +colvars: ( -0.0227246 , 0.0751716 , -0.0173043 ) +colvars: ( -0.0170123 , 0.0724067 , -0.0829303 ) +colvars: ( -0.0201489 , 0.0865836 , -0.101807 ) +colvars: ( -0.00870571 , 0.0464422 , -0.0831679 ) +colvars: ( -0.0187076 , 0.0667001 , -0.0351397 ) +colvars: ( -0.022497 , 0.0839954 , -0.0586742 ) +colvars: ( -0.0246095 , 0.0929421 , -0.0687797 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 18. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 18. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atoms_new_colvar_forces = { ( -7.15143246749638e-02 , 3.03607143562019e-01 , -3.99266458606129e-01 ), ( 1.27511738446594e-02 , 3.00967629854831e-02 , -2.38127471469929e-01 ), ( -4.18863071949037e-02 , 9.32301455194097e-02 , 8.81628918987510e-02 ), ( -9.70895404804677e-02 , 2.49908041041692e-01 , 6.59713718888419e-02 ), ( -1.88725880515165e-02 , 9.92228346931220e-02 , -1.71872787066905e-01 ), ( 7.09670536741436e-02 , -1.85486495457679e-01 , -3.87969474637418e-02 ), ( 1.03600953886065e-02 , -9.93144409185911e-02 , 2.54966692370490e-01 ), ( -4.10379422641936e-02 , 6.15825267191375e-02 , 1.91648394424666e-01 ), ( 6.61910179362997e-02 , -1.89870815465685e-01 , 3.08332055522194e-02 ), ( 1.15081183601858e-01 , -3.91707048313628e-01 , 2.73856265793050e-01 ), ( 2.46774375424239e-02 , -9.93924532683559e-02 , 9.58370334057540e-02 ), ( 2.66500535243150e-02 , -9.72209778665420e-02 , 5.96137627610270e-02 ), ( 1.24681376732403e-02 , -5.57608422003375e-02 , 7.24674929744035e-02 ), ( 1.26076824836146e-02 , -5.36224387337502e-02 , 6.12952593688761e-02 ), ( 5.62539094638128e-03 , -3.50561345523898e-02 , 7.56316999753237e-02 ), ( -8.60606560277206e-03 , 9.53712138345240e-03 , 7.55675193204442e-02 ), ( -2.08543446117501e-03 , -2.78615340021712e-03 , 4.04226285887231e-02 ), ( -5.77487538308468e-03 , 9.76017420918320e-03 , 3.61300350716817e-02 ), ( 2.70138528408105e-03 , -1.30014125518310e-02 , 1.96922867703026e-02 ), ( 8.97908516827588e-03 , -2.19969142018477e-02 , -2.65871231424575e-02 ), ( 8.68487447282498e-03 , -2.37680120333839e-02 , -1.49066296522007e-02 ), ( 6.55363705774327e-03 , -1.35293937357806e-02 , -3.03613858553427e-02 ), ( 1.50526198911460e-02 , -4.66653732768597e-02 , -2.10512603376900e-03 ), ( 2.77299143813737e-02 , -8.85219509446862e-02 , 7.20549150444689e-03 ), ( 1.43478752729337e-02 , -4.69610108498508e-02 , 8.75330557484605e-03 ), ( 1.42932681641806e-02 , -4.41264084608804e-02 , -2.80083205314169e-03 ), ( 9.38971606170557e-03 , -3.71491334276232e-02 , 3.35616067674381e-02 ), ( -7.12546262469615e-04 , -1.54013014397138e-02 , 7.64908271177000e-02 ), ( -3.72927860592955e-03 , 4.08981429157061e-03 , 3.29319617386191e-02 ), ( -5.79295740178263e-03 , 1.11354132169146e-02 , 3.04101252621499e-02 ), ( -7.30076957302218e-03 , 1.79113599273376e-02 , 2.15049483746605e-02 ), ( -1.63859058028266e-02 , 5.21459645145339e-02 , -3.55241297422584e-03 ), ( -9.83317150417715e-03 , 3.57919846305960e-02 , -2.16488481834581e-02 ), ( -1.38825585085550e-02 , 5.00342849475707e-02 , -2.84074398206996e-02 ), ( -2.06827442900071e-03 , 1.48642117794079e-02 , -3.63755080607341e-02 ), ( 1.04902107573028e-02 , -1.59566230977413e-02 , -7.33221264395743e-02 ), ( 4.31488123513660e-03 , -9.60525185674116e-04 , -5.44635132252315e-02 ), ( 3.27250278479952e-03 , 5.85914181832615e-03 , -6.98826067047735e-02 ), ( 7.12741052770944e-03 , -1.50453533016599e-02 , -3.15817248280361e-02 ), ( 1.31993193745071e-02 , -4.16884063363824e-02 , 1.48789399052293e-03 ), ( 5.54304324758436e-04 , 1.50953505055301e-03 , -1.40799929296691e-02 ), ( 4.87659795907501e-04 , 3.07695750800323e-03 , -1.99737071226953e-02 ), ( -6.49910304176036e-03 , 2.04035182113293e-02 , -1.98666442130940e-04 ), ( -2.05638510973712e-02 , 5.77453732012774e-02 , 2.89275614275456e-02 ), ( -1.90138229562706e-02 , 6.32310314419597e-02 , -1.59301210133700e-02 ), ( -2.27246458259210e-02 , 7.51715617639337e-02 , -1.73043097713146e-02 ), ( -1.70122524685426e-02 , 7.24067493443881e-02 , -8.29303072212397e-02 ), ( -2.01489048049457e-02 , 8.65835663076626e-02 , -1.01806981860336e-01 ), ( -8.70570647921074e-03 , 4.64421864114534e-02 , -8.31679002836408e-02 ), ( -1.87075793223643e-02 , 6.67000943942084e-02 , -3.51396666630672e-02 ), ( -2.46094849727014e-02 , 9.29421201465667e-02 , -6.87796670346709e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 18, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 19 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 19, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 19, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 19, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 19, atoms_positions[size = 51] = { ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 ), ( 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 ), ( 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 ), ( 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 ), ( 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 ), ( 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 ), ( -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 ), ( -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 ), ( -3.70748943344948e+00 , 4.16903006825168e-02 , 5.43600413888779e+00 ), ( -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ), ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 ), ( 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 ), ( 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 ), ( 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 ), ( 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 ), ( 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 ), ( 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 ), ( 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 ), ( 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 ), ( 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 ), ( 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 ), ( 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 ), ( 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 ), ( 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 ), ( 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 ), ( 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 ), ( 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 ), ( 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 ), ( 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 ), ( -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 ), ( 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 ), ( 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 ), ( -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 ), ( -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 ), ( -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 ), ( -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 ), ( -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 ), ( -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 ), ( -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 ), ( -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 ), ( -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 ), ( -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 ), ( -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 ), ( -2.38818462389786e+00 , -3.15034590810127e-01 , 6.17323190730087e+00 ), ( -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 ), ( -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 ), ( -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 ), ( -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 ), ( -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 ), ( -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 ), ( -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ) } +colvars: Step 19, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_ids[size = 0] = +colvars: Step 19, atom_groups_refcount[size = 0] = +colvars: Step 19, atom_groups_masses[size = 0] = +colvars: Step 19, atom_groups_charges[size = 0] = +colvars: Step 19, atom_groups_coms[size = 0] = +colvars: Step 19, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 19, volmaps_ids[size = 0] = +colvars: Step 19, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 19 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687067e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687067e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.238446 , 17.1992 , 17.2761 , 18.0322 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.238446 , 17.1992 , 17.2761 , 18.0322 ) to colvar "one". +colvars: Adding total bias energy: 11.4937 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.238446 , 17.1992 , 17.2761 , 18.0322 ) +colvars: Applying force on main group : +colvars: ( -0.0914707 , 0.385609 , -0.482845 ) +colvars: ( 0.015285 , 0.0381361 , -0.307758 ) +colvars: ( -0.0459678 , 0.10412 , 0.0969107 ) +colvars: ( -0.11686 , 0.311083 , 0.0706998 ) +colvars: ( -0.0220502 , 0.120402 , -0.220332 ) +colvars: ( 0.0843059 , -0.226597 , -0.0427713 ) +colvars: ( 0.0080256 , -0.105981 , 0.315591 ) +colvars: ( -0.0496875 , 0.0836534 , 0.214167 ) +colvars: ( 0.0809202 , -0.234458 , 0.0231773 ) +colvars: ( 0.1375 , -0.475966 , 0.33316 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246813 , -0.0994258 , 0.0959358 ) +colvars: ( 0.0200629 , -0.0819689 , 0.0829822 ) +colvars: ( 0.026646 , -0.0972576 , 0.0596657 ) +colvars: ( 0.0124695 , -0.0557562 , 0.0725248 ) +colvars: ( 0.0126092 , -0.0536279 , 0.0613489 ) +colvars: ( 0.00562681 , -0.0350233 , 0.0756789 ) +colvars: ( -0.00249684 , -0.00812038 , 0.0694567 ) +colvars: ( -0.00860415 , 0.00962177 , 0.0755927 ) +colvars: ( -0.00208655 , -0.00274152 , 0.0404309 ) +colvars: ( -0.00577449 , 0.00980914 , 0.0361369 ) +colvars: ( 0.00269566 , -0.0129723 , 0.0196798 ) +colvars: ( 0.00401591 , -0.010591 , -0.00871806 ) +colvars: ( 0.00896498 , -0.0219935 , -0.0266451 ) +colvars: ( 0.00867631 , -0.0237772 , -0.0149358 ) +colvars: ( 0.0065445 , -0.0135404 , -0.0304032 ) +colvars: ( 0.0150454 , -0.0466942 , -0.0021121 ) +colvars: ( 0.0197596 , -0.0608316 , -0.00492218 ) +colvars: ( 0.0277241 , -0.0885971 , 0.00722998 ) +colvars: ( 0.0143461 , -0.0470011 , 0.00877355 ) +colvars: ( 0.0142916 , -0.0441759 , -0.00278498 ) +colvars: ( 0.0093917 , -0.0371663 , 0.0336002 ) +colvars: ( 0.00325039 , -0.0212642 , 0.0482137 ) +colvars: ( -0.000702702 , -0.0153787 , 0.0765648 ) +colvars: ( -0.00372363 , 0.00410665 , 0.0329642 ) +colvars: ( -0.00578554 , 0.0111507 , 0.0304456 ) +colvars: ( -0.00729785 , 0.017944 , 0.0215143 ) +colvars: ( -0.0133433 , 0.0408943 , 0.00412601 ) +colvars: ( -0.0163872 , 0.0522106 , -0.00358746 ) +colvars: ( -0.00983437 , 0.035817 , -0.0216798 ) +colvars: ( -0.0138827 , 0.0500649 , -0.0284434 ) +colvars: ( -0.00207303 , 0.0148629 , -0.0364151 ) +colvars: ( 0.00225124 , 0.00679636 , -0.0603372 ) +colvars: ( 0.0104787 , -0.0160066 , -0.0733857 ) +colvars: ( 0.00431024 , -0.00100084 , -0.0544993 ) +colvars: ( 0.00326729 , 0.0058129 , -0.069929 ) +colvars: ( 0.007126 , -0.0150916 , -0.0315889 ) +colvars: ( 0.00864414 , -0.0219447 , -0.0224765 ) +colvars: ( 0.0132037 , -0.0417553 , 0.00153019 ) +colvars: ( 0.000559622 , 0.00147419 , -0.0140614 ) +colvars: ( 0.000494052 , 0.00303273 , -0.019953 ) +colvars: ( -0.00649192 , 0.0203982 , -0.000178086 ) +colvars: ( -0.0146969 , 0.0442903 , 0.00782102 ) +colvars: ( -0.0205512 , 0.0577936 , 0.0289605 ) +colvars: ( -0.0190057 , 0.0632568 , -0.0159333 ) +colvars: ( -0.0227146 , 0.0752021 , -0.0173057 ) +colvars: ( -0.0170137 , 0.0724113 , -0.083 ) +colvars: ( -0.0201519 , 0.0865916 , -0.101897 ) +colvars: ( -0.00870791 , 0.0464183 , -0.0832269 ) +colvars: ( -0.0187037 , 0.0667269 , -0.0351689 ) +colvars: ( -0.0224956 , 0.0840283 , -0.0587307 ) +colvars: ( -0.0246115 , 0.0929889 , -0.0688587 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 19. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 19. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atoms_new_colvar_forces = { ( -7.14077590702325e-02 , 3.03639970618158e-01 , -3.99862623514067e-01 ), ( 1.27881311797386e-02 , 3.00156744122845e-02 , -2.38301254790407e-01 ), ( -4.19519028873145e-02 , 9.35290707918833e-02 , 8.81926041657879e-02 ), ( -9.71004375206781e-02 , 2.50250971830372e-01 , 6.57776690911295e-02 ), ( -1.87998622166412e-02 , 9.91374485926363e-02 , -1.72118839430279e-01 ), ( 7.09626200046807e-02 , -1.85703030420809e-01 , -3.86453310144055e-02 ), ( 1.02768410340877e-02 , -9.91850800704239e-02 , 2.55253853212102e-01 ), ( -4.10433812807933e-02 , 6.17087230475973e-02 , 1.91690812071477e-01 ), ( 6.62233150611980e-02 , -1.90167721803567e-01 , 3.09983544618496e-02 ), ( 1.15003966443554e-01 , -3.91937648056864e-01 , 2.74429662774009e-01 ), ( 2.46812974419315e-02 , -9.94258146412512e-02 , 9.59357593321758e-02 ), ( 2.66459609072608e-02 , -9.72575765949008e-02 , 5.96657296750887e-02 ), ( 1.24695131914519e-02 , -5.57562195730972e-02 , 7.25248107254090e-02 ), ( 1.26092198409545e-02 , -5.36278872660035e-02 , 6.13488949830409e-02 ), ( 5.62681147971932e-03 , -3.50232748733177e-02 , 7.56788968781099e-02 ), ( -8.60415005884939e-03 , 9.62176625969064e-03 , 7.55926821951814e-02 ), ( -2.08655279010191e-03 , -2.74151909885105e-03 , 4.04309135482712e-02 ), ( -5.77449105629113e-03 , 9.80913615447255e-03 , 3.61368984787320e-02 ), ( 2.69566274999494e-03 , -1.29722622520675e-02 , 1.96797958058926e-02 ), ( 8.96497685882790e-03 , -2.19934906690526e-02 , -2.66451373083052e-02 ), ( 8.67631064794137e-03 , -2.37772038243613e-02 , -1.49358354286275e-02 ), ( 6.54449571419079e-03 , -1.35403908603913e-02 , -3.04031721925375e-02 ), ( 1.50454384630021e-02 , -4.66942483082077e-02 , -2.11209871448282e-03 ), ( 2.77241036133913e-02 , -8.85971246913936e-02 , 7.22997775690739e-03 ), ( 1.43461138727377e-02 , -4.70010830247044e-02 , 8.77355335079919e-03 ), ( 1.42916168907112e-02 , -4.41759052969429e-02 , -2.78498300656853e-03 ), ( 9.39169571445058e-03 , -3.71662534556160e-02 , 3.36002219154809e-02 ), ( -7.02702203154147e-04 , -1.53787093342839e-02 , 7.65647743355095e-02 ), ( -3.72362969097915e-03 , 4.10664783797948e-03 , 3.29642053334804e-02 ), ( -5.78554254176952e-03 , 1.11507318324770e-02 , 3.04456069939037e-02 ), ( -7.29784765745149e-03 , 1.79439584046955e-02 , 2.15143492971677e-02 ), ( -1.63872029943874e-02 , 5.22105740129331e-02 , -3.58746379327103e-03 ), ( -9.83436728933798e-03 , 3.58169908716224e-02 , -2.16798178840036e-02 ), ( -1.38826941479590e-02 , 5.00648597055764e-02 , -2.84434181671928e-02 ), ( -2.07303470268060e-03 , 1.48629103736301e-02 , -3.64151138487412e-02 ), ( 1.04786554117137e-02 , -1.60066238108003e-02 , -7.33856896007905e-02 ), ( 4.31023778396208e-03 , -1.00084497686633e-03 , -5.44992546381540e-02 ), ( 3.26728614384986e-03 , 5.81290388986927e-03 , -6.99290438725339e-02 ), ( 7.12599788830755e-03 , -1.50915587910003e-02 , -3.15889400834817e-02 ), ( 1.32036800757807e-02 , -4.17552991830073e-02 , 1.53018914256155e-03 ), ( 5.59622310848577e-04 , 1.47419140054324e-03 , -1.40614251650752e-02 ), ( 4.94051785359338e-04 , 3.03273025975034e-03 , -1.99529580396408e-02 ), ( -6.49191624788353e-03 , 2.03981522284860e-02 , -1.78085695653553e-04 ), ( -2.05511764922100e-02 , 5.77936243785591e-02 , 2.89605276578092e-02 ), ( -1.90057197022633e-02 , 6.32567607724533e-02 , -1.59332941394231e-02 ), ( -2.27145709982415e-02 , 7.52020714968192e-02 , -1.73056614158674e-02 ), ( -1.70136933099124e-02 , 7.24112968951756e-02 , -8.29999768120056e-02 ), ( -2.01519254267428e-02 , 8.65915569665777e-02 , -1.01896782591472e-01 ), ( -8.70791333279080e-03 , 4.64182692798261e-02 , -8.32269283153985e-02 ), ( -1.87036946668894e-02 , 6.67269139196540e-02 , -3.51688999413350e-02 ), ( -2.46114542240917e-02 , 9.29888646440582e-02 , -6.88587137781561e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 19, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 20 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 20, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 20, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643353998e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780256e+00 , -3.16614240925533e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +colvars: Step 20, atom_groups_refcount[size = 0] = +colvars: Step 20, atom_groups_masses[size = 0] = +colvars: Step 20, atom_groups_charges[size = 0] = +colvars: Step 20, atom_groups_coms[size = 0] = +colvars: Step 20, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_ids[size = 0] = +colvars: Step 20, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 20 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.233415 , 17.2076 , 17.2731 , 18.0383 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.233415 , 17.2076 , 17.2731 , 18.0383 ) to colvar "one". +colvars: Adding total bias energy: 11.4987 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.233415 , 17.2076 , 17.2731 , 18.0383 ) +colvars: Applying force on main group : +colvars: ( -0.0913396 , 0.385649 , -0.483413 ) +colvars: ( 0.0153156 , 0.0380779 , -0.307957 ) +colvars: ( -0.0460269 , 0.10441 , 0.0968747 ) +colvars: ( -0.116844 , 0.311391 , 0.0704888 ) +colvars: ( -0.0219711 , 0.120302 , -0.220545 ) +colvars: ( 0.0842827 , -0.226789 , -0.0426138 ) +colvars: ( 0.0079403 , -0.105844 , 0.315844 ) +colvars: ( -0.0496811 , 0.0837394 , 0.214219 ) +colvars: ( 0.0809344 , -0.234762 , 0.0233814 ) +colvars: ( 0.137389 , -0.476175 , 0.333721 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246764 , -0.0994603 , 0.0960262 ) +colvars: ( 0.0200575 , -0.081987 , 0.0830467 ) +colvars: ( 0.0266365 , -0.0972981 , 0.0597107 ) +colvars: ( 0.0124661 , -0.055756 , 0.0725744 ) +colvars: ( 0.0126062 , -0.053636 , 0.0613964 ) +colvars: ( 0.00562478 , -0.0349973 , 0.0757171 ) +colvars: ( -0.00249657 , -0.00807268 , 0.0694821 ) +colvars: ( -0.00860292 , 0.00969555 , 0.0756074 ) +colvars: ( -0.00208776 , -0.00270415 , 0.0404328 ) +colvars: ( -0.0057739 , 0.00985182 , 0.0361383 ) +colvars: ( 0.00269105 , -0.0129509 , 0.019662 ) +colvars: ( 0.00400949 , -0.0105822 , -0.0087584 ) +colvars: ( 0.00895487 , -0.0219985 , -0.0267055 ) +colvars: ( 0.00866948 , -0.0237906 , -0.0149662 ) +colvars: ( 0.0065381 , -0.0135548 , -0.0304446 ) +colvars: ( 0.0150379 , -0.0467256 , -0.00212057 ) +colvars: ( 0.0197518 , -0.0608843 , -0.00491806 ) +colvars: ( 0.0277145 , -0.0886706 , 0.00725391 ) +colvars: ( 0.0143418 , -0.0470397 , 0.00879345 ) +colvars: ( 0.0142877 , -0.0442223 , -0.00276785 ) +colvars: ( 0.00939022 , -0.0371829 , 0.0336364 ) +colvars: ( 0.00325256 , -0.0212633 , 0.0482639 ) +colvars: ( -0.000698145 , -0.0153563 , 0.0766331 ) +colvars: ( -0.00372007 , 0.0041238 , 0.0329943 ) +colvars: ( -0.00578039 , 0.0111679 , 0.0304799 ) +colvars: ( -0.007295 , 0.0179744 , 0.0215214 ) +colvars: ( -0.0133397 , 0.0409385 , 0.00411059 ) +colvars: ( -0.0163845 , 0.0522691 , -0.00362466 ) +colvars: ( -0.00983258 , 0.0358406 , -0.0217096 ) +colvars: ( -0.0138792 , 0.0500947 , -0.0284772 ) +colvars: ( -0.00207475 , 0.0148609 , -0.0364524 ) +colvars: ( 0.00224746 , 0.00677197 , -0.0603866 ) +colvars: ( 0.0104709 , -0.0160556 , -0.0734437 ) +colvars: ( 0.00430769 , -0.00103735 , -0.0545293 ) +colvars: ( 0.00326495 , 0.00577162 , -0.0699681 ) +colvars: ( 0.00712437 , -0.0151328 , -0.0315917 ) +colvars: ( 0.00864399 , -0.021995 , -0.0224582 ) +colvars: ( 0.0132037 , -0.0418137 , 0.00157607 ) +colvars: ( 0.000563179 , 0.00144649 , -0.0140382 ) +colvars: ( 0.000498434 , 0.00299805 , -0.0199262 ) +colvars: ( -0.00648605 , 0.0203983 , -0.000154656 ) +colvars: ( -0.0146875 , 0.0443143 , 0.00784744 ) +colvars: ( -0.0205396 , 0.0578448 , 0.0289934 ) +colvars: ( -0.0189963 , 0.0632872 , -0.0159325 ) +colvars: ( -0.0227031 , 0.0752383 , -0.0173023 ) +colvars: ( -0.0170092 , 0.0724201 , -0.083061 ) +colvars: ( -0.0201473 , 0.0866037 , -0.101977 ) +colvars: ( -0.00870557 , 0.0464005 , -0.0832767 ) +colvars: ( -0.0186966 , 0.0667567 , -0.0351936 ) +colvars: ( -0.0224888 , 0.0840635 , -0.0587812 ) +colvars: ( -0.024606 , 0.0930351 , -0.0689323 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 20. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800976e-02 , 3.00052379356398e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500016e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827239e-02 , 1.91760996033175e-01 ), ( 6.62468727487264e-02 , -1.90448081926945e-01 , 3.12288455216891e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807518e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489682e-02 ), ( 1.24661136135099e-02 , -5.57559811144077e-02 , 7.25743621949595e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332648e-03 , -3.49973301865401e-02 , 7.57170861826678e-02 ), ( -8.60292310050451e-03 , 9.69554753037329e-03 , 7.56073713177290e-02 ), ( -2.08776469672693e-03 , -2.70415172113726e-03 , 4.04328246755312e-02 ), ( -5.77389521453808e-03 , 9.85182430390034e-03 , 3.61382862311481e-02 ), ( 2.69104804092522e-03 , -1.29509138532636e-02 , 1.96620498003799e-02 ), ( 8.95486758503643e-03 , -2.19984645975748e-02 , -2.67054922301013e-02 ), ( 8.66947656368631e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541540e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516852e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879235e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703576e-03 , -3.71828583991163e-02 , 3.36363523912982e-02 ), ( -6.98144545634527e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600069e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540628e-03 , 1.11679149109105e-02 , 3.04799282045032e-02 ), ( -7.29500058088394e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040445e-02 , -3.62466193947452e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308239e-02 ), ( -2.07475381329403e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505723e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288624e-03 , -1.03735135095862e-03 , -5.45293145217132e-02 ), ( 3.26495468493790e-03 , 5.77162454807394e-03 , -6.99680928834496e-02 ), ( 7.12436996401245e-03 , -1.51327555336419e-02 , -3.15916578475219e-02 ), ( 1.32036569636365e-02 , -4.18136663470712e-02 , 1.57606808925123e-03 ), ( 5.63178713376314e-04 , 1.44649438052724e-03 , -1.40381831264554e-02 ), ( 4.98434308056258e-04 , 2.99804808326457e-03 , -1.99261927958005e-02 ), ( -6.48604874882728e-03 , 2.03983070643249e-02 , -1.54655641113355e-04 ), ( -2.05396268108372e-02 , 5.78448103620468e-02 , 2.89933897342497e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654819e-03 , 4.64004872660570e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278477e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Saving collective variables state to "test.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped new file mode 100644 index 000000000..db11936b1 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,17 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x ( 0.99975884202595 , 0.01402736950034 , 0.011979408737928 , -0.011915723314925 ) +} + +restraint { + configuration { + step 20 + name harmonic1 + } +} + diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj new file mode 100644 index 000000000..ca2c7beb2 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one + 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( -3.25898609205420e-01 , 1.69798809632672e+01 , 1.71828081280911e+01 , 1.81199165160869e+01 ) + 1 ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ) ( -3.21564188520062e-01 , 1.69819486822241e+01 , 1.71859144849276e+01 , 1.81247073526383e+01 ) + 2 ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ) ( -3.17383070027282e-01 , 1.69856435072818e+01 , 1.71892246235753e+01 , 1.81275786557577e+01 ) + 3 ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ) ( -3.13410121312395e-01 , 1.69909293641043e+01 , 1.71929002393502e+01 , 1.81282997059461e+01 ) + 4 ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ) ( -3.09649515116043e-01 , 1.69977772313853e+01 , 1.71971079225853e+01 , 1.81267357994661e+01 ) + 5 ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ) ( -3.06058986795120e-01 , 1.70061638839744e+01 , 1.72019887637082e+01 , 1.81228667161400e+01 ) + 6 ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ) ( -3.02559854946980e-01 , 1.70160600442246e+01 , 1.72076310908889e+01 , 1.81167997183534e+01 ) + 7 ( 9.99619179084481e-01 , 1.92861231851382e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ) ( -2.99050775133683e-01 , 1.70274127639097e+01 , 1.72140507063916e+01 , 1.81087735951856e+01 ) + 8 ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ) ( -2.95423022186405e-01 , 1.70401276827003e+01 , 1.72211809136720e+01 , 1.80991515946418e+01 ) + 9 ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ) ( -2.91575342533006e-01 , 1.70540561294731e+01 , 1.72288725006022e+01 , 1.80884027962568e+01 ) + 10 ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ) ( -2.87426720479198e-01 , 1.70689904989372e+01 , 1.72369024184678e+01 , 1.80770732028938e+01 ) + 11 ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ) ( -2.82925613878243e-01 , 1.70846693215076e+01 , 1.72449893116233e+01 , 1.80657495280640e+01 ) + 12 ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ) ( -2.78054513150077e-01 , 1.71007911361289e+01 , 1.72528140290677e+01 , 1.80550200826245e+01 ) + 13 ( 9.99711367452522e-01 , 1.66424815610562e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ) ( -2.72829776587463e-01 , 1.71170334040853e+01 , 1.72600431390157e+01 , 1.80454376062023e+01 ) + 14 ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ) ( -2.67298305818362e-01 , 1.71330704047432e+01 , 1.72663532826131e+01 , 1.80374879075006e+01 ) + 15 ( 9.99735732840256e-01 , 1.57202526155576e-02 , 1.18858573400358e-02 , -1.18348863683820e-02 ) ( -2.61533691909663e-01 , 1.71485840824799e+01 , 1.72714541741650e+01 , 1.80315661983211e+01 ) + 16 ( 9.99744979701586e-01 , 1.52939094147335e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ) ( -2.55633883245562e-01 , 1.71632652563580e+01 , 1.72751084768322e+01 , 1.80279610546862e+01 ) + 17 ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652891e-02 , -1.16317231514313e-02 ) ( -2.49720405143540e-01 , 1.71768080432236e+01 , 1.72771475989308e+01 , 1.80268447892810e+01 ) + 18 ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ) ( -2.43937108749464e-01 , 1.71889046690184e+01 , 1.72774832629947e+01 , 1.80282687528248e+01 ) + 19 ( 9.99758962093459e-01 , 1.42609660687067e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ) ( -2.38445587445625e-01 , 1.71992487761229e+01 , 1.72761151637582e+01 , 1.80321624270782e+01 ) + 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ) ( -2.33415112386271e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..39c528f4c --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out @@ -0,0 +1,4871 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Called colvarcript::init_commands() +colvars: Defined command "cv_addenergy", with help string: +colvars: Add an energy to the MD engine (no effect in VMD) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: E : float - Amount of energy to add +colvars: Defined command "cv_bias", with help string: +colvars: Prefix for bias-specific commands +colvars: Defined command "cv_colvar", with help string: +colvars: Prefix for colvar-specific commands +colvars: Defined command "cv_config", with help string: +colvars: Read configuration from the given string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf : string - Configuration string +colvars: Defined command "cv_configfile", with help string: +colvars: Read configuration from a file +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: conf_file : string - Path to configuration file +colvars: Defined command "cv_delete", with help string: +colvars: Delete this Colvars module instance (VMD only) +colvars: Defined command "cv_featurereport", with help string: +colvars: Return a summary of Colvars features used so far and their citations +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: report : string - Feature report and citations +colvars: +colvars: Defined command "cv_frame", with help string: +colvars: Get or set current frame number (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: frame : integer - Frame number (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: frame : integer - Frame number +colvars: +colvars: Defined command "cv_getatomappliedforces", with help string: +colvars: Get the list of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic forces +colvars: +colvars: Defined command "cv_getatomappliedforcesmax", with help string: +colvars: Get the maximum norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesmaxid", with help string: +colvars: Get the atom ID with the largest applied force +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: id : int - ID of the atom with the maximum atomic force +colvars: +colvars: Defined command "cv_getatomappliedforcesrms", with help string: +colvars: Get the root-mean-square norm of forces applied by Colvars to atoms +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - RMS atomic force +colvars: +colvars: Defined command "cv_resetatomappliedforces", with help string: +colvars: Reset forces applied by Colvars to atoms +colvars: Defined command "cv_getatomids", with help string: +colvars: Get the list of indices of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "cv_getatomcharges", with help string: +colvars: Get the list of charges of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: charges : array of floats - Atomic charges +colvars: +colvars: Defined command "cv_getatommasses", with help string: +colvars: Get the list of masses of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: masses : array of floats - Atomic masses +colvars: +colvars: Defined command "cv_getatompositions", with help string: +colvars: Get the list of cached positions of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: positions : array of arrays of floats - Atomic positions +colvars: +colvars: Defined command "cv_getatomtotalforces", with help string: +colvars: Get the list of cached total forces of atoms used in Colvars +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: forces : array of arrays of floats - Atomic total foces +colvars: +colvars: Defined command "cv_getconfig", with help string: +colvars: Get the module's configuration string read so far +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "cv_getenergy", with help string: +colvars: Get the current Colvars energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Amount of energy (internal units) +colvars: +colvars: Defined command "cv_getnumactiveatomgroups", with help string: +colvars: Get the number of atom groups that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atom groups +colvars: +colvars: Defined command "cv_getnumactiveatoms", with help string: +colvars: Get the number of atoms that currently have positive ref counts +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getnumatoms", with help string: +colvars: Get the number of requested atoms, including those not in use now +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: count : integer - Total number of atoms +colvars: +colvars: Defined command "cv_getstepabsolute", with help string: +colvars: Get the current step number of the simulation (including restarts) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Absolute step number +colvars: +colvars: Defined command "cv_getsteprelative", with help string: +colvars: Get the current step number from the start of this job +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: step : int - Relative step number +colvars: +colvars: Defined command "cv_help", with help string: +colvars: Get the help string of the Colvars scripting interface +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "cv_languageversion", with help string: +colvars: Get the C++ language version number +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - C++ language version +colvars: +colvars: Defined command "cv_list", with help string: +colvars: Return a list of all variables or biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: param : string - "colvars" or "biases"; default is "colvars" (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of elements +colvars: +colvars: Defined command "cv_listcommands", with help string: +colvars: Get the list of script functions, prefixed with "cv_", "colvar_" or "bias_" +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of commands +colvars: +colvars: Defined command "cv_listindexfiles", with help string: +colvars: Get a list of the index files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of index file names +colvars: +colvars: Defined command "cv_listinputfiles", with help string: +colvars: Get a list of all input/configuration files loaded in this session +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: list : sequence of strings - List of file names +colvars: +colvars: Defined command "cv_load", with help string: +colvars: Load data from a state file into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Path to existing state file or input prefix +colvars: Defined command "cv_loadfromstring", with help string: +colvars: Load state data from a string into all matching colvars and biases +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "cv_molid", with help string: +colvars: Get or set the molecule ID on which Colvars is defined (VMD only) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: molid : integer - New molecule ID; -1 means undefined (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: molid : integer - Current molecule ID +colvars: +colvars: Defined command "cv_printframe", with help string: +colvars: Return the values that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: values : string - The values +colvars: +colvars: Defined command "cv_printframelabels", with help string: +colvars: Return the labels that would be written to colvars.traj +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Labels : string - The labels +colvars: +colvars: Defined command "cv_reset", with help string: +colvars: Delete all internal configuration +colvars: Defined command "cv_resetindexgroups", with help string: +colvars: Clear the index groups loaded so far, allowing to replace them +colvars: Defined command "cv_save", with help string: +colvars: Change the prefix of all output files and save them +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Output prefix with trailing ".colvars.state" gets removed) +colvars: Defined command "cv_savetostring", with help string: +colvars: Write the Colvars state to a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The saved state +colvars: +colvars: Defined command "cv_targettemperature", with help string: +colvars: Get/set target temperature, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: T : float - New target temperature in K (internal use) (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: T : float - Current target temperature in K +colvars: +colvars: Defined command "cv_timestep", with help string: +colvars: Get/set integration timestep, overriding internally what the MD engine reports +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: dt : float - New integration timestep in MD engine units (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: dt : float - Current integration timestep in MD engine units +colvars: +colvars: Defined command "cv_units", with help string: +colvars: Get or set the current Colvars unit system +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: units : string - The new unit system (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: units : string - The current unit system +colvars: +colvars: Defined command "cv_update", with help string: +colvars: Recalculate colvars and biases +colvars: Defined command "cv_version", with help string: +colvars: Get the Colvars Module version string +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: version : string - Colvars version +colvars: +colvars: Defined command "colvar_addforce", with help string: +colvars: Apply the given force onto this colvar (no effects outside run) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: force : float or array - Applied force; must match colvar dimensionality +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float or array - Applied force; matches colvar dimensionality +colvars: +colvars: Defined command "colvar_communicateforces", with help string: +colvars: Communicate bias forces from this colvar to atoms +colvars: Defined command "colvar_cvcflags", with help string: +colvars: Enable or disable individual components by setting their active flags +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: flags : integer array - Zero/nonzero value disables/enables the CVC +colvars: Defined command "colvar_delete", with help string: +colvars: Delete this colvar, along with all biases that depend on it +colvars: Defined command "colvar_get", with help string: +colvars: Get the value of the given feature for this colvar +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "colvar_getappliedforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Applied force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_resetbiasforce", with help string: +colvars: Return the total of the forces applied to this colvar +colvars: Defined command "colvar_getatomgroups", with help string: +colvars: Return the atom indices used by this colvar as a list of lists +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: groups : array of arrays of ints - Atom indices +colvars: +colvars: Defined command "colvar_getatomids", with help string: +colvars: Return the list of atom indices used by this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: indices : array of ints - Atom indices +colvars: +colvars: Defined command "colvar_getconfig", with help string: +colvars: Return the configuration string of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "colvar_getgradients", with help string: +colvars: Return the atomic gradients of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: gradients : array of arrays of floats - Atomic gradients +colvars: +colvars: Defined command "colvar_gettotalforce", with help string: +colvars: Return the sum of internal and external forces to this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: force : float - Total force; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_getvolmapids", with help string: +colvars: Return the list of volumetric map indices used by this colvar +colvars: Defined command "colvar_help", with help string: +colvars: Get a help summary or the help string of one colvar subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "colvar_modifycvcs", with help string: +colvars: Modify configuration of individual components by passing string arguments +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: confs : sequence of strings - New configurations; empty strings are skipped +colvars: Defined command "colvar_run_ave", with help string: +colvars: Get the current running average of the value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Averaged value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_set", with help string: +colvars: Set the given feature of this colvar to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "colvar_state", with help string: +colvars: Print a string representation of the feature state of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The feature state +colvars: +colvars: Defined command "colvar_type", with help string: +colvars: Get the type description of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type description +colvars: +colvars: Defined command "colvar_update", with help string: +colvars: Recompute this colvar and return its up-to-date value +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_value", with help string: +colvars: Get the current value of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: value : float or array - Current value; matches the colvar dimensionality +colvars: +colvars: Defined command "colvar_width", with help string: +colvars: Get the width of this colvar +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: width : float - Value of the width +colvars: +colvars: Defined command "bias_bin", with help string: +colvars: Get the current grid bin index (flattened if more than 1d) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: bin : integer - Bin index +colvars: +colvars: Defined command "bias_bincount", with help string: +colvars: Get the number of samples at the given grid bin (1D ABF only for now) +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: index : integer - Grid index; defaults to current bin (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: samples : integer - Number of samples +colvars: +colvars: Defined command "bias_local_sample_count", with help string: +colvars: Get the number of samples around the current binsamples : integer - Number of samples +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: radius : integer - Sum over radius bins around current bin (optional) +colvars: Defined command "bias_binnum", with help string: +colvars: Get the total number of grid points of this bias (1D ABF only for now) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: Bins : integer - Number of grid points +colvars: +colvars: Defined command "bias_delete", with help string: +colvars: Delete this bias +colvars: Defined command "bias_energy", with help string: +colvars: Get the current energy of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Defined command "bias_get", with help string: +colvars: Get the value of the given feature for this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : 1/0 - State of the given feature +colvars: +colvars: Defined command "bias_getconfig", with help string: +colvars: Return the configuration string of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: conf : string - Current configuration string +colvars: +colvars: Defined command "bias_help", with help string: +colvars: Get a help summary or the help string of one bias subcommand +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: command : string - Get the help string of this specific command (optional) +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: help : string - Help string +colvars: +colvars: Defined command "bias_load", with help string: +colvars: Load data into this bias +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Read from a file with this name or prefix +colvars: Defined command "bias_loadfromstring", with help string: +colvars: Load state data into this bias from a string +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: buffer : string - String buffer containing the state information +colvars: Defined command "bias_save", with help string: +colvars: Save data from this bias into a file with the given prefix +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: prefix : string - Prefix for the state file of this bias +colvars: Defined command "bias_savetostring", with help string: +colvars: Save data from this bias into a string and return it +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - The bias state +colvars: +colvars: Defined command "bias_set", with help string: +colvars: Set the given feature of this bias to a new value +colvars: +colvars: Parameters +colvars: ---------- +colvars: +colvars: feature : string - Name of the feature +colvars: value : string - String representation of the new feature value +colvars: Defined command "bias_share", with help string: +colvars: Share bias information with other replicas (multiple-walker scheme) +colvars: Defined command "bias_state", with help string: +colvars: Print a string representation of the feature state of this bias +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: state : string - String representation of the bias features +colvars: +colvars: Defined command "bias_type", with help string: +colvars: Print the type of this bias object +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: type : string - Type of this bias object (e.g. metadynamics) +colvars: +colvars: Defined command "bias_update", with help string: +colvars: Recompute this bias and return its up-to-date energy +colvars: +colvars: Returns +colvars: ------- +colvars: +colvars: E : float - Energy value +colvars: +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: Called script run with 3 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: configfile +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: test.in +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "configfile" +colvars: Executing script function "cv_configfile" +colvars: Using simple-cast script::obj_to_str(): result = "test.in" +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: Looking for the keyword "logLevel" and its value. +colvars: Keyword "logLevel" not found. +colvars: Looking for the keyword "units" and its value. +colvars: Keyword "units" not found. +colvars: # units = "" [default] +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword value = "index.ndx". +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: Looking for the keyword "indexFile" and its value. +colvars: Keyword "indexFile" not found. +colvars: Looking for the keyword "smp" and its value. +colvars: Keyword "smp" not found. +colvars: # smp = on [default] +colvars: Looking for the keyword "analysis" and its value. +colvars: Keyword "analysis" not found. +colvars: Looking for the keyword "debugGradientsStepSize" and its value. +colvars: Keyword "debugGradientsStepSize" not found. +colvars: Looking for the keyword "monitorEigenvalueCrossing" and its value. +colvars: Keyword "monitorEigenvalueCrossing" not found. +colvars: Looking for the keyword "eigenvalueCrossingThreshold" and its value. +colvars: Keyword "eigenvalueCrossingThreshold" not found. +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword value = "1". +colvars: Looking for the keyword "colvarsTrajFrequency" and its value. +colvars: Keyword "colvarsTrajFrequency" not found. +colvars: # colvarsTrajFrequency = 1 +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword value = "10". +colvars: Looking for the keyword "colvarsRestartFrequency" and its value. +colvars: Keyword "colvarsRestartFrequency" not found. +colvars: # colvarsRestartFrequency = 10 +colvars: Looking for the keyword "scriptedColvarForces" and its value. +colvars: Keyword "scriptedColvarForces" not found. +colvars: # scriptedColvarForces = off [default] +colvars: Looking for the keyword "scriptingAfterBiases" and its value. +colvars: Keyword "scriptingAfterBiases" not found. +colvars: # scriptingAfterBiases = off [default] +colvars: Looking for the keyword "sourceTclFile" and its value. +colvars: Keyword "sourceTclFile" not found. +colvars: # sourceTclFile = "" [default] +colvars: Initializing the collective variables. +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: orientation { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "one" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: ". +colvars: Initializing a new "orientation" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "orientation" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "orientation" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "orientation" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = on +colvars: DEPS: atom group atoms enabling "center_to_reference" +colvars: DEPS: feature "center_to_reference" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword value = "yes". +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = on +colvars: DEPS: atom group atoms enabling "rotate_to_origin" +colvars: DEPS: feature "rotate_to_origin" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "RMSD_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "RMSD_atoms" +colvars: Adding atom 4 for collective variables calculation. +colvars: Adding atom 14 for collective variables calculation. +colvars: Adding atom 24 for collective variables calculation. +colvars: Adding atom 34 for collective variables calculation. +colvars: Adding atom 44 for collective variables calculation. +colvars: Adding atom 54 for collective variables calculation. +colvars: Adding atom 64 for collective variables calculation. +colvars: Adding atom 74 for collective variables calculation. +colvars: Adding atom 84 for collective variables calculation. +colvars: Adding atom 99 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "refPositionsGroup" and its value. +colvars: Keyword "refPositionsGroup" not found. +colvars: Looking for the keyword "fittingGroup" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Within atom group "atoms": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Adding atom 1 for collective variables calculation. +colvars: Adding atom 6 for collective variables calculation. +colvars: Adding atom 10 for collective variables calculation. +colvars: Adding atom 11 for collective variables calculation. +colvars: Adding atom 12 for collective variables calculation. +colvars: Adding atom 16 for collective variables calculation. +colvars: Adding atom 20 for collective variables calculation. +colvars: Adding atom 21 for collective variables calculation. +colvars: Adding atom 22 for collective variables calculation. +colvars: Adding atom 26 for collective variables calculation. +colvars: Adding atom 30 for collective variables calculation. +colvars: Adding atom 31 for collective variables calculation. +colvars: Adding atom 32 for collective variables calculation. +colvars: Adding atom 36 for collective variables calculation. +colvars: Adding atom 40 for collective variables calculation. +colvars: Adding atom 41 for collective variables calculation. +colvars: Adding atom 42 for collective variables calculation. +colvars: Adding atom 46 for collective variables calculation. +colvars: Adding atom 50 for collective variables calculation. +colvars: Adding atom 51 for collective variables calculation. +colvars: Adding atom 52 for collective variables calculation. +colvars: Adding atom 56 for collective variables calculation. +colvars: Adding atom 60 for collective variables calculation. +colvars: Adding atom 61 for collective variables calculation. +colvars: Adding atom 62 for collective variables calculation. +colvars: Adding atom 66 for collective variables calculation. +colvars: Adding atom 70 for collective variables calculation. +colvars: Adding atom 71 for collective variables calculation. +colvars: Adding atom 72 for collective variables calculation. +colvars: Adding atom 76 for collective variables calculation. +colvars: Adding atom 80 for collective variables calculation. +colvars: Adding atom 81 for collective variables calculation. +colvars: Adding atom 82 for collective variables calculation. +colvars: Adding atom 86 for collective variables calculation. +colvars: Adding atom 90 for collective variables calculation. +colvars: Adding atom 91 for collective variables calculation. +colvars: Adding atom 92 for collective variables calculation. +colvars: Adding atom 93 for collective variables calculation. +colvars: Adding atom 94 for collective variables calculation. +colvars: Adding atom 97 for collective variables calculation. +colvars: Adding atom 101 for collective variables calculation. +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group atoms enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units. +colvars: Warning: atom group "atoms" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group atoms enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group atoms enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group atoms enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group atoms enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: DEPS: unnamed cvc of type "orientation" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "orientation" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "rmsd_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "rmsd_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Centering the reference coordinates on the origin by subtracting the center of geometry at ( -0.9999 , -2 , -3 ); it is assumed that each atom is the closest periodic image to the center of geometry. +colvars: Looking for the keyword "closestToQuaternion" and its value. +colvars: Keyword "closestToQuaternion" not found. +colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default] +colvars: Configuration string for "orientation": " +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: ". +colvars: Done initializing a "orientation" component, named "orientation0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 4-dimensional unit quaternion with 4 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: orientation { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: Initializing the collective variables biases. +colvars: Looking for the keyword "abf" and its value. +colvars: Keyword "abf" not found. +colvars: Looking for the keyword "abmd" and its value. +colvars: Keyword "abmd" not found. +colvars: Looking for the keyword "ALB" and its value. +colvars: Keyword "ALB" not found. +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword value = " +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +colvars: forceConstant 10.0 +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "harmonic1" [default] +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "colvars" and its value. +colvars: Keyword "colvars" not found. +colvars: # colvars = { one } +colvars: Applying this bias to collective variable "one". +colvars: Looking for the keyword "stepZeroData" and its value. +colvars: Keyword "stepZeroData" not found. +colvars: # stepZeroData = off [default] +colvars: DEPS: disabling feature "step_zero_data" in bias harmonic1 +colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword "outputEnergy" not found. +colvars: # outputEnergy = off [default] +colvars: Looking for the keyword "outputFreq" and its value. +colvars: Keyword "outputFreq" not found. +colvars: # outputFreq = 10 [default] +colvars: Looking for the keyword "bypassExtendedLagrangian" and its value. +colvars: Keyword "bypassExtendedLagrangian" not found. +colvars: DEPS: disabling feature "bypass_extended_Lagrangian_coordinates" in bias harmonic1 +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "scaledBiasingForce" and its value. +colvars: Keyword "scaledBiasingForce" not found. +colvars: DEPS: disabling feature "scale_biasing_force" in bias harmonic1 +colvars: DEPS: bias harmonic1 enabling "active" +colvars: DEPS: colvar one testing "active" +colvars: DEPS: re-enabling children's active +colvars: DEPS: colvar one enabling "active" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in bias harmonic1 enabled, ref_count = 1. +colvars: Features of "bias harmonic1" (refcount) +colvars: - ON active +colvars: - awake +colvars: - step_zero_data +colvars: - apply_force +colvars: - bypass_extended_Lagrangian_coordinates +colvars: - obtain_total_force +colvars: - output_accumulated_work +colvars: - history_dependent +colvars: - time_dependent +colvars: - require_scalar_variables +colvars: - calculate_a_PMF +colvars: - calculate_TI_samples +colvars: - write_TI_samples_ +colvars: - write_TI_PMF +colvars: - scale_biasing_force +colvars: - Bias on extended-Lagrangian variables +colvars: * child 1 +colvars: Features of "colvar one" (refcount) +colvars: - ON active (1) +colvars: - awake +colvars: - gradient +colvars: - collect_gradient +colvars: - collect_atom_ids +colvars: - velocity_from_finite_differences +colvars: - total_force +colvars: - total_force_calculation +colvars: - subtract_applied_force_from_total_force +colvars: - Jacobian_derivative +colvars: - hide_Jacobian_force +colvars: - extended_Lagrangian +colvars: - external +colvars: - Langevin_dynamics +colvars: - output_energy +colvars: - ON output_value +colvars: - output_velocity +colvars: - ON output_applied_force +colvars: - output_total_force +colvars: - lower_boundary +colvars: - upper_boundary +colvars: - hard_lower_boundary +colvars: - hard_upper_boundary +colvars: - reflecting_lower_boundary +colvars: - reflecting_upper_boundary +colvars: - grid +colvars: - running_average +colvars: - correlation_function +colvars: - scripted +colvars: - custom_function +colvars: - periodic +colvars: - ON single_component +colvars: - scalar +colvars: - ON linear (1) +colvars: - ON homogeneous +colvars: - multiple_timestep +colvars: * child 1 +colvars: Features of "cvc "orientation0001" of type "orientation"" (refcount) +colvars: - ON active +colvars: - scalar +colvars: - periodic +colvars: - defined_width +colvars: - defined_lower_boundary +colvars: - defined_upper_boundary +colvars: - ON explicit_atom_groups +colvars: - gradient +colvars: - explicit_gradient +colvars: - inverse_gradient +colvars: - Jacobian_derivative +colvars: - total_force_from_one_group +colvars: - debug_gradient +colvars: - ON use_minimum-image_with_PBCs +colvars: - function_of_centers_of_mass +colvars: - scalable_calculation +colvars: - scalable_calculation_of_centers_of_mass +colvars: - collect_atom_ids +colvars: * child 1 +colvars: Features of "atom group atoms" (refcount) +colvars: - active +colvars: - ON center_to_reference +colvars: - center_to_origin +colvars: - ON rotate_to_origin +colvars: - ON fitting_group +colvars: - ON explicit_atom_gradient (1) +colvars: - ON fit_gradients +colvars: - atomic_forces +colvars: - scalable_group +colvars: - scalable_group_center_of_mass +colvars: - collect_atom_ids +colvars: DEPS: bias harmonic1 enabling "apply_force" +colvars: DEPS: colvar one enabling "gradient" +colvars: DEPS: cvc "orientation0001" of type "orientation" enabling "gradient" +colvars: DEPS: feature "gradient" in cvc "orientation0001" of type "orientation" enabled, ref_count = 1. +colvars: DEPS: feature "gradient" in colvar one enabled, ref_count = 1. +colvars: DEPS: feature "apply_force" in bias harmonic1 enabled, ref_count = 1. +colvars: Looking for the keyword "writeTISamples" and its value. +colvars: Keyword "writeTISamples" not found. +colvars: # writeTISamples = off [default] +colvars: DEPS: disabling feature "write_TI_samples_" in bias harmonic1 +colvars: Looking for the keyword "writeTIPMF" and its value. +colvars: Keyword "writeTIPMF" not found. +colvars: # writeTIPMF = off [default] +colvars: DEPS: disabling feature "write_TI_PMF" in bias harmonic1 +colvars: Initializing a new restraint bias. +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword value = "(0.9, 0.5, 0.5, 0.5)". +colvars: Looking for the keyword "centers" and its value. +colvars: Keyword "centers" not found. +colvars: # centers = { ( 0.720577 , 0.40032 , 0.40032 , 0.40032 ) } +colvars: colvarbias_restraint: parsing initial centers, i = 0. +colvars: colvarbias_restraint: parsing target centers. +colvars: Looking for the keyword "targetCenters" and its value. +colvars: Keyword "targetCenters" not found. +colvars: # targetCenters = { ( 0.720577 , 0.40032 , 0.40032 , 0.40032 ) } [default] +colvars: Looking for the keyword "outputCenters" and its value. +colvars: Keyword "outputCenters" not found. +colvars: # outputCenters = off [default] +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword value = "10.0". +colvars: Looking for the keyword "forceConstant" and its value. +colvars: Keyword "forceConstant" not found. +colvars: # forceConstant = 10 +colvars: Looking for the keyword "decoupling" and its value. +colvars: Keyword "decoupling" not found. +colvars: # decoupling = off [default] +colvars: Looking for the keyword "targetForceConstant" and its value. +colvars: Keyword "targetForceConstant" not found. +colvars: # targetForceConstant = -1 [default] +colvars: The force constant for colvar "one" will be rescaled to 40 according to the specified width (0.5). +colvars: Configuration string for "harmonic": " +colvars: +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +colvars: forceConstant 10.0 +colvars: ". +colvars: Looking for the keyword "harmonic" and its value. +colvars: Keyword "harmonic" not found. +colvars: Looking for the keyword "harmonicWalls" and its value. +colvars: Keyword "harmonicWalls" not found. +colvars: Looking for the keyword "histogram" and its value. +colvars: Keyword "histogram" not found. +colvars: Looking for the keyword "histogramRestraint" and its value. +colvars: Keyword "histogramRestraint" not found. +colvars: Looking for the keyword "linear" and its value. +colvars: Keyword "linear" not found. +colvars: Looking for the keyword "metadynamics" and its value. +colvars: Keyword "metadynamics" not found. +colvars: Looking for the keyword "reweightaMD" and its value. +colvars: Keyword "reweightaMD" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: Configuration string for "colvarmodule": " +colvars: colvarsTrajFrequency 1 +colvars: colvarsRestartFrequency 10 +colvars: indexFile index.ndx +colvars: colvar { +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: orientation { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: refPositionsFile rmsd_atoms_refpos.xyz +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +colvars: forceConstant 10.0 +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Harmonic colvar bias implementation: +colvars: - Moving frame of reference: +colvars: - Optimal rotation via flexible fitting: +colvars: - orientation colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Called script run with 3 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "load" +colvars: load +colvars: Using simple-cast script::obj_to_str(): result = "test.colvars.state" +colvars: test.colvars.state +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "load" +colvars: Executing script function "cv_load" +colvars: Using simple-cast script::obj_to_str(): result = "test.colvars.state" +colvars: ---------------------------------------------------------------------- +colvars: Loading state from text file "test.colvars.state". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Looking for the keyword "version" and its value. +colvars: Keyword value = "2024-06-04". +colvars: Looking for the keyword "version" and its value. +colvars: Keyword "version" not found. +colvars: Looking for the keyword "units" and its value. +colvars: Keyword "units" not found. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 0.99975884202595 , 0.01402736950034 , 0.011979408737928 , -0.011915723314925 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "one" from value: ( 0.999759 , 0.0140274 , 0.0119794 , -0.0119157 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "harmonic1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Looking for the keyword "step" and its value. +colvars: Keyword value = "20". +colvars: Looking for the keyword "step" and its value. +colvars: Keyword "step" not found. +colvars: Restarted harmonic bias "harmonic1" with step number 20. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (51 atoms). +colvars: updating group data (0 scalable groups, 0 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 20 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 20, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 20, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643353998e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780256e+00 , -3.16614240925533e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +colvars: Step 20, atom_groups_refcount[size = 0] = +colvars: Step 20, atom_groups_masses[size = 0] = +colvars: Step 20, atom_groups_charges[size = 0] = +colvars: Step 20, atom_groups_coms[size = 0] = +colvars: Step 20, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_ids[size = 0] = +colvars: Step 20, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 20 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.233415 , 17.2076 , 17.2731 , 18.0383 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.233415 , 17.2076 , 17.2731 , 18.0383 ) to colvar "one". +colvars: Adding total bias energy: 11.4987 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.233415 , 17.2076 , 17.2731 , 18.0383 ) +colvars: Applying force on main group : +colvars: ( -0.0913396 , 0.385649 , -0.483413 ) +colvars: ( 0.0153156 , 0.0380779 , -0.307957 ) +colvars: ( -0.0460269 , 0.10441 , 0.0968747 ) +colvars: ( -0.116844 , 0.311391 , 0.0704888 ) +colvars: ( -0.0219711 , 0.120302 , -0.220545 ) +colvars: ( 0.0842827 , -0.226789 , -0.0426138 ) +colvars: ( 0.0079403 , -0.105844 , 0.315844 ) +colvars: ( -0.0496811 , 0.0837394 , 0.214219 ) +colvars: ( 0.0809344 , -0.234762 , 0.0233814 ) +colvars: ( 0.137389 , -0.476175 , 0.333721 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246764 , -0.0994603 , 0.0960262 ) +colvars: ( 0.0200575 , -0.081987 , 0.0830467 ) +colvars: ( 0.0266365 , -0.0972981 , 0.0597107 ) +colvars: ( 0.0124661 , -0.055756 , 0.0725744 ) +colvars: ( 0.0126062 , -0.053636 , 0.0613964 ) +colvars: ( 0.00562478 , -0.0349973 , 0.0757171 ) +colvars: ( -0.00249657 , -0.00807268 , 0.0694821 ) +colvars: ( -0.00860292 , 0.00969555 , 0.0756074 ) +colvars: ( -0.00208776 , -0.00270415 , 0.0404328 ) +colvars: ( -0.0057739 , 0.00985182 , 0.0361383 ) +colvars: ( 0.00269105 , -0.0129509 , 0.019662 ) +colvars: ( 0.00400949 , -0.0105822 , -0.0087584 ) +colvars: ( 0.00895487 , -0.0219985 , -0.0267055 ) +colvars: ( 0.00866948 , -0.0237906 , -0.0149662 ) +colvars: ( 0.0065381 , -0.0135548 , -0.0304446 ) +colvars: ( 0.0150379 , -0.0467256 , -0.00212057 ) +colvars: ( 0.0197518 , -0.0608843 , -0.00491806 ) +colvars: ( 0.0277145 , -0.0886706 , 0.00725391 ) +colvars: ( 0.0143418 , -0.0470397 , 0.00879345 ) +colvars: ( 0.0142877 , -0.0442223 , -0.00276785 ) +colvars: ( 0.00939022 , -0.0371829 , 0.0336364 ) +colvars: ( 0.00325256 , -0.0212633 , 0.0482639 ) +colvars: ( -0.000698145 , -0.0153563 , 0.0766331 ) +colvars: ( -0.00372007 , 0.0041238 , 0.0329943 ) +colvars: ( -0.00578039 , 0.0111679 , 0.0304799 ) +colvars: ( -0.007295 , 0.0179744 , 0.0215214 ) +colvars: ( -0.0133397 , 0.0409385 , 0.00411059 ) +colvars: ( -0.0163845 , 0.0522691 , -0.00362466 ) +colvars: ( -0.00983258 , 0.0358406 , -0.0217096 ) +colvars: ( -0.0138792 , 0.0500947 , -0.0284772 ) +colvars: ( -0.00207475 , 0.0148609 , -0.0364524 ) +colvars: ( 0.00224746 , 0.00677197 , -0.0603866 ) +colvars: ( 0.0104709 , -0.0160556 , -0.0734437 ) +colvars: ( 0.00430769 , -0.00103735 , -0.0545293 ) +colvars: ( 0.00326495 , 0.00577162 , -0.0699681 ) +colvars: ( 0.00712437 , -0.0151328 , -0.0315917 ) +colvars: ( 0.00864399 , -0.021995 , -0.0224582 ) +colvars: ( 0.0132037 , -0.0418137 , 0.00157607 ) +colvars: ( 0.000563179 , 0.00144649 , -0.0140382 ) +colvars: ( 0.000498434 , 0.00299805 , -0.0199262 ) +colvars: ( -0.00648605 , 0.0203983 , -0.000154656 ) +colvars: ( -0.0146875 , 0.0443143 , 0.00784744 ) +colvars: ( -0.0205396 , 0.0578448 , 0.0289934 ) +colvars: ( -0.0189963 , 0.0632872 , -0.0159325 ) +colvars: ( -0.0227031 , 0.0752383 , -0.0173023 ) +colvars: ( -0.0170092 , 0.0724201 , -0.083061 ) +colvars: ( -0.0201473 , 0.0866037 , -0.101977 ) +colvars: ( -0.00870557 , 0.0464005 , -0.0832767 ) +colvars: ( -0.0186966 , 0.0667567 , -0.0351936 ) +colvars: ( -0.0224888 , 0.0840635 , -0.0587812 ) +colvars: ( -0.024606 , 0.0930351 , -0.0689323 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 20. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800976e-02 , 3.00052379356398e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500016e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827239e-02 , 1.91760996033175e-01 ), ( 6.62468727487264e-02 , -1.90448081926945e-01 , 3.12288455216891e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807518e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489682e-02 ), ( 1.24661136135099e-02 , -5.57559811144077e-02 , 7.25743621949595e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332648e-03 , -3.49973301865401e-02 , 7.57170861826678e-02 ), ( -8.60292310050451e-03 , 9.69554753037329e-03 , 7.56073713177290e-02 ), ( -2.08776469672693e-03 , -2.70415172113726e-03 , 4.04328246755312e-02 ), ( -5.77389521453808e-03 , 9.85182430390034e-03 , 3.61382862311481e-02 ), ( 2.69104804092522e-03 , -1.29509138532636e-02 , 1.96620498003799e-02 ), ( 8.95486758503643e-03 , -2.19984645975748e-02 , -2.67054922301013e-02 ), ( 8.66947656368631e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541540e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516852e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879235e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703576e-03 , -3.71828583991163e-02 , 3.36363523912982e-02 ), ( -6.98144545634527e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600069e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540628e-03 , 1.11679149109105e-02 , 3.04799282045032e-02 ), ( -7.29500058088394e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040445e-02 , -3.62466193947452e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308239e-02 ), ( -2.07475381329403e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505723e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288624e-03 , -1.03735135095862e-03 , -5.45293145217132e-02 ), ( 3.26495468493790e-03 , 5.77162454807394e-03 , -6.99680928834496e-02 ), ( 7.12436996401245e-03 , -1.51327555336419e-02 , -3.15916578475219e-02 ), ( 1.32036569636365e-02 , -4.18136663470712e-02 , 1.57606808925123e-03 ), ( 5.63178713376314e-04 , 1.44649438052724e-03 , -1.40381831264554e-02 ), ( 4.98434308056258e-04 , 2.99804808326457e-03 , -1.99261927958005e-02 ), ( -6.48604874882728e-03 , 2.03983070643249e-02 , -1.54655641113355e-04 ), ( -2.05396268108372e-02 , 5.78448103620468e-02 , 2.89933897342497e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654819e-03 , 4.64004872660570e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278477e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 20, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 21 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 21, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 21, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 21, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 21, atoms_positions[size = 51] = { ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 ), ( 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 ), ( 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 ), ( 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 ), ( 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 ), ( 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 ), ( -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 ), ( -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 ), ( -3.69409231538776e+00 , 5.15006269291782e-02 , 5.43762393708684e+00 ), ( -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ), ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 ), ( 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 ), ( 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 ), ( 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 ), ( 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 ), ( 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 ), ( 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 ), ( 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 ), ( 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 ), ( 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 ), ( 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 ), ( 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 ), ( 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 ), ( 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 ), ( 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 ), ( 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 ), ( 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 ), ( 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 ), ( 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 ), ( -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 ), ( 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 ), ( 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 ), ( -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 ), ( -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 ), ( -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 ), ( -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 ), ( -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 ), ( -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 ), ( -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 ), ( -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 ), ( -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 ), ( -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 ), ( -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 ), ( -2.39058560242180e+00 , -3.18609476113618e-01 , 6.16957497599152e+00 ), ( -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 ), ( -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 ), ( -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265566e+00 ), ( -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 ), ( -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 ), ( -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 ), ( -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ) } +colvars: Step 21, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_ids[size = 0] = +colvars: Step 21, atom_groups_refcount[size = 0] = +colvars: Step 21, atom_groups_masses[size = 0] = +colvars: Step 21, atom_groups_charges[size = 0] = +colvars: Step 21, atom_groups_coms[size = 0] = +colvars: Step 21, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 21, volmaps_ids[size = 0] = +colvars: Step 21, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 21 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.229007 , 17.2136 , 17.2687 , 18.0465 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.229007 , 17.2136 , 17.2687 , 18.0465 ) to colvar "one". +colvars: Adding total bias energy: 11.5031 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.229007 , 17.2136 , 17.2687 , 18.0465 ) +colvars: Applying force on main group : +colvars: ( -0.0911855 , 0.385681 , -0.483872 ) +colvars: ( 0.0153436 , 0.0380978 , -0.308144 ) +colvars: ( -0.0460885 , 0.104701 , 0.0967372 ) +colvars: ( -0.11681 , 0.311605 , 0.0702682 ) +colvars: ( -0.0218806 , 0.120191 , -0.220668 ) +colvars: ( 0.084245 , -0.226906 , -0.0424669 ) +colvars: ( 0.00784608 , -0.105726 , 0.316006 ) +colvars: ( -0.0496637 , 0.083727 , 0.214293 ) +colvars: ( 0.0809419 , -0.235048 , 0.0236444 ) +colvars: ( 0.137251 , -0.476324 , 0.334203 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246626 , -0.0994935 , 0.0961067 ) +colvars: ( 0.0200455 , -0.0820075 , 0.083102 ) +colvars: ( 0.0266219 , -0.0973406 , 0.0597488 ) +colvars: ( 0.0124578 , -0.0557595 , 0.0726154 ) +colvars: ( 0.0125984 , -0.0536459 , 0.061437 ) +colvars: ( 0.00561903 , -0.0349787 , 0.0757458 ) +colvars: ( -0.00249859 , -0.00803416 , 0.0694984 ) +colvars: ( -0.00860289 , 0.00975608 , 0.0756115 ) +colvars: ( -0.00208923 , -0.0026753 , 0.0404288 ) +colvars: ( -0.00577334 , 0.00988678 , 0.0361344 ) +colvars: ( 0.00268768 , -0.0129383 , 0.0196405 ) +colvars: ( 0.00400624 , -0.0105813 , -0.00879944 ) +colvars: ( 0.00894944 , -0.0220123 , -0.0267649 ) +colvars: ( 0.00866483 , -0.0238081 , -0.0149959 ) +colvars: ( 0.00653496 , -0.0135726 , -0.0304835 ) +colvars: ( 0.0150303 , -0.0467585 , -0.00212921 ) +colvars: ( 0.0197427 , -0.0609346 , -0.00491311 ) +colvars: ( 0.0277018 , -0.0887396 , 0.0072778 ) +colvars: ( 0.0143353 , -0.0470752 , 0.00881294 ) +colvars: ( 0.0142818 , -0.0442636 , -0.00274953 ) +colvars: ( 0.00938523 , -0.0371979 , 0.0336692 ) +colvars: ( 0.00325026 , -0.0212607 , 0.0483094 ) +colvars: ( -0.000699503 , -0.0153341 , 0.0766933 ) +colvars: ( -0.00371898 , 0.004141 , 0.033021 ) +colvars: ( -0.00577794 , 0.0111867 , 0.0305114 ) +colvars: ( -0.00729252 , 0.0180018 , 0.0215256 ) +colvars: ( -0.0133342 , 0.0409778 , 0.00409386 ) +colvars: ( -0.0163781 , 0.0523192 , -0.00366306 ) +colvars: ( -0.00982784 , 0.0358615 , -0.0217376 ) +colvars: ( -0.0138723 , 0.0501225 , -0.0285084 ) +colvars: ( -0.00207317 , 0.0148577 , -0.036486 ) +colvars: ( 0.00224792 , 0.00674885 , -0.0604294 ) +colvars: ( 0.0104678 , -0.0161024 , -0.0734936 ) +colvars: ( 0.00430768 , -0.00106911 , -0.0545527 ) +colvars: ( 0.00326601 , 0.0057363 , -0.0699986 ) +colvars: ( 0.00712281 , -0.0151675 , -0.0315898 ) +colvars: ( 0.00864209 , -0.0220358 , -0.0224358 ) +colvars: ( 0.0131993 , -0.041861 , 0.0016239 ) +colvars: ( 0.000564876 , 0.00142763 , -0.0140117 ) +colvars: ( 0.0005007 , 0.00297437 , -0.0198951 ) +colvars: ( -0.00648182 , 0.0204042 , -0.000130015 ) +colvars: ( -0.0146797 , 0.0443429 , 0.00787407 ) +colvars: ( -0.02053 , 0.0578974 , 0.0290236 ) +colvars: ( -0.0189861 , 0.0633211 , -0.0159292 ) +colvars: ( -0.0226909 , 0.075279 , -0.0172961 ) +colvars: ( -0.0169985 , 0.0724322 , -0.0831126 ) +colvars: ( -0.0201348 , 0.0866187 , -0.102045 ) +colvars: ( -0.00869839 , 0.0463889 , -0.0833164 ) +colvars: ( -0.0186865 , 0.0667879 , -0.0352142 ) +colvars: ( -0.0224765 , 0.0840991 , -0.0588253 ) +colvars: ( -0.0245932 , 0.0930782 , -0.068999 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 21. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 21. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atoms_new_colvar_forces = { ( -7.11399384318308e-02 , 3.03673714596804e-01 , -4.00770119886634e-01 ), ( 1.28450168410534e-02 , 3.00636017805382e-02 , -2.38645544534817e-01 ), ( -4.20822670353576e-02 , 9.41200209059076e-02 , 8.79377349508916e-02 ), ( -9.70668784584833e-02 , 2.50670455049784e-01 , 6.53550388999108e-02 ), ( -1.86302899611748e-02 , 9.89303159690965e-02 , -1.72358620278118e-01 ), ( 7.09108063101488e-02 , -1.85927916967423e-01 , -3.83730584164822e-02 ), ( 1.00940002734312e-02 , -9.89773108191159e-02 , 2.55576585814222e-01 ), ( -4.10215749964445e-02 , 6.16911466781240e-02 , 1.91856870875936e-01 ), ( 6.62622265583337e-02 , -1.90705006891368e-01 , 3.15184935556135e-02 ), ( 1.14774657066217e-01 , -3.92224428801080e-01 , 2.75377184594162e-01 ), ( 2.46625873851910e-02 , -9.94934972823231e-02 , 9.61066727823309e-02 ), ( 2.66219319601746e-02 , -9.73405519568489e-02 , 5.97487570195681e-02 ), ( 1.24577915943817e-02 , -5.57595264132078e-02 , 7.26154388026603e-02 ), ( 1.25983778171294e-02 , -5.36459257873875e-02 , 6.14369978247319e-02 ), ( 5.61903440744207e-03 , -3.49787311352311e-02 , 7.57458071852306e-02 ), ( -8.60288899774203e-03 , 9.75608155101247e-03 , 7.56115259176666e-02 ), ( -2.08923468684039e-03 , -2.67530457899125e-03 , 4.04287964932554e-02 ), ( -5.77333835969325e-03 , 9.88677812731997e-03 , 3.61343701273132e-02 ), ( 2.68767850620089e-03 , -1.29382633507289e-02 , 1.96404769055550e-02 ), ( 8.94944167110717e-03 , -2.20122654388583e-02 , -2.67648727689499e-02 ), ( 8.66483279553808e-03 , -2.38081467999426e-02 , -1.49959487368345e-02 ), ( 6.53495529803232e-03 , -1.35726331970709e-02 , -3.04835083292054e-02 ), ( 1.50303446132429e-02 , -4.67584847450611e-02 , -2.12920998279260e-03 ), ( 2.77018244289007e-02 , -8.87395931998711e-02 , 7.27779809261198e-03 ), ( 1.43352800222162e-02 , -4.70751609713203e-02 , 8.81293743885319e-03 ), ( 1.42817640632689e-02 , -4.42636422522604e-02 , -2.74952806030974e-03 ), ( 9.38522823558223e-03 , -3.71979422433983e-02 , 3.36691841968735e-02 ), ( -6.99503281119027e-04 , -1.53341150642310e-02 , 7.66932516135838e-02 ), ( -3.71897519690294e-03 , 4.14100412747780e-03 , 3.30209727953179e-02 ), ( -5.77794268053231e-03 , 1.11867179676655e-02 , 3.05114126724248e-02 ), ( -7.29252056176346e-03 , 1.80017851832736e-02 , 2.15255686424141e-02 ), ( -1.63781366214478e-02 , 5.23192063260294e-02 , -3.66306391685652e-03 ), ( -9.82784133106717e-03 , 3.58615231332486e-02 , -2.17375544901125e-02 ), ( -1.38723121061425e-02 , 5.01224906323065e-02 , -2.85083949342105e-02 ), ( -2.07316713877926e-03 , 1.48577122015172e-02 , -3.64859747436524e-02 ), ( 1.04678431390518e-02 , -1.61024070956970e-02 , -7.34936428665872e-02 ), ( 4.30768009091327e-03 , -1.06911031799013e-03 , -5.45527250787330e-02 ), ( 3.26600819838429e-03 , 5.73629579028582e-03 , -6.99986217017486e-02 ), ( 7.12281125111273e-03 , -1.51675396442752e-02 , -3.15898239456440e-02 ), ( 1.31993145017299e-02 , -4.18609641559936e-02 , 1.62390103359614e-03 ), ( 5.64876125100682e-04 , 1.42763294196247e-03 , -1.40117013302236e-02 ), ( 5.00700080314879e-04 , 2.97437334002883e-03 , -1.98951338246220e-02 ), ( -6.48182242008077e-03 , 2.04041914680348e-02 , -1.30015240503235e-04 ), ( -2.05300318216163e-02 , 5.78974351383434e-02 , 2.90236424552306e-02 ), ( -1.89861081468300e-02 , 6.33210745824364e-02 , -1.59292058110389e-02 ), ( -2.26909264798947e-02 , 7.52790104786259e-02 , -1.72961210714088e-02 ), ( -1.69985052661349e-02 , 7.24322155695334e-02 , -8.31125713403870e-02 ), ( -2.01347960952781e-02 , 8.66187159297856e-02 , -1.02044870208897e-01 ), ( -8.69838837231288e-03 , 4.63888524456888e-02 , -8.33163867525161e-02 ), ( -1.86864572755115e-02 , 6.67879237282488e-02 , -3.52141881593768e-02 ), ( -2.45931675112201e-02 , 9.30781934665973e-02 , -6.89990142792918e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 21, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 22 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 22, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 22, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 22, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 22, atoms_positions[size = 51] = { ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 ), ( 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 ), ( 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 ), ( 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 ), ( 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 ), ( 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 ), ( -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 ), ( -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 ), ( -3.68858938020335e+00 , 5.71185724985548e-02 , 5.44106122479227e+00 ), ( -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ), ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 ), ( 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 ), ( 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 ), ( 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 ), ( 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 ), ( 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 ), ( 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 ), ( 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 ), ( 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 ), ( 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 ), ( 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 ), ( 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 ), ( 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 ), ( 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 ), ( 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 ), ( 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 ), ( 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 ), ( 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 ), ( 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 ), ( -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 ), ( 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 ), ( 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 ), ( -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 ), ( -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 ), ( -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 ), ( -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 ), ( -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 ), ( -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 ), ( -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 ), ( -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 ), ( -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 ), ( -5.49635790878409e+00 , 8.04534957780670e-01 , 3.33283357586958e+00 ), ( -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 ), ( -2.39123986166853e+00 , -3.20694772050752e-01 , 6.16685140323704e+00 ), ( -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 ), ( -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 ), ( -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 ), ( -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 ), ( -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 ), ( -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 ), ( -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ) } +colvars: Step 22, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_ids[size = 0] = +colvars: Step 22, atom_groups_refcount[size = 0] = +colvars: Step 22, atom_groups_masses[size = 0] = +colvars: Step 22, atom_groups_charges[size = 0] = +colvars: Step 22, atom_groups_coms[size = 0] = +colvars: Step 22, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 22, volmaps_ids[size = 0] = +colvars: Step 22, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 22 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072403e-02 , -1.24385326679425e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072403e-02 , -1.24385326679425e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.225354 , 17.2172 , 17.2632 , 18.0562 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.225354 , 17.2172 , 17.2632 , 18.0562 ) to colvar "one". +colvars: Adding total bias energy: 11.5066 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.225354 , 17.2172 , 17.2632 , 18.0562 ) +colvars: Applying force on main group : +colvars: ( -0.0910113 , 0.385703 , -0.484216 ) +colvars: ( 0.0153711 , 0.0381921 , -0.308315 ) +colvars: ( -0.0461528 , 0.104985 , 0.0965041 ) +colvars: ( -0.116762 , 0.311723 , 0.0700421 ) +colvars: ( -0.02178 , 0.12007 , -0.220702 ) +colvars: ( 0.0841964 , -0.226946 , -0.0423329 ) +colvars: ( 0.00774329 , -0.10563 , 0.316076 ) +colvars: ( -0.0496388 , 0.08362 , 0.214385 ) +colvars: ( 0.0809445 , -0.235308 , 0.0239595 ) +colvars: ( 0.13709 , -0.47641 , 0.334599 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246401 , -0.0995232 , 0.0961757 ) +colvars: ( 0.0200273 , -0.0820288 , 0.0831474 ) +colvars: ( 0.0266028 , -0.0973827 , 0.0597805 ) +colvars: ( 0.0124446 , -0.0557661 , 0.0726477 ) +colvars: ( 0.012586 , -0.0536567 , 0.0614702 ) +colvars: ( 0.00560942 , -0.0349676 , 0.0757651 ) +colvars: ( -0.00250328 , -0.00800591 , 0.0695056 ) +colvars: ( -0.00860459 , 0.00980138 , 0.0756056 ) +colvars: ( -0.00209115 , -0.00265596 , 0.0404196 ) +colvars: ( -0.00577312 , 0.00991277 , 0.0361256 ) +colvars: ( 0.00268564 , -0.0129349 , 0.0196168 ) +colvars: ( 0.00400645 , -0.0105887 , -0.00883872 ) +colvars: ( 0.00894926 , -0.022035 , -0.0268197 ) +colvars: ( 0.0086628 , -0.0238294 , -0.0150229 ) +colvars: ( 0.0065355 , -0.0135936 , -0.0305178 ) +colvars: ( 0.0150234 , -0.0467916 , -0.00213659 ) +colvars: ( 0.0197332 , -0.0609807 , -0.00490641 ) +colvars: ( 0.0276867 , -0.0888011 , 0.00730219 ) +colvars: ( 0.0143268 , -0.047106 , 0.00883198 ) +colvars: ( 0.0142743 , -0.0442983 , -0.00273019 ) +colvars: ( 0.00937682 , -0.0372105 , 0.033698 ) +colvars: ( 0.00324329 , -0.0212559 , 0.0483485 ) +colvars: ( -0.000707235 , -0.0153122 , 0.0767431 ) +colvars: ( -0.00372065 , 0.00415795 , 0.033043 ) +colvars: ( -0.00577859 , 0.0112068 , 0.0305384 ) +colvars: ( -0.00729073 , 0.0180251 , 0.0215266 ) +colvars: ( -0.0133273 , 0.0410107 , 0.00407599 ) +colvars: ( -0.0163684 , 0.0523585 , -0.0037016 ) +colvars: ( -0.00982031 , 0.0358787 , -0.0217631 ) +colvars: ( -0.0138622 , 0.0501466 , -0.0285365 ) +colvars: ( -0.00206812 , 0.0148532 , -0.0365148 ) +colvars: ( 0.00225301 , 0.00672729 , -0.0604641 ) +colvars: ( 0.0104701 , -0.016146 , -0.0735332 ) +colvars: ( 0.00431059 , -0.00109532 , -0.0545688 ) +colvars: ( 0.00327088 , 0.00570774 , -0.0700198 ) +colvars: ( 0.00712165 , -0.0151947 , -0.0315836 ) +colvars: ( 0.00863873 , -0.0220654 , -0.0224102 ) +colvars: ( 0.0131909 , -0.041895 , 0.00167184 ) +colvars: ( 0.000564699 , 0.0014185 , -0.0139837 ) +colvars: ( 0.000500837 , 0.0029628 , -0.0198619 ) +colvars: ( -0.00647952 , 0.0204158 , -0.000106 ) +colvars: ( -0.014674 , 0.0443753 , 0.00789855 ) +colvars: ( -0.0205232 , 0.0579499 , 0.0290487 ) +colvars: ( -0.0189757 , 0.0633572 , -0.0159251 ) +colvars: ( -0.0226787 , 0.0753225 , -0.0172892 ) +colvars: ( -0.0169819 , 0.0724463 , -0.0831542 ) +colvars: ( -0.0201146 , 0.0866349 , -0.102101 ) +colvars: ( -0.00868627 , 0.0463831 , -0.0833457 ) +colvars: ( -0.0186738 , 0.0668192 , -0.0352312 ) +colvars: ( -0.0224593 , 0.0841331 , -0.0588629 ) +colvars: ( -0.0245733 , 0.0931158 , -0.0690579 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 22. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 22. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atoms_new_colvar_forces = { ( -7.09839898778747e-02 , 3.03674063527600e-01 , -4.01068648115013e-01 ), ( 1.28677757638464e-02 , 3.01861976186923e-02 , -2.38809348309205e-01 ), ( -4.21463674859759e-02 , 9.43967829010162e-02 , 8.76653672693452e-02 ), ( -9.70292248461032e-02 , 2.50742449438027e-01 , 6.51357190727136e-02 ), ( -1.85367305319293e-02 , 9.88144120703526e-02 , -1.72353345630284e-01 ), ( 7.08691073007723e-02 , -1.85935576884942e-01 , -3.82568663452623e-02 ), ( 9.99629817433116e-03 , -9.89023847961850e-02 , 2.55611691378657e-01 ), ( -4.10000890482683e-02 , 6.15546231916447e-02 , 1.91974826016933e-01 ), ( 6.62704276258434e-02 , -1.90932830035544e-01 , 3.18580020079369e-02 ), ( 1.14630750534917e-01 , -3.92276752466799e-01 , 2.75736313750346e-01 ), ( 2.46401348458040e-02 , -9.95231922332751e-02 , 9.61756954601184e-02 ), ( 2.66028495666390e-02 , -9.73827270437477e-02 , 5.97805459313106e-02 ), ( 1.24445918472298e-02 , -5.57660823956985e-02 , 7.26477167044874e-02 ), ( 1.25859818519026e-02 , -5.36566849366138e-02 , 6.14702165822492e-02 ), ( 5.60941666979545e-03 , -3.49676476401050e-02 , 7.57650503878028e-02 ), ( -8.60459043493706e-03 , 9.80137872000443e-03 , 7.56056143106273e-02 ), ( -2.09115201198730e-03 , -2.65595958743230e-03 , 4.04196007616606e-02 ), ( -5.77311642017532e-03 , 9.91276524030936e-03 , 3.61256035860894e-02 ), ( 2.68564234612565e-03 , -1.29349024719858e-02 , 1.96168163142232e-02 ), ( 8.94925864416897e-03 , -2.20349749067143e-02 , -2.68197445771303e-02 ), ( 8.66280149401488e-03 , -2.38293607684870e-02 , -1.50229481919147e-02 ), ( 6.53549642564501e-03 , -1.35935670322821e-02 , -3.05178145405584e-02 ), ( 1.50234208571289e-02 , -4.67916092089625e-02 , -2.13659458865095e-03 ), ( 2.76867464932990e-02 , -8.88011036791123e-02 , 7.30219119954996e-03 ), ( 1.43268298943310e-02 , -4.71060008041501e-02 , 8.83198042196747e-03 ), ( 1.42742680267957e-02 , -4.42983138073421e-02 , -2.73019093925149e-03 ), ( 9.37682487194692e-03 , -3.72105131562461e-02 , 3.36980129801635e-02 ), ( -7.07234928782565e-04 , -1.53121732294138e-02 , 7.67431469878513e-02 ), ( -3.72064813930677e-03 , 4.15794740228741e-03 , 3.30429937869084e-02 ), ( -5.77858592433563e-03 , 1.12068079161518e-02 , 3.05383925376817e-02 ), ( -7.29072954144173e-03 , 1.80250877442325e-02 , 2.15265738678377e-02 ), ( -1.63683809363363e-02 , 5.23584897961350e-02 , -3.70159935424319e-03 ), ( -9.82031195706153e-03 , 3.58787450236741e-02 , -2.17630809852664e-02 ), ( -1.38621548995544e-02 , 5.01466473790395e-02 , -2.85364839098933e-02 ), ( -2.06812117531274e-03 , 1.48531610368221e-02 , -3.65147867450562e-02 ), ( 1.04701424349007e-02 , -1.61460182290016e-02 , -7.35332062826640e-02 ), ( 4.31059150250448e-03 , -1.09531770379866e-03 , -5.45687792002220e-02 ), ( 3.27087578265066e-03 , 5.70773713995558e-03 , -7.00198422700666e-02 ), ( 7.12165311897483e-03 , -1.51946850165027e-02 , -3.15836085513172e-02 ), ( 1.31909349580735e-02 , -4.18949630055120e-02 , 1.67183642219017e-03 ), ( 5.64699401698968e-04 , 1.41850132131441e-03 , -1.39836938535898e-02 ), ( 5.00837441823005e-04 , 2.96280077134345e-03 , -1.98618599951808e-02 ), ( -6.47952298250982e-03 , 2.04157888640752e-02 , -1.05999642867334e-04 ), ( -2.05232494824155e-02 , 5.79498507924875e-02 , 2.90487025878773e-02 ), ( -1.89756580163051e-02 , 6.33571912361918e-02 , -1.59250752374072e-02 ), ( -2.26786531673934e-02 , 7.53225391086036e-02 , -1.72891702626615e-02 ), ( -1.69818816397503e-02 , 7.24462974551710e-02 , -8.31541664771447e-02 ), ( -2.01145633252694e-02 , 8.66349326960424e-02 , -1.02100887695110e-01 ), ( -8.68627168332184e-03 , 4.63831438807106e-02 , -8.33457370302980e-02 ), ( -1.86738034866789e-02 , 6.68192172662539e-02 , -3.52312486009207e-02 ), ( -2.45733259321368e-02 , 9.31157815017149e-02 , -6.90578829953477e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 22, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 23 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 23, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 23, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 23, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 23, atoms_positions[size = 51] = { ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 ), ( 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 ), ( 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 ), ( 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 ), ( 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 ), ( 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 ), ( -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 ), ( -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 ), ( -3.68392264400780e+00 , 6.26974696338532e-02 , 5.44598583975169e+00 ), ( -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ), ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 ), ( 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 ), ( 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 ), ( 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 ), ( 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 ), ( 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 ), ( 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 ), ( 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 ), ( 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 ), ( 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 ), ( 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 ), ( 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 ), ( 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 ), ( 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 ), ( 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 ), ( 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 ), ( 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 ), ( 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 ), ( 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 ), ( -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 ), ( 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 ), ( 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 ), ( -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 ), ( -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 ), ( -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 ), ( -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 ), ( -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 ), ( -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 ), ( -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 ), ( -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 ), ( -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 ), ( -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 ), ( -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 ), ( -2.39140303069694e+00 , -3.22564541882358e-01 , 6.16358793333041e+00 ), ( -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 ), ( -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 ), ( -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 ), ( -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 ), ( -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 ), ( -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 ), ( -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ) } +colvars: Step 23, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_ids[size = 0] = +colvars: Step 23, atom_groups_refcount[size = 0] = +colvars: Step 23, atom_groups_masses[size = 0] = +colvars: Step 23, atom_groups_charges[size = 0] = +colvars: Step 23, atom_groups_coms[size = 0] = +colvars: Step 23, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 23, volmaps_ids[size = 0] = +colvars: Step 23, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 23 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.222545 , 17.2183 , 17.2568 , 18.067 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.222545 , 17.2183 , 17.2568 , 18.067 ) to colvar "one". +colvars: Adding total bias energy: 11.5092 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.222545 , 17.2183 , 17.2568 , 18.067 ) +colvars: Applying force on main group : +colvars: ( -0.0908201 , 0.385714 , -0.484446 ) +colvars: ( 0.0154006 , 0.0383537 , -0.308467 ) +colvars: ( -0.04622 , 0.105257 , 0.0961868 ) +colvars: ( -0.116708 , 0.311748 , 0.0698151 ) +colvars: ( -0.0216711 , 0.119944 , -0.220652 ) +colvars: ( 0.0841413 , -0.226914 , -0.042213 ) +colvars: ( 0.00763224 , -0.105555 , 0.316058 ) +colvars: ( -0.0496109 , 0.0834271 , 0.214493 ) +colvars: ( 0.080944 , -0.235538 , 0.0243166 ) +colvars: ( 0.136912 , -0.476435 , 0.334909 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0246097 , -0.0995472 , 0.0962325 ) +colvars: ( 0.0200032 , -0.0820492 , 0.0831831 ) +colvars: ( 0.0265801 , -0.0974225 , 0.059807 ) +colvars: ( 0.0124268 , -0.0557747 , 0.0726714 ) +colvars: ( 0.0125693 , -0.0536673 , 0.061496 ) +colvars: ( 0.00559595 , -0.0349639 , 0.0757754 ) +colvars: ( -0.00251088 , -0.00798848 , 0.0695044 ) +colvars: ( -0.00860853 , 0.00983018 , 0.0755907 ) +colvars: ( -0.00209371 , -0.00264664 , 0.0404063 ) +colvars: ( -0.00577354 , 0.00992899 , 0.0361127 ) +colvars: ( 0.00268496 , -0.012941 , 0.019593 ) +colvars: ( 0.00401022 , -0.0106045 , -0.00887379 ) +colvars: ( 0.00895464 , -0.0220662 , -0.0268667 ) +colvars: ( 0.0086637 , -0.0238537 , -0.0150453 ) +colvars: ( 0.00653999 , -0.0136172 , -0.0305456 ) +colvars: ( 0.0150176 , -0.0468238 , -0.00214131 ) +colvars: ( 0.0197239 , -0.0610207 , -0.00489711 ) +colvars: ( 0.0276703 , -0.0888527 , 0.00732764 ) +colvars: ( 0.014317 , -0.0471309 , 0.00885057 ) +colvars: ( 0.0142657 , -0.0443249 , -0.00271007 ) +colvars: ( 0.00936529 , -0.0372197 , 0.0337223 ) +colvars: ( 0.0032317 , -0.0212485 , 0.0483801 ) +colvars: ( -0.000721504 , -0.0152905 , 0.0767811 ) +colvars: ( -0.00372528 , 0.00417433 , 0.0330594 ) +colvars: ( -0.00578257 , 0.0112278 , 0.0305594 ) +colvars: ( -0.00728994 , 0.0180436 , 0.0215242 ) +colvars: ( -0.0133196 , 0.0410358 , 0.0040572 ) +colvars: ( -0.0163559 , 0.0523853 , -0.00373915 ) +colvars: ( -0.00981031 , 0.0358913 , -0.0217857 ) +colvars: ( -0.0138492 , 0.050166 , -0.0285613 ) +colvars: ( -0.00205963 , 0.014847 , -0.0365379 ) +colvars: ( 0.00226292 , 0.00670751 , -0.0604894 ) +colvars: ( 0.0104783 , -0.0161855 , -0.0735606 ) +colvars: ( 0.0043167 , -0.00111542 , -0.0545772 ) +colvars: ( 0.00327983 , 0.00568646 , -0.0700315 ) +colvars: ( 0.00712124 , -0.0152133 , -0.0315734 ) +colvars: ( 0.0086343 , -0.0220826 , -0.0223829 ) +colvars: ( 0.013179 , -0.0419141 , 0.00171796 ) +colvars: ( 0.000562737 , 0.00141951 , -0.013956 ) +colvars: ( 0.000498954 , 0.00296383 , -0.0198286 ) +colvars: ( -0.00647935 , 0.0204328 , -8.44655e-05 ) +colvars: ( -0.0146711 , 0.0444104 , 0.00791859 ) +colvars: ( -0.0205201 , 0.0580004 , 0.0290662 ) +colvars: ( -0.0189656 , 0.0633941 , -0.0159219 ) +colvars: ( -0.0226671 , 0.0753672 , -0.0172837 ) +colvars: ( -0.0169597 , 0.0724611 , -0.0831859 ) +colvars: ( -0.0200871 , 0.0866508 , -0.102144 ) +colvars: ( -0.00866934 , 0.0463829 , -0.083365 ) +colvars: ( -0.0186592 , 0.066849 , -0.0352456 ) +colvars: ( -0.0224379 , 0.0841636 , -0.0588943 ) +colvars: ( -0.0245472 , 0.0931456 , -0.0691082 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 23. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 23. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atoms_new_colvar_forces = { ( -7.08168814937949e-02 , 3.03664452472894e-01 , -4.01263051701776e-01 ), ( 1.28897282159372e-02 , 3.03652461049389e-02 , -2.38962907009597e-01 ), ( -4.22098006472154e-02 , 9.46520341380242e-02 , 8.73129850632795e-02 ), ( -9.69836961545911e-02 , 2.50727137133401e-01 , 6.49179539830782e-02 ), ( -1.84393958034465e-02 , 9.86949573833386e-02 , -1.72272185409953e-01 ), ( 7.08217601806615e-02 , -1.85878656231815e-01 , -3.81557494152707e-02 ), ( 9.89515936319978e-03 , -9.88477114743486e-02 , 2.55569065601461e-01 ), ( -4.09765694460841e-02 , 6.13444540424882e-02 , 1.92109707586131e-01 ), ( 6.62729002147716e-02 , -1.91127572587650e-01 , 3.22352067094027e-02 ), ( 1.14473689844909e-01 , -3.92271189494705e-01 , 2.76014821802483e-01 ), ( 2.46097378880774e-02 , -9.95472081172002e-02 , 9.62325265867954e-02 ), ( 2.65800661415529e-02 , -9.74224674168166e-02 , 5.98069715723355e-02 ), ( 1.24268052531842e-02 , -5.57747491404972e-02 , 7.26713718002168e-02 ), ( 1.25692908517025e-02 , -5.36672888971867e-02 , 6.14959932071031e-02 ), ( 5.59595460705682e-03 , -3.49639005947200e-02 , 7.57753564150521e-02 ), ( -8.60853344063534e-03 , 9.83018051445575e-03 , 7.55907061791914e-02 ), ( -2.09370541899715e-03 , -2.64663879970087e-03 , 4.04063346386015e-02 ), ( -5.77353689472604e-03 , 9.92898655659039e-03 , 3.61127372741654e-02 ), ( 2.68495661875314e-03 , -1.29409636173138e-02 , 1.95929838330084e-02 ), ( 8.95464052648906e-03 , -2.20662135786371e-02 , -2.68667237089156e-02 ), ( 8.66369655000775e-03 , -2.38537280061534e-02 , -1.50453182585348e-02 ), ( 6.53999219691608e-03 , -1.36172289972066e-02 , -3.05455555170775e-02 ), ( 1.50176159970732e-02 , -4.68238119845228e-02 , -2.14130988594835e-03 ), ( 2.76703023716468e-02 , -8.88526582257362e-02 , 7.32763641562823e-03 ), ( 1.43169910754908e-02 , -4.71308548263177e-02 , 8.85056798528954e-03 ), ( 1.42657338744872e-02 , -4.43248724469114e-02 , -2.71006633727085e-03 ), ( 9.36528608667769e-03 , -3.72197152508182e-02 , 3.37223434971326e-02 ), ( -7.21504131285960e-04 , -1.52905347062471e-02 , 7.67810657807839e-02 ), ( -3.72528256564419e-03 , 4.17432885242505e-03 , 3.30593835387063e-02 ), ( -5.78257112165283e-03 , 1.12277726999349e-02 , 3.05594093243620e-02 ), ( -7.28993979152106e-03 , 1.80436025627073e-02 , 2.15242117056218e-02 ), ( -1.63558940654101e-02 , 5.23852695599543e-02 , -3.73915389641007e-03 ), ( -9.81031471026572e-03 , 3.58912916496682e-02 , -2.17857056962443e-02 ), ( -1.38492253162238e-02 , 5.01659601331753e-02 , -2.85612669585644e-02 ), ( -2.05962857627378e-03 , 1.48469797126605e-02 , -3.65378567014535e-02 ), ( 1.04783374291988e-02 , -1.61854613034706e-02 , -7.35606117525264e-02 ), ( 4.31670110681340e-03 , -1.11542447291207e-03 , -5.45771754964243e-02 ), ( 3.27982880802864e-03 , 5.68645760642483e-03 , -7.00314830313078e-02 ), ( 7.12123613458920e-03 , -1.52133335041448e-02 , -3.15734429379239e-02 ), ( 1.31790365397598e-02 , -4.19140962086650e-02 , 1.71795596493783e-03 ), ( 5.62737062255140e-04 , 1.41951133743413e-03 , -1.39560183089449e-02 ), ( 4.98953902161183e-04 , 2.96382598398074e-03 , -1.98286454303239e-02 ), ( -6.47935157763106e-03 , 2.04327935768267e-02 , -8.44654753454989e-05 ), ( -2.05200517884924e-02 , 5.80004004527264e-02 , 2.90662088850963e-02 ), ( -1.89655968658880e-02 , 6.33940538126061e-02 , -1.59219105336479e-02 ), ( -2.26670637582555e-02 , 7.53671927014898e-02 , -1.72837048580549e-02 ), ( -1.69597158830491e-02 , 7.24610787203845e-02 , -8.31859201087093e-02 ), ( -2.00871048374524e-02 , 8.66507978883153e-02 , -1.02144384436106e-01 ), ( -8.66934268082574e-03 , 4.63828731985594e-02 , -8.33650111463787e-02 ), ( -1.86591940279770e-02 , 6.68490223519342e-02 , -3.52456476594086e-02 ), ( -2.45472378440625e-02 , 9.31456187363587e-02 , -6.91082336777466e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 23, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 24 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 24, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 24, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 24, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 24, atoms_positions[size = 51] = { ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 ), ( 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 ), ( 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 ), ( 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 ), ( 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 ), ( 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 ), ( -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 ), ( -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 ), ( -3.68005965040029e+00 , 6.78907924099859e-02 , 5.45204135176785e+00 ), ( -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ), ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 ), ( 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 ), ( 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 ), ( 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 ), ( 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 ), ( 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 ), ( 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 ), ( 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 ), ( 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 ), ( 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 ), ( 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 ), ( 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 ), ( 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 ), ( 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 ), ( 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 ), ( 3.75816832389218e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 ), ( 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 ), ( 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 ), ( 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 ), ( -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 ), ( 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 ), ( 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 ), ( -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 ), ( -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 ), ( -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 ), ( -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 ), ( -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 ), ( -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 ), ( -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 ), ( -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 ), ( -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 ), ( -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 ), ( -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 ), ( -2.39101064153575e+00 , -3.23953535315118e-01 , 6.15985323826371e+00 ), ( -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 ), ( -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 ), ( -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 ), ( -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 ), ( -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 ), ( -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 ), ( -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ) } +colvars: Step 24, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_ids[size = 0] = +colvars: Step 24, atom_groups_refcount[size = 0] = +colvars: Step 24, atom_groups_masses[size = 0] = +colvars: Step 24, atom_groups_charges[size = 0] = +colvars: Step 24, atom_groups_coms[size = 0] = +colvars: Step 24, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 24, volmaps_ids[size = 0] = +colvars: Step 24, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 24 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756126e-02 , 1.27630697470619e-02 , -1.31113665114322e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756126e-02 , 1.27630697470619e-02 , -1.31113665114322e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.220603 , 17.2172 , 17.25 , 18.0784 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.220603 , 17.2172 , 17.25 , 18.0784 ) to colvar "one". +colvars: Adding total bias energy: 11.5109 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.220603 , 17.2172 , 17.25 , 18.0784 ) +colvars: Applying force on main group : +colvars: ( -0.0906157 , 0.385714 , -0.48457 ) +colvars: ( 0.0154351 , 0.0385714 , -0.308599 ) +colvars: ( -0.0462903 , 0.105509 , 0.0958017 ) +colvars: ( -0.116651 , 0.311688 , 0.0695912 ) +colvars: ( -0.0215556 , 0.119814 , -0.22053 ) +colvars: ( 0.0840843 , -0.226818 , -0.0421076 ) +colvars: ( 0.00751337 , -0.105502 , 0.315964 ) +colvars: ( -0.0495844 , 0.0831619 , 0.21461 ) +colvars: ( 0.0809424 , -0.235734 , 0.0247035 ) +colvars: ( 0.136722 , -0.476403 , 0.335136 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0245726 , -0.0995639 , 0.0962772 ) +colvars: ( 0.0199744 , -0.0820673 , 0.0832098 ) +colvars: ( 0.0265546 , -0.0974578 , 0.0598293 ) +colvars: ( 0.012405 , -0.0557846 , 0.0726871 ) +colvars: ( 0.0125489 , -0.0536768 , 0.0615148 ) +colvars: ( 0.0055789 , -0.0349669 , 0.0757779 ) +colvars: ( -0.00252151 , -0.00798183 , 0.0694959 ) +colvars: ( -0.00861512 , 0.00984223 , 0.0755685 ) +colvars: ( -0.00209706 , -0.00264726 , 0.0403904 ) +colvars: ( -0.00577489 , 0.00993524 , 0.0360968 ) +colvars: ( 0.00268555 , -0.012956 , 0.0195709 ) +colvars: ( 0.00401748 , -0.0106281 , -0.00890248 ) +colvars: ( 0.00896558 , -0.0221051 , -0.0269029 ) +colvars: ( 0.00866766 , -0.0238805 , -0.0150614 ) +colvars: ( 0.00654848 , -0.013643 , -0.0305652 ) +colvars: ( 0.0150134 , -0.046854 , -0.00214212 ) +colvars: ( 0.0197155 , -0.0610534 , -0.00488454 ) +colvars: ( 0.0276536 , -0.0888924 , 0.00735459 ) +colvars: ( 0.0143064 , -0.0471488 , 0.00886871 ) +colvars: ( 0.0142568 , -0.0443424 , -0.00268945 ) +colvars: ( 0.00935109 , -0.0372249 , 0.033742 ) +colvars: ( 0.00321579 , -0.0212386 , 0.0484033 ) +colvars: ( -0.000742094 , -0.0152693 , 0.0768061 ) +colvars: ( -0.0037329 , 0.00418987 , 0.0330695 ) +colvars: ( -0.00578996 , 0.0112491 , 0.0305734 ) +colvars: ( -0.00729042 , 0.0180569 , 0.0215185 ) +colvars: ( -0.0133115 , 0.0410522 , 0.0040378 ) +colvars: ( -0.0163415 , 0.0523986 , -0.00377466 ) +colvars: ( -0.00979833 , 0.0358985 , -0.0218051 ) +colvars: ( -0.0138342 , 0.0501795 , -0.0285827 ) +colvars: ( -0.00204791 , 0.0148391 , -0.0365546 ) +colvars: ( 0.00227757 , 0.00668967 , -0.0605048 ) +colvars: ( 0.0104926 , -0.01622 , -0.0735749 ) +colvars: ( 0.00432611 , -0.00112924 , -0.0545781 ) +colvars: ( 0.00329291 , 0.00567254 , -0.0700339 ) +colvars: ( 0.00712187 , -0.0152232 , -0.03156 ) +colvars: ( 0.00862927 , -0.0220872 , -0.0223552 ) +colvars: ( 0.0131644 , -0.0419177 , 0.00176044 ) +colvars: ( 0.000559194 , 0.00143045 , -0.0139305 ) +colvars: ( 0.00049529 , 0.00297717 , -0.0197978 ) +colvars: ( -0.00648138 , 0.0204546 , -6.71144e-05 ) +colvars: ( -0.0146711 , 0.044447 , 0.00793218 ) +colvars: ( -0.020521 , 0.0580476 , 0.0290743 ) +colvars: ( -0.0189565 , 0.0634302 , -0.0159214 ) +colvars: ( -0.0226569 , 0.0754112 , -0.0172819 ) +colvars: ( -0.0169328 , 0.0724753 , -0.0832086 ) +colvars: ( -0.0200534 , 0.0866648 , -0.102176 ) +colvars: ( -0.00864801 , 0.0463873 , -0.0833752 ) +colvars: ( -0.0186433 , 0.066876 , -0.0352584 ) +colvars: ( -0.0224131 , 0.084189 , -0.0589202 ) +colvars: ( -0.0245161 , 0.0931661 , -0.06915 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 24. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 24. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atoms_new_colvar_forces = { ( -7.06413071230504e-02 , 3.03646376177113e-01 , -4.01360271764822e-01 ), ( 1.29135699454975e-02 , 3.05895907970704e-02 , -2.39103012853669e-01 ), ( -4.22727893177429e-02 , 9.48806486655140e-02 , 8.68992202535935e-02 ), ( -9.69353995896309e-02 , 2.50634381681781e-01 , 6.47066866422256e-02 ), ( -1.83397783484814e-02 , 9.85756742630302e-02 , -1.72126442430389e-01 ), ( 7.07728219511373e-02 , -1.85765887475988e-01 , -3.80697774318616e-02 ), ( 9.79094825409427e-03 , -9.88124633185437e-02 , 2.55459166370171e-01 ), ( -4.09551734426115e-02 , 6.10746932338372e-02 , 1.92255054495674e-01 ), ( 6.62713061540428e-02 , -1.91287333337422e-01 , 3.26356316955038e-02 ), ( 1.14308608904662e-01 , -3.92214125425127e-01 , 2.76215371150626e-01 ), ( 2.45725920232996e-02 , -9.95638546443988e-02 , 9.62771812753496e-02 ), ( 2.65546467078898e-02 , -9.74578351767044e-02 , 5.98293143046422e-02 ), ( 1.24049987615565e-02 , -5.57845532030435e-02 , 7.26871465513840e-02 ), ( 1.25488921727912e-02 , -5.36768078818011e-02 , 6.15147514345488e-02 ), ( 5.57889542473557e-03 , -3.49669023596321e-02 , 7.57778613512468e-02 ), ( -8.61511790943967e-03 , 9.84223056552993e-03 , 7.55684853155769e-02 ), ( -2.09705915825774e-03 , -2.64725710136185e-03 , 4.03903767810113e-02 ), ( -5.77488506394999e-03 , 9.93524199145594e-03 , 3.60968052014861e-02 ), ( 2.68555107386696e-03 , -1.29560057336035e-02 , 1.95709202788530e-02 ), ( 8.96558132413488e-03 , -2.21050689084729e-02 , -2.69029309665138e-02 ), ( 8.66766398808846e-03 , -2.38805017462989e-02 , -1.50614381521955e-02 ), ( 6.54848333975446e-03 , -1.36430392009208e-02 , -3.05652148041553e-02 ), ( 1.50134061346635e-02 , -4.68539729865604e-02 , -2.14212405348145e-03 ), ( 2.76535944622938e-02 , -8.88924111111195e-02 , 7.35459163320720e-03 ), ( 1.43063692881742e-02 , -4.71487915327259e-02 , 8.86870857810112e-03 ), ( 1.42567773634181e-02 , -4.43424413314667e-02 , -2.68944979509767e-03 ), ( 9.35108517815967e-03 , -3.72249354736576e-02 , 3.37419691915580e-02 ), ( -7.42093767884166e-04 , -1.52692752516169e-02 , 7.68061137984732e-02 ), ( -3.73289987962753e-03 , 4.18986710243482e-03 , 3.30695277218438e-02 ), ( -5.78995808229406e-03 , 1.12491380714132e-02 , 3.05733940861192e-02 ), ( -7.29041607322479e-03 , 1.80568906634082e-02 , 2.15185307159462e-02 ), ( -1.63414772366860e-02 , 5.23986257872083e-02 , -3.77465749262824e-03 ), ( -9.79832819666986e-03 , 3.58985454533797e-02 , -2.18051356045120e-02 ), ( -1.38341517731008e-02 , 5.01795107928477e-02 , -2.85827133571873e-02 ), ( -2.04790718474561e-03 , 1.48390673158269e-02 , -3.65546209718068e-02 ), ( 1.04926098671793e-02 , -1.62200191491437e-02 , -7.35748831065827e-02 ), ( 4.32610626512208e-03 , -1.12923962307860e-03 , -5.45781232758893e-02 ), ( 3.29291015644961e-03 , 5.67254452054351e-03 , -7.00339106044753e-02 ), ( 7.12187254119930e-03 , -1.52231512708809e-02 , -3.15600301609801e-02 ), ( 1.31643703507535e-02 , -4.19177461698118e-02 , 1.76043709113814e-03 ), ( 5.59193791564009e-04 , 1.43044841286948e-03 , -1.39305256747123e-02 ), ( 4.95289569726371e-04 , 2.97716813520240e-03 , -1.97977791071556e-02 ), ( -6.48138398004286e-03 , 2.04545723962382e-02 , -6.71144154469031e-05 ), ( -2.05210193315769e-02 , 5.80475595770238e-02 , 2.90742990478969e-02 ), ( -1.89565419805277e-02 , 6.34302052679531e-02 , -1.59214405626776e-02 ), ( -2.26568850688841e-02 , 7.54112231480941e-02 , -1.72818588807229e-02 ), ( -1.69327803850088e-02 , 7.24752813498580e-02 , -8.32085865792704e-02 ), ( -2.00533740645507e-02 , 8.66648297314470e-02 , -1.02175971750392e-01 ), ( -8.64801089252043e-03 , 4.63872708123076e-02 , -8.33751561955853e-02 ), ( -1.86433498800995e-02 , 6.68759703471642e-02 , -3.52584071050765e-02 ), ( -2.45160572636472e-02 , 9.31660631528296e-02 , -6.91499678688890e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 24, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 25 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 25, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 25, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 25, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 25, atoms_positions[size = 51] = { ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 ), ( 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 ), ( 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 ), ( 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 ), ( 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 ), ( 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 ), ( -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 ), ( -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 ), ( -3.67692497938528e+00 , 7.24104000983907e-02 , 5.45877291154939e+00 ), ( -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ), ( 8.30509683048428e+00 , 4.19726743115743e-02 , -7.29420068900795e-01 ), ( 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 ), ( 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 ), ( 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 ), ( 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 ), ( 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 ), ( 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 ), ( 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 ), ( 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 ), ( 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 ), ( 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 ), ( 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 ), ( 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 ), ( 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 ), ( 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 ), ( 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 ), ( 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 ), ( 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 ), ( 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 ), ( -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 ), ( 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 ), ( 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 ), ( -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 ), ( -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 ), ( -5.34273816020180e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 ), ( -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 ), ( -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 ), ( -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 ), ( -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 ), ( -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 ), ( -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 ), ( -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 ), ( -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 ), ( -2.39001770562881e+00 , -3.24650284743471e-01 , 6.15574359469104e+00 ), ( -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 ), ( -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 ), ( -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 ), ( -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 ), ( -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 ), ( -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 ), ( -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ) } +colvars: Step 25, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_ids[size = 0] = +colvars: Step 25, atom_groups_refcount[size = 0] = +colvars: Step 25, atom_groups_masses[size = 0] = +colvars: Step 25, atom_groups_charges[size = 0] = +colvars: Step 25, atom_groups_coms[size = 0] = +colvars: Step 25, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 25, volmaps_ids[size = 0] = +colvars: Step 25, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 25 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876203e-02 , 1.29777530480417e-02 , -1.34613291247888e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876203e-02 , 1.29777530480417e-02 , -1.34613291247888e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.219486 , 17.214 , 17.2433 , 18.0897 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.219486 , 17.214 , 17.2433 , 18.0897 ) to colvar "one". +colvars: Adding total bias energy: 11.5117 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.219486 , 17.214 , 17.2433 , 18.0897 ) +colvars: Applying force on main group : +colvars: ( -0.0904019 , 0.385704 , -0.484602 ) +colvars: ( 0.0154771 , 0.0388302 , -0.308709 ) +colvars: ( -0.0463635 , 0.105738 , 0.0953698 ) +colvars: ( -0.116598 , 0.311557 , 0.0693746 ) +colvars: ( -0.0214355 , 0.119686 , -0.22035 ) +colvars: ( 0.08403 , -0.22667 , -0.0420161 ) +colvars: ( 0.00738743 , -0.105468 , 0.315807 ) +colvars: ( -0.0495642 , 0.0828429 , 0.214732 ) +colvars: ( 0.0809418 , -0.235896 , 0.0251056 ) +colvars: ( 0.136527 , -0.476323 , 0.335288 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0245304 , -0.0995721 , 0.0963105 ) +colvars: ( 0.0199419 , -0.0820818 , 0.0832288 ) +colvars: ( 0.0265278 , -0.0974873 , 0.0598491 ) +colvars: ( 0.01238 , -0.0557945 , 0.0726963 ) +colvars: ( 0.0125256 , -0.0536844 , 0.0615274 ) +colvars: ( 0.00555872 , -0.0349756 , 0.0757743 ) +colvars: ( -0.00253506 , -0.00798516 , 0.0694818 ) +colvars: ( -0.00862459 , 0.00983841 , 0.0755412 ) +colvars: ( -0.00210133 , -0.00265706 , 0.0403733 ) +colvars: ( -0.0057774 , 0.00993201 , 0.0360791 ) +colvars: ( 0.00268726 , -0.012979 , 0.0195524 ) +colvars: ( 0.00402788 , -0.0106585 , -0.00892308 ) +colvars: ( 0.0089817 , -0.0221501 , -0.0269263 ) +colvars: ( 0.00867465 , -0.0239088 , -0.0150701 ) +colvars: ( 0.00656075 , -0.0136703 , -0.0305759 ) +colvars: ( 0.0150112 , -0.0468811 , -0.0021381 ) +colvars: ( 0.0197088 , -0.0610779 , -0.00486829 ) +colvars: ( 0.0276378 , -0.0889194 , 0.00738337 ) +colvars: ( 0.0142956 , -0.0471594 , 0.00888643 ) +colvars: ( 0.0142481 , -0.0443508 , -0.00266869 ) +colvars: ( 0.00933488 , -0.0372259 , 0.033757 ) +colvars: ( 0.00319616 , -0.021226 , 0.0484179 ) +colvars: ( -0.000768369 , -0.0152485 , 0.0768183 ) +colvars: ( -0.00374333 , 0.00420433 , 0.0330733 ) +colvars: ( -0.00580058 , 0.0112704 , 0.0305798 ) +colvars: ( -0.00729235 , 0.0180649 , 0.0215098 ) +colvars: ( -0.0133036 , 0.0410599 , 0.00401815 ) +colvars: ( -0.0163261 , 0.0523986 , -0.00380717 ) +colvars: ( -0.00978497 , 0.0359003 , -0.0218213 ) +colvars: ( -0.0138177 , 0.0501868 , -0.028601 ) +colvars: ( -0.00203339 , 0.0148295 , -0.036565 ) +colvars: ( 0.00229658 , 0.00667381 , -0.0605105 ) +colvars: ( 0.0105127 , -0.0162493 , -0.073576 ) +colvars: ( 0.00433869 , -0.00113699 , -0.0545724 ) +colvars: ( 0.0033099 , 0.00566561 , -0.0700282 ) +colvars: ( 0.00712382 , -0.0152244 , -0.0315443 ) +colvars: ( 0.00862418 , -0.0220796 , -0.0223286 ) +colvars: ( 0.0131479 , -0.0419064 , 0.0017977 ) +colvars: ( 0.000554388 , 0.00145041 , -0.0139089 ) +colvars: ( 0.000490214 , 0.0030017 , -0.0197714 ) +colvars: ( -0.00648555 , 0.0204802 , -5.53434e-05 ) +colvars: ( -0.0146744 , 0.0444839 , 0.00793778 ) +colvars: ( -0.0205265 , 0.0580901 , 0.0290718 ) +colvars: ( -0.0189491 , 0.0634643 , -0.0159252 ) +colvars: ( -0.0226488 , 0.075453 , -0.0172855 ) +colvars: ( -0.0169022 , 0.0724877 , -0.0832236 ) +colvars: ( -0.0200147 , 0.0866758 , -0.102197 ) +colvars: ( -0.00862298 , 0.0463953 , -0.0833778 ) +colvars: ( -0.0186271 , 0.0668989 , -0.0352706 ) +colvars: ( -0.0223862 , 0.0842082 , -0.0589417 ) +colvars: ( -0.0244813 , 0.0931762 , -0.0691836 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 25. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 25. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atoms_new_colvar_forces = { ( -7.04600443638350e-02 , 3.03621747458522e-01 , -4.01373682028472e-01 ), ( 1.29420506857990e-02 , 3.08450317799853e-02 , -2.39227221868054e-01 ), ( -4.23355906274468e-02 , 9.50793160624865e-02 , 8.64467007486022e-02 ), ( -9.68894888293516e-02 , 2.50479150966912e-01 , 6.45062578129430e-02 ), ( -1.82393338200141e-02 , 9.84602010337278e-02 , -1.71931658781829e-01 ), ( 7.07263478012350e-02 , -1.85609672059077e-01 , -3.79978980760433e-02 ), ( 9.68400550810395e-03 , -9.87944561148575e-02 , 2.55296819269015e-01 ), ( -4.09399777928876e-02 , 6.07633323078663e-02 , 1.92403592972447e-01 ), ( 6.62674376926360e-02 , -1.91412527838396e-01 , 3.30433713295305e-02 ), ( 1.14140727837322e-01 , -3.92115243802243e-01 , 2.76345875640083e-01 ), ( 2.45303535326015e-02 , -9.95720517518532e-02 , 9.63105281691544e-02 ), ( 2.65278426707223e-02 , -9.74872741208498e-02 , 5.98491237917058e-02 ), ( 1.23800078595191e-02 , -5.57945041990638e-02 , 7.26963423269235e-02 ), ( 1.25256232080886e-02 , -5.36844439703333e-02 , 6.15274102361732e-02 ), ( 5.55871954717282e-03 , -3.49756477161695e-02 , 7.57742636763354e-02 ), ( -8.62458743879690e-03 , 9.83841075458373e-03 , 7.55411808127872e-02 ), ( -2.10133459875127e-03 , -2.65705587569525e-03 , 4.03733078812120e-02 ), ( -5.77739600858532e-03 , 9.93201495398463e-03 , 3.60790735980493e-02 ), ( 2.68726300921175e-03 , -1.29789758403624e-02 , 1.95524417854630e-02 ), ( 8.98170264457940e-03 , -2.21500931356781e-02 , -2.69262680091887e-02 ), ( 8.67464681814413e-03 , -2.39087709180257e-02 , -1.50701443449332e-02 ), ( 6.56074612158967e-03 , -1.36702589485719e-02 , -3.05758637567222e-02 ), ( 1.50111682037605e-02 , -4.68811361083810e-02 , -2.13810104570518e-03 ), ( 2.76377619824812e-02 , -8.89193875459930e-02 , 7.38337491409857e-03 ), ( 1.42956328492329e-02 , -4.71593898002372e-02 , 8.88642649261350e-03 ), ( 1.42480549426660e-02 , -4.43507918114741e-02 , -2.66868998230111e-03 ), ( 9.33487811850630e-03 , -3.72258735497682e-02 , 3.37570127503085e-02 ), ( -7.68369119173232e-04 , -1.52484894295288e-02 , 7.68183269009158e-02 ), ( -3.74332602967186e-03 , 4.20432533857040e-03 , 3.30732666132640e-02 ), ( -5.80058286933925e-03 , 1.12703919993963e-02 , 3.05797902919004e-02 ), ( -7.29234650113121e-03 , 1.80648763741093e-02 , 2.15098284387671e-02 ), ( -1.63260769480337e-02 , 5.23986038060843e-02 , -3.80716611556856e-03 ), ( -9.78497055648197e-03 , 3.59002867510908e-02 , -2.18212967568863e-02 ), ( -1.38177140907220e-02 , 5.01868220910697e-02 , -2.86010179352413e-02 ), ( -2.03339071916587e-03 , 1.48294691070948e-02 , -3.65649683550387e-02 ), ( 1.05127471287825e-02 , -1.62492873763924e-02 , -7.35760043117993e-02 ), ( 4.33869355337769e-03 , -1.13698546157586e-03 , -5.45723770452254e-02 ), ( 3.30989754432303e-03 , 5.66560766362083e-03 , -7.00281639538081e-02 ), ( 7.12381538260144e-03 , -1.52244133889981e-02 , -3.15443190776360e-02 ), ( 1.31478892206905e-02 , -4.19063984404894e-02 , 1.79769937088844e-03 ), ( 5.54388479922571e-04 , 1.45041162698806e-03 , -1.39089157145296e-02 ), ( 4.90214236116323e-04 , 3.00169662343023e-03 , -1.97713882165925e-02 ), ( -6.48554752146523e-03 , 2.04801681670990e-02 , -5.53434019236648e-05 ), ( -2.05264663856608e-02 , 5.80900538781189e-02 , 2.90718102447906e-02 ), ( -1.89490503248258e-02 , 6.34642763608981e-02 , -1.59251829016669e-02 ), ( -2.26487578411400e-02 , 7.54529703717811e-02 , -1.72854851773508e-02 ), ( -1.69021686492795e-02 , 7.24877434965380e-02 , -8.32235613476903e-02 ), ( -2.00147470785519e-02 , 8.66757664758654e-02 , -1.02197102389267e-01 ), ( -8.62297525244981e-03 , 4.63953041892996e-02 , -8.33777736619381e-02 ), ( -1.86270819201374e-02 , 6.68989416403371e-02 , -3.52706493301954e-02 ), ( -2.44812912922878e-02 , 9.31762079245552e-02 , -6.91835824823653e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 25, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 26 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 26, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 26, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 26, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 26, atoms_positions[size = 51] = { ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 ), ( 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 ), ( 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 ), ( 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 ), ( 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 ), ( 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 ), ( -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 ), ( -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 ), ( -3.67441092319199e+00 , 7.60406688373052e-02 , 5.46566218960245e+00 ), ( -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ), ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 ), ( 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459835e-01 ), ( 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 ), ( 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 ), ( 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 ), ( 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 ), ( 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 ), ( 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 ), ( 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 ), ( 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 ), ( 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 ), ( 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 ), ( 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 ), ( 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 ), ( 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 ), ( 3.83975554418138e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 ), ( 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 ), ( 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 ), ( 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 ), ( -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 ), ( 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 ), ( 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 ), ( -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 ), ( -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 ), ( -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 ), ( -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 ), ( -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 ), ( -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 ), ( -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 ), ( -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 ), ( -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 ), ( -5.48945484200930e+00 , 7.77049854240672e-01 , 3.33760630244013e+00 ), ( -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 ), ( -2.38839256737456e+00 , -3.24502407433314e-01 , 6.15138672061077e+00 ), ( -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 ), ( -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983191e+00 ), ( -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 ), ( -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 ), ( -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 ), ( -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 ), ( -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ) } +colvars: Step 26, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_ids[size = 0] = +colvars: Step 26, atom_groups_refcount[size = 0] = +colvars: Step 26, atom_groups_masses[size = 0] = +colvars: Step 26, atom_groups_charges[size = 0] = +colvars: Step 26, atom_groups_coms[size = 0] = +colvars: Step 26, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 26, volmaps_ids[size = 0] = +colvars: Step 26, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 26 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.219086 , 17.2092 , 17.237 , 18.1004 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.219086 , 17.2092 , 17.237 , 18.1004 ) to colvar "one". +colvars: Adding total bias energy: 11.5118 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.219086 , 17.2092 , 17.237 , 18.1004 ) +colvars: Applying force on main group : +colvars: ( -0.0901832 , 0.385685 , -0.484565 ) +colvars: ( 0.015529 , 0.0391122 , -0.308798 ) +colvars: ( -0.0464393 , 0.105941 , 0.094915 ) +colvars: ( -0.116555 , 0.311375 , 0.0691684 ) +colvars: ( -0.0213131 , 0.119563 , -0.220131 ) +colvars: ( 0.0839829 , -0.226485 , -0.0419367 ) +colvars: ( 0.00725547 , -0.10545 , 0.315608 ) +colvars: ( -0.0495543 , 0.0824925 , 0.214853 ) +colvars: ( 0.0809439 , -0.236026 , 0.0255078 ) +colvars: ( 0.136334 , -0.476208 , 0.335379 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.024485 , -0.0995714 , 0.0963342 ) +colvars: ( 0.0199072 , -0.0820919 , 0.0832421 ) +colvars: ( 0.026501 , -0.0975097 , 0.0598681 ) +colvars: ( 0.0123529 , -0.0558037 , 0.0727007 ) +colvars: ( 0.0125005 , -0.0536896 , 0.0615353 ) +colvars: ( 0.00553612 , -0.0349888 , 0.0757667 ) +colvars: ( -0.00255128 , -0.00799704 , 0.0694642 ) +colvars: ( -0.00863701 , 0.0098207 , 0.0755114 ) +colvars: ( -0.0021066 , -0.00267464 , 0.0403568 ) +colvars: ( -0.00578124 , 0.00992045 , 0.036061 ) +colvars: ( 0.00268985 , -0.0130083 , 0.0195391 ) +colvars: ( 0.00404088 , -0.0106941 , -0.00893444 ) +colvars: ( 0.00900227 , -0.0221994 , -0.0269356 ) +colvars: ( 0.00868438 , -0.0239375 , -0.0150708 ) +colvars: ( 0.0065763 , -0.013698 , -0.0305772 ) +colvars: ( 0.0150112 , -0.0469046 , -0.00212867 ) +colvars: ( 0.0197042 , -0.0610941 , -0.00484826 ) +colvars: ( 0.0276239 , -0.0889335 , 0.00741414 ) +colvars: ( 0.0142855 , -0.0471628 , 0.00890376 ) +colvars: ( 0.0142402 , -0.0443504 , -0.00264817 ) +colvars: ( 0.00931746 , -0.0372226 , 0.0337679 ) +colvars: ( 0.00317367 , -0.021211 , 0.0484244 ) +colvars: ( -0.000799309 , -0.0152283 , 0.0768187 ) +colvars: ( -0.0037562 , 0.00421753 , 0.0330709 ) +colvars: ( -0.00581406 , 0.011291 , 0.0305786 ) +colvars: ( -0.00729583 , 0.0180679 , 0.0214986 ) +colvars: ( -0.0132967 , 0.0410592 , 0.00399866 ) +colvars: ( -0.0163107 , 0.0523862 , -0.00383593 ) +colvars: ( -0.00977096 , 0.0358967 , -0.0218343 ) +colvars: ( -0.0138008 , 0.0501879 , -0.0286166 ) +colvars: ( -0.00201671 , 0.0148184 , -0.0365692 ) +colvars: ( 0.00231924 , 0.00665986 , -0.0605074 ) +colvars: ( 0.0105381 , -0.0162732 , -0.0735649 ) +colvars: ( 0.00435414 , -0.00113929 , -0.0545612 ) +colvars: ( 0.00333031 , 0.0056648 , -0.0700159 ) +colvars: ( 0.00712724 , -0.015218 , -0.0315274 ) +colvars: ( 0.00861958 , -0.0220612 , -0.0223047 ) +colvars: ( 0.0131307 , -0.0418816 , 0.00182851 ) +colvars: ( 0.000548735 , 0.00147786 , -0.0138926 ) +colvars: ( 0.000484205 , 0.00303549 , -0.0197513 ) +colvars: ( -0.00649162 , 0.0205084 , -5.01451e-05 ) +colvars: ( -0.0146808 , 0.0445198 , 0.00793446 ) +colvars: ( -0.0205364 , 0.0581269 , 0.0290584 ) +colvars: ( -0.0189436 , 0.0634951 , -0.0159343 ) +colvars: ( -0.0226432 , 0.075491 , -0.017296 ) +colvars: ( -0.0168692 , 0.0724975 , -0.0832328 ) +colvars: ( -0.0199729 , 0.0866826 , -0.10221 ) +colvars: ( -0.00859519 , 0.0464057 , -0.083375 ) +colvars: ( -0.0186112 , 0.0669171 , -0.0352835 ) +colvars: ( -0.0223586 , 0.0842205 , -0.0589601 ) +colvars: ( -0.0244447 , 0.0931759 , -0.0692101 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 26. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 26. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atoms_new_colvar_forces = { ( -7.02759487121494e-02 , 3.03592903297381e-01 , -4.01322595058309e-01 ), ( 1.29777444484042e-02 , 3.11151912550363e-02 , -2.39334291295019e-01 ), ( -4.23984621351553e-02 , 9.52467395890064e-02 , 8.59805584984231e-02 ), ( -9.68508821319136e-02 , 2.50280691303569e-01 , 6.43201527675708e-02 ), ( -1.81394624860404e-02 , 9.83519274233092e-02 , -1.71706731179628e-01 ), ( 7.06861711244203e-02 , -1.85425392448265e-01 , -3.79380381448007e-02 ), ( 9.57471239129270e-03 , -9.87903314213212e-02 , 2.55100464157634e-01 ), ( -4.09347057274910e-02 , 6.04312464191056e-02 , 1.92547924833260e-01 ), ( 6.62631407386995e-02 , -1.91505902765397e-01 , 3.34422263795947e-02 ), ( 1.13975178390395e-01 , -3.91987080180140e-01 , 2.76419259062611e-01 ), ( 2.44850402010076e-02 , -9.95713974916157e-02 , 9.63342285937298e-02 ), ( 2.65010124687372e-02 , -9.75097049166922e-02 , 5.98681079194398e-02 ), ( 1.23528879662618e-02 , -5.58036520957835e-02 , 7.27007292311104e-02 ), ( 1.25005219271507e-02 , -5.36895785441518e-02 , 6.15353199422810e-02 ), ( 5.53611543404053e-03 , -3.49887682495593e-02 , 7.57667076403760e-02 ), ( -8.63700702604890e-03 , 9.82070089447021e-03 , 7.55114158522256e-02 ), ( -2.10659992708688e-03 , -2.67464113977565e-03 , 4.03568019629268e-02 ), ( -5.78123646494342e-03 , 9.92045066551187e-03 , 3.60609548302388e-02 ), ( 2.68984652041441e-03 , -1.30082658740007e-02 , 1.95391125026404e-02 ), ( 9.00226957835603e-03 , -2.21993856296152e-02 , -2.69355681840099e-02 ), ( 8.68438349470703e-03 , -2.39375135194768e-02 , -1.50708149285185e-02 ), ( 6.57630028948228e-03 , -1.36980342382398e-02 , -3.05772297762471e-02 ), ( 1.50111517137013e-02 , -4.69045680137091e-02 , -2.12866950333661e-03 ), ( 2.76239043083305e-02 , -8.89335499142471e-02 , 7.41413710602707e-03 ), ( 1.42854688295579e-02 , -4.71627686040402e-02 , 8.90375783411516e-03 ), ( 1.42402199047629e-02 , -4.43503631938378e-02 , -2.64816707932507e-03 ), ( 9.31746414113780e-03 , -3.72225620105006e-02 , 3.37679174239998e-02 ), ( -7.99308945475918e-04 , -1.52282832043496e-02 , 7.68186726665386e-02 ), ( -3.75619772566365e-03 , 4.21752672172109e-03 , 3.30709088042420e-02 ), ( -5.81406267630258e-03 , 1.12910157251468e-02 , 3.05785957286102e-02 ), ( -7.29582728360610e-03 , 1.80678557646107e-02 , 2.14986330080878e-02 ), ( -1.63107240894460e-02 , 5.23862202541373e-02 , -3.83592521087051e-03 ), ( -9.77096127551217e-03 , 3.58967100268294e-02 , -2.18343387088895e-02 ), ( -1.38007947251377e-02 , 5.01878895330269e-02 , -2.86165861734204e-02 ), ( -2.01670542625995e-03 , 1.48183742544679e-02 , -3.65692494411242e-02 ), ( 1.05381451549543e-02 , -1.62732033203028e-02 , -7.35649265176478e-02 ), ( 4.35413995448841e-03 , -1.13928950370447e-03 , -5.45611871279412e-02 ), ( 3.33031042288602e-03 , 5.66479643420804e-03 , -7.00158856017225e-02 ), ( 7.12723901359867e-03 , -1.52179938195833e-02 , -3.15274406212481e-02 ), ( 1.31306877600108e-02 , -4.18816228571182e-02 , 1.82851326350305e-03 ), ( 5.48734989236870e-04 , 1.47786091102192e-03 , -1.38926182011663e-02 ), ( 4.84204918059284e-04 , 3.03549036454787e-03 , -1.97512896041410e-02 ), ( -6.49162233900808e-03 , 2.05083540598446e-02 , -5.01450680240982e-05 ), ( -2.05364121159091e-02 , 5.81269386311858e-02 , 2.90583664730193e-02 ), ( -1.89435793931410e-02 , 6.34950680085711e-02 , -1.59343341897455e-02 ), ( -2.26431912621753e-02 , 7.54909620571149e-02 , -1.72960215224767e-02 ), ( -1.68692306396098e-02 , 7.24974880057940e-02 , -8.32327838657938e-02 ), ( -1.99729416336030e-02 , 8.66826413894369e-02 , -1.02209969773827e-01 ), ( -8.59518558707567e-03 , 4.64057351138899e-02 , -8.33750094210587e-02 ), ( -1.86112386515313e-02 , 6.69171340762310e-02 , -3.52835165863774e-02 ), ( -2.44447077038081e-02 , 9.31759407762520e-02 , -6.92101336975360e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 26, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 27 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 27, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 27, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 27, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 27, atoms_positions[size = 51] = { ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 ), ( 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 ), ( 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 ), ( 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 ), ( 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 ), ( 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 ), ( -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 ), ( -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 ), ( -3.67239157969653e+00 , 7.86444043011857e-02 , 5.47216870495720e+00 ), ( -4.81061183134772e+00 , 3.26599326572317e+00 , 7.26118632650396e+00 ), ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 ), ( 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 ), ( 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 ), ( 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321918e-01 ), ( 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 ), ( 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 ), ( 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 ), ( 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 ), ( 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 ), ( 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 ), ( 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 ), ( 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 ), ( 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 ), ( 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 ), ( 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 ), ( 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 ), ( 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 ), ( 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 ), ( 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 ), ( -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 ), ( 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 ), ( 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 ), ( -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 ), ( -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 ), ( -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 ), ( -7.19299148831412e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 ), ( -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 ), ( -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 ), ( -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 ), ( -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 ), ( -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 ), ( -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 ), ( -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 ), ( -2.38611115771939e+00 , -3.23414419937704e-01 , 6.14694225305598e+00 ), ( -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 ), ( -5.36207760113481e+00 , 5.84976302002794e-01 , 7.21438869028155e+00 ), ( -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 ), ( -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 ), ( -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 ), ( -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 ), ( -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ) } +colvars: Step 27, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_ids[size = 0] = +colvars: Step 27, atom_groups_refcount[size = 0] = +colvars: Step 27, atom_groups_masses[size = 0] = +colvars: Step 27, atom_groups_charges[size = 0] = +colvars: Step 27, atom_groups_coms[size = 0] = +colvars: Step 27, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 27, volmaps_ids[size = 0] = +colvars: Step 27, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 27 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.219239 , 17.2034 , 17.2317 , 18.1101 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.219239 , 17.2034 , 17.2317 , 18.1101 ) to colvar "one". +colvars: Adding total bias energy: 11.5114 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.219239 , 17.2034 , 17.2317 , 18.1101 ) +colvars: Applying force on main group : +colvars: ( -0.089964 , 0.38566 , -0.484483 ) +colvars: ( 0.0155926 , 0.0393983 , -0.30887 ) +colvars: ( -0.0465174 , 0.106117 , 0.0944626 ) +colvars: ( -0.116526 , 0.311163 , 0.0689755 ) +colvars: ( -0.0211908 , 0.119448 , -0.219896 ) +colvars: ( 0.0839469 , -0.226281 , -0.0418671 ) +colvars: ( 0.00711886 , -0.105444 , 0.315388 ) +colvars: ( -0.0495585 , 0.0821349 , 0.214966 ) +colvars: ( 0.0809504 , -0.236126 , 0.0258951 ) +colvars: ( 0.136148 , -0.47607 , 0.33543 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0244389 , -0.0995621 , 0.0963506 ) +colvars: ( 0.0198721 , -0.082097 , 0.0832519 ) +colvars: ( 0.0264755 , -0.0975246 , 0.059888 ) +colvars: ( 0.0123248 , -0.0558111 , 0.0727024 ) +colvars: ( 0.0124747 , -0.0536918 , 0.0615401 ) +colvars: ( 0.00551192 , -0.0350046 , 0.0757576 ) +colvars: ( -0.00256972 , -0.00801547 , 0.0694455 ) +colvars: ( -0.00865227 , 0.00979196 , 0.075482 ) +colvars: ( -0.00211287 , -0.00269813 , 0.0403425 ) +colvars: ( -0.0057865 , 0.00990223 , 0.0360439 ) +colvars: ( 0.002693 , -0.0130419 , 0.0195322 ) +colvars: ( 0.00405574 , -0.0107329 , -0.00893605 ) +colvars: ( 0.00902627 , -0.0222508 , -0.0269306 ) +colvars: ( 0.00869644 , -0.0239657 , -0.0150634 ) +colvars: ( 0.00659446 , -0.0137255 , -0.0305697 ) +colvars: ( 0.0150135 , -0.0469238 , -0.00211363 ) +colvars: ( 0.0197023 , -0.0611022 , -0.0048246 ) +colvars: ( 0.027613 , -0.0889357 , 0.00744686 ) +colvars: ( 0.0142765 , -0.0471595 , 0.00892075 ) +colvars: ( 0.0142339 , -0.0443422 , -0.00262826 ) +colvars: ( 0.00929972 , -0.0372153 , 0.0337754 ) +colvars: ( 0.00314937 , -0.0211942 , 0.0484237 ) +colvars: ( -0.0008336 , -0.0152088 , 0.0768089 ) +colvars: ( -0.003771 , 0.00422936 , 0.0330632 ) +colvars: ( -0.00582984 , 0.0113105 , 0.0305703 ) +colvars: ( -0.00730086 , 0.0180664 , 0.0214856 ) +colvars: ( -0.0132912 , 0.0410511 , 0.00397973 ) +colvars: ( -0.0162965 , 0.0523633 , -0.00386041 ) +colvars: ( -0.00975707 , 0.0358884 , -0.0218446 ) +colvars: ( -0.0137843 , 0.0501831 , -0.02863 ) +colvars: ( -0.00199862 , 0.0148061 , -0.0365682 ) +colvars: ( 0.00234464 , 0.00664768 , -0.060497 ) +colvars: ( 0.0105679 , -0.016292 , -0.0735434 ) +colvars: ( 0.00437195 , -0.00113711 , -0.0545462 ) +colvars: ( 0.00335346 , 0.00566889 , -0.0699992 ) +colvars: ( 0.00713223 , -0.0152053 , -0.0315106 ) +colvars: ( 0.00861599 , -0.0220342 , -0.0222845 ) +colvars: ( 0.0131139 , -0.0418459 , 0.00185206 ) +colvars: ( 0.000542707 , 0.00151077 , -0.0138827 ) +colvars: ( 0.000477805 , 0.00307603 , -0.0197389 ) +colvars: ( -0.00649927 , 0.0205377 , -5.2071e-05 ) +colvars: ( -0.0146901 , 0.0445534 , 0.00792188 ) +colvars: ( -0.0205506 , 0.0581576 , 0.0290343 ) +colvars: ( -0.0189405 , 0.0635216 , -0.0159497 ) +colvars: ( -0.0226405 , 0.075524 , -0.0173144 ) +colvars: ( -0.0168355 , 0.0725038 , -0.0832386 ) +colvars: ( -0.0199299 , 0.0866848 , -0.102217 ) +colvars: ( -0.00856576 , 0.0464172 , -0.0833694 ) +colvars: ( -0.0185967 , 0.0669301 , -0.0352981 ) +colvars: ( -0.0223316 , 0.0842257 , -0.058977 ) +colvars: ( -0.0244082 , 0.0931659 , -0.0692311 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 27. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 27. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atoms_new_colvar_forces = { ( -7.00918839295064e-02 , 3.03562631602812e-01 , -4.01230929831610e-01 ), ( 1.30228758705242e-02 , 3.13827887370110e-02 , -2.39424491797733e-01 ), ( -4.24616685652880e-02 , 9.53835979703357e-02 , 8.55264993388502e-02 ), ( -9.68240429627762e-02 , 2.50061075123733e-01 , 6.41508540355183e-02 ), ( -1.80414634629806e-02 , 9.82538668968961e-02 , -1.71472514960320e-01 ), ( 7.06557321135335e-02 , -1.85230277861217e-01 , -3.78873518772363e-02 ), ( 9.46350321907650e-03 , -9.87959399798595e-02 , 2.54890867620378e-01 ), ( -4.09425282344282e-02 , 6.01006350600721e-02 , 1.92681282419908e-01 ), ( 6.62602546982738e-02 , -1.91572278981195e-01 , 3.38169510399862e-02 ), ( 1.13816818760197e-01 , -3.91844223708385e-01 , 2.76452516683183e-01 ), ( 2.44388756577774e-02 , -9.95621342458959e-02 , 9.63505584456550e-02 ), ( 2.64755279440645e-02 , -9.75245532058121e-02 , 5.98880018253482e-02 ), ( 1.23248315375857e-02 , -5.58111427214885e-02 , 7.27023861546839e-02 ), ( 1.24747461734146e-02 , -5.36917952096011e-02 , 6.15401343699062e-02 ), ( 5.51192150634254e-03 , -3.50046483383724e-02 , 7.57575991860129e-02 ), ( -8.65227008336139e-03 , 9.79196214590065e-03 , 7.54819945039508e-02 ), ( -2.11286820065884e-03 , -2.69812507500008e-03 , 4.03425028835691e-02 ), ( -5.78649800221506e-03 , 9.90222838177424e-03 , 3.60438978525862e-02 ), ( 2.69299629720132e-03 , -1.30418621694614e-02 , 1.95321561354718e-02 ), ( 9.02626661697228e-03 , -2.22507545160550e-02 , -2.69306034571754e-02 ), ( 8.69644116503100e-03 , -2.39656725403336e-02 , -1.50633697361967e-02 ), ( 6.59446000905699e-03 , -1.37254617346516e-02 , -3.05696631273867e-02 ), ( 1.50134732127959e-02 , -4.69237871938746e-02 , -2.11363340989586e-03 ), ( 2.76130137525994e-02 , -8.89357221272514e-02 , 7.44686468199215e-03 ), ( 1.42765376002831e-02 , -4.71595341482906e-02 , 8.92074709266032e-03 ), ( 1.42338803726940e-02 , -4.43421789389268e-02 , -2.62826389885197e-03 ), ( 9.29972386139693e-03 , -3.72153352269306e-02 , 3.37753908498073e-02 ), ( -8.33599916874233e-04 , -1.52087633395627e-02 , 7.68089093286441e-02 ), ( -3.77100007712009e-03 , 4.22936205944202e-03 , 3.30631726198432e-02 ), ( -5.82983732798803e-03 , 1.13105190175713e-02 , 3.05703186441769e-02 ), ( -7.30086314368950e-03 , 1.80664473965964e-02 , 2.14856482153999e-02 ), ( -1.62964605632924e-02 , 5.23633164766681e-02 , -3.86040699596929e-03 ), ( -9.75706736775822e-03 , 3.58883761599068e-02 , -2.18446064193114e-02 ), ( -1.37843146647957e-02 , 5.01831413928922e-02 , -2.86299893752881e-02 ), ( -1.99861537665627e-03 , 1.48060903079009e-02 , -3.65682156413178e-02 ), ( 1.05678765369072e-02 , -1.62920244012486e-02 , -7.35434253074627e-02 ), ( 4.37194853737757e-03 , -1.13711218922162e-03 , -5.45461735948314e-02 ), ( 3.35345912840901e-03 , 5.66889059294423e-03 , -6.99991598096522e-02 ), ( 7.13223287626544e-03 , -1.52052602553789e-02 , -3.15106149149864e-02 ), ( 1.31139199664390e-02 , -4.18458818185023e-02 , 1.85205753754504e-03 ), ( 5.42706815934916e-04 , 1.51076931287781e-03 , -1.38827152006991e-02 ), ( 4.77805130120424e-04 , 3.07602707525113e-03 , -1.97388884158322e-02 ), ( -6.49926788211310e-03 , 2.05377353834856e-02 , -5.20710086762654e-05 ), ( -2.05506026036694e-02 , 5.81576335292180e-02 , 2.90343421506679e-02 ), ( -1.89404668103573e-02 , 6.35216142070820e-02 , -1.59497126415629e-02 ), ( -2.26405419833073e-02 , 7.55239927482679e-02 , -1.73144238866618e-02 ), ( -1.68354683467430e-02 , 7.25037673134110e-02 , -8.32385599157364e-02 ), ( -1.99298828125147e-02 , 8.66848171303143e-02 , -1.02217297110141e-01 ), ( -8.56576446939229e-03 , 4.64172138931442e-02 , -8.33693617236000e-02 ), ( -1.85966500629948e-02 , 6.69300872459209e-02 , -3.52980902148761e-02 ), ( -2.44082025097931e-02 , 9.31658827650885e-02 , -6.92311193427338e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 27, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 28 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 28, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 28, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 28, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 28, atoms_positions[size = 51] = { ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371142e-01 ), ( 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 ), ( 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 ), ( 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 ), ( 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 ), ( 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 ), ( -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 ), ( -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 ), ( -3.67073843017742e+00 , 8.01608924560728e-02 , 5.47777368326127e+00 ), ( -4.81202089485083e+00 , 3.27314869824355e+00 , 7.25929534791218e+00 ), ( 8.29937250565104e+00 , 4.23866805000533e-02 , -7.17159057051135e-01 ), ( 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828406e-01 ), ( 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 ), ( 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 ), ( 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 ), ( 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 ), ( 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 ), ( 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 ), ( 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 ), ( 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 ), ( 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 ), ( 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 ), ( 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 ), ( 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 ), ( 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 ), ( 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 ), ( 2.07308013451524e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 ), ( 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 ), ( 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 ), ( -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 ), ( 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 ), ( 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 ), ( -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 ), ( -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 ), ( -5.42011744036733e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 ), ( -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638271e+00 ), ( -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 ), ( -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 ), ( -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 ), ( -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 ), ( -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 ), ( -5.48235415482577e+00 , 7.64556077951691e-01 , 3.34059019506604e+00 ), ( -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 ), ( -2.38315281417864e+00 , -3.21340415243169e-01 , 6.14259769946699e+00 ), ( -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 ), ( -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 ), ( -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 ), ( -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 ), ( -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 ), ( -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 ), ( -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ) } +colvars: Step 28, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_ids[size = 0] = +colvars: Step 28, atom_groups_refcount[size = 0] = +colvars: Step 28, atom_groups_masses[size = 0] = +colvars: Step 28, atom_groups_charges[size = 0] = +colvars: Step 28, atom_groups_coms[size = 0] = +colvars: Step 28, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 28, volmaps_ids[size = 0] = +colvars: Step 28, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 28 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092545e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092545e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.219748 , 17.1971 , 17.2276 , 18.1182 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.219748 , 17.1971 , 17.2276 , 18.1182 ) to colvar "one". +colvars: Adding total bias energy: 11.5106 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.219748 , 17.1971 , 17.2276 , 18.1182 ) +colvars: Applying force on main group : +colvars: ( -0.0897487 , 0.385631 , -0.484386 ) +colvars: ( 0.015669 , 0.0396693 , -0.308928 ) +colvars: ( -0.0465972 , 0.106265 , 0.0940367 ) +colvars: ( -0.116516 , 0.310946 , 0.0687975 ) +colvars: ( -0.0210708 , 0.119345 , -0.219667 ) +colvars: ( 0.0839256 , -0.226079 , -0.0418043 ) +colvars: ( 0.00697909 , -0.105444 , 0.31517 ) +colvars: ( -0.0495798 , 0.0817944 , 0.215067 ) +colvars: ( 0.0809625 , -0.236202 , 0.0262542 ) +colvars: ( 0.135977 , -0.475926 , 0.335459 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243941 , -0.099545 , 0.0963622 ) +colvars: ( 0.0198381 , -0.0820968 , 0.0832606 ) +colvars: ( 0.0264527 , -0.0975317 , 0.0599104 ) +colvars: ( 0.0122971 , -0.0558163 , 0.0727035 ) +colvars: ( 0.0124495 , -0.0536909 , 0.0615436 ) +colvars: ( 0.00548705 , -0.0350216 , 0.0757494 ) +colvars: ( -0.00258984 , -0.00803817 , 0.0694281 ) +colvars: ( -0.00867013 , 0.00975559 , 0.0754557 ) +colvars: ( -0.0021201 , -0.00272534 , 0.0403319 ) +colvars: ( -0.0057932 , 0.00987935 , 0.0360293 ) +colvars: ( 0.00269638 , -0.0130776 , 0.0195324 ) +colvars: ( 0.00407168 , -0.0107731 , -0.00892795 ) +colvars: ( 0.00905252 , -0.0223019 , -0.026912 ) +colvars: ( 0.00871028 , -0.0239922 , -0.0150482 ) +colvars: ( 0.00661442 , -0.0137517 , -0.030554 ) +colvars: ( 0.0150181 , -0.0469386 , -0.00209313 ) +colvars: ( 0.0197034 , -0.0611031 , -0.00479768 ) +colvars: ( 0.0276059 , -0.0889274 , 0.00748141 ) +colvars: ( 0.0142694 , -0.0471507 , 0.00893745 ) +colvars: ( 0.0142296 , -0.0443277 , -0.00260933 ) +colvars: ( 0.00928255 , -0.0372048 , 0.0337803 ) +colvars: ( 0.00312437 , -0.021176 , 0.0484174 ) +colvars: ( -0.000869776 , -0.01519 , 0.0767913 ) +colvars: ( -0.00378713 , 0.00423979 , 0.0330511 ) +colvars: ( -0.00584724 , 0.0113285 , 0.0305559 ) +colvars: ( -0.00730738 , 0.0180615 , 0.0214717 ) +colvars: ( -0.0132876 , 0.0410371 , 0.00396175 ) +colvars: ( -0.0162843 , 0.0523323 , -0.00388032 ) +colvars: ( -0.00974404 , 0.0358761 , -0.0218526 ) +colvars: ( -0.0137692 , 0.0501733 , -0.0286419 ) +colvars: ( -0.00197995 , 0.014793 , -0.0365629 ) +colvars: ( 0.00237175 , 0.00663703 , -0.060481 ) +colvars: ( 0.0106008 , -0.0163063 , -0.0735138 ) +colvars: ( 0.00439151 , -0.00113163 , -0.0545291 ) +colvars: ( 0.00337853 , 0.00567645 , -0.0699803 ) +colvars: ( 0.00713881 , -0.0151879 , -0.031495 ) +colvars: ( 0.00861389 , -0.0220012 , -0.0222693 ) +colvars: ( 0.0130987 , -0.0418022 , 0.00186792 ) +colvars: ( 0.000536791 , 0.00154685 , -0.0138799 ) +colvars: ( 0.000471572 , 0.00312047 , -0.0197351 ) +colvars: ( -0.00650807 , 0.0205669 , -6.12559e-05 ) +colvars: ( -0.014702 , 0.0445837 , 0.00790024 ) +colvars: ( -0.0205686 , 0.0581819 , 0.0290007 ) +colvars: ( -0.0189399 , 0.0635432 , -0.0159718 ) +colvars: ( -0.022641 , 0.0755512 , -0.0173412 ) +colvars: ( -0.0168024 , 0.0725061 , -0.0832433 ) +colvars: ( -0.0198875 , 0.086682 , -0.102222 ) +colvars: ( -0.0085359 , 0.0464284 , -0.0833634 ) +colvars: ( -0.0185841 , 0.0669377 , -0.0353153 ) +colvars: ( -0.0223065 , 0.0842241 , -0.058994 ) +colvars: ( -0.0243736 , 0.0931472 , -0.0692483 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 28. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 28. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atoms_new_colvar_forces = { ( -6.99105964745414e-02 , 3.03534108224077e-01 , -4.01125198858137e-01 ), ( 1.30792098250532e-02 , 3.16310929373661e-02 , -2.39499701615836e-01 ), ( -4.25255029736803e-02 , 9.54922740032261e-02 , 8.51087057351073e-02 ), ( -9.68128132349850e-02 , 2.49843308955989e-01 , 6.39997898630516e-02 ), ( -1.79464748638226e-02 , 9.81685466429824e-02 , -1.71250102556514e-01 ), ( 7.06379507910652e-02 , -1.85041970185675e-01 , -3.78425579319191e-02 ), ( 9.35083933511790e-03 , -9.88068220395378e-02 , 2.54689455152915e-01 ), ( -4.09659433594163e-02 , 5.97932072032175e-02 , 1.92798200103656e-01 ), ( 6.62605501454588e-02 , -1.91618026165443e-01 , 3.41544371557535e-02 ), ( 1.13670038704103e-01 , -3.91702187892016e-01 , 2.76465205814139e-01 ), ( 2.43941032937985e-02 , -9.95450315112680e-02 , 9.63621500021452e-02 ), ( 2.64526804358145e-02 , -9.75317185173844e-02 , 5.99104372755897e-02 ), ( 1.22970656157734e-02 , -5.58162675354601e-02 , 7.27035002216812e-02 ), ( 1.24494756477064e-02 , -5.36908802348386e-02 , 6.15436432653573e-02 ), ( 5.48704688714376e-03 , -3.50215844750732e-02 , 7.57493863140233e-02 ), ( -8.67012952291998e-03 , 9.75558764555574e-03 , 7.54556612518544e-02 ), ( -2.12010225636095e-03 , -2.72534424138995e-03 , 4.03319038952513e-02 ), ( -5.79320046768154e-03 , 9.87935351909539e-03 , 3.60292720624457e-02 ), ( 2.69638236344813e-03 , -1.30775617081468e-02 , 1.95324137553816e-02 ), ( 9.05251869178128e-03 , -2.23019324748084e-02 , -2.69119622158068e-02 ), ( 8.71027637037681e-03 , -2.39922447972659e-02 , -1.50481952882849e-02 ), ( 6.61441724671008e-03 , -1.37516683392467e-02 , -3.05540177540563e-02 ), ( 1.50181321585705e-02 , -4.69385652870097e-02 , -2.09312910608297e-03 ), ( 2.76059252628942e-02 , -8.89273993060487e-02 , 7.48140988776515e-03 ), ( 1.42694316016934e-02 , -4.71506609950198e-02 , 8.93744511963322e-03 ), ( 1.42295639585641e-02 , -4.43276814589434e-02 , -2.60933393989567e-03 ), ( 9.28254514352050e-03 , -3.72047576822429e-02 , 3.37803143159950e-02 ), ( -8.69775702737491e-04 , -1.51900253011091e-02 , 7.67913363669554e-02 ), ( -3.78712761698228e-03 , 4.23979009716207e-03 , 3.30510708702083e-02 ), ( -5.84723852640201e-03 , 1.13284759700188e-02 , 3.05558632441676e-02 ), ( -7.30738149450517e-03 , 1.80614978519294e-02 , 2.14716730988585e-02 ), ( -1.62842633958380e-02 , 5.23322937967764e-02 , -3.88032006840828e-03 ), ( -9.74404228898785e-03 , 3.58761140757968e-02 , -2.18525871928399e-02 ), ( -1.37691637380410e-02 , 5.01733408163495e-02 , -2.86418995399456e-02 ), ( -1.97994657736161e-03 , 1.47930001175436e-02 , -3.65629037841475e-02 ), ( 1.06008081770661e-02 , -1.63062648103744e-02 , -7.35138432584534e-02 ), ( 4.39151001737965e-03 , -1.13162558162393e-03 , -5.45291484906228e-02 ), ( 3.37852500415077e-03 , 5.67644658806253e-03 , -6.99802892637869e-02 ), ( 7.13880736625240e-03 , -1.51878963709950e-02 , -3.14950444881112e-02 ), ( 1.30987062537573e-02 , -4.18022069940880e-02 , 1.86792386817925e-03 ), ( 5.36790918205760e-04 , 1.54685236917992e-03 , -1.38799100920889e-02 ), ( 4.71571839629201e-04 , 3.12046790390119e-03 , -1.97351320604518e-02 ), ( -6.50806934625518e-03 , 2.05668835560401e-02 , -6.12559491181550e-05 ), ( -2.05685759895296e-02 , 5.81819166560511e-02 , 2.90007198523593e-02 ), ( -1.89399299546582e-02 , 6.35432232945508e-02 , -1.59717550759216e-02 ), ( -2.26410185265841e-02 , 7.55511789495086e-02 , -1.73411688823523e-02 ), ( -1.68024096378493e-02 , 7.25060849069893e-02 , -8.32433362384075e-02 ), ( -1.98875385771560e-02 , 8.66819831532424e-02 , -1.02222056961599e-01 ), ( -8.53590432797544e-03 , 4.64283976982095e-02 , -8.33634418048039e-02 ), ( -1.85840756007226e-02 , 6.69376673267996e-02 , -3.53153210594370e-02 ), ( -2.43736486000415e-02 , 9.31472296453879e-02 , -6.92483050154469e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 28, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 29 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 29, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 29, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 29, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 29, atoms_positions[size = 51] = { ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754424e-01 ), ( 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 ), ( 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 ), ( 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 ), ( 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 ), ( 8.65304397854146e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 ), ( -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 ), ( -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 ), ( -3.66933507872099e+00 , 8.05977535935299e-02 , 5.48202248684294e+00 ), ( -4.81296950008506e+00 , 3.27902937016758e+00 , 7.25609311672234e+00 ), ( 8.29622457456575e+00 , 4.23601649414827e-02 , -7.12749794942444e-01 ), ( 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 ), ( 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 ), ( 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 ), ( 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 ), ( 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 ), ( 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 ), ( 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 ), ( 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 ), ( 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 ), ( 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 ), ( 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 ), ( 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 ), ( 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 ), ( 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 ), ( 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 ), ( 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 ), ( 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 ), ( 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 ), ( -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 ), ( 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 ), ( 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 ), ( -3.54512396787449e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 ), ( -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 ), ( -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 ), ( -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 ), ( -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 ), ( -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 ), ( -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 ), ( -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 ), ( -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 ), ( -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 ), ( -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 ), ( -2.37949805223028e+00 , -3.18274942149998e-01 , 6.13855939203602e+00 ), ( -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 ), ( -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 ), ( -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 ), ( -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 ), ( -6.64854667858963e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 ), ( -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 ), ( -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ) } +colvars: Step 29, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_ids[size = 0] = +colvars: Step 29, atom_groups_refcount[size = 0] = +colvars: Step 29, atom_groups_masses[size = 0] = +colvars: Step 29, atom_groups_charges[size = 0] = +colvars: Step 29, atom_groups_coms[size = 0] = +colvars: Step 29, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 29, volmaps_ids[size = 0] = +colvars: Step 29, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 29 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601430e-02 , -1.45578300084090e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601430e-02 , -1.45578300084090e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.220399 , 17.191 , 17.225 , 18.1245 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.220399 , 17.191 , 17.225 , 18.1245 ) to colvar "one". +colvars: Adding total bias energy: 11.5097 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.220399 , 17.191 , 17.225 , 18.1245 ) +colvars: Applying force on main group : +colvars: ( -0.0895413 , 0.385602 , -0.484303 ) +colvars: ( 0.015759 , 0.0399081 , -0.308977 ) +colvars: ( -0.0466782 , 0.106389 , 0.0936585 ) +colvars: ( -0.116528 , 0.310747 , 0.0686354 ) +colvars: ( -0.0209552 , 0.119255 , -0.219466 ) +colvars: ( 0.0839214 , -0.225896 , -0.0417453 ) +colvars: ( 0.00683767 , -0.105446 , 0.314978 ) +colvars: ( -0.0496204 , 0.081493 , 0.215155 ) +colvars: ( 0.0809815 , -0.23626 , 0.0265745 ) +colvars: ( 0.135823 , -0.475792 , 0.33549 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243528 , -0.0995212 , 0.0963717 ) +colvars: ( 0.0198067 , -0.0820915 , 0.0832706 ) +colvars: ( 0.0264336 , -0.0975315 , 0.0599368 ) +colvars: ( 0.0122707 , -0.0558185 , 0.0727062 ) +colvars: ( 0.0124258 , -0.0536868 , 0.0615476 ) +colvars: ( 0.00546239 , -0.035038 , 0.0757443 ) +colvars: ( -0.00261105 , -0.00806282 , 0.0694142 ) +colvars: ( -0.00869024 , 0.0097151 , 0.0754349 ) +colvars: ( -0.00212822 , -0.00275411 , 0.0403262 ) +colvars: ( -0.0058013 , 0.00985391 , 0.0360183 ) +colvars: ( 0.00269969 , -0.0131132 , 0.0195403 ) +colvars: ( 0.00408789 , -0.0108124 , -0.00891064 ) +colvars: ( 0.00907983 , -0.0223508 , -0.0268808 ) +colvars: ( 0.00872531 , -0.0240164 , -0.015026 ) +colvars: ( 0.00663534 , -0.0137759 , -0.0305315 ) +colvars: ( 0.015025 , -0.0469489 , -0.00206755 ) +colvars: ( 0.0197077 , -0.0610978 , -0.00476801 ) +colvars: ( 0.0276033 , -0.0889105 , 0.00751754 ) +colvars: ( 0.0142646 , -0.0471373 , 0.00895391 ) +colvars: ( 0.0142277 , -0.0443085 , -0.00259167 ) +colvars: ( 0.00926675 , -0.0371915 , 0.0337836 ) +colvars: ( 0.00309975 , -0.0211572 , 0.0484068 ) +colvars: ( -0.000906372 , -0.0151721 , 0.0767685 ) +colvars: ( -0.00380396 , 0.00424883 , 0.0330358 ) +colvars: ( -0.00586557 , 0.0113446 , 0.0305364 ) +colvars: ( -0.00731526 , 0.018054 , 0.0214575 ) +colvars: ( -0.0132863 , 0.0410186 , 0.00394503 ) +colvars: ( -0.016275 , 0.0522958 , -0.0038956 ) +colvars: ( -0.00973257 , 0.0358609 , -0.0218588 ) +colvars: ( -0.0137561 , 0.0501595 , -0.028653 ) +colvars: ( -0.0019615 , 0.0147795 , -0.0365545 ) +colvars: ( 0.0023995 , 0.00662764 , -0.0604615 ) +colvars: ( 0.0106357 , -0.0163166 , -0.0734788 ) +colvars: ( 0.00441218 , -0.00112407 , -0.0545119 ) +colvars: ( 0.00340465 , 0.00568597 , -0.0699616 ) +colvars: ( 0.00714691 , -0.0151677 , -0.0314818 ) +colvars: ( 0.00861366 , -0.0219646 , -0.0222597 ) +colvars: ( 0.013086 , -0.0417538 , 0.00187608 ) +colvars: ( 0.000531439 , 0.00158383 , -0.0138845 ) +colvars: ( 0.000466019 , 0.00316598 , -0.0197405 ) +colvars: ( -0.00651759 , 0.0205945 , -7.74867e-05 ) +colvars: ( -0.0147159 , 0.0446098 , 0.00787016 ) +colvars: ( -0.0205898 , 0.0581999 , 0.0289589 ) +colvars: ( -0.0189421 , 0.0635595 , -0.0160006 ) +colvars: ( -0.0226447 , 0.075572 , -0.0173763 ) +colvars: ( -0.0167715 , 0.0725042 , -0.0832495 ) +colvars: ( -0.0198478 , 0.0866741 , -0.102227 ) +colvars: ( -0.00850676 , 0.0464381 , -0.0833597 ) +colvars: ( -0.0185742 , 0.06694 , -0.035336 ) +colvars: ( -0.0222847 , 0.0842162 , -0.0590125 ) +colvars: ( -0.0243427 , 0.0931215 , -0.0692635 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 29. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 29. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atoms_new_colvar_forces = { ( -6.97345673689353e-02 , 3.03510657206574e-01 , -4.01032117490141e-01 ), ( 1.31479927636834e-02 , 3.18452841780117e-02 , -2.39563239519030e-01 ), ( -4.25902939322404e-02 , 9.55764008556160e-02 , 8.47478780569349e-02 ), ( -9.68202824772278e-02 , 2.49649279092987e-01 , 6.38673507909631e-02 ), ( -1.78554209094392e-02 , 9.80978947661689e-02 , -1.71059030797415e-01 ), ( 7.06351339216980e-02 , -1.84876997886692e-01 , -3.78002906708560e-02 ), ( 9.23717210815472e-03 , -9.88186635802035e-02 , 2.54516498207081e-01 ), ( -4.10067185999413e-02 , 5.95284116782757e-02 , 1.92894973903991e-01 ), ( 6.62656509213339e-02 , -1.91650327349241e-01 , 3.44446751551083e-02 ), ( 1.13538570672861e-01 , -3.91576043794114e-01 , 2.76477610737634e-01 ), ( 2.43528011759160e-02 , -9.95212184108119e-02 , 9.63717066493160e-02 ), ( 2.64335990853690e-02 , -9.75315010313773e-02 , 5.99368309122805e-02 ), ( 1.22707479665203e-02 , -5.58185019853083e-02 , 7.27061619717733e-02 ), ( 1.24258135329339e-02 , -5.36868050421806e-02 , 6.15475967226827e-02 ), ( 5.46238658459673e-03 , -3.50379570239896e-02 , 7.57443415325614e-02 ), ( -8.69024268940156e-03 , 9.71509594049825e-03 , 7.54348715011720e-02 ), ( -2.12822387245308e-03 , -2.75410877718619e-03 , 4.03262459211456e-02 ), ( -5.80130253688933e-03 , 9.85391482653324e-03 , 3.60182615787236e-02 ), ( 2.69968905367764e-03 , -1.31132121873080e-02 , 1.95403438129169e-02 ), ( 9.07983140495067e-03 , -2.23508072022709e-02 , -2.68808418768290e-02 ), ( 8.72530906787373e-03 , -2.40163686340764e-02 , -1.50260205641190e-02 ), ( 6.63533929943794e-03 , -1.37758914733351e-02 , -3.05314804783749e-02 ), ( 1.50250412334631e-02 , -4.69489069415381e-02 , -2.06754550118032e-03 ), ( 2.76032855445120e-02 , -8.89104932973903e-02 , 7.51753913090130e-03 ), ( 1.42646426422054e-02 , -4.71373373917235e-02 , 8.95390893414003e-03 ), ( 1.42276919791724e-02 , -4.43085252454197e-02 , -2.59167092550324e-03 ), ( 9.26674921618978e-03 , -3.71915296398978e-02 , 3.37836374872139e-02 ), ( -9.06372128229056e-04 , -1.51721407720698e-02 , 7.67684938038021e-02 ), ( -3.80395529749382e-03 , 4.24883243177135e-03 , 3.30357666004564e-02 ), ( -5.86557141109127e-03 , 1.13445570023479e-02 , 3.05363750307080e-02 ), ( -7.31525519485768e-03 , 1.80539646497407e-02 , 2.14575122079536e-02 ), ( -1.62749765161026e-02 , 5.22957913864255e-02 , -3.89559645051791e-03 ), ( -9.73256717086334e-03 , 3.58608957287872e-02 , -2.18588455272024e-02 ), ( -1.37561356846093e-02 , 5.01594555083329e-02 , -2.86530175657035e-02 ), ( -1.96150471330579e-03 , 1.47795103338105e-02 , -3.65544936694368e-02 ), ( 1.06357415268573e-02 , -1.63166088971694e-02 , -7.34787770018302e-02 ), ( 4.41217592686858e-03 , -1.12407025410037e-03 , -5.45119214454607e-02 ), ( 3.40465355615724e-03 , 5.68596742599340e-03 , -6.99615536721609e-02 ), ( 7.14690794577242e-03 , -1.51676910384938e-02 , -3.14818108612719e-02 ), ( 1.30860440731738e-02 , -4.17538157142368e-02 , 1.87607969243244e-03 ), ( 5.31438886239974e-04 , 1.58382764422033e-03 , -1.38845375267955e-02 ), ( 4.66019431914596e-04 , 3.16597921279863e-03 , -1.97405139078286e-02 ), ( -6.51759358566815e-03 , 2.05944778805003e-02 , -7.74867141769462e-05 ), ( -2.05897522873165e-02 , 5.81998881002601e-02 , 2.89588835151015e-02 ), ( -1.89420811869476e-02 , 6.35594972111328e-02 , -1.60005578066733e-02 ), ( -2.26447048361701e-02 , 7.55719886654578e-02 , -1.73763109801339e-02 ), ( -1.67714821195974e-02 , 7.25041952445797e-02 , -8.32494688284707e-02 ), ( -1.98477539008037e-02 , 8.66741240236254e-02 , -1.02227174905627e-01 ), ( -8.50675931255932e-03 , 4.64380716891990e-02 , -8.33597300696781e-02 ), ( -1.85741622090217e-02 , 6.69400231747561e-02 , -3.53359787198467e-02 ), ( -2.43427495803689e-02 , 9.31215377117312e-02 , -6.92635303807293e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 29, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 30 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 30, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 30, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 30, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 30, atoms_positions[size = 51] = { ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641626e-01 ), ( 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 ), ( 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 ), ( 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 ), ( 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 ), ( 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 ), ( -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 ), ( -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 ), ( -3.66808902897429e+00 , 8.00192656616480e-02 , 5.48456203544387e+00 ), ( -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ), ( 8.29230184427869e+00 , 4.21861224833246e-02 , -7.08174413023012e-01 ), ( 7.01074964451227e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 ), ( 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 ), ( 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 ), ( 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 ), ( 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 ), ( 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 ), ( 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 ), ( 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 ), ( 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 ), ( 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 ), ( 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 ), ( 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 ), ( 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 ), ( 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 ), ( 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 ), ( 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 ), ( 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 ), ( 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 ), ( -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 ), ( 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 ), ( 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 ), ( -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 ), ( -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 ), ( -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 ), ( -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633871e+00 ), ( -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 ), ( -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 ), ( -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 ), ( -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160168e-01 ), ( -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 ), ( -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 ), ( -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 ), ( -2.37512825645772e+00 , -3.14245448646485e-01 , 6.13503886138837e+00 ), ( -4.48049343311408e+00 , 9.23291002542476e-01 , 6.42458367171772e+00 ), ( -5.35769724718959e+00 , 5.73458684568046e-01 , 7.20401421961488e+00 ), ( -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 ), ( -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 ), ( -6.63855361839081e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 ), ( -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 ), ( -4.01878208177308e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ) } +colvars: Step 30, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_ids[size = 0] = +colvars: Step 30, atom_groups_refcount[size = 0] = +colvars: Step 30, atom_groups_masses[size = 0] = +colvars: Step 30, atom_groups_charges[size = 0] = +colvars: Step 30, atom_groups_coms[size = 0] = +colvars: Step 30, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 30, volmaps_ids[size = 0] = +colvars: Step 30, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 30 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.220986 , 17.1855 , 17.2243 , 18.1288 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.220986 , 17.1855 , 17.2243 , 18.1288 ) to colvar "one". +colvars: Adding total bias energy: 11.509 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.220986 , 17.1855 , 17.2243 , 18.1288 ) +colvars: Applying force on main group : +colvars: ( -0.0893451 , 0.385577 , -0.48426 ) +colvars: ( 0.0158627 , 0.0401008 , -0.309025 ) +colvars: ( -0.04676 , 0.10649 , 0.0933446 ) +colvars: ( -0.116564 , 0.310586 , 0.0684891 ) +colvars: ( -0.0208455 , 0.119181 , -0.219309 ) +colvars: ( 0.0839365 , -0.225747 , -0.0416872 ) +colvars: ( 0.006696 , -0.105447 , 0.31483 ) +colvars: ( -0.0496814 , 0.0812491 , 0.215226 ) +colvars: ( 0.0810083 , -0.236308 , 0.0268488 ) +colvars: ( 0.135692 , -0.475682 , 0.335543 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243167 , -0.099492 , 0.0963817 ) +colvars: ( 0.0197793 , -0.0820812 , 0.0832837 ) +colvars: ( 0.0264192 , -0.0975245 , 0.0599683 ) +colvars: ( 0.0122469 , -0.0558175 , 0.0727122 ) +colvars: ( 0.0124047 , -0.0536797 , 0.0615536 ) +colvars: ( 0.00543875 , -0.0350524 , 0.0757444 ) +colvars: ( -0.0026328 , -0.00808731 , 0.0694056 ) +colvars: ( -0.00871222 , 0.00967375 , 0.0754216 ) +colvars: ( -0.00213712 , -0.00278243 , 0.0403264 ) +colvars: ( -0.00581071 , 0.00982786 , 0.0360118 ) +colvars: ( 0.00270265 , -0.0131469 , 0.0195561 ) +colvars: ( 0.00410366 , -0.0108494 , -0.00888492 ) +colvars: ( 0.00910712 , -0.0223956 , -0.0268388 ) +colvars: ( 0.00874099 , -0.0240374 , -0.0149978 ) +colvars: ( 0.00665646 , -0.0137975 , -0.0305034 ) +colvars: ( 0.0150341 , -0.046955 , -0.00203743 ) +colvars: ( 0.0197152 , -0.0610877 , -0.00473617 ) +colvars: ( 0.0276055 , -0.0888871 , 0.00755499 ) +colvars: ( 0.0142625 , -0.0471208 , 0.0089702 ) +colvars: ( 0.0142286 , -0.0442864 , -0.00257548 ) +colvars: ( 0.00925303 , -0.0371764 , 0.0337863 ) +colvars: ( 0.00307649 , -0.0211382 , 0.0483935 ) +colvars: ( -0.000942067 , -0.0151551 , 0.0767429 ) +colvars: ( -0.0038209 , 0.00425657 , 0.0330184 ) +colvars: ( -0.00588419 , 0.0113586 , 0.0305131 ) +colvars: ( -0.00732433 , 0.0180448 , 0.0214439 ) +colvars: ( -0.0132876 , 0.0409974 , 0.00392981 ) +colvars: ( -0.0162693 , 0.0522564 , -0.00390637 ) +colvars: ( -0.0097232 , 0.0358437 , -0.021864 ) +colvars: ( -0.0137459 , 0.0501425 , -0.028664 ) +colvars: ( -0.001944 , 0.014766 , -0.0365442 ) +colvars: ( 0.00242693 , 0.00661922 , -0.0604406 ) +colvars: ( 0.0106715 , -0.0163238 , -0.0734408 ) +colvars: ( 0.00443333 , -0.00111562 , -0.0544961 ) +colvars: ( 0.00343104 , 0.00569606 , -0.069945 ) +colvars: ( 0.00715643 , -0.0151463 , -0.0314718 ) +colvars: ( 0.00861558 , -0.0219272 , -0.0222562 ) +colvars: ( 0.0130767 , -0.0417037 , 0.00187681 ) +colvars: ( 0.000527024 , 0.00161965 , -0.0138966 ) +colvars: ( 0.000461571 , 0.00321003 , -0.0197551 ) +colvars: ( -0.00652744 , 0.0206194 , -0.000100291 ) +colvars: ( -0.0147314 , 0.0446312 , 0.00783254 ) +colvars: ( -0.0206135 , 0.0582119 , 0.0289104 ) +colvars: ( -0.018947 , 0.0635703 , -0.0160359 ) +colvars: ( -0.0226516 , 0.0755862 , -0.0174196 ) +colvars: ( -0.0167439 , 0.0724981 , -0.083259 ) +colvars: ( -0.0198121 , 0.0866615 , -0.102235 ) +colvars: ( -0.00847935 , 0.0464452 , -0.0833604 ) +colvars: ( -0.0185674 , 0.0669375 , -0.0353606 ) +colvars: ( -0.0222671 , 0.0842029 , -0.0590339 ) +colvars: ( -0.0243169 , 0.0930905 , -0.0692785 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 30. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 30. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atoms_new_colvar_forces = { ( -6.95658913699924e-02 , 3.03495304700360e-01 , -4.00976200210173e-01 ), ( 1.32299191340559e-02 , 3.20134991645447e-02 , -2.39619452468059e-01 ), ( -4.26563766265219e-02 , 9.56403093898097e-02 , 8.44596854250561e-02 ), ( -9.68486750504376e-02 , 2.49497835273790e-01 , 6.37529442829732e-02 ), ( -1.77689888890507e-02 , 9.80431135295305e-02 , -1.70915677049662e-01 ), ( 7.06489024165661e-02 , -1.84749376697780e-01 , -3.77573986335530e-02 ), ( 9.12292858715042e-03 , -9.88276270229263e-02 , 2.54389414476489e-01 ), ( -4.10658673366000e-02 , 5.93219876485636e-02 , 1.92969834008387e-01 ), ( 6.62769371505774e-02 , -1.91676334263824e-01 , 3.46813751733085e-02 ), ( 1.13425333979248e-01 , -3.91478967299099e-01 , 2.76508875738693e-01 ), ( 2.43167271106807e-02 , -9.94920033544715e-02 , 9.63817440640522e-02 ), ( 2.64191895603649e-02 , -9.75245060047425e-02 , 5.99683035376166e-02 ), ( 1.22468789126365e-02 , -5.58175258139927e-02 , 7.27121898589340e-02 ), ( 1.24047035902619e-02 , -5.36796957632884e-02 , 6.15535517723070e-02 ), ( 5.43874680066886e-03 , -3.50523789955920e-02 , 7.57443798203501e-02 ), ( -8.71221758731420e-03 , 9.67375370300251e-03 , 7.54216052589434e-02 ), ( -2.13712409634063e-03 , -2.78243053067266e-03 , 4.03264445359764e-02 ), ( -5.81071492969707e-03 , 9.82785816537381e-03 , 3.60117830588854e-02 ), ( 2.70265027945472e-03 , -1.31469274539607e-02 , 1.95560512477302e-02 ), ( 9.10712044392774e-03 , -2.23956228363689e-02 , -2.68388150373631e-02 ), ( 8.74099287762604e-03 , -2.40373952913405e-02 , -1.49977781270839e-02 ), ( 6.65645930329754e-03 , -1.37975462710417e-02 , -3.05033911886318e-02 ), ( 1.50340605582740e-02 , -4.69550160873604e-02 , -2.03743106755413e-03 ), ( 2.76055388989486e-02 , -8.88870722111463e-02 , 7.55498700718659e-03 ), ( 1.42625395994906e-02 , -4.71208094237405e-02 , 8.97020314867174e-03 ), ( 1.42285636033123e-02 , -4.42863738174125e-02 , -2.57548378640847e-03 ), ( 9.25302873951539e-03 , -3.71763907190270e-02 , 3.37862797711345e-02 ), ( -9.42067296947512e-04 , -1.51551450565181e-02 , 7.67428731176359e-02 ), ( -3.82090419229272e-03 , 4.25656589375703e-03 , 3.30184313118940e-02 ), ( -5.88419054784475e-03 , 1.13585528504002e-02 , 3.05130825138278e-02 ), ( -7.32432688702300e-03 , 1.80448026433321e-02 , 2.14438932885341e-02 ), ( -1.62692581172610e-02 , 5.22563759057720e-02 , -3.90636550782251e-03 ), ( -9.72320285482906e-03 , 3.58437115716669e-02 , -2.18639600318727e-02 ), ( -1.37458764867003e-02 , 5.01425240534089e-02 , -2.86640083889571e-02 ), ( -1.94400216674573e-03 , 1.47660014403295e-02 , -3.65441692936174e-02 ), ( 1.06715441245246e-02 , -1.63238233771593e-02 , -7.34407746919613e-02 ), ( 4.43332716670918e-03 , -1.11562187529326e-03 , -5.44961240911917e-02 ), ( 3.43104066974840e-03 , 5.69605899859925e-03 , -6.99449935137132e-02 ), ( 7.15643203676903e-03 , -1.51463397957204e-02 , -3.14717894247689e-02 ), ( 1.30767350430219e-02 , -4.17037479203932e-02 , 1.87680844406153e-03 ), ( 5.27024352117541e-04 , 1.61965138324290e-03 , -1.38965999902881e-02 ), ( 4.61570877233452e-04 , 3.21002571734941e-03 , -1.97551106198276e-02 ), ( -6.52744180540112e-03 , 2.06194280345439e-02 , -1.00291408984661e-04 ), ( -2.06135237907966e-02 , 5.82119164551232e-02 , 2.89103990433041e-02 ), ( -1.89469500756803e-02 , 6.35703291381154e-02 , -1.60359417691587e-02 ), ( -2.26515916333778e-02 , 7.55862445647695e-02 , -1.74195690035389e-02 ), ( -1.67439071198021e-02 , 7.24980841159223e-02 , -8.32590234227901e-02 ), ( -1.98121104958263e-02 , 8.66614672876918e-02 , -1.02235268950251e-01 ), ( -8.47935120434021e-03 , 4.64452483103734e-02 , -8.33603674838263e-02 ), ( -1.85674151530122e-02 , 6.69375262400478e-02 , -3.53606221186804e-02 ), ( -2.43169201023462e-02 , 9.30905017034529e-02 , -6.92785326262130e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 30, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 31 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 31, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 31, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 31, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 31, atoms_positions[size = 51] = { ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590915e-01 ), ( 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 ), ( 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 ), ( 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 ), ( 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 ), ( 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 ), ( -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 ), ( -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 ), ( -3.66693895104545e+00 , 7.85341863726525e-02 , 5.48517025875378e+00 ), ( -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ), ( 8.28755940062026e+00 , 4.18329711611075e-02 , -7.03446891225446e-01 ), ( 7.00850253516804e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 ), ( 6.14090877060161e+00 , -3.55929932388830e-01 , 8.11285689266245e-01 ), ( 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 ), ( 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 ), ( 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 ), ( 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 ), ( 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 ), ( 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 ), ( 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 ), ( 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 ), ( 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 ), ( 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 ), ( 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 ), ( 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 ), ( 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 ), ( 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 ), ( 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 ), ( 5.73958980727405e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 ), ( -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 ), ( 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 ), ( 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 ), ( -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 ), ( -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 ), ( -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 ), ( -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 ), ( -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 ), ( -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 ), ( -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 ), ( -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697041e-01 ), ( -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 ), ( -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 ), ( -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 ), ( -2.37002722947734e+00 , -3.09308532077129e-01 , 6.13223591205862e+00 ), ( -4.48400436751533e+00 , 9.25990621860429e-01 , 6.42460287653144e+00 ), ( -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 ), ( -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 ), ( -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 ), ( -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876725e+00 ), ( -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 ), ( -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ) } +colvars: Step 31, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_ids[size = 0] = +colvars: Step 31, atom_groups_refcount[size = 0] = +colvars: Step 31, atom_groups_masses[size = 0] = +colvars: Step 31, atom_groups_charges[size = 0] = +colvars: Step 31, atom_groups_coms[size = 0] = +colvars: Step 31, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 31, volmaps_ids[size = 0] = +colvars: Step 31, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 31 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250314e-02 , -1.47660205688039e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250314e-02 , -1.47660205688039e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.221323 , 17.1811 , 17.2253 , 18.131 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.221323 , 17.1811 , 17.2253 , 18.131 ) to colvar "one". +colvars: Adding total bias energy: 11.5086 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.221323 , 17.1811 , 17.2253 , 18.131 ) +colvars: Applying force on main group : +colvars: ( -0.0891629 , 0.385557 , -0.484279 ) +colvars: ( 0.0159797 , 0.0402373 , -0.309077 ) +colvars: ( -0.0468425 , 0.106571 , 0.0931056 ) +colvars: ( -0.116625 , 0.310477 , 0.0683578 ) +colvars: ( -0.020743 , 0.119124 , -0.219211 ) +colvars: ( 0.0839717 , -0.225644 , -0.0416274 ) +colvars: ( 0.00655531 , -0.105442 , 0.314741 ) +colvars: ( -0.0497634 , 0.0810759 , 0.215282 ) +colvars: ( 0.0810436 , -0.23635 , 0.0270738 ) +colvars: ( 0.135587 , -0.475606 , 0.335635 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242872 , -0.0994587 , 0.0963944 ) +colvars: ( 0.0197567 , -0.0820666 , 0.0833017 ) +colvars: ( 0.0264101 , -0.0975115 , 0.0600056 ) +colvars: ( 0.0122262 , -0.0558132 , 0.072723 ) +colvars: ( 0.0123869 , -0.0536698 , 0.0615628 ) +colvars: ( 0.00541679 , -0.0350638 , 0.0757509 ) +colvars: ( -0.00265456 , -0.00810989 , 0.0694037 ) +colvars: ( -0.00873565 , 0.0096343 , 0.0754172 ) +colvars: ( -0.00214667 , -0.00280869 , 0.040333 ) +colvars: ( -0.00582131 , 0.00980282 , 0.0360104 ) +colvars: ( 0.00270507 , -0.0131772 , 0.0195793 ) +colvars: ( 0.00411844 , -0.0108826 , -0.0088518 ) +colvars: ( 0.0091335 , -0.0224351 , -0.0267876 ) +colvars: ( 0.00875687 , -0.0240549 , -0.0149645 ) +colvars: ( 0.00667714 , -0.0138163 , -0.0304711 ) +colvars: ( 0.015045 , -0.0469573 , -0.00200341 ) +colvars: ( 0.0197259 , -0.0610739 , -0.0047027 ) +colvars: ( 0.0276129 , -0.0888591 , 0.0075935 ) +colvars: ( 0.0142634 , -0.0471023 , 0.0089864 ) +colvars: ( 0.0142323 , -0.0442627 , -0.00256088 ) +colvars: ( 0.00924191 , -0.03716 , 0.0337891 ) +colvars: ( 0.00305534 , -0.0211196 , 0.048379 ) +colvars: ( -0.000975781 , -0.015139 , 0.0767167 ) +colvars: ( -0.00383749 , 0.00426312 , 0.0330001 ) +colvars: ( -0.00590255 , 0.0113704 , 0.0304872 ) +colvars: ( -0.00733443 , 0.0180349 , 0.0214314 ) +colvars: ( -0.0132916 , 0.0409749 , 0.00391623 ) +colvars: ( -0.0162675 , 0.0522163 , -0.00391293 ) +colvars: ( -0.00971636 , 0.0358255 , -0.0218685 ) +colvars: ( -0.0137389 , 0.0501235 , -0.0286755 ) +colvars: ( -0.00192801 , 0.0147528 , -0.036533 ) +colvars: ( 0.00245324 , 0.00661149 , -0.0604197 ) +colvars: ( 0.0107072 , -0.0163287 , -0.0734021 ) +colvars: ( 0.00445442 , -0.00110729 , -0.0544831 ) +colvars: ( 0.00345699 , 0.00570554 , -0.0699323 ) +colvars: ( 0.00716724 , -0.0151253 , -0.0314656 ) +colvars: ( 0.0086198 , -0.0218908 , -0.022259 ) +colvars: ( 0.0130713 , -0.0416546 , 0.00187065 ) +colvars: ( 0.000523814 , 0.00165269 , -0.0139158 ) +colvars: ( 0.000458524 , 0.00325058 , -0.0197786 ) +colvars: ( -0.00653729 , 0.020641 , -0.000129024 ) +colvars: ( -0.0147481 , 0.0446476 , 0.0077884 ) +colvars: ( -0.0206393 , 0.0582186 , 0.0288568 ) +colvars: ( -0.0189545 , 0.0635759 , -0.0160775 ) +colvars: ( -0.0226616 , 0.0755941 , -0.0174704 ) +colvars: ( -0.0167206 , 0.0724879 , -0.0832736 ) +colvars: ( -0.0197818 , 0.0866444 , -0.102248 ) +colvars: ( -0.0084545 , 0.0464492 , -0.083367 ) +colvars: ( -0.0185642 , 0.0669307 , -0.0353896 ) +colvars: ( -0.0222544 , 0.084185 , -0.0590592 ) +colvars: ( -0.0242972 , 0.0930558 , -0.0692948 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 31. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 31. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atoms_new_colvar_forces = { ( -6.94062311976976e-02 , 3.03490162526349e-01 , -4.00977684676539e-01 ), ( 1.33250914292943e-02 , 3.21274159113017e-02 , -2.39673124267053e-01 ), ( -4.27240173299418e-02 , 9.56884710025728e-02 , 8.42538100974747e-02 ), ( -9.68992403195541e-02 , 2.49403270880954e-01 , 6.36550646087563e-02 ), ( -1.76876529227756e-02 , 9.80045407383212e-02 , -1.70832054059996e-01 ), ( 7.06801261970315e-02 , -1.84669520776609e-01 , -3.77111455843510e-02 ), ( 9.00854828343869e-03 , -9.88304975182526e-02 , 2.54321406257577e-01 ), ( -4.11436258006877e-02 , 5.91850265153628e-02 , 1.93022819474710e-01 ), ( 6.62954345819473e-02 , -1.91702333806160e-01 , 3.48621933243010e-02 ), ( 1.13332338741391e-01 , -3.91420878955913e-01 , 2.76575377836213e-01 ), ( 2.42872148797992e-02 , -9.94587130056355e-02 , 9.63943991230486e-02 ), ( 2.64100966633783e-02 , -9.75115436907893e-02 , 6.00056349308210e-02 ), ( 1.22262415576413e-02 , -5.58132199905036e-02 , 7.27230076112159e-02 ), ( 1.23868742972013e-02 , -5.36697943768003e-02 , 6.15627630782520e-02 ), ( 5.41679282312664e-03 , -3.50637919502010e-02 , 7.57509344298476e-02 ), ( -8.73564860535173e-03 , 9.63430126607937e-03 , 7.54172439511873e-02 ), ( -2.14667172436306e-03 , -2.80868609548290e-03 , 4.03330489817440e-02 ), ( -5.82131170575600e-03 , 9.80282071643300e-03 , 3.60104340994009e-02 ), ( 2.70507434291429e-03 , -1.31772377559795e-02 , 1.95793288634017e-02 ), ( 9.13350434142546e-03 , -2.24351165446065e-02 , -2.67876251701295e-02 ), ( 8.75686636115701e-03 , -2.40549319003777e-02 , -1.49644833891818e-02 ), ( 6.67714140247193e-03 , -1.38162687868113e-02 , -3.04710927408924e-02 ), ( 1.50450251745692e-02 , -4.69572561816395e-02 , -2.00341070693012e-03 ), ( 2.76129239088779e-02 , -8.88591444165270e-02 , 7.59350369394594e-03 ), ( 1.42633561864486e-02 , -4.71022538320507e-02 , 8.98640238438215e-03 ), ( 1.42323483168066e-02 , -4.42627395145504e-02 , -2.56087965676218e-03 ), ( 9.24190630524867e-03 , -3.71600388875369e-02 , 3.37890553737084e-02 ), ( -9.75780785785191e-04 , -1.51390239570636e-02 , 7.67166922117845e-02 ), ( -3.83748876882388e-03 , 4.26311527955189e-03 , 3.30001325447189e-02 ), ( -5.90255480909130e-03 , 1.13703876236472e-02 , 3.04871677339910e-02 ), ( -7.33442811574979e-03 , 1.80348763776466e-02 , 2.14314056086946e-02 ), ( -1.62675478976216e-02 , 5.22163018395812e-02 , -3.91292521691018e-03 ), ( -9.71635845312025e-03 , 3.58254697071210e-02 , -2.18684742275428e-02 ), ( -1.37388511966618e-02 , 5.01235438545573e-02 , -2.86754534301744e-02 ), ( -1.92800700867435e-03 , 1.47527874968520e-02 , -3.65330096949882e-02 ), ( 1.07072451090726e-02 , -1.63286881274528e-02 , -7.34020992469165e-02 ), ( 4.45442382316415e-03 , -1.10729458237341e-03 , -5.44830805548990e-02 ), ( 3.45699477161343e-03 , 5.70554105771488e-03 , -6.99322518035784e-02 ), ( 7.16724311301136e-03 , -1.51252971866452e-02 , -3.14655922184140e-02 ), ( 1.30713373800647e-02 , -4.16545922190191e-02 , 1.87064785303078e-03 ), ( 5.23813753763795e-04 , 1.65268772039421e-03 , -1.39158135611629e-02 ), ( 4.58524248322317e-04 , 3.25057971335603e-03 , -1.97786328645290e-02 ), ( -6.53728779931365e-03 , 2.06409550101289e-02 , -1.29023632259624e-04 ), ( -2.06393235201968e-02 , 5.82185808423522e-02 , 2.88568299399628e-02 ), ( -1.89545031374289e-02 , 6.35758809325615e-02 , -1.60775201326768e-02 ), ( -2.26616033796460e-02 , 7.55941014081297e-02 , -1.74704140838847e-02 ), ( -1.67206283762288e-02 , 7.24879315487866e-02 , -8.32736354364718e-02 ), ( -1.97818320480012e-02 , 8.66444186321444e-02 , -1.02248462678572e-01 ), ( -8.45450440118757e-03 , 4.64492240552549e-02 , -8.33670099030260e-02 ), ( -1.85641815327470e-02 , 6.69307057568639e-02 , -3.53895893594843e-02 ), ( -2.42972071567756e-02 , 9.30557656449630e-02 , -6.92948157148458e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 31, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 32 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 32, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 32, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 32, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 32, atoms_positions[size = 51] = { ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155027e-01 ), ( 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 ), ( 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 ), ( 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451151e-02 ), ( 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 ), ( 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 ), ( -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 ), ( -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 ), ( -3.66585660784361e+00 , 7.62856477282831e-02 , 5.48377527024691e+00 ), ( -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ), ( 8.28198546168908e+00 , 4.12774609412898e-02 , -6.98594743896480e-01 ), ( 7.00719717014731e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 ), ( 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 ), ( 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 ), ( 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 ), ( 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 ), ( 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 ), ( 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 ), ( 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 ), ( 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 ), ( 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 ), ( 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 ), ( 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 ), ( 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 ), ( 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 ), ( 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 ), ( 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 ), ( 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 ), ( 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 ), ( -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 ), ( 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 ), ( 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 ), ( -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013817e+00 ), ( -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 ), ( -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 ), ( -7.53250040458546e-01 , 5.44646798686886e+00 , 2.48270190089130e+00 ), ( -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 ), ( -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 ), ( -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 ), ( -3.35494631132017e+00 , 8.82615575571746e-01 , 7.96973196127045e-01 ), ( -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 ), ( -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 ), ( -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 ), ( -2.36418473395890e+00 , -3.03550327204905e-01 , 6.13032039751402e+00 ), ( -4.48692880047466e+00 , 9.30938001369169e-01 , 6.42485932408154e+00 ), ( -5.35487679866182e+00 , 5.62926127628069e-01 , 7.19598206069251e+00 ), ( -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246735e+00 ), ( -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 ), ( -6.62216635512164e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 ), ( -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 ), ( -4.00962749496156e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ) } +colvars: Step 32, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_ids[size = 0] = +colvars: Step 32, atom_groups_refcount[size = 0] = +colvars: Step 32, atom_groups_masses[size = 0] = +colvars: Step 32, atom_groups_charges[size = 0] = +colvars: Step 32, atom_groups_coms[size = 0] = +colvars: Step 32, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 32, volmaps_ids[size = 0] = +colvars: Step 32, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 32 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919956e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919956e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.221261 , 17.1781 , 17.2283 , 18.1312 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.221261 , 17.1781 , 17.2283 , 18.1312 ) to colvar "one". +colvars: Adding total bias energy: 11.5086 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.221261 , 17.1781 , 17.2283 , 18.1312 ) +colvars: Applying force on main group : +colvars: ( -0.0889966 , 0.385544 , -0.484377 ) +colvars: ( 0.0161089 , 0.0403116 , -0.309138 ) +colvars: ( -0.0469251 , 0.106636 , 0.0929461 ) +colvars: ( -0.116712 , 0.310432 , 0.0682395 ) +colvars: ( -0.0206486 , 0.119083 , -0.21918 ) +colvars: ( 0.0840272 , -0.225596 , -0.0415636 ) +colvars: ( 0.00641675 , -0.105429 , 0.314721 ) +colvars: ( -0.0498658 , 0.0809809 , 0.215323 ) +colvars: ( 0.0810874 , -0.236392 , 0.0272497 ) +colvars: ( 0.135508 , -0.475571 , 0.335779 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242651 , -0.0994226 , 0.0964113 ) +colvars: ( 0.0197397 , -0.0820481 , 0.0833257 ) +colvars: ( 0.0264067 , -0.0974935 , 0.0600493 ) +colvars: ( 0.0122094 , -0.0558056 , 0.0727396 ) +colvars: ( 0.0123728 , -0.0536574 , 0.0615761 ) +colvars: ( 0.00539703 , -0.0350715 , 0.0757649 ) +colvars: ( -0.00267591 , -0.00812928 , 0.0694092 ) +colvars: ( -0.00876013 , 0.00959882 , 0.0754225 ) +colvars: ( -0.00215672 , -0.00283169 , 0.0403462 ) +colvars: ( -0.00583294 , 0.00978005 , 0.0360145 ) +colvars: ( 0.00270685 , -0.0132032 , 0.0196097 ) +colvars: ( 0.00413183 , -0.0109113 , -0.0088124 ) +colvars: ( 0.00915834 , -0.0224686 , -0.0267291 ) +colvars: ( 0.00877258 , -0.0240689 , -0.0149272 ) +colvars: ( 0.00669691 , -0.0138319 , -0.0304358 ) +colvars: ( 0.0150578 , -0.0469561 , -0.00196613 ) +colvars: ( 0.0197397 , -0.0610577 , -0.00466808 ) +colvars: ( 0.0276255 , -0.0888285 , 0.00763289 ) +colvars: ( 0.0142672 , -0.0470827 , 0.00900259 ) +colvars: ( 0.0142391 , -0.0442389 , -0.00254786 ) +colvars: ( 0.00923372 , -0.0371431 , 0.0337926 ) +colvars: ( 0.00303683 , -0.0211018 , 0.0483646 ) +colvars: ( -0.00100672 , -0.0151237 , 0.0766918 ) +colvars: ( -0.00385334 , 0.00426865 , 0.0329818 ) +colvars: ( -0.00592025 , 0.0113801 , 0.0304597 ) +colvars: ( -0.00734539 , 0.0180249 , 0.0214205 ) +colvars: ( -0.0132983 , 0.0409523 , 0.00390429 ) +colvars: ( -0.0162701 , 0.0521774 , -0.00391572 ) +colvars: ( -0.00971228 , 0.0358069 , -0.0218729 ) +colvars: ( -0.0137353 , 0.0501034 , -0.0286878 ) +colvars: ( -0.00191392 , 0.0147401 , -0.0365219 ) +colvars: ( 0.00247783 , 0.00660416 , -0.0604005 ) +colvars: ( 0.0107421 , -0.016332 , -0.0733646 ) +colvars: ( 0.00447503 , -0.0010999 , -0.0544737 ) +colvars: ( 0.00348196 , 0.00571349 , -0.0699245 ) +colvars: ( 0.00717918 , -0.0151057 , -0.0314635 ) +colvars: ( 0.00862636 , -0.0218573 , -0.0222678 ) +colvars: ( 0.0130701 , -0.0416083 , 0.00185834 ) +colvars: ( 0.000521954 , 0.00168178 , -0.0139416 ) +colvars: ( 0.000457039 , 0.00328621 , -0.0198105 ) +colvars: ( -0.00654689 , 0.0206586 , -0.000162922 ) +colvars: ( -0.0147657 , 0.0446592 , 0.00773883 ) +colvars: ( -0.0206667 , 0.0582206 , 0.0287996 ) +colvars: ( -0.0189647 , 0.0635765 , -0.0161247 ) +colvars: ( -0.0226746 , 0.075596 , -0.0175281 ) +colvars: ( -0.0167023 , 0.0724741 , -0.0832944 ) +colvars: ( -0.0197577 , 0.0866235 , -0.102268 ) +colvars: ( -0.00843282 , 0.0464496 , -0.0833808 ) +colvars: ( -0.0185646 , 0.0669202 , -0.035423 ) +colvars: ( -0.0222471 , 0.0841636 , -0.059089 ) +colvars: ( -0.0242843 , 0.0930188 , -0.0693136 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 32. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 32. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atoms_new_colvar_forces = { ( -6.92568715614583e-02 , 3.03495735434584e-01 , -4.01051034554086e-01 ), ( 1.34329507330979e-02 , 3.21823421820297e-02 , -2.39728800701794e-01 ), ( -4.27932942514774e-02 , 9.57250229757168e-02 , 8.41336611203875e-02 ), ( -9.69721359131866e-02 , 2.49374374044742e-01 , 6.35713681489005e-02 ), ( -1.76117481642180e-02 , 9.79815145584645e-02 , -1.70815129298603e-01 ), ( 7.07288562482511e-02 , -1.84643583954109e-01 , -3.76592985999826e-02 ), ( 8.89458290762086e-03 , -9.88246374575186e-02 , 2.54320588792076e-01 ), ( -4.12394038835748e-02 , 5.91236247152377e-02 , 1.93055401124770e-01 ), ( 6.63217004345557e-02 , -1.91733043548502e-01 , 3.49885686528138e-02 ), ( 1.13260661861210e-01 , -3.91407351480788e-01 , 2.76689535486305e-01 ), ( 2.42651317273264e-02 , -9.94225742000947e-02 , 9.64113282701169e-02 ), ( 2.64066904536132e-02 , -9.74935399270448e-02 , 6.00492513226762e-02 ), ( 1.22093769543052e-02 , -5.58056399140129e-02 , 7.27395848120445e-02 ), ( 1.23728157982682e-02 , -5.36574167094586e-02 , 6.15761281158678e-02 ), ( 5.39702675372179e-03 , -3.50714933498933e-02 , 7.57648994879827e-02 ), ( -8.76013321362389e-03 , 9.59882429321861e-03 , 7.54225173037756e-02 ), ( -2.15671749599581e-03 , -2.83168923198219e-03 , 4.03462312173627e-02 ), ( -5.83293595863409e-03 , 9.78005162701339e-03 , 3.60144735560437e-02 ), ( 2.70685449391100e-03 , -1.32031518159557e-02 , 1.96096956238938e-02 ), ( 9.15834484476424e-03 , -2.24685704740751e-02 , -2.67290524869441e-02 ), ( 8.77257569498755e-03 , -2.40688502387905e-02 , -1.49271558255535e-02 ), ( 6.69690925220352e-03 , -1.38319295185637e-02 , -3.04358373033775e-02 ), ( 1.50577581290483e-02 , -4.69561111251409e-02 , -1.96613008527341e-03 ), ( 2.76254746082904e-02 , -8.88285207379886e-02 , 7.63288568266023e-03 ), ( 1.42671870557170e-02 , -4.70826991952575e-02 , 9.00259338710698e-03 ), ( 1.42390841263955e-02 , -4.42388910447388e-02 , -2.54785637659202e-03 ), ( 9.23371743643695e-03 , -3.71430769112850e-02 , 3.37926316895198e-02 ), ( -1.00671645139512e-03 , -1.51237006633047e-02 , 7.66917667387033e-02 ), ( -3.85333757609561e-03 , 4.26864830346807e-03 , 3.29817680526447e-02 ), ( -5.92025145185637e-03 , 1.13801197645519e-02 , 3.04596874187430e-02 ), ( -7.34538833041085e-03 , 1.80249123828996e-02 , 2.14204667214301e-02 ), ( -1.62700547283456e-02 , 5.21773794390723e-02 , -3.91571878647396e-03 ), ( -9.71227876735541e-03 , 3.58069340024963e-02 , -2.18728681348969e-02 ), ( -1.37353309403861e-02 , 5.01033977158764e-02 , -2.86878254222996e-02 ), ( -1.91392124870542e-03 , 1.47400910989978e-02 , -3.65219256023002e-02 ), ( 1.07420773702121e-02 , -1.63319578513661e-02 , -7.33645921720010e-02 ), ( 4.47502720517409e-03 , -1.09989696158710e-03 , -5.44737391135987e-02 ), ( 3.48196414612037e-03 , 5.71349460324854e-03 , -6.99244915959539e-02 ), ( 7.17917766055985e-03 , -1.51057032137927e-02 , -3.14635424487425e-02 ), ( 1.30701470184094e-02 , -4.16083430400286e-02 , 1.85834248014843e-03 ), ( 5.21954160713210e-04 , 1.68178454324210e-03 , -1.39416476691109e-02 ), ( 4.57038802683104e-04 , 3.28621433002094e-03 , -1.98104713257074e-02 ), ( -6.54689474568868e-03 , 2.06586185232721e-02 , -1.62922115952703e-04 ), ( -2.06666564338070e-02 , 5.82206186454470e-02 , 2.87996216213028e-02 ), ( -1.89646538418560e-02 , 6.35765442851976e-02 , -1.61247498604394e-02 ), ( -2.26746116772884e-02 , 7.55960018013675e-02 , -1.75281356896499e-02 ), ( -1.67022826530015e-02 , 7.24740620594433e-02 , -8.32944414820944e-02 ), ( -1.97577450187155e-02 , 8.66234931154464e-02 , -1.02268290532814e-01 ), ( -8.43281840311426e-03 , 4.64495839359491e-02 , -8.33807577121063e-02 ), ( -1.85646447386543e-02 , 6.69201891596660e-02 , -3.54230015720242e-02 ), ( -2.42842584287525e-02 , 9.30187950246104e-02 , -6.93135803589043e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 32, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 33 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 33, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 33, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 33, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 33, atoms_positions[size = 51] = { ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120442e-01 ), ( 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 ), ( 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 ), ( 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729124e-02 ), ( 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 ), ( 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 ), ( -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 ), ( -3.81293200553925e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 ), ( -3.66484332642688e+00 , 7.34445121413667e-02 , 5.48046255017265e+00 ), ( -4.80937207857509e+00 , 3.28709350636303e+00 , 7.23093439006143e+00 ), ( 8.27559967802095e+00 , 4.05062115642719e-02 , -6.93657807517061e-01 ), ( 7.00691465518316e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 ), ( 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 ), ( 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 ), ( 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 ), ( 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 ), ( 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 ), ( 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 ), ( 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 ), ( 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 ), ( 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 ), ( 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 ), ( 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 ), ( 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 ), ( 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 ), ( 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 ), ( 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 ), ( 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 ), ( 5.72398418120017e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 ), ( -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 ), ( 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 ), ( 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 ), ( -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 ), ( -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 ), ( -5.35408684950861e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 ), ( -7.59767399943052e-01 , 5.45187321071623e+00 , 2.48446362740502e+00 ), ( -2.75044654362177e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 ), ( -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 ), ( -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 ), ( -3.35259279459821e+00 , 8.86544438418595e-01 , 7.90248627130321e-01 ), ( -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 ), ( -5.44785168837972e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 ), ( -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345538e+00 ), ( -2.35760224718149e+00 , -2.97089451023095e-01 , 6.12941517052038e+00 ), ( -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 ), ( -5.35378412302326e+00 , 5.56844942923712e-01 , 7.19187592084459e+00 ), ( -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 ), ( -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 ), ( -6.61603045936864e+00 , 3.16825299393760e+00 , 5.55235673570187e+00 ), ( -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 ), ( -4.00672772214133e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ) } +colvars: Step 33, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_ids[size = 0] = +colvars: Step 33, atom_groups_refcount[size = 0] = +colvars: Step 33, atom_groups_masses[size = 0] = +colvars: Step 33, atom_groups_charges[size = 0] = +colvars: Step 33, atom_groups_coms[size = 0] = +colvars: Step 33, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 33, volmaps_ids[size = 0] = +colvars: Step 33, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 33 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99690134322553e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99690134322553e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.220695 , 17.1766 , 17.233 , 18.1296 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.220695 , 17.1766 , 17.233 , 18.1296 ) to colvar "one". +colvars: Adding total bias energy: 11.5093 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.220695 , 17.1766 , 17.233 , 18.1296 ) +colvars: Applying force on main group : +colvars: ( -0.0888475 , 0.385537 , -0.48456 ) +colvars: ( 0.0162487 , 0.0403215 , -0.309213 ) +colvars: ( -0.0470076 , 0.106688 , 0.0928646 ) +colvars: ( -0.116823 , 0.310454 , 0.0681315 ) +colvars: ( -0.0205629 , 0.119057 , -0.219218 ) +colvars: ( 0.0841019 , -0.225604 , -0.041494 ) +colvars: ( 0.00628156 , -0.105405 , 0.314773 ) +colvars: ( -0.0499869 , 0.0809667 , 0.215352 ) +colvars: ( 0.0811396 , -0.236437 , 0.0273803 ) +colvars: ( 0.135456 , -0.475578 , 0.335983 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242509 , -0.0993847 , 0.0964337 ) +colvars: ( 0.0197286 , -0.0820264 , 0.0833563 ) +colvars: ( 0.0264091 , -0.0974715 , 0.0600992 ) +colvars: ( 0.0121966 , -0.055795 , 0.0727624 ) +colvars: ( 0.0123628 , -0.0536429 , 0.0615942 ) +colvars: ( 0.0053798 , -0.0350751 , 0.0757866 ) +colvars: ( -0.00269649 , -0.00814458 , 0.0694225 ) +colvars: ( -0.00878527 , 0.00956878 , 0.0754375 ) +colvars: ( -0.00216709 , -0.00285067 , 0.0403658 ) +colvars: ( -0.0058454 , 0.00976042 , 0.0360238 ) +colvars: ( 0.00270796 , -0.0132241 , 0.0196464 ) +colvars: ( 0.00414362 , -0.010935 , -0.00876792 ) +colvars: ( 0.00918123 , -0.0224958 , -0.0266649 ) +colvars: ( 0.00878787 , -0.0240793 , -0.0148868 ) +colvars: ( 0.00671544 , -0.0138446 , -0.0303988 ) +colvars: ( 0.0150721 , -0.0469522 , -0.00192624 ) +colvars: ( 0.0197564 , -0.06104 , -0.00463271 ) +colvars: ( 0.027643 , -0.0887968 , 0.00767298 ) +colvars: ( 0.014274 , -0.047063 , 0.00901887 ) +colvars: ( 0.0142487 , -0.0442158 , -0.00253631 ) +colvars: ( 0.00922862 , -0.037126 , 0.0337975 ) +colvars: ( 0.0030213 , -0.0210848 , 0.0483511 ) +colvars: ( -0.00103435 , -0.015109 , 0.0766695 ) +colvars: ( -0.00386819 , 0.00427337 , 0.0329641 ) +colvars: ( -0.00593699 , 0.0113879 , 0.0304316 ) +colvars: ( -0.00735703 , 0.0180155 , 0.0214113 ) +colvars: ( -0.0133077 , 0.0409305 , 0.0038939 ) +colvars: ( -0.0162768 , 0.052141 , -0.00391532 ) +colvars: ( -0.00971105 , 0.0357887 , -0.0218776 ) +colvars: ( -0.0137354 , 0.0500828 , -0.0287015 ) +colvars: ( -0.00190199 , 0.014728 , -0.0365116 ) +colvars: ( 0.00250028 , 0.00659697 , -0.0603838 ) +colvars: ( 0.0107755 , -0.0163344 , -0.0733296 ) +colvars: ( 0.00449479 , -0.00109404 , -0.0544687 ) +colvars: ( 0.00350553 , 0.00571925 , -0.0699224 ) +colvars: ( 0.00719204 , -0.0150884 , -0.0314657 ) +colvars: ( 0.00863515 , -0.0218276 , -0.0222823 ) +colvars: ( 0.0130732 , -0.0415664 , 0.00184082 ) +colvars: ( 0.000521478 , 0.00170625 , -0.0139733 ) +colvars: ( 0.00045714 , 0.00331608 , -0.0198497 ) +colvars: ( -0.00655611 , 0.0206723 , -0.000201135 ) +colvars: ( -0.0147839 , 0.0446663 , 0.00768494 ) +colvars: ( -0.0206951 , 0.0582189 , 0.0287401 ) +colvars: ( -0.0189773 , 0.0635729 , -0.016177 ) +colvars: ( -0.0226904 , 0.0755926 , -0.0175919 ) +colvars: ( -0.0166892 , 0.0724569 , -0.0833221 ) +colvars: ( -0.0197403 , 0.0865993 , -0.102296 ) +colvars: ( -0.00841468 , 0.0464462 , -0.0834022 ) +colvars: ( -0.0185688 , 0.0669067 , -0.0354608 ) +colvars: ( -0.0222453 , 0.0841395 , -0.0591237 ) +colvars: ( -0.0242783 , 0.0929808 , -0.0693357 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 33. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 33. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atoms_new_colvar_forces = { ( -6.91188567735979e-02 , 3.03510290930652e-01 , -4.01204144218599e-01 ), ( 1.35521762003070e-02 , 3.21768778512665e-02 , -2.39790134003717e-01 ), ( -4.28639525555757e-02 , 9.57534430612640e-02 , 8.40967235066483e-02 ), ( -9.70663031948216e-02 , 2.49414118682993e-01 , 6.34987583733795e-02 ), ( -1.75415795560571e-02 , 9.79722684267187e-02 , -1.70866696053046e-01 ), ( 7.07942495838553e-02 , -1.84673272750277e-01 , -3.76001166998724e-02 ), ( 8.78184374387501e-03 , -9.88077937155113e-02 , 2.54389666713542e-01 ), ( -4.13517014975361e-02 , 5.91390874827820e-02 , 1.93069939999040e-01 ), ( 6.63557173096008e-02 , -1.91771135913036e-01 , 3.50652281889722e-02 ), ( 1.13210481361609e-01 , -3.91438934081905e-01 , 2.76859144441299e-01 ), ( 2.42508944679387e-02 , -9.93846540337704e-02 , 9.64336947828106e-02 ), ( 2.64090719407573e-02 , -9.74714705706512e-02 , 6.00992361309366e-02 ), ( 1.21965933010758e-02 , -5.57949721748439e-02 , 7.27624373994067e-02 ), ( 1.23627885303054e-02 , -5.36429148072454e-02 , 6.15941847800253e-02 ), ( 5.37979546280219e-03 , -3.50750987052205e-02 , 7.57866353155475e-02 ), ( -8.78526662946197e-03 , 9.56877620746106e-03 , 7.54375158033274e-02 ), ( -2.16709293495136e-03 , -2.85067072987600e-03 , 4.03657995178171e-02 ), ( -5.84539818911868e-03 , 9.76042249153602e-03 , 3.60238306868930e-02 ), ( 2.70796487908087e-03 , -1.32241296979077e-02 , 1.96464215489824e-02 ), ( 9.18123224966560e-03 , -2.24957783523680e-02 , -2.66648685481025e-02 ), ( 8.78786656590287e-03 , -2.40792626679961e-02 , -1.48867932591327e-02 ), ( 6.71543577080716e-03 , -1.38446172953135e-02 , -3.03987599525088e-02 ), ( 1.50720661069986e-02 , -4.69521524401563e-02 , -1.92623704629728e-03 ), ( 2.76430209908363e-02 , -8.87967682589699e-02 , 7.67298256261929e-03 ), ( 1.42739897167352e-02 , -4.70630029142168e-02 , 9.01887453976425e-03 ), ( 1.42486787822643e-02 , -4.42158363168287e-02 , -2.53630561326753e-03 ), ( 9.22861705229511e-03 , -3.71259922873568e-02 , 3.37975218579997e-02 ), ( -1.03434697133724e-03 , -1.51090259593529e-02 , 7.66694860475731e-02 ), ( -3.86818586249688e-03 , 4.27337270826742e-03 , 3.29640520152657e-02 ), ( -5.93698751092329e-03 , 1.13879312616528e-02 , 3.04315529874885e-02 ), ( -7.35703194127185e-03 , 1.80154944915386e-02 , 2.14113196413313e-02 ), ( -1.62767618705796e-02 , 5.21409602254909e-02 , -3.91531965756657e-03 ), ( -9.71104920550145e-03 , 3.57887071932448e-02 , -2.18775513745859e-02 ), ( -1.37353980805760e-02 , 5.00828269242235e-02 , -2.87014844466074e-02 ), ( -1.90198879974778e-03 , 1.47280365461961e-02 , -3.65116461378042e-02 ), ( 1.07754626664859e-02 , -1.63343561723597e-02 , -7.33296483410145e-02 ), ( 4.49479215925103e-03 , -1.09404148493303e-03 , -5.44686669481052e-02 ), ( 3.50552735386582e-03 , 5.71924557998363e-03 , -6.99223907581774e-02 ), ( 7.19204308392409e-03 , -1.50883876037312e-02 , -3.14656795197780e-02 ), ( 1.30732051974001e-02 , -4.15663983506900e-02 , 1.84081814203581e-03 ), ( 5.21478005410687e-04 , 1.70625332202461e-03 , -1.39733493818603e-02 ), ( 4.57140419366897e-04 , 3.31607765582657e-03 , -1.98497263687156e-02 ), ( -6.55610910963487e-03 , 2.06722915485128e-02 , -2.01135264238115e-04 ), ( -2.06950886573350e-02 , 5.82188855341263e-02 , 2.87400696279859e-02 ), ( -1.89772593961475e-02 , 6.35728929566774e-02 , -1.61769549127555e-02 ), ( -2.26904308970779e-02 , 7.55926189084028e-02 , -1.75918705795380e-02 ), ( -1.66892107294848e-02 , 7.24568921030755e-02 , -8.33220787125385e-02 ), ( -1.97402932869575e-02 , 8.65992546836357e-02 , -1.02295692485758e-01 ), ( -8.41467779143524e-03 , 4.64461590623506e-02 , -8.34021574859847e-02 ), ( -1.85688269232122e-02 , 6.69066565879082e-02 , -3.54607731899792e-02 ), ( -2.42783345375781e-02 , 9.29808248567057e-02 , -6.93357136511408e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 33, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 34 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 34, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 34, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 34, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 34, atoms_positions[size = 51] = { ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213235e-01 ), ( 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 ), ( 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 ), ( 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547472e-02 ), ( 1.27341573009207e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 ), ( 9.03067744585786e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 ), ( -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 ), ( -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 ), ( -3.66392163061900e+00 , 7.02059845558150e-02 , 5.47546908453679e+00 ), ( -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ), ( 8.26845026355394e+00 , 3.95164634150700e-02 , -6.88685005072648e-01 ), ( 7.00769008928434e+00 , -2.07938515079511e+00 , -8.46089877311366e-01 ), ( 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548920e-01 ), ( 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 ), ( 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 ), ( 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 ), ( 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 ), ( 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 ), ( 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 ), ( 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 ), ( 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473450e+00 ), ( 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 ), ( 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 ), ( 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 ), ( 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 ), ( 4.23609800543256e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 ), ( 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 ), ( 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 ), ( 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 ), ( -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 ), ( 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 ), ( 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 ), ( -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 ), ( -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 ), ( -5.31089467087467e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 ), ( -7.65716766890360e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 ), ( -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 ), ( -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 ), ( -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 ), ( -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354262e-01 ), ( -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 ), ( -5.43935071235475e+00 , 7.31389248939757e-01 , 3.35509424924392e+00 ), ( -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 ), ( -2.35030078449157e+00 , -2.90079848836045e-01 , 6.12958271650988e+00 ), ( -4.49013169330158e+00 , 9.46193862990713e-01 , 6.42562713694847e+00 ), ( -5.35296372957695e+00 , 5.50304318713275e-01 , 7.18777295484910e+00 ), ( -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 ), ( -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 ), ( -6.61130571979379e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 ), ( -4.10966101472105e+00 , 2.25473453690066e+00 , 6.41773857390378e+00 ), ( -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721327e+00 ) } +colvars: Step 34, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_ids[size = 0] = +colvars: Step 34, atom_groups_refcount[size = 0] = +colvars: Step 34, atom_groups_masses[size = 0] = +colvars: Step 34, atom_groups_charges[size = 0] = +colvars: Step 34, atom_groups_coms[size = 0] = +colvars: Step 34, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 34, volmaps_ids[size = 0] = +colvars: Step 34, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 34 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111081e-02 , 1.30981148586897e-02 , -1.46120262321522e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111081e-02 , 1.30981148586897e-02 , -1.46120262321522e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.219558 , 17.1767 , 17.2392 , 18.1264 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.219558 , 17.1767 , 17.2392 , 18.1264 ) to colvar "one". +colvars: Adding total bias energy: 11.5105 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.219558 , 17.1767 , 17.2392 , 18.1264 ) +colvars: Applying force on main group : +colvars: ( -0.0887166 , 0.385532 , -0.484832 ) +colvars: ( 0.0163966 , 0.0402676 , -0.309303 ) +colvars: ( -0.047089 , 0.10673 , 0.0928551 ) +colvars: ( -0.116955 , 0.310542 , 0.0680304 ) +colvars: ( -0.0204864 , 0.119043 , -0.219323 ) +colvars: ( 0.084194 , -0.225666 , -0.0414171 ) +colvars: ( 0.00615123 , -0.105367 , 0.314896 ) +colvars: ( -0.050124 , 0.081031 , 0.215371 ) +colvars: ( 0.0811992 , -0.236486 , 0.0274716 ) +colvars: ( 0.13543 , -0.475625 , 0.336251 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242445 , -0.0993459 , 0.0964622 ) +colvars: ( 0.0197234 , -0.0820021 , 0.0833938 ) +colvars: ( 0.0264171 , -0.0974463 , 0.0601554 ) +colvars: ( 0.012188 , -0.0557815 , 0.0727917 ) +colvars: ( 0.0123569 , -0.0536267 , 0.0616171 ) +colvars: ( 0.00536532 , -0.0350745 , 0.075816 ) +colvars: ( -0.00271597 , -0.00815525 , 0.0694433 ) +colvars: ( -0.00881062 , 0.00954512 , 0.0754618 ) +colvars: ( -0.00217761 , -0.00286519 , 0.0403912 ) +colvars: ( -0.00585847 , 0.00974451 , 0.0360381 ) +colvars: ( 0.00270844 , -0.01324 , 0.0196885 ) +colvars: ( 0.00415371 , -0.0109537 , -0.00871964 ) +colvars: ( 0.00920193 , -0.0225169 , -0.0265969 ) +colvars: ( 0.00880255 , -0.0240865 , -0.0148444 ) +colvars: ( 0.0067325 , -0.0138546 , -0.0303609 ) +colvars: ( 0.0150877 , -0.046946 , -0.0018844 ) +colvars: ( 0.0197758 , -0.0610219 , -0.00459693 ) +colvars: ( 0.0276652 , -0.0887652 , 0.00771368 ) +colvars: ( 0.0142836 , -0.0470439 , 0.00903535 ) +colvars: ( 0.0142609 , -0.0441944 , -0.00252603 ) +colvars: ( 0.0092266 , -0.0371092 , 0.0338041 ) +colvars: ( 0.00300888 , -0.0210688 , 0.0483394 ) +colvars: ( -0.00105835 , -0.0150948 , 0.0766509 ) +colvars: ( -0.00388185 , 0.00427753 , 0.0329475 ) +colvars: ( -0.00595256 , 0.0113941 , 0.0304036 ) +colvars: ( -0.00736917 , 0.0180071 , 0.0214041 ) +colvars: ( -0.0133195 , 0.0409102 , 0.00388486 ) +colvars: ( -0.0162874 , 0.052108 , -0.00391242 ) +colvars: ( -0.00971261 , 0.0357713 , -0.0218829 ) +colvars: ( -0.013739 , 0.0500624 , -0.0287167 ) +colvars: ( -0.00189233 , 0.0147167 , -0.0365027 ) +colvars: ( 0.00252032 , 0.00658963 , -0.0603704 ) +colvars: ( 0.010807 , -0.0163366 , -0.0732983 ) +colvars: ( 0.00451344 , -0.00109019 , -0.0544681 ) +colvars: ( 0.00352735 , 0.0057223 , -0.0699262 ) +colvars: ( 0.00720561 , -0.0150739 , -0.0314718 ) +colvars: ( 0.00864595 , -0.0218025 , -0.0223017 ) +colvars: ( 0.0130803 , -0.0415297 , 0.00181918 ) +colvars: ( 0.000522321 , 0.00172577 , -0.01401 ) +colvars: ( 0.000458742 , 0.00333977 , -0.0198952 ) +colvars: ( -0.00656484 , 0.0206821 , -0.000242711 ) +colvars: ( -0.0148024 , 0.0446694 , 0.00762788 ) +colvars: ( -0.0207242 , 0.0582143 , 0.0286794 ) +colvars: ( -0.0189921 , 0.0635656 , -0.0162333 ) +colvars: ( -0.0227088 , 0.0755848 , -0.0176606 ) +colvars: ( -0.0166815 , 0.0724369 , -0.0833567 ) +colvars: ( -0.0197296 , 0.0865723 , -0.102331 ) +colvars: ( -0.00840029 , 0.046439 , -0.0834313 ) +colvars: ( -0.0185766 , 0.0668908 , -0.0355026 ) +colvars: ( -0.022249 , 0.0841135 , -0.0591633 ) +colvars: ( -0.0242794 , 0.0929429 , -0.0693618 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 34. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 34. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atoms_new_colvar_forces = { ( -6.89931515523720e-02 , 3.03529453435325e-01 , -4.01438225063418e-01 ), ( 1.36805804611951e-02 , 3.21123159144449e-02 , -2.39859338329955e-01 ), ( -4.29352667358211e-02 , 9.57764098729455e-02 , 8.41354087339802e-02 ), ( -9.71793493942814e-02 , 2.49519950404404e-01 , 6.34334958307605e-02 ), ( -1.74775293005199e-02 , 9.79738898846051e-02 , -1.70983723879155e-01 ), ( 7.08744938792751e-02 , -1.84756089859670e-01 , -3.75322777943504e-02 ), ( 8.67155116481982e-03 , -9.87778464994404e-02 , 2.54526116207477e-01 ), ( -4.14780086993959e-02 , 5.92285323448908e-02 , 1.93069092917232e-01 ), ( 6.63968084260576e-02 , -1.91817057413589e-01 , 3.50994591677031e-02 ), ( 1.13181130747263e-01 , -3.91510994669006e-01 , 2.77087216958719e-01 ), ( 2.42445286609735e-02 , -9.93458642506380e-02 , 9.64622242692801e-02 ), ( 2.64170912653268e-02 , -9.74463301627498e-02 , 6.01553510528831e-02 ), ( 1.21880001742566e-02 , -5.57814893760357e-02 , 7.27916733558242e-02 ), ( 1.23568551091888e-02 , -5.36266530279977e-02 , 6.16171486908459e-02 ), ( 5.36532119084151e-03 , -3.50744606060441e-02 , 7.58160218574634e-02 ), ( -8.81061897949867e-03 , 9.54511730651302e-03 , 7.54617555207575e-02 ), ( -2.17760511040056e-03 , -2.86518723913951e-03 , 4.03912296616751e-02 ), ( -5.85846868302164e-03 , 9.74450841827336e-03 , 3.60381370606483e-02 ), ( 2.70844461247052e-03 , -1.32399871433099e-02 , 1.96885363244457e-02 ), ( 9.20192687987025e-03 , -2.25169446455836e-02 , -2.65968732719788e-02 ), ( 8.80255120781469e-03 , -2.40864736018276e-02 , -1.48443959207891e-02 ), ( 6.73250208365005e-03 , -1.38545990414471e-02 , -3.03609130906804e-02 ), ( 1.50877199996254e-02 , -4.69460167158572e-02 , -1.88440003463209e-03 ), ( 2.76651864173050e-02 , -8.87652480873047e-02 , 7.71367668824415e-03 ), ( 1.42835896453966e-02 , -4.70438788226700e-02 , 9.03535000251388e-03 ), ( 1.42609120931696e-02 , -4.41943703904300e-02 , -2.52602727794592e-03 ), ( 9.22660325372610e-03 , -3.71091704512848e-02 , 3.38041040625322e-02 ), ( -1.05835313619203e-03 , -1.50947778879150e-02 , 7.66508781959285e-02 ), ( -3.88184605550169e-03 , 4.27753341324615e-03 , 3.29475466990499e-02 ), ( -5.95255522011071e-03 , 1.13941067628747e-02 , 3.04035631838731e-02 ), ( -7.36916549274786e-03 , 1.80070942161374e-02 , 2.14040567647014e-02 ), ( -1.62874444626766e-02 , 5.21080227589862e-02 , -3.91242232744703e-03 ), ( -9.71261338380347e-03 , 3.57712555200729e-02 , -2.18828726157710e-02 ), ( -1.37389641632307e-02 , 5.00624491635394e-02 , -2.87166885471019e-02 ), ( -1.89232631851091e-03 , 1.47166616758053e-02 , -3.65027479143405e-02 ), ( 1.08069515486647e-02 , -1.63365926908086e-02 , -7.32982874652060e-02 ), ( 4.51343606296248e-03 , -1.09019322499418e-03 , -5.44680977153746e-02 ), ( 3.52735490621465e-03 , 5.72230291359508e-03 , -6.99262007192625e-02 ), ( 7.20560809590541e-03 , -1.50739359573486e-02 , -3.14717893114619e-02 ), ( 1.30803256344867e-02 , -4.15296746745539e-02 , 1.81917584866729e-03 ), ( 5.22321157891290e-04 , 1.72577325068763e-03 , -1.40099506251826e-02 ), ( 4.58742355604884e-04 , 3.33977328082308e-03 , -1.98952188702455e-02 ), ( -6.56483596370069e-03 , 2.06820949494386e-02 , -2.42711121581346e-04 ), ( -2.07242020794929e-02 , 5.82143300984994e-02 , 2.86793663983974e-02 ), ( -1.89921052856702e-02 , 6.35656362416375e-02 , -1.62333176260830e-02 ), ( -2.27087976362070e-02 , 7.55847985706018e-02 , -1.76605909183659e-02 ), ( -1.66814979147063e-02 , 7.24368891060878e-02 , -8.33567348746792e-02 ), ( -1.97295924656961e-02 , 8.65722790102330e-02 , -1.02331076952250e-01 ), ( -8.40029022578601e-03 , 4.64389575616804e-02 , -8.34312592396013e-02 ), ( -1.85765957934514e-02 , 6.68908166789611e-02 , -3.55026209993640e-02 ), ( -2.42793529811600e-02 , 9.29428836853372e-02 , -6.93618229473791e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 34, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 35 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 35, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 35, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 35, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 35, atoms_positions[size = 51] = { ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518404e-01 ), ( 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 ), ( 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 ), ( 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 ), ( 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 ), ( 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 ), ( -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 ), ( -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 ), ( -3.66312344819816e+00 , 6.67877799859193e-02 , 5.46916433855244e+00 ), ( -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103287e+00 ), ( 8.26061045679133e+00 , 3.83159872376038e-02 , -6.83729575836184e-01 ), ( 7.00950811364951e+00 , -2.08340936270183e+00 , -8.38373555072615e-01 ), ( 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 ), ( 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 ), ( 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 ), ( 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 ), ( 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486681e+00 ), ( 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 ), ( 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 ), ( 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 ), ( 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 ), ( 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 ), ( 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 ), ( 3.13674411350812e+00 , 2.65473647538066e+00 , -1.53101934024696e+00 ), ( 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 ), ( 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 ), ( 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 ), ( 2.09321874616618e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 ), ( 5.70469478379835e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 ), ( -6.04067745585490e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 ), ( 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 ), ( 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 ), ( -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233233e+00 ), ( -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 ), ( -5.26037504488993e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 ), ( -7.70948015201457e-01 , 5.46443699617149e+00 , 2.48736122784712e+00 ), ( -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 ), ( -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 ), ( -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 ), ( -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293812e-01 ), ( -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 ), ( -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 ), ( -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306037e+00 ), ( -2.34232995666455e+00 , -2.82710935135214e-01 , 6.13081751615586e+00 ), ( -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958555e+00 ), ( -5.35241375743554e+00 , 5.43401369702619e-01 , 7.18368666862339e+00 ), ( -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 ), ( -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 ), ( -6.60792606081237e+00 , 3.17278933049612e+00 , 5.56077186656671e+00 ), ( -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 ), ( -4.00406811080273e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ) } +colvars: Step 35, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_ids[size = 0] = +colvars: Step 35, atom_groups_refcount[size = 0] = +colvars: Step 35, atom_groups_masses[size = 0] = +colvars: Step 35, atom_groups_charges[size = 0] = +colvars: Step 35, atom_groups_coms[size = 0] = +colvars: Step 35, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 35, volmaps_ids[size = 0] = +colvars: Step 35, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 35 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858438e-02 , 1.28715966499478e-02 , -1.44634565196466e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858438e-02 , 1.28715966499478e-02 , -1.44634565196466e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.217828 , 17.1783 , 17.2468 , 18.1219 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.217828 , 17.1783 , 17.2468 , 18.1219 ) to colvar "one". +colvars: Adding total bias energy: 11.5124 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.217828 , 17.1783 , 17.2468 , 18.1219 ) +colvars: Applying force on main group : +colvars: ( -0.0886047 , 0.385522 , -0.485186 ) +colvars: ( 0.0165491 , 0.0401529 , -0.309408 ) +colvars: ( -0.047168 , 0.106763 , 0.0929072 ) +colvars: ( -0.117105 , 0.310689 , 0.0679324 ) +colvars: ( -0.0204197 , 0.119036 , -0.219489 ) +colvars: ( 0.0843001 , -0.225778 , -0.0413317 ) +colvars: ( 0.00602767 , -0.105314 , 0.315083 ) +colvars: ( -0.0502732 , 0.0811681 , 0.21538 ) +colvars: ( 0.0812645 , -0.236538 , 0.0275314 ) +colvars: ( 0.135429 , -0.475701 , 0.33658 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242457 , -0.099307 , 0.0964973 ) +colvars: ( 0.0197239 , -0.0819759 , 0.083438 ) +colvars: ( 0.0264304 , -0.0974191 , 0.0602171 ) +colvars: ( 0.0121836 , -0.0557655 , 0.0728271 ) +colvars: ( 0.0123549 , -0.053609 , 0.061645 ) +colvars: ( 0.00535374 , -0.0350696 , 0.0758525 ) +colvars: ( -0.00273406 , -0.00816094 , 0.069471 ) +colvars: ( -0.00883571 , 0.00952851 , 0.0754943 ) +colvars: ( -0.00218803 , -0.002875 , 0.0404217 ) +colvars: ( -0.00587187 , 0.0097327 , 0.0360568 ) +colvars: ( 0.00270837 , -0.0132508 , 0.0197348 ) +colvars: ( 0.00416207 , -0.0109677 , -0.00866901 ) +colvars: ( 0.00922028 , -0.0225325 , -0.026527 ) +colvars: ( 0.00881646 , -0.0240909 , -0.014801 ) +colvars: ( 0.00674794 , -0.0138623 , -0.0303233 ) +colvars: ( 0.0151044 , -0.0469384 , -0.00184135 ) +colvars: ( 0.0197972 , -0.0610043 , -0.00456109 ) +colvars: ( 0.0276914 , -0.0887352 , 0.00775484 ) +colvars: ( 0.0142957 , -0.047026 , 0.00905212 ) +colvars: ( 0.0142754 , -0.0441752 , -0.00251675 ) +colvars: ( 0.00922755 , -0.0370929 , 0.0338127 ) +colvars: ( 0.00299961 , -0.0210538 , 0.0483301 ) +colvars: ( -0.00107854 , -0.0150807 , 0.0766367 ) +colvars: ( -0.00389417 , 0.00428141 , 0.0329327 ) +colvars: ( -0.00596679 , 0.011399 , 0.0303765 ) +colvars: ( -0.00738156 , 0.0180001 , 0.0213987 ) +colvars: ( -0.0133334 , 0.0408922 , 0.00387691 ) +colvars: ( -0.0163017 , 0.0520793 , -0.00390783 ) +colvars: ( -0.0097168 , 0.035755 , -0.0218891 ) +colvars: ( -0.0137458 , 0.0500428 , -0.0287336 ) +colvars: ( -0.00188496 , 0.0147059 , -0.0364957 ) +colvars: ( 0.00253775 , 0.00658184 , -0.0603607 ) +colvars: ( 0.0108361 , -0.0163394 , -0.0732713 ) +colvars: ( 0.0045307 , -0.00108873 , -0.054472 ) +colvars: ( 0.00354716 , 0.00572228 , -0.0699358 ) +colvars: ( 0.00721959 , -0.0150628 , -0.0314815 ) +colvars: ( 0.00865845 , -0.0217825 , -0.0223251 ) +colvars: ( 0.0130911 , -0.0414988 , 0.00179469 ) +colvars: ( 0.000524349 , 0.00174026 , -0.0140503 ) +colvars: ( 0.000461675 , 0.00335719 , -0.0199455 ) +colvars: ( -0.006573 , 0.0206883 , -0.000286565 ) +colvars: ( -0.0148209 , 0.0446691 , 0.00756892 ) +colvars: ( -0.0207535 , 0.058208 , 0.0286187 ) +colvars: ( -0.0190089 , 0.0635556 , -0.0162928 ) +colvars: ( -0.0227293 , 0.0755735 , -0.0177331 ) +colvars: ( -0.016679 , 0.0724146 , -0.0833982 ) +colvars: ( -0.0197255 , 0.0865432 , -0.102374 ) +colvars: ( -0.00838973 , 0.0464281 , -0.0834677 ) +colvars: ( -0.0185877 , 0.0668734 , -0.0355481 ) +colvars: ( -0.0222577 , 0.0840866 , -0.0592078 ) +colvars: ( -0.0242869 , 0.0929059 , -0.0693923 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 35. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 35. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atoms_new_colvar_forces = { ( -6.88807360946586e-02 , 3.03546174506848e-01 , -4.01748229755430e-01 ), ( 1.38150532480895e-02 , 3.19920050341430e-02 , -2.39936826947338e-01 ), ( -4.30059550048689e-02 , 9.57958483467742e-02 , 8.42381958230144e-02 ), ( -9.73074704360655e-02 , 2.49684520874827e-01 , 6.33713523707342e-02 ), ( -1.74201151791814e-02 , 9.79823778111991e-02 , -1.71159035993790e-01 ), ( 7.09667533396045e-02 , -1.84885894825296e-01 , -3.74547956787869e-02 ), ( 8.56541917378931e-03 , -9.87326138352739e-02 , 2.54722745980557e-01 ), ( -4.16147347248275e-02 , 5.93856644975063e-02 , 1.93055283348347e-01 ), ( 6.64435907168653e-02 , -1.91869163125823e-01 , 3.51002760286789e-02 ), ( 1.13171124872205e-01 , -3.91614114049827e-01 , 2.77372205308533e-01 ), ( 2.42457448834940e-02 , -9.93070224567197e-02 , 9.64972929017528e-02 ), ( 2.64303690231682e-02 , -9.74191373119857e-02 , 6.02170552240258e-02 ), ( 1.21835519220548e-02 , -5.57655192466588e-02 , 7.28270609870343e-02 ), ( 1.23549210045000e-02 , -5.36090050053975e-02 , 6.16449699320789e-02 ), ( 5.35374003500272e-03 , -3.50695784504462e-02 , 7.58525382532428e-02 ), ( -8.83570700232431e-03 , 9.52850693697147e-03 , 7.54942754737820e-02 ), ( -2.18803122140737e-03 , -2.87499821449638e-03 , 4.04217065934371e-02 ), ( -5.87186847068820e-03 , 9.73270279833235e-03 , 3.60567731097607e-02 ), ( 2.70837477367324e-03 , -1.32507681744094e-02 , 1.97348271046726e-02 ), ( 9.22027924498694e-03 , -2.25325482849989e-02 , -2.65269833710351e-02 ), ( 8.81646329246599e-03 , -2.40909194584065e-02 , -1.48010224744674e-02 ), ( 6.74794204665999e-03 , -1.38622651450867e-02 , -3.03233386338981e-02 ), ( 1.51044276345387e-02 , -4.69383939076473e-02 , -1.84135275144504e-03 ), ( 2.76913826852593e-02 , -8.87352085322906e-02 , 7.75483897287111e-03 ), ( 1.42956864003069e-02 , -4.70259579292682e-02 , 9.05211661372034e-03 ), ( 1.42754387286164e-02 , -4.41751623983650e-02 , -2.51675453633898e-03 ), ( 9.22754823332048e-03 , -3.70929337651855e-02 , 3.38126538002123e-02 ), ( -1.07854362508034e-03 , -1.50806771148120e-02 , 7.66367273623760e-02 ), ( -3.89416842781480e-03 , 4.28140636220416e-03 , 3.29327218643407e-02 ), ( -5.96678550441179e-03 , 1.13990052816781e-02 , 3.03764693573408e-02 ), ( -7.38156070100471e-03 , 1.80001190670400e-02 , 2.13986614634106e-02 ), ( -1.63016928856876e-02 , 5.20793173793130e-02 , -3.90783217966117e-03 ), ( -9.71679604441101e-03 , 3.57549618897123e-02 , -2.18891358294395e-02 ), ( -1.37457928463725e-02 , 5.00428092109121e-02 , -2.87336088867497e-02 ), ( -1.88496398780748e-03 , 1.47059454600983e-02 , -3.64957084247095e-02 ), ( 1.08361435000648e-02 , -1.63393854324176e-02 , -7.32712852290432e-02 ), ( 4.53069842551565e-03 , -1.08873278149813e-03 , -5.44720111056568e-02 ), ( 3.54715952514465e-03 , 5.72228164961963e-03 , -6.99358433688926e-02 ), ( 7.21959067154382e-03 , -1.50627862598159e-02 , -3.14814510290332e-02 ), ( 1.30911314699056e-02 , -4.14987884092740e-02 , 1.79469385094992e-03 ), ( 5.24348506408817e-04 , 1.74025786394996e-03 , -1.40502650952513e-02 ), ( 4.61674806489523e-04 , 3.35719489023765e-03 , -1.99454895684732e-02 ), ( -6.57300468365555e-03 , 2.06883139076784e-02 , -2.86564847277621e-04 ), ( -2.07535322945684e-02 , 5.82079798474097e-02 , 2.86187002618328e-02 ), ( -1.90088824990835e-02 , 6.35555827272411e-02 , -1.62928456142045e-02 ), ( -2.27293407292263e-02 , 7.55735124075078e-02 , -1.77330614847095e-02 ), ( -1.66790254550069e-02 , 7.24145550891492e-02 , -8.33982228687755e-02 ), ( -1.97254993582460e-02 , 8.65431509733358e-02 , -1.02374417573546e-01 ), ( -8.38973467101069e-03 , 4.64280970315202e-02 , -8.34677033511890e-02 ), ( -1.85876716559441e-02 , 6.68734057428191e-02 , -3.55480668376697e-02 ), ( -2.42869446603211e-02 , 9.29058765273728e-02 , -6.93922885498936e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 35, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 36 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 36, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 36, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 36, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 36, atoms_positions[size = 51] = { ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460808e-01 ), ( 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 ), ( 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 ), ( 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643877e-02 ), ( 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 ), ( 9.14913692767032e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 ), ( -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 ), ( -3.82286114827543e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 ), ( -3.66247706101863e+00 , 6.34272909613127e-02 , 5.46201921848078e+00 ), ( -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252679e+00 ), ( 8.25217464544869e+00 , 3.69221958155763e-02 , -6.78843503334926e-01 ), ( 7.01230109825313e+00 , -2.08771896240021e+00 , -8.30893615702845e-01 ), ( 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221474e-01 ), ( 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 ), ( 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 ), ( 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 ), ( 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 ), ( 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 ), ( 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 ), ( 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 ), ( 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981678e+00 ), ( 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 ), ( 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 ), ( 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 ), ( 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 ), ( 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 ), ( 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 ), ( 2.09467021666479e+00 , -1.09528109816073e+00 , 2.02995905011222e+00 ), ( 5.69529133519057e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 ), ( -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 ), ( 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 ), ( 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 ), ( -3.55712677434050e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 ), ( -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 ), ( -5.20464387542565e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 ), ( -7.75358318910474e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 ), ( -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 ), ( -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 ), ( -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 ), ( -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839781e-01 ), ( -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 ), ( -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 ), ( -3.35934410802697e+00 , 7.13844953536182e-01 , 4.17234104677063e+00 ), ( -2.33377676810807e+00 , -2.75203274913520e-01 , 6.13304533363275e+00 ), ( -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 ), ( -5.35209341374793e+00 , 5.36256909713220e-01 , 7.17960272686383e+00 ), ( -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394096e+00 ), ( -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 ), ( -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 ), ( -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 ), ( -4.00404855626916e+00 , 4.62566455159043e+00 , 7.28513526460300e+00 ) } +colvars: Step 36, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_ids[size = 0] = +colvars: Step 36, atom_groups_refcount[size = 0] = +colvars: Step 36, atom_groups_masses[size = 0] = +colvars: Step 36, atom_groups_charges[size = 0] = +colvars: Step 36, atom_groups_coms[size = 0] = +colvars: Step 36, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 36, volmaps_ids[size = 0] = +colvars: Step 36, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 36 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956246e-02 , 1.26183883681986e-02 , -1.42839286474994e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956246e-02 , 1.26183883681986e-02 , -1.42839286474994e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.215512 , 17.1814 , 17.2553 , 18.1165 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.215512 , 17.1814 , 17.2553 , 18.1165 ) to colvar "one". +colvars: Adding total bias energy: 11.515 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.215512 , 17.1814 , 17.2553 , 18.1165 ) +colvars: Applying force on main group : +colvars: ( -0.0885123 , 0.3855 , -0.485612 ) +colvars: ( 0.0167021 , 0.0399823 , -0.309526 ) +colvars: ( -0.0472429 , 0.10679 , 0.0930085 ) +colvars: ( -0.117266 , 0.310885 , 0.0678334 ) +colvars: ( -0.0203634 , 0.119033 , -0.219706 ) +colvars: ( 0.0844161 , -0.225931 , -0.0412367 ) +colvars: ( 0.00591321 , -0.105243 , 0.315324 ) +colvars: ( -0.0504294 , 0.0813694 , 0.215382 ) +colvars: ( 0.0813332 , -0.23659 , 0.0275681 ) +colvars: ( 0.135449 , -0.475794 , 0.336965 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.024254 , -0.0992689 , 0.096539 ) +colvars: ( 0.0197298 , -0.0819484 , 0.0834884 ) +colvars: ( 0.0264483 , -0.097391 , 0.0602835 ) +colvars: ( 0.0121831 , -0.0557474 , 0.0728681 ) +colvars: ( 0.0123568 , -0.0535904 , 0.0616774 ) +colvars: ( 0.00534513 , -0.0350605 , 0.0758953 ) +colvars: ( -0.00275044 , -0.00816139 , 0.0695047 ) +colvars: ( -0.00885998 , 0.00951947 , 0.0755337 ) +colvars: ( -0.00219812 , -0.00287996 , 0.0404562 ) +colvars: ( -0.00588527 , 0.00972532 , 0.0360789 ) +colvars: ( 0.00270785 , -0.0132566 , 0.0197838 ) +colvars: ( 0.00416873 , -0.0109771 , -0.00861765 ) +colvars: ( 0.00923616 , -0.0225432 , -0.0264573 ) +colvars: ( 0.00882942 , -0.0240931 , -0.0147578 ) +colvars: ( 0.00676159 , -0.0138681 , -0.0302871 ) +colvars: ( 0.0151218 , -0.04693 , -0.00179794 ) +colvars: ( 0.0198203 , -0.060988 , -0.00452557 ) +colvars: ( 0.0277208 , -0.0887079 , 0.00779627 ) +colvars: ( 0.0143099 , -0.0470099 , 0.00906924 ) +colvars: ( 0.0142918 , -0.0441588 , -0.00250819 ) +colvars: ( 0.00923122 , -0.0370776 , 0.0338234 ) +colvars: ( 0.00299343 , -0.0210397 , 0.0483238 ) +colvars: ( -0.00109479 , -0.0150664 , 0.0766277 ) +colvars: ( -0.00390501 , 0.00428529 , 0.03292 ) +colvars: ( -0.00597951 , 0.011403 , 0.030351 ) +colvars: ( -0.00739394 , 0.017995 , 0.0213951 ) +colvars: ( -0.0133489 , 0.040877 , 0.00386976 ) +colvars: ( -0.0163189 , 0.0520555 , -0.00390245 ) +colvars: ( -0.00972332 , 0.0357402 , -0.0218966 ) +colvars: ( -0.0137555 , 0.0500244 , -0.0287523 ) +colvars: ( -0.00187988 , 0.0146958 , -0.036491 ) +colvars: ( 0.0025524 , 0.00657329 , -0.0603553 ) +colvars: ( 0.0108626 , -0.0163435 , -0.0732493 ) +colvars: ( 0.00454631 , -0.00109 , -0.0544802 ) +colvars: ( 0.00356466 , 0.00571885 , -0.069951 ) +colvars: ( 0.00723365 , -0.0150553 , -0.0314941 ) +colvars: ( 0.00867222 , -0.0217679 , -0.0223513 ) +colvars: ( 0.0131051 , -0.0414742 , 0.00176882 ) +colvars: ( 0.00052738 , 0.00174973 , -0.0140929 ) +colvars: ( 0.000465716 , 0.00336837 , -0.0199988 ) +colvars: ( -0.00658054 , 0.0206913 , -0.000331446 ) +colvars: ( -0.0148392 , 0.0446663 , 0.00750948 ) +colvars: ( -0.0207825 , 0.0582009 , 0.0285594 ) +colvars: ( -0.0190272 , 0.0635436 , -0.0163543 ) +colvars: ( -0.0227516 , 0.0755598 , -0.0178078 ) +colvars: ( -0.0166815 , 0.0723904 , -0.0834461 ) +colvars: ( -0.0197277 , 0.0865125 , -0.102425 ) +colvars: ( -0.008383 , 0.0464138 , -0.0835108 ) +colvars: ( -0.0186016 , 0.0668552 , -0.0355964 ) +colvars: ( -0.0222711 , 0.0840595 , -0.0592566 ) +colvars: ( -0.0243005 , 0.0928707 , -0.0694273 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 36. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 36. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atoms_new_colvar_forces = { ( -6.87825515010302e-02 , 3.03551175854197e-01 , -4.02123591707848e-01 ), ( 1.39516159518603e-02 , 3.18209001221920e-02 , -2.40021075355466e-01 ), ( -4.30741931969209e-02 , 9.58131187992767e-02 , 8.43908110464439e-02 ), ( -9.74454677719412e-02 , 2.49896651123009e-01 , 6.33078221622214e-02 ), ( -1.73699557572936e-02 , 9.79928227747052e-02 , -1.71382115313688e-01 ), ( 7.10671728779809e-02 , -1.85053619004943e-01 , -3.73669781672519e-02 ), ( 8.46560683046808e-03 , -9.86698209726457e-02 , 2.54968457116350e-01 ), ( -4.17572287925473e-02 , 5.96014738190170e-02 , 1.93030343635103e-01 ), ( 6.64939874414992e-02 , -1.91924129005420e-01 , 3.50776228827208e-02 ), ( 1.13178124270782e-01 , -3.91734979956619e-01 , 2.77708435582395e-01 ), ( 2.42540016505370e-02 , -9.92689443102836e-02 , 9.65390072894102e-02 ), ( 2.64483115922368e-02 , -9.73909658951079e-02 , 6.02835162651832e-02 ), ( 1.21830809877307e-02 , -5.57474384223472e-02 , 7.28680948982734e-02 ), ( 1.23567667227087e-02 , -5.35903711954581e-02 , 6.16773865701317e-02 ), ( 5.34512949395847e-03 , -3.50605336726781e-02 , 7.58953439322042e-02 ), ( -8.85997764673843e-03 , 9.51947116101916e-03 , 7.55337438274853e-02 ), ( -2.19811885413010e-03 , -2.87995808817898e-03 , 4.04561704955643e-02 ), ( -5.88526593724566e-03 , 9.72531991195740e-03 , 3.60789200428813e-02 ), ( 2.70785417124687e-03 , -1.32566301520369e-02 , 1.97838389513108e-02 ), ( 9.23615813287942e-03 , -2.25432107077568e-02 , -2.64573206711712e-02 ), ( 8.82941764911573e-03 , -2.40931117783055e-02 , -1.47578476036868e-02 ), ( 6.76159384954824e-03 , -1.38680730198555e-02 , -3.02871414148130e-02 ), ( 1.51218095131350e-02 , -4.69300222271671e-02 , -1.79794353022244e-03 ), ( 2.77208071616533e-02 , -8.87078872996008e-02 , 7.79627322118805e-03 ), ( 1.43098597663197e-02 , -4.70098544163797e-02 , 9.06924461340023e-03 ), ( 1.42917926844773e-02 , -4.41588435488001e-02 , -2.50818581251333e-03 ), ( 9.23122439443106e-03 , -3.70775907849662e-02 , 3.38233725284600e-02 ), ( -1.09478835120119e-03 , -1.50664198922653e-02 , 7.66276922034176e-02 ), ( -3.90500816429111e-03 , 4.28528625123975e-03 , 3.29200157247979e-02 ), ( -5.97950807729433e-03 , 1.14030284170730e-02 , 3.03510423802199e-02 ), ( -7.39394176377097e-03 , 1.79949563178355e-02 , 2.13950536392084e-02 ), ( -1.63189362527715e-02 , 5.20555115448216e-02 , -3.90244624481999e-03 ), ( -9.72332312549996e-03 , 3.57401858757540e-02 , -2.18966122390077e-02 ), ( -1.37555195126383e-02 , 5.00244400005668e-02 , -2.87523394191009e-02 ), ( -1.87987996734087e-03 , 1.46958439822277e-02 , -3.64909585650040e-02 ), ( 1.08626211982598e-02 , -1.63434687790130e-02 , -7.32493095287909e-02 ), ( 4.54630977618069e-03 , -1.09000456952993e-03 , -5.44802162169457e-02 ), ( 3.56465799952970e-03 , 5.71884565694859e-03 , -6.99510120052419e-02 ), ( 7.23365133628510e-03 , -1.50553158520898e-02 , -3.14940893290122e-02 ), ( 1.31050916705081e-02 , -4.14742340010639e-02 , 1.76882071273220e-03 ), ( 5.27380256966284e-04 , 1.74973163386150e-03 , -1.40928889578658e-02 ), ( 4.65715758364314e-04 , 3.36837393393765e-03 , -1.99988030791925e-02 ), ( -6.58053681650212e-03 , 2.06913214588559e-02 , -3.31446169875402e-04 ), ( -2.07825151365776e-02 , 5.82009297448728e-02 , 2.85593613051498e-02 ), ( -1.90271656243260e-02 , 6.35436180091860e-02 , -1.63543335215463e-02 ), ( -2.27515526488475e-02 , 7.55598273573979e-02 , -1.78077907924695e-02 ), ( -1.66815106120319e-02 , 7.23904387415431e-02 , -8.34460512800944e-02 ), ( -1.97276671460812e-02 , 8.65124958483396e-02 , -1.02425344852602e-01 ), ( -8.38299757725755e-03 , 4.64137645103610e-02 , -8.35108075184974e-02 ), ( -1.86016314754188e-02 , 6.68552036549514e-02 , -3.55964346198361e-02 ), ( -2.43005014289642e-02 , 9.28706910473661e-02 , -6.94273071096894e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 36, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 37 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 37, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 37, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 37, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 37, atoms_positions[size = 51] = { ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171618e-01 ), ( 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 ), ( 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 ), ( 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588425e-02 ), ( 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 ), ( 9.19169465945245e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 ), ( -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 ), ( -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 ), ( -3.66199545735369e+00 , 6.03753664064912e-02 , 5.45456574948843e+00 ), ( -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931395e+00 ), ( 8.24325423950952e+00 , 3.53606340058558e-02 , -6.74071896755363e-01 ), ( 7.01595064911502e+00 , -2.09226237248072e+00 , -8.23713639498106e-01 ), ( 6.10178478736824e+00 , -3.17827591276147e-01 , 8.15561834792713e-01 ), ( 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 ), ( 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 ), ( 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 ), ( 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 ), ( 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 ), ( 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757520e+00 ), ( 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 ), ( 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 ), ( 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 ), ( 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 ), ( 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 ), ( 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 ), ( 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 ), ( 2.01981272765407e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 ), ( 2.09593922434932e+00 , -1.09517162307367e+00 , 2.02627695012513e+00 ), ( 5.68648106130873e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 ), ( -6.10998899499221e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 ), ( 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 ), ( 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 ), ( -3.53783966258115e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 ), ( -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 ), ( -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 ), ( -7.78897366273469e-01 , 5.47909401918027e+00 , 2.48909074021991e+00 ), ( -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 ), ( -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 ), ( -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 ), ( -3.34173659956129e+00 , 9.09242156894626e-01 , 7.66376749024154e-01 ), ( -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 ), ( -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 ), ( -3.35601110578621e+00 , 7.08982263935928e-01 , 4.17614644200216e+00 ), ( -2.32477219663653e+00 , -2.67799335468043e-01 , 6.13612947330243e+00 ), ( -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 ), ( -5.35192634835997e+00 , 5.29009862298982e-01 , 7.17548197632397e+00 ), ( -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 ), ( -7.04702908508777e+00 , 4.30002272437193e+00 , 7.52014167082679e+00 ), ( -6.60462930316152e+00 , 3.17780650929997e+00 , 5.56735921475796e+00 ), ( -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 ), ( -4.00464293001051e+00 , 4.63648260149376e+00 , 7.28600629551503e+00 ) } +colvars: Step 37, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_ids[size = 0] = +colvars: Step 37, atom_groups_refcount[size = 0] = +colvars: Step 37, atom_groups_masses[size = 0] = +colvars: Step 37, atom_groups_charges[size = 0] = +colvars: Step 37, atom_groups_coms[size = 0] = +colvars: Step 37, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 37, volmaps_ids[size = 0] = +colvars: Step 37, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 37 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905548e-02 , -1.40858436164589e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905548e-02 , -1.40858436164589e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.212649 , 17.1858 , 17.2644 , 18.1106 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.212649 , 17.1858 , 17.2644 , 18.1106 ) to colvar "one". +colvars: Adding total bias energy: 11.5181 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.212649 , 17.1858 , 17.2644 , 18.1106 ) +colvars: Applying force on main group : +colvars: ( -0.0884397 , 0.385454 , -0.486093 ) +colvars: ( 0.0168504 , 0.0397618 , -0.309652 ) +colvars: ( -0.0473115 , 0.106812 , 0.0931446 ) +colvars: ( -0.117431 , 0.311116 , 0.0677293 ) +colvars: ( -0.0203179 , 0.119026 , -0.219961 ) +colvars: ( 0.0845366 , -0.226113 , -0.0411315 ) +colvars: ( 0.00581037 , -0.105151 , 0.315603 ) +colvars: ( -0.0505867 , 0.0816238 , 0.215374 ) +colvars: ( 0.0814022 , -0.236639 , 0.0275905 ) +colvars: ( 0.135487 , -0.475891 , 0.337396 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242685 , -0.0992325 , 0.0965872 ) +colvars: ( 0.0197404 , -0.0819204 , 0.0835444 ) +colvars: ( 0.0264701 , -0.097363 , 0.0603536 ) +colvars: ( 0.0121863 , -0.0557277 , 0.072914 ) +colvars: ( 0.0123621 , -0.0535712 , 0.061714 ) +colvars: ( 0.00533951 , -0.0350475 , 0.0759433 ) +colvars: ( -0.00276479 , -0.00815638 , 0.0695433 ) +colvars: ( -0.00888282 , 0.00951848 , 0.0755786 ) +colvars: ( -0.0022076 , -0.00287996 , 0.0404934 ) +colvars: ( -0.00589829 , 0.00972264 , 0.0361036 ) +colvars: ( 0.00270698 , -0.0132578 , 0.0198339 ) +colvars: ( 0.0041737 , -0.0109825 , -0.00856736 ) +colvars: ( 0.00924941 , -0.0225496 , -0.0263902 ) +colvars: ( 0.00884119 , -0.0240936 , -0.0147162 ) +colvars: ( 0.00677328 , -0.0138725 , -0.0302535 ) +colvars: ( 0.0151394 , -0.0469217 , -0.00175516 ) +colvars: ( 0.0198442 , -0.0609742 , -0.00449087 ) +colvars: ( 0.0277524 , -0.0886846 , 0.00783767 ) +colvars: ( 0.0143256 , -0.0469962 , 0.00908676 ) +colvars: ( 0.0143094 , -0.0441461 , -0.00250002 ) +colvars: ( 0.00923732 , -0.0370635 , 0.0338364 ) +colvars: ( 0.00299025 , -0.0210266 , 0.048321 ) +colvars: ( -0.00110699 , -0.0150517 , 0.0766244 ) +colvars: ( -0.00391421 , 0.00428947 , 0.0329099 ) +colvars: ( -0.00599054 , 0.0114066 , 0.0303281 ) +colvars: ( -0.00740599 , 0.017992 , 0.0213931 ) +colvars: ( -0.0133656 , 0.0408652 , 0.00386308 ) +colvars: ( -0.0163385 , 0.0520373 , -0.00389722 ) +colvars: ( -0.00973183 , 0.0357273 , -0.0219055 ) +colvars: ( -0.0137677 , 0.0500079 , -0.0287729 ) +colvars: ( -0.00187701 , 0.0146863 , -0.0364889 ) +colvars: ( 0.00256413 , 0.0065637 , -0.0603543 ) +colvars: ( 0.0108859 , -0.0163496 , -0.073233 ) +colvars: ( 0.00455999 , -0.00109433 , -0.0544924 ) +colvars: ( 0.00357957 , 0.0057117 , -0.0699712 ) +colvars: ( 0.0072474 , -0.0150519 , -0.031509 ) +colvars: ( 0.00868676 , -0.0217592 , -0.0223791 ) +colvars: ( 0.0131215 , -0.0414565 , 0.00174314 ) +colvars: ( 0.000531213 , 0.00175426 , -0.0141362 ) +colvars: ( 0.000470617 , 0.00337339 , -0.0200532 ) +colvars: ( -0.00658733 , 0.0206915 , -0.000375934 ) +colvars: ( -0.0148569 , 0.0446618 , 0.00745122 ) +colvars: ( -0.0208105 , 0.0581943 , 0.0285028 ) +colvars: ( -0.0190464 , 0.0635307 , -0.0164163 ) +colvars: ( -0.0227748 , 0.0755449 , -0.017883 ) +colvars: ( -0.0166885 , 0.0723652 , -0.0834995 ) +colvars: ( -0.0197356 , 0.086481 , -0.102483 ) +colvars: ( -0.00837998 , 0.0463962 , -0.0835596 ) +colvars: ( -0.0186179 , 0.0668371 , -0.0356468 ) +colvars: ( -0.0222885 , 0.0840332 , -0.0593092 ) +colvars: ( -0.0243192 , 0.0928383 , -0.0694669 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 37. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 37. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atoms_new_colvar_forces = { ( -6.86992555484974e-02 , 3.03533865507726e-01 , -4.02549057467857e-01 ), ( 1.40856347083700e-02 , 3.16054533617281e-02 , -2.40108723882893e-01 ), ( -4.31377610411099e-02 , 9.58292762145927e-02 , 8.45772221147907e-02 ), ( -9.75869154560516e-02 , 2.50142296885573e-01 , 6.32383876309269e-02 ), ( -1.73276221003673e-02 , 9.79997153046434e-02 , -1.71639856633221e-01 ), ( 7.11709823308420e-02 , -1.85247971867427e-01 , -3.72684595182543e-02 ), ( 8.37449646162987e-03 , -9.85873004139697e-02 , 2.55249027610009e-01 ), ( -4.18999502863235e-02 , 5.98646644222401e-02 , 1.92995396989750e-01 ), ( 6.65453214330516e-02 , -1.91977552169553e-01 , 3.50417318547983e-02 ), ( 1.13198840831002e-01 , -3.91857648237532e-01 , 2.78086587467602e-01 ), ( 2.42685311116601e-02 , -9.92325269053165e-02 , 9.65872421316358e-02 ), ( 2.64701156863432e-02 , -9.73629786194261e-02 , 6.03536160863482e-02 ), ( 1.21863057138768e-02 , -5.57276902573276e-02 , 7.29140401008523e-02 ), ( 1.23620577888413e-02 , -5.35712074899439e-02 , 6.17139569187324e-02 ), ( 5.33950914573618e-03 , -3.50474741441835e-02 , 7.59433411582639e-02 ), ( -8.88281993356189e-03 , 9.51847849516835e-03 , 7.55785515708698e-02 ), ( -2.20759731463681e-03 , -2.87996413681205e-03 , 4.04933637879491e-02 ), ( -5.89828602420452e-03 , 9.72264454596837e-03 , 3.61036089633233e-02 ), ( 2.70697939545164e-03 , -1.32577794042574e-02 , 1.98338955000179e-02 ), ( 9.24941364417830e-03 , -2.25496043655818e-02 , -2.63902426068050e-02 ), ( 8.84119091067351e-03 , -2.40935956604268e-02 , -1.47161864940914e-02 ), ( 6.77327853075890e-03 , -1.38725010943118e-02 , -3.02535239169240e-02 ), ( 1.51393890116988e-02 , -4.69216812545930e-02 , -1.75516266427916e-03 ), ( 2.77524492898462e-02 , -8.86845708413805e-02 , 7.83766833850180e-03 ), ( 1.43255768269100e-02 , -4.69962060586814e-02 , 9.08675655639762e-03 ), ( 1.43093962067837e-02 , -4.41460571780060e-02 , -2.50001761113216e-03 ), ( 9.23731630260701e-03 , -3.70634757084186e-02 , 3.38363984449440e-02 ), ( -1.10699471847077e-03 , -1.50517238825784e-02 , 7.66243735456773e-02 ), ( -3.91421362763155e-03 , 4.28946728051717e-03 , 3.29098700792866e-02 ), ( -5.99053525305987e-03 , 1.14065895810092e-02 , 3.03281077571817e-02 ), ( -7.40598527053743e-03 , 1.79919911555435e-02 , 2.13931244285798e-02 ), ( -1.63384629373081e-02 , 5.20372766884958e-02 , -3.89721869762519e-03 ), ( -9.73183297611762e-03 , 3.57273056791311e-02 , -2.19055389368894e-02 ), ( -1.37676619415743e-02 , 5.00079066655861e-02 , -2.87728945664571e-02 ), ( -1.87701437763671e-03 , 1.46863241700003e-02 , -3.64889093585485e-02 ), ( 1.08859301674395e-02 , -1.63495717571680e-02 , -7.32330047742821e-02 ), ( 4.55998687637418e-03 , -1.09432736090071e-03 , -5.44924110293288e-02 ), ( 3.57956536940772e-03 , 5.71169649747299e-03 , -6.99712434611576e-02 ), ( 7.24739952063045e-03 , -1.50518827154552e-02 , -3.15090206351926e-02 ), ( 1.31215493743308e-02 , -4.14564908669138e-02 , 1.74314223554916e-03 ), ( 5.31212991272961e-04 , 1.75425920777903e-03 , -1.41362226136182e-02 ), ( 4.70616521599423e-04 , 3.37339310139416e-03 , -2.00531767539541e-02 ), ( -6.58732737457220e-03 , 2.06915304154358e-02 , -3.75933503541312e-04 ), ( -2.08104666769918e-02 , 5.81943213728344e-02 , 2.85028017920970e-02 ), ( -1.90464014201955e-02 , 6.35306924938405e-02 , -1.64163462385557e-02 ), ( -2.27747747072922e-02 , 7.55448881774991e-02 , -1.78830097269419e-02 ), ( -1.66885178805266e-02 , 7.23651669999104e-02 , -8.34994688828352e-02 ), ( -1.97355628115301e-02 , 8.64810282483968e-02 , -1.02483200962999e-01 ), ( -8.37997841556806e-03 , 4.63962179161769e-02 , -8.35596291533627e-02 ), ( -1.86179094057264e-02 , 6.68370515009343e-02 , -3.56468487901190e-02 ), ( -2.43191986518237e-02 , 9.28382805005676e-02 , -6.94669041832188e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 37, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 38 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 38, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 38, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 38, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 38, atoms_positions[size = 51] = { ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114381e-01 ), ( 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 ), ( 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 ), ( 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556786e-02 ), ( 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975422e+00 ), ( 9.22097757526461e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 ), ( -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 ), ( -3.82716365577602e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 ), ( -3.66166853640507e+00 , 5.78854680676884e-02 , 5.44735153195077e+00 ), ( -4.79230652547135e+00 , 3.27021253565707e+00 , 7.18706754003824e+00 ), ( 8.23397334242518e+00 , 3.36629988416887e-02 , -6.69448059688789e-01 ), ( 7.02029295911994e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 ), ( 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545464e-01 ), ( 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 ), ( 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 ), ( 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 ), ( 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 ), ( 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522920e+00 ), ( 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 ), ( 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 ), ( 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 ), ( 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 ), ( 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868302e-01 ), ( 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 ), ( 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 ), ( 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 ), ( 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 ), ( 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 ), ( 5.67827189361794e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 ), ( -6.13967788582873e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 ), ( 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 ), ( 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 ), ( -3.51365065386000e-01 , 2.88588961715295e+00 , 4.91640875050460e+00 ), ( -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 ), ( -5.08771410005460e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 ), ( -7.81567996234711e-01 , 5.48701616412022e+00 , 2.48946663787883e+00 ), ( -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 ), ( -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 ), ( -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 ), ( -3.33868648611506e+00 , 9.16055538251035e-01 , 7.61631047253214e-01 ), ( -4.27757651872762e+00 , 1.01649290349519e+00 , 3.23714639246471e+00 ), ( -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 ), ( -3.35274399292602e+00 , 7.04100676066046e-01 , 4.17999176321870e+00 ), ( -2.31549361557950e+00 , -2.60750067046298e-01 , 6.13988294900187e+00 ), ( -4.48330176893684e+00 , 9.82575531416186e-01 , 6.42533908148497e+00 ), ( -5.35180750527742e+00 , 5.21809458288691e-01 , 7.17126620866168e+00 ), ( -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304484e+00 ), ( -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 ), ( -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 ), ( -4.12563405115866e+00 , 2.25335610553221e+00 , 6.43205928200358e+00 ), ( -4.00561105971608e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ) } +colvars: Step 38, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_ids[size = 0] = +colvars: Step 38, atom_groups_refcount[size = 0] = +colvars: Step 38, atom_groups_masses[size = 0] = +colvars: Step 38, atom_groups_charges[size = 0] = +colvars: Step 38, atom_groups_coms[size = 0] = +colvars: Step 38, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 38, volmaps_ids[size = 0] = +colvars: Step 38, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 38 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865609e-02 , 1.20819700460899e-02 , -1.38821562016640e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865609e-02 , 1.20819700460899e-02 , -1.38821562016640e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.209302 , 17.1913 , 17.2736 , 18.1046 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.209302 , 17.1913 , 17.2736 , 18.1046 ) to colvar "one". +colvars: Adding total bias energy: 11.5217 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.209302 , 17.1913 , 17.2736 , 18.1046 ) +colvars: Applying force on main group : +colvars: ( -0.088386 , 0.385376 , -0.48661 ) +colvars: ( 0.016989 , 0.0394997 , -0.30978 ) +colvars: ( -0.0473713 , 0.106829 , 0.0933004 ) +colvars: ( -0.117593 , 0.311369 , 0.0676164 ) +colvars: ( -0.0202833 , 0.119012 , -0.22024 ) +colvars: ( 0.0846555 , -0.226313 , -0.0410159 ) +colvars: ( 0.0057215 , -0.105036 , 0.315906 ) +colvars: ( -0.0507384 , 0.0819183 , 0.215358 ) +colvars: ( 0.0814678 , -0.236681 , 0.0276068 ) +colvars: ( 0.135538 , -0.475974 , 0.337859 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0242883 , -0.0991988 , 0.0966416 ) +colvars: ( 0.0197551 , -0.0818928 , 0.083605 ) +colvars: ( 0.0264948 , -0.0973364 , 0.060426 ) +colvars: ( 0.0121928 , -0.0557068 , 0.0729639 ) +colvars: ( 0.0123703 , -0.053552 , 0.0617541 ) +colvars: ( 0.00533681 , -0.0350307 , 0.0759952 ) +colvars: ( -0.00277681 , -0.00814581 , 0.0695855 ) +colvars: ( -0.00890361 , 0.00952589 , 0.0756269 ) +colvars: ( -0.0022162 , -0.00287498 , 0.0405319 ) +colvars: ( -0.00591054 , 0.00972491 , 0.0361298 ) +colvars: ( 0.00270583 , -0.0132545 , 0.0198832 ) +colvars: ( 0.00417699 , -0.0109841 , -0.00852009 ) +colvars: ( 0.00925989 , -0.0225524 , -0.0263283 ) +colvars: ( 0.00885153 , -0.0240929 , -0.0146775 ) +colvars: ( 0.00678282 , -0.013876 , -0.0302238 ) +colvars: ( 0.0151566 , -0.0469142 , -0.00171412 ) +colvars: ( 0.0198682 , -0.0609637 , -0.00445757 ) +colvars: ( 0.0277851 , -0.0886666 , 0.00787858 ) +colvars: ( 0.0143422 , -0.0469857 , 0.00910461 ) +colvars: ( 0.0143276 , -0.0441374 , -0.00249197 ) +colvars: ( 0.00924542 , -0.037051 , 0.0338518 ) +colvars: ( 0.0029899 , -0.0210144 , 0.0483224 ) +colvars: ( -0.00111514 , -0.0150364 , 0.0766273 ) +colvars: ( -0.00392164 , 0.00429422 , 0.0329027 ) +colvars: ( -0.00599968 , 0.0114101 , 0.0303085 ) +colvars: ( -0.00741734 , 0.0179916 , 0.0213927 ) +colvars: ( -0.0133828 , 0.0408575 , 0.0038566 ) +colvars: ( -0.0163594 , 0.0520253 , -0.00389311 ) +colvars: ( -0.00974188 , 0.0357167 , -0.0219161 ) +colvars: ( -0.0137816 , 0.0499938 , -0.0287952 ) +colvars: ( -0.00187626 , 0.0146774 , -0.0364899 ) +colvars: ( 0.00257281 , 0.00655283 , -0.0603581 ) +colvars: ( 0.0109056 , -0.0163584 , -0.073223 ) +colvars: ( 0.00457146 , -0.00110196 , -0.0545082 ) +colvars: ( 0.00359163 , 0.00570062 , -0.0699959 ) +colvars: ( 0.00726042 , -0.0150528 , -0.0315255 ) +colvars: ( 0.00870154 , -0.0217566 , -0.022407 ) +colvars: ( 0.0131397 , -0.041446 , 0.00171931 ) +colvars: ( 0.000535632 , 0.00175395 , -0.0141785 ) +colvars: ( 0.000476118 , 0.0033724 , -0.0201065 ) +colvars: ( -0.00659325 , 0.0206894 , -0.000418477 ) +colvars: ( -0.0148733 , 0.0446565 , 0.00739593 ) +colvars: ( -0.0208366 , 0.0581893 , 0.0284506 ) +colvars: ( -0.0190659 , 0.0635178 , -0.0164772 ) +colvars: ( -0.0227982 , 0.0755299 , -0.0179567 ) +colvars: ( -0.0166994 , 0.0723395 , -0.0835575 ) +colvars: ( -0.0197484 , 0.0864496 , -0.102547 ) +colvars: ( -0.00838046 , 0.0463758 , -0.083613 ) +colvars: ( -0.0186358 , 0.0668199 , -0.0356982 ) +colvars: ( -0.0223088 , 0.0840088 , -0.0593647 ) +colvars: ( -0.024342 , 0.0928097 , -0.0695109 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 38. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 38. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atoms_new_colvar_forces = { ( -6.86308206116251e-02 , 3.03483614991524e-01 , -4.03005467230188e-01 ), ( 1.42122004866687e-02 , 3.13538650225890e-02 , -2.40194902047227e-01 ), ( -4.31943237080591e-02 , 9.58453152835204e-02 , 8.47803175901869e-02 ), ( -9.77245156213514e-02 , 2.50405352501500e-01 , 6.31588211970295e-02 ), ( -1.72933931549215e-02 , 9.79973607673578e-02 , -1.71917156945550e-01 ), ( 7.12727321448884e-02 , -1.85456026954594e-01 , -3.71593100693835e-02 ), ( 8.29430983007023e-03 , -9.84834160035740e-02 , 2.55547810067643e-01 ), ( -4.20368158050724e-02 , 6.01617567264364e-02 , 1.92950990770399e-01 ), ( 6.65945023408876e-02 , -1.92024618939844e-01 , 3.50027046417249e-02 ), ( 1.13228932734361e-01 , -3.91964986992019e-01 , 2.78494124440071e-01 ), ( 2.42883201820208e-02 , -9.91987813394096e-02 , 9.66416199757184e-02 ), ( 2.64947648348943e-02 , -9.73364338961823e-02 , 6.04259622476607e-02 ), ( 1.21928076457344e-02 , -5.57068145202949e-02 , 7.29639460351480e-02 ), ( 1.23703282478627e-02 , -5.35520485838743e-02 , 6.17540627985405e-02 ), ( 5.33680830935799e-03 , -3.50306520250388e-02 , 7.59952094602463e-02 ), ( -8.90361352233686e-03 , 9.52588864838620e-03 , 7.56268806698402e-02 ), ( -2.21620231280117e-03 , -2.87498061072691e-03 , 4.05318787135928e-02 ), ( -5.91053580061553e-03 , 9.72490617764336e-03 , 3.61297622980792e-02 ), ( 2.70583315529539e-03 , -1.32544772276849e-02 , 1.98831553338981e-02 ), ( 9.25989089906256e-03 , -2.25524231939905e-02 , -2.63282702430853e-02 ), ( 8.85153296477523e-03 , -2.40929295219061e-02 , -1.46774587577451e-02 ), ( 6.78281666744161e-03 , -1.38760216221009e-02 , -3.02237522299002e-02 ), ( 1.51566055711864e-02 , -4.69141735790477e-02 , -1.71412442695696e-03 ), ( 2.77851147346442e-02 , -8.86665700485733e-02 , 7.87857868564020e-03 ), ( 1.43422027572354e-02 , -4.69856650191699e-02 , 9.10461085344261e-03 ), ( 1.43275767180269e-02 , -4.41374431611392e-02 , -2.49197110163824e-03 ), ( 9.24541543566428e-03 , -3.70509593640707e-02 , 3.38517921818639e-02 ), ( -1.11514134289475e-03 , -1.50363761218496e-02 , 7.66272962861233e-02 ), ( -3.92164379332093e-03 , 4.29421869707042e-03 , 3.29027198923366e-02 ), ( -5.99967910186779e-03 , 1.14100882546170e-02 , 3.03085239625797e-02 ), ( -7.41733786811938e-03 , 1.79915865282469e-02 , 2.13927487362460e-02 ), ( -1.63594388549170e-02 , 5.20252755586254e-02 , -3.89310930664072e-03 ), ( -9.74187732357990e-03 , 3.57167216706750e-02 , -2.19161002769431e-02 ), ( -1.37816216212824e-02 , 4.99938096396475e-02 , -2.87951941243782e-02 ), ( -1.87625613950849e-03 , 1.46773844030486e-02 , -3.64899362824451e-02 ), ( 1.09056209410314e-02 , -1.63583620058828e-02 , -7.32229830172713e-02 ), ( 4.57146300390369e-03 , -1.10195764427394e-03 , -5.45081993441415e-02 ), ( 3.59163170697867e-03 , 5.70061800575529e-03 , -6.99959399808052e-02 ), ( 7.26041751542734e-03 , -1.50528004946293e-02 , -3.15254859290255e-02 ), ( 1.31397398961161e-02 , -4.14460138981811e-02 , 1.71931122698228e-03 ), ( 5.35631856761167e-04 , 1.75395146515928e-03 , -1.41785278298944e-02 ), ( 4.76117787198403e-04 , 3.37239514763850e-03 , -2.01064513441219e-02 ), ( -6.59324679933046e-03 , 2.06893842474070e-02 , -4.18476613147334e-04 ), ( -2.08366128212283e-02 , 5.81893019564111e-02 , 2.84506088586252e-02 ), ( -1.90659163881719e-02 , 6.35178090703331e-02 , -1.64772486067613e-02 ), ( -2.27982067233440e-02 , 7.55299015632439e-02 , -1.79567088892806e-02 ), ( -1.66994361211408e-02 , 7.23394764221848e-02 , -8.35574744904818e-02 ), ( -1.97484391686671e-02 , 8.64495918792105e-02 , -1.02547043382609e-01 ), ( -8.38045756030608e-03 , 4.63758256138758e-02 , -8.36129911674441e-02 ), ( -1.86357970883621e-02 , 6.68198521875454e-02 , -3.56982452867784e-02 ), ( -2.43419891146704e-02 , 9.28096803384051e-02 , -6.95109079997762e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 38, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 39 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 39, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 39, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 39, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 39, atoms_positions[size = 51] = { ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116680e-01 ), ( 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 ), ( 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 ), ( 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925346e-02 ), ( 1.30134291871750e+00 , 1.65124561639393e-01 , 1.66688264750347e+00 ), ( 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 ), ( -1.46198923284116e+00 , 4.48031715232442e+00 , 3.40319926113214e+00 ), ( -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 ), ( -3.66146058229158e+00 , 5.61986142826135e-02 , 5.44089379923338e+00 ), ( -4.78936447974314e+00 , 3.26644842590914e+00 , 7.18028305985000e+00 ), ( 8.22446419823708e+00 , 3.18649479383654e-02 , -6.64989816298089e-01 ), ( 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 ), ( 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254841e-01 ), ( 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 ), ( 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 ), ( 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 ), ( 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 ), ( 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 ), ( 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 ), ( 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 ), ( 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 ), ( 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991723e+00 ), ( 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 ), ( 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 ), ( 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528189e-01 ), ( 4.37681313203302e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 ), ( 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 ), ( 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 ), ( 5.67045576176349e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 ), ( -6.16431681139151e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 ), ( 1.29461765027047e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 ), ( 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 ), ( -3.48478472967696e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 ), ( -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 ), ( -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 ), ( -7.83422856191321e-01 , 5.49518347305934e+00 , 2.48952532366079e+00 ), ( -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 ), ( -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 ), ( -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 ), ( -3.33555341340174e+00 , 9.23051989092355e-01 , 7.57539942689168e-01 ), ( -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702990e+00 ), ( -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 ), ( -3.34976062208996e+00 , 6.99485565685802e-01 , 4.18343622948658e+00 ), ( -2.30616158940055e+00 , -2.54299022897341e-01 , 6.14408467519650e+00 ), ( -4.47912226138258e+00 , 9.89222211089517e-01 , 6.42454983767422e+00 ), ( -5.35161281557211e+00 , 5.14805563214697e-01 , 7.16688596353334e+00 ), ( -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 ), ( -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 ), ( -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 ), ( -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231195e+00 ), ( -4.00670158436285e+00 , 4.65485176981042e+00 , 7.28690738849569e+00 ) } +colvars: Step 39, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_ids[size = 0] = +colvars: Step 39, atom_groups_refcount[size = 0] = +colvars: Step 39, atom_groups_masses[size = 0] = +colvars: Step 39, atom_groups_charges[size = 0] = +colvars: Step 39, atom_groups_coms[size = 0] = +colvars: Step 39, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 39, volmaps_ids[size = 0] = +colvars: Step 39, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 39 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.205562 , 17.1978 , 17.2824 , 18.0989 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.205562 , 17.1978 , 17.2824 , 18.0989 ) to colvar "one". +colvars: Adding total bias energy: 11.5258 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.205562 , 17.1978 , 17.2824 , 18.0989 ) +colvars: Applying force on main group : +colvars: ( -0.088349 , 0.385258 , -0.487139 ) +colvars: ( 0.0171129 , 0.0392063 , -0.309903 ) +colvars: ( -0.0474205 , 0.106845 , 0.0934601 ) +colvars: ( -0.117742 , 0.311626 , 0.0674918 ) +colvars: ( -0.0202591 , 0.118984 , -0.220526 ) +colvars: ( 0.0847664 , -0.226518 , -0.0408902 ) +colvars: ( 0.00564816 , -0.104898 , 0.316213 ) +colvars: ( -0.0508777 , 0.0822372 , 0.215331 ) +colvars: ( 0.0815265 , -0.236712 , 0.0276249 ) +colvars: ( 0.135594 , -0.476027 , 0.338338 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243121 , -0.0991688 , 0.0967014 ) +colvars: ( 0.0197729 , -0.0818665 , 0.0836688 ) +colvars: ( 0.026521 , -0.0973126 , 0.0604989 ) +colvars: ( 0.012202 , -0.0556855 , 0.0730166 ) +colvars: ( 0.0123809 , -0.0535335 , 0.0617969 ) +colvars: ( 0.00533681 , -0.0350105 , 0.0760494 ) +colvars: ( -0.00278631 , -0.00812977 , 0.0696297 ) +colvars: ( -0.00892181 , 0.00954179 , 0.0756767 ) +colvars: ( -0.00222371 , -0.00286513 , 0.0405702 ) +colvars: ( -0.00592164 , 0.00973218 , 0.0361562 ) +colvars: ( 0.00270448 , -0.0132471 , 0.0199297 ) +colvars: ( 0.00417866 , -0.0109825 , -0.0084778 ) +colvars: ( 0.00926749 , -0.0225524 , -0.0262739 ) +colvars: ( 0.00886021 , -0.0240917 , -0.0146431 ) +colvars: ( 0.00679008 , -0.0138791 , -0.030199 ) +colvars: ( 0.0151729 , -0.0469083 , -0.00167599 ) +colvars: ( 0.0198913 , -0.0609574 , -0.00442633 ) +colvars: ( 0.0278175 , -0.0886551 , 0.00791845 ) +colvars: ( 0.014359 , -0.0469788 , 0.0091227 ) +colvars: ( 0.0143456 , -0.0441336 , -0.00248381 ) +colvars: ( 0.009255 , -0.0370404 , 0.0338695 ) +colvars: ( 0.00299208 , -0.0210033 , 0.0483282 ) +colvars: ( -0.00111936 , -0.0150203 , 0.0766368 ) +colvars: ( -0.00392721 , 0.00429976 , 0.0328989 ) +colvars: ( -0.0060068 , 0.0114139 , 0.0302931 ) +colvars: ( -0.00742765 , 0.017994 , 0.0213938 ) +colvars: ( -0.0133998 , 0.0408542 , 0.00385004 ) +colvars: ( -0.0163809 , 0.05202 , -0.00389102 ) +colvars: ( -0.00975292 , 0.0357088 , -0.0219284 ) +colvars: ( -0.0137967 , 0.0499827 , -0.028819 ) +colvars: ( -0.00187741 , 0.0146691 , -0.0364943 ) +colvars: ( 0.00257847 , 0.00654055 , -0.0603668 ) +colvars: ( 0.0109213 , -0.0163704 , -0.0732197 ) +colvars: ( 0.00458055 , -0.00111301 , -0.0545271 ) +colvars: ( 0.00360072 , 0.00568557 , -0.0700243 ) +colvars: ( 0.0072723 , -0.0150583 , -0.0315427 ) +colvars: ( 0.00871597 , -0.0217602 , -0.0224335 ) +colvars: ( 0.0131588 , -0.0414431 , 0.00169894 ) +colvars: ( 0.000540413 , 0.00174905 , -0.014218 ) +colvars: ( 0.000481955 , 0.00336568 , -0.0201564 ) +colvars: ( -0.00659816 , 0.0206854 , -0.000457496 ) +colvars: ( -0.0148882 , 0.0446512 , 0.00734545 ) +colvars: ( -0.0208602 , 0.058187 , 0.0284044 ) +colvars: ( -0.0190849 , 0.063506 , -0.0165353 ) +colvars: ( -0.0228209 , 0.0755161 , -0.0180268 ) +colvars: ( -0.0167134 , 0.0723142 , -0.0836188 ) +colvars: ( -0.0197653 , 0.0864192 , -0.102616 ) +colvars: ( -0.00838404 , 0.0463531 , -0.0836695 ) +colvars: ( -0.0186545 , 0.0668045 , -0.0357494 ) +colvars: ( -0.0223311 , 0.0839872 , -0.059422 ) +colvars: ( -0.0243676 , 0.0927859 , -0.0695589 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 39. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 39. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atoms_new_colvar_forces = { ( -6.85760792996511e-02 , 3.03391190372132e-01 , -4.03470465038437e-01 ), ( 1.43266319462628e-02 , 3.10765577955413e-02 , -2.40273727195948e-01 ), ( -4.32418115472582e-02 , 9.58623311770646e-02 , 8.49822855712108e-02 ), ( -9.78506393239423e-02 , 2.50668249779756e-01 , 6.30654919349158e-02 ), ( -1.72669714438694e-02 , 9.79803550809251e-02 , -1.72197348799224e-01 ), ( 7.13666644571403e-02 , -1.85663666663476e-01 , -3.70401934232006e-02 ), ( 8.22663282605443e-03 , -9.83576242859787e-02 , 2.55846331786987e-01 ), ( -4.21617012069782e-02 , 6.04769641875639e-02 , 1.92897427331650e-01 ), ( 6.66383033413407e-02 , -1.92060723280848e-01 , 3.49703055971520e-02 ), ( 1.13262969450724e-01 , -3.92040115424842e-01 , 2.78915680074420e-01 ), ( 2.43120615818260e-02 , -9.91687871383144e-02 , 9.67014422689911e-02 ), ( 2.65210286567995e-02 , -9.73126436762223e-02 , 6.04989195122588e-02 ), ( 1.22019876372007e-02 , -5.56854705073975e-02 , 7.30166371651342e-02 ), ( 1.23809460844627e-02 , -5.35335097256021e-02 , 6.17968896446734e-02 ), ( 5.33680866413092e-03 , -3.50104986769918e-02 , 7.60494168987403e-02 ), ( -8.92180929547350e-03 , 9.54178500425490e-03 , 7.56767473291031e-02 ), ( -2.22371115869817e-03 , -2.86513208581145e-03 , 4.05702084627808e-02 ), ( -5.92164461686849e-03 , 9.73218229005266e-03 , 3.61562278670125e-02 ), ( 2.70448252725674e-03 , -1.32471106341959e-02 , 1.99297111740999e-02 ), ( 9.26749253439040e-03 , -2.25524145633818e-02 , -2.62739003345519e-02 ), ( 8.86020893235893e-03 , -2.40916843932129e-02 , -1.46430826543643e-02 ), ( 6.79008106829284e-03 , -1.38790942151789e-02 , -3.01990451011923e-02 ), ( 1.51728533578124e-02 , -4.69082884526167e-02 , -1.67599335757655e-03 ), ( 2.78174735877192e-02 , -8.86550992426879e-02 , 7.91844579743056e-03 ), ( 1.43590192425672e-02 , -4.69788314968345e-02 , 9.12269597050372e-03 ), ( 1.43455946611162e-02 , -4.41335513916129e-02 , -2.48380726608012e-03 ), ( 9.25500305278820e-03 , -3.70404219689552e-02 , 3.38695002708129e-02 ), ( -1.11936165716947e-03 , -1.50202702602189e-02 , 7.66368011977586e-02 ), ( -3.92721222202764e-03 , 4.29975912649857e-03 , 3.28989332702641e-02 ), ( -6.00679980196902e-03 , 1.14138917306432e-02 , 3.02930976450661e-02 ), ( -7.42765119826021e-03 , 1.79940255100832e-02 , 2.13937723184561e-02 ), ( -1.63809278079067e-02 , 5.20200431521570e-02 , -3.89101834427693e-03 ), ( -9.75291630201696e-03 , 3.57088137252074e-02 , -2.19283949849110e-02 ), ( -1.37966814091787e-02 , 4.99827360070345e-02 , -2.88190408100287e-02 ), ( -1.87740684913841e-03 , 1.46690549469220e-02 , -3.64943197340017e-02 ), ( 1.09213485123973e-02 , -1.63703636169440e-02 , -7.32197132080785e-02 ), ( 4.58054909200228e-03 , -1.11301381598280e-03 , -5.45270632193023e-02 ), ( 3.60071564144867e-03 , 5.68556530723015e-03 , -7.00243396038003e-02 ), ( 7.27230082340127e-03 , -1.50582502822533e-02 , -3.15426687678145e-02 ), ( 1.31588021489714e-02 , -4.14431027325793e-02 , 1.69893986732976e-03 ), ( 5.40413457436416e-04 , 1.74904516444129e-03 , -1.42180257520665e-02 ), ( 4.81955385624926e-04 , 3.36568253909044e-03 , -2.01564103345881e-02 ), ( -6.59816426575166e-03 , 2.06853833091742e-02 , -4.57496077723121e-04 ), ( -2.08601693150008e-02 , 5.81869588982627e-02 , 2.84043742803996e-02 ), ( -1.90849481901457e-02 , 6.35059990249224e-02 , -1.65352950682017e-02 ), ( -2.28209467504911e-02 , 7.55161082636293e-02 , -1.80267509733149e-02 ), ( -1.67134328831536e-02 , 7.23142221324330e-02 , -8.36188006345148e-02 ), ( -1.97652753228754e-02 , 8.64191632927915e-02 , -1.02615606437546e-01 ), ( -8.38403595659010e-03 , 4.63531251980092e-02 , -8.36694766979938e-02 ), ( -1.86544506501744e-02 , 6.68045394632732e-02 , -3.57494057868076e-02 ), ( -2.43675801969378e-02 , 9.27859360530459e-02 , -6.95588936316066e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 39, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: getnumatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumatoms" +colvars: Executing script function "cv_getnumatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: getnumactiveatoms +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatoms" +colvars: Executing script function "cv_getnumactiveatoms" +colvars: Called script run with 2 args: +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: cv +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: getnumactiveatomgroups +colvars: Using simple-cast script::obj_to_str(): result = "cv" +colvars: Using simple-cast script::obj_to_str(): result = "getnumactiveatomgroups" +colvars: Executing script function "cv_getnumactiveatomgroups" +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 40 +colvars: Updating atomic data arrays. +colvars: Updating positions arrays. +colvars: Updating group positions arrays. +colvars: Updating grid objects. +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } +colvars: Step 40, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 40, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 40, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 40, atoms_positions[size = 51] = { ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543952e-01 ), ( 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 ), ( 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 ), ( 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145887e-02 ), ( 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 ), ( 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 ), ( -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 ), ( -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 ), ( -3.66131282078092e+00 , 5.55259716682067e-02 , 5.43563780321032e+00 ), ( -4.78721531273729e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ), ( 8.21486247008991e+00 , 3.00039497048982e-02 , -6.60697462712691e-01 ), ( 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 ), ( 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528584e-01 ), ( 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 ), ( 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 ), ( 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 ), ( 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 ), ( 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896024e+00 ), ( 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 ), ( 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 ), ( 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 ), ( 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 ), ( 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 ), ( 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883072e+00 ), ( 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 ), ( 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 ), ( 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049652e+00 ), ( 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 ), ( 5.66268392317115e-01 , 6.44411030333317e-01 , 2.93545758947663e+00 ), ( -6.18281281150509e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 ), ( 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 ), ( 2.02515014278286e+00 , 2.79394318413906e+00 , 5.72833915031846e+00 ), ( -3.45150604495940e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 ), ( -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 ), ( -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 ), ( -7.84558308207992e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 ), ( -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 ), ( -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 ), ( -2.72175683744147e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 ), ( -3.33238449414696e+00 , 9.30098455178845e-01 , 7.54153994227607e-01 ), ( -4.27817669645113e+00 , 1.01230827582552e+00 , 3.22603647756983e+00 ), ( -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 ), ( -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427901e+00 ), ( -2.29703042167363e+00 , -2.48666237490765e-01 , 6.14849732461339e+00 ), ( -4.47429163821902e+00 , 9.93809554940078e-01 , 6.42347308377283e+00 ), ( -5.35121077038599e+00 , 5.08137902098546e-01 , 7.16226945729229e+00 ), ( -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781003e+00 ), ( -7.05853462677926e+00 , 4.28980729398598e+00 , 7.51013468005025e+00 ), ( -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 ), ( -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704306e+00 ), ( -4.00767500939248e+00 , 4.66160981547132e+00 , 7.28700289556107e+00 ) } +colvars: Step 40, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_ids[size = 0] = +colvars: Step 40, atom_groups_refcount[size = 0] = +colvars: Step 40, atom_groups_masses[size = 0] = +colvars: Step 40, atom_groups_charges[size = 0] = +colvars: Step 40, atom_groups_coms[size = 0] = +colvars: Step 40, atom_groups_total_forces[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: Step 40, volmaps_ids[size = 0] = +colvars: Step 40, volmaps_values[size = 0] = +colvars: ---------------------------------------------------------------------- +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module, step no. 40 +colvars: Calculating collective variables. +colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629676e-02 , 1.15959419288222e-02 , -1.35102502789138e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629676e-02 , 1.15959419288222e-02 , -1.35102502789138e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( -0.201549 , 17.205 , 17.2905 , 18.0939 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( -0.201549 , 17.205 , 17.2905 , 18.0939 ) to colvar "one". +colvars: Adding total bias energy: 11.53 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( -0.201549 , 17.205 , 17.2905 , 18.0939 ) +colvars: Applying force on main group : +colvars: ( -0.0883248 , 0.385093 , -0.487654 ) +colvars: ( 0.0172183 , 0.0388953 , -0.310013 ) +colvars: ( -0.0474577 , 0.10686 , 0.0936071 ) +colvars: ( -0.117871 , 0.311869 , 0.0673534 ) +colvars: ( -0.0202436 , 0.118937 , -0.220801 ) +colvars: ( 0.084863 , -0.226712 , -0.0407557 ) +colvars: ( 0.00559067 , -0.104738 , 0.316505 ) +colvars: ( -0.0509985 , 0.082562 , 0.215293 ) +colvars: ( 0.0815747 , -0.236729 , 0.0276524 ) +colvars: ( 0.135649 , -0.476037 , 0.338813 ) +colvars: Calculating fit forces. +colvars: Done calculating fit forces. +colvars: Applying force on the fitting group of main group: +colvars: ( 0.0243381 , -0.0991436 , 0.0967656 ) +colvars: ( 0.0197924 , -0.0818427 , 0.0837345 ) +colvars: ( 0.0265475 , -0.0972929 , 0.0605707 ) +colvars: ( 0.012213 , -0.0556644 , 0.0730707 ) +colvars: ( 0.0123931 , -0.0535163 , 0.0618414 ) +colvars: ( 0.00533908 , -0.0349877 , 0.0761042 ) +colvars: ( -0.00279328 , -0.00810871 , 0.0696743 ) +colvars: ( -0.00893702 , 0.00956575 , 0.075726 ) +colvars: ( -0.00222998 , -0.00285083 , 0.0406068 ) +colvars: ( -0.00593131 , 0.00974426 , 0.0361818 ) +colvars: ( 0.00270299 , -0.0132363 , 0.0199717 ) +colvars: ( 0.00417884 , -0.0109782 , -0.00844224 ) +colvars: ( 0.00927227 , -0.0225505 , -0.0262293 ) +colvars: ( 0.00886706 , -0.0240905 , -0.0146143 ) +colvars: ( 0.00679507 , -0.0138822 , -0.0301804 ) +colvars: ( 0.0151875 , -0.0469047 , -0.00164186 ) +colvars: ( 0.0199127 , -0.0609561 , -0.00439774 ) +colvars: ( 0.0278481 , -0.0886511 , 0.00795666 ) +colvars: ( 0.0143753 , -0.0469761 , 0.00914084 ) +colvars: ( 0.0143627 , -0.0441347 , -0.00247533 ) +colvars: ( 0.00926543 , -0.0370322 , 0.0338893 ) +colvars: ( 0.00299633 , -0.0209932 , 0.0483387 ) +colvars: ( -0.00112005 , -0.0150034 , 0.0766529 ) +colvars: ( -0.00393094 , 0.00430623 , 0.0328987 ) +colvars: ( -0.00601187 , 0.0114183 , 0.0302825 ) +colvars: ( -0.00743663 , 0.0179994 , 0.021396 ) +colvars: ( -0.0134158 , 0.0408557 , 0.00384319 ) +colvars: ( -0.0164019 , 0.0520218 , -0.00389172 ) +colvars: ( -0.00976432 , 0.0357039 , -0.0219424 ) +colvars: ( -0.013812 , 0.0499752 , -0.0288441 ) +colvars: ( -0.00188014 , 0.0146614 , -0.0365022 ) +colvars: ( 0.0025813 , 0.00652686 , -0.0603804 ) +colvars: ( 0.010933 , -0.0163859 , -0.0732233 ) +colvars: ( 0.00458721 , -0.00112738 , -0.0545483 ) +colvars: ( 0.00360687 , 0.00566677 , -0.0700555 ) +colvars: ( 0.00728271 , -0.0150682 , -0.0315597 ) +colvars: ( 0.0087295 , -0.02177 , -0.0224574 ) +colvars: ( 0.0131778 , -0.0414477 , 0.00168347 ) +colvars: ( 0.000545322 , 0.00174003 , -0.014253 ) +colvars: ( 0.000487858 , 0.00335387 , -0.0202009 ) +colvars: ( -0.00660199 , 0.0206801 , -0.000491529 ) +colvars: ( -0.014901 , 0.0446469 , 0.00730146 ) +colvars: ( -0.0208805 , 0.0581882 , 0.0283655 ) +colvars: ( -0.0191027 , 0.0634963 , -0.0165888 ) +colvars: ( -0.0228421 , 0.0755047 , -0.0180911 ) +colvars: ( -0.0167294 , 0.0722903 , -0.0836819 ) +colvars: ( -0.0197847 , 0.0863908 , -0.102687 ) +colvars: ( -0.00839007 , 0.0463289 , -0.0837274 ) +colvars: ( -0.0186729 , 0.066792 , -0.035799 ) +colvars: ( -0.0223541 , 0.0839695 , -0.0594797 ) +colvars: ( -0.0243944 , 0.092768 , -0.0696101 ) +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 40. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" +colvars: colvarmodule::end_of_step(), step = 40. +colvars: End of step for colvar "one". +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atoms_new_colvar_forces = { ( -6.85323667607085e-02 , 3.03250085633828e-01 , -4.03919244566743e-01 ), ( 1.44250120644039e-02 , 3.07866206325814e-02 , -2.40338909060198e-01 ), ( -4.32788268105407e-02 , 9.58815639835368e-02 , 8.51648417941772e-02 ), ( -9.79580001908215e-02 , 2.50912438003103e-01 , 6.29556416781234e-02 ), ( -1.72472401057155e-02 , 9.79440595116233e-02 , -1.72462588377445e-01 ), ( 7.14471883024387e-02 , -1.85855959156371e-01 , -3.69125172216922e-02 ), ( 8.17196163325179e-03 , -9.82110268157001e-02 , 2.56124884008761e-01 ), ( -4.22690273374395e-02 , 6.07920779777388e-02 , 1.92835186870276e-01 ), ( 6.66737009441522e-02 , -1.92081954588494e-01 , 3.49538806817385e-02 ), ( 1.13294551779845e-01 , -3.92067691417467e-01 , 2.79333500624614e-01 ), ( 2.43381070971489e-02 , -9.91435684382055e-02 , 9.67656042693870e-02 ), ( 2.65474804688020e-02 , -9.72928771737138e-02 , 6.05706743700988e-02 ), ( 1.22130220545263e-02 , -5.56644363052377e-02 , 7.30706999847849e-02 ), ( 1.23930794636728e-02 , -5.35162574221356e-02 , 6.18414015927799e-02 ), ( 5.33908232466113e-03 , -3.49877052428895e-02 , 7.61042263482980e-02 ), ( -8.93702422432012e-03 , 9.56574591985604e-03 , 7.57260345722720e-02 ), ( -2.22998076945108e-03 , -2.85083274124680e-03 , 4.06068065590374e-02 ), ( -5.93131133315950e-03 , 9.74426221995694e-03 , 3.61818108984666e-02 ), ( 2.70298600701359e-03 , -1.32362980851642e-02 , 1.99717264345225e-02 ), ( 9.27227028404926e-03 , -2.25504503061479e-02 , -2.62293277894644e-02 ), ( 8.86706074728804e-03 , -2.40904542112200e-02 , -1.46143142955973e-02 ), ( 6.79506980951520e-03 , -1.38821750859600e-02 , -3.01804053172093e-02 ), ( 1.51875404530745e-02 , -4.69047478317858e-02 , -1.64186260049467e-03 ), ( 2.78481343112598e-02 , -8.86510812523361e-02 , 7.95666205544641e-03 ), ( 1.43752539372569e-02 , -4.69761437538032e-02 , 9.14083867651916e-03 ), ( 1.43626830924914e-02 , -4.41347053823263e-02 , -2.47532915565276e-03 ), ( 9.26543336548817e-03 , -3.70321914229107e-02 , 3.38893091282548e-02 ), ( -1.12004885949660e-03 , -1.50034226484375e-02 , 7.66528774929137e-02 ), ( -3.93094451591357e-03 , 4.30623483933488e-03 , 3.28987164124701e-02 ), ( -6.01187124969791e-03 , 1.14183247352517e-02 , 3.02824521939553e-02 ), ( -7.43662755693067e-03 , 1.79994313113881e-02 , 2.13959799540316e-02 ), ( -1.64019199467728e-02 , 5.20217936348420e-02 , -3.89171641232288e-03 ), ( -9.76431618508571e-03 , 3.57038612670258e-02 , -2.19423983487685e-02 ), ( -1.38120095259618e-02 , 4.99751669683366e-02 , -2.88441005754843e-02 ), ( -1.88013590503811e-03 , 1.46613779011853e-02 , -3.65021572613942e-02 ), ( 1.09330016456256e-02 , -1.63858682409413e-02 , -7.32233385220953e-02 ), ( 4.58720889823015e-03 , -1.12738473805357e-03 , -5.45483074608205e-02 ), ( 3.60687333466525e-03 , 5.66676925795172e-03 , -7.00554557812025e-02 ), ( 7.28270763577972e-03 , -1.50681561528744e-02 , -3.15597043389583e-02 ), ( 1.31777917031141e-02 , -4.14476897041726e-02 , 1.68346700673696e-03 ), ( 5.45322168857217e-04 , 1.74002562910155e-03 , -1.42530289183739e-02 ), ( 4.87858268944159e-04 , 3.35386962129515e-03 , -2.02009403001517e-02 ), ( -6.60198593674321e-03 , 2.06801299134617e-02 , -4.91529279330384e-04 ), ( -2.08804561740570e-02 , 5.81882353586720e-02 , 2.83654816899834e-02 ), ( -1.91027000722412e-02 , 6.34962788800136e-02 , -1.65887744997137e-02 ), ( -2.28420590270769e-02 , 7.55047340022035e-02 , -1.80910514907058e-02 ), ( -1.67294107746415e-02 , 7.22903490015903e-02 , -8.36818944736092e-02 ), ( -1.97847172876338e-02 , 8.63908043813334e-02 , -1.02687251415262e-01 ), ( -8.39007040909995e-03 , 4.63288740292679e-02 , -8.37274147395396e-02 ), ( -1.86729126279069e-02 , 6.67920120077291e-02 , -3.57990212161275e-02 ), ( -2.43944182091028e-02 , 9.27679514953860e-02 , -6.96101218792903e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Step 40, volmaps_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +colvars: Saving collective variables state to "test.restart.colvars.state". +colvars: Using colvarproxy_namd::output_stream() +colvars: Writing formatted state for bias "harmonic1" diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped new file mode 100644 index 000000000..28d381db9 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,17 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x ( 0.99973970766145 , 0.014266190562968 , 0.011595941928822 , -0.013510250278914 ) +} + +restraint { + configuration { + step 40 + name harmonic1 + } +} + diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj new file mode 100644 index 000000000..cae2fd3bb --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one + 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ) ( -2.33415112386271e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) + 21 ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ) ( -2.29006853143000e-01 , 1.72135778158611e+01 , 1.72687267375248e+01 , 1.80464864475683e+01 ) + 22 ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072403e-02 , -1.24385326679425e-02 ) ( -2.25354457213011e-01 , 1.72171754135474e+01 , 1.72631618101901e+01 , 1.80562099325717e+01 ) + 23 ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ) ( -2.22544779088946e-01 , 1.72183237124724e+01 , 1.72567883292804e+01 , 1.80670193605806e+01 ) + 24 ( 9.99737489847089e-01 , 1.37893985756126e-02 , 1.27630697470619e-02 , -1.31113665114322e-02 ) ( -2.20603106002609e-01 , 1.72171554509598e+01 , 1.72500128724119e+01 , 1.80783704448867e+01 ) + 25 ( 9.99728636259111e-01 , 1.38933216876203e-02 , 1.29777530480417e-02 , -1.34613291247888e-02 ) ( -2.19486355870299e-01 , 1.72139646676619e+01 , 1.72432756028464e+01 , 1.80896940912098e+01 ) + 26 ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ) ( -2.19085878573173e-01 , 1.72091896600299e+01 , 1.72370208696570e+01 , 1.81004332960232e+01 ) + 27 ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ) ( -2.19239183005156e-01 , 1.72033736955944e+01 , 1.72316668936004e+01 , 1.81100807759075e+01 ) + 28 ( 9.99702390065719e-01 , 1.44141469092545e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ) ( -2.19748019832374e-01 , 1.71971104079588e+01 , 1.72275783419924e+01 , 1.81182129845822e+01 ) + 29 ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601430e-02 , -1.45578300084090e-02 ) ( -2.20399336095059e-01 , 1.71909839939957e+01 , 1.72250446125594e+01 , 1.81245164741949e+01 ) + 30 ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ) ( -2.20985728454130e-01 , 1.71855148115988e+01 , 1.72242650771018e+01 , 1.81288036297547e+01 ) + 31 ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250314e-02 , -1.47660205688039e-02 ) ( -2.21322757293946e-01 , 1.71811189756810e+01 , 1.72253411048109e+01 , 1.81310165171552e+01 ) + 32 ( 9.99688177857407e-01 , 1.49982495919956e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ) ( -2.21261370441172e-01 , 1.71780870762712e+01 , 1.72282738490838e+01 , 1.81312195438593e+01 ) + 33 ( 9.99690134322553e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ) ( -2.20694541572399e-01 , 1.71765830291102e+01 , 1.72329665905616e+01 , 1.81295834415202e+01 ) + 34 ( 9.99694127613340e-01 , 1.50525510111081e-02 , 1.30981148586897e-02 , -1.46120262321522e-02 ) ( -2.19558217033344e-01 , 1.71766598040325e+01 , 1.72392306187359e+01 , 1.81263642820461e+01 ) + 35 ( 9.99699846006243e-01 , 1.50116061858438e-02 , 1.28715966499478e-02 , -1.44634565196466e-02 ) ( -2.17827764309674e-01 , 1.71782851045968e+01 , 1.72467940429680e+01 , 1.81218814860652e+01 ) + 36 ( 9.99706901952671e-01 , 1.49283570956246e-02 , 1.26183883681986e-02 , -1.42839286474994e-02 ) ( -2.15512239618473e-01 , 1.71813676827162e+01 , 1.72553133391491e+01 , 1.81164979377424e+01 ) + 37 ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905548e-02 , -1.40858436164589e-02 ) ( -2.12649201856729e-01 , 1.71857754415149e+01 , 1.72643878203920e+01 , 1.81106036446139e+01 ) + 38 ( 9.99723286500429e-01 , 1.46513537865609e-02 , 1.20819700460899e-02 , -1.38821562016640e-02 ) ( -2.09302245721531e-01 , 1.71913399553369e+01 , 1.72735773588976e+01 , 1.81046024388439e+01 ) + 39 ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ) ( -2.05561935701077e-01 , 1.71978476772161e+01 , 1.72824235036234e+01 , 1.80988996968902e+01 ) + 40 ( 9.99739707661452e-01 , 1.42661905629676e-02 , 1.15959419288222e-02 , -1.35102502789138e-02 ) ( -2.01548974416543e-01 , 1.72050238188529e+01 , 1.72904735673894e+01 , 1.80938885690596e+01 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/namd-version.txt b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/namd-version.txt new file mode 100644 index 000000000..e1d311c69 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/namd-version.txt @@ -0,0 +1,3 @@ +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-06-04. +colvars: Using NAMD interface, version "2023-12-05". diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in new file mode 100644 index 000000000..6ea85dcd3 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in @@ -0,0 +1,31 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + orientation { + atoms { + indexGroup RMSD_atoms + centerToReference yes + rotateToReference yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + refPositionsFile rmsd_atoms_refpos.xyz + } +} + +harmonic { + colvars one + centers (0.9, 0.5, 0.5, 0.5) + forceConstant 10.0 +} From 147f6c80c0dedb92dfc8e1d93c9b50f8e16874df Mon Sep 17 00:00:00 2001 From: HanatoK Date: Tue, 17 Sep 2024 22:00:47 -0500 Subject: [PATCH 09/14] refactor: eliminate the buffer of fitting group forces --- src/colvaratoms.cpp | 93 ++++++++++++++++++++------------------------- src/colvaratoms.h | 44 +++++++++++++++------ 2 files changed, 74 insertions(+), 63 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index e4a507ef5..0b939cf34 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -921,15 +921,6 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) void cvm::atom_group::do_feature_side_effects(int id) { - // If enabled features are changed upstream, the features below should be refreshed - switch (id) { - case f_ag_fit_gradients: - if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) { - atom_group *group_for_fit = fitting_group ? fitting_group : this; - group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::atom_pos(0.0, 0.0, 0.0)); - } - break; - } } @@ -1218,15 +1209,22 @@ void cvm::atom_group::calc_fit_gradients() cvm::log("Calculating fit gradients.\n"); cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - auto accessor = [this](size_t i){return atoms[i].grad;}; + if (group_for_fit->fit_gradients.size() != group_for_fit->size()) { + group_for_fit->fit_gradients.assign(group_for_fit->size(), 0); + } else { + std::fill(group_for_fit->fit_gradients.begin(), + group_for_fit->fit_gradients.end(), 0); + } + auto accessor_main = [this](size_t i){return atoms[i].grad;}; + auto accessor_fitting = [&group_for_fit](size_t j, const cvm::rvector& grad){group_for_fit->fit_gradients[j] += grad;}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl(group_for_fit->fit_gradients, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (cvm::debug()) cvm::log("Done calculating fit gradients.\n"); @@ -1234,14 +1232,11 @@ void cvm::atom_group::calc_fit_gradients() template + typename main_force_accessor_T, typename fitting_force_accessor_T> void cvm::atom_group::calc_fit_forces_impl( - std::vector& forces_on_fitting_group, - main_force_accessor_T accessor) const { + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const { const cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - if (forces_on_fitting_group.size() != group_for_fit->size()) { - forces_on_fitting_group.assign(group_for_fit->size(), 0); - } // the center of geometry contribution to the gradients cvm::rvector atom_grad; // the rotation matrix contribution to the gradients @@ -1253,7 +1248,7 @@ void cvm::atom_group::calc_fit_forces_impl( for (size_t i = 0; i < size(); i++) { cvm::atom_pos pos_orig; if (B_ag_center) { - atom_grad += accessor(i); + atom_grad += accessor_main(i); if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); } else { if (B_ag_rotate) pos_orig = atoms[i].pos; @@ -1261,7 +1256,7 @@ void cvm::atom_group::calc_fit_forces_impl( if (B_ag_rotate) { // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i cvm::quaternion const dxdq = - rot.q.position_derivative_inner(pos_orig, accessor(i)); + rot.q.position_derivative_inner(pos_orig, accessor_main(i)); sum_dxdq[0] += dxdq[0]; sum_dxdq[1] += dxdq[1]; sum_dxdq[2] += dxdq[2]; @@ -1275,38 +1270,37 @@ void cvm::atom_group::calc_fit_forces_impl( // loop 2: iterate over the fitting group if (B_ag_rotate) rot_deriv->prepare_derivative(rotation_derivative_dldq::use_dq); for (size_t j = 0; j < group_for_fit->size(); j++) { + cvm::rvector fitting_force_grad{0, 0, 0}; if (B_ag_center) { - forces_on_fitting_group[j] = atom_grad; + fitting_force_grad += atom_grad; } if (B_ag_rotate) { rot_deriv->calc_derivative_wrt_group1(j, nullptr, &dq0_1); // multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients - forces_on_fitting_group[j] += sum_dxdq[0] * dq0_1[0] + - sum_dxdq[1] * dq0_1[1] + - sum_dxdq[2] * dq0_1[2] + - sum_dxdq[3] * dq0_1[3]; + fitting_force_grad += sum_dxdq[0] * dq0_1[0] + + sum_dxdq[1] * dq0_1[1] + + sum_dxdq[2] * dq0_1[2] + + sum_dxdq[3] * dq0_1[3]; + } + if (cvm::debug()) { + cvm::log(cvm::to_str(fitting_force_grad)); } + accessor_fitting(j, fitting_force_grad); } } - +template void cvm::atom_group::calc_fit_forces( - const std::vector& forces_on_main_group, - std::vector& forces_on_fitting_group) const { - if (cvm::debug()) - cvm::log("Calculating fit forces.\n"); - auto accessor = [&forces_on_main_group](size_t i){return forces_on_main_group[i];}; + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const { if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl(forces_on_fitting_group, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl(forces_on_fitting_group, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_forces_impl(forces_on_fitting_group, accessor); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_forces_impl(forces_on_fitting_group, accessor); - - if (cvm::debug()) - cvm::log("Done calculating fit forces.\n"); + calc_fit_forces_impl(accessor_main, accessor_fitting); } @@ -1500,12 +1494,6 @@ m_has_fitting_force(m_ag->is_enabled(f_ag_center) || m_ag->is_enabled(f_ag_rotat std::fill(m_ag->group_forces.begin(), m_ag->group_forces.end(), 0); } - if (m_ag->fitting_group_forces.size() != m_group_for_fit->size()) { - m_ag->fitting_group_forces.assign(m_group_for_fit->size(), 0); - } else { - std::fill(m_ag->fitting_group_forces.begin(), - m_ag->fitting_group_forces.end(), 0); - } } } @@ -1542,15 +1530,16 @@ void cvm::atom_group::group_force_object::apply_force_with_fitting_group() { // group, but checking this flag can mimic results that the users expect (if // "enableFitGradients no" then there is no force on the fitting group). if (m_ag->is_enabled(f_ag_fit_gradients)) { - m_ag->calc_fit_forces(m_ag->group_forces, m_ag->fitting_group_forces); + auto accessor_main = [this](size_t i){return m_ag->group_forces[i];}; + auto accessor_fitting = [this](size_t j, const cvm::rvector& fitting_force){ + (*(m_group_for_fit))[j].apply_force(fitting_force); + }; if (cvm::debug()) { cvm::log("Applying force on the fitting group of main group" + m_ag->name + ":\n"); } - for (size_t ia = 0; ia < m_group_for_fit->size(); ia++) { - (*(m_group_for_fit))[ia].apply_force(m_ag->fitting_group_forces[ia]); - if (cvm::debug()) { - cvm::log(cvm::to_str(m_ag->fitting_group_forces[ia])); - } + m_ag->calc_fit_forces(accessor_main, accessor_fitting); + if (cvm::debug()) { + cvm::log("Done applying force on the fitting group of main group" + m_ag->name + ":\n"); } } } diff --git a/src/colvaratoms.h b/src/colvaratoms.h index 5c96b307e..bb1c10ed5 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -257,8 +257,8 @@ class colvarmodule::atom_group /// \brief Index in the colvarproxy arrays (if the group is scalable) int index; + /// \brief The forces acting on the group atoms (stored mainly used for calculating the fitting group forces) std::vector group_forces; - std::vector fitting_group_forces; public: @@ -514,25 +514,47 @@ class colvarmodule::atom_group /// \brief Calculate the derivatives of the fitting transformation void calc_fit_gradients(); - void calc_fit_forces( - const std::vector& forces_on_main_group, - std::vector& forces_on_fitting_group) const; - -/*! @brief Actual implementation of `calc_fit_gradients`. The template is +/*! @brief Actual implementation of `calc_fit_gradients` and + * `calc_fit_forces`. The template is * used to avoid branching inside the loops in case that the CPU * branch prediction is broken (or further migration to GPU code). * @tparam B_ag_center Centered the reference to origin? This should follow * the value of `is_enabled(f_ag_center)`. * @tparam B_ag_rotate Calculate the optimal rotation? This should follow * the value of `is_enabled(f_ag_rotate)`. + * @tparam main_force_accessor_T The type of accessor of the main + * group forces or gradients. + * @tparam fitting_force_accessor_T The type of accessor of the fitting group + * forces or gradients. + * @param accessor_main The accessor of the main group forces or gradients. + * accessor_main(i) should return the i-th force or gradient of the + * main group. + * @param accessor_fitting The accessor of the fitting group forces or gradients. + * accessor_fitting(j, v) should store/apply the j-th atom gradient or + * force in the fitting group. */ - // template void calc_fit_gradients_impl(); - template + typename main_force_accessor_T, typename fitting_force_accessor_T> void calc_fit_forces_impl( - std::vector& forces_on_fitting_group, - main_force_accessor_T accessor) const; + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const; + +/*! @brief Calculate or apply the fitting group forces from the main group forces. + * @tparam main_force_accessor_T The type of accessor of the main + * group forces or gradients. + * @tparam fitting_force_accessor_T The type of accessor of the fitting group + * forces or gradients. + * @param accessor_main The accessor of the main group forces or gradients. + * accessor_main(i) should return the i-th force or gradient of the + * main group. + * @param accessor_fitting The accessor of the fitting group forces or gradients. + * accessor_fitting(j, v) should store/apply the j-th atom gradient or + * force in the fitting group. + */ + template + void calc_fit_forces( + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const; /// \brief Derivatives of the fitting transformation std::vector fit_gradients; From e6a4e1621803d8e851b0978905439441e88824ca Mon Sep 17 00:00:00 2001 From: HanatoK Date: Mon, 23 Sep 2024 15:47:55 -0500 Subject: [PATCH 10/14] test: compare the results from Colvars with those of pytorch This commit dumps the Cartesian coordinates of each frame, which can be read by the compare_with_pytorch.py. compare_with_pytorch.py then calculates the forces on the main and the fitting groups by symbolic gradients, and compares them with the Colvars debug output. --- .../AutoDiff/test.colvars.out | 2465 +++++++++++++++- .../AutoDiff/test.colvars.state.stripped | 10 + .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 2562 ++++++++++++++++- .../test.restart.colvars.state.stripped | 12 +- .../AutoDiff/test.restart.colvars.traj | 44 +- .../compare_with_pytorch.py | 245 ++ .../test.in | 20 +- 8 files changed, 5112 insertions(+), 290 deletions(-) create mode 100644 namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out index f146e17b2..9b22d5849 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out @@ -1274,9 +1274,647 @@ colvars: refPositionsFile rmsd_atoms_refpos.xyz colvars: } colvars: ". colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "main" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "RMSD_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "RMSD_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 30 individual components. +colvars: DEPS: disabling feature "scalar" in colvar main +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: feature "linear" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "single_component" +colvars: DEPS: feature "single_component" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar main +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar main +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar main +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar main enabling "output_value" +colvars: DEPS: feature "output_value" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar main +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar main +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar main +colvars: DEPS: colvar main enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar main testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar main testing "linear" +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "main". +colvars: Configuration string for "colvar": " +colvars: +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar fitting enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar fitting +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting +colvars: DEPS: colvar fitting enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar fitting testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar fitting testing "linear" +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "fitting". +colvars: Configuration string for "colvar": " +colvars: +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. colvars: Keyword "colvar" not found. colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. +colvars: Collective variables initialized, 3 in total. colvars: Initializing the collective variables biases. colvars: Looking for the keyword "abf" and its value. colvars: Keyword "abf" not found. @@ -1496,7 +2134,23 @@ colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: } colvars: refPositionsFile rmsd_atoms_refpos.xyz colvars: } -colvars: } +colvars: } +colvars: colvar { +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } colvars: harmonic { colvars: colvars one colvars: centers (0.9, 0.5, 0.5, 0.5) @@ -1518,6 +2172,7 @@ colvars: - Colvars-NAMD interface: colvars: - Harmonic colvar bias implementation: colvars: - Moving frame of reference: colvars: - Optimal rotation via flexible fitting: +colvars: - cartesian colvar component: colvars: - orientation colvar component: colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 colvars: @@ -1533,6 +2188,8 @@ colvars: updating target temperature (T = 0 K). colvars: Current simulation parameters: initial step = 0, integration timestep = 1 colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "main":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "fitting":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: ---------------------------------------------------------------------- colvars: colvarproxy_namd, step no. 0 @@ -1542,7 +2199,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 0, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 0, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 0, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 0, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 0, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 0, atoms_positions[size = 51] = { ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 ), ( 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 ), ( 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 ), ( 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 ), ( 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 ), ( 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 ), ( -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 ), ( -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 ), ( -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 ), ( -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ), ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 ), ( 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 ), ( 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 ), ( 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ), ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 ), ( 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 ), ( 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 ), ( 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ), ( 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 ), ( 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 ), ( 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 ), ( 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 ), ( 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 ), ( 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 ), ( 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 ), ( 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 ), ( 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 ), ( 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 ), ( 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 ), ( -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 ), ( 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 ), ( 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 ), ( -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 ), ( -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 ), ( -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 ), ( -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 ), ( -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 ), ( -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 ), ( -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 ), ( -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 ), ( -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 ), ( -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 ), ( -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 ), ( -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 ), ( -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 ), ( -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 ), ( -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 ), ( -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 ), ( -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 ), ( -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 ), ( -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) } @@ -1564,15 +2221,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating fit gradients. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "main" has value ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -1585,6 +2313,10 @@ colvars: Adding total bias energy: 11.4 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -1600,8 +2332,6 @@ colvars: ( 0.00831741 , -0.109858 , 0.306951 ) colvars: ( -0.0487266 , 0.074898 , 0.215487 ) colvars: ( 0.0806562 , -0.231591 , 0.0243652 ) colvars: ( 0.136965 , -0.472311 , 0.321252 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242619 , -0.099509 , 0.0941691 ) colvars: ( 0.0197743 , -0.0822842 , 0.0814769 ) @@ -1654,6 +2384,7 @@ colvars: ( -0.0085258 , 0.0471754 , -0.0819464 ) colvars: ( -0.0185683 , 0.0667252 , -0.0343222 ) colvars: ( -0.0222448 , 0.0840291 , -0.0574973 ) colvars: ( -0.0242478 , 0.0927893 , -0.0674521 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 0. colvars: colvarmodule::write_traj_files() @@ -1661,6 +2392,8 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: colvarmodule::end_of_step(), step = 0. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- colvars: Step 0, atoms_new_colvar_forces = { ( -7.17112331393693e-02 , 3.05098327565957e-01 , -3.87711644832293e-01 ), ( 1.19555459248557e-02 , 3.65941097357604e-02 , -2.36512628285003e-01 ), ( -4.16513128784966e-02 , 9.10770464245731e-02 , 8.22518324392786e-02 ), ( -9.62168257886831e-02 , 2.41917479955852e-01 , 6.78847980688516e-02 ), ( -1.89845157517858e-02 , 9.98710219002420e-02 , -1.64599111102358e-01 ), ( 7.03301603774896e-02 , -1.79535932890023e-01 , -4.14067432161946e-02 ), ( 1.07471104828031e-02 , -1.02577848089066e-01 , 2.47364312690905e-01 ), ( -4.02256833871764e-02 , 5.38601721942073e-02 , 1.93139708020977e-01 ), ( 6.58704306067279e-02 , -1.87291492706406e-01 , 3.23878619810793e-02 ), ( 1.14720183887631e-01 , -3.88281468777201e-01 , 2.63754453050035e-01 ), ( 2.42618507983615e-02 , -9.95090220875313e-02 , 9.41691127788629e-02 ), ( 2.64140528573990e-02 , -9.72948413283316e-02 , 5.83337189788877e-02 ), ( 1.22660085012390e-02 , -5.62309126513698e-02 , 7.13109049758973e-02 ), ( 1.24027961622539e-02 , -5.39033622796542e-02 , 6.02813703425287e-02 ), ( 5.50365180277709e-03 , -3.58654134074757e-02 , 7.45595484006017e-02 ), ( -8.56869612739025e-03 , 8.15418354809084e-03 , 7.47590614158032e-02 ), ( -2.04345135727017e-03 , -3.57842067967311e-03 , 3.99322594237481e-02 ), ( -5.72407370686545e-03 , 8.98773129963851e-03 , 3.57708956627444e-02 ), ( 2.80344276950839e-03 , -1.36159740030154e-02 , 1.93567445096325e-02 ), ( 9.22210196636199e-03 , -2.22622813867358e-02 , -2.64859467986244e-02 ), ( 8.79316761791039e-03 , -2.38089040285720e-02 , -1.49202518973436e-02 ), ( 6.70562195329319e-03 , -1.34686650666172e-02 , -3.01395709833031e-02 ), ( 1.50473126186007e-02 , -4.65247806418302e-02 , -2.39287487045654e-03 ), ( 2.75363017231425e-02 , -8.78760894143468e-02 , 6.57333075023515e-03 ), ( 1.42160293860021e-02 , -4.66103438169562e-02 , 8.36819326569623e-03 ), ( 1.41623599363496e-02 , -4.35929741103034e-02 , -3.03504901951588e-03 ), ( 9.21986652441758e-03 , -3.71107050197726e-02 , 3.29673234888841e-02 ), ( -9.63775655681931e-04 , -1.58643052576496e-02 , 7.55701254462465e-02 ), ( -3.83069289063363e-03 , 3.84917215687278e-03 , 3.26059455401106e-02 ), ( -5.91198486374499e-03 , 1.09771288603378e-02 , 3.01642040800903e-02 ), ( -7.28976560942452e-03 , 1.74875351287834e-02 , 2.13767345680998e-02 ), ( -1.61562664646153e-02 , 5.13986449348097e-02 , -3.21420801068685e-03 ), ( -9.68017103615191e-03 , 3.56109507442153e-02 , -2.11960333401958e-02 ), ( -1.37049814773182e-02 , 4.98621539927025e-02 , -2.77874076093298e-02 ), ( -1.91792500276001e-03 , 1.49750007080970e-02 , -3.58941052675410e-02 ), ( 1.06647740597758e-02 , -1.52501737314967e-02 , -7.26305692651966e-02 ), ( 4.39025313827158e-03 , -2.89712934588417e-04 , -5.38644244704754e-02 ), ( 3.37835546017515e-03 , 6.67816083650675e-03 , -6.90684195578746e-02 ), ( 7.08425965807474e-03 , -1.43615244078311e-02 , -3.13117755624624e-02 ), ( 1.29337999684502e-02 , -4.08166651615065e-02 , 1.25159424194878e-03 ), ( 4.21517000834667e-04 , 2.14779898690001e-03 , -1.38787149564562e-02 ), ( 3.30986545488312e-04 , 3.88313347866908e-03 , -1.96891054554931e-02 ), ( -6.59621209084941e-03 , 2.06662848702344e-02 , -3.74608751278817e-05 ), ( -2.06331572427302e-02 , 5.73693700933228e-02 , 2.89999395613771e-02 ), ( -1.89787290812637e-02 , 6.32653631722135e-02 , -1.53318322023093e-02 ), ( -2.26926653990437e-02 , 7.52153031654799e-02 , -1.66095079265972e-02 ), ( -1.67511882905597e-02 , 7.28367292485312e-02 , -8.15558389781937e-02 ), ( -1.98067264091487e-02 , 8.70491413541379e-02 , -1.00140043772665e-01 ), ( -8.52580045706230e-03 , 4.71754189750805e-02 , -8.19464349448593e-02 ), ( -1.85683188859792e-02 , 6.67251710260006e-02 , -3.43221673997345e-02 ), ( -2.42477887341905e-02 , 9.27892795207383e-02 , -6.74521030822303e-02 ) } colvars: ---------------------------------------------------------------------- @@ -1700,7 +2433,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 1, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 1, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 1, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 1, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 1, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 1, atoms_positions[size = 51] = { ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 ), ( 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 ), ( 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 ), ( 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 ), ( 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 ), ( 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 ), ( -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 ), ( -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 ), ( -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 ), ( -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ), ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 ), ( 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 ), ( 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 ), ( 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 ), ( 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 ), ( 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 ), ( 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 ), ( 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 ), ( 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 ), ( 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 ), ( 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 ), ( 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 ), ( 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 ), ( 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 ), ( 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 ), ( 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 ), ( 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 ), ( 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 ), ( 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 ), ( -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 ), ( 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 ), ( 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 ), ( -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 ), ( -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 ), ( -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 ), ( -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 ), ( -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 ), ( -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 ), ( -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 ), ( -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 ), ( -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 ), ( -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 ), ( -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 ), ( -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 ), ( -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 ), ( -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 ), ( -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 ), ( -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 ), ( -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 ), ( -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 ), ( -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ) } @@ -1721,16 +2454,87 @@ colvars: Collective variables module, step no. 1 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 , 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 , 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 , 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 , 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 , 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 , 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 , 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 , 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 , 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 , 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 , 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 , 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 , 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 , 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 , -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 , 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 , -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 , -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 , -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 , -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 , -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 , -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 , -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 , -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 , -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 , -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 , -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 , -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 , -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 , -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 , -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 , -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 , 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 , 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 , 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 , 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 , 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 , 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 , 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 , 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 , 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 , 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 , 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 , 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 , 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 , 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 , -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 , 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 , -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 , -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 , -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 , -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 , -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 , -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 , -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 , -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 , -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 , -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 , -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 , -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 , -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 , -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 , -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 , -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -1743,6 +2547,10 @@ colvars: Adding total bias energy: 11.4044 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -1758,8 +2566,6 @@ colvars: ( 0.0082118 , -0.109708 , 0.307032 ) colvars: ( -0.0487751 , 0.0750392 , 0.215444 ) colvars: ( 0.0805998 , -0.231596 , 0.0244957 ) colvars: ( 0.136782 , -0.472199 , 0.321545 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242477 , -0.0994947 , 0.0942202 ) colvars: ( 0.0197636 , -0.0822787 , 0.081522 ) @@ -1812,12 +2618,15 @@ colvars: ( -0.00851097 , 0.0471709 , -0.0819763 ) colvars: ( -0.0185701 , 0.066731 , -0.0343585 ) colvars: ( -0.0222411 , 0.0840279 , -0.0575417 ) colvars: ( -0.0242402 , 0.0927787 , -0.0674981 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 1. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 1. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- colvars: Step 1, atoms_new_colvar_forces = { ( -7.15151729651260e-02 , 3.04899243481533e-01 , -3.87916030963302e-01 ), ( 1.20368649362899e-02 , 3.64235792090596e-02 , -2.36533693202075e-01 ), ( -4.16415878718478e-02 , 9.11022438626934e-02 , 8.22174068287411e-02 ), ( -9.61659395369152e-02 , 2.41989972764637e-01 , 6.77382993270643e-02 ), ( -1.89170945988754e-02 , 9.97945490695020e-02 , -1.64675032270572e-01 ), ( 7.02945076928405e-02 , -1.79595291976670e-01 , -4.12934261331383e-02 ), ( 1.06593636141036e-02 , -1.02444767354498e-01 , 2.47440239914315e-01 ), ( -4.02691431255613e-02 , 5.40107887471147e-02 , 1.93099494398337e-01 ), ( 6.58001964113642e-02 , -1.87274572435745e-01 , 3.24910083791860e-02 ), ( 1.14541196581312e-01 , -3.88171056981776e-01 , 2.64003649424930e-01 ), ( 2.42477192528996e-02 , -9.94947081114131e-02 , 9.42201611607529e-02 ), ( 2.64136166976736e-02 , -9.72996799526701e-02 , 5.83863996262244e-02 ), ( 1.22548721116594e-02 , -5.62266396301048e-02 , 7.13435168350051e-02 ), ( 1.23936399651521e-02 , -5.38979530864836e-02 , 6.03110988177678e-02 ), ( 5.49001413551297e-03 , -3.58637287706379e-02 , 7.45844785550286e-02 ), ( -8.58662775485298e-03 , 8.15197217862955e-03 , 7.47658701006714e-02 ), ( -2.05061868858449e-03 , -3.58458690191429e-03 , 3.99413123521106e-02 ), ( -5.73267269837427e-03 , 8.98459258558919e-03 , 3.57726717890164e-02 ), ( 2.80515992656613e-03 , -1.36318939949399e-02 , 1.93713053854992e-02 ), ( 9.24091216374164e-03 , -2.22963827594714e-02 , -2.64665663613212e-02 ), ( 8.80524457636114e-03 , -2.38284772346292e-02 , -1.49041760335850e-02 ), ( 6.72044863046050e-03 , -1.34897386302215e-02 , -3.01294931954585e-02 ), ( 1.50576435827247e-02 , -4.65389127767602e-02 , -2.36711837470063e-03 ), ( 2.75472753380666e-02 , -8.78822788846253e-02 , 6.61567117283608e-03 ), ( 1.42197676549019e-02 , -4.66103962861243e-02 , 8.39005985454352e-03 ), ( 1.41681378086040e-02 , -4.35920831820608e-02 , -3.01634853592154e-03 ), ( 9.21461496103597e-03 , -3.71036824034249e-02 , 3.29854494207997e-02 ), ( -9.86126451234636e-04 , -1.58417642622825e-02 , 7.55784048787670e-02 ), ( -3.84239612560993e-03 , 3.86150425286693e-03 , 3.26037689714234e-02 ), ( -5.92521514581768e-03 , 1.09937156748894e-02 , 3.01569322569409e-02 ), ( -7.29812275527947e-03 , 1.74916709978540e-02 , 2.13701287787168e-02 ), ( -1.61590546113848e-02 , 5.13892040394262e-02 , -3.23396497301815e-03 ), ( -9.67788551506929e-03 , 3.56052475625837e-02 , -2.12124757482175e-02 ), ( -1.37034108862765e-02 , 4.98582644999593e-02 , -2.78117321811795e-02 ), ( -1.90789273977489e-03 , 1.49631727913749e-02 , -3.59009302348894e-02 ), ( 1.06906045511525e-02 , -1.52740011368780e-02 , -7.26241198821211e-02 ), ( 4.40529849774725e-03 , -2.97823815696022e-04 , -5.38681586639291e-02 ), ( 3.39643922578235e-03 , 6.66896241573230e-03 , -6.90768027297062e-02 ), ( 7.09321783492851e-03 , -1.43609832339387e-02 , -3.13096039888957e-02 ), ( 1.29336183664370e-02 , -4.07998296242983e-02 , 1.26359385658362e-03 ), ( 4.19979277285392e-04 , 2.16348662453615e-03 , -1.38873734861057e-02 ), ( 3.29655166819156e-04 , 3.90209739378588e-03 , -1.97005199557689e-02 ), ( -6.60377269842420e-03 , 2.06837283573336e-02 , -5.32553285992549e-05 ), ( -2.06544209370330e-02 , 5.73950938853213e-02 , 2.89683973885608e-02 ), ( -1.89875466809821e-02 , 6.32816036261560e-02 , -1.53681222592533e-02 ), ( -2.27038413337324e-02 , 7.52356909090834e-02 , -1.66528519569391e-02 ), ( -1.67393048554064e-02 , 7.28311918128840e-02 , -8.15966907597996e-02 ), ( -1.97909234720973e-02 , 8.70391604498609e-02 , -1.00187941489201e-01 ), ( -8.51097375894001e-03 , 4.71708543895567e-02 , -8.19762682790733e-02 ), ( -1.85700756693449e-02 , 6.67309773118485e-02 , -3.43585040385876e-02 ), ( -2.42401880848779e-02 , 9.27786645334536e-02 , -6.74981184484641e-02 ) } colvars: ---------------------------------------------------------------------- @@ -1857,7 +2666,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 2, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 2, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 2, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 2, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 2, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 2, atoms_positions[size = 51] = { ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 ), ( 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 ), ( 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 ), ( 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 ), ( 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 ), ( 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 ), ( -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 ), ( -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 ), ( -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 ), ( -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ), ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 ), ( 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 ), ( 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 ), ( 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 ), ( 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 ), ( 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 ), ( 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 ), ( 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 ), ( 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 ), ( 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 ), ( 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 ), ( 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 ), ( 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 ), ( 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 ), ( 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 ), ( 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 ), ( 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 ), ( 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 ), ( 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 ), ( -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 ), ( 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 ), ( 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 ), ( -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 ), ( -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 ), ( -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 ), ( -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 ), ( -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 ), ( -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 ), ( -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 ), ( -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 ), ( -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 ), ( -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 ), ( -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 ), ( -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 ), ( -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 ), ( -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 ), ( -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 ), ( -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 ), ( -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 ), ( -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 ), ( -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ) } @@ -1878,16 +2687,87 @@ colvars: Collective variables module, step no. 2 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Colvar component no. 1 within colvar "main" has value ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ). +colvars: Calculating gradients of colvar "main". colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 , 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 , 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 , 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 , 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 , 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 , 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 , 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 , 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 , 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 , 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 , 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 , 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 , 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 , 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 , -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 , 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 , -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 , -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 , -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 , -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 , -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 , -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 , -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 , -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 , -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 , -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 , -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 , -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 , -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 , -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 , -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 , -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 , 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 , 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 , 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 , 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 , 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 , 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 , 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 , 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 , 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 , 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 , 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 , 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 , 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 , 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 , -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 , 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 , -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 , -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 , -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 , -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 , -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 , -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 , -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 , -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 , -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 , -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 , -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 , -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 , -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 , -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 , -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 , -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -1900,6 +2780,10 @@ colvars: Adding total bias energy: 11.4086 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -1915,8 +2799,6 @@ colvars: ( 0.00813549 , -0.109536 , 0.307174 ) colvars: ( -0.048817 , 0.0752539 , 0.215389 ) colvars: ( 0.0805502 , -0.231606 , 0.0245895 ) colvars: ( 0.136645 , -0.472109 , 0.321893 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242404 , -0.0994785 , 0.0942791 ) colvars: ( 0.0197577 , -0.0822678 , 0.0815733 ) @@ -1969,12 +2851,15 @@ colvars: ( -0.00850116 , 0.0471568 , -0.0820123 ) colvars: ( -0.0185724 , 0.0667338 , -0.0343967 ) colvars: ( -0.0222404 , 0.0840242 , -0.0575902 ) colvars: ( -0.0242373 , 0.0927691 , -0.0675498 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 2. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 2. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- colvars: Step 2, atoms_new_colvar_forces = { ( -7.13662406347475e-02 , 3.04690881238521e-01 , -3.88189014550433e-01 ), ( 1.21024777996464e-02 , 3.62012543772250e-02 , -2.36560385329191e-01 ), ( -4.16270344260805e-02 , 9.11317483620320e-02 , 8.22453445505728e-02 ), ( -9.61258643475432e-02 , 2.42118549983633e-01 , 6.75964639859510e-02 ), ( -1.88692093361642e-02 , 9.97197189297282e-02 , -1.64805343769547e-01 ), ( 7.02674381185762e-02 , -1.79697300167168e-01 , -4.11729051286209e-02 ), ( 1.05951211671063e-02 , -1.02292489843847e-01 , 2.47571722543744e-01 ), ( -4.03059854417923e-02 , 5.42236285493406e-02 , 1.93046549392435e-01 ), ( 6.57408551090289e-02 , -1.87266309856294e-01 , 3.25601520815156e-02 ), ( 1.14404466188646e-01 , -3.88084904837303e-01 , 2.64302707504789e-01 ), ( 2.42403744165811e-02 , -9.94785187554915e-02 , 9.42791291950214e-02 ), ( 2.64150718872813e-02 , -9.73002134525345e-02 , 5.84427219892992e-02 ), ( 1.22480322060636e-02 , -5.62157918593996e-02 , 7.13815477024520e-02 ), ( 1.23883380687533e-02 , -5.38885112017688e-02 , 6.03455655484888e-02 ), ( 5.48062002843824e-03 , -3.58514915394607e-02 , 7.46148407252745e-02 ), ( -8.60056519272734e-03 , 8.16670443437686e-03 , 7.47778066468873e-02 ), ( -2.05645685993396e-03 , -3.58005212530679e-03 , 3.99526483103971e-02 ), ( -5.73963473120446e-03 , 8.99109627006217e-03 , 3.57767175444479e-02 ), ( 2.80549872017285e-03 , -1.36374684939331e-02 , 1.93857966829495e-02 ), ( 9.25294348776421e-03 , -2.23212932966850e-02 , -2.64521663051807e-02 ), ( 8.81336594162522e-03 , -2.38438300993918e-02 , -1.48909470506634e-02 ), ( 6.73030250851154e-03 , -1.35078732001586e-02 , -3.01234731955913e-02 ), ( 1.50653818005725e-02 , -4.65512686167406e-02 , -2.34284311242762e-03 ), ( 2.75570538265062e-02 , -8.78929598017612e-02 , 6.65785423175934e-03 ), ( 1.42236341148245e-02 , -4.66134370995714e-02 , 8.41248205826075e-03 ), ( 1.41735565627240e-02 , -4.35966335485880e-02 , -2.99781666970647e-03 ), ( 9.21202377418917e-03 , -3.70972210496742e-02 , 3.30065277669219e-02 ), ( -1.00090754604269e-03 , -1.58167028261417e-02 , 7.55940860707059e-02 ), ( -3.85036480540487e-03 , 3.87472044758625e-03 , 3.26050293851104e-02 ), ( -5.93416109216629e-03 , 1.10093226221347e-02 , 3.01533130775972e-02 ), ( -7.30451303321866e-03 , 1.74998354864693e-02 , 2.13654311507231e-02 ), ( -1.61630628639610e-02 , 5.13889365763393e-02 , -3.25476401672865e-03 ), ( -9.67740222362291e-03 , 3.56016733585189e-02 , -2.12309147297704e-02 ), ( -1.37036427268514e-02 , 4.98557230830785e-02 , -2.78383479874705e-02 ), ( -1.90156928795647e-03 , 1.49514486553429e-02 , -3.59113664694244e-02 ), ( 1.07086125914830e-02 , -1.53022610381287e-02 , -7.26250027034179e-02 ), ( 4.41605431417831e-03 , -3.12810190896927e-04 , -5.38764592683203e-02 ), ( 3.40925420915234e-03 , 6.65106748886611e-03 , -6.90909274179423e-02 ), ( 7.10036528785388e-03 , -1.43684525078162e-02 , -3.13096231913525e-02 ), ( 1.29357293014539e-02 , -4.07951303363235e-02 , 1.27717136871923e-03 ), ( 4.20013690039623e-04 , 2.16888898682387e-03 , -1.38956021720835e-02 ), ( 3.30067539764028e-04 , 3.90817206331382e-03 , -1.97116211345700e-02 ), ( -6.60857296101589e-03 , 2.06946733874849e-02 , -6.74622074879811e-05 ), ( -2.06697591996960e-02 , 5.74197879098366e-02 , 2.89412848935110e-02 ), ( -1.89943446265396e-02 , 6.32931538792098e-02 , -1.54039897267542e-02 ), ( -2.27123621770474e-02 , 7.52502973237281e-02 , -1.66954809253169e-02 ), ( -1.67323700772781e-02 , 7.28193141294979e-02 , -8.16437923409835e-02 ), ( -1.97816905755823e-02 , 8.70227179902238e-02 , -1.00243802160594e-01 ), ( -8.50116034360863e-03 , 4.71568068651273e-02 , -8.20123108275631e-02 ), ( -1.85724328597233e-02 , 6.67337512843182e-02 , -3.43967090628983e-02 ), ( -2.42373452910282e-02 , 9.27690520615654e-02 , -6.75498229534928e-02 ) } colvars: ---------------------------------------------------------------------- @@ -2014,7 +2899,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 3, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 3, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 3, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 3, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 3, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 3, atoms_positions[size = 51] = { ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 ), ( 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 ), ( 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 ), ( 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 ), ( 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 ), ( 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 ), ( -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 ), ( -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 ), ( -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 ), ( -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ), ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 ), ( 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 ), ( 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 ), ( 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 ), ( 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 ), ( 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 ), ( 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 ), ( 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 ), ( 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 ), ( 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 ), ( 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 ), ( 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 ), ( 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 ), ( 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 ), ( 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 ), ( 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 ), ( 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 ), ( 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 ), ( 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 ), ( -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 ), ( 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 ), ( 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 ), ( -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 ), ( -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 ), ( -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 ), ( -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 ), ( -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 ), ( -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 ), ( -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 ), ( -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 ), ( -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 ), ( -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 ), ( -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 ), ( -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 ), ( -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 ), ( -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 ), ( -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 ), ( -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 ), ( -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 ), ( -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 ), ( -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ) } @@ -2035,16 +2920,87 @@ colvars: Collective variables module, step no. 3 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 , 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 , 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 , 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 , 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 , 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 , 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 , 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 , 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 , 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 , 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 , 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 , 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 , 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 , 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 , -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 , 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 , -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 , -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 , -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 , -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 , -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 , -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 , -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 , -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 , -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 , -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 , -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 , -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 , -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 , -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 , -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 , -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 , 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 , 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 , 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 , 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 , 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 , 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 , 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 , 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 , 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 , 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 , 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 , 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 , 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 , 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 , -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 , 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 , -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 , -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 , -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 , -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 , -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 , -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 , -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 , -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 , -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 , -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 , -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 , -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 , -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 , -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 , -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 , -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2057,6 +3013,10 @@ colvars: Adding total bias energy: 11.4128 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2072,8 +3032,6 @@ colvars: ( 0.0080871 , -0.109346 , 0.307379 ) colvars: ( -0.0488551 , 0.0755417 , 0.215322 ) colvars: ( 0.0805094 , -0.23162 , 0.0246419 ) colvars: ( 0.136555 , -0.472047 , 0.322292 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.02424 , -0.0994602 , 0.0943451 ) colvars: ( 0.0197569 , -0.0822515 , 0.0816304 ) @@ -2126,12 +3084,15 @@ colvars: ( -0.00849626 , 0.0471338 , -0.0820545 ) colvars: ( -0.0185757 , 0.0667331 , -0.0344369 ) colvars: ( -0.0222427 , 0.0840176 , -0.0576426 ) colvars: ( -0.0242395 , 0.0927599 , -0.0676063 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 3. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 3. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- colvars: Step 3, atoms_new_colvar_forces = { ( -7.12644910002888e-02 , 3.04480391919715e-01 , -3.88530416773670e-01 ), ( 1.21543402350703e-02 , 3.59283757073496e-02 , -2.36592346550597e-01 ), ( -4.16092138833091e-02 , 9.11640888447168e-02 , 8.23416306242972e-02 ), ( -9.61000764313615e-02 , 2.42305695294195e-01 , 6.74632194161953e-02 ), ( -1.88405647185787e-02 , 9.96498172188486e-02 , -1.64992595806876e-01 ), ( 7.02514835169250e-02 , -1.79844182937403e-01 , -4.10469774921604e-02 ), ( 1.05532653731170e-02 , -1.02124362545298e-01 , 2.47761381423188e-01 ), ( -4.03387808327078e-02 , 5.44992483058144e-02 , 1.92980165253870e-01 ), ( 6.56942024572184e-02 , -1.87268005160499e-01 , 3.25895903711645e-02 ), ( 1.14312103245404e-01 , -3.88029814824987e-01 , 2.64649278438540e-01 ), ( 2.42399874948257e-02 , -9.94601615884302e-02 , 9.43450526358905e-02 ), ( 2.64187832067172e-02 , -9.72959614091883e-02 , 5.85026645399138e-02 ), ( 1.22455016217257e-02 , -5.61985927602022e-02 , 7.14248035735868e-02 ), ( 1.23869408467411e-02 , -5.38750852851352e-02 , 6.03844516287721e-02 ), ( 5.47533482913114e-03 , -3.58293646823109e-02 , 7.46507658907643e-02 ), ( -8.61093066863975e-03 , 8.19691911326328e-03 , 7.47955564010663e-02 ), ( -2.06113077404795e-03 , -3.56556978390652e-03 , 3.99668789943306e-02 ), ( -5.74519237302200e-03 , 9.00641804914424e-03 , 3.57835237496780e-02 ), ( 2.80447863484305e-03 , -1.36331338607282e-02 , 1.94012145925844e-02 ), ( 9.25852941616702e-03 , -2.23368932576550e-02 , -2.64410106981663e-02 ), ( 8.81779507607160e-03 , -2.38547195085519e-02 , -1.48796460307627e-02 ), ( 6.73545618225761e-03 , -1.35227630184473e-02 , -3.01205268766796e-02 ), ( 1.50708708581964e-02 , -4.65613398889311e-02 , -2.31954133071604e-03 ), ( 2.75661986728460e-02 , -8.79069437037276e-02 , 6.69966718119029e-03 ), ( 1.42278972265037e-02 , -4.66188536979522e-02 , 8.43518305129557e-03 ), ( 1.41789197697816e-02 , -4.36058466193783e-02 , -2.97984094516618e-03 ), ( 9.21216484792188e-03 , -3.70911405406308e-02 , 3.30300824801763e-02 ), ( -1.00842453813973e-03 , -1.57897001341701e-02 , 7.56161841724666e-02 ), ( -3.85480601482357e-03 , 3.88845033974037e-03 , 3.26092204945920e-02 ), ( -5.93907177018090e-03 , 1.10235923365747e-02 , 3.01526170963657e-02 ), ( -7.30916548846552e-03 , 1.75114619452427e-02 , 2.13626571248804e-02 ), ( -1.61686021542056e-02 , 5.13968697461965e-02 , -3.27568354660324e-03 ), ( -9.67884364851469e-03 , 3.55998969369253e-02 , -2.12508875909159e-02 ), ( -1.37058643655233e-02 , 4.98541172211488e-02 , -2.78668434034106e-02 ), ( -1.89885720037668e-03 , 1.49399596092170e-02 , -3.59248246074874e-02 ), ( 1.07192981146069e-02 , -1.53339454667564e-02 , -7.26323591285075e-02 ), ( 4.42280297726436e-03 , -3.33908263890920e-04 , -5.38891907297017e-02 ), ( 3.41711373116267e-03 , 6.62536545954213e-03 , -6.91106420905072e-02 ), ( 7.10595226173296e-03 , -1.43831502417926e-02 , -3.13121755456011e-02 ), ( 1.29403714170504e-02 , -4.08015816582177e-02 , 1.29101937417115e-03 ), ( 4.21650163844445e-04 , 2.16452996514270e-03 , -1.39044294702790e-02 ), ( 3.32265751315244e-04 , 3.90201987778178e-03 , -1.97236621643520e-02 ), ( -6.61077765359962e-03 , 2.06991412040919e-02 , -8.09922488427135e-05 ), ( -2.06797382433100e-02 , 5.74425477014770e-02 , 2.89176437746283e-02 ), ( -1.89994930796128e-02 , 6.32995810538052e-02 , -1.54400667540050e-02 ), ( -2.27186777545924e-02 , 7.52586020414951e-02 , -1.67382012788684e-02 ), ( -1.67304543184278e-02 , 7.28011998778589e-02 , -8.16968210356079e-02 ), ( -1.97790932339822e-02 , 8.69999150277857e-02 , -1.00307053543935e-01 ), ( -8.49625951876390e-03 , 4.71338235969838e-02 , -8.20544860518998e-02 ), ( -1.85756727929090e-02 , 6.67331167231479e-02 , -3.44368813268715e-02 ), ( -2.42395254710581e-02 , 9.27598757209877e-02 , -6.76063492614180e-02 ) } colvars: ---------------------------------------------------------------------- @@ -2171,7 +3132,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 4, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 4, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 4, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 4, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 4, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 4, atoms_positions[size = 51] = { ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 ), ( 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 ), ( 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 ), ( 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 ), ( 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 ), ( 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 ), ( -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 ), ( -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 ), ( -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 ), ( -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ), ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 ), ( 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 ), ( 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 ), ( 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 ), ( 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 ), ( 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 ), ( 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 ), ( 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 ), ( 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 ), ( 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 ), ( 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 ), ( 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 ), ( 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 ), ( 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 ), ( 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 ), ( 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 ), ( 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 ), ( 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 ), ( 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 ), ( -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 ), ( 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 ), ( 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 ), ( -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 ), ( -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 ), ( -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 ), ( -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 ), ( -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 ), ( -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 ), ( -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 ), ( -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 ), ( -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 ), ( -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 ), ( -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 ), ( -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 ), ( -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 ), ( -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 ), ( -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 ), ( -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 ), ( -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 ), ( -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 ), ( -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ) } @@ -2191,17 +3152,88 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 4 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 , 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 , 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 , 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 , 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 , 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 , 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 , 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 , 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 , 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 , 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 , 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 , 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 , 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 , 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 , -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 , 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 , -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 , -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 , -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 , -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 , -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 , -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 , -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 , -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 , -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 , -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 , -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 , -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 , -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 , -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 , -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 , -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 , 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 , 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 , 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 , 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 , 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 , 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 , 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 , 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 , 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 , 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 , 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 , 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 , 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 , 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 , -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 , 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 , -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 , -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 , -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 , -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 , -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 , -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 , -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 , -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 , -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 , -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 , -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 , -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 , -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 , -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 , -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 , -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2214,6 +3246,10 @@ colvars: Adding total bias energy: 11.4167 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2229,8 +3265,6 @@ colvars: ( 0.00806427 , -0.109141 , 0.307649 ) colvars: ( -0.0488924 , 0.0759017 , 0.215243 ) colvars: ( 0.0804791 , -0.23164 , 0.0246495 ) colvars: ( 0.136513 , -0.47202 , 0.32274 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242467 , -0.0994396 , 0.0944171 ) colvars: ( 0.0197612 , -0.0822299 , 0.0816931 ) @@ -2283,12 +3317,15 @@ colvars: ( -0.00849614 , 0.0471027 , -0.0821028 ) colvars: ( -0.0185801 , 0.0667289 , -0.0344791 ) colvars: ( -0.0222485 , 0.084008 , -0.0576986 ) colvars: ( -0.024247 , 0.0927508 , -0.067667 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 4. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 4. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- colvars: Step 4, atoms_new_colvar_forces = { ( -7.12080210552797e-02 , 3.04274726531718e-01 , -3.88940587640774e-01 ), ( 1.21950269985741e-02 , 3.56064499150579e-02 , -2.36629571966559e-01 ), ( -4.15896800926495e-02 , 9.11984131701159e-02 , 8.25110748151548e-02 ), ( -9.60913610694842e-02 , 2.42553891617927e-01 , 6.73416799725295e-02 ), ( -1.88301065662091e-02 , 9.95877660607348e-02 , -1.65239019876376e-01 ), ( 7.02486546083075e-02 , -1.80038089572669e-01 , -4.09170337765094e-02 ), ( 1.05318019430700e-02 , -1.01943502700610e-01 , 2.48011589427611e-01 ), ( -4.03702441420600e-02 , 5.48377999542595e-02 , 1.92899941686077e-01 ), ( 6.56614060203969e-02 , -1.87281426243981e-01 , 3.25748774948746e-02 ), ( 1.14264326869696e-01 , -3.88012490794451e-01 , 2.65041892347769e-01 ), ( 2.42467051015945e-02 , -9.94396336710934e-02 , 9.44171391294592e-02 ), ( 2.64251678200815e-02 , -9.72867887154741e-02 , 5.85662658018812e-02 ), ( 1.22472752364769e-02 , -5.61754900662332e-02 , 7.14731700813468e-02 ), ( 1.23894843053070e-02 , -5.38579145569750e-02 , 6.04275201891246e-02 ), ( 5.47399239743080e-03 , -3.57982173847452e-02 , 7.46924353005460e-02 ), ( -8.61820629816763e-03 , 8.24101256205583e-03 , 7.48197995077387e-02 ), ( -2.06481714081862e-03 , -3.54201942450395e-03 , 3.99845925012198e-02 ), ( -5.74960578369700e-03 , 9.02966184445511e-03 , 3.57935634859857e-02 ), ( 2.80215815799665e-03 , -1.36194994617910e-02 , 1.94184830640624e-02 ), ( 9.25813419184906e-03 , -2.23432881756588e-02 , -2.64315357010282e-02 ), ( 8.81887984484594e-03 , -2.38610548708190e-02 , -1.48694441646478e-02 ), ( 6.73627359909724e-03 , -1.35342143700938e-02 , -3.01197791283318e-02 ), ( 1.50745344951528e-02 , -4.65688049220078e-02 , -2.29674594399060e-03 ), ( 2.75753596529584e-02 , -8.79232773311727e-02 , 6.74093354014295e-03 ), ( 1.42328598821259e-02 , -4.66261458490982e-02 , 8.45792361108824e-03 ), ( 1.41845692241518e-02 , -4.36190215434519e-02 , -2.96277053426434e-03 ), ( 9.21509811267395e-03 , -3.70853528776646e-02 , 3.30557103690731e-02 ), ( -1.00908817873593e-03 , -1.57613613752127e-02 , 7.56438621946769e-02 ), ( -3.85598849795090e-03 , 3.90235192006697e-03 , 3.26159055815450e-02 ), ( -5.94027352971036e-03 , 1.10362439836852e-02 , 3.01542014974282e-02 ), ( -7.31235222693024e-03 , 1.75260063960574e-02 , 2.13618346567090e-02 ), ( -1.61760008919845e-02 , 5.14120787753115e-02 , -3.29589385739106e-03 ), ( -9.68233173784903e-03 , 3.55996626468111e-02 , -2.12719940992636e-02 ), ( -1.37102747661633e-02 , 4.98531642203748e-02 , -2.78968717294853e-02 ), ( -1.89961262970978e-03 , 1.49288570247522e-02 , -3.59407974062863e-02 ), ( 1.07232945874884e-02 , -1.53680987893684e-02 , -7.26454605633824e-02 ), ( 4.42589088117630e-03 , -3.60305744266164e-04 , -5.39062707052113e-02 ), ( 3.42040381532136e-03 , 6.59283053457814e-03 , -6.91358624396322e-02 ), ( 7.11026470043291e-03 , -1.44042598923488e-02 , -3.13175947834697e-02 ), ( 1.29477734767760e-02 , -4.08181704267577e-02 , 1.30395382414031e-03 ), ( 4.24885994011587e-04 , 2.15107073748631e-03 , -1.39148029314400e-02 ), ( 3.36253599568686e-04 , 3.88447745033494e-03 , -1.97377999334930e-02 ), ( -6.61061592184173e-03 , 2.06973135737414e-02 , -9.46778005412389e-05 ), ( -2.06850655568149e-02 , 5.74627047385668e-02 , 2.88966154320564e-02 ), ( -1.90034487268360e-02 , 6.33007217508657e-02 , -1.54769495934924e-02 ), ( -2.27233448939688e-02 , 7.52604092524772e-02 , -1.67817706510836e-02 ), ( -1.67336131493115e-02 , 7.27772224080956e-02 , -8.17555554242184e-02 ), ( -1.97831682663396e-02 , 8.69711573163882e-02 , -1.00377263119591e-01 ), ( -8.49613558415377e-03 , 4.71026760275649e-02 , -8.21027934280728e-02 ), ( -1.85801247869260e-02 , 6.67289400821420e-02 , -3.44791463843032e-02 ), ( -2.42469940229704e-02 , 9.27508182648225e-02 , -6.76669719294010e-02 ) } colvars: ---------------------------------------------------------------------- @@ -2328,7 +3365,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 5, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 5, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 5, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 5, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 5, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 5, atoms_positions[size = 51] = { ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 ), ( 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 ), ( 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 ), ( 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 ), ( 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 ), ( 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 ), ( -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 ), ( -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 ), ( -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 ), ( -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ), ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 ), ( 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 ), ( 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 ), ( 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 ), ( 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 ), ( 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 ), ( 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 ), ( 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 ), ( 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 ), ( 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 ), ( 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 ), ( 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 ), ( 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 ), ( 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 ), ( 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 ), ( 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 ), ( 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 ), ( 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 ), ( 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 ), ( -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 ), ( 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 ), ( 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 ), ( -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 ), ( -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 ), ( -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 ), ( -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 ), ( -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 ), ( -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 ), ( -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 ), ( -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 ), ( -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 ), ( -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 ), ( -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 ), ( -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 ), ( -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 ), ( -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 ), ( -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 ), ( -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 ), ( -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 ), ( -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 ), ( -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ) } @@ -2349,16 +3386,87 @@ colvars: Collective variables module, step no. 5 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 , 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 , 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 , 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 , 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 , 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 , 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 , 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 , 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 , 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 , 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 , 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 , 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 , 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 , 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 , -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 , 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 , -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 , -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 , -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 , -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 , -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 , -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 , -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 , -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 , -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 , -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 , -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 , -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 , -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 , -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 , -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 , -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 , 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 , 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 , 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 , 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 , 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 , 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 , 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 , 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 , 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 , 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 , 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 , 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 , 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 , 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 , -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 , 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 , -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 , -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 , -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 , -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 , -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 , -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 , -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 , -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 , -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 , -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 , -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 , -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 , -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 , -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 , -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 , -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2371,6 +3479,10 @@ colvars: Adding total bias energy: 11.4206 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2386,8 +3498,6 @@ colvars: ( 0.0080638 , -0.108924 , 0.307986 ) colvars: ( -0.0489315 , 0.0763321 , 0.215154 ) colvars: ( 0.0804605 , -0.231668 , 0.0246104 ) colvars: ( 0.136517 , -0.472035 , 0.323238 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242606 , -0.0994173 , 0.0944948 ) colvars: ( 0.0197707 , -0.0822038 , 0.0817612 ) @@ -2440,12 +3550,15 @@ colvars: ( -0.0085006 , 0.0470643 , -0.0821573 ) colvars: ( -0.0185861 , 0.0667214 , -0.0345236 ) colvars: ( -0.0222579 , 0.0839955 , -0.057758 ) colvars: ( -0.0242599 , 0.0927419 , -0.0677312 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 5. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 5. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- colvars: Step 5, atoms_new_colvar_forces = { ( -7.11930917715262e-02 , 3.04080402889663e-01 , -3.89420117659556e-01 ), ( 1.22274699460667e-02 , 3.52378104756379e-02 , -2.36672496748529e-01 ), ( -4.15700140483639e-02 , 9.12349296696296e-02 , 8.27563970021866e-02 ), ( -9.61016217912612e-02 , 2.42865160914319e-01 , 6.72337999946861e-02 ), ( -1.88360121209974e-02 , 9.95358134491225e-02 , -1.65545997411328e-01 ), ( 7.02602719142824e-02 , -1.80280636028130e-01 , -4.07839832834661e-02 ), ( 1.05279361141261e-02 , -1.01752713338897e-01 , 2.48323952446562e-01 ), ( -4.04029387005403e-02 , 5.52382955877266e-02 , 1.92806022433958e-01 ), ( 6.56430458681339e-02 , -1.87308994968492e-01 , 3.25135719017205e-02 ), ( 1.14259433857731e-01 , -3.88039115593396e-01 , 2.65479921768059e-01 ), ( 2.42605798564394e-02 , -9.94172883871254e-02 , 9.44948179787660e-02 ), ( 2.64346007973788e-02 , -9.72729724027510e-02 , 5.86335564201711e-02 ), ( 1.22532987785135e-02 , -5.61471444227930e-02 , 7.15265885148806e-02 ), ( 1.23959564254596e-02 , -5.38374384588434e-02 , 6.04746134511424e-02 ), ( 5.47639039529515e-03 , -3.57590564742181e-02 , 7.47400233883485e-02 ), ( -8.62288446849312e-03 , 8.29741139291352e-03 , 7.48511040577863e-02 ), ( -2.06769030098720e-03 , -3.51031338390929e-03 , 4.00062583395601e-02 ), ( -5.75313344233234e-03 , 9.05996009845718e-03 , 3.58072218150797e-02 ), ( 2.79862073872496e-03 , -1.35972818387436e-02 , 1.94383059596313e-02 ), ( 9.25229494769087e-03 , -2.23407885089335e-02 , -2.64225913728223e-02 ), ( 8.81700552361751e-03 , -2.38629084835913e-02 , -1.48597374907990e-02 ), ( 6.73316724776024e-03 , -1.35421597401508e-02 , -3.01205976460819e-02 ), ( 1.50768098167967e-02 , -4.65735796171252e-02 , -2.27412576343031e-03 ), ( 2.75851638634807e-02 , -8.79413881509297e-02 , 6.78148943275173e-03 ), ( 1.42388046236963e-02 , -4.66350043773231e-02 , 8.48051060091069e-03 ), ( 1.41908282837240e-02 , -4.36356336581280e-02 , -2.94688817210362e-03 ), ( 9.22084526028328e-03 , -3.70798975284593e-02 , 3.30831159893830e-02 ), ( -1.00338374270740e-03 , -1.57322786602175e-02 , 7.56765366312058e-02 ), ( -3.85421467521831e-03 , 3.91614128972128e-03 , 3.26247802985022e-02 ), ( -5.93813236113047e-03 , 1.10470979535649e-02 , 3.01576079069810e-02 ), ( -7.31435281678647e-03 , 1.75430114049752e-02 , 2.13630069306248e-02 ), ( -1.61855455840492e-02 , 5.14338186761766e-02 , -3.31475159770605e-03 ), ( -9.68795659419696e-03 , 3.56008411236023e-02 , -2.12939333607702e-02 ), ( -1.37170377970814e-02 , 4.98527717794188e-02 , -2.79281712479423e-02 ), ( -1.90365092081225e-03 , 1.49183129164942e-02 , -3.59589220985608e-02 ), ( 1.07212998249860e-02 , -1.54039102464941e-02 , -7.26638156649286e-02 ), ( 4.42569541964384e-03 , -3.91221119058605e-04 , -5.39276752213949e-02 ), ( 3.41955036969028e-03 , 6.55443034604825e-03 , -6.91665708908388e-02 ), ( 7.11358937522634e-03 , -1.44310237929892e-02 , -3.13261600722330e-02 ), ( 1.29581107015235e-02 , -4.08439956241160e-02 , 1.31506744524187e-03 ), ( 4.29688150890716e-04 , 2.12923211316452e-03 , -1.39274449810552e-02 ), ( 3.41999448111169e-04 , 3.85645860323836e-03 , -1.97549178900757e-02 ), ( -6.60834719336973e-03 , 2.06895144376888e-02 , -1.09137290942866e-04 ), ( -2.06864898021626e-02 , 5.74799121391366e-02 , 2.88775969811894e-02 ), ( -1.90066753015798e-02 , 6.32967248326141e-02 , -1.55150723924351e-02 ), ( -2.27269315783031e-02 , 7.52558980269329e-02 , -1.68267407696857e-02 ), ( -1.67418411274645e-02 , 7.27480314369913e-02 , -8.18198566656224e-02 ), ( -1.97938715038249e-02 , 8.69371697033174e-02 , -1.00454140405606e-01 ), ( -8.50060401083803e-03 , 4.70643098012962e-02 , -8.21572711273281e-02 ), ( -1.85860961724292e-02 , 6.67213789483478e-02 , -3.45235959012453e-02 ), ( -2.42599397228173e-02 , 9.27419047946174e-02 , -6.77311545628400e-02 ) } colvars: ---------------------------------------------------------------------- @@ -2485,10 +3598,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 6, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 6, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 6, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 6, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 6, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 6, atoms_positions[size = 51] = { ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 ), ( 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 ), ( 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 ), ( 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 ), ( 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 ), ( 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 ), ( -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 ), ( -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 ), ( -3.77765611267382e+00 , 9.58922869679192e-02 , 5.48159808807106e+00 ), ( -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ), ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 ), ( 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 ), ( 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 ), ( 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 ), ( 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 ), ( 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 ), ( 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 ), ( 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 ), ( 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 ), ( 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 ), ( 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 ), ( 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 ), ( 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 ), ( 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 ), ( 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 ), ( 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 ), ( 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 ), ( 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 ), ( 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 ), ( -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 ), ( 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 ), ( 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 ), ( -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 ), ( -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 ), ( -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 ), ( -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 ), ( -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 ), ( -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 ), ( -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 ), ( -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 ), ( -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 ), ( -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 ), ( -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 ), ( -2.40918974321356e+00 , -3.98829720444864e-01 , 6.14201010890720e+00 ), ( -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 ), ( -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 ), ( -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 ), ( -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 ), ( -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 ), ( -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 ), ( -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ) } +colvars: Step 6, atoms_positions[size = 51] = { ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 ), ( 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 ), ( 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 ), ( 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 ), ( 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 ), ( 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 ), ( -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 ), ( -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 ), ( -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 ), ( -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ), ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 ), ( 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 ), ( 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 ), ( 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 ), ( 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 ), ( 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 ), ( 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 ), ( 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 ), ( 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 ), ( 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 ), ( 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 ), ( 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 ), ( 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 ), ( 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 ), ( 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 ), ( 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 ), ( 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 ), ( 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 ), ( 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 ), ( -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 ), ( 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 ), ( 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 ), ( -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 ), ( -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 ), ( -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 ), ( -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 ), ( -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 ), ( -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 ), ( -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 ), ( -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 ), ( -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 ), ( -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 ), ( -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 ), ( -2.40918974321355e+00 , -3.98829720444863e-01 , 6.14201010890720e+00 ), ( -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 ), ( -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 ), ( -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 ), ( -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 ), ( -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 ), ( -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 ), ( -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ) } colvars: Step 6, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 6, atom_groups_ids[size = 0] = @@ -2506,16 +3619,87 @@ colvars: Collective variables module, step no. 6 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ). +colvars: Calculating gradients of colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ). colvars: Calculating gradients of colvar "one". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 , 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 , 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 , 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 , 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 , 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 , 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 , 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 , 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 , 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 , 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 , 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 , 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 , 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 , 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 , -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 , 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 , -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 , -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 , -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 , -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 , -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 , -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 , -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 , -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 , -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -2.40918974321355e+00 , -3.98829720444863e-01 , 6.14201010890720e+00 , -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 , -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 , -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 , -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 , -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 , -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 , -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 , 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 , 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 , 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 , 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 , 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 , 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 , 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 , 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 , 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 , 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 , 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 , 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 , 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 , 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 , -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 , 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 , -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 , -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 , -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 , -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 , -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 , -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 , -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 , -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 , -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -2.40918974321355e+00 , -3.98829720444863e-01 , 6.14201010890720e+00 , -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 , -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 , -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 , -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 , -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 , -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 , -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2528,6 +3712,10 @@ colvars: Adding total bias energy: 11.4245 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2543,8 +3731,6 @@ colvars: ( 0.00808168 , -0.1087 , 0.308388 ) colvars: ( -0.0489749 , 0.076829 , 0.215056 ) colvars: ( 0.0804539 , -0.231708 , 0.0245252 ) colvars: ( 0.136565 , -0.472096 , 0.323784 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242815 , -0.0993938 , 0.0945777 ) colvars: ( 0.0197853 , -0.0821738 , 0.0818345 ) @@ -2597,14 +3783,17 @@ colvars: ( -0.00850939 , 0.0470198 , -0.0822179 ) colvars: ( -0.0185938 , 0.0667109 , -0.0345702 ) colvars: ( -0.0222711 , 0.0839807 , -0.0578208 ) colvars: ( -0.0242784 , 0.0927335 , -0.0677985 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 6. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 6. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 6, atoms_new_colvar_forces = { ( -7.12142262303992e-02 , 3.03903301715952e-01 , -3.89969129550351e-01 ), ( 1.22547356452154e-02 , 3.48262951672449e-02 , -2.36721963920782e-01 ), ( -4.15518674361304e-02 , 9.12751560648350e-02 , 8.30772582640576e-02 ), ( -9.61317320933757e-02 , 2.43240346979410e-01 , 6.71401363520435e-02 ), ( -1.88556777097379e-02 , 9.94952870708496e-02 , -1.65913347874103e-01 ), ( 7.02868318338666e-02 , -1.80572282391047e-01 , -4.06482640014998e-02 ), ( 1.05381289914210e-02 , -1.01554511095457e-01 , 2.48698582925828e-01 ), ( -4.04390358015067e-02 , 5.56977300193671e-02 , 1.92699294429561e-01 ), ( 6.56391566883627e-02 , -1.87353793800463e-01 , 3.24058940221479e-02 ), ( 1.14293775414791e-01 , -3.88114795924072e-01 , 2.65963163735460e-01 ), ( 2.42814729749294e-02 , -9.93938454081909e-02 , 9.45777245589051e-02 ), ( 2.64473139563615e-02 , -9.72552236470947e-02 , 5.87044852956407e-02 ), ( 1.22634185313900e-02 , -5.61144142202651e-02 , 7.15849993395887e-02 ), ( 1.24062468740887e-02 , -5.38142909992530e-02 , 6.05256176470266e-02 ), ( 5.48226526174387e-03 , -3.57129885325301e-02 , 7.47936140876123e-02 ), ( -8.62544006295661e-03 , 8.36465137573990e-03 , 7.48898030521818e-02 ), ( -2.06991625388785e-03 , -3.47135619509694e-03 , 4.00321364199732e-02 ), ( -5.75601257738078e-03 , 9.09651790518482e-03 , 3.58247231259840e-02 ), ( 2.79396502781401e-03 , -1.35672817619064e-02 , 1.94610539947598e-02 ), ( 9.24159279432054e-03 , -2.23299181608012e-02 , -2.64135889483069e-02 ), ( 8.81256516211875e-03 , -2.38605293913080e-02 , -1.48502275938890e-02 ), ( 6.72657734904849e-03 , -1.35466756974881e-02 , -3.01226642825190e-02 ), ( 1.50780930352461e-02 , -4.65758441774542e-02 , -2.25154451988601e-03 ), ( 2.75961135614895e-02 , -8.79611454331461e-02 , 6.82117273635850e-03 ), ( 1.42459402549000e-02 , -4.66453423016032e-02 , 8.50280256995158e-03 ), ( 1.41979492402755e-02 , -4.36553747142220e-02 , -2.93238398181345e-03 ), ( 9.22935271210501e-03 , -3.70749488738609e-02 , 3.31121184968349e-02 ), ( -9.91874405938820e-04 , -1.57029967626075e-02 , 7.57139032005495e-02 ), ( -3.84980968726094e-03 , 3.92961372844109e-03 , 3.26356944825281e-02 ), ( -5.93303553292433e-03 , 1.10560962669028e-02 , 3.01626091603370e-02 ), ( -7.31542887547997e-03 , 1.75621364522944e-02 , 2.13662184603644e-02 ), ( -1.61974194508721e-02 , 5.14615739051055e-02 , -3.33186857750587e-03 ), ( -9.69573856621546e-03 , 3.56034451247036e-02 , -2.13165194953996e-02 ), ( -1.37262291647893e-02 , 4.98530577430511e-02 , -2.79605666016103e-02 ), ( -1.91073603828273e-03 , 1.49085110410628e-02 , -3.59790018535196e-02 ), ( 1.07140432385856e-02 , -1.54407701911095e-02 , -7.26871956581507e-02 ), ( 4.42261271019296e-03 , -4.25945906022851e-04 , -5.39534073383785e-02 ), ( 3.41501168760075e-03 , 6.51107644294852e-03 , -6.92027722989708e-02 ), ( 7.11618928681651e-03 , -1.44627849641822e-02 , -3.13380424647115e-02 ), ( 1.29714546559885e-02 , -4.08783185679446e-02 , 1.32383933489511e-03 ), ( 4.35990744562135e-04 , 2.09976734191281e-03 , -1.39427446383950e-02 ), ( 3.49433995726928e-04 , 3.81891985606553e-03 , -1.97754914609517e-02 ), ( -6.60423860307249e-03 , 2.06762093489714e-02 , -1.24683954910893e-04 ), ( -2.06847286332335e-02 , 5.74941934675936e-02 , 2.88603238042472e-02 ), ( -1.90095738981270e-02 , 6.32880734562383e-02 , -1.55546171706953e-02 ), ( -2.27299338339649e-02 , 7.52456489187880e-02 , -1.68733466161828e-02 ), ( -1.67550040694721e-02 , 7.27145435033735e-02 , -8.18896108779006e-02 ), ( -1.98109971023338e-02 , 8.68989856646780e-02 , -1.00537483379429e-01 ), ( -8.50939441170506e-03 , 4.70198123865680e-02 , -8.22179224442125e-02 ), ( -1.85938018440016e-02 , 6.67108998990059e-02 , -3.45702310150741e-02 ), ( -2.42783793459124e-02 , 9.27335282708393e-02 , -6.77985489776879e-02 ) } +colvars: Step 6, atoms_new_colvar_forces = { ( -7.12142262303992e-02 , 3.03903301715951e-01 , -3.89969129550351e-01 ), ( 1.22547356452154e-02 , 3.48262951672449e-02 , -2.36721963920782e-01 ), ( -4.15518674361304e-02 , 9.12751560648350e-02 , 8.30772582640576e-02 ), ( -9.61317320933757e-02 , 2.43240346979410e-01 , 6.71401363520435e-02 ), ( -1.88556777097379e-02 , 9.94952870708496e-02 , -1.65913347874103e-01 ), ( 7.02868318338666e-02 , -1.80572282391047e-01 , -4.06482640014998e-02 ), ( 1.05381289914209e-02 , -1.01554511095457e-01 , 2.48698582925828e-01 ), ( -4.04390358015067e-02 , 5.56977300193672e-02 , 1.92699294429561e-01 ), ( 6.56391566883627e-02 , -1.87353793800463e-01 , 3.24058940221479e-02 ), ( 1.14293775414791e-01 , -3.88114795924072e-01 , 2.65963163735460e-01 ), ( 2.42814729749294e-02 , -9.93938454081909e-02 , 9.45777245589051e-02 ), ( 2.64473139563615e-02 , -9.72552236470947e-02 , 5.87044852956407e-02 ), ( 1.22634185313900e-02 , -5.61144142202651e-02 , 7.15849993395887e-02 ), ( 1.24062468740887e-02 , -5.38142909992529e-02 , 6.05256176470266e-02 ), ( 5.48226526174388e-03 , -3.57129885325300e-02 , 7.47936140876123e-02 ), ( -8.62544006295660e-03 , 8.36465137573996e-03 , 7.48898030521818e-02 ), ( -2.06991625388785e-03 , -3.47135619509690e-03 , 4.00321364199732e-02 ), ( -5.75601257738078e-03 , 9.09651790518486e-03 , 3.58247231259840e-02 ), ( 2.79396502781401e-03 , -1.35672817619064e-02 , 1.94610539947598e-02 ), ( 9.24159279432052e-03 , -2.23299181608012e-02 , -2.64135889483069e-02 ), ( 8.81256516211873e-03 , -2.38605293913080e-02 , -1.48502275938890e-02 ), ( 6.72657734904847e-03 , -1.35466756974881e-02 , -3.01226642825190e-02 ), ( 1.50780930352461e-02 , -4.65758441774542e-02 , -2.25154451988603e-03 ), ( 2.75961135614895e-02 , -8.79611454331461e-02 , 6.82117273635849e-03 ), ( 1.42459402548999e-02 , -4.66453423016032e-02 , 8.50280256995158e-03 ), ( 1.41979492402755e-02 , -4.36553747142220e-02 , -2.93238398181345e-03 ), ( 9.22935271210501e-03 , -3.70749488738609e-02 , 3.31121184968349e-02 ), ( -9.91874405938806e-04 , -1.57029967626075e-02 , 7.57139032005495e-02 ), ( -3.84980968726093e-03 , 3.92961372844109e-03 , 3.26356944825281e-02 ), ( -5.93303553292432e-03 , 1.10560962669028e-02 , 3.01626091603370e-02 ), ( -7.31542887547996e-03 , 1.75621364522944e-02 , 2.13662184603644e-02 ), ( -1.61974194508721e-02 , 5.14615739051056e-02 , -3.33186857750588e-03 ), ( -9.69573856621547e-03 , 3.56034451247036e-02 , -2.13165194953996e-02 ), ( -1.37262291647893e-02 , 4.98530577430511e-02 , -2.79605666016103e-02 ), ( -1.91073603828273e-03 , 1.49085110410628e-02 , -3.59790018535196e-02 ), ( 1.07140432385856e-02 , -1.54407701911095e-02 , -7.26871956581507e-02 ), ( 4.42261271019295e-03 , -4.25945906022867e-04 , -5.39534073383785e-02 ), ( 3.41501168760073e-03 , 6.51107644294849e-03 , -6.92027722989708e-02 ), ( 7.11618928681650e-03 , -1.44627849641823e-02 , -3.13380424647115e-02 ), ( 1.29714546559885e-02 , -4.08783185679446e-02 , 1.32383933489513e-03 ), ( 4.35990744562140e-04 , 2.09976734191279e-03 , -1.39427446383950e-02 ), ( 3.49433995726934e-04 , 3.81891985606549e-03 , -1.97754914609517e-02 ), ( -6.60423860307248e-03 , 2.06762093489713e-02 , -1.24683954910883e-04 ), ( -2.06847286332335e-02 , 5.74941934675936e-02 , 2.88603238042472e-02 ), ( -1.90095738981270e-02 , 6.32880734562383e-02 , -1.55546171706953e-02 ), ( -2.27299338339649e-02 , 7.52456489187880e-02 , -1.68733466161828e-02 ), ( -1.67550040694721e-02 , 7.27145435033735e-02 , -8.18896108779006e-02 ), ( -1.98109971023338e-02 , 8.68989856646780e-02 , -1.00537483379429e-01 ), ( -8.50939441170508e-03 , 4.70198123865680e-02 , -8.22179224442125e-02 ), ( -1.85938018440016e-02 , 6.67108998990059e-02 , -3.45702310150741e-02 ), ( -2.42783793459124e-02 , 9.27335282708393e-02 , -6.77985489776879e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 6, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2642,7 +3831,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 7, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 7, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 7, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 7, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 7, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 7, atoms_positions[size = 51] = { ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 ), ( 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 ), ( 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 ), ( 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 ), ( 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 ), ( 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 ), ( -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 ), ( -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 ), ( -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 ), ( -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ), ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 ), ( 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 ), ( 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 ), ( 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 ), ( 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 ), ( 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 ), ( 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 ), ( 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 ), ( 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 ), ( 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 ), ( 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 ), ( 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 ), ( 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 ), ( 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 ), ( 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 ), ( 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 ), ( 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 ), ( 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 ), ( 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 ), ( -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 ), ( 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 ), ( 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 ), ( -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 ), ( -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 ), ( -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 ), ( -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 ), ( -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 ), ( -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 ), ( -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 ), ( -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 ), ( -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 ), ( -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 ), ( -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 ), ( -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 ), ( -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 ), ( -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 ), ( -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 ), ( -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 ), ( -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 ), ( -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 ), ( -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ) } @@ -2663,16 +3852,87 @@ colvars: Collective variables module, step no. 7 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851382e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851381e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 , 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 , 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 , 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 , 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 , 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 , 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 , 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 , 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 , 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 , 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 , 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 , 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 , 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 , 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 , -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 , 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 , -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 , -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 , -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 , -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 , -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 , -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 , -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 , -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 , -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 , -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 , -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 , -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 , -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 , -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 , -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 , -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851382e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). +colvars: Colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851381e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 , 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 , 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 , 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 , 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 , 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 , 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 , 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 , 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 , 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 , 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 , 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 , 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 , 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 , 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 , -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 , 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 , -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 , -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 , -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 , -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 , -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 , -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 , -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 , -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 , -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 , -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 , -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 , -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 , -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 , -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 , -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 , -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2685,6 +3945,10 @@ colvars: Adding total bias energy: 11.4284 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2700,8 +3964,6 @@ colvars: ( 0.0081132 , -0.108469 , 0.308855 ) colvars: ( -0.0490242 , 0.0773859 , 0.21495 ) colvars: ( 0.0804595 , -0.231765 , 0.0243971 ) colvars: ( 0.13665 , -0.472208 , 0.324378 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.024309 , -0.0993703 , 0.0946656 ) colvars: ( 0.0198048 , -0.0821413 , 0.0819129 ) @@ -2754,14 +4016,17 @@ colvars: ( -0.00852211 , 0.0469704 , -0.0822846 ) colvars: ( -0.0186033 , 0.0666983 , -0.0346189 ) colvars: ( -0.022288 , 0.0839646 , -0.0578867 ) colvars: ( -0.0243021 , 0.0927264 , -0.067869 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 7. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 7. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 7, atoms_new_colvar_forces = { ( -7.12643629297238e-02 , 3.03748456819681e-01 , -3.90586407900473e-01 ), ( 1.22798357354463e-02 , 3.43778085240194e-02 , -2.36779111668178e-01 ), ( -4.15369806328073e-02 , 9.13219268139160e-02 , 8.34694649792221e-02 ), ( -9.61814499206716e-02 , 2.43678342667974e-01 , 6.70597490320277e-02 ), ( -1.88857517066456e-02 , 9.94664433603135e-02 , -1.66338638098737e-01 ), ( 7.03279301363652e-02 , -1.80911714089215e-01 , -4.05099162241549e-02 ), ( 1.05581846145116e-02 , -1.01351207901457e-01 , 2.49133378748631e-01 ), ( -4.04801416450276e-02 , 5.62103343343931e-02 , 1.92581516655001e-01 ), ( 6.56492670474172e-02 , -1.87419378224912e-01 , 3.22551691858706e-02 ), ( 1.14361816218885e-01 , -3.88242959643882e-01 , 2.66491224123914e-01 ), ( 2.43089604741000e-02 , -9.93703389638662e-02 , 9.46656398079234e-02 ), ( 2.64633115886798e-02 , -9.72346559646698e-02 , 5.87788599655936e-02 ), ( 1.22773304643787e-02 , -5.60783277865503e-02 , 7.16482732771626e-02 ), ( 1.24200974597789e-02 , -5.37892737835383e-02 , 6.05804114728067e-02 ), ( 5.49126095479498e-03 , -3.56612002445239e-02 , 7.48531138676495e-02 ), ( -8.62632024734143e-03 , 8.44138021182978e-03 , 7.49358821822966e-02 ), ( -2.07165217509811e-03 , -3.42604475726389e-03 , 4.00622073248809e-02 ), ( -5.75844877153946e-03 , 9.13861103854014e-03 , 3.58460704568341e-02 ), ( 2.78830006708309e-03 , -1.35303913001015e-02 , 1.94867025441894e-02 ), ( 9.22664704378498e-03 , -2.23114382528987e-02 , -2.64045420530178e-02 ), ( 8.80594631376906e-03 , -2.38543535758261e-02 , -1.48409418464280e-02 ), ( 6.71696820112536e-03 , -1.35479989898134e-02 , -3.01259814853927e-02 ), ( 1.50787036067345e-02 , -4.65760405505027e-02 , -2.22907699732126e-03 ), ( 2.76085096907280e-02 , -8.79828374284035e-02 , 6.85982871925103e-03 ), ( 1.42543599808695e-02 , -4.66572795962589e-02 , 8.52471407991168e-03 ), ( 1.42060734830385e-02 , -4.36781388833885e-02 , -2.91933397806574e-03 ), ( 9.24045584481542e-03 , -3.70707957299862e-02 , 3.31426363027339e-02 ), ( -9.75223585295903e-04 , -1.56739823609264e-02 , 7.57558939840136e-02 ), ( -3.84312252210567e-03 , 3.94265579472863e-03 , 3.26486365211450e-02 ), ( -5.92538821370363e-03 , 1.10633157410566e-02 , 3.01692052913536e-02 ), ( -7.31580955849081e-03 , 1.75831579539413e-02 , 2.13714897525162e-02 ), ( -1.62116519386518e-02 , 5.14950342863534e-02 , -3.34714876103202e-03 ), ( -9.70559411338392e-03 , 3.56076117306303e-02 , -2.13396788115715e-02 ), ( -1.37377903715564e-02 , 4.98543287436506e-02 , -2.79939571721177e-02 ), ( -1.92056274355791e-03 , 1.48996290499974e-02 , -3.60009908034978e-02 ), ( 1.07022807165507e-02 , -1.54782919591166e-02 , -7.27155880541698e-02 ), ( 4.41705954600045e-03 , -4.63856402268637e-04 , -5.39834426064317e-02 ), ( 3.40728678849276e-03 , 6.46360802827689e-03 , -6.92444234215556e-02 ), ( 7.11828967127039e-03 , -1.44989851915113e-02 , -3.13532550881224e-02 ), ( 1.29877290166139e-02 , -4.09205362039969e-02 , 1.33018961029170e-03 ), ( 4.43689718407329e-04 , 2.06347307826286e-03 , -1.39606995589762e-02 ), ( 3.58444950702431e-04 , 3.77287300218497e-03 , -1.97995143891150e-02 ), ( -6.59855400003896e-03 , 2.06580134531092e-02 , -1.41289081215119e-04 ), ( -2.06804274679637e-02 , 5.75059489194441e-02 , 2.88448741084997e-02 ), ( -1.90124333628416e-02 , 6.32755773639386e-02 , -1.55954735441749e-02 ), ( -2.27327171854041e-02 , 7.52306358455108e-02 , -1.69214580765575e-02 ), ( -1.67727728860836e-02 , 7.26779069784233e-02 , -8.19646548939965e-02 ), ( -1.98340970554791e-02 , 8.68579024560199e-02 , -1.00627094487174e-01 ), ( -8.52210798867692e-03 , 4.69703868264598e-02 , -8.22846297106069e-02 ), ( -1.86033074160002e-02 , 6.66982592868968e-02 , -3.46189230904566e-02 ), ( -2.43020708962544e-02 , 9.27264054753276e-02 , -6.78689601911793e-02 ) } +colvars: Step 7, atoms_new_colvar_forces = { ( -7.12643629297239e-02 , 3.03748456819681e-01 , -3.90586407900473e-01 ), ( 1.22798357354463e-02 , 3.43778085240195e-02 , -2.36779111668179e-01 ), ( -4.15369806328073e-02 , 9.13219268139160e-02 , 8.34694649792220e-02 ), ( -9.61814499206716e-02 , 2.43678342667974e-01 , 6.70597490320277e-02 ), ( -1.88857517066456e-02 , 9.94664433603135e-02 , -1.66338638098737e-01 ), ( 7.03279301363652e-02 , -1.80911714089215e-01 , -4.05099162241549e-02 ), ( 1.05581846145115e-02 , -1.01351207901457e-01 , 2.49133378748630e-01 ), ( -4.04801416450276e-02 , 5.62103343343931e-02 , 1.92581516655002e-01 ), ( 6.56492670474172e-02 , -1.87419378224912e-01 , 3.22551691858707e-02 ), ( 1.14361816218885e-01 , -3.88242959643882e-01 , 2.66491224123914e-01 ), ( 2.43089604741000e-02 , -9.93703389638662e-02 , 9.46656398079235e-02 ), ( 2.64633115886798e-02 , -9.72346559646698e-02 , 5.87788599655936e-02 ), ( 1.22773304643787e-02 , -5.60783277865503e-02 , 7.16482732771626e-02 ), ( 1.24200974597789e-02 , -5.37892737835383e-02 , 6.05804114728067e-02 ), ( 5.49126095479498e-03 , -3.56612002445240e-02 , 7.48531138676496e-02 ), ( -8.62632024734144e-03 , 8.44138021182977e-03 , 7.49358821822966e-02 ), ( -2.07165217509811e-03 , -3.42604475726390e-03 , 4.00622073248809e-02 ), ( -5.75844877153946e-03 , 9.13861103854014e-03 , 3.58460704568341e-02 ), ( 2.78830006708309e-03 , -1.35303913001015e-02 , 1.94867025441895e-02 ), ( 9.22664704378498e-03 , -2.23114382528987e-02 , -2.64045420530178e-02 ), ( 8.80594631376906e-03 , -2.38543535758261e-02 , -1.48409418464280e-02 ), ( 6.71696820112536e-03 , -1.35479989898134e-02 , -3.01259814853926e-02 ), ( 1.50787036067345e-02 , -4.65760405505027e-02 , -2.22907699732124e-03 ), ( 2.76085096907280e-02 , -8.79828374284034e-02 , 6.85982871925105e-03 ), ( 1.42543599808695e-02 , -4.66572795962589e-02 , 8.52471407991169e-03 ), ( 1.42060734830385e-02 , -4.36781388833885e-02 , -2.91933397806573e-03 ), ( 9.24045584481543e-03 , -3.70707957299862e-02 , 3.31426363027339e-02 ), ( -9.75223585295899e-04 , -1.56739823609265e-02 , 7.57558939840137e-02 ), ( -3.84312252210567e-03 , 3.94265579472862e-03 , 3.26486365211450e-02 ), ( -5.92538821370363e-03 , 1.10633157410566e-02 , 3.01692052913536e-02 ), ( -7.31580955849081e-03 , 1.75831579539413e-02 , 2.13714897525162e-02 ), ( -1.62116519386518e-02 , 5.14950342863534e-02 , -3.34714876103200e-03 ), ( -9.70559411338393e-03 , 3.56076117306303e-02 , -2.13396788115714e-02 ), ( -1.37377903715564e-02 , 4.98543287436506e-02 , -2.79939571721177e-02 ), ( -1.92056274355792e-03 , 1.48996290499974e-02 , -3.60009908034978e-02 ), ( 1.07022807165507e-02 , -1.54782919591166e-02 , -7.27155880541698e-02 ), ( 4.41705954600045e-03 , -4.63856402268646e-04 , -5.39834426064317e-02 ), ( 3.40728678849276e-03 , 6.46360802827689e-03 , -6.92444234215556e-02 ), ( 7.11828967127039e-03 , -1.44989851915113e-02 , -3.13532550881224e-02 ), ( 1.29877290166139e-02 , -4.09205362039969e-02 , 1.33018961029169e-03 ), ( 4.43689718407328e-04 , 2.06347307826285e-03 , -1.39606995589763e-02 ), ( 3.58444950702430e-04 , 3.77287300218497e-03 , -1.97995143891151e-02 ), ( -6.59855400003897e-03 , 2.06580134531091e-02 , -1.41289081215124e-04 ), ( -2.06804274679637e-02 , 5.75059489194441e-02 , 2.88448741084997e-02 ), ( -1.90124333628416e-02 , 6.32755773639386e-02 , -1.55954735441749e-02 ), ( -2.27327171854041e-02 , 7.52306358455108e-02 , -1.69214580765575e-02 ), ( -1.67727728860836e-02 , 7.26779069784233e-02 , -8.19646548939965e-02 ), ( -1.98340970554791e-02 , 8.68579024560199e-02 , -1.00627094487174e-01 ), ( -8.52210798867692e-03 , 4.69703868264598e-02 , -8.22846297106070e-02 ), ( -1.86033074160002e-02 , 6.66982592868968e-02 , -3.46189230904566e-02 ), ( -2.43020708962544e-02 , 9.27264054753276e-02 , -6.78689601911793e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 7, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2799,10 +4064,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 8, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 8, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 8, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 8, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 8, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 8, atoms_positions[size = 51] = { ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 ), ( 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 ), ( 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 ), ( 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 ), ( 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 ), ( 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 ), ( -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 ), ( -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 ), ( -3.77960603765112e+00 , 8.28285620991697e-02 , 5.48323895924115e+00 ), ( -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ), ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 ), ( 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 ), ( 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 ), ( 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 ), ( 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 ), ( 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 ), ( 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 ), ( 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 ), ( 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 ), ( 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 ), ( 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 ), ( 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 ), ( 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 ), ( 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 ), ( 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 ), ( 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 ), ( 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 ), ( 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 ), ( 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 ), ( -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 ), ( 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 ), ( 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 ), ( -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 ), ( -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 ), ( -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 ), ( -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 ), ( -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 ), ( -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 ), ( -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 ), ( -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 ), ( -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 ), ( -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 ), ( -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 ), ( -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 ), ( -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 ), ( -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 ), ( -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 ), ( -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 ), ( -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 ), ( -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 ), ( -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ) } +colvars: Step 8, atoms_positions[size = 51] = { ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 ), ( 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 ), ( 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 ), ( 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 ), ( 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 ), ( 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 ), ( -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 ), ( -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 ), ( -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 ), ( -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ), ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 ), ( 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 ), ( 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 ), ( 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 ), ( 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 ), ( 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 ), ( 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 ), ( 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 ), ( 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 ), ( 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 ), ( 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 ), ( 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 ), ( 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 ), ( 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 ), ( 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 ), ( 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 ), ( 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 ), ( 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 ), ( 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 ), ( -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 ), ( 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 ), ( 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 ), ( -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 ), ( -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 ), ( -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 ), ( -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 ), ( -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 ), ( -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 ), ( -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 ), ( -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 ), ( -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 ), ( -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 ), ( -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 ), ( -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 ), ( -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 ), ( -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 ), ( -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 ), ( -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 ), ( -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 ), ( -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 ), ( -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ) } colvars: Step 8, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 8, atom_groups_ids[size = 0] = @@ -2820,16 +4085,87 @@ colvars: Collective variables module, step no. 8 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 , 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 , 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 , 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 , 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 , 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 , 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 , 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 , 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 , 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 , 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 , 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 , 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 , 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 , 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 , -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 , 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 , -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 , -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 , -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 , -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 , -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 , -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 , -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 , -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 , -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 , -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 , -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 , -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 , -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 , -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 , -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 , -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 , 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 , 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 , 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 , 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 , 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 , 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 , 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 , 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 , 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 , 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 , 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 , 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 , 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 , 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 , -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 , 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 , -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 , -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 , -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 , -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 , -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 , -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 , -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 , -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 , -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 , -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 , -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 , -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 , -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 , -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 , -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 , -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2842,6 +4178,10 @@ colvars: Adding total bias energy: 11.4325 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2857,8 +4197,6 @@ colvars: ( 0.00815306 , -0.108235 , 0.309381 ) colvars: ( -0.0490804 , 0.0779933 , 0.214839 ) colvars: ( 0.0804766 , -0.231843 , 0.0242323 ) colvars: ( 0.136765 , -0.472373 , 0.325018 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243423 , -0.099348 , 0.0947584 ) colvars: ( 0.0198284 , -0.0821074 , 0.081996 ) @@ -2911,14 +4249,17 @@ colvars: ( -0.00853819 , 0.0469173 , -0.0823571 ) colvars: ( -0.0186145 , 0.0666844 , -0.0346694 ) colvars: ( -0.0223082 , 0.0839483 , -0.0579556 ) colvars: ( -0.0243305 , 0.0927215 , -0.0679423 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 8. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 8. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 8, atoms_new_colvar_forces = { ( -7.13351423072813e-02 , 3.03619825792168e-01 , -3.91268617939964e-01 ), ( 1.23055499660459e-02 , 3.39005917766654e-02 , -2.36845225742551e-01 ), ( -4.15271491397816e-02 , 9.13791618604164e-02 , 8.39245305411536e-02 ), ( -9.62494045652913e-02 , 2.44175455092806e-01 , 6.69902520302190e-02 ), ( -1.89222535399380e-02 , 9.94484271845722e-02 , -1.66816690819095e-01 ), ( 7.03822543304743e-02 , -1.81295378894829e-01 , -4.03686971085317e-02 ), ( 1.05834154712841e-02 , -1.01144992174696e-01 , 2.49623497290294e-01 ), ( -4.05271851974778e-02 , 5.67671746608100e-02 , 1.92455361027341e-01 ), ( 6.56724380837020e-02 , -1.87509424162519e-01 , 3.20679681604365e-02 ), ( 1.14456342649259e-01 , -3.88424805112912e-01 , 2.67062889902466e-01 ), ( 2.43422720664008e-02 , -9.93480134779912e-02 , 9.47584074895654e-02 ), ( 2.64823207884572e-02 , -9.72127013570269e-02 , 5.88563122381287e-02 ), ( 1.22945465945720e-02 , -5.60400376600130e-02 , 7.17161479237924e-02 ), ( 1.24370696655174e-02 , -5.37633069113443e-02 , 6.06388129855506e-02 ), ( 5.50290662739556e-03 , -3.56049421041010e-02 , 7.49181815458750e-02 ), ( -8.62594279342891e-03 , 8.52631563305037e-03 , 7.49889010438598e-02 ), ( -2.07304727561448e-03 , -3.37528964129998e-03 , 4.00961351411889e-02 ), ( -5.76061164789090e-03 , 9.18555649372059e-03 , 3.58710078036011e-02 ), ( 2.78174471784882e-03 , -1.34876115706387e-02 , 1.95148242584832e-02 ), ( 9.20812060560969e-03 , -2.22863671904897e-02 , -2.63960131935175e-02 ), ( 8.79752854486906e-03 , -2.38450026309958e-02 , -1.48322003035765e-02 ), ( 6.70483229466327e-03 , -1.35465340002202e-02 , -3.01308249087184e-02 ), ( 1.50788672216310e-02 , -4.65748402463062e-02 , -2.20698674250555e-03 ), ( 2.76224099666520e-02 , -8.80070809511392e-02 , 6.89732827922291e-03 ), ( 1.42640174897213e-02 , -4.66710917663395e-02 , 8.54621834415305e-03 ), ( 1.42152092039004e-02 , -4.37039689431695e-02 , -2.90768681103621e-03 ), ( 9.25385553881755e-03 , -3.70677988178844e-02 , 3.31746574587554e-02 ), ( -9.54216635819503e-04 , -1.56455971443211e-02 , 7.58025888278881e-02 ), ( -3.83453115114318e-03 , 3.95524868266385e-03 , 3.26636909607623e-02 ), ( -5.91561681798440e-03 , 1.10689709469262e-02 , 3.01775794099485e-02 ), ( -7.31568557729522e-03 , 1.76059473675832e-02 , 2.13787882331402e-02 ), ( -1.62280883237696e-02 , 5.15340202994481e-02 , -3.36079177638941e-03 ), ( -9.71731425170028e-03 , 3.56135592412924e-02 , -2.13634329163894e-02 ), ( -1.37515004753704e-02 , 4.98570258920335e-02 , -2.80282978586587e-02 ), ( -1.93274202187645e-03 , 1.48918151276390e-02 , -3.60249531028628e-02 ), ( 1.06868010425364e-02 , -1.55163054887531e-02 , -7.27491027760079e-02 ), ( 4.40947940082497e-03 , -5.04406089998529e-04 , -5.40176678525476e-02 ), ( 3.39692613696997e-03 , 6.41279540689519e-03 , -6.92913568633798e-02 ), ( 7.12007193986920e-03 , -1.45391352614655e-02 , -3.13716172491232e-02 ), ( 1.30066812693670e-02 , -4.09701058428207e-02 , 1.33447796586508e-03 ), ( 4.52637477376300e-04 , 2.02121811019220e-03 , -1.39809114433900e-02 ), ( 3.68871321751038e-04 , 3.71941944337004e-03 , -1.98264904541570e-02 ), ( -6.59155139229773e-03 , 2.06356960691847e-02 , -1.58597446801256e-04 ), ( -2.06741434674982e-02 , 5.75159193607012e-02 , 2.88316092525700e-02 ), ( -1.90154049605807e-02 , 6.32603313301188e-02 , -1.56372478319434e-02 ), ( -2.27354870994093e-02 , 7.52121778503086e-02 , -1.69705931059206e-02 ), ( -1.67945805077401e-02 , 7.26394386828972e-02 , -8.20447054617395e-02 ), ( -1.98624280707300e-02 , 8.68154008280787e-02 , -1.00722691225296e-01 ), ( -8.53818784940369e-03 , 4.69173202401636e-02 , -8.23570774196875e-02 ), ( -1.86144965450949e-02 , 6.66844476645428e-02 , -3.46693975793695e-02 ), ( -2.43304588010985e-02 , 9.27214764030263e-02 , -6.79422921811020e-02 ) } +colvars: Step 8, atoms_new_colvar_forces = { ( -7.13351423072814e-02 , 3.03619825792168e-01 , -3.91268617939964e-01 ), ( 1.23055499660459e-02 , 3.39005917766654e-02 , -2.36845225742551e-01 ), ( -4.15271491397816e-02 , 9.13791618604163e-02 , 8.39245305411535e-02 ), ( -9.62494045652913e-02 , 2.44175455092806e-01 , 6.69902520302190e-02 ), ( -1.89222535399380e-02 , 9.94484271845721e-02 , -1.66816690819095e-01 ), ( 7.03822543304743e-02 , -1.81295378894829e-01 , -4.03686971085317e-02 ), ( 1.05834154712841e-02 , -1.01144992174696e-01 , 2.49623497290294e-01 ), ( -4.05271851974779e-02 , 5.67671746608100e-02 , 1.92455361027341e-01 ), ( 6.56724380837020e-02 , -1.87509424162519e-01 , 3.20679681604366e-02 ), ( 1.14456342649259e-01 , -3.88424805112911e-01 , 2.67062889902466e-01 ), ( 2.43422720664008e-02 , -9.93480134779911e-02 , 9.47584074895654e-02 ), ( 2.64823207884572e-02 , -9.72127013570268e-02 , 5.88563122381287e-02 ), ( 1.22945465945720e-02 , -5.60400376600130e-02 , 7.17161479237924e-02 ), ( 1.24370696655175e-02 , -5.37633069113443e-02 , 6.06388129855506e-02 ), ( 5.50290662739558e-03 , -3.56049421041009e-02 , 7.49181815458750e-02 ), ( -8.62594279342890e-03 , 8.52631563305040e-03 , 7.49889010438597e-02 ), ( -2.07304727561448e-03 , -3.37528964129997e-03 , 4.00961351411889e-02 ), ( -5.76061164789089e-03 , 9.18555649372060e-03 , 3.58710078036011e-02 ), ( 2.78174471784882e-03 , -1.34876115706386e-02 , 1.95148242584832e-02 ), ( 9.20812060560968e-03 , -2.22863671904896e-02 , -2.63960131935174e-02 ), ( 8.79752854486906e-03 , -2.38450026309957e-02 , -1.48322003035765e-02 ), ( 6.70483229466327e-03 , -1.35465340002202e-02 , -3.01308249087184e-02 ), ( 1.50788672216310e-02 , -4.65748402463062e-02 , -2.20698674250556e-03 ), ( 2.76224099666520e-02 , -8.80070809511392e-02 , 6.89732827922292e-03 ), ( 1.42640174897213e-02 , -4.66710917663395e-02 , 8.54621834415306e-03 ), ( 1.42152092039004e-02 , -4.37039689431695e-02 , -2.90768681103621e-03 ), ( 9.25385553881756e-03 , -3.70677988178844e-02 , 3.31746574587554e-02 ), ( -9.54216635819487e-04 , -1.56455971443210e-02 , 7.58025888278880e-02 ), ( -3.83453115114317e-03 , 3.95524868266385e-03 , 3.26636909607623e-02 ), ( -5.91561681798440e-03 , 1.10689709469262e-02 , 3.01775794099485e-02 ), ( -7.31568557729521e-03 , 1.76059473675832e-02 , 2.13787882331402e-02 ), ( -1.62280883237696e-02 , 5.15340202994481e-02 , -3.36079177638940e-03 ), ( -9.71731425170029e-03 , 3.56135592412924e-02 , -2.13634329163894e-02 ), ( -1.37515004753704e-02 , 4.98570258920335e-02 , -2.80282978586587e-02 ), ( -1.93274202187645e-03 , 1.48918151276390e-02 , -3.60249531028628e-02 ), ( 1.06868010425364e-02 , -1.55163054887531e-02 , -7.27491027760079e-02 ), ( 4.40947940082496e-03 , -5.04406089998534e-04 , -5.40176678525476e-02 ), ( 3.39692613696996e-03 , 6.41279540689518e-03 , -6.92913568633797e-02 ), ( 7.12007193986919e-03 , -1.45391352614655e-02 , -3.13716172491232e-02 ), ( 1.30066812693670e-02 , -4.09701058428207e-02 , 1.33447796586508e-03 ), ( 4.52637477376299e-04 , 2.02121811019218e-03 , -1.39809114433900e-02 ), ( 3.68871321751043e-04 , 3.71941944337000e-03 , -1.98264904541570e-02 ), ( -6.59155139229773e-03 , 2.06356960691847e-02 , -1.58597446801268e-04 ), ( -2.06741434674982e-02 , 5.75159193607011e-02 , 2.88316092525700e-02 ), ( -1.90154049605807e-02 , 6.32603313301187e-02 , -1.56372478319434e-02 ), ( -2.27354870994093e-02 , 7.52121778503086e-02 , -1.69705931059206e-02 ), ( -1.67945805077401e-02 , 7.26394386828972e-02 , -8.20447054617394e-02 ), ( -1.98624280707300e-02 , 8.68154008280787e-02 , -1.00722691225296e-01 ), ( -8.53818784940370e-03 , 4.69173202401635e-02 , -8.23570774196874e-02 ), ( -1.86144965450949e-02 , 6.66844476645427e-02 , -3.46693975793695e-02 ), ( -2.43304588010985e-02 , 9.27214764030262e-02 , -6.79422921811020e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 8, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2956,7 +4297,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 9, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 9, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 9, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 9, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 9, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 9, atoms_positions[size = 51] = { ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 ), ( 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 ), ( 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 ), ( 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 ), ( 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 ), ( 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 ), ( -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 ), ( -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 ), ( -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 ), ( -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ), ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 ), ( 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 ), ( 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 ), ( 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 ), ( 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 ), ( 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 ), ( 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 ), ( 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 ), ( 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 ), ( 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 ), ( 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 ), ( 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 ), ( 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 ), ( 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 ), ( 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 ), ( 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 ), ( 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 ), ( 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 ), ( 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 ), ( -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 ), ( 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 ), ( 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 ), ( -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 ), ( -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 ), ( -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 ), ( -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 ), ( -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 ), ( -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 ), ( -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 ), ( -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 ), ( -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 ), ( -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 ), ( -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 ), ( -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 ), ( -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 ), ( -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 ), ( -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 ), ( -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 ), ( -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 ), ( -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 ), ( -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ) } @@ -2977,16 +4318,87 @@ colvars: Collective variables module, step no. 9 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 , 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 , 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 , 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 , 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 , 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 , 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 , 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 , 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 , 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 , 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 , 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 , 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 , 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 , 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 , -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 , 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 , -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 , -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 , -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 , -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 , -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 , -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 , -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 , -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 , -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 , -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 , -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 , -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 , -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 , -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 , -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 , -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 , 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 , 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 , 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 , 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 , 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 , 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 , 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 , 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 , 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 , 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 , 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 , 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 , 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 , 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 , -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 , 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 , -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 , -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 , -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 , -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 , -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 , -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 , -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 , -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 , -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 , -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 , -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 , -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 , -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 , -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 , -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 , -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2999,6 +4411,10 @@ colvars: Adding total bias energy: 11.4369 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3014,8 +4430,6 @@ colvars: ( 0.0081957 , -0.108001 , 0.309959 ) colvars: ( -0.0491436 , 0.0786383 , 0.214725 ) colvars: ( 0.0805042 , -0.231946 , 0.0240398 ) colvars: ( 0.1369 , -0.472592 , 0.325703 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243803 , -0.0993282 , 0.0948558 ) colvars: ( 0.0198555 , -0.0820737 , 0.0820835 ) @@ -3068,14 +4482,17 @@ colvars: ( -0.00855692 , 0.0468619 , -0.0824347 ) colvars: ( -0.0186271 , 0.0666706 , -0.0347212 ) colvars: ( -0.022331 , 0.083933 , -0.058027 ) colvars: ( -0.0243627 , 0.0927198 , -0.0680185 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 9. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 9. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 9, atoms_new_colvar_forces = { ( -7.14173720653988e-02 , 3.03520052049550e-01 , -3.92009785651569e-01 ), ( 1.23342420189076e-02 , 3.34051155343946e-02 , -2.36921588255221e-01 ), ( -4.15241266423430e-02 , 9.14514427042298e-02 , 8.44297030591048e-02 ), ( -9.63331533612291e-02 , 2.44725046427125e-01 , 6.69280120891987e-02 ), ( -1.89607984864655e-02 , 9.94393414177422e-02 , -1.67339404363429e-01 ), ( 7.04476436573704e-02 , -1.81717278785775e-01 , -4.02242178643844e-02 ), ( 1.06089134397880e-02 , -1.00937973904036e-01 , 2.50161143716076e-01 ), ( -4.05803503902119e-02 , 5.73562046068344e-02 , 1.92324357692035e-01 ), ( 6.57073059950226e-02 , -1.87627270111012e-01 , 3.18539040038509e-02 ), ( 1.14568853707169e-01 , -3.88658891277373e-01 , 2.67675620853643e-01 ), ( 2.43802816273955e-02 , -9.93281874098511e-02 , 9.48558475196411e-02 ), ( 2.65037845454748e-02 , -9.71909867682365e-02 , 5.89362890305024e-02 ), ( 1.23143907242286e-02 , -5.60007579469611e-02 , 7.17881814673141e-02 ), ( 1.24565401286085e-02 , -5.37373630896944e-02 , 6.07005352450290e-02 ), ( 5.51661482992866e-03 , -3.55455043228472e-02 , 7.49881872869175e-02 ), ( -8.62469301701959e-03 , 8.61819191963210e-03 , 7.50479617281995e-02 ), ( -2.07424105302506e-03 , -3.32003763727391e-03 , 4.01332666040667e-02 ), ( -5.76263256060389e-03 , 9.23667566792743e-03 , 3.58990112766273e-02 ), ( 2.77442962802959e-03 , -1.34400622886135e-02 , 1.95446294702857e-02 ), ( 9.18672312511947e-03 , -2.22559787396961e-02 , -2.63889931974540e-02 ), ( 8.78768419625598e-03 , -2.38332647478740e-02 , -1.48245460439309e-02 ), ( 6.69069192888830e-03 , -1.35428452060799e-02 , -3.01376619569618e-02 ), ( 1.50787137839697e-02 , -4.65730867592132e-02 , -2.18567840461604e-03 ), ( 2.76376217799769e-02 , -8.80346894842445e-02 , 6.93358865624687e-03 ), ( 1.42747227515129e-02 , -4.66871377959406e-02 , 8.56734570785393e-03 ), ( 1.42252270283724e-02 , -4.37329821937682e-02 , -2.89726261151907e-03 ), ( 9.26911427579752e-03 , -3.70663365654842e-02 , 3.32082031893863e-02 ), ( -9.29764348433053e-04 , -1.56180778191128e-02 , 7.58541079446727e-02 ), ( -3.82444347630877e-03 , 3.96746298948432e-03 , 3.26809834852590e-02 ), ( -5.90417007842335e-03 , 1.10734044656187e-02 , 3.01880303085622e-02 ), ( -7.31520771406639e-03 , 1.76304377592534e-02 , 2.13880036242598e-02 ), ( -1.62463832765021e-02 , 5.15783873773705e-02 , -3.37326477439167e-03 ), ( -9.73056072304787e-03 , 3.56215314413404e-02 , -2.13878722217663e-02 ), ( -1.37669713898938e-02 , 4.98616515224360e-02 , -2.80635756631084e-02 ), ( -1.94679852005065e-03 , 1.48851647538967e-02 , -3.60510088394936e-02 ), ( 1.06684267389560e-02 , -1.55548296526290e-02 , -7.27878605475704e-02 ), ( 4.40034243909777e-03 , -5.47109796954654e-04 , -5.40558287094212e-02 ), ( 3.38453211590400e-03 , 6.35935043890287e-03 , -6.93432179144250e-02 ), ( 7.12167142475610e-03 , -1.45827751867512e-02 , -3.13927394832841e-02 ), ( 1.30278759427845e-02 , -4.10264554725312e-02 , 1.33745297410011e-03 ), ( 4.62640012449616e-04 , 1.97396863527872e-03 , -1.40026278660333e-02 ), ( 3.80499989890732e-04 , 3.65978008219712e-03 , -1.98554826335770e-02 ), ( -6.58348401757125e-03 , 2.06101712556980e-02 , -1.75982618459987e-04 ), ( -2.06663438231585e-02 , 5.75251140088467e-02 , 2.88210760175877e-02 ), ( -1.90184995833039e-02 , 6.32436419183766e-02 , -1.56793092131453e-02 ), ( -2.27382858128587e-02 , 7.51918527306527e-02 , -1.70199767768858e-02 ), ( -1.68196160872486e-02 , 7.26005373823680e-02 , -8.21293047577027e-02 ), ( -1.98949441245263e-02 , 8.67730382686525e-02 , -1.00823829224095e-01 ), ( -8.55691582416121e-03 , 4.68619408623113e-02 , -8.24346991593812e-02 ), ( -1.86270664811170e-02 , 6.66706057166005e-02 , -3.47212383429930e-02 ), ( -2.43626649786876e-02 , 9.27197710252338e-02 , -6.80184858556002e-02 ) } +colvars: Step 9, atoms_new_colvar_forces = { ( -7.14173720653988e-02 , 3.03520052049551e-01 , -3.92009785651569e-01 ), ( 1.23342420189076e-02 , 3.34051155343946e-02 , -2.36921588255221e-01 ), ( -4.15241266423430e-02 , 9.14514427042299e-02 , 8.44297030591049e-02 ), ( -9.63331533612292e-02 , 2.44725046427125e-01 , 6.69280120891988e-02 ), ( -1.89607984864654e-02 , 9.94393414177423e-02 , -1.67339404363429e-01 ), ( 7.04476436573704e-02 , -1.81717278785775e-01 , -4.02242178643844e-02 ), ( 1.06089134397880e-02 , -1.00937973904036e-01 , 2.50161143716076e-01 ), ( -4.05803503902119e-02 , 5.73562046068344e-02 , 1.92324357692035e-01 ), ( 6.57073059950226e-02 , -1.87627270111012e-01 , 3.18539040038509e-02 ), ( 1.14568853707169e-01 , -3.88658891277374e-01 , 2.67675620853643e-01 ), ( 2.43802816273955e-02 , -9.93281874098511e-02 , 9.48558475196411e-02 ), ( 2.65037845454748e-02 , -9.71909867682365e-02 , 5.89362890305023e-02 ), ( 1.23143907242286e-02 , -5.60007579469612e-02 , 7.17881814673141e-02 ), ( 1.24565401286085e-02 , -5.37373630896944e-02 , 6.07005352450290e-02 ), ( 5.51661482992865e-03 , -3.55455043228473e-02 , 7.49881872869175e-02 ), ( -8.62469301701959e-03 , 8.61819191963212e-03 , 7.50479617281995e-02 ), ( -2.07424105302506e-03 , -3.32003763727390e-03 , 4.01332666040666e-02 ), ( -5.76263256060389e-03 , 9.23667566792744e-03 , 3.58990112766273e-02 ), ( 2.77442962802959e-03 , -1.34400622886135e-02 , 1.95446294702857e-02 ), ( 9.18672312511947e-03 , -2.22559787396961e-02 , -2.63889931974540e-02 ), ( 8.78768419625598e-03 , -2.38332647478741e-02 , -1.48245460439309e-02 ), ( 6.69069192888831e-03 , -1.35428452060799e-02 , -3.01376619569618e-02 ), ( 1.50787137839697e-02 , -4.65730867592132e-02 , -2.18567840461609e-03 ), ( 2.76376217799769e-02 , -8.80346894842446e-02 , 6.93358865624684e-03 ), ( 1.42747227515129e-02 , -4.66871377959406e-02 , 8.56734570785393e-03 ), ( 1.42252270283724e-02 , -4.37329821937682e-02 , -2.89726261151908e-03 ), ( 9.26911427579751e-03 , -3.70663365654843e-02 , 3.32082031893864e-02 ), ( -9.29764348433053e-04 , -1.56180778191128e-02 , 7.58541079446727e-02 ), ( -3.82444347630877e-03 , 3.96746298948433e-03 , 3.26809834852590e-02 ), ( -5.90417007842336e-03 , 1.10734044656187e-02 , 3.01880303085623e-02 ), ( -7.31520771406639e-03 , 1.76304377592534e-02 , 2.13880036242598e-02 ), ( -1.62463832765020e-02 , 5.15783873773706e-02 , -3.37326477439168e-03 ), ( -9.73056072304786e-03 , 3.56215314413404e-02 , -2.13878722217663e-02 ), ( -1.37669713898938e-02 , 4.98616515224361e-02 , -2.80635756631084e-02 ), ( -1.94679852005065e-03 , 1.48851647538968e-02 , -3.60510088394936e-02 ), ( 1.06684267389560e-02 , -1.55548296526290e-02 , -7.27878605475705e-02 ), ( 4.40034243909777e-03 , -5.47109796954631e-04 , -5.40558287094212e-02 ), ( 3.38453211590400e-03 , 6.35935043890289e-03 , -6.93432179144250e-02 ), ( 7.12167142475610e-03 , -1.45827751867512e-02 , -3.13927394832841e-02 ), ( 1.30278759427845e-02 , -4.10264554725313e-02 , 1.33745297410013e-03 ), ( 4.62640012449613e-04 , 1.97396863527872e-03 , -1.40026278660333e-02 ), ( 3.80499989890731e-04 , 3.65978008219713e-03 , -1.98554826335769e-02 ), ( -6.58348401757126e-03 , 2.06101712556980e-02 , -1.75982618459972e-04 ), ( -2.06663438231585e-02 , 5.75251140088467e-02 , 2.88210760175877e-02 ), ( -1.90184995833039e-02 , 6.32436419183767e-02 , -1.56793092131453e-02 ), ( -2.27382858128587e-02 , 7.51918527306527e-02 , -1.70199767768858e-02 ), ( -1.68196160872486e-02 , 7.26005373823680e-02 , -8.21293047577027e-02 ), ( -1.98949441245263e-02 , 8.67730382686525e-02 , -1.00823829224095e-01 ), ( -8.55691582416120e-03 , 4.68619408623113e-02 , -8.24346991593813e-02 ), ( -1.86270664811170e-02 , 6.66706057166006e-02 , -3.47212383429930e-02 ), ( -2.43626649786876e-02 , 9.27197710252339e-02 , -6.80184858556002e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 9, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3113,7 +4530,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 10, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 10, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 10, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 10, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 10, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } colvars: Step 10, atoms_positions[size = 51] = { ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 ), ( 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 ), ( 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 ), ( 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 ), ( 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 ), ( 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 ), ( -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 ), ( -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 ), ( -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 ), ( -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ), ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 ), ( 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 ), ( 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 ), ( 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 ), ( 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 ), ( 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 ), ( 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 ), ( 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 ), ( 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 ), ( 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 ), ( 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 ), ( 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 ), ( 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 ), ( 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 ), ( 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 ), ( 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 ), ( 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 ), ( 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 ), ( 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 ), ( -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 ), ( 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 ), ( 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 ), ( -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 ), ( -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 ), ( -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 ), ( -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 ), ( -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 ), ( -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 ), ( -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 ), ( -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 ), ( -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 ), ( -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 ), ( -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 ), ( -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 ), ( -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 ), ( -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 ), ( -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 ), ( -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 ), ( -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 ), ( -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 ), ( -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ) } @@ -3134,16 +4551,87 @@ colvars: Collective variables module, step no. 10 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ). +colvars: Calculating gradients of colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ). +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 , 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 , 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 , 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 , 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 , 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 , 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 , 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 , 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 , 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 , 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 , 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 , 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 , 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 , 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 , -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 , 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 , -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 , -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 , -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 , -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 , -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 , -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 , -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 , -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 , -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 , -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 , -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 , -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 , -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 , -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 , -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 , -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 , 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 , 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 , 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 , 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 , 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 , 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 , 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 , 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 , 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 , 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 , 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 , 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 , 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 , 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 , -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 , 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 , -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 , -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 , -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 , -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 , -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 , -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 , -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 , -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 , -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 , -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 , -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 , -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 , -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 , -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 , -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 , -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3156,6 +4644,10 @@ colvars: Adding total bias energy: 11.4416 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3171,8 +4663,6 @@ colvars: ( 0.0082356 , -0.107768 , 0.310577 ) colvars: ( -0.0492129 , 0.0793055 , 0.214612 ) colvars: ( 0.0805409 , -0.232078 , 0.0238308 ) colvars: ( 0.137046 , -0.472861 , 0.326426 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0244216 , -0.0993121 , 0.0949577 ) colvars: ( 0.019885 , -0.0820416 , 0.0821746 ) @@ -3225,6 +4715,7 @@ colvars: ( -0.00857744 , 0.0468056 , -0.0825167 ) colvars: ( -0.0186405 , 0.0666579 , -0.0347739 ) colvars: ( -0.0223557 , 0.08392 , -0.0581005 ) colvars: ( -0.0243975 , 0.0927223 , -0.0680975 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 10. colvars: colvarmodule::write_traj_files() @@ -3235,8 +4726,10 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 10. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 10, atoms_new_colvar_forces = { ( -7.15016607715429e-02 , 3.03450248290296e-01 , -3.92801115143173e-01 ), ( 1.23676636514961e-02 , 3.29036024770242e-02 , -2.37009333522469e-01 ), ( -4.15294698469746e-02 , 9.15434694739862e-02 , 8.49684851875916e-02 ), ( -9.64292968119024e-02 , 2.45317517705941e-01 , 6.68684776651641e-02 ), ( -1.89969183888788e-02 , 9.94364123729832e-02 , -1.67895921441165e-01 ), ( 7.05212056674245e-02 , -1.82169054972534e-01 , -4.00760890945774e-02 ), ( 1.06299188456399e-02 , -1.00732179998986e-01 , 2.50735712205887e-01 ), ( -4.06390391411500e-02 , 5.79627727319512e-02 , 1.92192742745201e-01 ), ( 6.57521305972952e-02 , -1.87775429438928e-01 , 3.16250898809562e-02 ), ( 1.14690118965508e-01 , -3.88940933598096e-01 , 2.68325226130177e-01 ), ( 2.44215543618543e-02 , -9.93121128890011e-02 , 9.49576777085679e-02 ), ( 2.65268959319662e-02 , -9.71711911284568e-02 , 5.90180610098199e-02 ), ( 1.23360273326501e-02 , -5.59616922094030e-02 , 7.18637286173737e-02 ), ( 1.24777272206467e-02 , -5.37123954054054e-02 , 6.07651560900780e-02 ), ( 5.53170505664086e-03 , -3.54841808979951e-02 , 7.50622055553943e-02 ), ( -8.62291255185739e-03 , 8.71572042334931e-03 , 7.51117297407181e-02 ), ( -2.07535676767601e-03 , -3.26128095343410e-03 , 4.01726641337359e-02 ), ( -5.76460113859217e-03 , 9.29126628119511e-03 , 3.59293100500467e-02 ), ( 2.76649955079081e-03 , -1.33889700503236e-02 , 1.95750408014193e-02 ), ( 9.16320150588291e-03 , -2.22217657715012e-02 , -2.63847478136887e-02 ), ( 8.77677580102878e-03 , -2.38200554097055e-02 , -1.48186594740397e-02 ), ( 6.67509070954950e-03 , -1.35376306408063e-02 , -3.01470585284635e-02 ), ( 1.50782845708932e-02 , -4.65717205649901e-02 , -2.16564122789621e-03 ), ( 2.76537239190706e-02 , -8.80665291346259e-02 , 6.96858447717809e-03 ), ( 1.42861554171493e-02 , -4.67057844220242e-02 , 8.58817479450385e-03 ), ( 1.42358707997841e-02 , -4.37652957110214e-02 , -2.88776698081043e-03 ), ( 9.28567383034638e-03 , -3.70667515371096e-02 , 3.32432904895662e-02 ), ( -9.02878066972223e-04 , -1.55915280171617e-02 , 7.59105106601409e-02 ), ( -3.81328853416054e-03 , 3.97944496036692e-03 , 3.27006272124910e-02 ), ( -5.89151124666769e-03 , 1.10770632059042e-02 , 3.02008998913624e-02 ), ( -7.31448604032661e-03 , 1.76565883927560e-02 , 2.13989346487279e-02 ), ( -1.62660173524484e-02 , 5.16279375578137e-02 , -3.38524703866288e-03 ), ( -9.74488071294648e-03 , 3.56317430010617e-02 , -2.14131237375987e-02 ), ( -1.37836669147457e-02 , 4.98686933275603e-02 , -2.80997837478720e-02 ), ( -1.96218459227142e-03 , 1.48797039895180e-02 , -3.60792790294987e-02 ), ( 1.06479972601359e-02 , -1.55940292832885e-02 , -7.28318919398760e-02 ), ( 4.39013310678059e-03 , -5.91527552862357e-04 , -5.40974975810518e-02 ), ( 3.37074168129654e-03 , 6.30393571727351e-03 , -6.93994276341061e-02 ), ( 7.12317534535211e-03 , -1.46294393396425e-02 , -3.14160328614953e-02 ), ( 1.30507102522968e-02 , -4.10889103847666e-02 , 1.34016377943249e-03 ), ( 4.73458451596478e-04 , 1.92279396386442e-03 , -1.40248176248883e-02 ), ( 3.93066712348838e-04 , 3.59530102454662e-03 , -1.98852042495396e-02 ), ( -6.57460039163598e-03 , 2.05824681853941e-02 , -1.92624994433728e-04 ), ( -2.06574072402664e-02 , 5.75347116778676e-02 , 2.88139007127607e-02 ), ( -1.90216018460062e-02 , 6.32269308398371e-02 , -1.57208546495785e-02 ), ( -2.27410084662747e-02 , 7.51713819207301e-02 , -1.70686233836183e-02 ), ( -1.68468604051727e-02 , 7.25625867508809e-02 , -8.22177879392403e-02 ), ( -1.99303402800334e-02 , 8.67323329271237e-02 , -1.00929847872743e-01 ), ( -8.57744112834063e-03 , 4.68055646721169e-02 , -8.25166553580956e-02 ), ( -1.86405497075895e-02 , 6.66579250535560e-02 , -3.47739046838852e-02 ), ( -2.43975282009917e-02 , 9.27222723871716e-02 , -6.80974566358273e-02 ) } +colvars: Step 10, atoms_new_colvar_forces = { ( -7.15016607715429e-02 , 3.03450248290296e-01 , -3.92801115143173e-01 ), ( 1.23676636514961e-02 , 3.29036024770241e-02 , -2.37009333522469e-01 ), ( -4.15294698469745e-02 , 9.15434694739861e-02 , 8.49684851875917e-02 ), ( -9.64292968119024e-02 , 2.45317517705941e-01 , 6.68684776651641e-02 ), ( -1.89969183888788e-02 , 9.94364123729833e-02 , -1.67895921441165e-01 ), ( 7.05212056674244e-02 , -1.82169054972534e-01 , -4.00760890945773e-02 ), ( 1.06299188456399e-02 , -1.00732179998986e-01 , 2.50735712205887e-01 ), ( -4.06390391411500e-02 , 5.79627727319513e-02 , 1.92192742745201e-01 ), ( 6.57521305972952e-02 , -1.87775429438928e-01 , 3.16250898809561e-02 ), ( 1.14690118965508e-01 , -3.88940933598096e-01 , 2.68325226130177e-01 ), ( 2.44215543618544e-02 , -9.93121128890011e-02 , 9.49576777085680e-02 ), ( 2.65268959319662e-02 , -9.71711911284568e-02 , 5.90180610098199e-02 ), ( 1.23360273326501e-02 , -5.59616922094030e-02 , 7.18637286173737e-02 ), ( 1.24777272206467e-02 , -5.37123954054054e-02 , 6.07651560900780e-02 ), ( 5.53170505664087e-03 , -3.54841808979951e-02 , 7.50622055553943e-02 ), ( -8.62291255185738e-03 , 8.71572042334938e-03 , 7.51117297407181e-02 ), ( -2.07535676767600e-03 , -3.26128095343407e-03 , 4.01726641337359e-02 ), ( -5.76460113859216e-03 , 9.29126628119513e-03 , 3.59293100500467e-02 ), ( 2.76649955079081e-03 , -1.33889700503236e-02 , 1.95750408014193e-02 ), ( 9.16320150588288e-03 , -2.22217657715011e-02 , -2.63847478136887e-02 ), ( 8.77677580102877e-03 , -2.38200554097055e-02 , -1.48186594740397e-02 ), ( 6.67509070954949e-03 , -1.35376306408063e-02 , -3.01470585284635e-02 ), ( 1.50782845708932e-02 , -4.65717205649902e-02 , -2.16564122789622e-03 ), ( 2.76537239190706e-02 , -8.80665291346260e-02 , 6.96858447717808e-03 ), ( 1.42861554171493e-02 , -4.67057844220242e-02 , 8.58817479450385e-03 ), ( 1.42358707997841e-02 , -4.37652957110214e-02 , -2.88776698081043e-03 ), ( 9.28567383034640e-03 , -3.70667515371096e-02 , 3.32432904895662e-02 ), ( -9.02878066972215e-04 , -1.55915280171617e-02 , 7.59105106601410e-02 ), ( -3.81328853416053e-03 , 3.97944496036693e-03 , 3.27006272124911e-02 ), ( -5.89151124666768e-03 , 1.10770632059042e-02 , 3.02008998913624e-02 ), ( -7.31448604032661e-03 , 1.76565883927560e-02 , 2.13989346487279e-02 ), ( -1.62660173524484e-02 , 5.16279375578137e-02 , -3.38524703866288e-03 ), ( -9.74488071294648e-03 , 3.56317430010617e-02 , -2.14131237375987e-02 ), ( -1.37836669147457e-02 , 4.98686933275604e-02 , -2.80997837478720e-02 ), ( -1.96218459227142e-03 , 1.48797039895180e-02 , -3.60792790294987e-02 ), ( 1.06479972601358e-02 , -1.55940292832885e-02 , -7.28318919398761e-02 ), ( 4.39013310678057e-03 , -5.91527552862377e-04 , -5.40974975810518e-02 ), ( 3.37074168129652e-03 , 6.30393571727346e-03 , -6.93994276341061e-02 ), ( 7.12317534535211e-03 , -1.46294393396425e-02 , -3.14160328614953e-02 ), ( 1.30507102522968e-02 , -4.10889103847666e-02 , 1.34016377943251e-03 ), ( 4.73458451596487e-04 , 1.92279396386438e-03 , -1.40248176248883e-02 ), ( 3.93066712348846e-04 , 3.59530102454659e-03 , -1.98852042495396e-02 ), ( -6.57460039163597e-03 , 2.05824681853940e-02 , -1.92624994433700e-04 ), ( -2.06574072402663e-02 , 5.75347116778676e-02 , 2.88139007127607e-02 ), ( -1.90216018460062e-02 , 6.32269308398371e-02 , -1.57208546495785e-02 ), ( -2.27410084662747e-02 , 7.51713819207301e-02 , -1.70686233836183e-02 ), ( -1.68468604051727e-02 , 7.25625867508809e-02 , -8.22177879392403e-02 ), ( -1.99303402800334e-02 , 8.67323329271237e-02 , -1.00929847872743e-01 ), ( -8.57744112834064e-03 , 4.68055646721169e-02 , -8.25166553580956e-02 ), ( -1.86405497075895e-02 , 6.66579250535560e-02 , -3.47739046838852e-02 ), ( -2.43975282009917e-02 , 9.27222723871716e-02 , -6.80974566358273e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 10, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3274,10 +4767,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 11, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 11, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 11, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 11, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 11, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 11, atoms_positions[size = 51] = { ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 ), ( 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 ), ( 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 ), ( 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 ), ( 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 ), ( 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 ), ( -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 ), ( -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 ), ( -3.76978320280504e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 ), ( -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ), ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 ), ( 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 ), ( 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 ), ( 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 ), ( 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 ), ( 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 ), ( 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 ), ( 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 ), ( 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 ), ( 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 ), ( 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 ), ( 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 ), ( 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 ), ( 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 ), ( 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 ), ( 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 ), ( 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 ), ( 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 ), ( 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 ), ( -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 ), ( 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 ), ( 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 ), ( -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 ), ( -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 ), ( -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 ), ( -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 ), ( -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 ), ( -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 ), ( -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 ), ( -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 ), ( -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 ), ( -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 ), ( -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 ), ( -2.38523274426802e+00 , -3.45124047741376e-01 , 6.16281301316000e+00 ), ( -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 ), ( -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 ), ( -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 ), ( -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 ), ( -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 ), ( -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 ), ( -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ) } +colvars: Step 11, atoms_positions[size = 51] = { ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 ), ( 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 ), ( 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 ), ( 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 ), ( 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 ), ( 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 ), ( -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 ), ( -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 ), ( -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 ), ( -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ), ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 ), ( 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 ), ( 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 ), ( 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 ), ( 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 ), ( 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 ), ( 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 ), ( 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 ), ( 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 ), ( 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 ), ( 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 ), ( 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 ), ( 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 ), ( 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 ), ( 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 ), ( 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 ), ( 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 ), ( 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 ), ( 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 ), ( -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 ), ( 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 ), ( 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 ), ( -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 ), ( -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 ), ( -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 ), ( -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 ), ( -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 ), ( -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 ), ( -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 ), ( -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 ), ( -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 ), ( -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 ), ( -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 ), ( -2.38523274426801e+00 , -3.45124047741375e-01 , 6.16281301316000e+00 ), ( -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 ), ( -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 ), ( -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 ), ( -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 ), ( -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 ), ( -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 ), ( -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ) } colvars: Step 11, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 11, atom_groups_ids[size = 0] = @@ -3296,15 +4789,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ). +colvars: Calculating colvar components. colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 , 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 , 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 , 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 , 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 , 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 , 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 , 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 , 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 , 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 , 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 , 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 , 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 , 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 , 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 , -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 , 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 , -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 , -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 , -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 , -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 , -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 , -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 , -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 , -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 , -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -2.38523274426801e+00 , -3.45124047741375e-01 , 6.16281301316000e+00 , -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 , -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 , -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 , -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 , -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 , -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 , -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 , 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 , 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 , 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 , 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 , 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 , 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 , 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 , 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 , 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 , 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 , 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 , 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 , 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 , 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 , -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 , 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 , -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 , -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 , -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 , -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 , -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 , -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 , -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 , -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 , -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -2.38523274426801e+00 , -3.45124047741375e-01 , 6.16281301316000e+00 , -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 , -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 , -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 , -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 , -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 , -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 , -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3317,6 +4881,10 @@ colvars: Adding total bias energy: 11.4466 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3332,8 +4900,6 @@ colvars: ( 0.00826781 , -0.107538 , 0.311223 ) colvars: ( -0.0492868 , 0.0799779 , 0.214504 ) colvars: ( 0.0805848 , -0.232241 , 0.023618 ) colvars: ( 0.137192 , -0.473174 , 0.327181 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0244644 , -0.0993009 , 0.0950635 ) colvars: ( 0.0199155 , -0.0820124 , 0.0822687 ) @@ -3386,14 +4952,17 @@ colvars: ( -0.00859884 , 0.0467494 , -0.0826018 ) colvars: ( -0.0186544 , 0.0666476 , -0.0348268 ) colvars: ( -0.0223812 , 0.0839105 , -0.0581756 ) colvars: ( -0.0244337 , 0.0927298 , -0.068179 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 11. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 11. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 11, atoms_new_colvar_forces = { ( -7.15791435066877e-02 , 3.03409844462010e-01 , -3.93631147743522e-01 ), ( 1.24067694561056e-02 , 3.24092617088106e-02 , -2.37109313249408e-01 ), ( -4.15443493045436e-02 , 9.16594876814856e-02 , 8.55215908680847e-02 ), ( -9.65336402837815e-02 , 2.45940639162059e-01 , 6.68066014202904e-02 ), ( -1.90264360132423e-02 , 9.94362277505718e-02 , -1.68473121692907e-01 ), ( 7.05994752262471e-02 , -1.82640351786385e-01 , -3.99240593208833e-02 ), ( 1.06422393313364e-02 , -1.00529505736157e-01 , 2.51334253191404e-01 ), ( -4.07018668681346e-02 , 5.85704993383106e-02 , 1.92065217655378e-01 ), ( 6.58048500158185e-02 , -1.87955153690664e-01 , 3.13953139770057e-02 ), ( 1.14810836548122e-01 , -3.89263845763161e-01 , 2.69005747608971e-01 ), ( 2.44644420365523e-02 , -9.93008604362819e-02 , 9.50634540303171e-02 ), ( 2.65506639926814e-02 , -9.71549085398045e-02 , 5.91007414354449e-02 ), ( 1.23585185415142e-02 , -5.59239645083762e-02 , 7.19419408988772e-02 ), ( 1.24997439276150e-02 , -5.36892724561221e-02 , 6.08321053385152e-02 ), ( 5.54744932916615e-03 , -3.54222256237558e-02 , 7.51390424022061e-02 ), ( -8.62087934123943e-03 , 8.81757783726286e-03 , 7.51785053849694e-02 ), ( -2.07649081258038e-03 , -3.20004659983506e-03 , 4.02131668863943e-02 ), ( -5.76656001638264e-03 , 9.34859228802996e-03 , 3.59609344382249e-02 ), ( 2.75811391441253e-03 , -1.33356313310753e-02 , 1.96047867239134e-02 ), ( 9.13831399376691e-03 , -2.21853675629404e-02 , -2.63846638597659e-02 ), ( 8.76514693055518e-03 , -2.38063605419795e-02 , -1.48152755324360e-02 ), ( 6.65857259966534e-03 , -1.35316767744980e-02 , -3.01595939520679e-02 ), ( 1.50775434890925e-02 , -4.65716981852416e-02 , -2.14739829676821e-03 ), ( 2.76701085567005e-02 , -8.81033908999233e-02 , 7.00234061373576e-03 ), ( 1.42978914433128e-02 , -4.67273424783863e-02 , 8.60881480028640e-03 ), ( 1.42467794788397e-02 , -4.38009674766436e-02 , -2.87882066252855e-03 ), ( 9.30289142383668e-03 , -3.70693093754741e-02 , 3.32798991260648e-02 ), ( -8.74616788559080e-04 , -1.55659268803168e-02 , 7.59717207069584e-02 ), ( -3.80149697823639e-03 , 3.99139497661138e-03 , 3.27226818702287e-02 ), ( -5.87809955712979e-03 , 1.10804620992655e-02 , 3.02165111697874e-02 ), ( -7.31358799819382e-03 , 1.76843548454293e-02 , 2.14112914406596e-02 ), ( -1.62863320779151e-02 , 5.16823604558912e-02 , -3.39755451020750e-03 ), ( -9.75973706289892e-03 , 3.56443383847642e-02 , -2.14393173203162e-02 ), ( -1.38009410110882e-02 , 4.98785618144178e-02 , -2.81368949956214e-02 ), ( -1.97831014138354e-03 , 1.48753846947268e-02 , -3.61098401943824e-02 ), ( 1.06263319165018e-02 , -1.56341624769058e-02 , -7.28810696503613e-02 ), ( 4.37932488352575e-03 , -6.37252128288116e-04 , -5.41420695521195e-02 ), ( 3.35619138322246e-03 , 6.24716942821833e-03 , -6.94591804691144e-02 ), ( 7.12461969116057e-03 , -1.46786360570569e-02 , -3.14407424751560e-02 ), ( 1.30744491935402e-02 , -4.11566574770348e-02 , 1.34384855831247e-03 ), ( 4.84816048636935e-04 , 1.86884529652321e-03 , -1.40462649459062e-02 ), ( 4.06262902972105e-04 , 3.52742628407919e-03 , -1.99141343288618e-02 ), ( -6.56514050363635e-03 , 2.05536818096240e-02 , -2.07595716940279e-04 ), ( -2.06476219371302e-02 , 5.75459498804657e-02 , 2.88107008122013e-02 ), ( -1.90244943026149e-02 , 6.32116292719994e-02 , -1.57609754741589e-02 ), ( -2.27434304429232e-02 , 7.51525034805505e-02 , -1.71154202691943e-02 ), ( -1.68751559011819e-02 , 7.25268655901674e-02 , -8.23092755311854e-02 ), ( -1.99671400786953e-02 , 8.66946604746156e-02 , -1.01039844952936e-01 ), ( -8.59883664831505e-03 , 4.67494396675215e-02 , -8.26018445395924e-02 ), ( -1.86543551069504e-02 , 6.66475511479637e-02 , -3.48267535670694e-02 ), ( -2.44336835714561e-02 , 9.27298049549328e-02 , -6.81790385548220e-02 ) } +colvars: Step 11, atoms_new_colvar_forces = { ( -7.15791435066877e-02 , 3.03409844462010e-01 , -3.93631147743522e-01 ), ( 1.24067694561056e-02 , 3.24092617088106e-02 , -2.37109313249408e-01 ), ( -4.15443493045436e-02 , 9.16594876814856e-02 , 8.55215908680847e-02 ), ( -9.65336402837814e-02 , 2.45940639162059e-01 , 6.68066014202904e-02 ), ( -1.90264360132423e-02 , 9.94362277505718e-02 , -1.68473121692907e-01 ), ( 7.05994752262470e-02 , -1.82640351786385e-01 , -3.99240593208832e-02 ), ( 1.06422393313364e-02 , -1.00529505736157e-01 , 2.51334253191404e-01 ), ( -4.07018668681346e-02 , 5.85704993383106e-02 , 1.92065217655378e-01 ), ( 6.58048500158185e-02 , -1.87955153690664e-01 , 3.13953139770057e-02 ), ( 1.14810836548122e-01 , -3.89263845763161e-01 , 2.69005747608971e-01 ), ( 2.44644420365523e-02 , -9.93008604362819e-02 , 9.50634540303170e-02 ), ( 2.65506639926814e-02 , -9.71549085398046e-02 , 5.91007414354448e-02 ), ( 1.23585185415142e-02 , -5.59239645083762e-02 , 7.19419408988772e-02 ), ( 1.24997439276150e-02 , -5.36892724561222e-02 , 6.08321053385152e-02 ), ( 5.54744932916617e-03 , -3.54222256237558e-02 , 7.51390424022061e-02 ), ( -8.62087934123941e-03 , 8.81757783726286e-03 , 7.51785053849693e-02 ), ( -2.07649081258038e-03 , -3.20004659983505e-03 , 4.02131668863943e-02 ), ( -5.76656001638263e-03 , 9.34859228802995e-03 , 3.59609344382249e-02 ), ( 2.75811391441254e-03 , -1.33356313310754e-02 , 1.96047867239134e-02 ), ( 9.13831399376692e-03 , -2.21853675629404e-02 , -2.63846638597659e-02 ), ( 8.76514693055518e-03 , -2.38063605419795e-02 , -1.48152755324360e-02 ), ( 6.65857259966535e-03 , -1.35316767744980e-02 , -3.01595939520679e-02 ), ( 1.50775434890925e-02 , -4.65716981852416e-02 , -2.14739829676824e-03 ), ( 2.76701085567005e-02 , -8.81033908999233e-02 , 7.00234061373576e-03 ), ( 1.42978914433128e-02 , -4.67273424783863e-02 , 8.60881480028640e-03 ), ( 1.42467794788397e-02 , -4.38009674766436e-02 , -2.87882066252855e-03 ), ( 9.30289142383668e-03 , -3.70693093754740e-02 , 3.32798991260648e-02 ), ( -8.74616788559086e-04 , -1.55659268803168e-02 , 7.59717207069584e-02 ), ( -3.80149697823639e-03 , 3.99139497661139e-03 , 3.27226818702287e-02 ), ( -5.87809955712979e-03 , 1.10804620992656e-02 , 3.02165111697874e-02 ), ( -7.31358799819382e-03 , 1.76843548454293e-02 , 2.14112914406596e-02 ), ( -1.62863320779151e-02 , 5.16823604558912e-02 , -3.39755451020750e-03 ), ( -9.75973706289892e-03 , 3.56443383847642e-02 , -2.14393173203162e-02 ), ( -1.38009410110882e-02 , 4.98785618144178e-02 , -2.81368949956214e-02 ), ( -1.97831014138354e-03 , 1.48753846947269e-02 , -3.61098401943824e-02 ), ( 1.06263319165018e-02 , -1.56341624769058e-02 , -7.28810696503613e-02 ), ( 4.37932488352575e-03 , -6.37252128288097e-04 , -5.41420695521195e-02 ), ( 3.35619138322245e-03 , 6.24716942821834e-03 , -6.94591804691144e-02 ), ( 7.12461969116057e-03 , -1.46786360570569e-02 , -3.14407424751560e-02 ), ( 1.30744491935402e-02 , -4.11566574770348e-02 , 1.34384855831248e-03 ), ( 4.84816048636927e-04 , 1.86884529652323e-03 , -1.40462649459062e-02 ), ( 4.06262902972097e-04 , 3.52742628407923e-03 , -1.99141343288618e-02 ), ( -6.56514050363636e-03 , 2.05536818096240e-02 , -2.07595716940282e-04 ), ( -2.06476219371302e-02 , 5.75459498804657e-02 , 2.88107008122013e-02 ), ( -1.90244943026149e-02 , 6.32116292719994e-02 , -1.57609754741589e-02 ), ( -2.27434304429232e-02 , 7.51525034805505e-02 , -1.71154202691943e-02 ), ( -1.68751559011819e-02 , 7.25268655901675e-02 , -8.23092755311854e-02 ), ( -1.99671400786953e-02 , 8.66946604746157e-02 , -1.01039844952936e-01 ), ( -8.59883664831506e-03 , 4.67494396675215e-02 , -8.26018445395924e-02 ), ( -1.86543551069504e-02 , 6.66475511479637e-02 , -3.48267535670694e-02 ), ( -2.44336835714561e-02 , 9.27298049549328e-02 , -6.81790385548220e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 11, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3431,10 +5000,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 12, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 12, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 12, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 12, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 12, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 12, atoms_positions[size = 51] = { ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 ), ( 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 ), ( 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 ), ( 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 ), ( 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 ), ( 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 ), ( -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 ), ( -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 ), ( -3.76368207226495e+00 , 5.16946302547613e-02 , 5.47019231775250e+00 ), ( -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ), ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 ), ( 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 ), ( 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 ), ( 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 ), ( 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 ), ( 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 ), ( 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 ), ( 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 ), ( 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 ), ( 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 ), ( 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 ), ( 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 ), ( 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 ), ( 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 ), ( 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 ), ( 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 ), ( 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 ), ( 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 ), ( 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 ), ( -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 ), ( 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 ), ( 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 ), ( -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 ), ( -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 ), ( -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 ), ( -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 ), ( -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 ), ( -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 ), ( -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 ), ( -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 ), ( -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 ), ( -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 ), ( -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 ), ( -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 ), ( -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 ), ( -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 ), ( -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 ), ( -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 ), ( -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 ), ( -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 ), ( -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ) } +colvars: Step 12, atoms_positions[size = 51] = { ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 ), ( 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 ), ( 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 ), ( 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 ), ( 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 ), ( 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 ), ( -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 ), ( -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 ), ( -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 ), ( -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ), ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 ), ( 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 ), ( 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 ), ( 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 ), ( 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 ), ( 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 ), ( 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 ), ( 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 ), ( 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 ), ( 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 ), ( 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 ), ( 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 ), ( 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 ), ( 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 ), ( 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 ), ( 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 ), ( 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 ), ( 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 ), ( 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 ), ( -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 ), ( 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 ), ( 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 ), ( -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 ), ( -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 ), ( -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 ), ( -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 ), ( -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 ), ( -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 ), ( -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 ), ( -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 ), ( -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 ), ( -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 ), ( -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 ), ( -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 ), ( -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 ), ( -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 ), ( -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 ), ( -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 ), ( -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 ), ( -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 ), ( -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ) } colvars: Step 12, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 12, atom_groups_ids[size = 0] = @@ -3452,16 +5021,87 @@ colvars: Collective variables module, step no. 12 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 , 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 , 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 , 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 , 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 , 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 , 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 , 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 , 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 , 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 , 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 , 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 , 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 , 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 , 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 , -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 , 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 , -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 , -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 , -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 , -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 , -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 , -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 , -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 , -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 , -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 , -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 , -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 , -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 , -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 , -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 , -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 , -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 , 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 , 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 , 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 , 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 , 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 , 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 , 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 , 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 , 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 , 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 , 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 , 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 , 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 , 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 , -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 , 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 , -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 , -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 , -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 , -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 , -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 , -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 , -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 , -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 , -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 , -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 , -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 , -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 , -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 , -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 , -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 , -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3474,6 +5114,10 @@ colvars: Adding total bias energy: 11.452 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3489,8 +5133,6 @@ colvars: ( 0.00828836 , -0.107313 , 0.311882 ) colvars: ( -0.0493627 , 0.0806373 , 0.214404 ) colvars: ( 0.0806337 , -0.232438 , 0.0234152 ) colvars: ( 0.137329 , -0.473524 , 0.327961 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0245072 , -0.0992953 , 0.0951725 ) colvars: ( 0.0199458 , -0.0819872 , 0.0823646 ) @@ -3543,14 +5185,17 @@ colvars: ( -0.00862017 , 0.0466947 , -0.0826889 ) colvars: ( -0.0186678 , 0.0666405 , -0.0348791 ) colvars: ( -0.0224065 , 0.0839055 , -0.0582514 ) colvars: ( -0.0244697 , 0.092743 , -0.0682629 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 12. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 12. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 12, atoms_new_colvar_forces = { ( -7.16421680750279e-02 , 3.03396548751539e-01 , -3.94486220717945e-01 ), ( 1.24515909749765e-02 , 3.19353701028632e-02 , -2.37221977925211e-01 ), ( -4.15693683146454e-02 , 9.18027746722944e-02 , 8.60682081256656e-02 ), ( -9.66413963586872e-02 , 2.46580175116835e-01 , 6.67373004675042e-02 ), ( -1.90458239292532e-02 , 9.94350184313190e-02 , -1.69056362419433e-01 ), ( 7.06786042823088e-02 , -1.83119401980232e-01 , -3.97681292658151e-02 ), ( 1.06426346587686e-02 , -1.00331643510678e-01 , 2.51942191228478e-01 ), ( -4.07667108107428e-02 , 5.91623733313463e-02 , 1.91946646728410e-01 ), ( 6.58631416517817e-02 , -1.88166122049303e-01 , 3.11790396547625e-02 ), ( 1.14922285106495e-01 , -3.89618039834855e-01 , 2.69709548896305e-01 ), ( 2.45072064690875e-02 , -9.92952513398520e-02 , 9.51725380397601e-02 ), ( 2.65739974674320e-02 , -9.71435419165180e-02 , 5.91833122237861e-02 ), ( 1.23808965877678e-02 , -5.58885675058319e-02 , 7.20217919193645e-02 ), ( 1.25216656406114e-02 , -5.36687337202716e-02 , 6.09006716071648e-02 ), ( 5.56312902213689e-03 , -3.53608099000057e-02 , 7.52172944233855e-02 ), ( -8.61878532719258e-03 , 8.92242158732669e-03 , 7.52463376805511e-02 ), ( -2.07770157462097e-03 , -3.13736891666858e-03 , 4.02534722876006e-02 ), ( -5.76850016691932e-03 , 9.40789227218322e-03 , 3.59927854806369e-02 ), ( 2.74944431517631e-03 , -1.32813564898526e-02 , 1.96325014128747e-02 ), ( 9.11279236113812e-03 , -2.21484706889497e-02 , -2.63901170934250e-02 ), ( 8.75310807004707e-03 , -2.37931703636637e-02 , -1.48151159553400e-02 ), ( 6.64165272602963e-03 , -1.35258005651302e-02 , -3.01757967596976e-02 ), ( 1.50763901547272e-02 , -4.65739180996560e-02 , -2.13146940458401e-03 ), ( 2.76860357759323e-02 , -8.81459002274344e-02 , 7.03490641253196e-03 ), ( 1.43094379929380e-02 , -4.67520260279631e-02 , 8.62938073013700e-03 ), ( 1.42575165045805e-02 , -4.38399629483993e-02 , -2.87000166804047e-03 ), ( 9.32008697586987e-03 , -3.70741783280618e-02 , 3.33179476827688e-02 ), ( -8.46017739415173e-04 , -1.55411561800035e-02 , 7.60374898142788e-02 ), ( -3.78947514792484e-03 , 4.00354032955485e-03 , 3.27471322944332e-02 ), ( -5.86436487064504e-03 , 1.10841396046405e-02 , 3.02351262515298e-02 ), ( -7.31253639742771e-03 , 1.77136686845677e-02 , 2.14247141411940e-02 ), ( -1.63065776924027e-02 , 5.17412136033583e-02 , -3.41105376001136e-03 ), ( -9.77454806826517e-03 , 3.56593718965960e-02 , -2.14665548734431e-02 ), ( -1.38180877017203e-02 , 4.98915524044661e-02 , -2.81748384597231e-02 ), ( -1.99458201197298e-03 , 1.48720940467247e-02 , -3.61426953349021e-02 ), ( 1.06041811229485e-02 , -1.56755236088371e-02 , -7.29350852936609e-02 ), ( 4.36834845946130e-03 , -6.83900191805435e-04 , -5.41887880626872e-02 ), ( 3.34147327126993e-03 , 6.18962776423781e-03 , -6.95214782203114e-02 ), ( 7.12598681052463e-03 , -1.47298439811097e-02 , -3.14660014810572e-02 ), ( 1.30982744407057e-02 , -4.12287535926886e-02 , 1.34981438346011e-03 ), ( 4.96410404255612e-04 , 1.81331109876103e-03 , -1.40656698696598e-02 ), ( 4.19748344476731e-04 , 3.45764211772422e-03 , -1.99406416982656e-02 ), ( -6.55532830509409e-03 , 2.05249114086253e-02 , -2.19934544421123e-04 ), ( -2.06371808932977e-02 , 5.75600182245067e-02 , 2.88120279806772e-02 ), ( -1.90268865001024e-02 , 6.31990805317706e-02 , -1.57987157085620e-02 ), ( -2.27452399178175e-02 , 7.51368540083220e-02 , -1.71592008838816e-02 ), ( -1.69032961322243e-02 , 7.24944830113589e-02 , -8.24026922858791e-02 ), ( -2.00038076931115e-02 , 8.66611845674294e-02 , -1.01152684539195e-01 ), ( -8.62016999247503e-03 , 4.66946998990970e-02 , -8.26889476000254e-02 ), ( -1.86678199864865e-02 , 6.66405053489124e-02 , -3.48790635755432e-02 ), ( -2.44696659839757e-02 , 9.27429691514109e-02 , -6.82629424665394e-02 ) } +colvars: Step 12, atoms_new_colvar_forces = { ( -7.16421680750278e-02 , 3.03396548751539e-01 , -3.94486220717945e-01 ), ( 1.24515909749766e-02 , 3.19353701028634e-02 , -2.37221977925211e-01 ), ( -4.15693683146455e-02 , 9.18027746722945e-02 , 8.60682081256656e-02 ), ( -9.66413963586872e-02 , 2.46580175116835e-01 , 6.67373004675043e-02 ), ( -1.90458239292532e-02 , 9.94350184313190e-02 , -1.69056362419433e-01 ), ( 7.06786042823088e-02 , -1.83119401980232e-01 , -3.97681292658151e-02 ), ( 1.06426346587686e-02 , -1.00331643510678e-01 , 2.51942191228477e-01 ), ( -4.07667108107428e-02 , 5.91623733313461e-02 , 1.91946646728410e-01 ), ( 6.58631416517817e-02 , -1.88166122049303e-01 , 3.11790396547625e-02 ), ( 1.14922285106495e-01 , -3.89618039834855e-01 , 2.69709548896305e-01 ), ( 2.45072064690875e-02 , -9.92952513398520e-02 , 9.51725380397601e-02 ), ( 2.65739974674320e-02 , -9.71435419165180e-02 , 5.91833122237861e-02 ), ( 1.23808965877677e-02 , -5.58885675058319e-02 , 7.20217919193645e-02 ), ( 1.25216656406114e-02 , -5.36687337202716e-02 , 6.09006716071647e-02 ), ( 5.56312902213688e-03 , -3.53608099000057e-02 , 7.52172944233854e-02 ), ( -8.61878532719259e-03 , 8.92242158732663e-03 , 7.52463376805510e-02 ), ( -2.07770157462097e-03 , -3.13736891666861e-03 , 4.02534722876005e-02 ), ( -5.76850016691932e-03 , 9.40789227218320e-03 , 3.59927854806369e-02 ), ( 2.74944431517631e-03 , -1.32813564898526e-02 , 1.96325014128746e-02 ), ( 9.11279236113813e-03 , -2.21484706889497e-02 , -2.63901170934249e-02 ), ( 8.75310807004707e-03 , -2.37931703636637e-02 , -1.48151159553400e-02 ), ( 6.64165272602964e-03 , -1.35258005651303e-02 , -3.01757967596976e-02 ), ( 1.50763901547272e-02 , -4.65739180996560e-02 , -2.13146940458401e-03 ), ( 2.76860357759323e-02 , -8.81459002274344e-02 , 7.03490641253195e-03 ), ( 1.43094379929380e-02 , -4.67520260279631e-02 , 8.62938073013699e-03 ), ( 1.42575165045805e-02 , -4.38399629483993e-02 , -2.87000166804047e-03 ), ( 9.32008697586987e-03 , -3.70741783280618e-02 , 3.33179476827687e-02 ), ( -8.46017739415180e-04 , -1.55411561800036e-02 , 7.60374898142787e-02 ), ( -3.78947514792484e-03 , 4.00354032955483e-03 , 3.27471322944331e-02 ), ( -5.86436487064504e-03 , 1.10841396046405e-02 , 3.02351262515297e-02 ), ( -7.31253639742772e-03 , 1.77136686845677e-02 , 2.14247141411940e-02 ), ( -1.63065776924027e-02 , 5.17412136033583e-02 , -3.41105376001136e-03 ), ( -9.77454806826517e-03 , 3.56593718965959e-02 , -2.14665548734431e-02 ), ( -1.38180877017203e-02 , 4.98915524044661e-02 , -2.81748384597231e-02 ), ( -1.99458201197298e-03 , 1.48720940467247e-02 , -3.61426953349021e-02 ), ( 1.06041811229486e-02 , -1.56755236088371e-02 , -7.29350852936609e-02 ), ( 4.36834845946131e-03 , -6.83900191805431e-04 , -5.41887880626871e-02 ), ( 3.34147327126994e-03 , 6.18962776423782e-03 , -6.95214782203114e-02 ), ( 7.12598681052463e-03 , -1.47298439811097e-02 , -3.14660014810572e-02 ), ( 1.30982744407057e-02 , -4.12287535926886e-02 , 1.34981438346009e-03 ), ( 4.96410404255614e-04 , 1.81331109876104e-03 , -1.40656698696598e-02 ), ( 4.19748344476729e-04 , 3.45764211772423e-03 , -1.99406416982656e-02 ), ( -6.55532830509409e-03 , 2.05249114086253e-02 , -2.19934544421135e-04 ), ( -2.06371808932977e-02 , 5.75600182245067e-02 , 2.88120279806772e-02 ), ( -1.90268865001024e-02 , 6.31990805317706e-02 , -1.57987157085621e-02 ), ( -2.27452399178175e-02 , 7.51368540083220e-02 , -1.71592008838816e-02 ), ( -1.69032961322243e-02 , 7.24944830113589e-02 , -8.24026922858791e-02 ), ( -2.00038076931115e-02 , 8.66611845674294e-02 , -1.01152684539195e-01 ), ( -8.62016999247501e-03 , 4.66946998990970e-02 , -8.26889476000254e-02 ), ( -1.86678199864865e-02 , 6.66405053489124e-02 , -3.48790635755432e-02 ), ( -2.44696659839757e-02 , 9.27429691514109e-02 , -6.82629424665393e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 12, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3588,10 +5233,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 13, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 13, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 13, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 13, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 13, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 13, atoms_positions[size = 51] = { ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 ), ( 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 ), ( 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 ), ( 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 ), ( 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 ), ( 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 ), ( -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 ), ( -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 ), ( -3.75656449248184e+00 , 4.54305739009394e-02 , 5.46430316905750e+00 ), ( -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ), ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 ), ( 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 ), ( 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 ), ( 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 ), ( 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 ), ( 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 ), ( 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 ), ( 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 ), ( 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 ), ( 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 ), ( 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 ), ( 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 ), ( 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 ), ( 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 ), ( 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 ), ( 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 ), ( 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 ), ( 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 ), ( 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 ), ( -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 ), ( 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 ), ( 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 ), ( -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 ), ( -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 ), ( -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 ), ( -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 ), ( -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 ), ( -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 ), ( -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 ), ( -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 ), ( -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 ), ( -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 ), ( -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 ), ( -2.38255516970056e+00 , -3.29059335914522e-01 , 6.16893615475952e+00 ), ( -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 ), ( -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 ), ( -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 ), ( -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 ), ( -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 ), ( -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 ), ( -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ) } +colvars: Step 13, atoms_positions[size = 51] = { ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 ), ( 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 ), ( 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 ), ( 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 ), ( 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 ), ( 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 ), ( -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 ), ( -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 ), ( -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 ), ( -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ), ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 ), ( 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 ), ( 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 ), ( 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 ), ( 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 ), ( 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 ), ( 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 ), ( 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 ), ( 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 ), ( 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 ), ( 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 ), ( 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 ), ( 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 ), ( 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 ), ( 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 ), ( 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 ), ( 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 ), ( 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 ), ( 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 ), ( -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 ), ( 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 ), ( 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 ), ( -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 ), ( -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 ), ( -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 ), ( -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 ), ( -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 ), ( -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 ), ( -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 ), ( -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 ), ( -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 ), ( -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 ), ( -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 ), ( -2.38255516970055e+00 , -3.29059335914521e-01 , 6.16893615475952e+00 ), ( -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 ), ( -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 ), ( -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 ), ( -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 ), ( -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 ), ( -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 ), ( -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ) } colvars: Step 13, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 13, atom_groups_ids[size = 0] = @@ -3609,16 +5254,87 @@ colvars: Collective variables module, step no. 13 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610562e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610561e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 , 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 , 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 , 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 , 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 , 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 , 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 , 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 , 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 , 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 , 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 , 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 , 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 , 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 , 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 , -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 , 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 , -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 , -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 , -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 , -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 , -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 , -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 , -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 , -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 , -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -2.38255516970055e+00 , -3.29059335914521e-01 , 6.16893615475952e+00 , -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 , -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 , -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 , -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 , -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 , -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 , -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610562e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). +colvars: Colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610561e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 , 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 , 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 , 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 , 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 , 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 , 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 , 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 , 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 , 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 , 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 , 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 , 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 , 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 , 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 , -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 , 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 , -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 , -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 , -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 , -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 , -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 , -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 , -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 , -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 , -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -2.38255516970055e+00 , -3.29059335914521e-01 , 6.16893615475952e+00 , -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 , -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 , -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 , -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 , -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 , -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 , -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3631,6 +5347,10 @@ colvars: Adding total bias energy: 11.4577 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3646,8 +5366,6 @@ colvars: ( 0.00829457 , -0.107094 , 0.312538 ) colvars: ( -0.0494376 , 0.0812664 , 0.214316 ) colvars: ( 0.0806852 , -0.232666 , 0.0232353 ) colvars: ( 0.137447 , -0.473898 , 0.328755 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0245481 , -0.0992958 , 0.0952841 ) colvars: ( 0.0199747 , -0.081967 , 0.0824613 ) @@ -3700,14 +5418,17 @@ colvars: ( -0.00864057 , 0.0466423 , -0.0827765 ) colvars: ( -0.0186803 , 0.0666376 , -0.0349301 ) colvars: ( -0.0224303 , 0.0839057 , -0.0583273 ) colvars: ( -0.024504 , 0.0927621 , -0.0683487 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 13. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 13. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 13, atoms_new_colvar_forces = { ( -7.16848023051113e-02 , 3.03406467638823e-01 , -3.95351133644467e-01 ), ( 1.25012248682017e-02 , 3.14943727627139e-02 , -2.37347290328934e-01 ), ( -4.16044411846217e-02 , 9.19752550270074e-02 , 8.65873739393493e-02 ), ( -9.67474317693075e-02 , 2.47220693613752e-01 , 6.66558943569052e-02 ), ( -1.90524738522307e-02 , 9.94289567745099e-02 , -1.69630346467483e-01 ), ( 7.07545776624680e-02 , -1.83593734852738e-01 , -3.96086306355424e-02 ), ( 1.06290758170036e-02 , -1.00140025421509e-01 , 2.52544176616428e-01 ), ( -4.08308398476370e-02 , 5.97218751038244e-02 , 1.91841739524069e-01 ), ( 6.59244950506003e-02 , -1.88406306432059e-01 , 3.09903758344904e-02 ), ( 1.15016863749082e-01 , -3.89991960993715e-01 , 2.70427575233416e-01 ), ( 2.45481445884070e-02 , -9.92958410899459e-02 , 9.52840930616265e-02 ), ( 2.65957911792211e-02 , -9.71382388271648e-02 , 5.92646586708680e-02 ), ( 1.24022347475679e-02 , -5.58563360999198e-02 , 7.21021236988898e-02 ), ( 1.25425974982060e-02 , -5.36513706759084e-02 , 6.09700270201490e-02 ), ( 5.57808745511938e-03 , -3.53009942223408e-02 , 7.52954309343477e-02 ), ( -8.61672322330426e-03 , 9.02891576978664e-03 , 7.53131644443017e-02 ), ( -2.07900302590006e-03 , -3.07425778523133e-03 , 4.02922287168525e-02 ), ( -5.77036135321706e-03 , 9.46839655898241e-03 , 3.60237167170881e-02 ), ( 2.74066918054248e-03 , -1.32274107216639e-02 , 1.96568235606399e-02 ), ( 9.08730461783739e-03 , -2.21127046888010e-02 , -2.64023654543353e-02 ), ( 8.74092384788639e-03 , -2.37814157636701e-02 , -1.48188371221037e-02 ), ( 6.62478995543603e-03 , -1.35207891048718e-02 , -3.01961009405069e-02 ), ( 1.50746759309285e-02 , -4.65791626355137e-02 , -2.11834520072257e-03 ), ( 2.77006951945339e-02 , -8.81944669602844e-02 , 7.06632082557573e-03 ), ( 1.43202720040025e-02 , -4.67799343049266e-02 , 8.64996682972771e-03 ), ( 1.42676038711970e-02 , -4.38821442318173e-02 , -2.86089251963269e-03 ), ( 9.33659139362305e-03 , -3.70814288695834e-02 , 3.33572802635675e-02 ), ( -8.18030508691837e-04 , -1.55170421736455e-02 , 7.61073953459294e-02 ), ( -3.77758137799796e-03 , 4.01610561392808e-03 , 3.27738837575518e-02 ), ( -5.85068443666082e-03 , 1.10886119627274e-02 , 3.02569227489172e-02 ), ( -7.31131086834053e-03 , 1.77444252210332e-02 , 2.14388024426093e-02 ), ( -1.63259668292790e-02 , 5.18039334556752e-02 , -3.42657571196879e-03 ), ( -9.78872925192463e-03 , 3.56768071899492e-02 , -2.14948856921123e-02 ), ( -1.38343934007992e-02 , 4.99078327240418e-02 , -2.82134820935630e-02 ), ( -2.01044257050174e-03 , 1.48696753973150e-02 , -3.61777607784963e-02 ), ( 1.05821837722758e-02 , -1.57183863544096e-02 , -7.29934628812077e-02 ), ( 4.35756463209935e-03 , -7.31103056545410e-04 , -5.42367928014887e-02 ), ( 3.32709631940647e-03 , 6.13185076270506e-03 , -6.95851912988013e-02 ), ( 7.12720782650704e-03 , -1.47825181119657e-02 , -3.14908973687674e-02 ), ( 1.31213393285447e-02 , -4.13041633119196e-02 , 1.35932021834392e-03 ), ( 5.07929024846427e-04 , 1.75736416947850e-03 , -1.40817469322971e-02 ), ( 4.33168120790732e-04 , 3.38741176200938e-03 , -1.99631079092444e-02 ), ( -6.54536392556075e-03 , 2.04972001762583e-02 , -2.28718574320056e-04 ), ( -2.06261824379717e-02 , 5.75779688968008e-02 , 2.88183375108143e-02 ), ( -1.90284464589579e-02 , 6.31904647620932e-02 , -1.58331227728328e-02 ), ( -2.27460733223221e-02 , 7.51258762596511e-02 , -1.71988077928391e-02 ), ( -1.69301143808959e-02 , 7.24663474530253e-02 , -8.24968095319391e-02 ), ( -2.00388592213415e-02 , 8.66328293638355e-02 , -1.01267035271360e-01 ), ( -8.64057100669299e-03 , 4.66423398936291e-02 , -8.27764979146890e-02 ), ( -1.86802642125722e-02 , 6.66376349052638e-02 , -3.49300618005685e-02 ), ( -2.45040168644952e-02 , 9.27621234713304e-02 , -6.83487328322347e-02 ) } +colvars: Step 13, atoms_new_colvar_forces = { ( -7.16848023051113e-02 , 3.03406467638824e-01 , -3.95351133644467e-01 ), ( 1.25012248682017e-02 , 3.14943727627139e-02 , -2.37347290328934e-01 ), ( -4.16044411846218e-02 , 9.19752550270075e-02 , 8.65873739393492e-02 ), ( -9.67474317693076e-02 , 2.47220693613752e-01 , 6.66558943569052e-02 ), ( -1.90524738522307e-02 , 9.94289567745098e-02 , -1.69630346467483e-01 ), ( 7.07545776624681e-02 , -1.83593734852738e-01 , -3.96086306355424e-02 ), ( 1.06290758170036e-02 , -1.00140025421509e-01 , 2.52544176616428e-01 ), ( -4.08308398476371e-02 , 5.97218751038243e-02 , 1.91841739524069e-01 ), ( 6.59244950506004e-02 , -1.88406306432059e-01 , 3.09903758344904e-02 ), ( 1.15016863749083e-01 , -3.89991960993715e-01 , 2.70427575233416e-01 ), ( 2.45481445884070e-02 , -9.92958410899460e-02 , 9.52840930616265e-02 ), ( 2.65957911792211e-02 , -9.71382388271649e-02 , 5.92646586708679e-02 ), ( 1.24022347475679e-02 , -5.58563360999198e-02 , 7.21021236988898e-02 ), ( 1.25425974982060e-02 , -5.36513706759085e-02 , 6.09700270201490e-02 ), ( 5.57808745511937e-03 , -3.53009942223408e-02 , 7.52954309343477e-02 ), ( -8.61672322330427e-03 , 9.02891576978659e-03 , 7.53131644443017e-02 ), ( -2.07900302590006e-03 , -3.07425778523136e-03 , 4.02922287168525e-02 ), ( -5.77036135321706e-03 , 9.46839655898241e-03 , 3.60237167170881e-02 ), ( 2.74066918054249e-03 , -1.32274107216640e-02 , 1.96568235606399e-02 ), ( 9.08730461783740e-03 , -2.21127046888010e-02 , -2.64023654543353e-02 ), ( 8.74092384788639e-03 , -2.37814157636701e-02 , -1.48188371221037e-02 ), ( 6.62478995543604e-03 , -1.35207891048719e-02 , -3.01961009405069e-02 ), ( 1.50746759309285e-02 , -4.65791626355137e-02 , -2.11834520072256e-03 ), ( 2.77006951945339e-02 , -8.81944669602844e-02 , 7.06632082557573e-03 ), ( 1.43202720040025e-02 , -4.67799343049266e-02 , 8.64996682972771e-03 ), ( 1.42676038711970e-02 , -4.38821442318173e-02 , -2.86089251963270e-03 ), ( 9.33659139362305e-03 , -3.70814288695834e-02 , 3.33572802635675e-02 ), ( -8.18030508691844e-04 , -1.55170421736455e-02 , 7.61073953459294e-02 ), ( -3.77758137799797e-03 , 4.01610561392807e-03 , 3.27738837575518e-02 ), ( -5.85068443666083e-03 , 1.10886119627274e-02 , 3.02569227489172e-02 ), ( -7.31131086834053e-03 , 1.77444252210332e-02 , 2.14388024426093e-02 ), ( -1.63259668292790e-02 , 5.18039334556752e-02 , -3.42657571196878e-03 ), ( -9.78872925192462e-03 , 3.56768071899492e-02 , -2.14948856921123e-02 ), ( -1.38343934007992e-02 , 4.99078327240418e-02 , -2.82134820935630e-02 ), ( -2.01044257050173e-03 , 1.48696753973150e-02 , -3.61777607784963e-02 ), ( 1.05821837722758e-02 , -1.57183863544096e-02 , -7.29934628812077e-02 ), ( 4.35756463209935e-03 , -7.31103056545404e-04 , -5.42367928014887e-02 ), ( 3.32709631940648e-03 , 6.13185076270507e-03 , -6.95851912988013e-02 ), ( 7.12720782650704e-03 , -1.47825181119657e-02 , -3.14908973687674e-02 ), ( 1.31213393285447e-02 , -4.13041633119196e-02 , 1.35932021834391e-03 ), ( 5.07929024846422e-04 , 1.75736416947850e-03 , -1.40817469322971e-02 ), ( 4.33168120790726e-04 , 3.38741176200941e-03 , -1.99631079092444e-02 ), ( -6.54536392556077e-03 , 2.04972001762583e-02 , -2.28718574320056e-04 ), ( -2.06261824379717e-02 , 5.75779688968008e-02 , 2.88183375108143e-02 ), ( -1.90284464589579e-02 , 6.31904647620932e-02 , -1.58331227728328e-02 ), ( -2.27460733223221e-02 , 7.51258762596511e-02 , -1.71988077928391e-02 ), ( -1.69301143808959e-02 , 7.24663474530252e-02 , -8.24968095319391e-02 ), ( -2.00388592213415e-02 , 8.66328293638355e-02 , -1.01267035271360e-01 ), ( -8.64057100669298e-03 , 4.66423398936291e-02 , -8.27764979146890e-02 ), ( -1.86802642125722e-02 , 6.66376349052638e-02 , -3.49300618005685e-02 ), ( -2.45040168644952e-02 , 9.27621234713303e-02 , -6.83487328322347e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 13, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3745,10 +5466,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 14, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 14, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 14, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 14, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 14, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 14, atoms_positions[size = 51] = { ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 ), ( 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 ), ( 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 ), ( 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 ), ( 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 ), ( 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 ), ( -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 ), ( -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 ), ( -3.74870489789954e+00 , 4.05644189334812e-02 , 5.45803072342270e+00 ), ( -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ), ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 ), ( 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 ), ( 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 ), ( 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 ), ( 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 ), ( 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 ), ( 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 ), ( 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 ), ( 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 ), ( 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 ), ( 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 ), ( 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 ), ( 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 ), ( 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 ), ( 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 ), ( 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 ), ( 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 ), ( 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 ), ( 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 ), ( -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 ), ( 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 ), ( 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 ), ( -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 ), ( -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 ), ( -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 ), ( -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 ), ( -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 ), ( -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 ), ( -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 ), ( -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 ), ( -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 ), ( -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 ), ( -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 ), ( -2.38241107657785e+00 , -3.23121881461260e-01 , 6.17120868209903e+00 ), ( -4.47207562252775e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 ), ( -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 ), ( -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 ), ( -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 ), ( -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 ), ( -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 ), ( -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ) } +colvars: Step 14, atoms_positions[size = 51] = { ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 ), ( 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 ), ( 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 ), ( 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 ), ( 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 ), ( 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 ), ( -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 ), ( -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 ), ( -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 ), ( -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ), ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 ), ( 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 ), ( 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 ), ( 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 ), ( 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 ), ( 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 ), ( 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 ), ( 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 ), ( 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 ), ( 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 ), ( 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 ), ( 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 ), ( 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 ), ( 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 ), ( 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 ), ( 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 ), ( 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 ), ( 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 ), ( 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 ), ( -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 ), ( 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 ), ( 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 ), ( -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 ), ( -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 ), ( -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 ), ( -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 ), ( -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 ), ( -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 ), ( -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 ), ( -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 ), ( -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 ), ( -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 ), ( -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 ), ( -2.38241107657785e+00 , -3.23121881461259e-01 , 6.17120868209903e+00 ), ( -4.47207562252774e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 ), ( -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 ), ( -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 ), ( -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 ), ( -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 ), ( -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 ), ( -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ) } colvars: Step 14, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 14, atom_groups_ids[size = 0] = @@ -3766,16 +5487,87 @@ colvars: Collective variables module, step no. 14 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 , 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 , 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 , 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 , 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 , 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 , 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 , 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 , 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 , 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 , 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 , 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 , 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 , 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 , 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 , -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 , 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 , -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 , -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 , -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 , -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 , -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 , -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 , -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 , -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 , -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -2.38241107657785e+00 , -3.23121881461259e-01 , 6.17120868209903e+00 , -4.47207562252774e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 , -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 , -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 , -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 , -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 , -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 , -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 , 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 , 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 , 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 , 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 , 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 , 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 , 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 , 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 , 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 , 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 , 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 , 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 , 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 , 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 , -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 , 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 , -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 , -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 , -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 , -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 , -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 , -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 , -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 , -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 , -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -2.38241107657785e+00 , -3.23121881461259e-01 , 6.17120868209903e+00 , -4.47207562252774e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 , -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 , -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 , -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 , -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 , -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 , -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3788,6 +5580,10 @@ colvars: Adding total bias energy: 11.4636 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3803,8 +5599,6 @@ colvars: ( 0.00828513 , -0.106883 , 0.313175 ) colvars: ( -0.0495078 , 0.0818492 , 0.214242 ) colvars: ( 0.0807368 , -0.232924 , 0.0230906 ) colvars: ( 0.13754 , -0.474285 , 0.329552 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0245857 , -0.0993029 , 0.0953971 ) colvars: ( 0.020001 , -0.0819523 , 0.0825574 ) @@ -3857,14 +5651,17 @@ colvars: ( -0.00865928 , 0.0465932 , -0.082863 ) colvars: ( -0.018691 , 0.0666396 , -0.034979 ) colvars: ( -0.0224517 , 0.0839118 , -0.0584022 ) colvars: ( -0.0245354 , 0.0927874 , -0.0684358 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 14. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 14. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 14, atoms_new_colvar_forces = { ( -7.17030729248560e-02 , 3.03434412847935e-01 , -3.96209881834245e-01 ), ( 1.25539674912846e-02 , 3.10971748466751e-02 , -2.37484688240301e-01 ), ( -4.16487740410050e-02 , 9.21772717626605e-02 , 8.70592462212864e-02 ), ( -9.68465681352754e-02 , 2.47846407485462e-01 , 6.65584771335487e-02 ), ( -1.90448258776952e-02 , 9.94144511414792e-02 , -1.70179970081159e-01 ), ( 7.08234560023367e-02 , -1.84050882202746e-01 , -3.94462726906446e-02 ), ( 1.06008164335397e-02 , -9.99558236220789e-02 , 2.53124929639883e-01 ), ( -4.08911448281357e-02 , 6.02339263019856e-02 , 1.91754774692143e-01 ), ( 6.59863081703112e-02 , -1.88672016902237e-01 , 3.08421610939228e-02 ), ( 1.15088456013817e-01 , -3.90372791027753e-01 , 2.71149704495937e-01 ), ( 2.45856886529822e-02 , -9.93029314643077e-02 , 9.53970980947032e-02 ), ( 2.66150021200131e-02 , -9.71398604141635e-02 , 5.93436150137355e-02 ), ( 1.24217001709229e-02 , -5.58279443000605e-02 , 7.21817026324729e-02 ), ( 1.25617262932672e-02 , -5.36376273244229e-02 , 6.10392612117306e-02 ), ( 5.59176317587433e-03 , -3.52437222501083e-02 , 7.53718830903424e-02 ), ( -8.61469376918818e-03 , 9.13573878138333e-03 , 7.53769537257818e-02 ), ( -2.08036764354213e-03 , -3.01168138675437e-03 , 4.03281283495174e-02 ), ( -5.77204210497506e-03 , 9.52933492292574e-03 , 3.60526155123662e-02 ), ( 2.73196767940917e-03 , -1.31749730390552e-02 , 1.96764929056506e-02 ), ( 9.06243454595903e-03 , -2.20795588291178e-02 , -2.64224504586307e-02 ), ( 8.72881036570474e-03 , -2.37719186216426e-02 , -1.48269814368021e-02 ), ( 6.60837365683509e-03 , -1.35173489297917e-02 , -3.02208077794285e-02 ), ( 1.50722263329384e-02 , -4.65880566497031e-02 , -2.10846056423043e-03 ), ( 2.77132714691932e-02 , -8.82492552943065e-02 , 7.09658509678953e-03 ), ( 1.43298786671376e-02 , -4.68110431832540e-02 , 8.67062510312126e-03 ), ( 1.42765588857720e-02 , -4.39272648779111e-02 , -2.85112288428024e-03 ), ( 9.35178577309466e-03 , -3.70910423075215e-02 , 3.33976601877557e-02 ), ( -7.91476888628795e-04 , -1.54934024438347e-02 , 7.61808486456305e-02 ), ( -3.76611455213548e-03 , 4.02928451363875e-03 , 3.28027615403106e-02 ), ( -5.83737261763688e-03 , 1.10943335602030e-02 , 3.02819747857202e-02 ), ( -7.30985707112402e-03 , 1.77764718021673e-02 , 2.14531452840506e-02 ), ( -1.63437274011271e-02 , 5.18698487860540e-02 , -3.44483737933500e-03 ), ( -9.80172955653648e-03 , 3.56965236015377e-02 , -2.15242878391028e-02 ), ( -1.38491829664301e-02 , 4.99274418679334e-02 , -2.82526227196997e-02 ), ( -2.02539614964378e-03 , 1.48679519023049e-02 , -3.62148591869112e-02 ), ( 1.05608512952179e-02 , -1.57629483249763e-02 , -7.30555800588351e-02 ), ( 4.34725410231148e-03 , -7.78490150777868e-04 , -5.42851718364163e-02 ), ( 3.31346888814621e-03 , 6.07435944700226e-03 , -6.96491258062289e-02 ), ( 7.12817424489928e-03 , -1.48360902169562e-02 , -3.15145377778368e-02 ), ( 1.31428212464034e-02 , -4.13817917713363e-02 , 1.37346881309776e-03 ), ( 5.19064722109662e-04 , 1.70212341462858e-03 , -1.40933202424561e-02 ), ( 4.46170100063446e-04 , 3.31812885537241e-03 , -1.99800460475654e-02 ), ( -6.53542118172565e-03 , 2.04714903649538e-02 , -2.33128257942877e-04 ), ( -2.06146479410913e-02 , 5.76006473823990e-02 , 2.88299600818956e-02 ), ( -1.90288349421177e-02 , 6.31867488549733e-02 , -1.58633007683796e-02 ), ( -2.27455548385216e-02 , 7.51207571365791e-02 , -1.72331583835215e-02 ), ( -1.69545518180851e-02 , 7.24431631875390e-02 , -8.25902995953081e-02 ), ( -2.00709479746416e-02 , 8.66102831783137e-02 , -1.01381424086626e-01 ), ( -8.65927776259551e-03 , 4.65932132315996e-02 , -8.28629606271324e-02 ), ( -1.86910394658317e-02 , 6.66395860461118e-02 , -3.49789572629907e-02 ), ( -2.45353740469984e-02 , 9.27873903110001e-02 , -6.84358195053828e-02 ) } +colvars: Step 14, atoms_new_colvar_forces = { ( -7.17030729248560e-02 , 3.03434412847935e-01 , -3.96209881834245e-01 ), ( 1.25539674912846e-02 , 3.10971748466752e-02 , -2.37484688240301e-01 ), ( -4.16487740410050e-02 , 9.21772717626605e-02 , 8.70592462212863e-02 ), ( -9.68465681352754e-02 , 2.47846407485462e-01 , 6.65584771335486e-02 ), ( -1.90448258776952e-02 , 9.94144511414791e-02 , -1.70179970081159e-01 ), ( 7.08234560023367e-02 , -1.84050882202746e-01 , -3.94462726906446e-02 ), ( 1.06008164335397e-02 , -9.99558236220789e-02 , 2.53124929639883e-01 ), ( -4.08911448281357e-02 , 6.02339263019856e-02 , 1.91754774692143e-01 ), ( 6.59863081703112e-02 , -1.88672016902237e-01 , 3.08421610939229e-02 ), ( 1.15088456013817e-01 , -3.90372791027753e-01 , 2.71149704495937e-01 ), ( 2.45856886529822e-02 , -9.93029314643077e-02 , 9.53970980947032e-02 ), ( 2.66150021200131e-02 , -9.71398604141635e-02 , 5.93436150137355e-02 ), ( 1.24217001709229e-02 , -5.58279443000605e-02 , 7.21817026324729e-02 ), ( 1.25617262932672e-02 , -5.36376273244229e-02 , 6.10392612117306e-02 ), ( 5.59176317587432e-03 , -3.52437222501083e-02 , 7.53718830903424e-02 ), ( -8.61469376918818e-03 , 9.13573878138332e-03 , 7.53769537257818e-02 ), ( -2.08036764354214e-03 , -3.01168138675438e-03 , 4.03281283495174e-02 ), ( -5.77204210497506e-03 , 9.52933492292573e-03 , 3.60526155123662e-02 ), ( 2.73196767940916e-03 , -1.31749730390552e-02 , 1.96764929056506e-02 ), ( 9.06243454595903e-03 , -2.20795588291178e-02 , -2.64224504586307e-02 ), ( 8.72881036570473e-03 , -2.37719186216426e-02 , -1.48269814368021e-02 ), ( 6.60837365683509e-03 , -1.35173489297917e-02 , -3.02208077794285e-02 ), ( 1.50722263329384e-02 , -4.65880566497031e-02 , -2.10846056423043e-03 ), ( 2.77132714691932e-02 , -8.82492552943065e-02 , 7.09658509678953e-03 ), ( 1.43298786671376e-02 , -4.68110431832540e-02 , 8.67062510312127e-03 ), ( 1.42765588857720e-02 , -4.39272648779111e-02 , -2.85112288428024e-03 ), ( 9.35178577309465e-03 , -3.70910423075215e-02 , 3.33976601877557e-02 ), ( -7.91476888628810e-04 , -1.54934024438347e-02 , 7.61808486456305e-02 ), ( -3.76611455213548e-03 , 4.02928451363874e-03 , 3.28027615403106e-02 ), ( -5.83737261763688e-03 , 1.10943335602030e-02 , 3.02819747857202e-02 ), ( -7.30985707112403e-03 , 1.77764718021673e-02 , 2.14531452840506e-02 ), ( -1.63437274011271e-02 , 5.18698487860540e-02 , -3.44483737933499e-03 ), ( -9.80172955653648e-03 , 3.56965236015377e-02 , -2.15242878391028e-02 ), ( -1.38491829664301e-02 , 4.99274418679334e-02 , -2.82526227196997e-02 ), ( -2.02539614964378e-03 , 1.48679519023049e-02 , -3.62148591869112e-02 ), ( 1.05608512952179e-02 , -1.57629483249763e-02 , -7.30555800588351e-02 ), ( 4.34725410231149e-03 , -7.78490150777871e-04 , -5.42851718364163e-02 ), ( 3.31346888814621e-03 , 6.07435944700226e-03 , -6.96491258062289e-02 ), ( 7.12817424489928e-03 , -1.48360902169562e-02 , -3.15145377778368e-02 ), ( 1.31428212464034e-02 , -4.13817917713363e-02 , 1.37346881309776e-03 ), ( 5.19064722109667e-04 , 1.70212341462858e-03 , -1.40933202424561e-02 ), ( 4.46170100063452e-04 , 3.31812885537241e-03 , -1.99800460475654e-02 ), ( -6.53542118172565e-03 , 2.04714903649538e-02 , -2.33128257942889e-04 ), ( -2.06146479410913e-02 , 5.76006473823990e-02 , 2.88299600818957e-02 ), ( -1.90288349421176e-02 , 6.31867488549733e-02 , -1.58633007683796e-02 ), ( -2.27455548385216e-02 , 7.51207571365791e-02 , -1.72331583835215e-02 ), ( -1.69545518180850e-02 , 7.24431631875390e-02 , -8.25902995953081e-02 ), ( -2.00709479746416e-02 , 8.66102831783137e-02 , -1.01381424086626e-01 ), ( -8.65927776259550e-03 , 4.65932132315996e-02 , -8.28629606271324e-02 ), ( -1.86910394658317e-02 , 6.66395860461118e-02 , -3.49789572629907e-02 ), ( -2.45353740469984e-02 , 9.27873903110001e-02 , -6.84358195053828e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 14, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3902,10 +5699,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 15, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 15, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 15, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 15, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 15, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 15, atoms_positions[size = 51] = { ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 ), ( 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 ), ( 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 ), ( 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 ), ( 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 ), ( 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 ), ( -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 ), ( -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 ), ( -3.74037993756623e+00 , 3.73480401968941e-02 , 5.45181495688655e+00 ), ( -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ), ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 ), ( 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 ), ( 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 ), ( 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 ), ( 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 ), ( 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 ), ( 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 ), ( 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 ), ( 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 ), ( 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 ), ( 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 ), ( 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 ), ( 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 ), ( 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 ), ( 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 ), ( 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 ), ( 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 ), ( 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 ), ( 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 ), ( -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 ), ( 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 ), ( 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 ), ( -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 ), ( -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 ), ( -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 ), ( -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 ), ( -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 ), ( -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 ), ( -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 ), ( -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 ), ( -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 ), ( -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 ), ( -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 ), ( -2.38290213212965e+00 , -3.18712087726499e-01 , 6.17288759969147e+00 ), ( -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 ), ( -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 ), ( -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 ), ( -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 ), ( -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 ), ( -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 ), ( -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ) } +colvars: Step 15, atoms_positions[size = 51] = { ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 ), ( 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 ), ( 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 ), ( 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 ), ( 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 ), ( 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 ), ( -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 ), ( -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 ), ( -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 ), ( -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ), ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 ), ( 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 ), ( 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 ), ( 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 ), ( 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 ), ( 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 ), ( 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 ), ( 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 ), ( 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 ), ( 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 ), ( 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 ), ( 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 ), ( 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 ), ( 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 ), ( 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 ), ( 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 ), ( 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 ), ( 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 ), ( 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 ), ( -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 ), ( 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 ), ( 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 ), ( -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 ), ( -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 ), ( -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 ), ( -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 ), ( -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 ), ( -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 ), ( -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 ), ( -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 ), ( -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 ), ( -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 ), ( -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 ), ( -2.38290213212964e+00 , -3.18712087726498e-01 , 6.17288759969147e+00 ), ( -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 ), ( -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 ), ( -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 ), ( -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 ), ( -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 ), ( -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 ), ( -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ) } colvars: Step 15, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 15, atom_groups_ids[size = 0] = @@ -3923,16 +5720,87 @@ colvars: Collective variables module, step no. 15 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155576e-02 , 1.18858573400358e-02 , -1.18348863683820e-02 ). +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155577e-02 , 1.18858573400358e-02 , -1.18348863683821e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 , 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 , 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 , 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 , 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 , 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 , 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 , 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 , 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 , 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 , 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 , 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 , 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 , 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 , 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 , -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 , 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 , -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 , -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 , -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 , -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 , -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 , -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 , -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 , -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 , -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -2.38290213212964e+00 , -3.18712087726498e-01 , 6.17288759969147e+00 , -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 , -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 , -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 , -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 , -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 , -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 , -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155576e-02 , 1.18858573400358e-02 , -1.18348863683820e-02 ). +colvars: Colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155577e-02 , 1.18858573400358e-02 , -1.18348863683821e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 , 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 , 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 , 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 , 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 , 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 , 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 , 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 , 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 , 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 , 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 , 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 , 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 , 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 , 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 , -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 , 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 , -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 , -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 , -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 , -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 , -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 , -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 , -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 , -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 , -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -2.38290213212964e+00 , -3.18712087726498e-01 , 6.17288759969147e+00 , -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 , -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 , -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 , -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 , -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 , -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 , -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3945,6 +5813,10 @@ colvars: Adding total bias energy: 11.4698 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3960,8 +5832,6 @@ colvars: ( 0.00825998 , -0.106681 , 0.313778 ) colvars: ( -0.04957 , 0.0823715 , 0.214185 ) colvars: ( 0.080786 , -0.233207 , 0.0229914 ) colvars: ( 0.137602 , -0.474671 , 0.33034 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246185 , -0.0993166 , 0.0955104 ) colvars: ( 0.0200236 , -0.0819437 , 0.0826516 ) @@ -4014,14 +5884,17 @@ colvars: ( -0.00867565 , 0.046548 , -0.0829468 ) colvars: ( -0.0186996 , 0.0666468 , -0.035025 ) colvars: ( -0.0224698 , 0.083924 , -0.0584754 ) colvars: ( -0.0245625 , 0.0928186 , -0.0685235 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 15. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 15. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 15, atoms_new_colvar_forces = { ( -7.16949290049834e-02 , 3.03474386830269e-01 , -3.97046304863662e-01 ), ( 1.26075871768278e-02 , 3.07527449828283e-02 , -2.37633102868567e-01 ), ( -4.17009663573045e-02 , 9.24074981387009e-02 , 8.74661003276692e-02 ), ( -9.69339385370995e-02 , 2.48441896040349e-01 , 6.64422051068895e-02 ), ( -1.90223480977663e-02 , 9.93884227003578e-02 , -1.70691018987116e-01 ), ( 7.08816450632660e-02 , -1.84478966273026e-01 , -3.92821711082243e-02 ), ( 1.05582685074796e-02 , -9.97800400249164e-02 , 2.53669949381410e-01 ), ( -4.09444626684394e-02 , 6.06855197421953e-02 , 1.91689409105388e-01 ), ( 6.60460181362832e-02 , -1.88958089484125e-01 , 3.07452614062881e-02 ), ( 1.15132613755772e-01 , -3.90747225325214e-01 , 2.71865086326974e-01 ), ( 2.46184640764127e-02 , -9.93165721706982e-02 , 9.55103597383862e-02 ), ( 2.66307072466724e-02 , -9.71489574950985e-02 , 5.94190206706606e-02 ), ( 1.24385783576097e-02 , -5.58039125261095e-02 , 7.22592691180316e-02 ), ( 1.25783473850690e-02 , -5.36278041390523e-02 , 6.11074116288131e-02 ), ( 5.60369514890443e-03 , -3.51898383705384e-02 , 7.54451200188047e-02 ), ( -8.61263899903100e-03 , 9.24154583271543e-03 , 7.54358198108120e-02 ), ( -2.08174033617832e-03 , -2.95057966487033e-03 , 4.03599892786103e-02 ), ( -5.77342095425320e-03 , 9.58991721603904e-03 , 3.60784709629169e-02 ), ( 2.72351577197190e-03 , -1.31251301023363e-02 , 1.96904464620740e-02 ), ( 9.03869059047242e-03 , -2.20503408746778e-02 , -2.64510800630670e-02 ), ( 8.71694929791339e-03 , -2.37653627920194e-02 , -1.48399149504546e-02 ), ( 6.59273362777683e-03 , -1.35160743118100e-02 , -3.02500320355194e-02 ), ( 1.50688725450407e-02 , -4.66010358784319e-02 , -2.10215211531109e-03 ), ( 2.77230111502822e-02 , -8.83101398980123e-02 , 7.12565967045664e-03 ), ( 1.43377869775359e-02 , -4.68451858579056e-02 , 8.69135479693351e-03 ), ( 1.42839316102877e-02 , -4.39749472823456e-02 , -2.84039866961499e-03 ), ( 9.36512460506414e-03 , -3.71029112834419e-02 , 3.34387634313426e-02 ), ( -7.67051236185161e-04 , -1.54700848230630e-02 , 7.62570819365013e-02 ), ( -3.75532166399210e-03 , 4.04321632367066e-03 , 3.28334978472288e-02 ), ( -5.82469119645842e-03 , 1.11016688047768e-02 , 3.03102195604810e-02 ), ( -7.30810612237384e-03 , 1.78095870567290e-02 , 2.14673383326389e-02 ), ( -1.63591489797325e-02 , 5.19381615875535e-02 , -3.46637651232031e-03 ), ( -9.81305659264498e-03 , 3.57183112578093e-02 , -2.15546526463102e-02 ), ( -1.38618534791799e-02 , 4.99502805211779e-02 , -2.82919814203272e-02 ), ( -2.03901561513156e-03 , 1.48667419014925e-02 , -3.62537044187399e-02 ), ( 1.05405919753518e-02 , -1.58092773650867e-02 , -7.31206596138427e-02 ), ( 4.33763159321967e-03 , -8.25659687975372e-04 , -5.43329959677468e-02 ), ( 3.30091166802390e-03 , 6.01768930062787e-03 , -6.97120700059172e-02 ), ( 7.12876070240522e-03 , -1.48899474877114e-02 , -3.15361024336851e-02 ), ( 1.31619639603794e-02 , -4.14604738001422e-02 , 1.39310822023035e-03 ), ( 5.29527032387887e-04 , 1.64865096373702e-03 , -1.40994166020852e-02 ), ( 4.58418665716039e-04 , 3.25111466051151e-03 , -1.99902166450620e-02 ), ( -6.52565516598719e-03 , 2.04486038718644e-02 , -2.32521360264111e-04 ), ( -2.06025650233246e-02 , 5.76286370246274e-02 , 2.88470449160681e-02 ), ( -1.90277436193707e-02 , 6.31886535767905e-02 , -1.58884792059689e-02 ), ( -2.27433417372783e-02 , 7.51223872874197e-02 , -1.72613295599796e-02 ), ( -1.69756928755969e-02 , 7.24254347727082e-02 , -8.26817853858622e-02 ), ( -2.00989076652020e-02 , 8.65940068037253e-02 , -1.01494282967316e-01 ), ( -8.67565012061669e-03 , 4.65480494214555e-02 , -8.29467996197521e-02 ), ( -1.86995694597294e-02 , 6.66467836543689e-02 , -3.50249837064717e-02 ), ( -2.45625311202662e-02 , 9.28186466441078e-02 , -6.85234543224205e-02 ) } +colvars: Step 15, atoms_new_colvar_forces = { ( -7.16949290049834e-02 , 3.03474386830269e-01 , -3.97046304863662e-01 ), ( 1.26075871768279e-02 , 3.07527449828284e-02 , -2.37633102868567e-01 ), ( -4.17009663573045e-02 , 9.24074981387010e-02 , 8.74661003276692e-02 ), ( -9.69339385370995e-02 , 2.48441896040349e-01 , 6.64422051068895e-02 ), ( -1.90223480977663e-02 , 9.93884227003577e-02 , -1.70691018987116e-01 ), ( 7.08816450632660e-02 , -1.84478966273026e-01 , -3.92821711082244e-02 ), ( 1.05582685074796e-02 , -9.97800400249164e-02 , 2.53669949381410e-01 ), ( -4.09444626684395e-02 , 6.06855197421951e-02 , 1.91689409105388e-01 ), ( 6.60460181362832e-02 , -1.88958089484125e-01 , 3.07452614062881e-02 ), ( 1.15132613755772e-01 , -3.90747225325214e-01 , 2.71865086326974e-01 ), ( 2.46184640764127e-02 , -9.93165721706982e-02 , 9.55103597383862e-02 ), ( 2.66307072466724e-02 , -9.71489574950985e-02 , 5.94190206706605e-02 ), ( 1.24385783576097e-02 , -5.58039125261095e-02 , 7.22592691180316e-02 ), ( 1.25783473850690e-02 , -5.36278041390523e-02 , 6.11074116288130e-02 ), ( 5.60369514890443e-03 , -3.51898383705384e-02 , 7.54451200188047e-02 ), ( -8.61263899903098e-03 , 9.24154583271544e-03 , 7.54358198108119e-02 ), ( -2.08174033617832e-03 , -2.95057966487033e-03 , 4.03599892786103e-02 ), ( -5.77342095425320e-03 , 9.58991721603904e-03 , 3.60784709629169e-02 ), ( 2.72351577197190e-03 , -1.31251301023362e-02 , 1.96904464620740e-02 ), ( 9.03869059047243e-03 , -2.20503408746778e-02 , -2.64510800630671e-02 ), ( 8.71694929791340e-03 , -2.37653627920194e-02 , -1.48399149504546e-02 ), ( 6.59273362777682e-03 , -1.35160743118100e-02 , -3.02500320355194e-02 ), ( 1.50688725450407e-02 , -4.66010358784319e-02 , -2.10215211531110e-03 ), ( 2.77230111502822e-02 , -8.83101398980123e-02 , 7.12565967045663e-03 ), ( 1.43377869775359e-02 , -4.68451858579056e-02 , 8.69135479693351e-03 ), ( 1.42839316102877e-02 , -4.39749472823456e-02 , -2.84039866961499e-03 ), ( 9.36512460506414e-03 , -3.71029112834419e-02 , 3.34387634313426e-02 ), ( -7.67051236185160e-04 , -1.54700848230630e-02 , 7.62570819365013e-02 ), ( -3.75532166399210e-03 , 4.04321632367066e-03 , 3.28334978472288e-02 ), ( -5.82469119645842e-03 , 1.11016688047768e-02 , 3.03102195604810e-02 ), ( -7.30810612237383e-03 , 1.78095870567290e-02 , 2.14673383326389e-02 ), ( -1.63591489797325e-02 , 5.19381615875536e-02 , -3.46637651232032e-03 ), ( -9.81305659264498e-03 , 3.57183112578092e-02 , -2.15546526463102e-02 ), ( -1.38618534791799e-02 , 4.99502805211779e-02 , -2.82919814203272e-02 ), ( -2.03901561513156e-03 , 1.48667419014925e-02 , -3.62537044187399e-02 ), ( 1.05405919753518e-02 , -1.58092773650867e-02 , -7.31206596138427e-02 ), ( 4.33763159321967e-03 , -8.25659687975371e-04 , -5.43329959677468e-02 ), ( 3.30091166802390e-03 , 6.01768930062788e-03 , -6.97120700059172e-02 ), ( 7.12876070240522e-03 , -1.48899474877114e-02 , -3.15361024336851e-02 ), ( 1.31619639603794e-02 , -4.14604738001422e-02 , 1.39310822023036e-03 ), ( 5.29527032387889e-04 , 1.64865096373702e-03 , -1.40994166020852e-02 ), ( 4.58418665716035e-04 , 3.25111466051152e-03 , -1.99902166450619e-02 ), ( -6.52565516598718e-03 , 2.04486038718644e-02 , -2.32521360264095e-04 ), ( -2.06025650233246e-02 , 5.76286370246274e-02 , 2.88470449160681e-02 ), ( -1.90277436193707e-02 , 6.31886535767905e-02 , -1.58884792059689e-02 ), ( -2.27433417372783e-02 , 7.51223872874197e-02 , -1.72613295599796e-02 ), ( -1.69756928755969e-02 , 7.24254347727082e-02 , -8.26817853858621e-02 ), ( -2.00989076652020e-02 , 8.65940068037253e-02 , -1.01494282967316e-01 ), ( -8.67565012061669e-03 , 4.65480494214555e-02 , -8.29467996197520e-02 ), ( -1.86995694597294e-02 , 6.66467836543689e-02 , -3.50249837064717e-02 ), ( -2.45625311202662e-02 , 9.28186466441078e-02 , -6.85234543224205e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 15, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4059,10 +5932,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 16, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 16, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 16, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 16, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 16, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 16, atoms_positions[size = 51] = { ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 ), ( 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 ), ( 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 ), ( 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 ), ( 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 ), ( 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 ), ( -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 ), ( -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 ), ( -3.73185754983895e+00 , 3.59121509335080e-02 , 5.44610695064150e+00 ), ( -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ), ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 ), ( 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 ), ( 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 ), ( 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 ), ( 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 ), ( 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 ), ( 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 ), ( 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 ), ( 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 ), ( 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 ), ( 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 ), ( 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 ), ( 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 ), ( 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 ), ( 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 ), ( 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 ), ( 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 ), ( 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 ), ( 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 ), ( -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 ), ( 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 ), ( 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 ), ( -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 ), ( -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 ), ( -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 ), ( -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 ), ( -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 ), ( -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 ), ( -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 ), ( -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 ), ( -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 ), ( -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 ), ( -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 ), ( -2.38388494433047e+00 , -3.15826223986612e-01 , 6.17394163944166e+00 ), ( -4.46828024629854e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 ), ( -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 ), ( -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 ), ( -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 ), ( -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 ), ( -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 ), ( -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ) } +colvars: Step 16, atoms_positions[size = 51] = { ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 ), ( 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 ), ( 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 ), ( 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 ), ( 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 ), ( 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 ), ( -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 ), ( -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 ), ( -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 ), ( -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ), ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 ), ( 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 ), ( 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 ), ( 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 ), ( 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 ), ( 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 ), ( 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 ), ( 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 ), ( 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 ), ( 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 ), ( 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 ), ( 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 ), ( 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 ), ( 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 ), ( 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 ), ( 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 ), ( 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 ), ( 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 ), ( 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 ), ( -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 ), ( 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 ), ( 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 ), ( -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 ), ( -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 ), ( -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 ), ( -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 ), ( -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 ), ( -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 ), ( -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 ), ( -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 ), ( -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 ), ( -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 ), ( -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 ), ( -2.38388494433046e+00 , -3.15826223986610e-01 , 6.17394163944166e+00 ), ( -4.46828024629853e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 ), ( -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 ), ( -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 ), ( -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 ), ( -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 ), ( -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 ), ( -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ) } colvars: Step 16, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 16, atom_groups_ids[size = 0] = @@ -4081,15 +5954,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147335e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147334e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: Calculating colvar components. +colvars: Calculating colvar components. colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 , 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 , 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 , 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 , 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 , 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 , 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 , 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 , 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 , 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 , 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 , 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 , 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 , 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 , 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 , -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 , 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 , -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 , -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 , -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 , -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 , -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 , -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 , -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 , -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 , -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -2.38388494433046e+00 , -3.15826223986610e-01 , 6.17394163944166e+00 , -4.46828024629853e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 , -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 , -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 , -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 , -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 , -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 , -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147335e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: Colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147334e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 , 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 , 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 , 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 , 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 , 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 , 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 , 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 , 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 , 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 , 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 , 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 , 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 , 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 , 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 , -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 , 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 , -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 , -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 , -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 , -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 , -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 , -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 , -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 , -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 , -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -2.38388494433046e+00 , -3.15826223986610e-01 , 6.17394163944166e+00 , -4.46828024629853e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 , -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 , -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 , -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 , -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 , -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 , -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4102,6 +6046,10 @@ colvars: Adding total bias energy: 11.476 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4117,8 +6065,6 @@ colvars: ( 0.00822 , -0.106488 , 0.314333 ) colvars: ( -0.0496209 , 0.0828217 , 0.214148 ) colvars: ( 0.0808304 , -0.233509 , 0.0229457 ) colvars: ( 0.13763 , -0.475045 , 0.331108 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246453 , -0.0993365 , 0.0956225 ) colvars: ( 0.0200417 , -0.0819413 , 0.0827426 ) @@ -4171,14 +6117,17 @@ colvars: ( -0.00868915 , 0.0465075 , -0.0830265 ) colvars: ( -0.0187054 , 0.0666594 , -0.0350675 ) colvars: ( -0.0224837 , 0.0839423 , -0.0585457 ) colvars: ( -0.0245845 , 0.0928555 , -0.0686107 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 16. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 16. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 16, atoms_new_colvar_forces = { ( -7.16599920626334e-02 , 3.03520189493113e-01 , -3.97844554110196e-01 ), ( 1.26596866495085e-02 , 3.04680490772270e-02 , -2.37791019205751e-01 ), ( -4.17592178733622e-02 , 9.26629575009943e-02 , 8.77929809589357e-02 ), ( -9.70053794347984e-02 , 2.48992623070873e-01 , 6.63054983454753e-02 ), ( -1.89853945294203e-02 , 9.93485496391636e-02 , -1.71150647534301e-01 ), ( 7.09261775017845e-02 , -1.84867108646044e-01 , -3.91178688867081e-02 ), ( 1.05027258080738e-02 , -9.96136798939432e-02 , 2.54166018544938e-01 ), ( -4.09879563722719e-02 , 6.10659904102845e-02 , 1.91648579072606e-01 ), ( 6.61012658667263e-02 , -1.89258161381491e-01 , 3.07081105841715e-02 ), ( 1.15146596997167e-01 , -3.91102227968993e-01 , 2.72562397837632e-01 ), ( 2.46453030855937e-02 , -9.93365220421225e-02 , 9.56225083588144e-02 ), ( 2.66421414788933e-02 , -9.71657300342827e-02 , 5.94897841061073e-02 ), ( 1.24522694746926e-02 , -5.57846102591163e-02 , 7.23335698331391e-02 ), ( 1.25918663087693e-02 , -5.36220502851586e-02 , 6.11734810795629e-02 ), ( 5.61350142569207e-03 , -3.51401203977188e-02 , 7.55136988866750e-02 ), ( -8.61049745184722e-03 , 9.34488100012722e-03 , 7.54880974356862e-02 ), ( -2.08306110857869e-03 , -2.89191085757775e-03 , 4.03868197279044e-02 ), ( -5.77438653909533e-03 , 9.64928220907090e-03 , 3.61004204614304e-02 ), ( 2.71548615893903e-03 , -1.30789072162389e-02 , 1.96979142124408e-02 ), ( 9.01654505317238e-03 , -2.20261826877445e-02 , -2.64884795675305e-02 ), ( 8.70551878740282e-03 , -2.37622854338400e-02 , -1.48577425980512e-02 ), ( 6.57817314530783e-03 , -1.35174371713845e-02 , -3.02836212361381e-02 ), ( 1.50644910475842e-02 , -4.66183167563982e-02 , -2.09959283310227e-03 ), ( 2.77292875578808e-02 , -8.83766259112437e-02 , 7.15349274759623e-03 ), ( 1.43436005142690e-02 , -4.68820099433303e-02 , 8.71210519613895e-03 ), ( 1.42893406669391e-02 , -4.40246300593357e-02 , -2.82851322219024e-03 ), ( 9.37614206359767e-03 , -3.71168203279471e-02 , 3.34801668491546e-02 ), ( -7.45360757258770e-04 , -1.54469884200433e-02 , 7.63350951705038e-02 ), ( -3.74542386156819e-03 , 4.05796942472545e-03 , 3.28656966491896e-02 ), ( -5.81287991845205e-03 , 1.11108772852015e-02 , 3.03413992192289e-02 ), ( -7.30600279987892e-03 , 1.78434469740859e-02 , 2.14809824211243e-02 ), ( -1.63716194505806e-02 , 5.20078778820190e-02 , -3.49150141876508e-03 ), ( -9.82228967181317e-03 , 3.57418436312302e-02 , -2.15857699885616e-02 ), ( -1.38718942693465e-02 , 4.99760774537983e-02 , -2.83312021543967e-02 ), ( -2.05092887520623e-03 , 1.48658588304507e-02 , -3.62938698788685e-02 ), ( 1.05217736834276e-02 , -1.58572613080413e-02 , -7.31877103025308e-02 ), ( 4.32888255023710e-03 , -8.72137630605562e-04 , -5.43793223663522e-02 ), ( 3.28969909537636e-03 , 5.96243711290139e-03 , -6.97728044235884e-02 ), ( 7.12885665987957e-03 , -1.49433842714813e-02 , -3.15548733162422e-02 ), ( 1.31781063569408e-02 , -4.15389021041050e-02 , 1.41874342019564e-03 ), ( 5.39047621159523e-04 , 1.59798991413936e-03 , -1.40993565514254e-02 ), ( 4.69602162734557e-04 , 3.18766520365176e-03 , -1.99927400393244e-02 ), ( -6.51622058373523e-03 , 2.04292485461563e-02 , -2.26519647382126e-04 ), ( -2.05899546307361e-02 , 5.76622094085089e-02 , 2.88694586745091e-02 ), ( -1.90249363443350e-02 , 6.31966262801517e-02 , -1.59081022548893e-02 ), ( -2.27391746568829e-02 , 7.51313288340186e-02 , -1.72826679888529e-02 ), ( -1.69927675860640e-02 , 7.24134595931748e-02 , -8.27698731950902e-02 ), ( -2.01217530075865e-02 , 8.65842216823478e-02 , -1.01603973274608e-01 ), ( -8.68915196928373e-03 , 4.65074767613662e-02 , -8.30265180199556e-02 ), ( -1.87053800613670e-02 , 6.66594018957552e-02 , -3.50674513075242e-02 ), ( -2.45844639056470e-02 , 9.28554718936520e-02 , -6.86107244708341e-02 ) } +colvars: Step 16, atoms_new_colvar_forces = { ( -7.16599920626333e-02 , 3.03520189493113e-01 , -3.97844554110196e-01 ), ( 1.26596866495085e-02 , 3.04680490772271e-02 , -2.37791019205751e-01 ), ( -4.17592178733622e-02 , 9.26629575009944e-02 , 8.77929809589356e-02 ), ( -9.70053794347984e-02 , 2.48992623070873e-01 , 6.63054983454752e-02 ), ( -1.89853945294203e-02 , 9.93485496391635e-02 , -1.71150647534301e-01 ), ( 7.09261775017845e-02 , -1.84867108646044e-01 , -3.91178688867081e-02 ), ( 1.05027258080738e-02 , -9.96136798939432e-02 , 2.54166018544938e-01 ), ( -4.09879563722719e-02 , 6.10659904102842e-02 , 1.91648579072607e-01 ), ( 6.61012658667264e-02 , -1.89258161381491e-01 , 3.07081105841716e-02 ), ( 1.15146596997166e-01 , -3.91102227968993e-01 , 2.72562397837632e-01 ), ( 2.46453030855937e-02 , -9.93365220421225e-02 , 9.56225083588144e-02 ), ( 2.66421414788933e-02 , -9.71657300342827e-02 , 5.94897841061073e-02 ), ( 1.24522694746926e-02 , -5.57846102591163e-02 , 7.23335698331391e-02 ), ( 1.25918663087693e-02 , -5.36220502851586e-02 , 6.11734810795629e-02 ), ( 5.61350142569206e-03 , -3.51401203977188e-02 , 7.55136988866750e-02 ), ( -8.61049745184722e-03 , 9.34488100012719e-03 , 7.54880974356862e-02 ), ( -2.08306110857868e-03 , -2.89191085757777e-03 , 4.03868197279044e-02 ), ( -5.77438653909533e-03 , 9.64928220907088e-03 , 3.61004204614304e-02 ), ( 2.71548615893904e-03 , -1.30789072162389e-02 , 1.96979142124408e-02 ), ( 9.01654505317240e-03 , -2.20261826877445e-02 , -2.64884795675305e-02 ), ( 8.70551878740283e-03 , -2.37622854338400e-02 , -1.48577425980512e-02 ), ( 6.57817314530784e-03 , -1.35174371713845e-02 , -3.02836212361381e-02 ), ( 1.50644910475842e-02 , -4.66183167563982e-02 , -2.09959283310228e-03 ), ( 2.77292875578808e-02 , -8.83766259112437e-02 , 7.15349274759623e-03 ), ( 1.43436005142690e-02 , -4.68820099433303e-02 , 8.71210519613895e-03 ), ( 1.42893406669391e-02 , -4.40246300593357e-02 , -2.82851322219024e-03 ), ( 9.37614206359767e-03 , -3.71168203279471e-02 , 3.34801668491546e-02 ), ( -7.45360757258783e-04 , -1.54469884200433e-02 , 7.63350951705038e-02 ), ( -3.74542386156819e-03 , 4.05796942472545e-03 , 3.28656966491896e-02 ), ( -5.81287991845206e-03 , 1.11108772852015e-02 , 3.03413992192289e-02 ), ( -7.30600279987893e-03 , 1.78434469740859e-02 , 2.14809824211243e-02 ), ( -1.63716194505806e-02 , 5.20078778820190e-02 , -3.49150141876509e-03 ), ( -9.82228967181316e-03 , 3.57418436312302e-02 , -2.15857699885616e-02 ), ( -1.38718942693465e-02 , 4.99760774537983e-02 , -2.83312021543967e-02 ), ( -2.05092887520622e-03 , 1.48658588304507e-02 , -3.62938698788685e-02 ), ( 1.05217736834276e-02 , -1.58572613080413e-02 , -7.31877103025308e-02 ), ( 4.32888255023710e-03 , -8.72137630605546e-04 , -5.43793223663522e-02 ), ( 3.28969909537636e-03 , 5.96243711290140e-03 , -6.97728044235884e-02 ), ( 7.12885665987956e-03 , -1.49433842714813e-02 , -3.15548733162422e-02 ), ( 1.31781063569408e-02 , -4.15389021041050e-02 , 1.41874342019563e-03 ), ( 5.39047621159515e-04 , 1.59798991413939e-03 , -1.40993565514254e-02 ), ( 4.69602162734545e-04 , 3.18766520365181e-03 , -1.99927400393244e-02 ), ( -6.51622058373524e-03 , 2.04292485461563e-02 , -2.26519647382133e-04 ), ( -2.05899546307361e-02 , 5.76622094085089e-02 , 2.88694586745090e-02 ), ( -1.90249363443350e-02 , 6.31966262801517e-02 , -1.59081022548893e-02 ), ( -2.27391746568829e-02 , 7.51313288340186e-02 , -1.72826679888529e-02 ), ( -1.69927675860640e-02 , 7.24134595931749e-02 , -8.27698731950902e-02 ), ( -2.01217530075865e-02 , 8.65842216823478e-02 , -1.01603973274608e-01 ), ( -8.68915196928372e-03 , 4.65074767613662e-02 , -8.30265180199556e-02 ), ( -1.87053800613670e-02 , 6.66594018957553e-02 , -3.50674513075242e-02 ), ( -2.45844639056470e-02 , 9.28554718936520e-02 , -6.86107244708341e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 16, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4216,10 +6165,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 17, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 17, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 17, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 17, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 17, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 17, atoms_positions[size = 51] = { ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 ), ( 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 ), ( 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 ), ( 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 ), ( 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 ), ( 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 ), ( -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 ), ( -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 ), ( -3.72338871222330e+00 , 3.62579539864891e-02 , 5.44133506196972e+00 ), ( -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ), ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 ), ( 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 ), ( 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 ), ( 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 ), ( 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 ), ( 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 ), ( 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 ), ( 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 ), ( 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 ), ( 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 ), ( 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 ), ( 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 ), ( 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 ), ( 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 ), ( 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 ), ( 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 ), ( 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 ), ( 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 ), ( 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 ), ( -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 ), ( 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 ), ( 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 ), ( -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 ), ( -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 ), ( -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 ), ( -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 ), ( -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 ), ( -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 ), ( -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 ), ( -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 ), ( -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 ), ( -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 ), ( -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 ), ( -2.38520263482904e+00 , -3.14375701461254e-01 , 6.17435317935263e+00 ), ( -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 ), ( -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 ), ( -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 ), ( -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 ), ( -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 ), ( -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 ), ( -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ) } +colvars: Step 17, atoms_positions[size = 51] = { ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 ), ( 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 ), ( 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 ), ( 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 ), ( 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 ), ( 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 ), ( -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 ), ( -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 ), ( -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 ), ( -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ), ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 ), ( 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 ), ( 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 ), ( 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 ), ( 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 ), ( 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 ), ( 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 ), ( 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 ), ( 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 ), ( 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 ), ( 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 ), ( 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 ), ( 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 ), ( 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 ), ( 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 ), ( 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 ), ( 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 ), ( 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 ), ( 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 ), ( -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 ), ( 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 ), ( 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 ), ( -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 ), ( -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 ), ( -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 ), ( -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 ), ( -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 ), ( -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 ), ( -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 ), ( -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 ), ( -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 ), ( -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 ), ( -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 ), ( -2.38520263482903e+00 , -3.14375701461253e-01 , 6.17435317935263e+00 ), ( -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 ), ( -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 ), ( -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 ), ( -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 ), ( -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 ), ( -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 ), ( -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ) } colvars: Step 17, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 17, atom_groups_ids[size = 0] = @@ -4237,16 +6186,87 @@ colvars: Collective variables module, step no. 17 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652891e-02 , -1.16317231514313e-02 ). +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652892e-02 , -1.16317231514313e-02 ). +colvars: Done calculating gradients of colvar "main". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 , 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 , 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 , 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 , 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 , 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 , 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 , 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 , 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 , 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 , 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 , 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 , 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 , 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 , 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 , -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 , 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 , -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 , -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 , -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 , -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 , -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 , -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 , -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 , -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 , -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -2.38520263482903e+00 , -3.14375701461253e-01 , 6.17435317935263e+00 , -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 , -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 , -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 , -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 , -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 , -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 , -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652891e-02 , -1.16317231514313e-02 ). +colvars: Colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652892e-02 , -1.16317231514313e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 , 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 , 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 , 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 , 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 , 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 , 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 , 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 , 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 , 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 , 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 , 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 , 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 , 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 , 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 , -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 , 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 , -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 , -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 , -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 , -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 , -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 , -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 , -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 , -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 , -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -2.38520263482903e+00 , -3.14375701461253e-01 , 6.17435317935263e+00 , -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 , -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 , -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 , -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 , -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 , -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 , -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4259,6 +6279,10 @@ colvars: Adding total bias energy: 11.4822 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4274,8 +6298,6 @@ colvars: ( 0.00816662 , -0.106306 , 0.314827 ) colvars: ( -0.0496581 , 0.0831902 , 0.214132 ) colvars: ( 0.0808682 , -0.233823 , 0.0229594 ) colvars: ( 0.137622 , -0.475392 , 0.331842 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246652 , -0.0993622 , 0.095732 ) colvars: ( 0.0200547 , -0.081945 , 0.0828289 ) @@ -4328,14 +6350,17 @@ colvars: ( -0.00869932 , 0.046472 , -0.0831007 ) colvars: ( -0.0187081 , 0.0666773 , -0.0351058 ) colvars: ( -0.0224929 , 0.0839663 , -0.0586123 ) colvars: ( -0.0246003 , 0.0928971 , -0.0686965 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 17. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 17. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 17, atoms_new_colvar_forces = { ( -7.15991844821387e-02 , 3.03566046493554e-01 , -3.98589394335568e-01 ), ( 1.27080880761104e-02 , 3.02482168390730e-02 , -2.37956547495991e-01 ), ( -4.18215965128955e-02 , 9.29391300559080e-02 , 8.80280661517742e-02 ), ( -9.70578106655439e-02 , 2.49485275638335e-01 , 6.61481548320792e-02 ), ( -1.89349892460271e-02 , 9.92934578601701e-02 , -1.71547671981010e-01 ), ( 7.09549756938869e-02 , -1.85205681928521e-01 , -3.89553397840212e-02 ), ( 1.04360069804476e-02 , -9.94579562621154e-02 , 2.54601524564221e-01 ), ( -4.10194911993123e-02 , 6.13670159681508e-02 , 1.91634456228622e-01 ), ( 6.61500758622970e-02 , -1.89564992241884e-01 , 3.07364530191408e-02 ), ( 1.15129312716163e-01 , -3.91425701068371e-01 , 2.73230025879347e-01 ), ( 2.46652291494805e-02 , -9.93621704587275e-02 , 9.57319835750408e-02 ), ( 2.66487201515362e-02 , -9.71899657435523e-02 , 5.95549496710853e-02 ), ( 1.24622672888664e-02 , -5.57702453559136e-02 , 7.24033746190143e-02 ), ( 1.26017842784006e-02 , -5.36203395040831e-02 , 6.12364446426536e-02 ), ( 5.62084309259653e-03 , -3.50953115725839e-02 , 7.55762909057078e-02 ), ( -8.60826813568425e-03 , 9.44406645854298e-03 , 7.55323767690547e-02 ), ( -2.08429098101708e-03 , -2.83671367062415e-03 , 4.04078631431500e-02 ), ( -5.77487048564608e-03 , 9.70643059913455e-03 , 3.61177754946845e-02 ), ( 2.70805118577230e-03 , -1.30373194634878e-02 , 1.96985074289443e-02 ), ( 8.99648984984500e-03 , -2.20080768587484e-02 , -2.65342276660742e-02 ), ( 8.69473273520900e-03 , -2.37630816502961e-02 , -1.48802114220181e-02 ), ( 6.56501421850286e-03 , -1.35217932541125e-02 , -3.03210592179036e-02 ), ( 1.50590452715200e-02 , -4.66398655552029e-02 , -2.10071241619051e-03 ), ( 2.77316589065012e-02 , -8.84477423995499e-02 , 7.18007358178622e-03 ), ( 1.43470225305447e-02 , -4.69209172028335e-02 , 8.73278967907638e-03 ), ( 1.42925048375785e-02 , -4.40754955097007e-02 , -2.81534258881913e-03 ), ( 9.38444695561450e-03 , -3.71324088332392e-02 , 3.35213337177348e-02 ), ( -7.26987884782412e-04 , -1.54240642662770e-02 , 7.64135749901223e-02 ), ( -3.73665213056787e-03 , 4.07353264834061e-03 , 3.28987833829794e-02 ), ( -5.80219750707640e-03 , 1.11221101587789e-02 , 3.03749870854370e-02 ), ( -7.30353687369275e-03 , 1.78775846305822e-02 , 2.14936665260160e-02 ), ( -1.63806520613838e-02 , 5.20777052185658e-02 , -3.52025758798728e-03 ), ( -9.82908388362489e-03 , 3.57666323257724e-02 , -2.16173158817409e-02 ), ( -1.38788964719874e-02 , 5.00043362505760e-02 , -2.83698539092528e-02 ), ( -2.06079367882705e-03 , 1.48650968594908e-02 , -3.63347462413643e-02 ), ( 1.05048058308129e-02 , -1.59065676245395e-02 , -7.32554311863814e-02 ), ( 4.32121096086670e-03 , -9.17335633906932e-04 , -5.44231732871726e-02 ), ( 3.28011518369856e-03 , 5.90930783998450e-03 , -6.98300821185564e-02 ), ( 7.12840086648953e-03 , -1.49955402368339e-02 , -3.15702448585199e-02 ), ( 1.31906996331723e-02 , -4.16155160943026e-02 , 1.45046337050661e-03 ), ( 5.47380948155791e-04 , 1.55122543651114e-03 , -1.40928369624719e-02 ), ( 4.79435149741417e-04 , 3.12912676270520e-03 , -1.99871975294202e-02 ), ( -6.50729574857995e-03 , 2.04140395217321e-02 , -2.15099640596013e-04 ), ( -2.05769479255007e-02 , 5.77012793802570e-02 , 2.88966554445180e-02 ), ( -1.90202892635905e-02 , 6.32108127600351e-02 , -1.59219288397588e-02 ), ( -2.27329271959792e-02 , 7.51477831841043e-02 , -1.72969138581540e-02 ), ( -1.70051329242468e-02 , 7.24073007431202e-02 , -8.28531707934524e-02 ), ( -2.01386533689387e-02 , 8.65808706267130e-02 , -1.01708791742204e-01 ), ( -8.69931533541390e-03 , 4.64720375584738e-02 , -8.31006752311498e-02 ), ( -1.87081206453085e-02 , 6.66773226446364e-02 , -3.51058027924910e-02 ), ( -2.46003337460445e-02 , 9.28970579261590e-02 , -6.86965453344270e-02 ) } +colvars: Step 17, atoms_new_colvar_forces = { ( -7.15991844821387e-02 , 3.03566046493554e-01 , -3.98589394335568e-01 ), ( 1.27080880761104e-02 , 3.02482168390730e-02 , -2.37956547495990e-01 ), ( -4.18215965128955e-02 , 9.29391300559080e-02 , 8.80280661517742e-02 ), ( -9.70578106655439e-02 , 2.49485275638335e-01 , 6.61481548320793e-02 ), ( -1.89349892460272e-02 , 9.92934578601701e-02 , -1.71547671981010e-01 ), ( 7.09549756938869e-02 , -1.85205681928521e-01 , -3.89553397840212e-02 ), ( 1.04360069804477e-02 , -9.94579562621154e-02 , 2.54601524564221e-01 ), ( -4.10194911993123e-02 , 6.13670159681508e-02 , 1.91634456228622e-01 ), ( 6.61500758622970e-02 , -1.89564992241884e-01 , 3.07364530191407e-02 ), ( 1.15129312716163e-01 , -3.91425701068371e-01 , 2.73230025879347e-01 ), ( 2.46652291494805e-02 , -9.93621704587276e-02 , 9.57319835750408e-02 ), ( 2.66487201515362e-02 , -9.71899657435524e-02 , 5.95549496710853e-02 ), ( 1.24622672888664e-02 , -5.57702453559136e-02 , 7.24033746190143e-02 ), ( 1.26017842784006e-02 , -5.36203395040831e-02 , 6.12364446426536e-02 ), ( 5.62084309259652e-03 , -3.50953115725840e-02 , 7.55762909057078e-02 ), ( -8.60826813568425e-03 , 9.44406645854299e-03 , 7.55323767690547e-02 ), ( -2.08429098101708e-03 , -2.83671367062416e-03 , 4.04078631431500e-02 ), ( -5.77487048564609e-03 , 9.70643059913453e-03 , 3.61177754946845e-02 ), ( 2.70805118577230e-03 , -1.30373194634879e-02 , 1.96985074289443e-02 ), ( 8.99648984984501e-03 , -2.20080768587484e-02 , -2.65342276660742e-02 ), ( 8.69473273520900e-03 , -2.37630816502961e-02 , -1.48802114220181e-02 ), ( 6.56501421850287e-03 , -1.35217932541125e-02 , -3.03210592179037e-02 ), ( 1.50590452715200e-02 , -4.66398655552029e-02 , -2.10071241619051e-03 ), ( 2.77316589065011e-02 , -8.84477423995500e-02 , 7.18007358178622e-03 ), ( 1.43470225305447e-02 , -4.69209172028335e-02 , 8.73278967907639e-03 ), ( 1.42925048375785e-02 , -4.40754955097007e-02 , -2.81534258881912e-03 ), ( 9.38444695561449e-03 , -3.71324088332392e-02 , 3.35213337177348e-02 ), ( -7.26987884782428e-04 , -1.54240642662770e-02 , 7.64135749901224e-02 ), ( -3.73665213056788e-03 , 4.07353264834062e-03 , 3.28987833829794e-02 ), ( -5.80219750707640e-03 , 1.11221101587789e-02 , 3.03749870854370e-02 ), ( -7.30353687369275e-03 , 1.78775846305822e-02 , 2.14936665260160e-02 ), ( -1.63806520613838e-02 , 5.20777052185658e-02 , -3.52025758798729e-03 ), ( -9.82908388362489e-03 , 3.57666323257724e-02 , -2.16173158817409e-02 ), ( -1.38788964719874e-02 , 5.00043362505760e-02 , -2.83698539092529e-02 ), ( -2.06079367882705e-03 , 1.48650968594908e-02 , -3.63347462413643e-02 ), ( 1.05048058308129e-02 , -1.59065676245395e-02 , -7.32554311863814e-02 ), ( 4.32121096086671e-03 , -9.17335633906933e-04 , -5.44231732871726e-02 ), ( 3.28011518369857e-03 , 5.90930783998450e-03 , -6.98300821185564e-02 ), ( 7.12840086648953e-03 , -1.49955402368339e-02 , -3.15702448585199e-02 ), ( 1.31906996331723e-02 , -4.16155160943026e-02 , 1.45046337050662e-03 ), ( 5.47380948155791e-04 , 1.55122543651116e-03 , -1.40928369624718e-02 ), ( 4.79435149741411e-04 , 3.12912676270521e-03 , -1.99871975294202e-02 ), ( -6.50729574857995e-03 , 2.04140395217321e-02 , -2.15099640596014e-04 ), ( -2.05769479255007e-02 , 5.77012793802570e-02 , 2.88966554445180e-02 ), ( -1.90202892635905e-02 , 6.32108127600351e-02 , -1.59219288397588e-02 ), ( -2.27329271959792e-02 , 7.51477831841043e-02 , -1.72969138581540e-02 ), ( -1.70051329242468e-02 , 7.24073007431202e-02 , -8.28531707934525e-02 ), ( -2.01386533689387e-02 , 8.65808706267130e-02 , -1.01708791742204e-01 ), ( -8.69931533541390e-03 , 4.64720375584738e-02 , -8.31006752311498e-02 ), ( -1.87081206453085e-02 , 6.66773226446364e-02 , -3.51058027924910e-02 ), ( -2.46003337460445e-02 , 9.28970579261591e-02 , -6.86965453344270e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 17, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4373,10 +6398,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 18, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 18, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 18, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 18, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 18, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 18, atoms_positions[size = 51] = { ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 ), ( 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 ), ( 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 ), ( 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 ), ( 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 ), ( 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 ), ( -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 ), ( -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 ), ( -3.71520050105914e+00 , 3.82616194620359e-02 , 5.43787192954506e+00 ), ( -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ), ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 ), ( 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 ), ( 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 ), ( 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 ), ( 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 ), ( 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 ), ( 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 ), ( 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 ), ( 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 ), ( 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 ), ( 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 ), ( 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 ), ( 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 ), ( 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 ), ( 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 ), ( 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 ), ( 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 ), ( 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 ), ( 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 ), ( -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 ), ( 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 ), ( 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 ), ( -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 ), ( -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 ), ( -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 ), ( -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 ), ( -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 ), ( -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 ), ( -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 ), ( -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 ), ( -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 ), ( -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 ), ( -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 ), ( -2.38669067542351e+00 , -3.14191400105748e-01 , 6.17411576908559e+00 ), ( -4.46409638252639e+00 , 9.98162053848096e-01 , 6.44369645585639e+00 ), ( -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 ), ( -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 ), ( -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 ), ( -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 ), ( -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 ), ( -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ) } +colvars: Step 18, atoms_positions[size = 51] = { ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 ), ( 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 ), ( 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 ), ( 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 ), ( 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 ), ( 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 ), ( -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 ), ( -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 ), ( -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 ), ( -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ), ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 ), ( 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 ), ( 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 ), ( 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 ), ( 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 ), ( 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 ), ( 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 ), ( 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 ), ( 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 ), ( 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 ), ( 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 ), ( 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 ), ( 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 ), ( 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 ), ( 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 ), ( 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 ), ( 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 ), ( 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 ), ( 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 ), ( -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 ), ( 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 ), ( 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 ), ( -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 ), ( -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 ), ( -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 ), ( -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 ), ( -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 ), ( -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 ), ( -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 ), ( -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 ), ( -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 ), ( -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 ), ( -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 ), ( -2.38669067542350e+00 , -3.14191400105746e-01 , 6.17411576908559e+00 ), ( -4.46409638252639e+00 , 9.98162053848095e-01 , 6.44369645585639e+00 ), ( -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 ), ( -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 ), ( -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 ), ( -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 ), ( -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 ), ( -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ) } colvars: Step 18, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 18, atom_groups_ids[size = 0] = @@ -4394,16 +6419,87 @@ colvars: Collective variables module, step no. 18 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 , 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 , 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 , 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 , 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 , 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 , 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 , 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 , 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 , 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 , 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 , 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 , 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 , 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 , 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 , -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 , 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 , -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 , -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 , -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 , -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 , -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 , -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 , -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 , -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 , -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -2.38669067542350e+00 , -3.14191400105746e-01 , 6.17411576908559e+00 , -4.46409638252639e+00 , 9.98162053848095e-01 , 6.44369645585639e+00 , -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 , -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 , -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 , -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 , -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 , -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 , 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 , 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 , 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 , 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 , 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 , 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 , 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 , 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 , 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 , 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 , 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 , 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 , 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 , 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 , -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 , 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 , -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 , -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 , -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 , -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 , -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 , -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 , -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 , -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 , -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -2.38669067542350e+00 , -3.14191400105746e-01 , 6.17411576908559e+00 , -4.46409638252639e+00 , 9.98162053848095e-01 , 6.44369645585639e+00 , -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 , -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 , -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 , -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 , -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 , -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4416,6 +6512,10 @@ colvars: Adding total bias energy: 11.4881 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4431,8 +6531,6 @@ colvars: ( 0.00810137 , -0.106136 , 0.31525 ) colvars: ( -0.0496803 , 0.0834693 , 0.214138 ) colvars: ( 0.0808983 , -0.234142 , 0.0230362 ) colvars: ( 0.137578 , -0.475702 , 0.33253 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246774 , -0.0993925 , 0.095837 ) colvars: ( 0.0200619 , -0.0819545 , 0.0829092 ) @@ -4485,14 +6583,17 @@ colvars: ( -0.00870571 , 0.0464422 , -0.0831679 ) colvars: ( -0.0187076 , 0.0667001 , -0.0351397 ) colvars: ( -0.022497 , 0.0839954 , -0.0586742 ) colvars: ( -0.0246095 , 0.0929421 , -0.0687797 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 18. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 18. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 18, atoms_new_colvar_forces = { ( -7.15143246749638e-02 , 3.03607143562019e-01 , -3.99266458606129e-01 ), ( 1.27511738446594e-02 , 3.00967629854831e-02 , -2.38127471469929e-01 ), ( -4.18863071949037e-02 , 9.32301455194097e-02 , 8.81628918987510e-02 ), ( -9.70895404804677e-02 , 2.49908041041692e-01 , 6.59713718888419e-02 ), ( -1.88725880515165e-02 , 9.92228346931220e-02 , -1.71872787066905e-01 ), ( 7.09670536741436e-02 , -1.85486495457679e-01 , -3.87969474637418e-02 ), ( 1.03600953886065e-02 , -9.93144409185911e-02 , 2.54966692370490e-01 ), ( -4.10379422641936e-02 , 6.15825267191375e-02 , 1.91648394424666e-01 ), ( 6.61910179362997e-02 , -1.89870815465685e-01 , 3.08332055522194e-02 ), ( 1.15081183601858e-01 , -3.91707048313628e-01 , 2.73856265793050e-01 ), ( 2.46774375424239e-02 , -9.93924532683559e-02 , 9.58370334057540e-02 ), ( 2.66500535243150e-02 , -9.72209778665420e-02 , 5.96137627610270e-02 ), ( 1.24681376732403e-02 , -5.57608422003375e-02 , 7.24674929744035e-02 ), ( 1.26076824836146e-02 , -5.36224387337502e-02 , 6.12952593688761e-02 ), ( 5.62539094638128e-03 , -3.50561345523898e-02 , 7.56316999753237e-02 ), ( -8.60606560277206e-03 , 9.53712138345240e-03 , 7.55675193204442e-02 ), ( -2.08543446117501e-03 , -2.78615340021712e-03 , 4.04226285887231e-02 ), ( -5.77487538308468e-03 , 9.76017420918320e-03 , 3.61300350716817e-02 ), ( 2.70138528408105e-03 , -1.30014125518310e-02 , 1.96922867703026e-02 ), ( 8.97908516827588e-03 , -2.19969142018477e-02 , -2.65871231424575e-02 ), ( 8.68487447282498e-03 , -2.37680120333839e-02 , -1.49066296522007e-02 ), ( 6.55363705774327e-03 , -1.35293937357806e-02 , -3.03613858553427e-02 ), ( 1.50526198911460e-02 , -4.66653732768597e-02 , -2.10512603376900e-03 ), ( 2.77299143813737e-02 , -8.85219509446862e-02 , 7.20549150444689e-03 ), ( 1.43478752729337e-02 , -4.69610108498508e-02 , 8.75330557484605e-03 ), ( 1.42932681641806e-02 , -4.41264084608804e-02 , -2.80083205314169e-03 ), ( 9.38971606170557e-03 , -3.71491334276232e-02 , 3.35616067674381e-02 ), ( -7.12546262469615e-04 , -1.54013014397138e-02 , 7.64908271177000e-02 ), ( -3.72927860592955e-03 , 4.08981429157061e-03 , 3.29319617386191e-02 ), ( -5.79295740178263e-03 , 1.11354132169146e-02 , 3.04101252621499e-02 ), ( -7.30076957302218e-03 , 1.79113599273376e-02 , 2.15049483746605e-02 ), ( -1.63859058028266e-02 , 5.21459645145339e-02 , -3.55241297422584e-03 ), ( -9.83317150417715e-03 , 3.57919846305960e-02 , -2.16488481834581e-02 ), ( -1.38825585085550e-02 , 5.00342849475707e-02 , -2.84074398206996e-02 ), ( -2.06827442900071e-03 , 1.48642117794079e-02 , -3.63755080607341e-02 ), ( 1.04902107573028e-02 , -1.59566230977413e-02 , -7.33221264395743e-02 ), ( 4.31488123513660e-03 , -9.60525185674116e-04 , -5.44635132252315e-02 ), ( 3.27250278479952e-03 , 5.85914181832615e-03 , -6.98826067047735e-02 ), ( 7.12741052770944e-03 , -1.50453533016599e-02 , -3.15817248280361e-02 ), ( 1.31993193745071e-02 , -4.16884063363824e-02 , 1.48789399052293e-03 ), ( 5.54304324758436e-04 , 1.50953505055301e-03 , -1.40799929296691e-02 ), ( 4.87659795907501e-04 , 3.07695750800323e-03 , -1.99737071226953e-02 ), ( -6.49910304176036e-03 , 2.04035182113293e-02 , -1.98666442130940e-04 ), ( -2.05638510973712e-02 , 5.77453732012774e-02 , 2.89275614275456e-02 ), ( -1.90138229562706e-02 , 6.32310314419597e-02 , -1.59301210133700e-02 ), ( -2.27246458259210e-02 , 7.51715617639337e-02 , -1.73043097713146e-02 ), ( -1.70122524685426e-02 , 7.24067493443881e-02 , -8.29303072212397e-02 ), ( -2.01489048049457e-02 , 8.65835663076626e-02 , -1.01806981860336e-01 ), ( -8.70570647921074e-03 , 4.64421864114534e-02 , -8.31679002836408e-02 ), ( -1.87075793223643e-02 , 6.67000943942084e-02 , -3.51396666630672e-02 ), ( -2.46094849727014e-02 , 9.29421201465667e-02 , -6.87796670346709e-02 ) } +colvars: Step 18, atoms_new_colvar_forces = { ( -7.15143246749638e-02 , 3.03607143562019e-01 , -3.99266458606129e-01 ), ( 1.27511738446594e-02 , 3.00967629854831e-02 , -2.38127471469929e-01 ), ( -4.18863071949037e-02 , 9.32301455194097e-02 , 8.81628918987510e-02 ), ( -9.70895404804677e-02 , 2.49908041041692e-01 , 6.59713718888419e-02 ), ( -1.88725880515165e-02 , 9.92228346931219e-02 , -1.71872787066905e-01 ), ( 7.09670536741436e-02 , -1.85486495457679e-01 , -3.87969474637418e-02 ), ( 1.03600953886065e-02 , -9.93144409185911e-02 , 2.54966692370490e-01 ), ( -4.10379422641935e-02 , 6.15825267191375e-02 , 1.91648394424666e-01 ), ( 6.61910179362998e-02 , -1.89870815465685e-01 , 3.08332055522194e-02 ), ( 1.15081183601858e-01 , -3.91707048313628e-01 , 2.73856265793050e-01 ), ( 2.46774375424239e-02 , -9.93924532683559e-02 , 9.58370334057540e-02 ), ( 2.66500535243150e-02 , -9.72209778665420e-02 , 5.96137627610270e-02 ), ( 1.24681376732403e-02 , -5.57608422003375e-02 , 7.24674929744034e-02 ), ( 1.26076824836146e-02 , -5.36224387337503e-02 , 6.12952593688761e-02 ), ( 5.62539094638127e-03 , -3.50561345523897e-02 , 7.56316999753237e-02 ), ( -8.60606560277205e-03 , 9.53712138345241e-03 , 7.55675193204442e-02 ), ( -2.08543446117501e-03 , -2.78615340021712e-03 , 4.04226285887230e-02 ), ( -5.77487538308468e-03 , 9.76017420918321e-03 , 3.61300350716817e-02 ), ( 2.70138528408105e-03 , -1.30014125518309e-02 , 1.96922867703026e-02 ), ( 8.97908516827587e-03 , -2.19969142018477e-02 , -2.65871231424575e-02 ), ( 8.68487447282497e-03 , -2.37680120333839e-02 , -1.49066296522007e-02 ), ( 6.55363705774326e-03 , -1.35293937357806e-02 , -3.03613858553427e-02 ), ( 1.50526198911460e-02 , -4.66653732768597e-02 , -2.10512603376900e-03 ), ( 2.77299143813737e-02 , -8.85219509446862e-02 , 7.20549150444689e-03 ), ( 1.43478752729337e-02 , -4.69610108498508e-02 , 8.75330557484605e-03 ), ( 1.42932681641806e-02 , -4.41264084608804e-02 , -2.80083205314169e-03 ), ( 9.38971606170556e-03 , -3.71491334276232e-02 , 3.35616067674381e-02 ), ( -7.12546262469610e-04 , -1.54013014397138e-02 , 7.64908271177000e-02 ), ( -3.72927860592954e-03 , 4.08981429157061e-03 , 3.29319617386191e-02 ), ( -5.79295740178263e-03 , 1.11354132169146e-02 , 3.04101252621499e-02 ), ( -7.30076957302218e-03 , 1.79113599273376e-02 , 2.15049483746605e-02 ), ( -1.63859058028266e-02 , 5.21459645145339e-02 , -3.55241297422586e-03 ), ( -9.83317150417714e-03 , 3.57919846305960e-02 , -2.16488481834581e-02 ), ( -1.38825585085550e-02 , 5.00342849475707e-02 , -2.84074398206996e-02 ), ( -2.06827442900072e-03 , 1.48642117794079e-02 , -3.63755080607341e-02 ), ( 1.04902107573028e-02 , -1.59566230977413e-02 , -7.33221264395743e-02 ), ( 4.31488123513660e-03 , -9.60525185674127e-04 , -5.44635132252315e-02 ), ( 3.27250278479951e-03 , 5.85914181832614e-03 , -6.98826067047734e-02 ), ( 7.12741052770944e-03 , -1.50453533016600e-02 , -3.15817248280361e-02 ), ( 1.31993193745071e-02 , -4.16884063363824e-02 , 1.48789399052296e-03 ), ( 5.54304324758442e-04 , 1.50953505055299e-03 , -1.40799929296691e-02 ), ( 4.87659795907501e-04 , 3.07695750800322e-03 , -1.99737071226952e-02 ), ( -6.49910304176036e-03 , 2.04035182113293e-02 , -1.98666442130922e-04 ), ( -2.05638510973712e-02 , 5.77453732012774e-02 , 2.89275614275457e-02 ), ( -1.90138229562706e-02 , 6.32310314419597e-02 , -1.59301210133700e-02 ), ( -2.27246458259210e-02 , 7.51715617639337e-02 , -1.73043097713145e-02 ), ( -1.70122524685426e-02 , 7.24067493443881e-02 , -8.29303072212396e-02 ), ( -2.01489048049457e-02 , 8.65835663076626e-02 , -1.01806981860336e-01 ), ( -8.70570647921074e-03 , 4.64421864114534e-02 , -8.31679002836407e-02 ), ( -1.87075793223643e-02 , 6.67000943942084e-02 , -3.51396666630672e-02 ), ( -2.46094849727014e-02 , 9.29421201465667e-02 , -6.87796670346709e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 18, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4530,10 +6631,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 19, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 19, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 19, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 19, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 19, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 19, atoms_positions[size = 51] = { ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 ), ( 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 ), ( 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 ), ( 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 ), ( 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 ), ( 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 ), ( -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 ), ( -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 ), ( -3.70748943344948e+00 , 4.16903006825168e-02 , 5.43600413888779e+00 ), ( -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ), ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 ), ( 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 ), ( 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 ), ( 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 ), ( 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 ), ( 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 ), ( 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 ), ( 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 ), ( 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 ), ( 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 ), ( 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 ), ( 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 ), ( 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 ), ( 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 ), ( 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 ), ( 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 ), ( 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 ), ( 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 ), ( 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 ), ( -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 ), ( 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 ), ( 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 ), ( -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 ), ( -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 ), ( -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 ), ( -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 ), ( -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 ), ( -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 ), ( -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 ), ( -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 ), ( -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 ), ( -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 ), ( -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 ), ( -2.38818462389786e+00 , -3.15034590810127e-01 , 6.17323190730087e+00 ), ( -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 ), ( -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 ), ( -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 ), ( -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 ), ( -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 ), ( -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 ), ( -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ) } +colvars: Step 19, atoms_positions[size = 51] = { ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 ), ( 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 ), ( 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 ), ( 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 ), ( 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 ), ( 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 ), ( -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 ), ( -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 ), ( -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 ), ( -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ), ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 ), ( 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 ), ( 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 ), ( 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 ), ( 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 ), ( 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 ), ( 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 ), ( 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 ), ( 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 ), ( 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 ), ( 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 ), ( 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 ), ( 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 ), ( 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 ), ( 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 ), ( 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 ), ( 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 ), ( 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 ), ( 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 ), ( -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 ), ( 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 ), ( 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 ), ( -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 ), ( -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 ), ( -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 ), ( -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 ), ( -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 ), ( -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 ), ( -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 ), ( -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 ), ( -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 ), ( -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 ), ( -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 ), ( -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 ), ( -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 ), ( -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 ), ( -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 ), ( -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 ), ( -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 ), ( -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 ), ( -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ) } colvars: Step 19, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 19, atom_groups_ids[size = 0] = @@ -4552,15 +6653,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687067e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687068e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 , 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 , 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 , 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 , 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 , 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 , 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 , 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 , 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 , 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 , 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 , 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 , 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 , 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 , 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 , -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 , 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 , -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 , -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 , -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 , -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 , -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 , -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 , -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 , -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 , -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 , -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 , -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 , -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 , -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 , -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 , -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 , -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687067e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). +colvars: Colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687068e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 , 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 , 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 , 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 , 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 , 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 , 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 , 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 , 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 , 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 , 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 , 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 , 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 , 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 , 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 , -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 , 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 , -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 , -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 , -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 , -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 , -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 , -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 , -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 , -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 , -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 , -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 , -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 , -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 , -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 , -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 , -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 , -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4573,6 +6745,10 @@ colvars: Adding total bias energy: 11.4937 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4588,8 +6764,6 @@ colvars: ( 0.0080256 , -0.105981 , 0.315591 ) colvars: ( -0.0496875 , 0.0836534 , 0.214167 ) colvars: ( 0.0809202 , -0.234458 , 0.0231773 ) colvars: ( 0.1375 , -0.475966 , 0.33316 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246813 , -0.0994258 , 0.0959358 ) colvars: ( 0.0200629 , -0.0819689 , 0.0829822 ) @@ -4642,14 +6816,17 @@ colvars: ( -0.00870791 , 0.0464183 , -0.0832269 ) colvars: ( -0.0187037 , 0.0667269 , -0.0351689 ) colvars: ( -0.0224956 , 0.0840283 , -0.0587307 ) colvars: ( -0.0246115 , 0.0929889 , -0.0688587 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 19. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 19. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 19, atoms_new_colvar_forces = { ( -7.14077590702325e-02 , 3.03639970618158e-01 , -3.99862623514067e-01 ), ( 1.27881311797386e-02 , 3.00156744122845e-02 , -2.38301254790407e-01 ), ( -4.19519028873145e-02 , 9.35290707918833e-02 , 8.81926041657879e-02 ), ( -9.71004375206781e-02 , 2.50250971830372e-01 , 6.57776690911295e-02 ), ( -1.87998622166412e-02 , 9.91374485926363e-02 , -1.72118839430279e-01 ), ( 7.09626200046807e-02 , -1.85703030420809e-01 , -3.86453310144055e-02 ), ( 1.02768410340877e-02 , -9.91850800704239e-02 , 2.55253853212102e-01 ), ( -4.10433812807933e-02 , 6.17087230475973e-02 , 1.91690812071477e-01 ), ( 6.62233150611980e-02 , -1.90167721803567e-01 , 3.09983544618496e-02 ), ( 1.15003966443554e-01 , -3.91937648056864e-01 , 2.74429662774009e-01 ), ( 2.46812974419315e-02 , -9.94258146412512e-02 , 9.59357593321758e-02 ), ( 2.66459609072608e-02 , -9.72575765949008e-02 , 5.96657296750887e-02 ), ( 1.24695131914519e-02 , -5.57562195730972e-02 , 7.25248107254090e-02 ), ( 1.26092198409545e-02 , -5.36278872660035e-02 , 6.13488949830409e-02 ), ( 5.62681147971932e-03 , -3.50232748733177e-02 , 7.56788968781099e-02 ), ( -8.60415005884939e-03 , 9.62176625969064e-03 , 7.55926821951814e-02 ), ( -2.08655279010191e-03 , -2.74151909885105e-03 , 4.04309135482712e-02 ), ( -5.77449105629113e-03 , 9.80913615447255e-03 , 3.61368984787320e-02 ), ( 2.69566274999494e-03 , -1.29722622520675e-02 , 1.96797958058926e-02 ), ( 8.96497685882790e-03 , -2.19934906690526e-02 , -2.66451373083052e-02 ), ( 8.67631064794137e-03 , -2.37772038243613e-02 , -1.49358354286275e-02 ), ( 6.54449571419079e-03 , -1.35403908603913e-02 , -3.04031721925375e-02 ), ( 1.50454384630021e-02 , -4.66942483082077e-02 , -2.11209871448282e-03 ), ( 2.77241036133913e-02 , -8.85971246913936e-02 , 7.22997775690739e-03 ), ( 1.43461138727377e-02 , -4.70010830247044e-02 , 8.77355335079919e-03 ), ( 1.42916168907112e-02 , -4.41759052969429e-02 , -2.78498300656853e-03 ), ( 9.39169571445058e-03 , -3.71662534556160e-02 , 3.36002219154809e-02 ), ( -7.02702203154147e-04 , -1.53787093342839e-02 , 7.65647743355095e-02 ), ( -3.72362969097915e-03 , 4.10664783797948e-03 , 3.29642053334804e-02 ), ( -5.78554254176952e-03 , 1.11507318324770e-02 , 3.04456069939037e-02 ), ( -7.29784765745149e-03 , 1.79439584046955e-02 , 2.15143492971677e-02 ), ( -1.63872029943874e-02 , 5.22105740129331e-02 , -3.58746379327103e-03 ), ( -9.83436728933798e-03 , 3.58169908716224e-02 , -2.16798178840036e-02 ), ( -1.38826941479590e-02 , 5.00648597055764e-02 , -2.84434181671928e-02 ), ( -2.07303470268060e-03 , 1.48629103736301e-02 , -3.64151138487412e-02 ), ( 1.04786554117137e-02 , -1.60066238108003e-02 , -7.33856896007905e-02 ), ( 4.31023778396208e-03 , -1.00084497686633e-03 , -5.44992546381540e-02 ), ( 3.26728614384986e-03 , 5.81290388986927e-03 , -6.99290438725339e-02 ), ( 7.12599788830755e-03 , -1.50915587910003e-02 , -3.15889400834817e-02 ), ( 1.32036800757807e-02 , -4.17552991830073e-02 , 1.53018914256155e-03 ), ( 5.59622310848577e-04 , 1.47419140054324e-03 , -1.40614251650752e-02 ), ( 4.94051785359338e-04 , 3.03273025975034e-03 , -1.99529580396408e-02 ), ( -6.49191624788353e-03 , 2.03981522284860e-02 , -1.78085695653553e-04 ), ( -2.05511764922100e-02 , 5.77936243785591e-02 , 2.89605276578092e-02 ), ( -1.90057197022633e-02 , 6.32567607724533e-02 , -1.59332941394231e-02 ), ( -2.27145709982415e-02 , 7.52020714968192e-02 , -1.73056614158674e-02 ), ( -1.70136933099124e-02 , 7.24112968951756e-02 , -8.29999768120056e-02 ), ( -2.01519254267428e-02 , 8.65915569665777e-02 , -1.01896782591472e-01 ), ( -8.70791333279080e-03 , 4.64182692798261e-02 , -8.32269283153985e-02 ), ( -1.87036946668894e-02 , 6.67269139196540e-02 , -3.51688999413350e-02 ), ( -2.46114542240917e-02 , 9.29888646440582e-02 , -6.88587137781561e-02 ) } +colvars: Step 19, atoms_new_colvar_forces = { ( -7.14077590702326e-02 , 3.03639970618158e-01 , -3.99862623514067e-01 ), ( 1.27881311797386e-02 , 3.00156744122846e-02 , -2.38301254790407e-01 ), ( -4.19519028873146e-02 , 9.35290707918833e-02 , 8.81926041657877e-02 ), ( -9.71004375206781e-02 , 2.50250971830372e-01 , 6.57776690911294e-02 ), ( -1.87998622166412e-02 , 9.91374485926363e-02 , -1.72118839430279e-01 ), ( 7.09626200046807e-02 , -1.85703030420808e-01 , -3.86453310144054e-02 ), ( 1.02768410340876e-02 , -9.91850800704239e-02 , 2.55253853212102e-01 ), ( -4.10433812807934e-02 , 6.17087230475970e-02 , 1.91690812071477e-01 ), ( 6.62233150611981e-02 , -1.90167721803567e-01 , 3.09983544618496e-02 ), ( 1.15003966443554e-01 , -3.91937648056864e-01 , 2.74429662774009e-01 ), ( 2.46812974419315e-02 , -9.94258146412512e-02 , 9.59357593321758e-02 ), ( 2.66459609072608e-02 , -9.72575765949007e-02 , 5.96657296750887e-02 ), ( 1.24695131914519e-02 , -5.57562195730971e-02 , 7.25248107254090e-02 ), ( 1.26092198409545e-02 , -5.36278872660035e-02 , 6.13488949830409e-02 ), ( 5.62681147971932e-03 , -3.50232748733177e-02 , 7.56788968781099e-02 ), ( -8.60415005884939e-03 , 9.62176625969063e-03 , 7.55926821951814e-02 ), ( -2.08655279010192e-03 , -2.74151909885105e-03 , 4.04309135482712e-02 ), ( -5.77449105629113e-03 , 9.80913615447252e-03 , 3.61368984787320e-02 ), ( 2.69566274999494e-03 , -1.29722622520676e-02 , 1.96797958058926e-02 ), ( 8.96497685882790e-03 , -2.19934906690525e-02 , -2.66451373083052e-02 ), ( 8.67631064794138e-03 , -2.37772038243613e-02 , -1.49358354286275e-02 ), ( 6.54449571419080e-03 , -1.35403908603913e-02 , -3.04031721925374e-02 ), ( 1.50454384630021e-02 , -4.66942483082076e-02 , -2.11209871448278e-03 ), ( 2.77241036133913e-02 , -8.85971246913935e-02 , 7.22997775690740e-03 ), ( 1.43461138727377e-02 , -4.70010830247043e-02 , 8.77355335079920e-03 ), ( 1.42916168907113e-02 , -4.41759052969429e-02 , -2.78498300656853e-03 ), ( 9.39169571445058e-03 , -3.71662534556159e-02 , 3.36002219154809e-02 ), ( -7.02702203154160e-04 , -1.53787093342839e-02 , 7.65647743355094e-02 ), ( -3.72362969097916e-03 , 4.10664783797948e-03 , 3.29642053334803e-02 ), ( -5.78554254176953e-03 , 1.11507318324770e-02 , 3.04456069939036e-02 ), ( -7.29784765745150e-03 , 1.79439584046955e-02 , 2.15143492971677e-02 ), ( -1.63872029943874e-02 , 5.22105740129330e-02 , -3.58746379327102e-03 ), ( -9.83436728933798e-03 , 3.58169908716224e-02 , -2.16798178840036e-02 ), ( -1.38826941479590e-02 , 5.00648597055764e-02 , -2.84434181671928e-02 ), ( -2.07303470268060e-03 , 1.48629103736301e-02 , -3.64151138487412e-02 ), ( 1.04786554117137e-02 , -1.60066238108003e-02 , -7.33856896007904e-02 ), ( 4.31023778396208e-03 , -1.00084497686633e-03 , -5.44992546381539e-02 ), ( 3.26728614384987e-03 , 5.81290388986927e-03 , -6.99290438725339e-02 ), ( 7.12599788830756e-03 , -1.50915587910003e-02 , -3.15889400834817e-02 ), ( 1.32036800757807e-02 , -4.17552991830072e-02 , 1.53018914256153e-03 ), ( 5.59622310848572e-04 , 1.47419140054326e-03 , -1.40614251650752e-02 ), ( 4.94051785359337e-04 , 3.03273025975037e-03 , -1.99529580396408e-02 ), ( -6.49191624788353e-03 , 2.03981522284860e-02 , -1.78085695653598e-04 ), ( -2.05511764922100e-02 , 5.77936243785590e-02 , 2.89605276578091e-02 ), ( -1.90057197022633e-02 , 6.32567607724533e-02 , -1.59332941394232e-02 ), ( -2.27145709982415e-02 , 7.52020714968191e-02 , -1.73056614158674e-02 ), ( -1.70136933099124e-02 , 7.24112968951755e-02 , -8.29999768120055e-02 ), ( -2.01519254267428e-02 , 8.65915569665776e-02 , -1.01896782591472e-01 ), ( -8.70791333279080e-03 , 4.64182692798261e-02 , -8.32269283153985e-02 ), ( -1.87036946668894e-02 , 6.67269139196539e-02 , -3.51688999413350e-02 ), ( -2.46114542240917e-02 , 9.29888646440581e-02 , -6.88587137781561e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 19, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4687,10 +6864,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 20, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 20, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 20, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 20, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 20, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643353998e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780256e+00 , -3.16614240925533e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } +colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_ids[size = 0] = @@ -4709,15 +6886,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). +colvars: Calculating colvar components. colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4730,6 +6978,10 @@ colvars: Adding total bias energy: 11.4987 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4745,8 +6997,6 @@ colvars: ( 0.0079403 , -0.105844 , 0.315844 ) colvars: ( -0.0496811 , 0.0837394 , 0.214219 ) colvars: ( 0.0809344 , -0.234762 , 0.0233814 ) colvars: ( 0.137389 , -0.476175 , 0.333721 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246764 , -0.0994603 , 0.0960262 ) colvars: ( 0.0200575 , -0.081987 , 0.0830467 ) @@ -4799,6 +7049,7 @@ colvars: ( -0.00870557 , 0.0464005 , -0.0832767 ) colvars: ( -0.0186966 , 0.0667567 , -0.0351936 ) colvars: ( -0.0224888 , 0.0840635 , -0.0587812 ) colvars: ( -0.024606 , 0.0930351 , -0.0689323 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 20. colvars: colvarmodule::write_traj_files() @@ -4809,8 +7060,10 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 20. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800976e-02 , 3.00052379356398e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500016e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827239e-02 , 1.91760996033175e-01 ), ( 6.62468727487264e-02 , -1.90448081926945e-01 , 3.12288455216891e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807518e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489682e-02 ), ( 1.24661136135099e-02 , -5.57559811144077e-02 , 7.25743621949595e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332648e-03 , -3.49973301865401e-02 , 7.57170861826678e-02 ), ( -8.60292310050451e-03 , 9.69554753037329e-03 , 7.56073713177290e-02 ), ( -2.08776469672693e-03 , -2.70415172113726e-03 , 4.04328246755312e-02 ), ( -5.77389521453808e-03 , 9.85182430390034e-03 , 3.61382862311481e-02 ), ( 2.69104804092522e-03 , -1.29509138532636e-02 , 1.96620498003799e-02 ), ( 8.95486758503643e-03 , -2.19984645975748e-02 , -2.67054922301013e-02 ), ( 8.66947656368631e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541540e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516852e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879235e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703576e-03 , -3.71828583991163e-02 , 3.36363523912982e-02 ), ( -6.98144545634527e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600069e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540628e-03 , 1.11679149109105e-02 , 3.04799282045032e-02 ), ( -7.29500058088394e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040445e-02 , -3.62466193947452e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308239e-02 ), ( -2.07475381329403e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505723e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288624e-03 , -1.03735135095862e-03 , -5.45293145217132e-02 ), ( 3.26495468493790e-03 , 5.77162454807394e-03 , -6.99680928834496e-02 ), ( 7.12436996401245e-03 , -1.51327555336419e-02 , -3.15916578475219e-02 ), ( 1.32036569636365e-02 , -4.18136663470712e-02 , 1.57606808925123e-03 ), ( 5.63178713376314e-04 , 1.44649438052724e-03 , -1.40381831264554e-02 ), ( 4.98434308056258e-04 , 2.99804808326457e-03 , -1.99261927958005e-02 ), ( -6.48604874882728e-03 , 2.03983070643249e-02 , -1.54655641113355e-04 ), ( -2.05396268108372e-02 , 5.78448103620468e-02 , 2.89933897342497e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654819e-03 , 4.64004872660570e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278477e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } +colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800977e-02 , 3.00052379356399e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500017e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827238e-02 , 1.91760996033175e-01 ), ( 6.62468727487265e-02 , -1.90448081926945e-01 , 3.12288455216890e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807517e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489683e-02 ), ( 1.24661136135099e-02 , -5.57559811144078e-02 , 7.25743621949596e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332647e-03 , -3.49973301865402e-02 , 7.57170861826678e-02 ), ( -8.60292310050453e-03 , 9.69554753037324e-03 , 7.56073713177290e-02 ), ( -2.08776469672694e-03 , -2.70415172113731e-03 , 4.04328246755312e-02 ), ( -5.77389521453809e-03 , 9.85182430390029e-03 , 3.61382862311481e-02 ), ( 2.69104804092523e-03 , -1.29509138532637e-02 , 1.96620498003800e-02 ), ( 8.95486758503647e-03 , -2.19984645975749e-02 , -2.67054922301013e-02 ), ( 8.66947656368633e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541543e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516849e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879236e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703577e-03 , -3.71828583991163e-02 , 3.36363523912981e-02 ), ( -6.98144545634549e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600071e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540629e-03 , 1.11679149109106e-02 , 3.04799282045032e-02 ), ( -7.29500058088395e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040444e-02 , -3.62466193947451e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308240e-02 ), ( -2.07475381329402e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505724e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288625e-03 , -1.03735135095860e-03 , -5.45293145217132e-02 ), ( 3.26495468493792e-03 , 5.77162454807398e-03 , -6.99680928834496e-02 ), ( 7.12436996401246e-03 , -1.51327555336419e-02 , -3.15916578475220e-02 ), ( 1.32036569636365e-02 , -4.18136663470711e-02 , 1.57606808925122e-03 ), ( 5.63178713376306e-04 , 1.44649438052730e-03 , -1.40381831264554e-02 ), ( 4.98434308056249e-04 , 2.99804808326463e-03 , -1.99261927958005e-02 ), ( -6.48604874882730e-03 , 2.03983070643250e-02 , -1.54655641113389e-04 ), ( -2.05396268108373e-02 , 5.78448103620468e-02 , 2.89933897342496e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654820e-03 , 4.64004872660571e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278478e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped index db11936b1..f60bc06ed 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped @@ -8,6 +8,16 @@ colvar { x ( 0.99975884202595 , 0.01402736950034 , 0.011979408737928 , -0.011915723314925 ) } +colvar { + name main + x ( 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 ) +} + +colvar { + name fitting + x ( 8.3109067593225 , 0.041832105536949 , -0.74720152184922 , 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 7.0501314089404 , -2.0502351229669 , -0.93466980629676 , 6.1724025468072 , -0.37440006998022 , 0.72796068970041 , 4.9728901219597 , -0.15984013302521 , 0.72686147800692 , 6.8514301642465 , -0.26741105895838 , 1.9083377792785 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 7.073607414672 , -0.35378704127878 , 4.3070951913435 , 5.2970773270167 , 1.0930675777403 , 3.3427298943302 , 4.1334323731907 , 1.0232724624507 , 3.6807757981069 , 5.8363306008465 , 2.2505141275817 , 2.9898069553745 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 6.3225154324575 , 4.5006943210992 , 2.3634882582325 , 3.8815799727105 , 3.7065612462023 , 2.0430944440883 , 2.7919894870931 , 4.1606818038692 , 2.4867320360913 , 3.9379247666863 , 3.2391551773311 , 0.73009137441107 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 3.0516504481894 , 2.7043614871659 , -1.5156733303712 , 1.5970874871384 , 2.1829728692071 , 0.44555677054977 , 0.37858437885899 , 2.5807264635357 , 0.51019557090508 , 2.04711677578 , 1.0703813637383 , 1.069206754706 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 2.0425329047304 , -1.1035104960071 , 2.0103674846849 , 0.56194901870408 , 0.61185187522511 , 2.9428132426689 , -0.60197676959252 , 0.34978459930961 , 3.1621649077962 , 1.3163590181237 , 1.3458687673819 , 3.7752112850979 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , 2.0804193492853 , 2.6881595598658 , 5.6815929959461 , -0.33660676483589 , 2.9148298650463 , 4.9681489667417 , -1.1362865907604 , 3.063001046068 , 5.8880007578731 , -0.51135551219128 , 3.535300553984 , 3.8464371088115 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -0.69985197514866 , 5.4140943569769 , 2.4638642323208 , -2.7601618038614 , 3.8895607334677 , 2.895793363421 , -3.8173497124104 , 4.5101036996167 , 2.8152773748772 , -2.6253924219612 , 2.6733261276654 , 2.4022619953018 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.3895014416165 , 0.8866696376631 , 0.87567133268272 , -4.322724391988 , 1.0702172791569 , 3.2141303643402 , -5.5001342374076 , 0.81893213505031 , 3.3310166100638 , -3.3688860558692 , 0.69174478744455 , 4.2057900990597 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -2.3895289778026 , -0.31661424092553 , 6.1717119733279 , -4.4607970213475 , 0.98729806770613 , 6.4413742570766 , -5.3579745601884 , 0.599067686148 , 7.2198955321113 , -6.2369282614895 , 3.6061273507614 , 6.7353796872239 , -6.9588258659327 , 4.2988412219219 , 7.4769553986534 , -6.7403993718841 , 3.1830257218785 , 5.5094675051539 , -4.1276723189508 , 2.2467034673003 , 6.4110909930055 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 , -4.0937877414092 , 4.5760013650879 , 7.2838298499369 ) +} + restraint { configuration { step 20 diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj index ca2c7beb2..bbd980fe3 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( -3.25898609205420e-01 , 1.69798809632672e+01 , 1.71828081280911e+01 , 1.81199165160869e+01 ) - 1 ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ) ( -3.21564188520062e-01 , 1.69819486822241e+01 , 1.71859144849276e+01 , 1.81247073526383e+01 ) - 2 ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ) ( -3.17383070027282e-01 , 1.69856435072818e+01 , 1.71892246235753e+01 , 1.81275786557577e+01 ) - 3 ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ) ( -3.13410121312395e-01 , 1.69909293641043e+01 , 1.71929002393502e+01 , 1.81282997059461e+01 ) - 4 ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ) ( -3.09649515116043e-01 , 1.69977772313853e+01 , 1.71971079225853e+01 , 1.81267357994661e+01 ) - 5 ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ) ( -3.06058986795120e-01 , 1.70061638839744e+01 , 1.72019887637082e+01 , 1.81228667161400e+01 ) - 6 ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ) ( -3.02559854946980e-01 , 1.70160600442246e+01 , 1.72076310908889e+01 , 1.81167997183534e+01 ) - 7 ( 9.99619179084481e-01 , 1.92861231851382e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ) ( -2.99050775133683e-01 , 1.70274127639097e+01 , 1.72140507063916e+01 , 1.81087735951856e+01 ) - 8 ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ) ( -2.95423022186405e-01 , 1.70401276827003e+01 , 1.72211809136720e+01 , 1.80991515946418e+01 ) - 9 ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ) ( -2.91575342533006e-01 , 1.70540561294731e+01 , 1.72288725006022e+01 , 1.80884027962568e+01 ) - 10 ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ) ( -2.87426720479198e-01 , 1.70689904989372e+01 , 1.72369024184678e+01 , 1.80770732028938e+01 ) - 11 ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ) ( -2.82925613878243e-01 , 1.70846693215076e+01 , 1.72449893116233e+01 , 1.80657495280640e+01 ) - 12 ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ) ( -2.78054513150077e-01 , 1.71007911361289e+01 , 1.72528140290677e+01 , 1.80550200826245e+01 ) - 13 ( 9.99711367452522e-01 , 1.66424815610562e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ) ( -2.72829776587463e-01 , 1.71170334040853e+01 , 1.72600431390157e+01 , 1.80454376062023e+01 ) - 14 ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ) ( -2.67298305818362e-01 , 1.71330704047432e+01 , 1.72663532826131e+01 , 1.80374879075006e+01 ) - 15 ( 9.99735732840256e-01 , 1.57202526155576e-02 , 1.18858573400358e-02 , -1.18348863683820e-02 ) ( -2.61533691909663e-01 , 1.71485840824799e+01 , 1.72714541741650e+01 , 1.80315661983211e+01 ) - 16 ( 9.99744979701586e-01 , 1.52939094147335e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ) ( -2.55633883245562e-01 , 1.71632652563580e+01 , 1.72751084768322e+01 , 1.80279610546862e+01 ) - 17 ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652891e-02 , -1.16317231514313e-02 ) ( -2.49720405143540e-01 , 1.71768080432236e+01 , 1.72771475989308e+01 , 1.80268447892810e+01 ) - 18 ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ) ( -2.43937108749464e-01 , 1.71889046690184e+01 , 1.72774832629947e+01 , 1.80282687528248e+01 ) - 19 ( 9.99758962093459e-01 , 1.42609660687067e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ) ( -2.38445587445625e-01 , 1.71992487761229e+01 , 1.72761151637582e+01 , 1.80321624270782e+01 ) - 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ) ( -2.33415112386271e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) +# step one fa_one main fitting + 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( -3.25898609205420e-01 , 1.69798809632672e+01 , 1.71828081280911e+01 , 1.81199165160869e+01 ) ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ) ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) + 1 ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ) ( -3.21564188520062e-01 , 1.69819486822241e+01 , 1.71859144849276e+01 , 1.81247073526383e+01 ) ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ) ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 , 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 , 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 , 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 , 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 , 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 , 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 , 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 , 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 , 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 , 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 , 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 , 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 , 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 , 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 , -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 , 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 , -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 , -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 , -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 , -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 , -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 , -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 , -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 , -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 , -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 , -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 , -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 , -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 , -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 , -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 , -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 , -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ) + 2 ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ) ( -3.17383070027282e-01 , 1.69856435072818e+01 , 1.71892246235753e+01 , 1.81275786557577e+01 ) ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ) ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 , 7.00115718441668e+00 , 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-3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 , -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 , -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 , -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 , -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 , -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 , -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 , -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 , -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 , -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 , -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ) + 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ) ( -2.33415112386265e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ) ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out index 39c528f4c..3a0585f3a 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out @@ -1274,9 +1274,647 @@ colvars: refPositionsFile rmsd_atoms_refpos.xyz colvars: } colvars: ". colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "main" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "RMSD_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "RMSD_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 30 individual components. +colvars: DEPS: disabling feature "scalar" in colvar main +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: feature "linear" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "single_component" +colvars: DEPS: feature "single_component" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar main +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar main +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar main +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar main enabling "output_value" +colvars: DEPS: feature "output_value" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar main +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar main +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar main +colvars: DEPS: colvar main enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar main testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar main testing "linear" +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "main". +colvars: Configuration string for "colvar": " +colvars: +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar fitting enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar fitting +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting +colvars: DEPS: colvar fitting enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar fitting testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar fitting testing "linear" +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "fitting". +colvars: Configuration string for "colvar": " +colvars: +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. colvars: Keyword "colvar" not found. colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. +colvars: Collective variables initialized, 3 in total. colvars: Initializing the collective variables biases. colvars: Looking for the keyword "abf" and its value. colvars: Keyword "abf" not found. @@ -1496,7 +2134,23 @@ colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: } colvars: refPositionsFile rmsd_atoms_refpos.xyz colvars: } -colvars: } +colvars: } +colvars: colvar { +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } colvars: harmonic { colvars: colvars one colvars: centers (0.9, 0.5, 0.5, 0.5) @@ -1518,6 +2172,7 @@ colvars: - Colvars-NAMD interface: colvars: - Harmonic colvar bias implementation: colvars: - Moving frame of reference: colvars: - Optimal rotation via flexible fitting: +colvars: - cartesian colvar component: colvars: - orientation colvar component: colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 colvars: @@ -1543,7 +2198,7 @@ colvars: Keyword value = "20". colvars: Looking for the keyword "step" and its value. colvars: Keyword "step" not found. colvars: Looking for the keyword "version" and its value. -colvars: Keyword value = "2024-06-04". +colvars: Keyword value = "2024-09-17". colvars: Looking for the keyword "version" and its value. colvars: Keyword "version" not found. colvars: Looking for the keyword "units" and its value. @@ -1558,6 +2213,39 @@ colvars: Looking for the keyword "x" and its value. colvars: Keyword "x" not found. colvars: Restarting collective variable "one" from value: ( 0.999759 , 0.0140274 , 0.0119794 , -0.0119157 ) colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "main": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "main" from value: ( 6.95697 , -0.549562 , -0.571673 , 6.15419 , -0.166072 , 3.18954 , 5.23832 , 3.57842 , 2.91984 , 2.66119 , 3.00667 , -0.104346 , 1.16849 , 0.116557 , 1.69698 , 0.843403 , 1.9786 , 5.02539 , -1.51786 , 4.53913 , 3.44518 , -3.77324 , 1.80375 , 2.00014 , -3.70041 , 0.046227 , 5.43591 , -4.80737 , 3.20639 , 7.24443 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting": this colvar is named "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 8.3109067593225 , 0.041832105536949 , -0.74720152184922 , 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 7.0501314089404 , -2.0502351229669 , -0.93466980629676 , 6.1724025468072 , -0.37440006998022 , 0.72796068970041 , 4.9728901219597 , -0.15984013302521 , 0.72686147800692 , 6.8514301642465 , -0.26741105895838 , 1.9083377792785 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 7.073607414672 , -0.35378704127878 , 4.3070951913435 , 5.2970773270167 , 1.0930675777403 , 3.3427298943302 , 4.1334323731907 , 1.0232724624507 , 3.6807757981069 , 5.8363306008465 , 2.2505141275817 , 2.9898069553745 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 6.3225154324575 , 4.5006943210992 , 2.3634882582325 , 3.8815799727105 , 3.7065612462023 , 2.0430944440883 , 2.7919894870931 , 4.1606818038692 , 2.4867320360913 , 3.9379247666863 , 3.2391551773311 , 0.73009137441107 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 3.0516504481894 , 2.7043614871659 , -1.5156733303712 , 1.5970874871384 , 2.1829728692071 , 0.44555677054977 , 0.37858437885899 , 2.5807264635357 , 0.51019557090508 , 2.04711677578 , 1.0703813637383 , 1.069206754706 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 2.0425329047304 , -1.1035104960071 , 2.0103674846849 , 0.56194901870408 , 0.61185187522511 , 2.9428132426689 , -0.60197676959252 , 0.34978459930961 , 3.1621649077962 , 1.3163590181237 , 1.3458687673819 , 3.7752112850979 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , 2.0804193492853 , 2.6881595598658 , 5.6815929959461 , -0.33660676483589 , 2.9148298650463 , 4.9681489667417 , -1.1362865907604 , 3.063001046068 , 5.8880007578731 , -0.51135551219128 , 3.535300553984 , 3.8464371088115 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -0.69985197514866 , 5.4140943569769 , 2.4638642323208 , -2.7601618038614 , 3.8895607334677 , 2.895793363421 , -3.8173497124104 , 4.5101036996167 , 2.8152773748772 , -2.6253924219612 , 2.6733261276654 , 2.4022619953018 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.3895014416165 , 0.8866696376631 , 0.87567133268272 , -4.322724391988 , 1.0702172791569 , 3.2141303643402 , -5.5001342374076 , 0.81893213505031 , 3.3310166100638 , -3.3688860558692 , 0.69174478744455 , 4.2057900990597 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -2.3895289778026 , -0.31661424092553 , 6.1717119733279 , -4.4607970213475 , 0.98729806770613 , 6.4413742570766 , -5.3579745601884 , 0.599067686148 , 7.2198955321113 , -6.2369282614895 , 3.6061273507614 , 6.7353796872239 , -6.9588258659327 , 4.2988412219219 , 7.4769553986534 , -6.7403993718841 , 3.1830257218785 , 5.5094675051539 , -4.1276723189508 , 2.2467034673003 , 6.4110909930055 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 , -4.0937877414092 , 4.5760013650879 , 7.2838298499369 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "fitting" from value: ( 8.31091 , 0.0418321 , -0.747202 , 6.95697 , -0.549562 , -0.571673 , 7.05013 , -2.05024 , -0.93467 , 6.1724 , -0.3744 , 0.727961 , 4.97289 , -0.15984 , 0.726861 , 6.85143 , -0.267411 , 1.90834 , 6.15419 , -0.166072 , 3.18954 , 7.07361 , -0.353787 , 4.3071 , 5.29708 , 1.09307 , 3.34273 , 4.13343 , 1.02327 , 3.68078 , 5.83633 , 2.25051 , 2.98981 , 5.23832 , 3.57842 , 2.91984 , 6.32252 , 4.50069 , 2.36349 , 3.88158 , 3.70656 , 2.04309 , 2.79199 , 4.16068 , 2.48673 , 3.93792 , 3.23916 , 0.730091 , 2.66119 , 3.00667 , -0.104346 , 3.05165 , 2.70436 , -1.51567 , 1.59709 , 2.18297 , 0.445557 , 0.378584 , 2.58073 , 0.510196 , 2.04712 , 1.07038 , 1.06921 , 1.16849 , 0.116557 , 1.69698 , 2.04253 , -1.10351 , 2.01037 , 0.561949 , 0.611852 , 2.94281 , -0.601977 , 0.349785 , 3.16216 , 1.31636 , 1.34587 , 3.77521 , 0.843403 , 1.9786 , 5.02539 , 2.08042 , 2.68816 , 5.68159 , -0.336607 , 2.91483 , 4.96815 , -1.13629 , 3.063 , 5.888 , -0.511356 , 3.5353 , 3.84644 , -1.51786 , 4.53913 , 3.44518 , -0.699852 , 5.41409 , 2.46386 , -2.76016 , 3.88956 , 2.89579 , -3.81735 , 4.5101 , 2.81528 , -2.62539 , 2.67333 , 2.40226 , -3.77324 , 1.80375 , 2.00014 , -3.3895 , 0.88667 , 0.875671 , -4.32272 , 1.07022 , 3.21413 , -5.50013 , 0.818932 , 3.33102 , -3.36889 , 0.691745 , 4.20579 , -3.70041 , 0.046227 , 5.43591 , -2.38953 , -0.316614 , 6.17171 , -4.4608 , 0.987298 , 6.44137 , -5.35797 , 0.599068 , 7.2199 , -6.23693 , 3.60613 , 6.73538 , -6.95883 , 4.29884 , 7.47696 , -6.7404 , 3.18303 , 5.50947 , -4.12767 , 2.2467 , 6.41109 , -4.80737 , 3.20639 , 7.24443 , -4.09379 , 4.576 , 7.28383 ) +colvars: Looking for the keyword "name" and its value. colvars: Keyword value = "harmonic1". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. @@ -1583,6 +2271,8 @@ colvars: updating target temperature (T = 0 K). colvars: Current simulation parameters: initial step = 20, integration timestep = 1 colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "main":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "fitting":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: ---------------------------------------------------------------------- colvars: colvarproxy_namd, step no. 20 @@ -1592,10 +2282,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 20, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 20, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 20, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 20, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 20, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643353998e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780256e+00 , -3.16614240925533e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } +colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_ids[size = 0] = @@ -1614,15 +2304,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ). +colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -1635,6 +2396,10 @@ colvars: Adding total bias energy: 11.4987 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -1650,8 +2415,6 @@ colvars: ( 0.0079403 , -0.105844 , 0.315844 ) colvars: ( -0.0496811 , 0.0837394 , 0.214219 ) colvars: ( 0.0809344 , -0.234762 , 0.0233814 ) colvars: ( 0.137389 , -0.476175 , 0.333721 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246764 , -0.0994603 , 0.0960262 ) colvars: ( 0.0200575 , -0.081987 , 0.0830467 ) @@ -1704,6 +2467,7 @@ colvars: ( -0.00870557 , 0.0464005 , -0.0832767 ) colvars: ( -0.0186966 , 0.0667567 , -0.0351936 ) colvars: ( -0.0224888 , 0.0840635 , -0.0587812 ) colvars: ( -0.024606 , 0.0930351 , -0.0689323 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 20. colvars: colvarmodule::write_traj_files() @@ -1711,8 +2475,10 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: colvarmodule::end_of_step(), step = 20. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800976e-02 , 3.00052379356398e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500016e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827239e-02 , 1.91760996033175e-01 ), ( 6.62468727487264e-02 , -1.90448081926945e-01 , 3.12288455216891e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807518e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489682e-02 ), ( 1.24661136135099e-02 , -5.57559811144077e-02 , 7.25743621949595e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332648e-03 , -3.49973301865401e-02 , 7.57170861826678e-02 ), ( -8.60292310050451e-03 , 9.69554753037329e-03 , 7.56073713177290e-02 ), ( -2.08776469672693e-03 , -2.70415172113726e-03 , 4.04328246755312e-02 ), ( -5.77389521453808e-03 , 9.85182430390034e-03 , 3.61382862311481e-02 ), ( 2.69104804092522e-03 , -1.29509138532636e-02 , 1.96620498003799e-02 ), ( 8.95486758503643e-03 , -2.19984645975748e-02 , -2.67054922301013e-02 ), ( 8.66947656368631e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541540e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516852e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879235e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703576e-03 , -3.71828583991163e-02 , 3.36363523912982e-02 ), ( -6.98144545634527e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600069e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540628e-03 , 1.11679149109105e-02 , 3.04799282045032e-02 ), ( -7.29500058088394e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040445e-02 , -3.62466193947452e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308239e-02 ), ( -2.07475381329403e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505723e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288624e-03 , -1.03735135095862e-03 , -5.45293145217132e-02 ), ( 3.26495468493790e-03 , 5.77162454807394e-03 , -6.99680928834496e-02 ), ( 7.12436996401245e-03 , -1.51327555336419e-02 , -3.15916578475219e-02 ), ( 1.32036569636365e-02 , -4.18136663470712e-02 , 1.57606808925123e-03 ), ( 5.63178713376314e-04 , 1.44649438052724e-03 , -1.40381831264554e-02 ), ( 4.98434308056258e-04 , 2.99804808326457e-03 , -1.99261927958005e-02 ), ( -6.48604874882728e-03 , 2.03983070643249e-02 , -1.54655641113355e-04 ), ( -2.05396268108372e-02 , 5.78448103620468e-02 , 2.89933897342497e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654819e-03 , 4.64004872660570e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278477e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } +colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800977e-02 , 3.00052379356399e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500017e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827238e-02 , 1.91760996033175e-01 ), ( 6.62468727487265e-02 , -1.90448081926945e-01 , 3.12288455216890e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807517e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489683e-02 ), ( 1.24661136135099e-02 , -5.57559811144078e-02 , 7.25743621949596e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332647e-03 , -3.49973301865402e-02 , 7.57170861826678e-02 ), ( -8.60292310050453e-03 , 9.69554753037324e-03 , 7.56073713177290e-02 ), ( -2.08776469672694e-03 , -2.70415172113731e-03 , 4.04328246755312e-02 ), ( -5.77389521453809e-03 , 9.85182430390029e-03 , 3.61382862311481e-02 ), ( 2.69104804092523e-03 , -1.29509138532637e-02 , 1.96620498003800e-02 ), ( 8.95486758503647e-03 , -2.19984645975749e-02 , -2.67054922301013e-02 ), ( 8.66947656368633e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541543e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516849e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879236e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703577e-03 , -3.71828583991163e-02 , 3.36363523912981e-02 ), ( -6.98144545634549e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600071e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540629e-03 , 1.11679149109106e-02 , 3.04799282045032e-02 ), ( -7.29500058088395e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040444e-02 , -3.62466193947451e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308240e-02 ), ( -2.07475381329402e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505724e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288625e-03 , -1.03735135095860e-03 , -5.45293145217132e-02 ), ( 3.26495468493792e-03 , 5.77162454807398e-03 , -6.99680928834496e-02 ), ( 7.12436996401246e-03 , -1.51327555336419e-02 , -3.15916578475220e-02 ), ( 1.32036569636365e-02 , -4.18136663470711e-02 , 1.57606808925122e-03 ), ( 5.63178713376306e-04 , 1.44649438052730e-03 , -1.40381831264554e-02 ), ( 4.98434308056249e-04 , 2.99804808326463e-03 , -1.99261927958005e-02 ), ( -6.48604874882730e-03 , 2.03983070643250e-02 , -1.54655641113389e-04 ), ( -2.05396268108373e-02 , 5.78448103620468e-02 , 2.89933897342496e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654820e-03 , 4.64004872660571e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278478e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -1750,10 +2516,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 21, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 21, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 21, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 21, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 21, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 21, atoms_positions[size = 51] = { ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 ), ( 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 ), ( 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 ), ( 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 ), ( 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 ), ( 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 ), ( -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 ), ( -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 ), ( -3.69409231538776e+00 , 5.15006269291782e-02 , 5.43762393708684e+00 ), ( -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ), ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 ), ( 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 ), ( 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 ), ( 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 ), ( 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 ), ( 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 ), ( 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 ), ( 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 ), ( 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 ), ( 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 ), ( 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 ), ( 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 ), ( 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 ), ( 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 ), ( 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 ), ( 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 ), ( 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 ), ( 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 ), ( 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 ), ( -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 ), ( 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 ), ( 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 ), ( -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 ), ( -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 ), ( -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 ), ( -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 ), ( -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 ), ( -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 ), ( -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 ), ( -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 ), ( -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 ), ( -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 ), ( -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 ), ( -2.39058560242180e+00 , -3.18609476113618e-01 , 6.16957497599152e+00 ), ( -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 ), ( -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 ), ( -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265566e+00 ), ( -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 ), ( -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 ), ( -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 ), ( -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ) } +colvars: Step 21, atoms_positions[size = 51] = { ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 ), ( 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 ), ( 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 ), ( 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 ), ( 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 ), ( 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 ), ( -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 ), ( -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 ), ( -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 ), ( -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ), ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 ), ( 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 ), ( 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 ), ( 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 ), ( 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 ), ( 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 ), ( 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 ), ( 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 ), ( 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 ), ( 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 ), ( 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 ), ( 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 ), ( 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 ), ( 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 ), ( 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 ), ( 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 ), ( 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 ), ( 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 ), ( 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 ), ( -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 ), ( 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 ), ( 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 ), ( -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 ), ( -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 ), ( -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 ), ( -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 ), ( -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 ), ( -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 ), ( -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 ), ( -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 ), ( -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 ), ( -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 ), ( -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 ), ( -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 ), ( -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 ), ( -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 ), ( -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 ), ( -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 ), ( -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 ), ( -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 ), ( -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ) } colvars: Step 21, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 21, atom_groups_ids[size = 0] = @@ -1771,16 +2537,87 @@ colvars: Collective variables module, step no. 21 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating colvar components. colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 , 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 , 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 , 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 , 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 , 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 , 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 , 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 , 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 , 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 , 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 , 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 , 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 , 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 , 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 , -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 , 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 , -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 , -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 , -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 , -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 , -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 , -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 , -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 , -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 , -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 , -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 , -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 , -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 , -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 , -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 , -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 , -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 , 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 , 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 , 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 , 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 , 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 , 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 , 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 , 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 , 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 , 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 , 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 , 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 , 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 , 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 , -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 , 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 , -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 , -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 , -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 , -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 , -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 , -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 , -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 , -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 , -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 , -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 , -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 , -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 , -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 , -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 , -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 , -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -1793,6 +2630,10 @@ colvars: Adding total bias energy: 11.5031 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -1808,8 +2649,6 @@ colvars: ( 0.00784608 , -0.105726 , 0.316006 ) colvars: ( -0.0496637 , 0.083727 , 0.214293 ) colvars: ( 0.0809419 , -0.235048 , 0.0236444 ) colvars: ( 0.137251 , -0.476324 , 0.334203 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246626 , -0.0994935 , 0.0961067 ) colvars: ( 0.0200455 , -0.0820075 , 0.083102 ) @@ -1862,14 +2701,17 @@ colvars: ( -0.00869839 , 0.0463889 , -0.0833164 ) colvars: ( -0.0186865 , 0.0667879 , -0.0352142 ) colvars: ( -0.0224765 , 0.0840991 , -0.0588253 ) colvars: ( -0.0245932 , 0.0930782 , -0.068999 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 21. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 21. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 21, atoms_new_colvar_forces = { ( -7.11399384318308e-02 , 3.03673714596804e-01 , -4.00770119886634e-01 ), ( 1.28450168410534e-02 , 3.00636017805382e-02 , -2.38645544534817e-01 ), ( -4.20822670353576e-02 , 9.41200209059076e-02 , 8.79377349508916e-02 ), ( -9.70668784584833e-02 , 2.50670455049784e-01 , 6.53550388999108e-02 ), ( -1.86302899611748e-02 , 9.89303159690965e-02 , -1.72358620278118e-01 ), ( 7.09108063101488e-02 , -1.85927916967423e-01 , -3.83730584164822e-02 ), ( 1.00940002734312e-02 , -9.89773108191159e-02 , 2.55576585814222e-01 ), ( -4.10215749964445e-02 , 6.16911466781240e-02 , 1.91856870875936e-01 ), ( 6.62622265583337e-02 , -1.90705006891368e-01 , 3.15184935556135e-02 ), ( 1.14774657066217e-01 , -3.92224428801080e-01 , 2.75377184594162e-01 ), ( 2.46625873851910e-02 , -9.94934972823231e-02 , 9.61066727823309e-02 ), ( 2.66219319601746e-02 , -9.73405519568489e-02 , 5.97487570195681e-02 ), ( 1.24577915943817e-02 , -5.57595264132078e-02 , 7.26154388026603e-02 ), ( 1.25983778171294e-02 , -5.36459257873875e-02 , 6.14369978247319e-02 ), ( 5.61903440744207e-03 , -3.49787311352311e-02 , 7.57458071852306e-02 ), ( -8.60288899774203e-03 , 9.75608155101247e-03 , 7.56115259176666e-02 ), ( -2.08923468684039e-03 , -2.67530457899125e-03 , 4.04287964932554e-02 ), ( -5.77333835969325e-03 , 9.88677812731997e-03 , 3.61343701273132e-02 ), ( 2.68767850620089e-03 , -1.29382633507289e-02 , 1.96404769055550e-02 ), ( 8.94944167110717e-03 , -2.20122654388583e-02 , -2.67648727689499e-02 ), ( 8.66483279553808e-03 , -2.38081467999426e-02 , -1.49959487368345e-02 ), ( 6.53495529803232e-03 , -1.35726331970709e-02 , -3.04835083292054e-02 ), ( 1.50303446132429e-02 , -4.67584847450611e-02 , -2.12920998279260e-03 ), ( 2.77018244289007e-02 , -8.87395931998711e-02 , 7.27779809261198e-03 ), ( 1.43352800222162e-02 , -4.70751609713203e-02 , 8.81293743885319e-03 ), ( 1.42817640632689e-02 , -4.42636422522604e-02 , -2.74952806030974e-03 ), ( 9.38522823558223e-03 , -3.71979422433983e-02 , 3.36691841968735e-02 ), ( -6.99503281119027e-04 , -1.53341150642310e-02 , 7.66932516135838e-02 ), ( -3.71897519690294e-03 , 4.14100412747780e-03 , 3.30209727953179e-02 ), ( -5.77794268053231e-03 , 1.11867179676655e-02 , 3.05114126724248e-02 ), ( -7.29252056176346e-03 , 1.80017851832736e-02 , 2.15255686424141e-02 ), ( -1.63781366214478e-02 , 5.23192063260294e-02 , -3.66306391685652e-03 ), ( -9.82784133106717e-03 , 3.58615231332486e-02 , -2.17375544901125e-02 ), ( -1.38723121061425e-02 , 5.01224906323065e-02 , -2.85083949342105e-02 ), ( -2.07316713877926e-03 , 1.48577122015172e-02 , -3.64859747436524e-02 ), ( 1.04678431390518e-02 , -1.61024070956970e-02 , -7.34936428665872e-02 ), ( 4.30768009091327e-03 , -1.06911031799013e-03 , -5.45527250787330e-02 ), ( 3.26600819838429e-03 , 5.73629579028582e-03 , -6.99986217017486e-02 ), ( 7.12281125111273e-03 , -1.51675396442752e-02 , -3.15898239456440e-02 ), ( 1.31993145017299e-02 , -4.18609641559936e-02 , 1.62390103359614e-03 ), ( 5.64876125100682e-04 , 1.42763294196247e-03 , -1.40117013302236e-02 ), ( 5.00700080314879e-04 , 2.97437334002883e-03 , -1.98951338246220e-02 ), ( -6.48182242008077e-03 , 2.04041914680348e-02 , -1.30015240503235e-04 ), ( -2.05300318216163e-02 , 5.78974351383434e-02 , 2.90236424552306e-02 ), ( -1.89861081468300e-02 , 6.33210745824364e-02 , -1.59292058110389e-02 ), ( -2.26909264798947e-02 , 7.52790104786259e-02 , -1.72961210714088e-02 ), ( -1.69985052661349e-02 , 7.24322155695334e-02 , -8.31125713403870e-02 ), ( -2.01347960952781e-02 , 8.66187159297856e-02 , -1.02044870208897e-01 ), ( -8.69838837231288e-03 , 4.63888524456888e-02 , -8.33163867525161e-02 ), ( -1.86864572755115e-02 , 6.67879237282488e-02 , -3.52141881593768e-02 ), ( -2.45931675112201e-02 , 9.30781934665973e-02 , -6.89990142792918e-02 ) } +colvars: Step 21, atoms_new_colvar_forces = { ( -7.11399384318308e-02 , 3.03673714596804e-01 , -4.00770119886634e-01 ), ( 1.28450168410534e-02 , 3.00636017805382e-02 , -2.38645544534818e-01 ), ( -4.20822670353576e-02 , 9.41200209059075e-02 , 8.79377349508917e-02 ), ( -9.70668784584834e-02 , 2.50670455049784e-01 , 6.53550388999108e-02 ), ( -1.86302899611748e-02 , 9.89303159690966e-02 , -1.72358620278118e-01 ), ( 7.09108063101489e-02 , -1.85927916967423e-01 , -3.83730584164822e-02 ), ( 1.00940002734312e-02 , -9.89773108191160e-02 , 2.55576585814222e-01 ), ( -4.10215749964445e-02 , 6.16911466781241e-02 , 1.91856870875936e-01 ), ( 6.62622265583337e-02 , -1.90705006891368e-01 , 3.15184935556135e-02 ), ( 1.14774657066217e-01 , -3.92224428801080e-01 , 2.75377184594162e-01 ), ( 2.46625873851911e-02 , -9.94934972823232e-02 , 9.61066727823309e-02 ), ( 2.66219319601747e-02 , -9.73405519568489e-02 , 5.97487570195681e-02 ), ( 1.24577915943817e-02 , -5.57595264132078e-02 , 7.26154388026604e-02 ), ( 1.25983778171294e-02 , -5.36459257873875e-02 , 6.14369978247319e-02 ), ( 5.61903440744207e-03 , -3.49787311352312e-02 , 7.57458071852306e-02 ), ( -8.60288899774205e-03 , 9.75608155101238e-03 , 7.56115259176666e-02 ), ( -2.08923468684040e-03 , -2.67530457899128e-03 , 4.04287964932555e-02 ), ( -5.77333835969326e-03 , 9.88677812731994e-03 , 3.61343701273132e-02 ), ( 2.68767850620090e-03 , -1.29382633507290e-02 , 1.96404769055550e-02 ), ( 8.94944167110720e-03 , -2.20122654388583e-02 , -2.67648727689498e-02 ), ( 8.66483279553809e-03 , -2.38081467999426e-02 , -1.49959487368344e-02 ), ( 6.53495529803234e-03 , -1.35726331970709e-02 , -3.04835083292054e-02 ), ( 1.50303446132429e-02 , -4.67584847450611e-02 , -2.12920998279256e-03 ), ( 2.77018244289008e-02 , -8.87395931998711e-02 , 7.27779809261200e-03 ), ( 1.43352800222162e-02 , -4.70751609713203e-02 , 8.81293743885319e-03 ), ( 1.42817640632689e-02 , -4.42636422522604e-02 , -2.74952806030974e-03 ), ( 9.38522823558224e-03 , -3.71979422433983e-02 , 3.36691841968735e-02 ), ( -6.99503281119043e-04 , -1.53341150642310e-02 , 7.66932516135838e-02 ), ( -3.71897519690295e-03 , 4.14100412747779e-03 , 3.30209727953179e-02 ), ( -5.77794268053234e-03 , 1.11867179676655e-02 , 3.05114126724248e-02 ), ( -7.29252056176348e-03 , 1.80017851832735e-02 , 2.15255686424142e-02 ), ( -1.63781366214478e-02 , 5.23192063260293e-02 , -3.66306391685651e-03 ), ( -9.82784133106718e-03 , 3.58615231332486e-02 , -2.17375544901125e-02 ), ( -1.38723121061425e-02 , 5.01224906323065e-02 , -2.85083949342105e-02 ), ( -2.07316713877925e-03 , 1.48577122015172e-02 , -3.64859747436524e-02 ), ( 1.04678431390519e-02 , -1.61024070956970e-02 , -7.34936428665872e-02 ), ( 4.30768009091328e-03 , -1.06911031799011e-03 , -5.45527250787330e-02 ), ( 3.26600819838431e-03 , 5.73629579028584e-03 , -6.99986217017486e-02 ), ( 7.12281125111274e-03 , -1.51675396442751e-02 , -3.15898239456440e-02 ), ( 1.31993145017299e-02 , -4.18609641559936e-02 , 1.62390103359611e-03 ), ( 5.64876125100676e-04 , 1.42763294196250e-03 , -1.40117013302236e-02 ), ( 5.00700080314872e-04 , 2.97437334002887e-03 , -1.98951338246221e-02 ), ( -6.48182242008078e-03 , 2.04041914680348e-02 , -1.30015240503271e-04 ), ( -2.05300318216164e-02 , 5.78974351383434e-02 , 2.90236424552305e-02 ), ( -1.89861081468300e-02 , 6.33210745824364e-02 , -1.59292058110389e-02 ), ( -2.26909264798947e-02 , 7.52790104786260e-02 , -1.72961210714089e-02 ), ( -1.69985052661349e-02 , 7.24322155695334e-02 , -8.31125713403870e-02 ), ( -2.01347960952781e-02 , 8.66187159297856e-02 , -1.02044870208897e-01 ), ( -8.69838837231290e-03 , 4.63888524456889e-02 , -8.33163867525162e-02 ), ( -1.86864572755115e-02 , 6.67879237282488e-02 , -3.52141881593768e-02 ), ( -2.45931675112202e-02 , 9.30781934665973e-02 , -6.89990142792918e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 21, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -1907,10 +2749,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 22, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 22, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 22, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 22, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 22, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 22, atoms_positions[size = 51] = { ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 ), ( 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 ), ( 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 ), ( 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 ), ( 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 ), ( 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 ), ( -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 ), ( -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 ), ( -3.68858938020335e+00 , 5.71185724985548e-02 , 5.44106122479227e+00 ), ( -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ), ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 ), ( 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 ), ( 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 ), ( 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 ), ( 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 ), ( 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 ), ( 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 ), ( 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 ), ( 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 ), ( 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 ), ( 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 ), ( 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 ), ( 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 ), ( 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 ), ( 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 ), ( 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 ), ( 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 ), ( 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 ), ( 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 ), ( -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 ), ( 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 ), ( 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 ), ( -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 ), ( -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 ), ( -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 ), ( -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 ), ( -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 ), ( -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 ), ( -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 ), ( -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 ), ( -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 ), ( -5.49635790878409e+00 , 8.04534957780670e-01 , 3.33283357586958e+00 ), ( -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 ), ( -2.39123986166853e+00 , -3.20694772050752e-01 , 6.16685140323704e+00 ), ( -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 ), ( -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 ), ( -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 ), ( -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 ), ( -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 ), ( -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 ), ( -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ) } +colvars: Step 22, atoms_positions[size = 51] = { ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 ), ( 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 ), ( 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 ), ( 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 ), ( 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 ), ( 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 ), ( -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 ), ( -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 ), ( -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 ), ( -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ), ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 ), ( 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 ), ( 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 ), ( 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 ), ( 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 ), ( 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 ), ( 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 ), ( 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 ), ( 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 ), ( 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 ), ( 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 ), ( 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 ), ( 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 ), ( 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 ), ( 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 ), ( 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 ), ( 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 ), ( 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 ), ( 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 ), ( -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 ), ( 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 ), ( 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 ), ( -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 ), ( -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 ), ( -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 ), ( -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 ), ( -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 ), ( -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 ), ( -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 ), ( -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 ), ( -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 ), ( -5.49635790878409e+00 , 8.04534957780669e-01 , 3.33283357586958e+00 ), ( -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 ), ( -2.39123986166852e+00 , -3.20694772050748e-01 , 6.16685140323704e+00 ), ( -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 ), ( -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 ), ( -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 ), ( -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 ), ( -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 ), ( -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 ), ( -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ) } colvars: Step 22, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 22, atom_groups_ids[size = 0] = @@ -1929,15 +2771,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072403e-02 , -1.24385326679425e-02 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072404e-02 , -1.24385326679425e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 , 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 , 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 , 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 , 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 , 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 , 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 , 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 , 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 , 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 , 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 , 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 , 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 , 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 , 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 , -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 , 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 , -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 , -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 , -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 , -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 , -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 , -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 , -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 , -5.49635790878409e+00 , 8.04534957780669e-01 , 3.33283357586958e+00 , -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -2.39123986166852e+00 , -3.20694772050748e-01 , 6.16685140323704e+00 , -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 , -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 , -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 , -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 , -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 , -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 , -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072403e-02 , -1.24385326679425e-02 ). +colvars: Colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072404e-02 , -1.24385326679425e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 , 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 , 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 , 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 , 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 , 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 , 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 , 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 , 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 , 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 , 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 , 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 , 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 , 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 , 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 , -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 , 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 , -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 , -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 , -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 , -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 , -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 , -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 , -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 , -5.49635790878409e+00 , 8.04534957780669e-01 , 3.33283357586958e+00 , -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -2.39123986166852e+00 , -3.20694772050748e-01 , 6.16685140323704e+00 , -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 , -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 , -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 , -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 , -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 , -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 , -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -1950,6 +2863,10 @@ colvars: Adding total bias energy: 11.5066 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -1965,8 +2882,6 @@ colvars: ( 0.00774329 , -0.10563 , 0.316076 ) colvars: ( -0.0496388 , 0.08362 , 0.214385 ) colvars: ( 0.0809445 , -0.235308 , 0.0239595 ) colvars: ( 0.13709 , -0.47641 , 0.334599 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246401 , -0.0995232 , 0.0961757 ) colvars: ( 0.0200273 , -0.0820288 , 0.0831474 ) @@ -2019,14 +2934,17 @@ colvars: ( -0.00868627 , 0.0463831 , -0.0833457 ) colvars: ( -0.0186738 , 0.0668192 , -0.0352312 ) colvars: ( -0.0224593 , 0.0841331 , -0.0588629 ) colvars: ( -0.0245733 , 0.0931158 , -0.0690579 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 22. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 22. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 22, atoms_new_colvar_forces = { ( -7.09839898778747e-02 , 3.03674063527600e-01 , -4.01068648115013e-01 ), ( 1.28677757638464e-02 , 3.01861976186923e-02 , -2.38809348309205e-01 ), ( -4.21463674859759e-02 , 9.43967829010162e-02 , 8.76653672693452e-02 ), ( -9.70292248461032e-02 , 2.50742449438027e-01 , 6.51357190727136e-02 ), ( -1.85367305319293e-02 , 9.88144120703526e-02 , -1.72353345630284e-01 ), ( 7.08691073007723e-02 , -1.85935576884942e-01 , -3.82568663452623e-02 ), ( 9.99629817433116e-03 , -9.89023847961850e-02 , 2.55611691378657e-01 ), ( -4.10000890482683e-02 , 6.15546231916447e-02 , 1.91974826016933e-01 ), ( 6.62704276258434e-02 , -1.90932830035544e-01 , 3.18580020079369e-02 ), ( 1.14630750534917e-01 , -3.92276752466799e-01 , 2.75736313750346e-01 ), ( 2.46401348458040e-02 , -9.95231922332751e-02 , 9.61756954601184e-02 ), ( 2.66028495666390e-02 , -9.73827270437477e-02 , 5.97805459313106e-02 ), ( 1.24445918472298e-02 , -5.57660823956985e-02 , 7.26477167044874e-02 ), ( 1.25859818519026e-02 , -5.36566849366138e-02 , 6.14702165822492e-02 ), ( 5.60941666979545e-03 , -3.49676476401050e-02 , 7.57650503878028e-02 ), ( -8.60459043493706e-03 , 9.80137872000443e-03 , 7.56056143106273e-02 ), ( -2.09115201198730e-03 , -2.65595958743230e-03 , 4.04196007616606e-02 ), ( -5.77311642017532e-03 , 9.91276524030936e-03 , 3.61256035860894e-02 ), ( 2.68564234612565e-03 , -1.29349024719858e-02 , 1.96168163142232e-02 ), ( 8.94925864416897e-03 , -2.20349749067143e-02 , -2.68197445771303e-02 ), ( 8.66280149401488e-03 , -2.38293607684870e-02 , -1.50229481919147e-02 ), ( 6.53549642564501e-03 , -1.35935670322821e-02 , -3.05178145405584e-02 ), ( 1.50234208571289e-02 , -4.67916092089625e-02 , -2.13659458865095e-03 ), ( 2.76867464932990e-02 , -8.88011036791123e-02 , 7.30219119954996e-03 ), ( 1.43268298943310e-02 , -4.71060008041501e-02 , 8.83198042196747e-03 ), ( 1.42742680267957e-02 , -4.42983138073421e-02 , -2.73019093925149e-03 ), ( 9.37682487194692e-03 , -3.72105131562461e-02 , 3.36980129801635e-02 ), ( -7.07234928782565e-04 , -1.53121732294138e-02 , 7.67431469878513e-02 ), ( -3.72064813930677e-03 , 4.15794740228741e-03 , 3.30429937869084e-02 ), ( -5.77858592433563e-03 , 1.12068079161518e-02 , 3.05383925376817e-02 ), ( -7.29072954144173e-03 , 1.80250877442325e-02 , 2.15265738678377e-02 ), ( -1.63683809363363e-02 , 5.23584897961350e-02 , -3.70159935424319e-03 ), ( -9.82031195706153e-03 , 3.58787450236741e-02 , -2.17630809852664e-02 ), ( -1.38621548995544e-02 , 5.01466473790395e-02 , -2.85364839098933e-02 ), ( -2.06812117531274e-03 , 1.48531610368221e-02 , -3.65147867450562e-02 ), ( 1.04701424349007e-02 , -1.61460182290016e-02 , -7.35332062826640e-02 ), ( 4.31059150250448e-03 , -1.09531770379866e-03 , -5.45687792002220e-02 ), ( 3.27087578265066e-03 , 5.70773713995558e-03 , -7.00198422700666e-02 ), ( 7.12165311897483e-03 , -1.51946850165027e-02 , -3.15836085513172e-02 ), ( 1.31909349580735e-02 , -4.18949630055120e-02 , 1.67183642219017e-03 ), ( 5.64699401698968e-04 , 1.41850132131441e-03 , -1.39836938535898e-02 ), ( 5.00837441823005e-04 , 2.96280077134345e-03 , -1.98618599951808e-02 ), ( -6.47952298250982e-03 , 2.04157888640752e-02 , -1.05999642867334e-04 ), ( -2.05232494824155e-02 , 5.79498507924875e-02 , 2.90487025878773e-02 ), ( -1.89756580163051e-02 , 6.33571912361918e-02 , -1.59250752374072e-02 ), ( -2.26786531673934e-02 , 7.53225391086036e-02 , -1.72891702626615e-02 ), ( -1.69818816397503e-02 , 7.24462974551710e-02 , -8.31541664771447e-02 ), ( -2.01145633252694e-02 , 8.66349326960424e-02 , -1.02100887695110e-01 ), ( -8.68627168332184e-03 , 4.63831438807106e-02 , -8.33457370302980e-02 ), ( -1.86738034866789e-02 , 6.68192172662539e-02 , -3.52312486009207e-02 ), ( -2.45733259321368e-02 , 9.31157815017149e-02 , -6.90578829953477e-02 ) } +colvars: Step 22, atoms_new_colvar_forces = { ( -7.09839898778747e-02 , 3.03674063527600e-01 , -4.01068648115013e-01 ), ( 1.28677757638464e-02 , 3.01861976186925e-02 , -2.38809348309205e-01 ), ( -4.21463674859759e-02 , 9.43967829010162e-02 , 8.76653672693451e-02 ), ( -9.70292248461031e-02 , 2.50742449438027e-01 , 6.51357190727135e-02 ), ( -1.85367305319293e-02 , 9.88144120703525e-02 , -1.72353345630284e-01 ), ( 7.08691073007723e-02 , -1.85935576884941e-01 , -3.82568663452623e-02 ), ( 9.99629817433111e-03 , -9.89023847961850e-02 , 2.55611691378657e-01 ), ( -4.10000890482683e-02 , 6.15546231916445e-02 , 1.91974826016933e-01 ), ( 6.62704276258435e-02 , -1.90932830035544e-01 , 3.18580020079369e-02 ), ( 1.14630750534917e-01 , -3.92276752466799e-01 , 2.75736313750346e-01 ), ( 2.46401348458040e-02 , -9.95231922332751e-02 , 9.61756954601184e-02 ), ( 2.66028495666390e-02 , -9.73827270437477e-02 , 5.97805459313105e-02 ), ( 1.24445918472298e-02 , -5.57660823956985e-02 , 7.26477167044874e-02 ), ( 1.25859818519026e-02 , -5.36566849366139e-02 , 6.14702165822491e-02 ), ( 5.60941666979545e-03 , -3.49676476401050e-02 , 7.57650503878028e-02 ), ( -8.60459043493705e-03 , 9.80137872000444e-03 , 7.56056143106272e-02 ), ( -2.09115201198730e-03 , -2.65595958743230e-03 , 4.04196007616605e-02 ), ( -5.77311642017531e-03 , 9.91276524030938e-03 , 3.61256035860894e-02 ), ( 2.68564234612566e-03 , -1.29349024719858e-02 , 1.96168163142232e-02 ), ( 8.94925864416898e-03 , -2.20349749067143e-02 , -2.68197445771304e-02 ), ( 8.66280149401487e-03 , -2.38293607684870e-02 , -1.50229481919147e-02 ), ( 6.53549642564500e-03 , -1.35935670322821e-02 , -3.05178145405584e-02 ), ( 1.50234208571289e-02 , -4.67916092089626e-02 , -2.13659458865097e-03 ), ( 2.76867464932989e-02 , -8.88011036791123e-02 , 7.30219119954995e-03 ), ( 1.43268298943310e-02 , -4.71060008041501e-02 , 8.83198042196748e-03 ), ( 1.42742680267957e-02 , -4.42983138073421e-02 , -2.73019093925148e-03 ), ( 9.37682487194691e-03 , -3.72105131562461e-02 , 3.36980129801635e-02 ), ( -7.07234928782566e-04 , -1.53121732294138e-02 , 7.67431469878513e-02 ), ( -3.72064813930677e-03 , 4.15794740228742e-03 , 3.30429937869084e-02 ), ( -5.77858592433564e-03 , 1.12068079161518e-02 , 3.05383925376817e-02 ), ( -7.29072954144173e-03 , 1.80250877442325e-02 , 2.15265738678377e-02 ), ( -1.63683809363363e-02 , 5.23584897961350e-02 , -3.70159935424319e-03 ), ( -9.82031195706152e-03 , 3.58787450236741e-02 , -2.17630809852663e-02 ), ( -1.38621548995544e-02 , 5.01466473790396e-02 , -2.85364839098933e-02 ), ( -2.06812117531274e-03 , 1.48531610368221e-02 , -3.65147867450562e-02 ), ( 1.04701424349007e-02 , -1.61460182290016e-02 , -7.35332062826640e-02 ), ( 4.31059150250448e-03 , -1.09531770379864e-03 , -5.45687792002220e-02 ), ( 3.27087578265066e-03 , 5.70773713995559e-03 , -7.00198422700665e-02 ), ( 7.12165311897482e-03 , -1.51946850165027e-02 , -3.15836085513172e-02 ), ( 1.31909349580735e-02 , -4.18949630055120e-02 , 1.67183642219021e-03 ), ( 5.64699401698964e-04 , 1.41850132131443e-03 , -1.39836938535898e-02 ), ( 5.00837441822996e-04 , 2.96280077134346e-03 , -1.98618599951807e-02 ), ( -6.47952298250981e-03 , 2.04157888640752e-02 , -1.05999642867301e-04 ), ( -2.05232494824155e-02 , 5.79498507924876e-02 , 2.90487025878773e-02 ), ( -1.89756580163051e-02 , 6.33571912361919e-02 , -1.59250752374072e-02 ), ( -2.26786531673934e-02 , 7.53225391086036e-02 , -1.72891702626615e-02 ), ( -1.69818816397503e-02 , 7.24462974551711e-02 , -8.31541664771447e-02 ), ( -2.01145633252694e-02 , 8.66349326960424e-02 , -1.02100887695110e-01 ), ( -8.68627168332183e-03 , 4.63831438807107e-02 , -8.33457370302980e-02 ), ( -1.86738034866789e-02 , 6.68192172662539e-02 , -3.52312486009206e-02 ), ( -2.45733259321368e-02 , 9.31157815017150e-02 , -6.90578829953477e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 22, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2064,10 +2982,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 23, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 23, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 23, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 23, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 23, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 23, atoms_positions[size = 51] = { ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 ), ( 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 ), ( 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 ), ( 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 ), ( 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 ), ( 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 ), ( -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 ), ( -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 ), ( -3.68392264400780e+00 , 6.26974696338532e-02 , 5.44598583975169e+00 ), ( -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ), ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 ), ( 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 ), ( 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 ), ( 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 ), ( 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 ), ( 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 ), ( 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 ), ( 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 ), ( 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 ), ( 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 ), ( 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 ), ( 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 ), ( 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 ), ( 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 ), ( 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 ), ( 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 ), ( 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 ), ( 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 ), ( 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 ), ( -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 ), ( 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 ), ( 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 ), ( -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 ), ( -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 ), ( -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 ), ( -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 ), ( -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 ), ( -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 ), ( -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 ), ( -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 ), ( -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 ), ( -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 ), ( -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 ), ( -2.39140303069694e+00 , -3.22564541882358e-01 , 6.16358793333041e+00 ), ( -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 ), ( -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 ), ( -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 ), ( -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 ), ( -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 ), ( -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 ), ( -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ) } +colvars: Step 23, atoms_positions[size = 51] = { ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 ), ( 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 ), ( 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 ), ( 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 ), ( 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 ), ( 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 ), ( -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 ), ( -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 ), ( -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 ), ( -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ), ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 ), ( 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 ), ( 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 ), ( 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 ), ( 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 ), ( 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 ), ( 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 ), ( 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 ), ( 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 ), ( 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 ), ( 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 ), ( 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 ), ( 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 ), ( 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 ), ( 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 ), ( 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 ), ( 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 ), ( 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 ), ( 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 ), ( -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 ), ( 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 ), ( 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 ), ( -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 ), ( -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 ), ( -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 ), ( -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 ), ( -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 ), ( -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 ), ( -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 ), ( -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 ), ( -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 ), ( -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 ), ( -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 ), ( -2.39140303069694e+00 , -3.22564541882353e-01 , 6.16358793333041e+00 ), ( -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 ), ( -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 ), ( -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 ), ( -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 ), ( -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 ), ( -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 ), ( -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ) } colvars: Step 23, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 23, atom_groups_ids[size = 0] = @@ -2085,16 +3003,87 @@ colvars: Collective variables module, step no. 23 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 , 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 , 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 , 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 , 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 , 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 , 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 , 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 , 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 , 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 , 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 , 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 , 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 , 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 , 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 , -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 , 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 , -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 , -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 , -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 , -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 , -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 , -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 , -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 , -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 , -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -2.39140303069694e+00 , -3.22564541882353e-01 , 6.16358793333041e+00 , -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 , -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 , -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 , -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 , -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 , -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 , -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 , 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 , 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 , 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 , 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 , 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 , 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 , 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 , 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 , 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 , 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 , 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 , 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 , 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 , 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 , -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 , 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 , -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 , -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 , -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 , -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 , -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 , -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 , -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 , -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 , -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -2.39140303069694e+00 , -3.22564541882353e-01 , 6.16358793333041e+00 , -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 , -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 , -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 , -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 , -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 , -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 , -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2107,6 +3096,10 @@ colvars: Adding total bias energy: 11.5092 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2122,8 +3115,6 @@ colvars: ( 0.00763224 , -0.105555 , 0.316058 ) colvars: ( -0.0496109 , 0.0834271 , 0.214493 ) colvars: ( 0.080944 , -0.235538 , 0.0243166 ) colvars: ( 0.136912 , -0.476435 , 0.334909 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0246097 , -0.0995472 , 0.0962325 ) colvars: ( 0.0200032 , -0.0820492 , 0.0831831 ) @@ -2176,14 +3167,17 @@ colvars: ( -0.00866934 , 0.0463829 , -0.083365 ) colvars: ( -0.0186592 , 0.066849 , -0.0352456 ) colvars: ( -0.0224379 , 0.0841636 , -0.0588943 ) colvars: ( -0.0245472 , 0.0931456 , -0.0691082 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 23. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 23. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 23, atoms_new_colvar_forces = { ( -7.08168814937949e-02 , 3.03664452472894e-01 , -4.01263051701776e-01 ), ( 1.28897282159372e-02 , 3.03652461049389e-02 , -2.38962907009597e-01 ), ( -4.22098006472154e-02 , 9.46520341380242e-02 , 8.73129850632795e-02 ), ( -9.69836961545911e-02 , 2.50727137133401e-01 , 6.49179539830782e-02 ), ( -1.84393958034465e-02 , 9.86949573833386e-02 , -1.72272185409953e-01 ), ( 7.08217601806615e-02 , -1.85878656231815e-01 , -3.81557494152707e-02 ), ( 9.89515936319978e-03 , -9.88477114743486e-02 , 2.55569065601461e-01 ), ( -4.09765694460841e-02 , 6.13444540424882e-02 , 1.92109707586131e-01 ), ( 6.62729002147716e-02 , -1.91127572587650e-01 , 3.22352067094027e-02 ), ( 1.14473689844909e-01 , -3.92271189494705e-01 , 2.76014821802483e-01 ), ( 2.46097378880774e-02 , -9.95472081172002e-02 , 9.62325265867954e-02 ), ( 2.65800661415529e-02 , -9.74224674168166e-02 , 5.98069715723355e-02 ), ( 1.24268052531842e-02 , -5.57747491404972e-02 , 7.26713718002168e-02 ), ( 1.25692908517025e-02 , -5.36672888971867e-02 , 6.14959932071031e-02 ), ( 5.59595460705682e-03 , -3.49639005947200e-02 , 7.57753564150521e-02 ), ( -8.60853344063534e-03 , 9.83018051445575e-03 , 7.55907061791914e-02 ), ( -2.09370541899715e-03 , -2.64663879970087e-03 , 4.04063346386015e-02 ), ( -5.77353689472604e-03 , 9.92898655659039e-03 , 3.61127372741654e-02 ), ( 2.68495661875314e-03 , -1.29409636173138e-02 , 1.95929838330084e-02 ), ( 8.95464052648906e-03 , -2.20662135786371e-02 , -2.68667237089156e-02 ), ( 8.66369655000775e-03 , -2.38537280061534e-02 , -1.50453182585348e-02 ), ( 6.53999219691608e-03 , -1.36172289972066e-02 , -3.05455555170775e-02 ), ( 1.50176159970732e-02 , -4.68238119845228e-02 , -2.14130988594835e-03 ), ( 2.76703023716468e-02 , -8.88526582257362e-02 , 7.32763641562823e-03 ), ( 1.43169910754908e-02 , -4.71308548263177e-02 , 8.85056798528954e-03 ), ( 1.42657338744872e-02 , -4.43248724469114e-02 , -2.71006633727085e-03 ), ( 9.36528608667769e-03 , -3.72197152508182e-02 , 3.37223434971326e-02 ), ( -7.21504131285960e-04 , -1.52905347062471e-02 , 7.67810657807839e-02 ), ( -3.72528256564419e-03 , 4.17432885242505e-03 , 3.30593835387063e-02 ), ( -5.78257112165283e-03 , 1.12277726999349e-02 , 3.05594093243620e-02 ), ( -7.28993979152106e-03 , 1.80436025627073e-02 , 2.15242117056218e-02 ), ( -1.63558940654101e-02 , 5.23852695599543e-02 , -3.73915389641007e-03 ), ( -9.81031471026572e-03 , 3.58912916496682e-02 , -2.17857056962443e-02 ), ( -1.38492253162238e-02 , 5.01659601331753e-02 , -2.85612669585644e-02 ), ( -2.05962857627378e-03 , 1.48469797126605e-02 , -3.65378567014535e-02 ), ( 1.04783374291988e-02 , -1.61854613034706e-02 , -7.35606117525264e-02 ), ( 4.31670110681340e-03 , -1.11542447291207e-03 , -5.45771754964243e-02 ), ( 3.27982880802864e-03 , 5.68645760642483e-03 , -7.00314830313078e-02 ), ( 7.12123613458920e-03 , -1.52133335041448e-02 , -3.15734429379239e-02 ), ( 1.31790365397598e-02 , -4.19140962086650e-02 , 1.71795596493783e-03 ), ( 5.62737062255140e-04 , 1.41951133743413e-03 , -1.39560183089449e-02 ), ( 4.98953902161183e-04 , 2.96382598398074e-03 , -1.98286454303239e-02 ), ( -6.47935157763106e-03 , 2.04327935768267e-02 , -8.44654753454989e-05 ), ( -2.05200517884924e-02 , 5.80004004527264e-02 , 2.90662088850963e-02 ), ( -1.89655968658880e-02 , 6.33940538126061e-02 , -1.59219105336479e-02 ), ( -2.26670637582555e-02 , 7.53671927014898e-02 , -1.72837048580549e-02 ), ( -1.69597158830491e-02 , 7.24610787203845e-02 , -8.31859201087093e-02 ), ( -2.00871048374524e-02 , 8.66507978883153e-02 , -1.02144384436106e-01 ), ( -8.66934268082574e-03 , 4.63828731985594e-02 , -8.33650111463787e-02 ), ( -1.86591940279770e-02 , 6.68490223519342e-02 , -3.52456476594086e-02 ), ( -2.45472378440625e-02 , 9.31456187363587e-02 , -6.91082336777466e-02 ) } +colvars: Step 23, atoms_new_colvar_forces = { ( -7.08168814937949e-02 , 3.03664452472894e-01 , -4.01263051701775e-01 ), ( 1.28897282159372e-02 , 3.03652461049390e-02 , -2.38962907009597e-01 ), ( -4.22098006472154e-02 , 9.46520341380242e-02 , 8.73129850632794e-02 ), ( -9.69836961545912e-02 , 2.50727137133401e-01 , 6.49179539830783e-02 ), ( -1.84393958034465e-02 , 9.86949573833386e-02 , -1.72272185409952e-01 ), ( 7.08217601806615e-02 , -1.85878656231814e-01 , -3.81557494152707e-02 ), ( 9.89515936319975e-03 , -9.88477114743486e-02 , 2.55569065601461e-01 ), ( -4.09765694460841e-02 , 6.13444540424881e-02 , 1.92109707586132e-01 ), ( 6.62729002147716e-02 , -1.91127572587650e-01 , 3.22352067094028e-02 ), ( 1.14473689844909e-01 , -3.92271189494705e-01 , 2.76014821802483e-01 ), ( 2.46097378880774e-02 , -9.95472081172002e-02 , 9.62325265867954e-02 ), ( 2.65800661415530e-02 , -9.74224674168165e-02 , 5.98069715723355e-02 ), ( 1.24268052531842e-02 , -5.57747491404972e-02 , 7.26713718002168e-02 ), ( 1.25692908517025e-02 , -5.36672888971867e-02 , 6.14959932071031e-02 ), ( 5.59595460705682e-03 , -3.49639005947200e-02 , 7.57753564150521e-02 ), ( -8.60853344063534e-03 , 9.83018051445572e-03 , 7.55907061791913e-02 ), ( -2.09370541899716e-03 , -2.64663879970091e-03 , 4.04063346386015e-02 ), ( -5.77353689472605e-03 , 9.92898655659034e-03 , 3.61127372741654e-02 ), ( 2.68495661875315e-03 , -1.29409636173138e-02 , 1.95929838330084e-02 ), ( 8.95464052648908e-03 , -2.20662135786371e-02 , -2.68667237089156e-02 ), ( 8.66369655000776e-03 , -2.38537280061534e-02 , -1.50453182585348e-02 ), ( 6.53999219691608e-03 , -1.36172289972066e-02 , -3.05455555170775e-02 ), ( 1.50176159970732e-02 , -4.68238119845228e-02 , -2.14130988594834e-03 ), ( 2.76703023716468e-02 , -8.88526582257361e-02 , 7.32763641562824e-03 ), ( 1.43169910754908e-02 , -4.71308548263177e-02 , 8.85056798528954e-03 ), ( 1.42657338744872e-02 , -4.43248724469113e-02 , -2.71006633727086e-03 ), ( 9.36528608667769e-03 , -3.72197152508182e-02 , 3.37223434971325e-02 ), ( -7.21504131285961e-04 , -1.52905347062471e-02 , 7.67810657807838e-02 ), ( -3.72528256564419e-03 , 4.17432885242504e-03 , 3.30593835387062e-02 ), ( -5.78257112165284e-03 , 1.12277726999349e-02 , 3.05594093243620e-02 ), ( -7.28993979152107e-03 , 1.80436025627073e-02 , 2.15242117056218e-02 ), ( -1.63558940654101e-02 , 5.23852695599543e-02 , -3.73915389641006e-03 ), ( -9.81031471026572e-03 , 3.58912916496682e-02 , -2.17857056962443e-02 ), ( -1.38492253162238e-02 , 5.01659601331753e-02 , -2.85612669585644e-02 ), ( -2.05962857627377e-03 , 1.48469797126605e-02 , -3.65378567014534e-02 ), ( 1.04783374291988e-02 , -1.61854613034706e-02 , -7.35606117525263e-02 ), ( 4.31670110681341e-03 , -1.11542447291206e-03 , -5.45771754964243e-02 ), ( 3.27982880802864e-03 , 5.68645760642483e-03 , -7.00314830313078e-02 ), ( 7.12123613458921e-03 , -1.52133335041448e-02 , -3.15734429379239e-02 ), ( 1.31790365397598e-02 , -4.19140962086650e-02 , 1.71795596493782e-03 ), ( 5.62737062255136e-04 , 1.41951133743415e-03 , -1.39560183089450e-02 ), ( 4.98953902161181e-04 , 2.96382598398075e-03 , -1.98286454303239e-02 ), ( -6.47935157763107e-03 , 2.04327935768268e-02 , -8.44654753455294e-05 ), ( -2.05200517884924e-02 , 5.80004004527264e-02 , 2.90662088850963e-02 ), ( -1.89655968658880e-02 , 6.33940538126061e-02 , -1.59219105336480e-02 ), ( -2.26670637582555e-02 , 7.53671927014898e-02 , -1.72837048580550e-02 ), ( -1.69597158830491e-02 , 7.24610787203844e-02 , -8.31859201087093e-02 ), ( -2.00871048374524e-02 , 8.66507978883153e-02 , -1.02144384436106e-01 ), ( -8.66934268082573e-03 , 4.63828731985594e-02 , -8.33650111463786e-02 ), ( -1.86591940279770e-02 , 6.68490223519342e-02 , -3.52456476594086e-02 ), ( -2.45472378440625e-02 , 9.31456187363586e-02 , -6.91082336777466e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 23, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2221,10 +3215,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 24, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 24, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 24, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 24, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 24, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 24, atoms_positions[size = 51] = { ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 ), ( 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 ), ( 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 ), ( 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 ), ( 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 ), ( 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 ), ( -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 ), ( -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 ), ( -3.68005965040029e+00 , 6.78907924099859e-02 , 5.45204135176785e+00 ), ( -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ), ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 ), ( 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 ), ( 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 ), ( 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 ), ( 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 ), ( 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 ), ( 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 ), ( 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 ), ( 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 ), ( 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 ), ( 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 ), ( 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 ), ( 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 ), ( 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 ), ( 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 ), ( 3.75816832389218e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 ), ( 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 ), ( 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 ), ( 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 ), ( -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 ), ( 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 ), ( 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 ), ( -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 ), ( -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 ), ( -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 ), ( -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 ), ( -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 ), ( -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 ), ( -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 ), ( -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 ), ( -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 ), ( -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 ), ( -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 ), ( -2.39101064153575e+00 , -3.23953535315118e-01 , 6.15985323826371e+00 ), ( -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 ), ( -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 ), ( -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 ), ( -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 ), ( -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 ), ( -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 ), ( -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ) } +colvars: Step 24, atoms_positions[size = 51] = { ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 ), ( 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 ), ( 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 ), ( 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 ), ( 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 ), ( 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 ), ( -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 ), ( -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 ), ( -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 ), ( -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ), ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 ), ( 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 ), ( 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 ), ( 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 ), ( 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 ), ( 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 ), ( 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 ), ( 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 ), ( 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 ), ( 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 ), ( 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 ), ( 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 ), ( 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 ), ( 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 ), ( 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 ), ( 3.75816832389217e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 ), ( 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 ), ( 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 ), ( 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 ), ( -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 ), ( 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 ), ( 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 ), ( -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 ), ( -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 ), ( -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 ), ( -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 ), ( -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 ), ( -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 ), ( -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 ), ( -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 ), ( -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 ), ( -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 ), ( -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 ), ( -2.39101064153575e+00 , -3.23953535315112e-01 , 6.15985323826371e+00 ), ( -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 ), ( -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 ), ( -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 ), ( -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 ), ( -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 ), ( -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 ), ( -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ) } colvars: Step 24, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 24, atom_groups_ids[size = 0] = @@ -2242,16 +3236,87 @@ colvars: Collective variables module, step no. 24 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756126e-02 , 1.27630697470619e-02 , -1.31113665114322e-02 ). +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756127e-02 , 1.27630697470618e-02 , -1.31113665114322e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 , 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 , 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 , 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 , 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 , 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 , 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 , 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 , 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 , 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 , 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 , 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 , 3.75816832389217e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 , 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 , 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 , -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 , 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 , -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 , -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 , -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 , -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 , -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 , -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 , -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 , -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 , -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -2.39101064153575e+00 , -3.23953535315112e-01 , 6.15985323826371e+00 , -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 , -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 , -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 , -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 , -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 , -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 , -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ). +colvars: Done calculating colvar "main". +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756126e-02 , 1.27630697470619e-02 , -1.31113665114322e-02 ). +colvars: Colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756127e-02 , 1.27630697470618e-02 , -1.31113665114322e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 , 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 , 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 , 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 , 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 , 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 , 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 , 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 , 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 , 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 , 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 , 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 , 3.75816832389217e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 , 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 , 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 , -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 , 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 , -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 , -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 , -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 , -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 , -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 , -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 , -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 , -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 , -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -2.39101064153575e+00 , -3.23953535315112e-01 , 6.15985323826371e+00 , -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 , -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 , -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 , -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 , -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 , -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 , -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2264,6 +3329,10 @@ colvars: Adding total bias energy: 11.5109 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2279,8 +3348,6 @@ colvars: ( 0.00751337 , -0.105502 , 0.315964 ) colvars: ( -0.0495844 , 0.0831619 , 0.21461 ) colvars: ( 0.0809424 , -0.235734 , 0.0247035 ) colvars: ( 0.136722 , -0.476403 , 0.335136 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0245726 , -0.0995639 , 0.0962772 ) colvars: ( 0.0199744 , -0.0820673 , 0.0832098 ) @@ -2333,14 +3400,17 @@ colvars: ( -0.00864801 , 0.0463873 , -0.0833752 ) colvars: ( -0.0186433 , 0.066876 , -0.0352584 ) colvars: ( -0.0224131 , 0.084189 , -0.0589202 ) colvars: ( -0.0245161 , 0.0931661 , -0.06915 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 24. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 24. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 24, atoms_new_colvar_forces = { ( -7.06413071230504e-02 , 3.03646376177113e-01 , -4.01360271764822e-01 ), ( 1.29135699454975e-02 , 3.05895907970704e-02 , -2.39103012853669e-01 ), ( -4.22727893177429e-02 , 9.48806486655140e-02 , 8.68992202535935e-02 ), ( -9.69353995896309e-02 , 2.50634381681781e-01 , 6.47066866422256e-02 ), ( -1.83397783484814e-02 , 9.85756742630302e-02 , -1.72126442430389e-01 ), ( 7.07728219511373e-02 , -1.85765887475988e-01 , -3.80697774318616e-02 ), ( 9.79094825409427e-03 , -9.88124633185437e-02 , 2.55459166370171e-01 ), ( -4.09551734426115e-02 , 6.10746932338372e-02 , 1.92255054495674e-01 ), ( 6.62713061540428e-02 , -1.91287333337422e-01 , 3.26356316955038e-02 ), ( 1.14308608904662e-01 , -3.92214125425127e-01 , 2.76215371150626e-01 ), ( 2.45725920232996e-02 , -9.95638546443988e-02 , 9.62771812753496e-02 ), ( 2.65546467078898e-02 , -9.74578351767044e-02 , 5.98293143046422e-02 ), ( 1.24049987615565e-02 , -5.57845532030435e-02 , 7.26871465513840e-02 ), ( 1.25488921727912e-02 , -5.36768078818011e-02 , 6.15147514345488e-02 ), ( 5.57889542473557e-03 , -3.49669023596321e-02 , 7.57778613512468e-02 ), ( -8.61511790943967e-03 , 9.84223056552993e-03 , 7.55684853155769e-02 ), ( -2.09705915825774e-03 , -2.64725710136185e-03 , 4.03903767810113e-02 ), ( -5.77488506394999e-03 , 9.93524199145594e-03 , 3.60968052014861e-02 ), ( 2.68555107386696e-03 , -1.29560057336035e-02 , 1.95709202788530e-02 ), ( 8.96558132413488e-03 , -2.21050689084729e-02 , -2.69029309665138e-02 ), ( 8.66766398808846e-03 , -2.38805017462989e-02 , -1.50614381521955e-02 ), ( 6.54848333975446e-03 , -1.36430392009208e-02 , -3.05652148041553e-02 ), ( 1.50134061346635e-02 , -4.68539729865604e-02 , -2.14212405348145e-03 ), ( 2.76535944622938e-02 , -8.88924111111195e-02 , 7.35459163320720e-03 ), ( 1.43063692881742e-02 , -4.71487915327259e-02 , 8.86870857810112e-03 ), ( 1.42567773634181e-02 , -4.43424413314667e-02 , -2.68944979509767e-03 ), ( 9.35108517815967e-03 , -3.72249354736576e-02 , 3.37419691915580e-02 ), ( -7.42093767884166e-04 , -1.52692752516169e-02 , 7.68061137984732e-02 ), ( -3.73289987962753e-03 , 4.18986710243482e-03 , 3.30695277218438e-02 ), ( -5.78995808229406e-03 , 1.12491380714132e-02 , 3.05733940861192e-02 ), ( -7.29041607322479e-03 , 1.80568906634082e-02 , 2.15185307159462e-02 ), ( -1.63414772366860e-02 , 5.23986257872083e-02 , -3.77465749262824e-03 ), ( -9.79832819666986e-03 , 3.58985454533797e-02 , -2.18051356045120e-02 ), ( -1.38341517731008e-02 , 5.01795107928477e-02 , -2.85827133571873e-02 ), ( -2.04790718474561e-03 , 1.48390673158269e-02 , -3.65546209718068e-02 ), ( 1.04926098671793e-02 , -1.62200191491437e-02 , -7.35748831065827e-02 ), ( 4.32610626512208e-03 , -1.12923962307860e-03 , -5.45781232758893e-02 ), ( 3.29291015644961e-03 , 5.67254452054351e-03 , -7.00339106044753e-02 ), ( 7.12187254119930e-03 , -1.52231512708809e-02 , -3.15600301609801e-02 ), ( 1.31643703507535e-02 , -4.19177461698118e-02 , 1.76043709113814e-03 ), ( 5.59193791564009e-04 , 1.43044841286948e-03 , -1.39305256747123e-02 ), ( 4.95289569726371e-04 , 2.97716813520240e-03 , -1.97977791071556e-02 ), ( -6.48138398004286e-03 , 2.04545723962382e-02 , -6.71144154469031e-05 ), ( -2.05210193315769e-02 , 5.80475595770238e-02 , 2.90742990478969e-02 ), ( -1.89565419805277e-02 , 6.34302052679531e-02 , -1.59214405626776e-02 ), ( -2.26568850688841e-02 , 7.54112231480941e-02 , -1.72818588807229e-02 ), ( -1.69327803850088e-02 , 7.24752813498580e-02 , -8.32085865792704e-02 ), ( -2.00533740645507e-02 , 8.66648297314470e-02 , -1.02175971750392e-01 ), ( -8.64801089252043e-03 , 4.63872708123076e-02 , -8.33751561955853e-02 ), ( -1.86433498800995e-02 , 6.68759703471642e-02 , -3.52584071050765e-02 ), ( -2.45160572636472e-02 , 9.31660631528296e-02 , -6.91499678688890e-02 ) } +colvars: Step 24, atoms_new_colvar_forces = { ( -7.06413071230504e-02 , 3.03646376177113e-01 , -4.01360271764822e-01 ), ( 1.29135699454975e-02 , 3.05895907970703e-02 , -2.39103012853669e-01 ), ( -4.22727893177430e-02 , 9.48806486655140e-02 , 8.68992202535934e-02 ), ( -9.69353995896309e-02 , 2.50634381681781e-01 , 6.47066866422256e-02 ), ( -1.83397783484814e-02 , 9.85756742630302e-02 , -1.72126442430389e-01 ), ( 7.07728219511373e-02 , -1.85765887475988e-01 , -3.80697774318616e-02 ), ( 9.79094825409427e-03 , -9.88124633185437e-02 , 2.55459166370171e-01 ), ( -4.09551734426115e-02 , 6.10746932338373e-02 , 1.92255054495674e-01 ), ( 6.62713061540428e-02 , -1.91287333337422e-01 , 3.26356316955038e-02 ), ( 1.14308608904662e-01 , -3.92214125425127e-01 , 2.76215371150626e-01 ), ( 2.45725920232996e-02 , -9.95638546443988e-02 , 9.62771812753496e-02 ), ( 2.65546467078899e-02 , -9.74578351767043e-02 , 5.98293143046423e-02 ), ( 1.24049987615565e-02 , -5.57845532030435e-02 , 7.26871465513840e-02 ), ( 1.25488921727912e-02 , -5.36768078818011e-02 , 6.15147514345488e-02 ), ( 5.57889542473557e-03 , -3.49669023596321e-02 , 7.57778613512469e-02 ), ( -8.61511790943968e-03 , 9.84223056552992e-03 , 7.55684853155769e-02 ), ( -2.09705915825774e-03 , -2.64725710136186e-03 , 4.03903767810113e-02 ), ( -5.77488506395000e-03 , 9.93524199145591e-03 , 3.60968052014862e-02 ), ( 2.68555107386697e-03 , -1.29560057336035e-02 , 1.95709202788530e-02 ), ( 8.96558132413490e-03 , -2.21050689084729e-02 , -2.69029309665138e-02 ), ( 8.66766398808848e-03 , -2.38805017462989e-02 , -1.50614381521955e-02 ), ( 6.54848333975447e-03 , -1.36430392009208e-02 , -3.05652148041552e-02 ), ( 1.50134061346635e-02 , -4.68539729865604e-02 , -2.14212405348141e-03 ), ( 2.76535944622938e-02 , -8.88924111111195e-02 , 7.35459163320721e-03 ), ( 1.43063692881742e-02 , -4.71487915327259e-02 , 8.86870857810114e-03 ), ( 1.42567773634181e-02 , -4.43424413314667e-02 , -2.68944979509766e-03 ), ( 9.35108517815968e-03 , -3.72249354736576e-02 , 3.37419691915580e-02 ), ( -7.42093767884172e-04 , -1.52692752516169e-02 , 7.68061137984732e-02 ), ( -3.73289987962753e-03 , 4.18986710243482e-03 , 3.30695277218438e-02 ), ( -5.78995808229407e-03 , 1.12491380714132e-02 , 3.05733940861192e-02 ), ( -7.29041607322480e-03 , 1.80568906634082e-02 , 2.15185307159462e-02 ), ( -1.63414772366860e-02 , 5.23986257872083e-02 , -3.77465749262822e-03 ), ( -9.79832819666987e-03 , 3.58985454533797e-02 , -2.18051356045120e-02 ), ( -1.38341517731008e-02 , 5.01795107928477e-02 , -2.85827133571873e-02 ), ( -2.04790718474561e-03 , 1.48390673158269e-02 , -3.65546209718068e-02 ), ( 1.04926098671793e-02 , -1.62200191491437e-02 , -7.35748831065827e-02 ), ( 4.32610626512208e-03 , -1.12923962307860e-03 , -5.45781232758893e-02 ), ( 3.29291015644962e-03 , 5.67254452054352e-03 , -7.00339106044753e-02 ), ( 7.12187254119930e-03 , -1.52231512708809e-02 , -3.15600301609801e-02 ), ( 1.31643703507535e-02 , -4.19177461698118e-02 , 1.76043709113810e-03 ), ( 5.59193791564009e-04 , 1.43044841286951e-03 , -1.39305256747124e-02 ), ( 4.95289569726373e-04 , 2.97716813520242e-03 , -1.97977791071556e-02 ), ( -6.48138398004286e-03 , 2.04545723962382e-02 , -6.71144154469311e-05 ), ( -2.05210193315769e-02 , 5.80475595770238e-02 , 2.90742990478969e-02 ), ( -1.89565419805277e-02 , 6.34302052679531e-02 , -1.59214405626777e-02 ), ( -2.26568850688841e-02 , 7.54112231480941e-02 , -1.72818588807230e-02 ), ( -1.69327803850088e-02 , 7.24752813498580e-02 , -8.32085865792704e-02 ), ( -2.00533740645507e-02 , 8.66648297314470e-02 , -1.02175971750392e-01 ), ( -8.64801089252043e-03 , 4.63872708123076e-02 , -8.33751561955853e-02 ), ( -1.86433498800995e-02 , 6.68759703471642e-02 , -3.52584071050766e-02 ), ( -2.45160572636472e-02 , 9.31660631528295e-02 , -6.91499678688890e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 24, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2378,10 +3448,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 25, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 25, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 25, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 25, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 25, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 25, atoms_positions[size = 51] = { ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 ), ( 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 ), ( 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 ), ( 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 ), ( 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 ), ( 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 ), ( -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 ), ( -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 ), ( -3.67692497938528e+00 , 7.24104000983907e-02 , 5.45877291154939e+00 ), ( -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ), ( 8.30509683048428e+00 , 4.19726743115743e-02 , -7.29420068900795e-01 ), ( 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 ), ( 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 ), ( 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 ), ( 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 ), ( 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 ), ( 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 ), ( 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 ), ( 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 ), ( 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 ), ( 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 ), ( 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 ), ( 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 ), ( 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 ), ( 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 ), ( 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 ), ( 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 ), ( 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 ), ( 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 ), ( -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 ), ( 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 ), ( 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 ), ( -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 ), ( -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 ), ( -5.34273816020180e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 ), ( -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 ), ( -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 ), ( -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 ), ( -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 ), ( -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 ), ( -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 ), ( -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 ), ( -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 ), ( -2.39001770562881e+00 , -3.24650284743471e-01 , 6.15574359469104e+00 ), ( -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 ), ( -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 ), ( -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 ), ( -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 ), ( -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 ), ( -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 ), ( -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ) } +colvars: Step 25, atoms_positions[size = 51] = { ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 ), ( 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 ), ( 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 ), ( 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 ), ( 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 ), ( 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 ), ( -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 ), ( -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 ), ( -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 ), ( -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ), ( 8.30509683048428e+00 , 4.19726743115742e-02 , -7.29420068900795e-01 ), ( 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 ), ( 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 ), ( 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 ), ( 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 ), ( 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 ), ( 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 ), ( 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 ), ( 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 ), ( 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 ), ( 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 ), ( 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 ), ( 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 ), ( 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 ), ( 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 ), ( 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 ), ( 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 ), ( 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 ), ( 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 ), ( -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 ), ( 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 ), ( 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 ), ( -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 ), ( -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 ), ( -5.34273816020181e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 ), ( -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 ), ( -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 ), ( -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 ), ( -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 ), ( -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 ), ( -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 ), ( -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 ), ( -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 ), ( -2.39001770562880e+00 , -3.24650284743465e-01 , 6.15574359469104e+00 ), ( -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 ), ( -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 ), ( -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 ), ( -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 ), ( -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 ), ( -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 ), ( -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ) } colvars: Step 25, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 25, atom_groups_ids[size = 0] = @@ -2400,15 +3470,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876203e-02 , 1.29777530480417e-02 , -1.34613291247888e-02 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876204e-02 , 1.29777530480416e-02 , -1.34613291247889e-02 ). +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30509683048428e+00 , 4.19726743115742e-02 , -7.29420068900795e-01 , 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 , 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 , 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 , 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 , 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 , 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 , 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 , 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 , 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 , 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 , 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 , 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 , 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 , 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 , -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 , 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 , -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 , -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 , -5.34273816020181e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 , -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 , -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 , -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 , -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 , -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 , -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -2.39001770562880e+00 , -3.24650284743465e-01 , 6.15574359469104e+00 , -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 , -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 , -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 , -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 , -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 , -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 , -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ). +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876203e-02 , 1.29777530480417e-02 , -1.34613291247888e-02 ). +colvars: Colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876204e-02 , 1.29777530480416e-02 , -1.34613291247889e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30509683048428e+00 , 4.19726743115742e-02 , -7.29420068900795e-01 , 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 , 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 , 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 , 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 , 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 , 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 , 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 , 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 , 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 , 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 , 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 , 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 , 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 , 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 , -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 , 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 , -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 , -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 , -5.34273816020181e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 , -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 , -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 , -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 , -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 , -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 , -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -2.39001770562880e+00 , -3.24650284743465e-01 , 6.15574359469104e+00 , -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 , -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 , -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 , -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 , -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 , -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 , -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2421,6 +3562,10 @@ colvars: Adding total bias energy: 11.5117 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2436,8 +3581,6 @@ colvars: ( 0.00738743 , -0.105468 , 0.315807 ) colvars: ( -0.0495642 , 0.0828429 , 0.214732 ) colvars: ( 0.0809418 , -0.235896 , 0.0251056 ) colvars: ( 0.136527 , -0.476323 , 0.335288 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0245304 , -0.0995721 , 0.0963105 ) colvars: ( 0.0199419 , -0.0820818 , 0.0832288 ) @@ -2490,14 +3633,17 @@ colvars: ( -0.00862298 , 0.0463953 , -0.0833778 ) colvars: ( -0.0186271 , 0.0668989 , -0.0352706 ) colvars: ( -0.0223862 , 0.0842082 , -0.0589417 ) colvars: ( -0.0244813 , 0.0931762 , -0.0691836 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 25. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 25. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 25, atoms_new_colvar_forces = { ( -7.04600443638350e-02 , 3.03621747458522e-01 , -4.01373682028472e-01 ), ( 1.29420506857990e-02 , 3.08450317799853e-02 , -2.39227221868054e-01 ), ( -4.23355906274468e-02 , 9.50793160624865e-02 , 8.64467007486022e-02 ), ( -9.68894888293516e-02 , 2.50479150966912e-01 , 6.45062578129430e-02 ), ( -1.82393338200141e-02 , 9.84602010337278e-02 , -1.71931658781829e-01 ), ( 7.07263478012350e-02 , -1.85609672059077e-01 , -3.79978980760433e-02 ), ( 9.68400550810395e-03 , -9.87944561148575e-02 , 2.55296819269015e-01 ), ( -4.09399777928876e-02 , 6.07633323078663e-02 , 1.92403592972447e-01 ), ( 6.62674376926360e-02 , -1.91412527838396e-01 , 3.30433713295305e-02 ), ( 1.14140727837322e-01 , -3.92115243802243e-01 , 2.76345875640083e-01 ), ( 2.45303535326015e-02 , -9.95720517518532e-02 , 9.63105281691544e-02 ), ( 2.65278426707223e-02 , -9.74872741208498e-02 , 5.98491237917058e-02 ), ( 1.23800078595191e-02 , -5.57945041990638e-02 , 7.26963423269235e-02 ), ( 1.25256232080886e-02 , -5.36844439703333e-02 , 6.15274102361732e-02 ), ( 5.55871954717282e-03 , -3.49756477161695e-02 , 7.57742636763354e-02 ), ( -8.62458743879690e-03 , 9.83841075458373e-03 , 7.55411808127872e-02 ), ( -2.10133459875127e-03 , -2.65705587569525e-03 , 4.03733078812120e-02 ), ( -5.77739600858532e-03 , 9.93201495398463e-03 , 3.60790735980493e-02 ), ( 2.68726300921175e-03 , -1.29789758403624e-02 , 1.95524417854630e-02 ), ( 8.98170264457940e-03 , -2.21500931356781e-02 , -2.69262680091887e-02 ), ( 8.67464681814413e-03 , -2.39087709180257e-02 , -1.50701443449332e-02 ), ( 6.56074612158967e-03 , -1.36702589485719e-02 , -3.05758637567222e-02 ), ( 1.50111682037605e-02 , -4.68811361083810e-02 , -2.13810104570518e-03 ), ( 2.76377619824812e-02 , -8.89193875459930e-02 , 7.38337491409857e-03 ), ( 1.42956328492329e-02 , -4.71593898002372e-02 , 8.88642649261350e-03 ), ( 1.42480549426660e-02 , -4.43507918114741e-02 , -2.66868998230111e-03 ), ( 9.33487811850630e-03 , -3.72258735497682e-02 , 3.37570127503085e-02 ), ( -7.68369119173232e-04 , -1.52484894295288e-02 , 7.68183269009158e-02 ), ( -3.74332602967186e-03 , 4.20432533857040e-03 , 3.30732666132640e-02 ), ( -5.80058286933925e-03 , 1.12703919993963e-02 , 3.05797902919004e-02 ), ( -7.29234650113121e-03 , 1.80648763741093e-02 , 2.15098284387671e-02 ), ( -1.63260769480337e-02 , 5.23986038060843e-02 , -3.80716611556856e-03 ), ( -9.78497055648197e-03 , 3.59002867510908e-02 , -2.18212967568863e-02 ), ( -1.38177140907220e-02 , 5.01868220910697e-02 , -2.86010179352413e-02 ), ( -2.03339071916587e-03 , 1.48294691070948e-02 , -3.65649683550387e-02 ), ( 1.05127471287825e-02 , -1.62492873763924e-02 , -7.35760043117993e-02 ), ( 4.33869355337769e-03 , -1.13698546157586e-03 , -5.45723770452254e-02 ), ( 3.30989754432303e-03 , 5.66560766362083e-03 , -7.00281639538081e-02 ), ( 7.12381538260144e-03 , -1.52244133889981e-02 , -3.15443190776360e-02 ), ( 1.31478892206905e-02 , -4.19063984404894e-02 , 1.79769937088844e-03 ), ( 5.54388479922571e-04 , 1.45041162698806e-03 , -1.39089157145296e-02 ), ( 4.90214236116323e-04 , 3.00169662343023e-03 , -1.97713882165925e-02 ), ( -6.48554752146523e-03 , 2.04801681670990e-02 , -5.53434019236648e-05 ), ( -2.05264663856608e-02 , 5.80900538781189e-02 , 2.90718102447906e-02 ), ( -1.89490503248258e-02 , 6.34642763608981e-02 , -1.59251829016669e-02 ), ( -2.26487578411400e-02 , 7.54529703717811e-02 , -1.72854851773508e-02 ), ( -1.69021686492795e-02 , 7.24877434965380e-02 , -8.32235613476903e-02 ), ( -2.00147470785519e-02 , 8.66757664758654e-02 , -1.02197102389267e-01 ), ( -8.62297525244981e-03 , 4.63953041892996e-02 , -8.33777736619381e-02 ), ( -1.86270819201374e-02 , 6.68989416403371e-02 , -3.52706493301954e-02 ), ( -2.44812912922878e-02 , 9.31762079245552e-02 , -6.91835824823653e-02 ) } +colvars: Step 25, atoms_new_colvar_forces = { ( -7.04600443638351e-02 , 3.03621747458522e-01 , -4.01373682028473e-01 ), ( 1.29420506857990e-02 , 3.08450317799853e-02 , -2.39227221868054e-01 ), ( -4.23355906274467e-02 , 9.50793160624864e-02 , 8.64467007486022e-02 ), ( -9.68894888293516e-02 , 2.50479150966912e-01 , 6.45062578129430e-02 ), ( -1.82393338200141e-02 , 9.84602010337278e-02 , -1.71931658781829e-01 ), ( 7.07263478012350e-02 , -1.85609672059077e-01 , -3.79978980760433e-02 ), ( 9.68400550810402e-03 , -9.87944561148575e-02 , 2.55296819269016e-01 ), ( -4.09399777928876e-02 , 6.07633323078664e-02 , 1.92403592972447e-01 ), ( 6.62674376926361e-02 , -1.91412527838396e-01 , 3.30433713295305e-02 ), ( 1.14140727837322e-01 , -3.92115243802243e-01 , 2.76345875640083e-01 ), ( 2.45303535326015e-02 , -9.95720517518532e-02 , 9.63105281691545e-02 ), ( 2.65278426707223e-02 , -9.74872741208499e-02 , 5.98491237917058e-02 ), ( 1.23800078595191e-02 , -5.57945041990639e-02 , 7.26963423269236e-02 ), ( 1.25256232080886e-02 , -5.36844439703333e-02 , 6.15274102361732e-02 ), ( 5.55871954717284e-03 , -3.49756477161695e-02 , 7.57742636763354e-02 ), ( -8.62458743879690e-03 , 9.83841075458371e-03 , 7.55411808127873e-02 ), ( -2.10133459875127e-03 , -2.65705587569528e-03 , 4.03733078812120e-02 ), ( -5.77739600858532e-03 , 9.93201495398462e-03 , 3.60790735980493e-02 ), ( 2.68726300921176e-03 , -1.29789758403624e-02 , 1.95524417854630e-02 ), ( 8.98170264457942e-03 , -2.21500931356782e-02 , -2.69262680091888e-02 ), ( 8.67464681814414e-03 , -2.39087709180257e-02 , -1.50701443449332e-02 ), ( 6.56074612158967e-03 , -1.36702589485719e-02 , -3.05758637567222e-02 ), ( 1.50111682037605e-02 , -4.68811361083810e-02 , -2.13810104570518e-03 ), ( 2.76377619824813e-02 , -8.89193875459930e-02 , 7.38337491409857e-03 ), ( 1.42956328492329e-02 , -4.71593898002372e-02 , 8.88642649261350e-03 ), ( 1.42480549426660e-02 , -4.43507918114741e-02 , -2.66868998230111e-03 ), ( 9.33487811850630e-03 , -3.72258735497682e-02 , 3.37570127503085e-02 ), ( -7.68369119173247e-04 , -1.52484894295288e-02 , 7.68183269009158e-02 ), ( -3.74332602967186e-03 , 4.20432533857040e-03 , 3.30732666132640e-02 ), ( -5.80058286933925e-03 , 1.12703919993963e-02 , 3.05797902919005e-02 ), ( -7.29234650113122e-03 , 1.80648763741093e-02 , 2.15098284387671e-02 ), ( -1.63260769480337e-02 , 5.23986038060843e-02 , -3.80716611556857e-03 ), ( -9.78497055648197e-03 , 3.59002867510908e-02 , -2.18212967568863e-02 ), ( -1.38177140907221e-02 , 5.01868220910697e-02 , -2.86010179352413e-02 ), ( -2.03339071916587e-03 , 1.48294691070948e-02 , -3.65649683550387e-02 ), ( 1.05127471287825e-02 , -1.62492873763924e-02 , -7.35760043117994e-02 ), ( 4.33869355337769e-03 , -1.13698546157585e-03 , -5.45723770452254e-02 ), ( 3.30989754432303e-03 , 5.66560766362085e-03 , -7.00281639538081e-02 ), ( 7.12381538260144e-03 , -1.52244133889981e-02 , -3.15443190776360e-02 ), ( 1.31478892206905e-02 , -4.19063984404894e-02 , 1.79769937088845e-03 ), ( 5.54388479922564e-04 , 1.45041162698810e-03 , -1.39089157145296e-02 ), ( 4.90214236116315e-04 , 3.00169662343026e-03 , -1.97713882165925e-02 ), ( -6.48554752146524e-03 , 2.04801681670990e-02 , -5.53434019236684e-05 ), ( -2.05264663856608e-02 , 5.80900538781189e-02 , 2.90718102447906e-02 ), ( -1.89490503248258e-02 , 6.34642763608981e-02 , -1.59251829016669e-02 ), ( -2.26487578411400e-02 , 7.54529703717812e-02 , -1.72854851773508e-02 ), ( -1.69021686492795e-02 , 7.24877434965381e-02 , -8.32235613476904e-02 ), ( -2.00147470785519e-02 , 8.66757664758654e-02 , -1.02197102389267e-01 ), ( -8.62297525244983e-03 , 4.63953041892996e-02 , -8.33777736619381e-02 ), ( -1.86270819201375e-02 , 6.68989416403372e-02 , -3.52706493301954e-02 ), ( -2.44812912922878e-02 , 9.31762079245552e-02 , -6.91835824823653e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 25, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2535,10 +3681,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 26, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 26, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 26, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 26, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 26, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 26, atoms_positions[size = 51] = { ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 ), ( 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 ), ( 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 ), ( 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 ), ( 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 ), ( 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 ), ( -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 ), ( -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 ), ( -3.67441092319199e+00 , 7.60406688373052e-02 , 5.46566218960245e+00 ), ( -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ), ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 ), ( 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459835e-01 ), ( 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 ), ( 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 ), ( 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 ), ( 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 ), ( 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 ), ( 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 ), ( 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 ), ( 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 ), ( 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 ), ( 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 ), ( 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 ), ( 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 ), ( 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 ), ( 3.83975554418138e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 ), ( 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 ), ( 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 ), ( 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 ), ( -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 ), ( 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 ), ( 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 ), ( -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 ), ( -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 ), ( -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 ), ( -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 ), ( -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 ), ( -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 ), ( -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 ), ( -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 ), ( -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 ), ( -5.48945484200930e+00 , 7.77049854240672e-01 , 3.33760630244013e+00 ), ( -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 ), ( -2.38839256737456e+00 , -3.24502407433314e-01 , 6.15138672061077e+00 ), ( -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 ), ( -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983191e+00 ), ( -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 ), ( -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 ), ( -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 ), ( -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 ), ( -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ) } +colvars: Step 26, atoms_positions[size = 51] = { ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 ), ( 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 ), ( 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 ), ( 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 ), ( 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 ), ( 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 ), ( -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 ), ( -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 ), ( -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 ), ( -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ), ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 ), ( 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459834e-01 ), ( 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 ), ( 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 ), ( 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 ), ( 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 ), ( 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 ), ( 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 ), ( 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 ), ( 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 ), ( 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 ), ( 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 ), ( 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 ), ( 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 ), ( 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 ), ( 3.83975554418137e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 ), ( 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 ), ( 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 ), ( 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 ), ( -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 ), ( 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 ), ( 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 ), ( -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 ), ( -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 ), ( -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 ), ( -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 ), ( -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 ), ( -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 ), ( -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 ), ( -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 ), ( -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 ), ( -5.48945484200930e+00 , 7.77049854240671e-01 , 3.33760630244013e+00 ), ( -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 ), ( -2.38839256737455e+00 , -3.24502407433307e-01 , 6.15138672061077e+00 ), ( -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 ), ( -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983190e+00 ), ( -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 ), ( -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 ), ( -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 ), ( -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 ), ( -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ) } colvars: Step 26, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 26, atom_groups_ids[size = 0] = @@ -2556,16 +3702,87 @@ colvars: Collective variables module, step no. 26 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 , 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459834e-01 , 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 , 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 , 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 , 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 , 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 , 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 , 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 , 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 , 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 , 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 , 3.83975554418137e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 , 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 , 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 , -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 , 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 , -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 , -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 , -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 , -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 , -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 , -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 , -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 , -5.48945484200930e+00 , 7.77049854240671e-01 , 3.33760630244013e+00 , -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -2.38839256737455e+00 , -3.24502407433307e-01 , 6.15138672061077e+00 , -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 , -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983190e+00 , -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 , -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 , -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 , -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 , -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 , 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459834e-01 , 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 , 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 , 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 , 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 , 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 , 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 , 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 , 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 , 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 , 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 , 3.83975554418137e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 , 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 , 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 , -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 , 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 , -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 , -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 , -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 , -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 , -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 , -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 , -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 , -5.48945484200930e+00 , 7.77049854240671e-01 , 3.33760630244013e+00 , -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -2.38839256737455e+00 , -3.24502407433307e-01 , 6.15138672061077e+00 , -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 , -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983190e+00 , -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 , -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 , -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 , -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 , -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2578,6 +3795,10 @@ colvars: Adding total bias energy: 11.5118 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2593,8 +3814,6 @@ colvars: ( 0.00725547 , -0.10545 , 0.315608 ) colvars: ( -0.0495543 , 0.0824925 , 0.214853 ) colvars: ( 0.0809439 , -0.236026 , 0.0255078 ) colvars: ( 0.136334 , -0.476208 , 0.335379 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.024485 , -0.0995714 , 0.0963342 ) colvars: ( 0.0199072 , -0.0820919 , 0.0832421 ) @@ -2647,14 +3866,17 @@ colvars: ( -0.00859519 , 0.0464057 , -0.083375 ) colvars: ( -0.0186112 , 0.0669171 , -0.0352835 ) colvars: ( -0.0223586 , 0.0842205 , -0.0589601 ) colvars: ( -0.0244447 , 0.0931759 , -0.0692101 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 26. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 26. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 26, atoms_new_colvar_forces = { ( -7.02759487121494e-02 , 3.03592903297381e-01 , -4.01322595058309e-01 ), ( 1.29777444484042e-02 , 3.11151912550363e-02 , -2.39334291295019e-01 ), ( -4.23984621351553e-02 , 9.52467395890064e-02 , 8.59805584984231e-02 ), ( -9.68508821319136e-02 , 2.50280691303569e-01 , 6.43201527675708e-02 ), ( -1.81394624860404e-02 , 9.83519274233092e-02 , -1.71706731179628e-01 ), ( 7.06861711244203e-02 , -1.85425392448265e-01 , -3.79380381448007e-02 ), ( 9.57471239129270e-03 , -9.87903314213212e-02 , 2.55100464157634e-01 ), ( -4.09347057274910e-02 , 6.04312464191056e-02 , 1.92547924833260e-01 ), ( 6.62631407386995e-02 , -1.91505902765397e-01 , 3.34422263795947e-02 ), ( 1.13975178390395e-01 , -3.91987080180140e-01 , 2.76419259062611e-01 ), ( 2.44850402010076e-02 , -9.95713974916157e-02 , 9.63342285937298e-02 ), ( 2.65010124687372e-02 , -9.75097049166922e-02 , 5.98681079194398e-02 ), ( 1.23528879662618e-02 , -5.58036520957835e-02 , 7.27007292311104e-02 ), ( 1.25005219271507e-02 , -5.36895785441518e-02 , 6.15353199422810e-02 ), ( 5.53611543404053e-03 , -3.49887682495593e-02 , 7.57667076403760e-02 ), ( -8.63700702604890e-03 , 9.82070089447021e-03 , 7.55114158522256e-02 ), ( -2.10659992708688e-03 , -2.67464113977565e-03 , 4.03568019629268e-02 ), ( -5.78123646494342e-03 , 9.92045066551187e-03 , 3.60609548302388e-02 ), ( 2.68984652041441e-03 , -1.30082658740007e-02 , 1.95391125026404e-02 ), ( 9.00226957835603e-03 , -2.21993856296152e-02 , -2.69355681840099e-02 ), ( 8.68438349470703e-03 , -2.39375135194768e-02 , -1.50708149285185e-02 ), ( 6.57630028948228e-03 , -1.36980342382398e-02 , -3.05772297762471e-02 ), ( 1.50111517137013e-02 , -4.69045680137091e-02 , -2.12866950333661e-03 ), ( 2.76239043083305e-02 , -8.89335499142471e-02 , 7.41413710602707e-03 ), ( 1.42854688295579e-02 , -4.71627686040402e-02 , 8.90375783411516e-03 ), ( 1.42402199047629e-02 , -4.43503631938378e-02 , -2.64816707932507e-03 ), ( 9.31746414113780e-03 , -3.72225620105006e-02 , 3.37679174239998e-02 ), ( -7.99308945475918e-04 , -1.52282832043496e-02 , 7.68186726665386e-02 ), ( -3.75619772566365e-03 , 4.21752672172109e-03 , 3.30709088042420e-02 ), ( -5.81406267630258e-03 , 1.12910157251468e-02 , 3.05785957286102e-02 ), ( -7.29582728360610e-03 , 1.80678557646107e-02 , 2.14986330080878e-02 ), ( -1.63107240894460e-02 , 5.23862202541373e-02 , -3.83592521087051e-03 ), ( -9.77096127551217e-03 , 3.58967100268294e-02 , -2.18343387088895e-02 ), ( -1.38007947251377e-02 , 5.01878895330269e-02 , -2.86165861734204e-02 ), ( -2.01670542625995e-03 , 1.48183742544679e-02 , -3.65692494411242e-02 ), ( 1.05381451549543e-02 , -1.62732033203028e-02 , -7.35649265176478e-02 ), ( 4.35413995448841e-03 , -1.13928950370447e-03 , -5.45611871279412e-02 ), ( 3.33031042288602e-03 , 5.66479643420804e-03 , -7.00158856017225e-02 ), ( 7.12723901359867e-03 , -1.52179938195833e-02 , -3.15274406212481e-02 ), ( 1.31306877600108e-02 , -4.18816228571182e-02 , 1.82851326350305e-03 ), ( 5.48734989236870e-04 , 1.47786091102192e-03 , -1.38926182011663e-02 ), ( 4.84204918059284e-04 , 3.03549036454787e-03 , -1.97512896041410e-02 ), ( -6.49162233900808e-03 , 2.05083540598446e-02 , -5.01450680240982e-05 ), ( -2.05364121159091e-02 , 5.81269386311858e-02 , 2.90583664730193e-02 ), ( -1.89435793931410e-02 , 6.34950680085711e-02 , -1.59343341897455e-02 ), ( -2.26431912621753e-02 , 7.54909620571149e-02 , -1.72960215224767e-02 ), ( -1.68692306396098e-02 , 7.24974880057940e-02 , -8.32327838657938e-02 ), ( -1.99729416336030e-02 , 8.66826413894369e-02 , -1.02209969773827e-01 ), ( -8.59518558707567e-03 , 4.64057351138899e-02 , -8.33750094210587e-02 ), ( -1.86112386515313e-02 , 6.69171340762310e-02 , -3.52835165863774e-02 ), ( -2.44447077038081e-02 , 9.31759407762520e-02 , -6.92101336975360e-02 ) } +colvars: Step 26, atoms_new_colvar_forces = { ( -7.02759487121496e-02 , 3.03592903297381e-01 , -4.01322595058309e-01 ), ( 1.29777444484041e-02 , 3.11151912550363e-02 , -2.39334291295019e-01 ), ( -4.23984621351551e-02 , 9.52467395890062e-02 , 8.59805584984231e-02 ), ( -9.68508821319136e-02 , 2.50280691303569e-01 , 6.43201527675709e-02 ), ( -1.81394624860405e-02 , 9.83519274233092e-02 , -1.71706731179628e-01 ), ( 7.06861711244202e-02 , -1.85425392448265e-01 , -3.79380381448007e-02 ), ( 9.57471239129273e-03 , -9.87903314213212e-02 , 2.55100464157634e-01 ), ( -4.09347057274910e-02 , 6.04312464191056e-02 , 1.92547924833260e-01 ), ( 6.62631407386996e-02 , -1.91505902765397e-01 , 3.34422263795946e-02 ), ( 1.13975178390395e-01 , -3.91987080180140e-01 , 2.76419259062611e-01 ), ( 2.44850402010076e-02 , -9.95713974916157e-02 , 9.63342285937298e-02 ), ( 2.65010124687372e-02 , -9.75097049166921e-02 , 5.98681079194398e-02 ), ( 1.23528879662618e-02 , -5.58036520957835e-02 , 7.27007292311104e-02 ), ( 1.25005219271507e-02 , -5.36895785441518e-02 , 6.15353199422810e-02 ), ( 5.53611543404054e-03 , -3.49887682495592e-02 , 7.57667076403759e-02 ), ( -8.63700702604888e-03 , 9.82070089447024e-03 , 7.55114158522256e-02 ), ( -2.10659992708687e-03 , -2.67464113977563e-03 , 4.03568019629268e-02 ), ( -5.78123646494341e-03 , 9.92045066551190e-03 , 3.60609548302388e-02 ), ( 2.68984652041441e-03 , -1.30082658740007e-02 , 1.95391125026403e-02 ), ( 9.00226957835600e-03 , -2.21993856296152e-02 , -2.69355681840099e-02 ), ( 8.68438349470702e-03 , -2.39375135194767e-02 , -1.50708149285185e-02 ), ( 6.57630028948226e-03 , -1.36980342382398e-02 , -3.05772297762471e-02 ), ( 1.50111517137013e-02 , -4.69045680137091e-02 , -2.12866950333664e-03 ), ( 2.76239043083305e-02 , -8.89335499142471e-02 , 7.41413710602703e-03 ), ( 1.42854688295579e-02 , -4.71627686040402e-02 , 8.90375783411515e-03 ), ( 1.42402199047629e-02 , -4.43503631938378e-02 , -2.64816707932508e-03 ), ( 9.31746414113780e-03 , -3.72225620105006e-02 , 3.37679174239998e-02 ), ( -7.99308945475898e-04 , -1.52282832043496e-02 , 7.68186726665386e-02 ), ( -3.75619772566364e-03 , 4.21752672172109e-03 , 3.30709088042420e-02 ), ( -5.81406267630256e-03 , 1.12910157251468e-02 , 3.05785957286102e-02 ), ( -7.29582728360609e-03 , 1.80678557646107e-02 , 2.14986330080878e-02 ), ( -1.63107240894460e-02 , 5.23862202541373e-02 , -3.83592521087052e-03 ), ( -9.77096127551217e-03 , 3.58967100268293e-02 , -2.18343387088894e-02 ), ( -1.38007947251377e-02 , 5.01878895330269e-02 , -2.86165861734203e-02 ), ( -2.01670542625997e-03 , 1.48183742544679e-02 , -3.65692494411242e-02 ), ( 1.05381451549542e-02 , -1.62732033203028e-02 , -7.35649265176479e-02 ), ( 4.35413995448840e-03 , -1.13928950370447e-03 , -5.45611871279412e-02 ), ( 3.33031042288600e-03 , 5.66479643420802e-03 , -7.00158856017225e-02 ), ( 7.12723901359866e-03 , -1.52179938195834e-02 , -3.15274406212481e-02 ), ( 1.31306877600108e-02 , -4.18816228571183e-02 , 1.82851326350306e-03 ), ( 5.48734989236875e-04 , 1.47786091102190e-03 , -1.38926182011663e-02 ), ( 4.84204918059289e-04 , 3.03549036454782e-03 , -1.97512896041410e-02 ), ( -6.49162233900807e-03 , 2.05083540598445e-02 , -5.01450680240616e-05 ), ( -2.05364121159090e-02 , 5.81269386311858e-02 , 2.90583664730193e-02 ), ( -1.89435793931410e-02 , 6.34950680085711e-02 , -1.59343341897455e-02 ), ( -2.26431912621753e-02 , 7.54909620571149e-02 , -1.72960215224767e-02 ), ( -1.68692306396098e-02 , 7.24974880057940e-02 , -8.32327838657938e-02 ), ( -1.99729416336030e-02 , 8.66826413894369e-02 , -1.02209969773827e-01 ), ( -8.59518558707570e-03 , 4.64057351138899e-02 , -8.33750094210587e-02 ), ( -1.86112386515312e-02 , 6.69171340762310e-02 , -3.52835165863774e-02 ), ( -2.44447077038081e-02 , 9.31759407762520e-02 , -6.92101336975360e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 26, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2692,10 +3914,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 27, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 27, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 27, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 27, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 27, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 27, atoms_positions[size = 51] = { ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 ), ( 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 ), ( 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 ), ( 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 ), ( 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 ), ( 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 ), ( -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 ), ( -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 ), ( -3.67239157969653e+00 , 7.86444043011857e-02 , 5.47216870495720e+00 ), ( -4.81061183134772e+00 , 3.26599326572317e+00 , 7.26118632650396e+00 ), ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 ), ( 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 ), ( 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 ), ( 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321918e-01 ), ( 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 ), ( 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 ), ( 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 ), ( 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 ), ( 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 ), ( 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 ), ( 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 ), ( 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 ), ( 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 ), ( 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 ), ( 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 ), ( 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 ), ( 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 ), ( 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 ), ( 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 ), ( -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 ), ( 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 ), ( 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 ), ( -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 ), ( -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 ), ( -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 ), ( -7.19299148831412e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 ), ( -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 ), ( -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 ), ( -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 ), ( -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 ), ( -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 ), ( -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 ), ( -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 ), ( -2.38611115771939e+00 , -3.23414419937704e-01 , 6.14694225305598e+00 ), ( -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 ), ( -5.36207760113481e+00 , 5.84976302002794e-01 , 7.21438869028155e+00 ), ( -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 ), ( -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 ), ( -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 ), ( -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 ), ( -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ) } +colvars: Step 27, atoms_positions[size = 51] = { ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 ), ( 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 ), ( 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 ), ( 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 ), ( 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 ), ( 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 ), ( -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 ), ( -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 ), ( -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 ), ( -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 ), ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 ), ( 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 ), ( 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 ), ( 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321919e-01 ), ( 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 ), ( 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 ), ( 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 ), ( 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 ), ( 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 ), ( 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 ), ( 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 ), ( 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 ), ( 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 ), ( 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 ), ( 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 ), ( 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 ), ( 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 ), ( 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 ), ( 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 ), ( -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 ), ( 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 ), ( 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 ), ( -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 ), ( -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 ), ( -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 ), ( -7.19299148831411e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 ), ( -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 ), ( -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 ), ( -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 ), ( -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 ), ( -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 ), ( -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 ), ( -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 ), ( -2.38611115771938e+00 , -3.23414419937697e-01 , 6.14694225305597e+00 ), ( -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 ), ( -5.36207760113481e+00 , 5.84976302002793e-01 , 7.21438869028155e+00 ), ( -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 ), ( -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 ), ( -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 ), ( -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 ), ( -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ) } colvars: Step 27, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 27, atom_groups_ids[size = 0] = @@ -2713,16 +3935,87 @@ colvars: Collective variables module, step no. 27 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 , 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 , 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 , 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321919e-01 , 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 , 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 , 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 , 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 , 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 , 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 , 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 , 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 , 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 , 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 , 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 , -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 , 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 , -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 , -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 , -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -7.19299148831411e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 , -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 , -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 , -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 , -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 , -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 , -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -2.38611115771938e+00 , -3.23414419937697e-01 , 6.14694225305597e+00 , -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 , -5.36207760113481e+00 , 5.84976302002793e-01 , 7.21438869028155e+00 , -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 , -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 , -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 , -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 , -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 , 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 , 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 , 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321919e-01 , 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 , 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 , 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 , 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 , 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 , 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 , 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 , 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 , 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 , 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 , 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 , -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 , 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 , -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 , -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 , -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -7.19299148831411e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 , -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 , -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 , -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 , -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 , -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 , -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -2.38611115771938e+00 , -3.23414419937697e-01 , 6.14694225305597e+00 , -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 , -5.36207760113481e+00 , 5.84976302002793e-01 , 7.21438869028155e+00 , -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 , -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 , -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 , -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 , -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2735,6 +4028,10 @@ colvars: Adding total bias energy: 11.5114 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2750,8 +4047,6 @@ colvars: ( 0.00711886 , -0.105444 , 0.315388 ) colvars: ( -0.0495585 , 0.0821349 , 0.214966 ) colvars: ( 0.0809504 , -0.236126 , 0.0258951 ) colvars: ( 0.136148 , -0.47607 , 0.33543 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0244389 , -0.0995621 , 0.0963506 ) colvars: ( 0.0198721 , -0.082097 , 0.0832519 ) @@ -2804,14 +4099,17 @@ colvars: ( -0.00856576 , 0.0464172 , -0.0833694 ) colvars: ( -0.0185967 , 0.0669301 , -0.0352981 ) colvars: ( -0.0223316 , 0.0842257 , -0.058977 ) colvars: ( -0.0244082 , 0.0931659 , -0.0692311 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 27. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 27. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 27, atoms_new_colvar_forces = { ( -7.00918839295064e-02 , 3.03562631602812e-01 , -4.01230929831610e-01 ), ( 1.30228758705242e-02 , 3.13827887370110e-02 , -2.39424491797733e-01 ), ( -4.24616685652880e-02 , 9.53835979703357e-02 , 8.55264993388502e-02 ), ( -9.68240429627762e-02 , 2.50061075123733e-01 , 6.41508540355183e-02 ), ( -1.80414634629806e-02 , 9.82538668968961e-02 , -1.71472514960320e-01 ), ( 7.06557321135335e-02 , -1.85230277861217e-01 , -3.78873518772363e-02 ), ( 9.46350321907650e-03 , -9.87959399798595e-02 , 2.54890867620378e-01 ), ( -4.09425282344282e-02 , 6.01006350600721e-02 , 1.92681282419908e-01 ), ( 6.62602546982738e-02 , -1.91572278981195e-01 , 3.38169510399862e-02 ), ( 1.13816818760197e-01 , -3.91844223708385e-01 , 2.76452516683183e-01 ), ( 2.44388756577774e-02 , -9.95621342458959e-02 , 9.63505584456550e-02 ), ( 2.64755279440645e-02 , -9.75245532058121e-02 , 5.98880018253482e-02 ), ( 1.23248315375857e-02 , -5.58111427214885e-02 , 7.27023861546839e-02 ), ( 1.24747461734146e-02 , -5.36917952096011e-02 , 6.15401343699062e-02 ), ( 5.51192150634254e-03 , -3.50046483383724e-02 , 7.57575991860129e-02 ), ( -8.65227008336139e-03 , 9.79196214590065e-03 , 7.54819945039508e-02 ), ( -2.11286820065884e-03 , -2.69812507500008e-03 , 4.03425028835691e-02 ), ( -5.78649800221506e-03 , 9.90222838177424e-03 , 3.60438978525862e-02 ), ( 2.69299629720132e-03 , -1.30418621694614e-02 , 1.95321561354718e-02 ), ( 9.02626661697228e-03 , -2.22507545160550e-02 , -2.69306034571754e-02 ), ( 8.69644116503100e-03 , -2.39656725403336e-02 , -1.50633697361967e-02 ), ( 6.59446000905699e-03 , -1.37254617346516e-02 , -3.05696631273867e-02 ), ( 1.50134732127959e-02 , -4.69237871938746e-02 , -2.11363340989586e-03 ), ( 2.76130137525994e-02 , -8.89357221272514e-02 , 7.44686468199215e-03 ), ( 1.42765376002831e-02 , -4.71595341482906e-02 , 8.92074709266032e-03 ), ( 1.42338803726940e-02 , -4.43421789389268e-02 , -2.62826389885197e-03 ), ( 9.29972386139693e-03 , -3.72153352269306e-02 , 3.37753908498073e-02 ), ( -8.33599916874233e-04 , -1.52087633395627e-02 , 7.68089093286441e-02 ), ( -3.77100007712009e-03 , 4.22936205944202e-03 , 3.30631726198432e-02 ), ( -5.82983732798803e-03 , 1.13105190175713e-02 , 3.05703186441769e-02 ), ( -7.30086314368950e-03 , 1.80664473965964e-02 , 2.14856482153999e-02 ), ( -1.62964605632924e-02 , 5.23633164766681e-02 , -3.86040699596929e-03 ), ( -9.75706736775822e-03 , 3.58883761599068e-02 , -2.18446064193114e-02 ), ( -1.37843146647957e-02 , 5.01831413928922e-02 , -2.86299893752881e-02 ), ( -1.99861537665627e-03 , 1.48060903079009e-02 , -3.65682156413178e-02 ), ( 1.05678765369072e-02 , -1.62920244012486e-02 , -7.35434253074627e-02 ), ( 4.37194853737757e-03 , -1.13711218922162e-03 , -5.45461735948314e-02 ), ( 3.35345912840901e-03 , 5.66889059294423e-03 , -6.99991598096522e-02 ), ( 7.13223287626544e-03 , -1.52052602553789e-02 , -3.15106149149864e-02 ), ( 1.31139199664390e-02 , -4.18458818185023e-02 , 1.85205753754504e-03 ), ( 5.42706815934916e-04 , 1.51076931287781e-03 , -1.38827152006991e-02 ), ( 4.77805130120424e-04 , 3.07602707525113e-03 , -1.97388884158322e-02 ), ( -6.49926788211310e-03 , 2.05377353834856e-02 , -5.20710086762654e-05 ), ( -2.05506026036694e-02 , 5.81576335292180e-02 , 2.90343421506679e-02 ), ( -1.89404668103573e-02 , 6.35216142070820e-02 , -1.59497126415629e-02 ), ( -2.26405419833073e-02 , 7.55239927482679e-02 , -1.73144238866618e-02 ), ( -1.68354683467430e-02 , 7.25037673134110e-02 , -8.32385599157364e-02 ), ( -1.99298828125147e-02 , 8.66848171303143e-02 , -1.02217297110141e-01 ), ( -8.56576446939229e-03 , 4.64172138931442e-02 , -8.33693617236000e-02 ), ( -1.85966500629948e-02 , 6.69300872459209e-02 , -3.52980902148761e-02 ), ( -2.44082025097931e-02 , 9.31658827650885e-02 , -6.92311193427338e-02 ) } +colvars: Step 27, atoms_new_colvar_forces = { ( -7.00918839295065e-02 , 3.03562631602812e-01 , -4.01230929831610e-01 ), ( 1.30228758705242e-02 , 3.13827887370110e-02 , -2.39424491797733e-01 ), ( -4.24616685652879e-02 , 9.53835979703357e-02 , 8.55264993388502e-02 ), ( -9.68240429627762e-02 , 2.50061075123733e-01 , 6.41508540355183e-02 ), ( -1.80414634629806e-02 , 9.82538668968962e-02 , -1.71472514960320e-01 ), ( 7.06557321135335e-02 , -1.85230277861217e-01 , -3.78873518772363e-02 ), ( 9.46350321907656e-03 , -9.87959399798596e-02 , 2.54890867620378e-01 ), ( -4.09425282344281e-02 , 6.01006350600723e-02 , 1.92681282419908e-01 ), ( 6.62602546982739e-02 , -1.91572278981195e-01 , 3.38169510399862e-02 ), ( 1.13816818760197e-01 , -3.91844223708385e-01 , 2.76452516683183e-01 ), ( 2.44388756577774e-02 , -9.95621342458959e-02 , 9.63505584456550e-02 ), ( 2.64755279440645e-02 , -9.75245532058120e-02 , 5.98880018253482e-02 ), ( 1.23248315375857e-02 , -5.58111427214885e-02 , 7.27023861546839e-02 ), ( 1.24747461734146e-02 , -5.36917952096011e-02 , 6.15401343699061e-02 ), ( 5.51192150634254e-03 , -3.50046483383724e-02 , 7.57575991860129e-02 ), ( -8.65227008336139e-03 , 9.79196214590068e-03 , 7.54819945039508e-02 ), ( -2.11286820065884e-03 , -2.69812507500006e-03 , 4.03425028835691e-02 ), ( -5.78649800221507e-03 , 9.90222838177424e-03 , 3.60438978525862e-02 ), ( 2.69299629720131e-03 , -1.30418621694614e-02 , 1.95321561354718e-02 ), ( 9.02626661697226e-03 , -2.22507545160550e-02 , -2.69306034571754e-02 ), ( 8.69644116503099e-03 , -2.39656725403336e-02 , -1.50633697361967e-02 ), ( 6.59446000905698e-03 , -1.37254617346516e-02 , -3.05696631273867e-02 ), ( 1.50134732127959e-02 , -4.69237871938746e-02 , -2.11363340989585e-03 ), ( 2.76130137525994e-02 , -8.89357221272514e-02 , 7.44686468199215e-03 ), ( 1.42765376002831e-02 , -4.71595341482906e-02 , 8.92074709266032e-03 ), ( 1.42338803726940e-02 , -4.43421789389268e-02 , -2.62826389885197e-03 ), ( 9.29972386139693e-03 , -3.72153352269306e-02 , 3.37753908498073e-02 ), ( -8.33599916874229e-04 , -1.52087633395627e-02 , 7.68089093286441e-02 ), ( -3.77100007712009e-03 , 4.22936205944202e-03 , 3.30631726198432e-02 ), ( -5.82983732798802e-03 , 1.13105190175712e-02 , 3.05703186441769e-02 ), ( -7.30086314368950e-03 , 1.80664473965964e-02 , 2.14856482153999e-02 ), ( -1.62964605632924e-02 , 5.23633164766681e-02 , -3.86040699596929e-03 ), ( -9.75706736775823e-03 , 3.58883761599068e-02 , -2.18446064193114e-02 ), ( -1.37843146647957e-02 , 5.01831413928922e-02 , -2.86299893752881e-02 ), ( -1.99861537665628e-03 , 1.48060903079009e-02 , -3.65682156413178e-02 ), ( 1.05678765369071e-02 , -1.62920244012486e-02 , -7.35434253074627e-02 ), ( 4.37194853737756e-03 , -1.13711218922164e-03 , -5.45461735948314e-02 ), ( 3.35345912840900e-03 , 5.66889059294422e-03 , -6.99991598096522e-02 ), ( 7.13223287626544e-03 , -1.52052602553789e-02 , -3.15106149149864e-02 ), ( 1.31139199664390e-02 , -4.18458818185023e-02 , 1.85205753754504e-03 ), ( 5.42706815934922e-04 , 1.51076931287779e-03 , -1.38827152006991e-02 ), ( 4.77805130120433e-04 , 3.07602707525109e-03 , -1.97388884158322e-02 ), ( -6.49926788211309e-03 , 2.05377353834856e-02 , -5.20710086762631e-05 ), ( -2.05506026036694e-02 , 5.81576335292180e-02 , 2.90343421506679e-02 ), ( -1.89404668103573e-02 , 6.35216142070820e-02 , -1.59497126415629e-02 ), ( -2.26405419833073e-02 , 7.55239927482679e-02 , -1.73144238866618e-02 ), ( -1.68354683467430e-02 , 7.25037673134109e-02 , -8.32385599157364e-02 ), ( -1.99298828125146e-02 , 8.66848171303143e-02 , -1.02217297110141e-01 ), ( -8.56576446939230e-03 , 4.64172138931442e-02 , -8.33693617236000e-02 ), ( -1.85966500629948e-02 , 6.69300872459209e-02 , -3.52980902148761e-02 ), ( -2.44082025097931e-02 , 9.31658827650885e-02 , -6.92311193427338e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 27, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2849,10 +4147,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 28, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 28, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 28, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 28, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 28, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 28, atoms_positions[size = 51] = { ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371142e-01 ), ( 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 ), ( 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 ), ( 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 ), ( 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 ), ( 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 ), ( -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 ), ( -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 ), ( -3.67073843017742e+00 , 8.01608924560728e-02 , 5.47777368326127e+00 ), ( -4.81202089485083e+00 , 3.27314869824355e+00 , 7.25929534791218e+00 ), ( 8.29937250565104e+00 , 4.23866805000533e-02 , -7.17159057051135e-01 ), ( 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828406e-01 ), ( 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 ), ( 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 ), ( 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 ), ( 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 ), ( 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 ), ( 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 ), ( 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 ), ( 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 ), ( 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 ), ( 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 ), ( 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 ), ( 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 ), ( 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 ), ( 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 ), ( 2.07308013451524e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 ), ( 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 ), ( 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 ), ( -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 ), ( 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 ), ( 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 ), ( -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 ), ( -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 ), ( -5.42011744036733e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 ), ( -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638271e+00 ), ( -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 ), ( -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 ), ( -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 ), ( -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 ), ( -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 ), ( -5.48235415482577e+00 , 7.64556077951691e-01 , 3.34059019506604e+00 ), ( -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 ), ( -2.38315281417864e+00 , -3.21340415243169e-01 , 6.14259769946699e+00 ), ( -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 ), ( -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 ), ( -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 ), ( -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 ), ( -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 ), ( -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 ), ( -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ) } +colvars: Step 28, atoms_positions[size = 51] = { ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 ), ( 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 ), ( 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 ), ( 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 ), ( 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 ), ( 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 ), ( -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 ), ( -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 ), ( -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 ), ( -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 ), ( 8.29937250565104e+00 , 4.23866805000532e-02 , -7.17159057051135e-01 ), ( 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828405e-01 ), ( 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 ), ( 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 ), ( 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 ), ( 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 ), ( 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 ), ( 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 ), ( 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 ), ( 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 ), ( 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 ), ( 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 ), ( 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 ), ( 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 ), ( 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 ), ( 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 ), ( 2.07308013451523e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 ), ( 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 ), ( 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 ), ( -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 ), ( 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 ), ( 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 ), ( -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 ), ( -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 ), ( -5.42011744036734e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 ), ( -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638270e+00 ), ( -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 ), ( -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 ), ( -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 ), ( -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 ), ( -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 ), ( -5.48235415482577e+00 , 7.64556077951690e-01 , 3.34059019506604e+00 ), ( -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 ), ( -2.38315281417863e+00 , -3.21340415243162e-01 , 6.14259769946698e+00 ), ( -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 ), ( -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 ), ( -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 ), ( -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 ), ( -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 ), ( -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 ), ( -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ) } colvars: Step 28, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 28, atom_groups_ids[size = 0] = @@ -2870,16 +4168,87 @@ colvars: Collective variables module, step no. 28 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092545e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092544e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.29937250565104e+00 , 4.23866805000532e-02 , -7.17159057051135e-01 , 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828405e-01 , 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 , 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 , 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 , 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 , 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 , 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 , 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 , 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 , 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 , 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 , 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 , 2.07308013451523e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 , 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 , -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 , 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 , -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 , -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 , -5.42011744036734e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638270e+00 , -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 , -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 , -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 , -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 , -5.48235415482577e+00 , 7.64556077951690e-01 , 3.34059019506604e+00 , -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -2.38315281417863e+00 , -3.21340415243162e-01 , 6.14259769946698e+00 , -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 , -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 , -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 , -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 , -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 , -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 , -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092545e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). +colvars: Colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092544e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.29937250565104e+00 , 4.23866805000532e-02 , -7.17159057051135e-01 , 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828405e-01 , 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 , 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 , 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 , 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 , 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 , 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 , 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 , 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 , 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 , 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 , 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 , 2.07308013451523e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 , 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 , -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 , 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 , -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 , -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 , -5.42011744036734e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638270e+00 , -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 , -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 , -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 , -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 , -5.48235415482577e+00 , 7.64556077951690e-01 , 3.34059019506604e+00 , -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -2.38315281417863e+00 , -3.21340415243162e-01 , 6.14259769946698e+00 , -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 , -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 , -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 , -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 , -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 , -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 , -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -2892,6 +4261,10 @@ colvars: Adding total bias energy: 11.5106 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -2907,8 +4280,6 @@ colvars: ( 0.00697909 , -0.105444 , 0.31517 ) colvars: ( -0.0495798 , 0.0817944 , 0.215067 ) colvars: ( 0.0809625 , -0.236202 , 0.0262542 ) colvars: ( 0.135977 , -0.475926 , 0.335459 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243941 , -0.099545 , 0.0963622 ) colvars: ( 0.0198381 , -0.0820968 , 0.0832606 ) @@ -2961,14 +4332,17 @@ colvars: ( -0.0085359 , 0.0464284 , -0.0833634 ) colvars: ( -0.0185841 , 0.0669377 , -0.0353153 ) colvars: ( -0.0223065 , 0.0842241 , -0.058994 ) colvars: ( -0.0243736 , 0.0931472 , -0.0692483 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 28. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 28. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 28, atoms_new_colvar_forces = { ( -6.99105964745414e-02 , 3.03534108224077e-01 , -4.01125198858137e-01 ), ( 1.30792098250532e-02 , 3.16310929373661e-02 , -2.39499701615836e-01 ), ( -4.25255029736803e-02 , 9.54922740032261e-02 , 8.51087057351073e-02 ), ( -9.68128132349850e-02 , 2.49843308955989e-01 , 6.39997898630516e-02 ), ( -1.79464748638226e-02 , 9.81685466429824e-02 , -1.71250102556514e-01 ), ( 7.06379507910652e-02 , -1.85041970185675e-01 , -3.78425579319191e-02 ), ( 9.35083933511790e-03 , -9.88068220395378e-02 , 2.54689455152915e-01 ), ( -4.09659433594163e-02 , 5.97932072032175e-02 , 1.92798200103656e-01 ), ( 6.62605501454588e-02 , -1.91618026165443e-01 , 3.41544371557535e-02 ), ( 1.13670038704103e-01 , -3.91702187892016e-01 , 2.76465205814139e-01 ), ( 2.43941032937985e-02 , -9.95450315112680e-02 , 9.63621500021452e-02 ), ( 2.64526804358145e-02 , -9.75317185173844e-02 , 5.99104372755897e-02 ), ( 1.22970656157734e-02 , -5.58162675354601e-02 , 7.27035002216812e-02 ), ( 1.24494756477064e-02 , -5.36908802348386e-02 , 6.15436432653573e-02 ), ( 5.48704688714376e-03 , -3.50215844750732e-02 , 7.57493863140233e-02 ), ( -8.67012952291998e-03 , 9.75558764555574e-03 , 7.54556612518544e-02 ), ( -2.12010225636095e-03 , -2.72534424138995e-03 , 4.03319038952513e-02 ), ( -5.79320046768154e-03 , 9.87935351909539e-03 , 3.60292720624457e-02 ), ( 2.69638236344813e-03 , -1.30775617081468e-02 , 1.95324137553816e-02 ), ( 9.05251869178128e-03 , -2.23019324748084e-02 , -2.69119622158068e-02 ), ( 8.71027637037681e-03 , -2.39922447972659e-02 , -1.50481952882849e-02 ), ( 6.61441724671008e-03 , -1.37516683392467e-02 , -3.05540177540563e-02 ), ( 1.50181321585705e-02 , -4.69385652870097e-02 , -2.09312910608297e-03 ), ( 2.76059252628942e-02 , -8.89273993060487e-02 , 7.48140988776515e-03 ), ( 1.42694316016934e-02 , -4.71506609950198e-02 , 8.93744511963322e-03 ), ( 1.42295639585641e-02 , -4.43276814589434e-02 , -2.60933393989567e-03 ), ( 9.28254514352050e-03 , -3.72047576822429e-02 , 3.37803143159950e-02 ), ( -8.69775702737491e-04 , -1.51900253011091e-02 , 7.67913363669554e-02 ), ( -3.78712761698228e-03 , 4.23979009716207e-03 , 3.30510708702083e-02 ), ( -5.84723852640201e-03 , 1.13284759700188e-02 , 3.05558632441676e-02 ), ( -7.30738149450517e-03 , 1.80614978519294e-02 , 2.14716730988585e-02 ), ( -1.62842633958380e-02 , 5.23322937967764e-02 , -3.88032006840828e-03 ), ( -9.74404228898785e-03 , 3.58761140757968e-02 , -2.18525871928399e-02 ), ( -1.37691637380410e-02 , 5.01733408163495e-02 , -2.86418995399456e-02 ), ( -1.97994657736161e-03 , 1.47930001175436e-02 , -3.65629037841475e-02 ), ( 1.06008081770661e-02 , -1.63062648103744e-02 , -7.35138432584534e-02 ), ( 4.39151001737965e-03 , -1.13162558162393e-03 , -5.45291484906228e-02 ), ( 3.37852500415077e-03 , 5.67644658806253e-03 , -6.99802892637869e-02 ), ( 7.13880736625240e-03 , -1.51878963709950e-02 , -3.14950444881112e-02 ), ( 1.30987062537573e-02 , -4.18022069940880e-02 , 1.86792386817925e-03 ), ( 5.36790918205760e-04 , 1.54685236917992e-03 , -1.38799100920889e-02 ), ( 4.71571839629201e-04 , 3.12046790390119e-03 , -1.97351320604518e-02 ), ( -6.50806934625518e-03 , 2.05668835560401e-02 , -6.12559491181550e-05 ), ( -2.05685759895296e-02 , 5.81819166560511e-02 , 2.90007198523593e-02 ), ( -1.89399299546582e-02 , 6.35432232945508e-02 , -1.59717550759216e-02 ), ( -2.26410185265841e-02 , 7.55511789495086e-02 , -1.73411688823523e-02 ), ( -1.68024096378493e-02 , 7.25060849069893e-02 , -8.32433362384075e-02 ), ( -1.98875385771560e-02 , 8.66819831532424e-02 , -1.02222056961599e-01 ), ( -8.53590432797544e-03 , 4.64283976982095e-02 , -8.33634418048039e-02 ), ( -1.85840756007226e-02 , 6.69376673267996e-02 , -3.53153210594370e-02 ), ( -2.43736486000415e-02 , 9.31472296453879e-02 , -6.92483050154469e-02 ) } +colvars: Step 28, atoms_new_colvar_forces = { ( -6.99105964745414e-02 , 3.03534108224077e-01 , -4.01125198858137e-01 ), ( 1.30792098250531e-02 , 3.16310929373660e-02 , -2.39499701615836e-01 ), ( -4.25255029736803e-02 , 9.54922740032261e-02 , 8.51087057351073e-02 ), ( -9.68128132349850e-02 , 2.49843308955989e-01 , 6.39997898630516e-02 ), ( -1.79464748638226e-02 , 9.81685466429824e-02 , -1.71250102556514e-01 ), ( 7.06379507910651e-02 , -1.85041970185675e-01 , -3.78425579319191e-02 ), ( 9.35083933511791e-03 , -9.88068220395377e-02 , 2.54689455152915e-01 ), ( -4.09659433594162e-02 , 5.97932072032176e-02 , 1.92798200103656e-01 ), ( 6.62605501454588e-02 , -1.91618026165443e-01 , 3.41544371557534e-02 ), ( 1.13670038704103e-01 , -3.91702187892015e-01 , 2.76465205814139e-01 ), ( 2.43941032937985e-02 , -9.95450315112680e-02 , 9.63621500021451e-02 ), ( 2.64526804358145e-02 , -9.75317185173843e-02 , 5.99104372755897e-02 ), ( 1.22970656157735e-02 , -5.58162675354601e-02 , 7.27035002216811e-02 ), ( 1.24494756477064e-02 , -5.36908802348386e-02 , 6.15436432653573e-02 ), ( 5.48704688714377e-03 , -3.50215844750731e-02 , 7.57493863140233e-02 ), ( -8.67012952291996e-03 , 9.75558764555577e-03 , 7.54556612518543e-02 ), ( -2.12010225636094e-03 , -2.72534424138993e-03 , 4.03319038952513e-02 ), ( -5.79320046768153e-03 , 9.87935351909541e-03 , 3.60292720624457e-02 ), ( 2.69638236344813e-03 , -1.30775617081468e-02 , 1.95324137553816e-02 ), ( 9.05251869178125e-03 , -2.23019324748083e-02 , -2.69119622158068e-02 ), ( 8.71027637037679e-03 , -2.39922447972658e-02 , -1.50481952882849e-02 ), ( 6.61441724671005e-03 , -1.37516683392467e-02 , -3.05540177540563e-02 ), ( 1.50181321585705e-02 , -4.69385652870096e-02 , -2.09312910608296e-03 ), ( 2.76059252628942e-02 , -8.89273993060486e-02 , 7.48140988776513e-03 ), ( 1.42694316016934e-02 , -4.71506609950198e-02 , 8.93744511963321e-03 ), ( 1.42295639585641e-02 , -4.43276814589433e-02 , -2.60933393989568e-03 ), ( 9.28254514352052e-03 , -3.72047576822429e-02 , 3.37803143159949e-02 ), ( -8.69775702737456e-04 , -1.51900253011091e-02 , 7.67913363669554e-02 ), ( -3.78712761698226e-03 , 4.23979009716207e-03 , 3.30510708702082e-02 ), ( -5.84723852640200e-03 , 1.13284759700188e-02 , 3.05558632441676e-02 ), ( -7.30738149450516e-03 , 1.80614978519294e-02 , 2.14716730988585e-02 ), ( -1.62842633958380e-02 , 5.23322937967764e-02 , -3.88032006840828e-03 ), ( -9.74404228898785e-03 , 3.58761140757968e-02 , -2.18525871928399e-02 ), ( -1.37691637380410e-02 , 5.01733408163495e-02 , -2.86418995399456e-02 ), ( -1.97994657736163e-03 , 1.47930001175436e-02 , -3.65629037841475e-02 ), ( 1.06008081770661e-02 , -1.63062648103744e-02 , -7.35138432584533e-02 ), ( 4.39151001737963e-03 , -1.13162558162395e-03 , -5.45291484906228e-02 ), ( 3.37852500415075e-03 , 5.67644658806250e-03 , -6.99802892637869e-02 ), ( 7.13880736625239e-03 , -1.51878963709950e-02 , -3.14950444881112e-02 ), ( 1.30987062537573e-02 , -4.18022069940880e-02 , 1.86792386817922e-03 ), ( 5.36790918205766e-04 , 1.54685236917990e-03 , -1.38799100920889e-02 ), ( 4.71571839629198e-04 , 3.12046790390116e-03 , -1.97351320604518e-02 ), ( -6.50806934625516e-03 , 2.05668835560400e-02 , -6.12559491181563e-05 ), ( -2.05685759895296e-02 , 5.81819166560511e-02 , 2.90007198523593e-02 ), ( -1.89399299546582e-02 , 6.35432232945508e-02 , -1.59717550759216e-02 ), ( -2.26410185265841e-02 , 7.55511789495086e-02 , -1.73411688823523e-02 ), ( -1.68024096378493e-02 , 7.25060849069892e-02 , -8.32433362384075e-02 ), ( -1.98875385771560e-02 , 8.66819831532423e-02 , -1.02222056961598e-01 ), ( -8.53590432797545e-03 , 4.64283976982095e-02 , -8.33634418048038e-02 ), ( -1.85840756007226e-02 , 6.69376673267996e-02 , -3.53153210594370e-02 ), ( -2.43736486000415e-02 , 9.31472296453878e-02 , -6.92483050154469e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 28, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3006,10 +4380,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 29, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 29, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 29, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 29, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 29, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 29, atoms_positions[size = 51] = { ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754424e-01 ), ( 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 ), ( 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 ), ( 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 ), ( 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 ), ( 8.65304397854146e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 ), ( -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 ), ( -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 ), ( -3.66933507872099e+00 , 8.05977535935299e-02 , 5.48202248684294e+00 ), ( -4.81296950008506e+00 , 3.27902937016758e+00 , 7.25609311672234e+00 ), ( 8.29622457456575e+00 , 4.23601649414827e-02 , -7.12749794942444e-01 ), ( 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 ), ( 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 ), ( 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 ), ( 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 ), ( 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 ), ( 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 ), ( 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 ), ( 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 ), ( 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 ), ( 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 ), ( 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 ), ( 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 ), ( 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 ), ( 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 ), ( 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 ), ( 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 ), ( 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 ), ( 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 ), ( -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 ), ( 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 ), ( 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 ), ( -3.54512396787449e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 ), ( -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 ), ( -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 ), ( -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 ), ( -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 ), ( -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 ), ( -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 ), ( -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 ), ( -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 ), ( -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 ), ( -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 ), ( -2.37949805223028e+00 , -3.18274942149998e-01 , 6.13855939203602e+00 ), ( -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 ), ( -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 ), ( -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 ), ( -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 ), ( -6.64854667858963e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 ), ( -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 ), ( -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ) } +colvars: Step 29, atoms_positions[size = 51] = { ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 ), ( 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 ), ( 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 ), ( 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 ), ( 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 ), ( 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 ), ( -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 ), ( -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 ), ( -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 ), ( -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 ), ( 8.29622457456575e+00 , 4.23601649414826e-02 , -7.12749794942444e-01 ), ( 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 ), ( 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 ), ( 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 ), ( 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 ), ( 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 ), ( 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 ), ( 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 ), ( 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 ), ( 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 ), ( 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 ), ( 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 ), ( 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 ), ( 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 ), ( 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 ), ( 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 ), ( 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 ), ( 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 ), ( 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 ), ( -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 ), ( 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 ), ( 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 ), ( -3.54512396787448e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 ), ( -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 ), ( -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 ), ( -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 ), ( -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 ), ( -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 ), ( -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 ), ( -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 ), ( -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 ), ( -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 ), ( -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 ), ( -2.37949805223027e+00 , -3.18274942149990e-01 , 6.13855939203602e+00 ), ( -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 ), ( -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 ), ( -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 ), ( -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 ), ( -6.64854667858964e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 ), ( -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 ), ( -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ) } colvars: Step 29, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 29, atom_groups_ids[size = 0] = @@ -3028,15 +4402,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601430e-02 , -1.45578300084090e-02 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601431e-02 , -1.45578300084090e-02 ). colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.29622457456575e+00 , 4.23601649414826e-02 , -7.12749794942444e-01 , 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 , 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 , 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 , 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 , 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 , 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 , 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 , 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 , 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 , 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 , 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 , 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 , 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 , 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 , -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 , 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 , -3.54512396787448e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 , -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 , -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 , -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 , -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 , -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 , -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 , -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 , -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -2.37949805223027e+00 , -3.18274942149990e-01 , 6.13855939203602e+00 , -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 , -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 , -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 , -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 , -6.64854667858964e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 , -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 , -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ). +colvars: Calculating gradients of colvar "fitting". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601430e-02 , -1.45578300084090e-02 ). +colvars: Colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601431e-02 , -1.45578300084090e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.29622457456575e+00 , 4.23601649414826e-02 , -7.12749794942444e-01 , 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 , 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 , 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 , 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 , 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 , 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 , 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 , 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 , 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 , 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 , 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 , 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 , 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 , 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 , -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 , 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 , -3.54512396787448e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 , -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 , -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 , -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 , -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 , -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 , -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 , -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 , -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -2.37949805223027e+00 , -3.18274942149990e-01 , 6.13855939203602e+00 , -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 , -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 , -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 , -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 , -6.64854667858964e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 , -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 , -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3049,6 +4494,10 @@ colvars: Adding total bias energy: 11.5097 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3064,8 +4513,6 @@ colvars: ( 0.00683767 , -0.105446 , 0.314978 ) colvars: ( -0.0496204 , 0.081493 , 0.215155 ) colvars: ( 0.0809815 , -0.23626 , 0.0265745 ) colvars: ( 0.135823 , -0.475792 , 0.33549 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243528 , -0.0995212 , 0.0963717 ) colvars: ( 0.0198067 , -0.0820915 , 0.0832706 ) @@ -3118,14 +4565,17 @@ colvars: ( -0.00850676 , 0.0464381 , -0.0833597 ) colvars: ( -0.0185742 , 0.06694 , -0.035336 ) colvars: ( -0.0222847 , 0.0842162 , -0.0590125 ) colvars: ( -0.0243427 , 0.0931215 , -0.0692635 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 29. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 29. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 29, atoms_new_colvar_forces = { ( -6.97345673689353e-02 , 3.03510657206574e-01 , -4.01032117490141e-01 ), ( 1.31479927636834e-02 , 3.18452841780117e-02 , -2.39563239519030e-01 ), ( -4.25902939322404e-02 , 9.55764008556160e-02 , 8.47478780569349e-02 ), ( -9.68202824772278e-02 , 2.49649279092987e-01 , 6.38673507909631e-02 ), ( -1.78554209094392e-02 , 9.80978947661689e-02 , -1.71059030797415e-01 ), ( 7.06351339216980e-02 , -1.84876997886692e-01 , -3.78002906708560e-02 ), ( 9.23717210815472e-03 , -9.88186635802035e-02 , 2.54516498207081e-01 ), ( -4.10067185999413e-02 , 5.95284116782757e-02 , 1.92894973903991e-01 ), ( 6.62656509213339e-02 , -1.91650327349241e-01 , 3.44446751551083e-02 ), ( 1.13538570672861e-01 , -3.91576043794114e-01 , 2.76477610737634e-01 ), ( 2.43528011759160e-02 , -9.95212184108119e-02 , 9.63717066493160e-02 ), ( 2.64335990853690e-02 , -9.75315010313773e-02 , 5.99368309122805e-02 ), ( 1.22707479665203e-02 , -5.58185019853083e-02 , 7.27061619717733e-02 ), ( 1.24258135329339e-02 , -5.36868050421806e-02 , 6.15475967226827e-02 ), ( 5.46238658459673e-03 , -3.50379570239896e-02 , 7.57443415325614e-02 ), ( -8.69024268940156e-03 , 9.71509594049825e-03 , 7.54348715011720e-02 ), ( -2.12822387245308e-03 , -2.75410877718619e-03 , 4.03262459211456e-02 ), ( -5.80130253688933e-03 , 9.85391482653324e-03 , 3.60182615787236e-02 ), ( 2.69968905367764e-03 , -1.31132121873080e-02 , 1.95403438129169e-02 ), ( 9.07983140495067e-03 , -2.23508072022709e-02 , -2.68808418768290e-02 ), ( 8.72530906787373e-03 , -2.40163686340764e-02 , -1.50260205641190e-02 ), ( 6.63533929943794e-03 , -1.37758914733351e-02 , -3.05314804783749e-02 ), ( 1.50250412334631e-02 , -4.69489069415381e-02 , -2.06754550118032e-03 ), ( 2.76032855445120e-02 , -8.89104932973903e-02 , 7.51753913090130e-03 ), ( 1.42646426422054e-02 , -4.71373373917235e-02 , 8.95390893414003e-03 ), ( 1.42276919791724e-02 , -4.43085252454197e-02 , -2.59167092550324e-03 ), ( 9.26674921618978e-03 , -3.71915296398978e-02 , 3.37836374872139e-02 ), ( -9.06372128229056e-04 , -1.51721407720698e-02 , 7.67684938038021e-02 ), ( -3.80395529749382e-03 , 4.24883243177135e-03 , 3.30357666004564e-02 ), ( -5.86557141109127e-03 , 1.13445570023479e-02 , 3.05363750307080e-02 ), ( -7.31525519485768e-03 , 1.80539646497407e-02 , 2.14575122079536e-02 ), ( -1.62749765161026e-02 , 5.22957913864255e-02 , -3.89559645051791e-03 ), ( -9.73256717086334e-03 , 3.58608957287872e-02 , -2.18588455272024e-02 ), ( -1.37561356846093e-02 , 5.01594555083329e-02 , -2.86530175657035e-02 ), ( -1.96150471330579e-03 , 1.47795103338105e-02 , -3.65544936694368e-02 ), ( 1.06357415268573e-02 , -1.63166088971694e-02 , -7.34787770018302e-02 ), ( 4.41217592686858e-03 , -1.12407025410037e-03 , -5.45119214454607e-02 ), ( 3.40465355615724e-03 , 5.68596742599340e-03 , -6.99615536721609e-02 ), ( 7.14690794577242e-03 , -1.51676910384938e-02 , -3.14818108612719e-02 ), ( 1.30860440731738e-02 , -4.17538157142368e-02 , 1.87607969243244e-03 ), ( 5.31438886239974e-04 , 1.58382764422033e-03 , -1.38845375267955e-02 ), ( 4.66019431914596e-04 , 3.16597921279863e-03 , -1.97405139078286e-02 ), ( -6.51759358566815e-03 , 2.05944778805003e-02 , -7.74867141769462e-05 ), ( -2.05897522873165e-02 , 5.81998881002601e-02 , 2.89588835151015e-02 ), ( -1.89420811869476e-02 , 6.35594972111328e-02 , -1.60005578066733e-02 ), ( -2.26447048361701e-02 , 7.55719886654578e-02 , -1.73763109801339e-02 ), ( -1.67714821195974e-02 , 7.25041952445797e-02 , -8.32494688284707e-02 ), ( -1.98477539008037e-02 , 8.66741240236254e-02 , -1.02227174905627e-01 ), ( -8.50675931255932e-03 , 4.64380716891990e-02 , -8.33597300696781e-02 ), ( -1.85741622090217e-02 , 6.69400231747561e-02 , -3.53359787198467e-02 ), ( -2.43427495803689e-02 , 9.31215377117312e-02 , -6.92635303807293e-02 ) } +colvars: Step 29, atoms_new_colvar_forces = { ( -6.97345673689355e-02 , 3.03510657206574e-01 , -4.01032117490141e-01 ), ( 1.31479927636833e-02 , 3.18452841780117e-02 , -2.39563239519030e-01 ), ( -4.25902939322403e-02 , 9.55764008556159e-02 , 8.47478780569350e-02 ), ( -9.68202824772279e-02 , 2.49649279092987e-01 , 6.38673507909632e-02 ), ( -1.78554209094393e-02 , 9.80978947661689e-02 , -1.71059030797415e-01 ), ( 7.06351339216979e-02 , -1.84876997886692e-01 , -3.78002906708561e-02 ), ( 9.23717210815477e-03 , -9.88186635802034e-02 , 2.54516498207081e-01 ), ( -4.10067185999412e-02 , 5.95284116782758e-02 , 1.92894973903991e-01 ), ( 6.62656509213339e-02 , -1.91650327349242e-01 , 3.44446751551082e-02 ), ( 1.13538570672862e-01 , -3.91576043794114e-01 , 2.76477610737634e-01 ), ( 2.43528011759160e-02 , -9.95212184108119e-02 , 9.63717066493160e-02 ), ( 2.64335990853690e-02 , -9.75315010313772e-02 , 5.99368309122805e-02 ), ( 1.22707479665203e-02 , -5.58185019853083e-02 , 7.27061619717733e-02 ), ( 1.24258135329339e-02 , -5.36868050421805e-02 , 6.15475967226826e-02 ), ( 5.46238658459673e-03 , -3.50379570239896e-02 , 7.57443415325614e-02 ), ( -8.69024268940156e-03 , 9.71509594049825e-03 , 7.54348715011720e-02 ), ( -2.12822387245308e-03 , -2.75410877718617e-03 , 4.03262459211456e-02 ), ( -5.80130253688933e-03 , 9.85391482653323e-03 , 3.60182615787236e-02 ), ( 2.69968905367764e-03 , -1.31132121873079e-02 , 1.95403438129169e-02 ), ( 9.07983140495067e-03 , -2.23508072022709e-02 , -2.68808418768289e-02 ), ( 8.72530906787373e-03 , -2.40163686340764e-02 , -1.50260205641190e-02 ), ( 6.63533929943793e-03 , -1.37758914733351e-02 , -3.05314804783748e-02 ), ( 1.50250412334631e-02 , -4.69489069415382e-02 , -2.06754550118032e-03 ), ( 2.76032855445120e-02 , -8.89104932973903e-02 , 7.51753913090128e-03 ), ( 1.42646426422054e-02 , -4.71373373917235e-02 , 8.95390893414003e-03 ), ( 1.42276919791724e-02 , -4.43085252454197e-02 , -2.59167092550324e-03 ), ( 9.26674921618978e-03 , -3.71915296398978e-02 , 3.37836374872139e-02 ), ( -9.06372128229042e-04 , -1.51721407720698e-02 , 7.67684938038020e-02 ), ( -3.80395529749381e-03 , 4.24883243177135e-03 , 3.30357666004564e-02 ), ( -5.86557141109127e-03 , 1.13445570023479e-02 , 3.05363750307080e-02 ), ( -7.31525519485768e-03 , 1.80539646497407e-02 , 2.14575122079536e-02 ), ( -1.62749765161026e-02 , 5.22957913864255e-02 , -3.89559645051793e-03 ), ( -9.73256717086334e-03 , 3.58608957287872e-02 , -2.18588455272024e-02 ), ( -1.37561356846092e-02 , 5.01594555083328e-02 , -2.86530175657035e-02 ), ( -1.96150471330580e-03 , 1.47795103338105e-02 , -3.65544936694368e-02 ), ( 1.06357415268573e-02 , -1.63166088971694e-02 , -7.34787770018302e-02 ), ( 4.41217592686858e-03 , -1.12407025410038e-03 , -5.45119214454608e-02 ), ( 3.40465355615724e-03 , 5.68596742599340e-03 , -6.99615536721609e-02 ), ( 7.14690794577242e-03 , -1.51676910384938e-02 , -3.14818108612719e-02 ), ( 1.30860440731738e-02 , -4.17538157142369e-02 , 1.87607969243245e-03 ), ( 5.31438886239974e-04 , 1.58382764422031e-03 , -1.38845375267955e-02 ), ( 4.66019431914596e-04 , 3.16597921279863e-03 , -1.97405139078286e-02 ), ( -6.51759358566815e-03 , 2.05944778805003e-02 , -7.74867141769325e-05 ), ( -2.05897522873164e-02 , 5.81998881002601e-02 , 2.89588835151015e-02 ), ( -1.89420811869476e-02 , 6.35594972111328e-02 , -1.60005578066733e-02 ), ( -2.26447048361701e-02 , 7.55719886654577e-02 , -1.73763109801340e-02 ), ( -1.67714821195974e-02 , 7.25041952445796e-02 , -8.32494688284707e-02 ), ( -1.98477539008037e-02 , 8.66741240236254e-02 , -1.02227174905627e-01 ), ( -8.50675931255931e-03 , 4.64380716891990e-02 , -8.33597300696780e-02 ), ( -1.85741622090217e-02 , 6.69400231747561e-02 , -3.53359787198467e-02 ), ( -2.43427495803689e-02 , 9.31215377117312e-02 , -6.92635303807292e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 29, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3163,10 +4613,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 30, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 30, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 30, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 30, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 30, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 30, atoms_positions[size = 51] = { ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641626e-01 ), ( 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 ), ( 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 ), ( 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 ), ( 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 ), ( 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 ), ( -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 ), ( -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 ), ( -3.66808902897429e+00 , 8.00192656616480e-02 , 5.48456203544387e+00 ), ( -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ), ( 8.29230184427869e+00 , 4.21861224833246e-02 , -7.08174413023012e-01 ), ( 7.01074964451227e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 ), ( 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 ), ( 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 ), ( 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 ), ( 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 ), ( 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 ), ( 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 ), ( 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 ), ( 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 ), ( 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 ), ( 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 ), ( 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 ), ( 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 ), ( 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 ), ( 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 ), ( 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 ), ( 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 ), ( 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 ), ( -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 ), ( 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 ), ( 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 ), ( -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 ), ( -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 ), ( -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 ), ( -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633871e+00 ), ( -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 ), ( -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 ), ( -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 ), ( -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160168e-01 ), ( -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 ), ( -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 ), ( -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 ), ( -2.37512825645772e+00 , -3.14245448646485e-01 , 6.13503886138837e+00 ), ( -4.48049343311408e+00 , 9.23291002542476e-01 , 6.42458367171772e+00 ), ( -5.35769724718959e+00 , 5.73458684568046e-01 , 7.20401421961488e+00 ), ( -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 ), ( -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 ), ( -6.63855361839081e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 ), ( -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 ), ( -4.01878208177308e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ) } +colvars: Step 30, atoms_positions[size = 51] = { ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 ), ( 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 ), ( 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 ), ( 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 ), ( 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 ), ( 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 ), ( -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 ), ( -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 ), ( -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 ), ( -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ), ( 8.29230184427869e+00 , 4.21861224833244e-02 , -7.08174413023012e-01 ), ( 7.01074964451226e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 ), ( 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 ), ( 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 ), ( 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 ), ( 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 ), ( 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 ), ( 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 ), ( 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 ), ( 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 ), ( 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 ), ( 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 ), ( 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 ), ( 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 ), ( 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 ), ( 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 ), ( 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 ), ( 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 ), ( 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 ), ( -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 ), ( 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 ), ( 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 ), ( -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 ), ( -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 ), ( -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 ), ( -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633870e+00 ), ( -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 ), ( -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 ), ( -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 ), ( -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160169e-01 ), ( -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 ), ( -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 ), ( -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 ), ( -2.37512825645771e+00 , -3.14245448646477e-01 , 6.13503886138836e+00 ), ( -4.48049343311408e+00 , 9.23291002542477e-01 , 6.42458367171772e+00 ), ( -5.35769724718959e+00 , 5.73458684568045e-01 , 7.20401421961488e+00 ), ( -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 ), ( -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 ), ( -6.63855361839082e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 ), ( -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 ), ( -4.01878208177307e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ) } colvars: Step 30, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 30, atom_groups_ids[size = 0] = @@ -3184,16 +4634,87 @@ colvars: Collective variables module, step no. 30 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Colvar component no. 1 within colvar "one" has value ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.29230184427869e+00 , 4.21861224833244e-02 , -7.08174413023012e-01 , 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 7.01074964451226e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 , 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 , 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 , 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 , 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 , 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 , 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 , 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 , 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 , 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 , 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 , 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 , 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 , 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 , -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 , 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 , -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 , -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 , -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633870e+00 , -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 , -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 , -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160169e-01 , -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 , -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 , -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -2.37512825645771e+00 , -3.14245448646477e-01 , 6.13503886138836e+00 , -4.48049343311408e+00 , 9.23291002542477e-01 , 6.42458367171772e+00 , -5.35769724718959e+00 , 5.73458684568045e-01 , 7.20401421961488e+00 , -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 , -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 , -6.63855361839082e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 , -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 , -4.01878208177307e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.29230184427869e+00 , 4.21861224833244e-02 , -7.08174413023012e-01 , 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 7.01074964451226e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 , 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 , 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 , 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 , 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 , 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 , 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 , 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 , 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 , 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 , 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 , 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 , 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 , 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 , -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 , 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 , -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 , -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 , -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633870e+00 , -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 , -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 , -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160169e-01 , -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 , -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 , -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -2.37512825645771e+00 , -3.14245448646477e-01 , 6.13503886138836e+00 , -4.48049343311408e+00 , 9.23291002542477e-01 , 6.42458367171772e+00 , -5.35769724718959e+00 , 5.73458684568045e-01 , 7.20401421961488e+00 , -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 , -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 , -6.63855361839082e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 , -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 , -4.01878208177307e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3206,6 +4727,10 @@ colvars: Adding total bias energy: 11.509 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3221,8 +4746,6 @@ colvars: ( 0.006696 , -0.105447 , 0.31483 ) colvars: ( -0.0496814 , 0.0812491 , 0.215226 ) colvars: ( 0.0810083 , -0.236308 , 0.0268488 ) colvars: ( 0.135692 , -0.475682 , 0.335543 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243167 , -0.099492 , 0.0963817 ) colvars: ( 0.0197793 , -0.0820812 , 0.0832837 ) @@ -3275,6 +4798,7 @@ colvars: ( -0.00847935 , 0.0464452 , -0.0833604 ) colvars: ( -0.0185674 , 0.0669375 , -0.0353606 ) colvars: ( -0.0222671 , 0.0842029 , -0.0590339 ) colvars: ( -0.0243169 , 0.0930905 , -0.0692785 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 30. colvars: colvarmodule::write_traj_files() @@ -3285,8 +4809,10 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 30. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 30, atoms_new_colvar_forces = { ( -6.95658913699924e-02 , 3.03495304700360e-01 , -4.00976200210173e-01 ), ( 1.32299191340559e-02 , 3.20134991645447e-02 , -2.39619452468059e-01 ), ( -4.26563766265219e-02 , 9.56403093898097e-02 , 8.44596854250561e-02 ), ( -9.68486750504376e-02 , 2.49497835273790e-01 , 6.37529442829732e-02 ), ( -1.77689888890507e-02 , 9.80431135295305e-02 , -1.70915677049662e-01 ), ( 7.06489024165661e-02 , -1.84749376697780e-01 , -3.77573986335530e-02 ), ( 9.12292858715042e-03 , -9.88276270229263e-02 , 2.54389414476489e-01 ), ( -4.10658673366000e-02 , 5.93219876485636e-02 , 1.92969834008387e-01 ), ( 6.62769371505774e-02 , -1.91676334263824e-01 , 3.46813751733085e-02 ), ( 1.13425333979248e-01 , -3.91478967299099e-01 , 2.76508875738693e-01 ), ( 2.43167271106807e-02 , -9.94920033544715e-02 , 9.63817440640522e-02 ), ( 2.64191895603649e-02 , -9.75245060047425e-02 , 5.99683035376166e-02 ), ( 1.22468789126365e-02 , -5.58175258139927e-02 , 7.27121898589340e-02 ), ( 1.24047035902619e-02 , -5.36796957632884e-02 , 6.15535517723070e-02 ), ( 5.43874680066886e-03 , -3.50523789955920e-02 , 7.57443798203501e-02 ), ( -8.71221758731420e-03 , 9.67375370300251e-03 , 7.54216052589434e-02 ), ( -2.13712409634063e-03 , -2.78243053067266e-03 , 4.03264445359764e-02 ), ( -5.81071492969707e-03 , 9.82785816537381e-03 , 3.60117830588854e-02 ), ( 2.70265027945472e-03 , -1.31469274539607e-02 , 1.95560512477302e-02 ), ( 9.10712044392774e-03 , -2.23956228363689e-02 , -2.68388150373631e-02 ), ( 8.74099287762604e-03 , -2.40373952913405e-02 , -1.49977781270839e-02 ), ( 6.65645930329754e-03 , -1.37975462710417e-02 , -3.05033911886318e-02 ), ( 1.50340605582740e-02 , -4.69550160873604e-02 , -2.03743106755413e-03 ), ( 2.76055388989486e-02 , -8.88870722111463e-02 , 7.55498700718659e-03 ), ( 1.42625395994906e-02 , -4.71208094237405e-02 , 8.97020314867174e-03 ), ( 1.42285636033123e-02 , -4.42863738174125e-02 , -2.57548378640847e-03 ), ( 9.25302873951539e-03 , -3.71763907190270e-02 , 3.37862797711345e-02 ), ( -9.42067296947512e-04 , -1.51551450565181e-02 , 7.67428731176359e-02 ), ( -3.82090419229272e-03 , 4.25656589375703e-03 , 3.30184313118940e-02 ), ( -5.88419054784475e-03 , 1.13585528504002e-02 , 3.05130825138278e-02 ), ( -7.32432688702300e-03 , 1.80448026433321e-02 , 2.14438932885341e-02 ), ( -1.62692581172610e-02 , 5.22563759057720e-02 , -3.90636550782251e-03 ), ( -9.72320285482906e-03 , 3.58437115716669e-02 , -2.18639600318727e-02 ), ( -1.37458764867003e-02 , 5.01425240534089e-02 , -2.86640083889571e-02 ), ( -1.94400216674573e-03 , 1.47660014403295e-02 , -3.65441692936174e-02 ), ( 1.06715441245246e-02 , -1.63238233771593e-02 , -7.34407746919613e-02 ), ( 4.43332716670918e-03 , -1.11562187529326e-03 , -5.44961240911917e-02 ), ( 3.43104066974840e-03 , 5.69605899859925e-03 , -6.99449935137132e-02 ), ( 7.15643203676903e-03 , -1.51463397957204e-02 , -3.14717894247689e-02 ), ( 1.30767350430219e-02 , -4.17037479203932e-02 , 1.87680844406153e-03 ), ( 5.27024352117541e-04 , 1.61965138324290e-03 , -1.38965999902881e-02 ), ( 4.61570877233452e-04 , 3.21002571734941e-03 , -1.97551106198276e-02 ), ( -6.52744180540112e-03 , 2.06194280345439e-02 , -1.00291408984661e-04 ), ( -2.06135237907966e-02 , 5.82119164551232e-02 , 2.89103990433041e-02 ), ( -1.89469500756803e-02 , 6.35703291381154e-02 , -1.60359417691587e-02 ), ( -2.26515916333778e-02 , 7.55862445647695e-02 , -1.74195690035389e-02 ), ( -1.67439071198021e-02 , 7.24980841159223e-02 , -8.32590234227901e-02 ), ( -1.98121104958263e-02 , 8.66614672876918e-02 , -1.02235268950251e-01 ), ( -8.47935120434021e-03 , 4.64452483103734e-02 , -8.33603674838263e-02 ), ( -1.85674151530122e-02 , 6.69375262400478e-02 , -3.53606221186804e-02 ), ( -2.43169201023462e-02 , 9.30905017034529e-02 , -6.92785326262130e-02 ) } +colvars: Step 30, atoms_new_colvar_forces = { ( -6.95658913699924e-02 , 3.03495304700359e-01 , -4.00976200210173e-01 ), ( 1.32299191340559e-02 , 3.20134991645447e-02 , -2.39619452468060e-01 ), ( -4.26563766265219e-02 , 9.56403093898097e-02 , 8.44596854250562e-02 ), ( -9.68486750504376e-02 , 2.49497835273790e-01 , 6.37529442829732e-02 ), ( -1.77689888890508e-02 , 9.80431135295304e-02 , -1.70915677049662e-01 ), ( 7.06489024165661e-02 , -1.84749376697780e-01 , -3.77573986335530e-02 ), ( 9.12292858715047e-03 , -9.88276270229263e-02 , 2.54389414476489e-01 ), ( -4.10658673366000e-02 , 5.93219876485636e-02 , 1.92969834008387e-01 ), ( 6.62769371505774e-02 , -1.91676334263824e-01 , 3.46813751733084e-02 ), ( 1.13425333979248e-01 , -3.91478967299099e-01 , 2.76508875738693e-01 ), ( 2.43167271106807e-02 , -9.94920033544715e-02 , 9.63817440640523e-02 ), ( 2.64191895603649e-02 , -9.75245060047426e-02 , 5.99683035376167e-02 ), ( 1.22468789126366e-02 , -5.58175258139928e-02 , 7.27121898589340e-02 ), ( 1.24047035902619e-02 , -5.36796957632884e-02 , 6.15535517723070e-02 ), ( 5.43874680066886e-03 , -3.50523789955921e-02 , 7.57443798203502e-02 ), ( -8.71221758731420e-03 , 9.67375370300251e-03 , 7.54216052589434e-02 ), ( -2.13712409634063e-03 , -2.78243053067266e-03 , 4.03264445359764e-02 ), ( -5.81071492969707e-03 , 9.82785816537380e-03 , 3.60117830588854e-02 ), ( 2.70265027945472e-03 , -1.31469274539608e-02 , 1.95560512477302e-02 ), ( 9.10712044392774e-03 , -2.23956228363689e-02 , -2.68388150373632e-02 ), ( 8.74099287762604e-03 , -2.40373952913405e-02 , -1.49977781270839e-02 ), ( 6.65645930329754e-03 , -1.37975462710417e-02 , -3.05033911886318e-02 ), ( 1.50340605582740e-02 , -4.69550160873604e-02 , -2.03743106755413e-03 ), ( 2.76055388989486e-02 , -8.88870722111463e-02 , 7.55498700718658e-03 ), ( 1.42625395994906e-02 , -4.71208094237406e-02 , 8.97020314867175e-03 ), ( 1.42285636033123e-02 , -4.42863738174126e-02 , -2.57548378640847e-03 ), ( 9.25302873951540e-03 , -3.71763907190270e-02 , 3.37862797711345e-02 ), ( -9.42067296947507e-04 , -1.51551450565181e-02 , 7.67428731176359e-02 ), ( -3.82090419229272e-03 , 4.25656589375704e-03 , 3.30184313118940e-02 ), ( -5.88419054784476e-03 , 1.13585528504002e-02 , 3.05130825138278e-02 ), ( -7.32432688702301e-03 , 1.80448026433321e-02 , 2.14438932885341e-02 ), ( -1.62692581172611e-02 , 5.22563759057720e-02 , -3.90636550782251e-03 ), ( -9.72320285482907e-03 , 3.58437115716669e-02 , -2.18639600318727e-02 ), ( -1.37458764867003e-02 , 5.01425240534089e-02 , -2.86640083889571e-02 ), ( -1.94400216674574e-03 , 1.47660014403295e-02 , -3.65441692936174e-02 ), ( 1.06715441245246e-02 , -1.63238233771593e-02 , -7.34407746919613e-02 ), ( 4.43332716670917e-03 , -1.11562187529326e-03 , -5.44961240911918e-02 ), ( 3.43104066974839e-03 , 5.69605899859925e-03 , -6.99449935137132e-02 ), ( 7.15643203676903e-03 , -1.51463397957204e-02 , -3.14717894247689e-02 ), ( 1.30767350430219e-02 , -4.17037479203933e-02 , 1.87680844406152e-03 ), ( 5.27024352117538e-04 , 1.61965138324291e-03 , -1.38965999902881e-02 ), ( 4.61570877233448e-04 , 3.21002571734941e-03 , -1.97551106198276e-02 ), ( -6.52744180540112e-03 , 2.06194280345440e-02 , -1.00291408984651e-04 ), ( -2.06135237907967e-02 , 5.82119164551233e-02 , 2.89103990433041e-02 ), ( -1.89469500756803e-02 , 6.35703291381154e-02 , -1.60359417691587e-02 ), ( -2.26515916333778e-02 , 7.55862445647695e-02 , -1.74195690035389e-02 ), ( -1.67439071198021e-02 , 7.24980841159224e-02 , -8.32590234227902e-02 ), ( -1.98121104958264e-02 , 8.66614672876918e-02 , -1.02235268950251e-01 ), ( -8.47935120434023e-03 , 4.64452483103734e-02 , -8.33603674838263e-02 ), ( -1.85674151530122e-02 , 6.69375262400479e-02 , -3.53606221186804e-02 ), ( -2.43169201023462e-02 , 9.30905017034529e-02 , -6.92785326262130e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 30, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3324,10 +4850,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 31, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 31, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 31, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 31, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 31, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 31, atoms_positions[size = 51] = { ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590915e-01 ), ( 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 ), ( 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 ), ( 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 ), ( 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 ), ( 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 ), ( -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 ), ( -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 ), ( -3.66693895104545e+00 , 7.85341863726525e-02 , 5.48517025875378e+00 ), ( -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ), ( 8.28755940062026e+00 , 4.18329711611075e-02 , -7.03446891225446e-01 ), ( 7.00850253516804e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 ), ( 6.14090877060161e+00 , -3.55929932388830e-01 , 8.11285689266245e-01 ), ( 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 ), ( 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 ), ( 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 ), ( 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 ), ( 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 ), ( 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 ), ( 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 ), ( 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 ), ( 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 ), ( 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 ), ( 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 ), ( 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 ), ( 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 ), ( 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 ), ( 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 ), ( 5.73958980727405e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 ), ( -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 ), ( 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 ), ( 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 ), ( -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 ), ( -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 ), ( -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 ), ( -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 ), ( -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 ), ( -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 ), ( -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 ), ( -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697041e-01 ), ( -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 ), ( -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 ), ( -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 ), ( -2.37002722947734e+00 , -3.09308532077129e-01 , 6.13223591205862e+00 ), ( -4.48400436751533e+00 , 9.25990621860429e-01 , 6.42460287653144e+00 ), ( -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 ), ( -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 ), ( -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 ), ( -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876725e+00 ), ( -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 ), ( -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ) } +colvars: Step 31, atoms_positions[size = 51] = { ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 ), ( 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 ), ( 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 ), ( 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 ), ( 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 ), ( 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 ), ( -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 ), ( -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 ), ( -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 ), ( -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ), ( 8.28755940062026e+00 , 4.18329711611074e-02 , -7.03446891225446e-01 ), ( 7.00850253516803e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 ), ( 6.14090877060161e+00 , -3.55929932388829e-01 , 8.11285689266245e-01 ), ( 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 ), ( 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 ), ( 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 ), ( 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 ), ( 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 ), ( 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 ), ( 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 ), ( 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 ), ( 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 ), ( 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 ), ( 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 ), ( 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 ), ( 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 ), ( 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 ), ( 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 ), ( 5.73958980727404e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 ), ( -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 ), ( 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 ), ( 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 ), ( -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 ), ( -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 ), ( -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 ), ( -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 ), ( -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 ), ( -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 ), ( -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 ), ( -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697042e-01 ), ( -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 ), ( -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 ), ( -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 ), ( -2.37002722947733e+00 , -3.09308532077121e-01 , 6.13223591205862e+00 ), ( -4.48400436751533e+00 , 9.25990621860430e-01 , 6.42460287653144e+00 ), ( -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 ), ( -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 ), ( -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 ), ( -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876726e+00 ), ( -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 ), ( -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ) } colvars: Step 31, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 31, atom_groups_ids[size = 0] = @@ -3345,16 +4871,87 @@ colvars: Collective variables module, step no. 31 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250314e-02 , -1.47660205688039e-02 ). +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250315e-02 , -1.47660205688038e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.28755940062026e+00 , 4.18329711611074e-02 , -7.03446891225446e-01 , 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 7.00850253516803e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 , 6.14090877060161e+00 , -3.55929932388829e-01 , 8.11285689266245e-01 , 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 , 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 , 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 , 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 , 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 , 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 , 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 , 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 , 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 , 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 , 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 , 5.73958980727404e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 , -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 , 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 , -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 , -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 , -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 , -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 , -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 , -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697042e-01 , -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 , -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 , -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -2.37002722947733e+00 , -3.09308532077121e-01 , 6.13223591205862e+00 , -4.48400436751533e+00 , 9.25990621860430e-01 , 6.42460287653144e+00 , -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 , -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 , -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 , -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876726e+00 , -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 , -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250314e-02 , -1.47660205688039e-02 ). +colvars: Colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250315e-02 , -1.47660205688038e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.28755940062026e+00 , 4.18329711611074e-02 , -7.03446891225446e-01 , 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 7.00850253516803e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 , 6.14090877060161e+00 , -3.55929932388829e-01 , 8.11285689266245e-01 , 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 , 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 , 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 , 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 , 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 , 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 , 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 , 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 , 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 , 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 , 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 , 5.73958980727404e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 , -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 , 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 , -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 , -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 , -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 , -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 , -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 , -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697042e-01 , -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 , -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 , -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -2.37002722947733e+00 , -3.09308532077121e-01 , 6.13223591205862e+00 , -4.48400436751533e+00 , 9.25990621860430e-01 , 6.42460287653144e+00 , -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 , -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 , -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 , -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876726e+00 , -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 , -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3367,6 +4964,10 @@ colvars: Adding total bias energy: 11.5086 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3382,8 +4983,6 @@ colvars: ( 0.00655531 , -0.105442 , 0.314741 ) colvars: ( -0.0497634 , 0.0810759 , 0.215282 ) colvars: ( 0.0810436 , -0.23635 , 0.0270738 ) colvars: ( 0.135587 , -0.475606 , 0.335635 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242872 , -0.0994587 , 0.0963944 ) colvars: ( 0.0197567 , -0.0820666 , 0.0833017 ) @@ -3436,14 +5035,17 @@ colvars: ( -0.0084545 , 0.0464492 , -0.083367 ) colvars: ( -0.0185642 , 0.0669307 , -0.0353896 ) colvars: ( -0.0222544 , 0.084185 , -0.0590592 ) colvars: ( -0.0242972 , 0.0930558 , -0.0692948 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 31. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 31. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 31, atoms_new_colvar_forces = { ( -6.94062311976976e-02 , 3.03490162526349e-01 , -4.00977684676539e-01 ), ( 1.33250914292943e-02 , 3.21274159113017e-02 , -2.39673124267053e-01 ), ( -4.27240173299418e-02 , 9.56884710025728e-02 , 8.42538100974747e-02 ), ( -9.68992403195541e-02 , 2.49403270880954e-01 , 6.36550646087563e-02 ), ( -1.76876529227756e-02 , 9.80045407383212e-02 , -1.70832054059996e-01 ), ( 7.06801261970315e-02 , -1.84669520776609e-01 , -3.77111455843510e-02 ), ( 9.00854828343869e-03 , -9.88304975182526e-02 , 2.54321406257577e-01 ), ( -4.11436258006877e-02 , 5.91850265153628e-02 , 1.93022819474710e-01 ), ( 6.62954345819473e-02 , -1.91702333806160e-01 , 3.48621933243010e-02 ), ( 1.13332338741391e-01 , -3.91420878955913e-01 , 2.76575377836213e-01 ), ( 2.42872148797992e-02 , -9.94587130056355e-02 , 9.63943991230486e-02 ), ( 2.64100966633783e-02 , -9.75115436907893e-02 , 6.00056349308210e-02 ), ( 1.22262415576413e-02 , -5.58132199905036e-02 , 7.27230076112159e-02 ), ( 1.23868742972013e-02 , -5.36697943768003e-02 , 6.15627630782520e-02 ), ( 5.41679282312664e-03 , -3.50637919502010e-02 , 7.57509344298476e-02 ), ( -8.73564860535173e-03 , 9.63430126607937e-03 , 7.54172439511873e-02 ), ( -2.14667172436306e-03 , -2.80868609548290e-03 , 4.03330489817440e-02 ), ( -5.82131170575600e-03 , 9.80282071643300e-03 , 3.60104340994009e-02 ), ( 2.70507434291429e-03 , -1.31772377559795e-02 , 1.95793288634017e-02 ), ( 9.13350434142546e-03 , -2.24351165446065e-02 , -2.67876251701295e-02 ), ( 8.75686636115701e-03 , -2.40549319003777e-02 , -1.49644833891818e-02 ), ( 6.67714140247193e-03 , -1.38162687868113e-02 , -3.04710927408924e-02 ), ( 1.50450251745692e-02 , -4.69572561816395e-02 , -2.00341070693012e-03 ), ( 2.76129239088779e-02 , -8.88591444165270e-02 , 7.59350369394594e-03 ), ( 1.42633561864486e-02 , -4.71022538320507e-02 , 8.98640238438215e-03 ), ( 1.42323483168066e-02 , -4.42627395145504e-02 , -2.56087965676218e-03 ), ( 9.24190630524867e-03 , -3.71600388875369e-02 , 3.37890553737084e-02 ), ( -9.75780785785191e-04 , -1.51390239570636e-02 , 7.67166922117845e-02 ), ( -3.83748876882388e-03 , 4.26311527955189e-03 , 3.30001325447189e-02 ), ( -5.90255480909130e-03 , 1.13703876236472e-02 , 3.04871677339910e-02 ), ( -7.33442811574979e-03 , 1.80348763776466e-02 , 2.14314056086946e-02 ), ( -1.62675478976216e-02 , 5.22163018395812e-02 , -3.91292521691018e-03 ), ( -9.71635845312025e-03 , 3.58254697071210e-02 , -2.18684742275428e-02 ), ( -1.37388511966618e-02 , 5.01235438545573e-02 , -2.86754534301744e-02 ), ( -1.92800700867435e-03 , 1.47527874968520e-02 , -3.65330096949882e-02 ), ( 1.07072451090726e-02 , -1.63286881274528e-02 , -7.34020992469165e-02 ), ( 4.45442382316415e-03 , -1.10729458237341e-03 , -5.44830805548990e-02 ), ( 3.45699477161343e-03 , 5.70554105771488e-03 , -6.99322518035784e-02 ), ( 7.16724311301136e-03 , -1.51252971866452e-02 , -3.14655922184140e-02 ), ( 1.30713373800647e-02 , -4.16545922190191e-02 , 1.87064785303078e-03 ), ( 5.23813753763795e-04 , 1.65268772039421e-03 , -1.39158135611629e-02 ), ( 4.58524248322317e-04 , 3.25057971335603e-03 , -1.97786328645290e-02 ), ( -6.53728779931365e-03 , 2.06409550101289e-02 , -1.29023632259624e-04 ), ( -2.06393235201968e-02 , 5.82185808423522e-02 , 2.88568299399628e-02 ), ( -1.89545031374289e-02 , 6.35758809325615e-02 , -1.60775201326768e-02 ), ( -2.26616033796460e-02 , 7.55941014081297e-02 , -1.74704140838847e-02 ), ( -1.67206283762288e-02 , 7.24879315487866e-02 , -8.32736354364718e-02 ), ( -1.97818320480012e-02 , 8.66444186321444e-02 , -1.02248462678572e-01 ), ( -8.45450440118757e-03 , 4.64492240552549e-02 , -8.33670099030260e-02 ), ( -1.85641815327470e-02 , 6.69307057568639e-02 , -3.53895893594843e-02 ), ( -2.42972071567756e-02 , 9.30557656449630e-02 , -6.92948157148458e-02 ) } +colvars: Step 31, atoms_new_colvar_forces = { ( -6.94062311976977e-02 , 3.03490162526349e-01 , -4.00977684676539e-01 ), ( 1.33250914292942e-02 , 3.21274159113017e-02 , -2.39673124267053e-01 ), ( -4.27240173299418e-02 , 9.56884710025727e-02 , 8.42538100974747e-02 ), ( -9.68992403195541e-02 , 2.49403270880954e-01 , 6.36550646087563e-02 ), ( -1.76876529227757e-02 , 9.80045407383212e-02 , -1.70832054059996e-01 ), ( 7.06801261970314e-02 , -1.84669520776609e-01 , -3.77111455843509e-02 ), ( 9.00854828343877e-03 , -9.88304975182525e-02 , 2.54321406257577e-01 ), ( -4.11436258006877e-02 , 5.91850265153628e-02 , 1.93022819474710e-01 ), ( 6.62954345819473e-02 , -1.91702333806160e-01 , 3.48621933243010e-02 ), ( 1.13332338741391e-01 , -3.91420878955912e-01 , 2.76575377836213e-01 ), ( 2.42872148797991e-02 , -9.94587130056355e-02 , 9.63943991230486e-02 ), ( 2.64100966633783e-02 , -9.75115436907893e-02 , 6.00056349308210e-02 ), ( 1.22262415576413e-02 , -5.58132199905036e-02 , 7.27230076112159e-02 ), ( 1.23868742972013e-02 , -5.36697943768003e-02 , 6.15627630782520e-02 ), ( 5.41679282312664e-03 , -3.50637919502010e-02 , 7.57509344298476e-02 ), ( -8.73564860535173e-03 , 9.63430126607933e-03 , 7.54172439511873e-02 ), ( -2.14667172436306e-03 , -2.80868609548291e-03 , 4.03330489817440e-02 ), ( -5.82131170575600e-03 , 9.80282071643299e-03 , 3.60104340994009e-02 ), ( 2.70507434291429e-03 , -1.31772377559795e-02 , 1.95793288634017e-02 ), ( 9.13350434142548e-03 , -2.24351165446065e-02 , -2.67876251701295e-02 ), ( 8.75686636115702e-03 , -2.40549319003777e-02 , -1.49644833891818e-02 ), ( 6.67714140247194e-03 , -1.38162687868113e-02 , -3.04710927408924e-02 ), ( 1.50450251745692e-02 , -4.69572561816395e-02 , -2.00341070693012e-03 ), ( 2.76129239088779e-02 , -8.88591444165270e-02 , 7.59350369394596e-03 ), ( 1.42633561864486e-02 , -4.71022538320507e-02 , 8.98640238438215e-03 ), ( 1.42323483168066e-02 , -4.42627395145504e-02 , -2.56087965676217e-03 ), ( 9.24190630524867e-03 , -3.71600388875370e-02 , 3.37890553737085e-02 ), ( -9.75780785785199e-04 , -1.51390239570636e-02 , 7.67166922117844e-02 ), ( -3.83748876882388e-03 , 4.26311527955188e-03 , 3.30001325447189e-02 ), ( -5.90255480909130e-03 , 1.13703876236472e-02 , 3.04871677339910e-02 ), ( -7.33442811574979e-03 , 1.80348763776466e-02 , 2.14314056086946e-02 ), ( -1.62675478976216e-02 , 5.22163018395812e-02 , -3.91292521691018e-03 ), ( -9.71635845312025e-03 , 3.58254697071210e-02 , -2.18684742275428e-02 ), ( -1.37388511966618e-02 , 5.01235438545573e-02 , -2.86754534301744e-02 ), ( -1.92800700867434e-03 , 1.47527874968520e-02 , -3.65330096949882e-02 ), ( 1.07072451090726e-02 , -1.63286881274528e-02 , -7.34020992469166e-02 ), ( 4.45442382316416e-03 , -1.10729458237341e-03 , -5.44830805548990e-02 ), ( 3.45699477161344e-03 , 5.70554105771486e-03 , -6.99322518035784e-02 ), ( 7.16724311301135e-03 , -1.51252971866452e-02 , -3.14655922184140e-02 ), ( 1.30713373800647e-02 , -4.16545922190191e-02 , 1.87064785303078e-03 ), ( 5.23813753763790e-04 , 1.65268772039422e-03 , -1.39158135611629e-02 ), ( 4.58524248322313e-04 , 3.25057971335604e-03 , -1.97786328645290e-02 ), ( -6.53728779931366e-03 , 2.06409550101289e-02 , -1.29023632259628e-04 ), ( -2.06393235201968e-02 , 5.82185808423522e-02 , 2.88568299399628e-02 ), ( -1.89545031374289e-02 , 6.35758809325615e-02 , -1.60775201326768e-02 ), ( -2.26616033796460e-02 , 7.55941014081297e-02 , -1.74704140838847e-02 ), ( -1.67206283762288e-02 , 7.24879315487867e-02 , -8.32736354364718e-02 ), ( -1.97818320480012e-02 , 8.66444186321444e-02 , -1.02248462678572e-01 ), ( -8.45450440118757e-03 , 4.64492240552550e-02 , -8.33670099030260e-02 ), ( -1.85641815327470e-02 , 6.69307057568639e-02 , -3.53895893594843e-02 ), ( -2.42972071567756e-02 , 9.30557656449630e-02 , -6.92948157148458e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 31, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3481,10 +5083,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 32, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 32, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 32, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 32, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 32, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 32, atoms_positions[size = 51] = { ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155027e-01 ), ( 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 ), ( 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 ), ( 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451151e-02 ), ( 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 ), ( 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 ), ( -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 ), ( -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 ), ( -3.66585660784361e+00 , 7.62856477282831e-02 , 5.48377527024691e+00 ), ( -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ), ( 8.28198546168908e+00 , 4.12774609412898e-02 , -6.98594743896480e-01 ), ( 7.00719717014731e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 ), ( 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 ), ( 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 ), ( 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 ), ( 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 ), ( 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 ), ( 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 ), ( 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 ), ( 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 ), ( 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 ), ( 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 ), ( 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 ), ( 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 ), ( 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 ), ( 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 ), ( 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 ), ( 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 ), ( 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 ), ( -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 ), ( 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 ), ( 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 ), ( -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013817e+00 ), ( -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 ), ( -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 ), ( -7.53250040458546e-01 , 5.44646798686886e+00 , 2.48270190089130e+00 ), ( -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 ), ( -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 ), ( -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 ), ( -3.35494631132017e+00 , 8.82615575571746e-01 , 7.96973196127045e-01 ), ( -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 ), ( -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 ), ( -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 ), ( -2.36418473395890e+00 , -3.03550327204905e-01 , 6.13032039751402e+00 ), ( -4.48692880047466e+00 , 9.30938001369169e-01 , 6.42485932408154e+00 ), ( -5.35487679866182e+00 , 5.62926127628069e-01 , 7.19598206069251e+00 ), ( -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246735e+00 ), ( -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 ), ( -6.62216635512164e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 ), ( -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 ), ( -4.00962749496156e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ) } +colvars: Step 32, atoms_positions[size = 51] = { ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 ), ( 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 ), ( 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 ), ( 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 ), ( 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 ), ( 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 ), ( -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 ), ( -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 ), ( -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 ), ( -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ), ( 8.28198546168908e+00 , 4.12774609412895e-02 , -6.98594743896480e-01 ), ( 7.00719717014730e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 ), ( 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 ), ( 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 ), ( 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 ), ( 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 ), ( 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 ), ( 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 ), ( 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 ), ( 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 ), ( 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 ), ( 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 ), ( 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 ), ( 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 ), ( 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 ), ( 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 ), ( 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 ), ( 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 ), ( 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 ), ( -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 ), ( 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 ), ( 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 ), ( -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013816e+00 ), ( -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 ), ( -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 ), ( -7.53250040458547e-01 , 5.44646798686886e+00 , 2.48270190089129e+00 ), ( -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 ), ( -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 ), ( -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 ), ( -3.35494631132017e+00 , 8.82615575571747e-01 , 7.96973196127046e-01 ), ( -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 ), ( -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 ), ( -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 ), ( -2.36418473395889e+00 , -3.03550327204897e-01 , 6.13032039751401e+00 ), ( -4.48692880047465e+00 , 9.30938001369170e-01 , 6.42485932408154e+00 ), ( -5.35487679866182e+00 , 5.62926127628068e-01 , 7.19598206069251e+00 ), ( -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246736e+00 ), ( -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 ), ( -6.62216635512165e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 ), ( -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 ), ( -4.00962749496155e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ) } colvars: Step 32, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 32, atom_groups_ids[size = 0] = @@ -3501,17 +5103,88 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 32 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919956e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919957e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.28198546168908e+00 , 4.12774609412895e-02 , -6.98594743896480e-01 , 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 7.00719717014730e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 , 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 , 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 , 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 , 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 , 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 , 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 , 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 , 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 , 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 , 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 , 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 , 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 , 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 , -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 , 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 , -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013816e+00 , -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 , -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -7.53250040458547e-01 , 5.44646798686886e+00 , 2.48270190089129e+00 , -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 , -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 , -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.35494631132017e+00 , 8.82615575571747e-01 , 7.96973196127046e-01 , -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 , -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 , -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -2.36418473395889e+00 , -3.03550327204897e-01 , 6.13032039751401e+00 , -4.48692880047465e+00 , 9.30938001369170e-01 , 6.42485932408154e+00 , -5.35487679866182e+00 , 5.62926127628068e-01 , 7.19598206069251e+00 , -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246736e+00 , -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 , -6.62216635512165e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 , -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 , -4.00962749496155e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919956e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). +colvars: Colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919957e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.28198546168908e+00 , 4.12774609412895e-02 , -6.98594743896480e-01 , 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 7.00719717014730e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 , 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 , 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 , 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 , 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 , 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 , 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 , 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 , 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 , 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 , 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 , 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 , 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 , 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 , -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 , 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 , -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013816e+00 , -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 , -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -7.53250040458547e-01 , 5.44646798686886e+00 , 2.48270190089129e+00 , -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 , -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 , -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.35494631132017e+00 , 8.82615575571747e-01 , 7.96973196127046e-01 , -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 , -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 , -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -2.36418473395889e+00 , -3.03550327204897e-01 , 6.13032039751401e+00 , -4.48692880047465e+00 , 9.30938001369170e-01 , 6.42485932408154e+00 , -5.35487679866182e+00 , 5.62926127628068e-01 , 7.19598206069251e+00 , -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246736e+00 , -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 , -6.62216635512165e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 , -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 , -4.00962749496155e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3524,6 +5197,10 @@ colvars: Adding total bias energy: 11.5086 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3539,8 +5216,6 @@ colvars: ( 0.00641675 , -0.105429 , 0.314721 ) colvars: ( -0.0498658 , 0.0809809 , 0.215323 ) colvars: ( 0.0810874 , -0.236392 , 0.0272497 ) colvars: ( 0.135508 , -0.475571 , 0.335779 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242651 , -0.0994226 , 0.0964113 ) colvars: ( 0.0197397 , -0.0820481 , 0.0833257 ) @@ -3593,14 +5268,17 @@ colvars: ( -0.00843282 , 0.0464496 , -0.0833808 ) colvars: ( -0.0185646 , 0.0669202 , -0.035423 ) colvars: ( -0.0222471 , 0.0841636 , -0.059089 ) colvars: ( -0.0242843 , 0.0930188 , -0.0693136 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 32. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 32. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 32, atoms_new_colvar_forces = { ( -6.92568715614583e-02 , 3.03495735434584e-01 , -4.01051034554086e-01 ), ( 1.34329507330979e-02 , 3.21823421820297e-02 , -2.39728800701794e-01 ), ( -4.27932942514774e-02 , 9.57250229757168e-02 , 8.41336611203875e-02 ), ( -9.69721359131866e-02 , 2.49374374044742e-01 , 6.35713681489005e-02 ), ( -1.76117481642180e-02 , 9.79815145584645e-02 , -1.70815129298603e-01 ), ( 7.07288562482511e-02 , -1.84643583954109e-01 , -3.76592985999826e-02 ), ( 8.89458290762086e-03 , -9.88246374575186e-02 , 2.54320588792076e-01 ), ( -4.12394038835748e-02 , 5.91236247152377e-02 , 1.93055401124770e-01 ), ( 6.63217004345557e-02 , -1.91733043548502e-01 , 3.49885686528138e-02 ), ( 1.13260661861210e-01 , -3.91407351480788e-01 , 2.76689535486305e-01 ), ( 2.42651317273264e-02 , -9.94225742000947e-02 , 9.64113282701169e-02 ), ( 2.64066904536132e-02 , -9.74935399270448e-02 , 6.00492513226762e-02 ), ( 1.22093769543052e-02 , -5.58056399140129e-02 , 7.27395848120445e-02 ), ( 1.23728157982682e-02 , -5.36574167094586e-02 , 6.15761281158678e-02 ), ( 5.39702675372179e-03 , -3.50714933498933e-02 , 7.57648994879827e-02 ), ( -8.76013321362389e-03 , 9.59882429321861e-03 , 7.54225173037756e-02 ), ( -2.15671749599581e-03 , -2.83168923198219e-03 , 4.03462312173627e-02 ), ( -5.83293595863409e-03 , 9.78005162701339e-03 , 3.60144735560437e-02 ), ( 2.70685449391100e-03 , -1.32031518159557e-02 , 1.96096956238938e-02 ), ( 9.15834484476424e-03 , -2.24685704740751e-02 , -2.67290524869441e-02 ), ( 8.77257569498755e-03 , -2.40688502387905e-02 , -1.49271558255535e-02 ), ( 6.69690925220352e-03 , -1.38319295185637e-02 , -3.04358373033775e-02 ), ( 1.50577581290483e-02 , -4.69561111251409e-02 , -1.96613008527341e-03 ), ( 2.76254746082904e-02 , -8.88285207379886e-02 , 7.63288568266023e-03 ), ( 1.42671870557170e-02 , -4.70826991952575e-02 , 9.00259338710698e-03 ), ( 1.42390841263955e-02 , -4.42388910447388e-02 , -2.54785637659202e-03 ), ( 9.23371743643695e-03 , -3.71430769112850e-02 , 3.37926316895198e-02 ), ( -1.00671645139512e-03 , -1.51237006633047e-02 , 7.66917667387033e-02 ), ( -3.85333757609561e-03 , 4.26864830346807e-03 , 3.29817680526447e-02 ), ( -5.92025145185637e-03 , 1.13801197645519e-02 , 3.04596874187430e-02 ), ( -7.34538833041085e-03 , 1.80249123828996e-02 , 2.14204667214301e-02 ), ( -1.62700547283456e-02 , 5.21773794390723e-02 , -3.91571878647396e-03 ), ( -9.71227876735541e-03 , 3.58069340024963e-02 , -2.18728681348969e-02 ), ( -1.37353309403861e-02 , 5.01033977158764e-02 , -2.86878254222996e-02 ), ( -1.91392124870542e-03 , 1.47400910989978e-02 , -3.65219256023002e-02 ), ( 1.07420773702121e-02 , -1.63319578513661e-02 , -7.33645921720010e-02 ), ( 4.47502720517409e-03 , -1.09989696158710e-03 , -5.44737391135987e-02 ), ( 3.48196414612037e-03 , 5.71349460324854e-03 , -6.99244915959539e-02 ), ( 7.17917766055985e-03 , -1.51057032137927e-02 , -3.14635424487425e-02 ), ( 1.30701470184094e-02 , -4.16083430400286e-02 , 1.85834248014843e-03 ), ( 5.21954160713210e-04 , 1.68178454324210e-03 , -1.39416476691109e-02 ), ( 4.57038802683104e-04 , 3.28621433002094e-03 , -1.98104713257074e-02 ), ( -6.54689474568868e-03 , 2.06586185232721e-02 , -1.62922115952703e-04 ), ( -2.06666564338070e-02 , 5.82206186454470e-02 , 2.87996216213028e-02 ), ( -1.89646538418560e-02 , 6.35765442851976e-02 , -1.61247498604394e-02 ), ( -2.26746116772884e-02 , 7.55960018013675e-02 , -1.75281356896499e-02 ), ( -1.67022826530015e-02 , 7.24740620594433e-02 , -8.32944414820944e-02 ), ( -1.97577450187155e-02 , 8.66234931154464e-02 , -1.02268290532814e-01 ), ( -8.43281840311426e-03 , 4.64495839359491e-02 , -8.33807577121063e-02 ), ( -1.85646447386543e-02 , 6.69201891596660e-02 , -3.54230015720242e-02 ), ( -2.42842584287525e-02 , 9.30187950246104e-02 , -6.93135803589043e-02 ) } +colvars: Step 32, atoms_new_colvar_forces = { ( -6.92568715614584e-02 , 3.03495735434584e-01 , -4.01051034554086e-01 ), ( 1.34329507330978e-02 , 3.21823421820298e-02 , -2.39728800701794e-01 ), ( -4.27932942514773e-02 , 9.57250229757168e-02 , 8.41336611203875e-02 ), ( -9.69721359131866e-02 , 2.49374374044742e-01 , 6.35713681489005e-02 ), ( -1.76117481642180e-02 , 9.79815145584645e-02 , -1.70815129298603e-01 ), ( 7.07288562482510e-02 , -1.84643583954109e-01 , -3.76592985999826e-02 ), ( 8.89458290762093e-03 , -9.88246374575186e-02 , 2.54320588792076e-01 ), ( -4.12394038835747e-02 , 5.91236247152376e-02 , 1.93055401124770e-01 ), ( 6.63217004345558e-02 , -1.91733043548502e-01 , 3.49885686528138e-02 ), ( 1.13260661861210e-01 , -3.91407351480788e-01 , 2.76689535486304e-01 ), ( 2.42651317273264e-02 , -9.94225742000947e-02 , 9.64113282701169e-02 ), ( 2.64066904536132e-02 , -9.74935399270448e-02 , 6.00492513226762e-02 ), ( 1.22093769543052e-02 , -5.58056399140130e-02 , 7.27395848120445e-02 ), ( 1.23728157982682e-02 , -5.36574167094586e-02 , 6.15761281158678e-02 ), ( 5.39702675372180e-03 , -3.50714933498933e-02 , 7.57648994879826e-02 ), ( -8.76013321362389e-03 , 9.59882429321861e-03 , 7.54225173037756e-02 ), ( -2.15671749599581e-03 , -2.83168923198219e-03 , 4.03462312173627e-02 ), ( -5.83293595863409e-03 , 9.78005162701337e-03 , 3.60144735560437e-02 ), ( 2.70685449391101e-03 , -1.32031518159557e-02 , 1.96096956238938e-02 ), ( 9.15834484476424e-03 , -2.24685704740751e-02 , -2.67290524869441e-02 ), ( 8.77257569498755e-03 , -2.40688502387905e-02 , -1.49271558255535e-02 ), ( 6.69690925220351e-03 , -1.38319295185637e-02 , -3.04358373033775e-02 ), ( 1.50577581290483e-02 , -4.69561111251409e-02 , -1.96613008527343e-03 ), ( 2.76254746082904e-02 , -8.88285207379886e-02 , 7.63288568266022e-03 ), ( 1.42671870557170e-02 , -4.70826991952575e-02 , 9.00259338710698e-03 ), ( 1.42390841263955e-02 , -4.42388910447388e-02 , -2.54785637659202e-03 ), ( 9.23371743643695e-03 , -3.71430769112850e-02 , 3.37926316895199e-02 ), ( -1.00671645139511e-03 , -1.51237006633047e-02 , 7.66917667387033e-02 ), ( -3.85333757609560e-03 , 4.26864830346807e-03 , 3.29817680526447e-02 ), ( -5.92025145185636e-03 , 1.13801197645519e-02 , 3.04596874187430e-02 ), ( -7.34538833041085e-03 , 1.80249123828996e-02 , 2.14204667214301e-02 ), ( -1.62700547283456e-02 , 5.21773794390723e-02 , -3.91571878647396e-03 ), ( -9.71227876735541e-03 , 3.58069340024963e-02 , -2.18728681348969e-02 ), ( -1.37353309403861e-02 , 5.01033977158764e-02 , -2.86878254222996e-02 ), ( -1.91392124870543e-03 , 1.47400910989978e-02 , -3.65219256023003e-02 ), ( 1.07420773702121e-02 , -1.63319578513661e-02 , -7.33645921720010e-02 ), ( 4.47502720517408e-03 , -1.09989696158711e-03 , -5.44737391135987e-02 ), ( 3.48196414612036e-03 , 5.71349460324854e-03 , -6.99244915959538e-02 ), ( 7.17917766055985e-03 , -1.51057032137927e-02 , -3.14635424487425e-02 ), ( 1.30701470184094e-02 , -4.16083430400286e-02 , 1.85834248014845e-03 ), ( 5.21954160713208e-04 , 1.68178454324210e-03 , -1.39416476691109e-02 ), ( 4.57038802683104e-04 , 3.28621433002093e-03 , -1.98104713257074e-02 ), ( -6.54689474568868e-03 , 2.06586185232721e-02 , -1.62922115952693e-04 ), ( -2.06666564338070e-02 , 5.82206186454471e-02 , 2.87996216213028e-02 ), ( -1.89646538418560e-02 , 6.35765442851976e-02 , -1.61247498604394e-02 ), ( -2.26746116772884e-02 , 7.55960018013675e-02 , -1.75281356896499e-02 ), ( -1.67022826530015e-02 , 7.24740620594433e-02 , -8.32944414820944e-02 ), ( -1.97577450187155e-02 , 8.66234931154465e-02 , -1.02268290532814e-01 ), ( -8.43281840311428e-03 , 4.64495839359491e-02 , -8.33807577121063e-02 ), ( -1.85646447386543e-02 , 6.69201891596660e-02 , -3.54230015720242e-02 ), ( -2.42842584287525e-02 , 9.30187950246104e-02 , -6.93135803589044e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 32, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3638,10 +5316,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 33, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 33, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 33, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 33, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 33, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 33, atoms_positions[size = 51] = { ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120442e-01 ), ( 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 ), ( 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 ), ( 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729124e-02 ), ( 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 ), ( 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 ), ( -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 ), ( -3.81293200553925e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 ), ( -3.66484332642688e+00 , 7.34445121413667e-02 , 5.48046255017265e+00 ), ( -4.80937207857509e+00 , 3.28709350636303e+00 , 7.23093439006143e+00 ), ( 8.27559967802095e+00 , 4.05062115642719e-02 , -6.93657807517061e-01 ), ( 7.00691465518316e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 ), ( 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 ), ( 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 ), ( 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 ), ( 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 ), ( 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 ), ( 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 ), ( 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 ), ( 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 ), ( 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 ), ( 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 ), ( 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 ), ( 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 ), ( 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 ), ( 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 ), ( 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 ), ( 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 ), ( 5.72398418120017e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 ), ( -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 ), ( 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 ), ( 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 ), ( -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 ), ( -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 ), ( -5.35408684950861e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 ), ( -7.59767399943052e-01 , 5.45187321071623e+00 , 2.48446362740502e+00 ), ( -2.75044654362177e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 ), ( -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 ), ( -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 ), ( -3.35259279459821e+00 , 8.86544438418595e-01 , 7.90248627130321e-01 ), ( -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 ), ( -5.44785168837972e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 ), ( -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345538e+00 ), ( -2.35760224718149e+00 , -2.97089451023095e-01 , 6.12941517052038e+00 ), ( -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 ), ( -5.35378412302326e+00 , 5.56844942923712e-01 , 7.19187592084459e+00 ), ( -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 ), ( -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 ), ( -6.61603045936864e+00 , 3.16825299393760e+00 , 5.55235673570187e+00 ), ( -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 ), ( -4.00672772214133e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ) } +colvars: Step 33, atoms_positions[size = 51] = { ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 ), ( 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 ), ( 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 ), ( 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 ), ( 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 ), ( 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 ), ( -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 ), ( -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 ), ( -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 ), ( -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 ), ( 8.27559967802095e+00 , 4.05062115642717e-02 , -6.93657807517061e-01 ), ( 7.00691465518315e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 ), ( 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 ), ( 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 ), ( 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 ), ( 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 ), ( 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 ), ( 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 ), ( 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 ), ( 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 ), ( 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 ), ( 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 ), ( 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 ), ( 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 ), ( 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 ), ( 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 ), ( 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 ), ( 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 ), ( 5.72398418120016e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 ), ( -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 ), ( 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 ), ( 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 ), ( -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 ), ( -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 ), ( -5.35408684950862e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 ), ( -7.59767399943053e-01 , 5.45187321071623e+00 , 2.48446362740501e+00 ), ( -2.75044654362178e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 ), ( -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 ), ( -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 ), ( -3.35259279459821e+00 , 8.86544438418596e-01 , 7.90248627130323e-01 ), ( -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 ), ( -5.44785168837973e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 ), ( -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345539e+00 ), ( -2.35760224718148e+00 , -2.97089451023085e-01 , 6.12941517052038e+00 ), ( -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 ), ( -5.35378412302326e+00 , 5.56844942923711e-01 , 7.19187592084459e+00 ), ( -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 ), ( -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 ), ( -6.61603045936865e+00 , 3.16825299393760e+00 , 5.55235673570188e+00 ), ( -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 ), ( -4.00672772214132e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ) } colvars: Step 33, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 33, atom_groups_ids[size = 0] = @@ -3659,16 +5337,87 @@ colvars: Collective variables module, step no. 33 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99690134322553e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99690134322554e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 ). +colvars: Calculating gradients of colvar "main". colvars: Calculating gradients of colvar "one". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.27559967802095e+00 , 4.05062115642717e-02 , -6.93657807517061e-01 , 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 7.00691465518315e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 , 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 , 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 , 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 , 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 , 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 , 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 , 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 , 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 , 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 , 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 , 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 , 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 , 5.72398418120016e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 , -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 , 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 , -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 , -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 , -5.35408684950862e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -7.59767399943053e-01 , 5.45187321071623e+00 , 2.48446362740501e+00 , -2.75044654362178e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 , -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 , -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.35259279459821e+00 , 8.86544438418596e-01 , 7.90248627130323e-01 , -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 , -5.44785168837973e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 , -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345539e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -2.35760224718148e+00 , -2.97089451023085e-01 , 6.12941517052038e+00 , -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 , -5.35378412302326e+00 , 5.56844942923711e-01 , 7.19187592084459e+00 , -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 , -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 , -6.61603045936865e+00 , 3.16825299393760e+00 , 5.55235673570188e+00 , -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 , -4.00672772214132e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99690134322553e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Colvar "one" has value ( 9.99690134322554e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.27559967802095e+00 , 4.05062115642717e-02 , -6.93657807517061e-01 , 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 7.00691465518315e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 , 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 , 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 , 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 , 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 , 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 , 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 , 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 , 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 , 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 , 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 , 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 , 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 , 5.72398418120016e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 , -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 , 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 , -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 , -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 , -5.35408684950862e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -7.59767399943053e-01 , 5.45187321071623e+00 , 2.48446362740501e+00 , -2.75044654362178e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 , -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 , -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.35259279459821e+00 , 8.86544438418596e-01 , 7.90248627130323e-01 , -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 , -5.44785168837973e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 , -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345539e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -2.35760224718148e+00 , -2.97089451023085e-01 , 6.12941517052038e+00 , -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 , -5.35378412302326e+00 , 5.56844942923711e-01 , 7.19187592084459e+00 , -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 , -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 , -6.61603045936865e+00 , 3.16825299393760e+00 , 5.55235673570188e+00 , -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 , -4.00672772214132e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3681,6 +5430,10 @@ colvars: Adding total bias energy: 11.5093 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3696,8 +5449,6 @@ colvars: ( 0.00628156 , -0.105405 , 0.314773 ) colvars: ( -0.0499869 , 0.0809667 , 0.215352 ) colvars: ( 0.0811396 , -0.236437 , 0.0273803 ) colvars: ( 0.135456 , -0.475578 , 0.335983 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242509 , -0.0993847 , 0.0964337 ) colvars: ( 0.0197286 , -0.0820264 , 0.0833563 ) @@ -3750,14 +5501,17 @@ colvars: ( -0.00841468 , 0.0464462 , -0.0834022 ) colvars: ( -0.0185688 , 0.0669067 , -0.0354608 ) colvars: ( -0.0222453 , 0.0841395 , -0.0591237 ) colvars: ( -0.0242783 , 0.0929808 , -0.0693357 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 33. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 33. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 33, atoms_new_colvar_forces = { ( -6.91188567735979e-02 , 3.03510290930652e-01 , -4.01204144218599e-01 ), ( 1.35521762003070e-02 , 3.21768778512665e-02 , -2.39790134003717e-01 ), ( -4.28639525555757e-02 , 9.57534430612640e-02 , 8.40967235066483e-02 ), ( -9.70663031948216e-02 , 2.49414118682993e-01 , 6.34987583733795e-02 ), ( -1.75415795560571e-02 , 9.79722684267187e-02 , -1.70866696053046e-01 ), ( 7.07942495838553e-02 , -1.84673272750277e-01 , -3.76001166998724e-02 ), ( 8.78184374387501e-03 , -9.88077937155113e-02 , 2.54389666713542e-01 ), ( -4.13517014975361e-02 , 5.91390874827820e-02 , 1.93069939999040e-01 ), ( 6.63557173096008e-02 , -1.91771135913036e-01 , 3.50652281889722e-02 ), ( 1.13210481361609e-01 , -3.91438934081905e-01 , 2.76859144441299e-01 ), ( 2.42508944679387e-02 , -9.93846540337704e-02 , 9.64336947828106e-02 ), ( 2.64090719407573e-02 , -9.74714705706512e-02 , 6.00992361309366e-02 ), ( 1.21965933010758e-02 , -5.57949721748439e-02 , 7.27624373994067e-02 ), ( 1.23627885303054e-02 , -5.36429148072454e-02 , 6.15941847800253e-02 ), ( 5.37979546280219e-03 , -3.50750987052205e-02 , 7.57866353155475e-02 ), ( -8.78526662946197e-03 , 9.56877620746106e-03 , 7.54375158033274e-02 ), ( -2.16709293495136e-03 , -2.85067072987600e-03 , 4.03657995178171e-02 ), ( -5.84539818911868e-03 , 9.76042249153602e-03 , 3.60238306868930e-02 ), ( 2.70796487908087e-03 , -1.32241296979077e-02 , 1.96464215489824e-02 ), ( 9.18123224966560e-03 , -2.24957783523680e-02 , -2.66648685481025e-02 ), ( 8.78786656590287e-03 , -2.40792626679961e-02 , -1.48867932591327e-02 ), ( 6.71543577080716e-03 , -1.38446172953135e-02 , -3.03987599525088e-02 ), ( 1.50720661069986e-02 , -4.69521524401563e-02 , -1.92623704629728e-03 ), ( 2.76430209908363e-02 , -8.87967682589699e-02 , 7.67298256261929e-03 ), ( 1.42739897167352e-02 , -4.70630029142168e-02 , 9.01887453976425e-03 ), ( 1.42486787822643e-02 , -4.42158363168287e-02 , -2.53630561326753e-03 ), ( 9.22861705229511e-03 , -3.71259922873568e-02 , 3.37975218579997e-02 ), ( -1.03434697133724e-03 , -1.51090259593529e-02 , 7.66694860475731e-02 ), ( -3.86818586249688e-03 , 4.27337270826742e-03 , 3.29640520152657e-02 ), ( -5.93698751092329e-03 , 1.13879312616528e-02 , 3.04315529874885e-02 ), ( -7.35703194127185e-03 , 1.80154944915386e-02 , 2.14113196413313e-02 ), ( -1.62767618705796e-02 , 5.21409602254909e-02 , -3.91531965756657e-03 ), ( -9.71104920550145e-03 , 3.57887071932448e-02 , -2.18775513745859e-02 ), ( -1.37353980805760e-02 , 5.00828269242235e-02 , -2.87014844466074e-02 ), ( -1.90198879974778e-03 , 1.47280365461961e-02 , -3.65116461378042e-02 ), ( 1.07754626664859e-02 , -1.63343561723597e-02 , -7.33296483410145e-02 ), ( 4.49479215925103e-03 , -1.09404148493303e-03 , -5.44686669481052e-02 ), ( 3.50552735386582e-03 , 5.71924557998363e-03 , -6.99223907581774e-02 ), ( 7.19204308392409e-03 , -1.50883876037312e-02 , -3.14656795197780e-02 ), ( 1.30732051974001e-02 , -4.15663983506900e-02 , 1.84081814203581e-03 ), ( 5.21478005410687e-04 , 1.70625332202461e-03 , -1.39733493818603e-02 ), ( 4.57140419366897e-04 , 3.31607765582657e-03 , -1.98497263687156e-02 ), ( -6.55610910963487e-03 , 2.06722915485128e-02 , -2.01135264238115e-04 ), ( -2.06950886573350e-02 , 5.82188855341263e-02 , 2.87400696279859e-02 ), ( -1.89772593961475e-02 , 6.35728929566774e-02 , -1.61769549127555e-02 ), ( -2.26904308970779e-02 , 7.55926189084028e-02 , -1.75918705795380e-02 ), ( -1.66892107294848e-02 , 7.24568921030755e-02 , -8.33220787125385e-02 ), ( -1.97402932869575e-02 , 8.65992546836357e-02 , -1.02295692485758e-01 ), ( -8.41467779143524e-03 , 4.64461590623506e-02 , -8.34021574859847e-02 ), ( -1.85688269232122e-02 , 6.69066565879082e-02 , -3.54607731899792e-02 ), ( -2.42783345375781e-02 , 9.29808248567057e-02 , -6.93357136511408e-02 ) } +colvars: Step 33, atoms_new_colvar_forces = { ( -6.91188567735980e-02 , 3.03510290930652e-01 , -4.01204144218599e-01 ), ( 1.35521762003069e-02 , 3.21768778512665e-02 , -2.39790134003718e-01 ), ( -4.28639525555756e-02 , 9.57534430612640e-02 , 8.40967235066482e-02 ), ( -9.70663031948216e-02 , 2.49414118682993e-01 , 6.34987583733795e-02 ), ( -1.75415795560572e-02 , 9.79722684267187e-02 , -1.70866696053046e-01 ), ( 7.07942495838554e-02 , -1.84673272750277e-01 , -3.76001166998724e-02 ), ( 8.78184374387509e-03 , -9.88077937155114e-02 , 2.54389666713542e-01 ), ( -4.13517014975361e-02 , 5.91390874827821e-02 , 1.93069939999040e-01 ), ( 6.63557173096009e-02 , -1.91771135913036e-01 , 3.50652281889724e-02 ), ( 1.13210481361609e-01 , -3.91438934081905e-01 , 2.76859144441299e-01 ), ( 2.42508944679388e-02 , -9.93846540337705e-02 , 9.64336947828107e-02 ), ( 2.64090719407573e-02 , -9.74714705706513e-02 , 6.00992361309367e-02 ), ( 1.21965933010758e-02 , -5.57949721748439e-02 , 7.27624373994068e-02 ), ( 1.23627885303054e-02 , -5.36429148072454e-02 , 6.15941847800254e-02 ), ( 5.37979546280222e-03 , -3.50750987052206e-02 , 7.57866353155476e-02 ), ( -8.78526662946196e-03 , 9.56877620746106e-03 , 7.54375158033274e-02 ), ( -2.16709293495136e-03 , -2.85067072987602e-03 , 4.03657995178171e-02 ), ( -5.84539818911867e-03 , 9.76042249153604e-03 , 3.60238306868930e-02 ), ( 2.70796487908088e-03 , -1.32241296979077e-02 , 1.96464215489824e-02 ), ( 9.18123224966560e-03 , -2.24957783523680e-02 , -2.66648685481025e-02 ), ( 8.78786656590287e-03 , -2.40792626679961e-02 , -1.48867932591327e-02 ), ( 6.71543577080716e-03 , -1.38446172953135e-02 , -3.03987599525088e-02 ), ( 1.50720661069986e-02 , -4.69521524401563e-02 , -1.92623704629729e-03 ), ( 2.76430209908363e-02 , -8.87967682589700e-02 , 7.67298256261931e-03 ), ( 1.42739897167352e-02 , -4.70630029142169e-02 , 9.01887453976427e-03 ), ( 1.42486787822643e-02 , -4.42158363168288e-02 , -2.53630561326753e-03 ), ( 9.22861705229513e-03 , -3.71259922873569e-02 , 3.37975218579997e-02 ), ( -1.03434697133723e-03 , -1.51090259593528e-02 , 7.66694860475731e-02 ), ( -3.86818586249688e-03 , 4.27337270826743e-03 , 3.29640520152657e-02 ), ( -5.93698751092329e-03 , 1.13879312616528e-02 , 3.04315529874886e-02 ), ( -7.35703194127185e-03 , 1.80154944915386e-02 , 2.14113196413313e-02 ), ( -1.62767618705796e-02 , 5.21409602254909e-02 , -3.91531965756660e-03 ), ( -9.71104920550146e-03 , 3.57887071932448e-02 , -2.18775513745860e-02 ), ( -1.37353980805760e-02 , 5.00828269242236e-02 , -2.87014844466075e-02 ), ( -1.90198879974780e-03 , 1.47280365461961e-02 , -3.65116461378043e-02 ), ( 1.07754626664859e-02 , -1.63343561723597e-02 , -7.33296483410146e-02 ), ( 4.49479215925102e-03 , -1.09404148493305e-03 , -5.44686669481053e-02 ), ( 3.50552735386580e-03 , 5.71924557998363e-03 , -6.99223907581775e-02 ), ( 7.19204308392410e-03 , -1.50883876037312e-02 , -3.14656795197781e-02 ), ( 1.30732051974002e-02 , -4.15663983506900e-02 , 1.84081814203583e-03 ), ( 5.21478005410681e-04 , 1.70625332202462e-03 , -1.39733493818603e-02 ), ( 4.57140419366889e-04 , 3.31607765582658e-03 , -1.98497263687156e-02 ), ( -6.55610910963488e-03 , 2.06722915485129e-02 , -2.01135264238113e-04 ), ( -2.06950886573350e-02 , 5.82188855341264e-02 , 2.87400696279859e-02 ), ( -1.89772593961475e-02 , 6.35728929566775e-02 , -1.61769549127556e-02 ), ( -2.26904308970780e-02 , 7.55926189084029e-02 , -1.75918705795381e-02 ), ( -1.66892107294848e-02 , 7.24568921030756e-02 , -8.33220787125386e-02 ), ( -1.97402932869575e-02 , 8.65992546836357e-02 , -1.02295692485758e-01 ), ( -8.41467779143527e-03 , 4.64461590623506e-02 , -8.34021574859848e-02 ), ( -1.85688269232122e-02 , 6.69066565879083e-02 , -3.54607731899793e-02 ), ( -2.42783345375781e-02 , 9.29808248567058e-02 , -6.93357136511408e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 33, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3795,10 +5549,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 34, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 34, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 34, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 34, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 34, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 34, atoms_positions[size = 51] = { ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213235e-01 ), ( 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 ), ( 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 ), ( 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547472e-02 ), ( 1.27341573009207e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 ), ( 9.03067744585786e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 ), ( -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 ), ( -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 ), ( -3.66392163061900e+00 , 7.02059845558150e-02 , 5.47546908453679e+00 ), ( -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ), ( 8.26845026355394e+00 , 3.95164634150700e-02 , -6.88685005072648e-01 ), ( 7.00769008928434e+00 , -2.07938515079511e+00 , -8.46089877311366e-01 ), ( 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548920e-01 ), ( 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 ), ( 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 ), ( 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 ), ( 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 ), ( 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 ), ( 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 ), ( 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 ), ( 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473450e+00 ), ( 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 ), ( 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 ), ( 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 ), ( 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 ), ( 4.23609800543256e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 ), ( 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 ), ( 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 ), ( 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 ), ( -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 ), ( 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 ), ( 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 ), ( -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 ), ( -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 ), ( -5.31089467087467e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 ), ( -7.65716766890360e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 ), ( -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 ), ( -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 ), ( -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 ), ( -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354262e-01 ), ( -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 ), ( -5.43935071235475e+00 , 7.31389248939757e-01 , 3.35509424924392e+00 ), ( -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 ), ( -2.35030078449157e+00 , -2.90079848836045e-01 , 6.12958271650988e+00 ), ( -4.49013169330158e+00 , 9.46193862990713e-01 , 6.42562713694847e+00 ), ( -5.35296372957695e+00 , 5.50304318713275e-01 , 7.18777295484910e+00 ), ( -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 ), ( -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 ), ( -6.61130571979379e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 ), ( -4.10966101472105e+00 , 2.25473453690066e+00 , 6.41773857390378e+00 ), ( -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721327e+00 ) } +colvars: Step 34, atoms_positions[size = 51] = { ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 ), ( 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 ), ( 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 ), ( 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 ), ( 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 ), ( 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 ), ( -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 ), ( -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 ), ( -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 ), ( -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ), ( 8.26845026355394e+00 , 3.95164634150697e-02 , -6.88685005072648e-01 ), ( 7.00769008928433e+00 , -2.07938515079511e+00 , -8.46089877311365e-01 ), ( 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548921e-01 ), ( 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 ), ( 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 ), ( 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 ), ( 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 ), ( 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 ), ( 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 ), ( 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 ), ( 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473451e+00 ), ( 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 ), ( 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 ), ( 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 ), ( 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 ), ( 4.23609800543255e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 ), ( 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 ), ( 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 ), ( 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 ), ( -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 ), ( 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 ), ( 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 ), ( -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 ), ( -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 ), ( -5.31089467087468e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 ), ( -7.65716766890362e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 ), ( -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 ), ( -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 ), ( -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 ), ( -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354263e-01 ), ( -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 ), ( -5.43935071235475e+00 , 7.31389248939756e-01 , 3.35509424924392e+00 ), ( -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 ), ( -2.35030078449156e+00 , -2.90079848836035e-01 , 6.12958271650987e+00 ), ( -4.49013169330158e+00 , 9.46193862990714e-01 , 6.42562713694847e+00 ), ( -5.35296372957695e+00 , 5.50304318713274e-01 , 7.18777295484910e+00 ), ( -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 ), ( -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 ), ( -6.61130571979380e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 ), ( -4.10966101472105e+00 , 2.25473453690065e+00 , 6.41773857390378e+00 ), ( -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721326e+00 ) } colvars: Step 34, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 34, atom_groups_ids[size = 0] = @@ -3815,17 +5569,88 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 34 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111081e-02 , 1.30981148586897e-02 , -1.46120262321522e-02 ). +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111080e-02 , 1.30981148586898e-02 , -1.46120262321522e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.26845026355394e+00 , 3.95164634150697e-02 , -6.88685005072648e-01 , 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 7.00769008928433e+00 , -2.07938515079511e+00 , -8.46089877311365e-01 , 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548921e-01 , 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 , 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 , 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 , 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 , 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 , 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473451e+00 , 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 , 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 , 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 , 4.23609800543255e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 , 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 , 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 , -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 , 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 , -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 , -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 , -5.31089467087468e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -7.65716766890362e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 , -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 , -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 , -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354263e-01 , -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 , -5.43935071235475e+00 , 7.31389248939756e-01 , 3.35509424924392e+00 , -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -2.35030078449156e+00 , -2.90079848836035e-01 , 6.12958271650987e+00 , -4.49013169330158e+00 , 9.46193862990714e-01 , 6.42562713694847e+00 , -5.35296372957695e+00 , 5.50304318713274e-01 , 7.18777295484910e+00 , -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 , -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 , -6.61130571979380e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 , -4.10966101472105e+00 , 2.25473453690065e+00 , 6.41773857390378e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 , -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721326e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111081e-02 , 1.30981148586897e-02 , -1.46120262321522e-02 ). +colvars: Colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111080e-02 , 1.30981148586898e-02 , -1.46120262321522e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.26845026355394e+00 , 3.95164634150697e-02 , -6.88685005072648e-01 , 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 7.00769008928433e+00 , -2.07938515079511e+00 , -8.46089877311365e-01 , 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548921e-01 , 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 , 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 , 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 , 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 , 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 , 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473451e+00 , 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 , 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 , 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 , 4.23609800543255e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 , 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 , 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 , -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 , 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 , -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 , -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 , -5.31089467087468e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -7.65716766890362e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 , -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 , -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 , -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354263e-01 , -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 , -5.43935071235475e+00 , 7.31389248939756e-01 , 3.35509424924392e+00 , -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -2.35030078449156e+00 , -2.90079848836035e-01 , 6.12958271650987e+00 , -4.49013169330158e+00 , 9.46193862990714e-01 , 6.42562713694847e+00 , -5.35296372957695e+00 , 5.50304318713274e-01 , 7.18777295484910e+00 , -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 , -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 , -6.61130571979380e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 , -4.10966101472105e+00 , 2.25473453690065e+00 , 6.41773857390378e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 , -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721326e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3838,6 +5663,10 @@ colvars: Adding total bias energy: 11.5105 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -3853,8 +5682,6 @@ colvars: ( 0.00615123 , -0.105367 , 0.314896 ) colvars: ( -0.050124 , 0.081031 , 0.215371 ) colvars: ( 0.0811992 , -0.236486 , 0.0274716 ) colvars: ( 0.13543 , -0.475625 , 0.336251 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242445 , -0.0993459 , 0.0964622 ) colvars: ( 0.0197234 , -0.0820021 , 0.0833938 ) @@ -3907,14 +5734,17 @@ colvars: ( -0.00840029 , 0.046439 , -0.0834313 ) colvars: ( -0.0185766 , 0.0668908 , -0.0355026 ) colvars: ( -0.022249 , 0.0841135 , -0.0591633 ) colvars: ( -0.0242794 , 0.0929429 , -0.0693618 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 34. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 34. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 34, atoms_new_colvar_forces = { ( -6.89931515523720e-02 , 3.03529453435325e-01 , -4.01438225063418e-01 ), ( 1.36805804611951e-02 , 3.21123159144449e-02 , -2.39859338329955e-01 ), ( -4.29352667358211e-02 , 9.57764098729455e-02 , 8.41354087339802e-02 ), ( -9.71793493942814e-02 , 2.49519950404404e-01 , 6.34334958307605e-02 ), ( -1.74775293005199e-02 , 9.79738898846051e-02 , -1.70983723879155e-01 ), ( 7.08744938792751e-02 , -1.84756089859670e-01 , -3.75322777943504e-02 ), ( 8.67155116481982e-03 , -9.87778464994404e-02 , 2.54526116207477e-01 ), ( -4.14780086993959e-02 , 5.92285323448908e-02 , 1.93069092917232e-01 ), ( 6.63968084260576e-02 , -1.91817057413589e-01 , 3.50994591677031e-02 ), ( 1.13181130747263e-01 , -3.91510994669006e-01 , 2.77087216958719e-01 ), ( 2.42445286609735e-02 , -9.93458642506380e-02 , 9.64622242692801e-02 ), ( 2.64170912653268e-02 , -9.74463301627498e-02 , 6.01553510528831e-02 ), ( 1.21880001742566e-02 , -5.57814893760357e-02 , 7.27916733558242e-02 ), ( 1.23568551091888e-02 , -5.36266530279977e-02 , 6.16171486908459e-02 ), ( 5.36532119084151e-03 , -3.50744606060441e-02 , 7.58160218574634e-02 ), ( -8.81061897949867e-03 , 9.54511730651302e-03 , 7.54617555207575e-02 ), ( -2.17760511040056e-03 , -2.86518723913951e-03 , 4.03912296616751e-02 ), ( -5.85846868302164e-03 , 9.74450841827336e-03 , 3.60381370606483e-02 ), ( 2.70844461247052e-03 , -1.32399871433099e-02 , 1.96885363244457e-02 ), ( 9.20192687987025e-03 , -2.25169446455836e-02 , -2.65968732719788e-02 ), ( 8.80255120781469e-03 , -2.40864736018276e-02 , -1.48443959207891e-02 ), ( 6.73250208365005e-03 , -1.38545990414471e-02 , -3.03609130906804e-02 ), ( 1.50877199996254e-02 , -4.69460167158572e-02 , -1.88440003463209e-03 ), ( 2.76651864173050e-02 , -8.87652480873047e-02 , 7.71367668824415e-03 ), ( 1.42835896453966e-02 , -4.70438788226700e-02 , 9.03535000251388e-03 ), ( 1.42609120931696e-02 , -4.41943703904300e-02 , -2.52602727794592e-03 ), ( 9.22660325372610e-03 , -3.71091704512848e-02 , 3.38041040625322e-02 ), ( -1.05835313619203e-03 , -1.50947778879150e-02 , 7.66508781959285e-02 ), ( -3.88184605550169e-03 , 4.27753341324615e-03 , 3.29475466990499e-02 ), ( -5.95255522011071e-03 , 1.13941067628747e-02 , 3.04035631838731e-02 ), ( -7.36916549274786e-03 , 1.80070942161374e-02 , 2.14040567647014e-02 ), ( -1.62874444626766e-02 , 5.21080227589862e-02 , -3.91242232744703e-03 ), ( -9.71261338380347e-03 , 3.57712555200729e-02 , -2.18828726157710e-02 ), ( -1.37389641632307e-02 , 5.00624491635394e-02 , -2.87166885471019e-02 ), ( -1.89232631851091e-03 , 1.47166616758053e-02 , -3.65027479143405e-02 ), ( 1.08069515486647e-02 , -1.63365926908086e-02 , -7.32982874652060e-02 ), ( 4.51343606296248e-03 , -1.09019322499418e-03 , -5.44680977153746e-02 ), ( 3.52735490621465e-03 , 5.72230291359508e-03 , -6.99262007192625e-02 ), ( 7.20560809590541e-03 , -1.50739359573486e-02 , -3.14717893114619e-02 ), ( 1.30803256344867e-02 , -4.15296746745539e-02 , 1.81917584866729e-03 ), ( 5.22321157891290e-04 , 1.72577325068763e-03 , -1.40099506251826e-02 ), ( 4.58742355604884e-04 , 3.33977328082308e-03 , -1.98952188702455e-02 ), ( -6.56483596370069e-03 , 2.06820949494386e-02 , -2.42711121581346e-04 ), ( -2.07242020794929e-02 , 5.82143300984994e-02 , 2.86793663983974e-02 ), ( -1.89921052856702e-02 , 6.35656362416375e-02 , -1.62333176260830e-02 ), ( -2.27087976362070e-02 , 7.55847985706018e-02 , -1.76605909183659e-02 ), ( -1.66814979147063e-02 , 7.24368891060878e-02 , -8.33567348746792e-02 ), ( -1.97295924656961e-02 , 8.65722790102330e-02 , -1.02331076952250e-01 ), ( -8.40029022578601e-03 , 4.64389575616804e-02 , -8.34312592396013e-02 ), ( -1.85765957934514e-02 , 6.68908166789611e-02 , -3.55026209993640e-02 ), ( -2.42793529811600e-02 , 9.29428836853372e-02 , -6.93618229473791e-02 ) } +colvars: Step 34, atoms_new_colvar_forces = { ( -6.89931515523722e-02 , 3.03529453435325e-01 , -4.01438225063418e-01 ), ( 1.36805804611950e-02 , 3.21123159144447e-02 , -2.39859338329955e-01 ), ( -4.29352667358211e-02 , 9.57764098729455e-02 , 8.41354087339803e-02 ), ( -9.71793493942812e-02 , 2.49519950404404e-01 , 6.34334958307607e-02 ), ( -1.74775293005200e-02 , 9.79738898846051e-02 , -1.70983723879155e-01 ), ( 7.08744938792751e-02 , -1.84756089859670e-01 , -3.75322777943504e-02 ), ( 8.67155116481996e-03 , -9.87778464994403e-02 , 2.54526116207477e-01 ), ( -4.14780086993958e-02 , 5.92285323448909e-02 , 1.93069092917231e-01 ), ( 6.63968084260576e-02 , -1.91817057413589e-01 , 3.50994591677031e-02 ), ( 1.13181130747263e-01 , -3.91510994669006e-01 , 2.77087216958719e-01 ), ( 2.42445286609735e-02 , -9.93458642506380e-02 , 9.64622242692801e-02 ), ( 2.64170912653268e-02 , -9.74463301627498e-02 , 6.01553510528831e-02 ), ( 1.21880001742566e-02 , -5.57814893760357e-02 , 7.27916733558242e-02 ), ( 1.23568551091888e-02 , -5.36266530279977e-02 , 6.16171486908459e-02 ), ( 5.36532119084152e-03 , -3.50744606060441e-02 , 7.58160218574634e-02 ), ( -8.81061897949866e-03 , 9.54511730651304e-03 , 7.54617555207575e-02 ), ( -2.17760511040056e-03 , -2.86518723913950e-03 , 4.03912296616751e-02 ), ( -5.85846868302164e-03 , 9.74450841827337e-03 , 3.60381370606483e-02 ), ( 2.70844461247052e-03 , -1.32399871433099e-02 , 1.96885363244457e-02 ), ( 9.20192687987023e-03 , -2.25169446455836e-02 , -2.65968732719789e-02 ), ( 8.80255120781468e-03 , -2.40864736018276e-02 , -1.48443959207891e-02 ), ( 6.73250208365004e-03 , -1.38545990414471e-02 , -3.03609130906804e-02 ), ( 1.50877199996254e-02 , -4.69460167158573e-02 , -1.88440003463211e-03 ), ( 2.76651864173050e-02 , -8.87652480873047e-02 , 7.71367668824414e-03 ), ( 1.42835896453966e-02 , -4.70438788226700e-02 , 9.03535000251388e-03 ), ( 1.42609120931696e-02 , -4.41943703904301e-02 , -2.52602727794592e-03 ), ( 9.22660325372609e-03 , -3.71091704512848e-02 , 3.38041040625322e-02 ), ( -1.05835313619202e-03 , -1.50947778879150e-02 , 7.66508781959285e-02 ), ( -3.88184605550168e-03 , 4.27753341324616e-03 , 3.29475466990500e-02 ), ( -5.95255522011070e-03 , 1.13941067628747e-02 , 3.04035631838731e-02 ), ( -7.36916549274786e-03 , 1.80070942161375e-02 , 2.14040567647014e-02 ), ( -1.62874444626766e-02 , 5.21080227589862e-02 , -3.91242232744704e-03 ), ( -9.71261338380347e-03 , 3.57712555200730e-02 , -2.18828726157710e-02 ), ( -1.37389641632307e-02 , 5.00624491635394e-02 , -2.87166885471019e-02 ), ( -1.89232631851091e-03 , 1.47166616758053e-02 , -3.65027479143405e-02 ), ( 1.08069515486647e-02 , -1.63365926908086e-02 , -7.32982874652060e-02 ), ( 4.51343606296246e-03 , -1.09019322499420e-03 , -5.44680977153746e-02 ), ( 3.52735490621464e-03 , 5.72230291359508e-03 , -6.99262007192625e-02 ), ( 7.20560809590540e-03 , -1.50739359573486e-02 , -3.14717893114619e-02 ), ( 1.30803256344866e-02 , -4.15296746745539e-02 , 1.81917584866731e-03 ), ( 5.22321157891290e-04 , 1.72577325068763e-03 , -1.40099506251826e-02 ), ( 4.58742355604879e-04 , 3.33977328082308e-03 , -1.98952188702454e-02 ), ( -6.56483596370068e-03 , 2.06820949494386e-02 , -2.42711121581312e-04 ), ( -2.07242020794929e-02 , 5.82143300984995e-02 , 2.86793663983974e-02 ), ( -1.89921052856701e-02 , 6.35656362416375e-02 , -1.62333176260830e-02 ), ( -2.27087976362070e-02 , 7.55847985706018e-02 , -1.76605909183659e-02 ), ( -1.66814979147063e-02 , 7.24368891060879e-02 , -8.33567348746792e-02 ), ( -1.97295924656961e-02 , 8.65722790102330e-02 , -1.02331076952250e-01 ), ( -8.40029022578602e-03 , 4.64389575616804e-02 , -8.34312592396013e-02 ), ( -1.85765957934514e-02 , 6.68908166789611e-02 , -3.55026209993640e-02 ), ( -2.42793529811600e-02 , 9.29428836853372e-02 , -6.93618229473791e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 34, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3952,10 +5782,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 35, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 35, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 35, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 35, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 35, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 35, atoms_positions[size = 51] = { ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518404e-01 ), ( 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 ), ( 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 ), ( 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 ), ( 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 ), ( 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 ), ( -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 ), ( -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 ), ( -3.66312344819816e+00 , 6.67877799859193e-02 , 5.46916433855244e+00 ), ( -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103287e+00 ), ( 8.26061045679133e+00 , 3.83159872376038e-02 , -6.83729575836184e-01 ), ( 7.00950811364951e+00 , -2.08340936270183e+00 , -8.38373555072615e-01 ), ( 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 ), ( 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 ), ( 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 ), ( 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 ), ( 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486681e+00 ), ( 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 ), ( 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 ), ( 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 ), ( 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 ), ( 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 ), ( 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 ), ( 3.13674411350812e+00 , 2.65473647538066e+00 , -1.53101934024696e+00 ), ( 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 ), ( 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 ), ( 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 ), ( 2.09321874616618e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 ), ( 5.70469478379835e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 ), ( -6.04067745585490e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 ), ( 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 ), ( 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 ), ( -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233233e+00 ), ( -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 ), ( -5.26037504488993e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 ), ( -7.70948015201457e-01 , 5.46443699617149e+00 , 2.48736122784712e+00 ), ( -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 ), ( -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 ), ( -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 ), ( -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293812e-01 ), ( -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 ), ( -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 ), ( -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306037e+00 ), ( -2.34232995666455e+00 , -2.82710935135214e-01 , 6.13081751615586e+00 ), ( -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958555e+00 ), ( -5.35241375743554e+00 , 5.43401369702619e-01 , 7.18368666862339e+00 ), ( -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 ), ( -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 ), ( -6.60792606081237e+00 , 3.17278933049612e+00 , 5.56077186656671e+00 ), ( -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 ), ( -4.00406811080273e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ) } +colvars: Step 35, atoms_positions[size = 51] = { ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 ), ( 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 ), ( 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 ), ( 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 ), ( 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 ), ( 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 ), ( -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 ), ( -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 ), ( -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 ), ( -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 ), ( 8.26061045679133e+00 , 3.83159872376033e-02 , -6.83729575836184e-01 ), ( 7.00950811364949e+00 , -2.08340936270183e+00 , -8.38373555072614e-01 ), ( 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 ), ( 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 ), ( 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 ), ( 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 ), ( 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486680e+00 ), ( 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 ), ( 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 ), ( 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 ), ( 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 ), ( 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 ), ( 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 ), ( 3.13674411350812e+00 , 2.65473647538067e+00 , -1.53101934024696e+00 ), ( 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 ), ( 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 ), ( 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 ), ( 2.09321874616617e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 ), ( 5.70469478379834e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 ), ( -6.04067745585491e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 ), ( 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 ), ( 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 ), ( -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233232e+00 ), ( -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 ), ( -5.26037504488994e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 ), ( -7.70948015201459e-01 , 5.46443699617149e+00 , 2.48736122784711e+00 ), ( -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 ), ( -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 ), ( -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 ), ( -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293814e-01 ), ( -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 ), ( -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 ), ( -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306038e+00 ), ( -2.34232995666454e+00 , -2.82710935135204e-01 , 6.13081751615585e+00 ), ( -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958556e+00 ), ( -5.35241375743554e+00 , 5.43401369702618e-01 , 7.18368666862339e+00 ), ( -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 ), ( -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 ), ( -6.60792606081237e+00 , 3.17278933049613e+00 , 5.56077186656671e+00 ), ( -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 ), ( -4.00406811080272e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ) } colvars: Step 35, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 35, atom_groups_ids[size = 0] = @@ -3973,16 +5803,87 @@ colvars: Collective variables module, step no. 35 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858438e-02 , 1.28715966499478e-02 , -1.44634565196466e-02 ). +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858439e-02 , 1.28715966499479e-02 , -1.44634565196466e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.26061045679133e+00 , 3.83159872376033e-02 , -6.83729575836184e-01 , 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 7.00950811364949e+00 , -2.08340936270183e+00 , -8.38373555072614e-01 , 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 , 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 , 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 , 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486680e+00 , 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 , 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 , 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 , 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 , 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 3.13674411350812e+00 , 2.65473647538067e+00 , -1.53101934024696e+00 , 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 , 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 , 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 2.09321874616617e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 , 5.70469478379834e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 , -6.04067745585491e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 , 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 , -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233232e+00 , -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 , -5.26037504488994e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -7.70948015201459e-01 , 5.46443699617149e+00 , 2.48736122784711e+00 , -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 , -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 , -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293814e-01 , -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 , -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 , -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306038e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -2.34232995666454e+00 , -2.82710935135204e-01 , 6.13081751615585e+00 , -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958556e+00 , -5.35241375743554e+00 , 5.43401369702618e-01 , 7.18368666862339e+00 , -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 , -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 , -6.60792606081237e+00 , 3.17278933049613e+00 , 5.56077186656671e+00 , -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 , -4.00406811080272e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858438e-02 , 1.28715966499478e-02 , -1.44634565196466e-02 ). +colvars: Colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858439e-02 , 1.28715966499479e-02 , -1.44634565196466e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.26061045679133e+00 , 3.83159872376033e-02 , -6.83729575836184e-01 , 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 7.00950811364949e+00 , -2.08340936270183e+00 , -8.38373555072614e-01 , 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 , 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 , 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 , 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486680e+00 , 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 , 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 , 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 , 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 , 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 3.13674411350812e+00 , 2.65473647538067e+00 , -1.53101934024696e+00 , 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 , 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 , 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 2.09321874616617e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 , 5.70469478379834e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 , -6.04067745585491e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 , 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 , -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233232e+00 , -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 , -5.26037504488994e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -7.70948015201459e-01 , 5.46443699617149e+00 , 2.48736122784711e+00 , -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 , -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 , -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293814e-01 , -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 , -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 , -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306038e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -2.34232995666454e+00 , -2.82710935135204e-01 , 6.13081751615585e+00 , -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958556e+00 , -5.35241375743554e+00 , 5.43401369702618e-01 , 7.18368666862339e+00 , -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 , -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 , -6.60792606081237e+00 , 3.17278933049613e+00 , 5.56077186656671e+00 , -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 , -4.00406811080272e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -3995,6 +5896,10 @@ colvars: Adding total bias energy: 11.5124 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4010,8 +5915,6 @@ colvars: ( 0.00602767 , -0.105314 , 0.315083 ) colvars: ( -0.0502732 , 0.0811681 , 0.21538 ) colvars: ( 0.0812645 , -0.236538 , 0.0275314 ) colvars: ( 0.135429 , -0.475701 , 0.33658 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242457 , -0.099307 , 0.0964973 ) colvars: ( 0.0197239 , -0.0819759 , 0.083438 ) @@ -4064,14 +5967,17 @@ colvars: ( -0.00838973 , 0.0464281 , -0.0834677 ) colvars: ( -0.0185877 , 0.0668734 , -0.0355481 ) colvars: ( -0.0222577 , 0.0840866 , -0.0592078 ) colvars: ( -0.0242869 , 0.0929059 , -0.0693923 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 35. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 35. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 35, atoms_new_colvar_forces = { ( -6.88807360946586e-02 , 3.03546174506848e-01 , -4.01748229755430e-01 ), ( 1.38150532480895e-02 , 3.19920050341430e-02 , -2.39936826947338e-01 ), ( -4.30059550048689e-02 , 9.57958483467742e-02 , 8.42381958230144e-02 ), ( -9.73074704360655e-02 , 2.49684520874827e-01 , 6.33713523707342e-02 ), ( -1.74201151791814e-02 , 9.79823778111991e-02 , -1.71159035993790e-01 ), ( 7.09667533396045e-02 , -1.84885894825296e-01 , -3.74547956787869e-02 ), ( 8.56541917378931e-03 , -9.87326138352739e-02 , 2.54722745980557e-01 ), ( -4.16147347248275e-02 , 5.93856644975063e-02 , 1.93055283348347e-01 ), ( 6.64435907168653e-02 , -1.91869163125823e-01 , 3.51002760286789e-02 ), ( 1.13171124872205e-01 , -3.91614114049827e-01 , 2.77372205308533e-01 ), ( 2.42457448834940e-02 , -9.93070224567197e-02 , 9.64972929017528e-02 ), ( 2.64303690231682e-02 , -9.74191373119857e-02 , 6.02170552240258e-02 ), ( 1.21835519220548e-02 , -5.57655192466588e-02 , 7.28270609870343e-02 ), ( 1.23549210045000e-02 , -5.36090050053975e-02 , 6.16449699320789e-02 ), ( 5.35374003500272e-03 , -3.50695784504462e-02 , 7.58525382532428e-02 ), ( -8.83570700232431e-03 , 9.52850693697147e-03 , 7.54942754737820e-02 ), ( -2.18803122140737e-03 , -2.87499821449638e-03 , 4.04217065934371e-02 ), ( -5.87186847068820e-03 , 9.73270279833235e-03 , 3.60567731097607e-02 ), ( 2.70837477367324e-03 , -1.32507681744094e-02 , 1.97348271046726e-02 ), ( 9.22027924498694e-03 , -2.25325482849989e-02 , -2.65269833710351e-02 ), ( 8.81646329246599e-03 , -2.40909194584065e-02 , -1.48010224744674e-02 ), ( 6.74794204665999e-03 , -1.38622651450867e-02 , -3.03233386338981e-02 ), ( 1.51044276345387e-02 , -4.69383939076473e-02 , -1.84135275144504e-03 ), ( 2.76913826852593e-02 , -8.87352085322906e-02 , 7.75483897287111e-03 ), ( 1.42956864003069e-02 , -4.70259579292682e-02 , 9.05211661372034e-03 ), ( 1.42754387286164e-02 , -4.41751623983650e-02 , -2.51675453633898e-03 ), ( 9.22754823332048e-03 , -3.70929337651855e-02 , 3.38126538002123e-02 ), ( -1.07854362508034e-03 , -1.50806771148120e-02 , 7.66367273623760e-02 ), ( -3.89416842781480e-03 , 4.28140636220416e-03 , 3.29327218643407e-02 ), ( -5.96678550441179e-03 , 1.13990052816781e-02 , 3.03764693573408e-02 ), ( -7.38156070100471e-03 , 1.80001190670400e-02 , 2.13986614634106e-02 ), ( -1.63016928856876e-02 , 5.20793173793130e-02 , -3.90783217966117e-03 ), ( -9.71679604441101e-03 , 3.57549618897123e-02 , -2.18891358294395e-02 ), ( -1.37457928463725e-02 , 5.00428092109121e-02 , -2.87336088867497e-02 ), ( -1.88496398780748e-03 , 1.47059454600983e-02 , -3.64957084247095e-02 ), ( 1.08361435000648e-02 , -1.63393854324176e-02 , -7.32712852290432e-02 ), ( 4.53069842551565e-03 , -1.08873278149813e-03 , -5.44720111056568e-02 ), ( 3.54715952514465e-03 , 5.72228164961963e-03 , -6.99358433688926e-02 ), ( 7.21959067154382e-03 , -1.50627862598159e-02 , -3.14814510290332e-02 ), ( 1.30911314699056e-02 , -4.14987884092740e-02 , 1.79469385094992e-03 ), ( 5.24348506408817e-04 , 1.74025786394996e-03 , -1.40502650952513e-02 ), ( 4.61674806489523e-04 , 3.35719489023765e-03 , -1.99454895684732e-02 ), ( -6.57300468365555e-03 , 2.06883139076784e-02 , -2.86564847277621e-04 ), ( -2.07535322945684e-02 , 5.82079798474097e-02 , 2.86187002618328e-02 ), ( -1.90088824990835e-02 , 6.35555827272411e-02 , -1.62928456142045e-02 ), ( -2.27293407292263e-02 , 7.55735124075078e-02 , -1.77330614847095e-02 ), ( -1.66790254550069e-02 , 7.24145550891492e-02 , -8.33982228687755e-02 ), ( -1.97254993582460e-02 , 8.65431509733358e-02 , -1.02374417573546e-01 ), ( -8.38973467101069e-03 , 4.64280970315202e-02 , -8.34677033511890e-02 ), ( -1.85876716559441e-02 , 6.68734057428191e-02 , -3.55480668376697e-02 ), ( -2.42869446603211e-02 , 9.29058765273728e-02 , -6.93922885498936e-02 ) } +colvars: Step 35, atoms_new_colvar_forces = { ( -6.88807360946587e-02 , 3.03546174506848e-01 , -4.01748229755430e-01 ), ( 1.38150532480894e-02 , 3.19920050341430e-02 , -2.39936826947338e-01 ), ( -4.30059550048689e-02 , 9.57958483467742e-02 , 8.42381958230143e-02 ), ( -9.73074704360656e-02 , 2.49684520874827e-01 , 6.33713523707341e-02 ), ( -1.74201151791814e-02 , 9.79823778111991e-02 , -1.71159035993790e-01 ), ( 7.09667533396044e-02 , -1.84885894825296e-01 , -3.74547956787869e-02 ), ( 8.56541917378938e-03 , -9.87326138352738e-02 , 2.54722745980557e-01 ), ( -4.16147347248274e-02 , 5.93856644975062e-02 , 1.93055283348347e-01 ), ( 6.64435907168653e-02 , -1.91869163125822e-01 , 3.51002760286789e-02 ), ( 1.13171124872205e-01 , -3.91614114049827e-01 , 2.77372205308533e-01 ), ( 2.42457448834941e-02 , -9.93070224567197e-02 , 9.64972929017528e-02 ), ( 2.64303690231682e-02 , -9.74191373119858e-02 , 6.02170552240258e-02 ), ( 1.21835519220548e-02 , -5.57655192466589e-02 , 7.28270609870343e-02 ), ( 1.23549210045000e-02 , -5.36090050053975e-02 , 6.16449699320789e-02 ), ( 5.35374003500274e-03 , -3.50695784504462e-02 , 7.58525382532428e-02 ), ( -8.83570700232429e-03 , 9.52850693697150e-03 , 7.54942754737820e-02 ), ( -2.18803122140736e-03 , -2.87499821449636e-03 , 4.04217065934371e-02 ), ( -5.87186847068819e-03 , 9.73270279833237e-03 , 3.60567731097607e-02 ), ( 2.70837477367325e-03 , -1.32507681744094e-02 , 1.97348271046725e-02 ), ( 9.22027924498692e-03 , -2.25325482849989e-02 , -2.65269833710352e-02 ), ( 8.81646329246599e-03 , -2.40909194584065e-02 , -1.48010224744675e-02 ), ( 6.74794204665998e-03 , -1.38622651450867e-02 , -3.03233386338982e-02 ), ( 1.51044276345387e-02 , -4.69383939076473e-02 , -1.84135275144506e-03 ), ( 2.76913826852593e-02 , -8.87352085322907e-02 , 7.75483897287110e-03 ), ( 1.42956864003069e-02 , -4.70259579292682e-02 , 9.05211661372034e-03 ), ( 1.42754387286164e-02 , -4.41751623983651e-02 , -2.51675453633897e-03 ), ( 9.22754823332049e-03 , -3.70929337651855e-02 , 3.38126538002124e-02 ), ( -1.07854362508031e-03 , -1.50806771148120e-02 , 7.66367273623761e-02 ), ( -3.89416842781478e-03 , 4.28140636220418e-03 , 3.29327218643407e-02 ), ( -5.96678550441178e-03 , 1.13990052816781e-02 , 3.03764693573409e-02 ), ( -7.38156070100469e-03 , 1.80001190670400e-02 , 2.13986614634107e-02 ), ( -1.63016928856876e-02 , 5.20793173793131e-02 , -3.90783217966120e-03 ), ( -9.71679604441101e-03 , 3.57549618897123e-02 , -2.18891358294395e-02 ), ( -1.37457928463725e-02 , 5.00428092109121e-02 , -2.87336088867498e-02 ), ( -1.88496398780749e-03 , 1.47059454600984e-02 , -3.64957084247095e-02 ), ( 1.08361435000648e-02 , -1.63393854324177e-02 , -7.32712852290432e-02 ), ( 4.53069842551564e-03 , -1.08873278149816e-03 , -5.44720111056568e-02 ), ( 3.54715952514462e-03 , 5.72228164961961e-03 , -6.99358433688927e-02 ), ( 7.21959067154380e-03 , -1.50627862598159e-02 , -3.14814510290332e-02 ), ( 1.30911314699056e-02 , -4.14987884092741e-02 , 1.79469385094998e-03 ), ( 5.24348506408816e-04 , 1.74025786394995e-03 , -1.40502650952513e-02 ), ( 4.61674806489519e-04 , 3.35719489023764e-03 , -1.99454895684731e-02 ), ( -6.57300468365554e-03 , 2.06883139076785e-02 , -2.86564847277578e-04 ), ( -2.07535322945683e-02 , 5.82079798474097e-02 , 2.86187002618328e-02 ), ( -1.90088824990835e-02 , 6.35555827272412e-02 , -1.62928456142045e-02 ), ( -2.27293407292263e-02 , 7.55735124075078e-02 , -1.77330614847094e-02 ), ( -1.66790254550069e-02 , 7.24145550891492e-02 , -8.33982228687755e-02 ), ( -1.97254993582460e-02 , 8.65431509733359e-02 , -1.02374417573546e-01 ), ( -8.38973467101070e-03 , 4.64280970315202e-02 , -8.34677033511890e-02 ), ( -1.85876716559441e-02 , 6.68734057428191e-02 , -3.55480668376697e-02 ), ( -2.42869446603211e-02 , 9.29058765273728e-02 , -6.93922885498936e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 35, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4109,10 +6015,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 36, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 36, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 36, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 36, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 36, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 36, atoms_positions[size = 51] = { ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460808e-01 ), ( 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 ), ( 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 ), ( 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643877e-02 ), ( 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 ), ( 9.14913692767032e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 ), ( -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 ), ( -3.82286114827543e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 ), ( -3.66247706101863e+00 , 6.34272909613127e-02 , 5.46201921848078e+00 ), ( -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252679e+00 ), ( 8.25217464544869e+00 , 3.69221958155763e-02 , -6.78843503334926e-01 ), ( 7.01230109825313e+00 , -2.08771896240021e+00 , -8.30893615702845e-01 ), ( 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221474e-01 ), ( 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 ), ( 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 ), ( 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 ), ( 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 ), ( 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 ), ( 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 ), ( 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 ), ( 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981678e+00 ), ( 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 ), ( 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 ), ( 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 ), ( 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 ), ( 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 ), ( 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 ), ( 2.09467021666479e+00 , -1.09528109816073e+00 , 2.02995905011222e+00 ), ( 5.69529133519057e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 ), ( -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 ), ( 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 ), ( 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 ), ( -3.55712677434050e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 ), ( -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 ), ( -5.20464387542565e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 ), ( -7.75358318910474e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 ), ( -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 ), ( -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 ), ( -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 ), ( -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839781e-01 ), ( -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 ), ( -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 ), ( -3.35934410802697e+00 , 7.13844953536182e-01 , 4.17234104677063e+00 ), ( -2.33377676810807e+00 , -2.75203274913520e-01 , 6.13304533363275e+00 ), ( -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 ), ( -5.35209341374793e+00 , 5.36256909713220e-01 , 7.17960272686383e+00 ), ( -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394096e+00 ), ( -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 ), ( -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 ), ( -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 ), ( -4.00404855626916e+00 , 4.62566455159043e+00 , 7.28513526460300e+00 ) } +colvars: Step 36, atoms_positions[size = 51] = { ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 ), ( 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 ), ( 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 ), ( 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 ), ( 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 ), ( 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 ), ( -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 ), ( -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 ), ( -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 ), ( -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 ), ( 8.25217464544869e+00 , 3.69221958155758e-02 , -6.78843503334926e-01 ), ( 7.01230109825312e+00 , -2.08771896240021e+00 , -8.30893615702844e-01 ), ( 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221475e-01 ), ( 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 ), ( 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 ), ( 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 ), ( 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 ), ( 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 ), ( 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 ), ( 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 ), ( 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981679e+00 ), ( 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 ), ( 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 ), ( 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 ), ( 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 ), ( 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 ), ( 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 ), ( 2.09467021666479e+00 , -1.09528109816072e+00 , 2.02995905011222e+00 ), ( 5.69529133519056e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 ), ( -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 ), ( 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 ), ( 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 ), ( -3.55712677434051e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 ), ( -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 ), ( -5.20464387542566e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 ), ( -7.75358318910477e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 ), ( -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 ), ( -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 ), ( -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 ), ( -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839784e-01 ), ( -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 ), ( -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 ), ( -3.35934410802697e+00 , 7.13844953536181e-01 , 4.17234104677064e+00 ), ( -2.33377676810806e+00 , -2.75203274913510e-01 , 6.13304533363274e+00 ), ( -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 ), ( -5.35209341374793e+00 , 5.36256909713219e-01 , 7.17960272686383e+00 ), ( -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394097e+00 ), ( -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 ), ( -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 ), ( -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 ), ( -4.00404855626915e+00 , 4.62566455159042e+00 , 7.28513526460300e+00 ) } colvars: Step 36, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 36, atom_groups_ids[size = 0] = @@ -4129,17 +6035,88 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 36 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956246e-02 , 1.26183883681986e-02 , -1.42839286474994e-02 ). +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956245e-02 , 1.26183883681986e-02 , -1.42839286474993e-02 ). +colvars: Done calculating gradients of colvar "main". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.25217464544869e+00 , 3.69221958155758e-02 , -6.78843503334926e-01 , 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 7.01230109825312e+00 , -2.08771896240021e+00 , -8.30893615702844e-01 , 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221475e-01 , 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 , 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 , 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 , 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 , 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 , 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981679e+00 , 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 , 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 , 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 , 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 , 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 2.09467021666479e+00 , -1.09528109816072e+00 , 2.02995905011222e+00 , 5.69529133519056e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 , -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 , 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 , -3.55712677434051e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 , -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 , -5.20464387542566e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -7.75358318910477e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 , -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 , -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 , -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839784e-01 , -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 , -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 , -3.35934410802697e+00 , 7.13844953536181e-01 , 4.17234104677064e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -2.33377676810806e+00 , -2.75203274913510e-01 , 6.13304533363274e+00 , -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 , -5.35209341374793e+00 , 5.36256909713219e-01 , 7.17960272686383e+00 , -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394097e+00 , -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 , -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 , -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 , -4.00404855626915e+00 , 4.62566455159042e+00 , 7.28513526460300e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956246e-02 , 1.26183883681986e-02 , -1.42839286474994e-02 ). +colvars: Colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956245e-02 , 1.26183883681986e-02 , -1.42839286474993e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.25217464544869e+00 , 3.69221958155758e-02 , -6.78843503334926e-01 , 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 7.01230109825312e+00 , -2.08771896240021e+00 , -8.30893615702844e-01 , 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221475e-01 , 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 , 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 , 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 , 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 , 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 , 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981679e+00 , 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 , 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 , 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 , 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 , 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 2.09467021666479e+00 , -1.09528109816072e+00 , 2.02995905011222e+00 , 5.69529133519056e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 , -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 , 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 , -3.55712677434051e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 , -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 , -5.20464387542566e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -7.75358318910477e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 , -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 , -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 , -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839784e-01 , -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 , -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 , -3.35934410802697e+00 , 7.13844953536181e-01 , 4.17234104677064e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -2.33377676810806e+00 , -2.75203274913510e-01 , 6.13304533363274e+00 , -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 , -5.35209341374793e+00 , 5.36256909713219e-01 , 7.17960272686383e+00 , -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394097e+00 , -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 , -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 , -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 , -4.00404855626915e+00 , 4.62566455159042e+00 , 7.28513526460300e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4152,6 +6129,10 @@ colvars: Adding total bias energy: 11.515 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4167,8 +6148,6 @@ colvars: ( 0.00591321 , -0.105243 , 0.315324 ) colvars: ( -0.0504294 , 0.0813694 , 0.215382 ) colvars: ( 0.0813332 , -0.23659 , 0.0275681 ) colvars: ( 0.135449 , -0.475794 , 0.336965 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.024254 , -0.0992689 , 0.096539 ) colvars: ( 0.0197298 , -0.0819484 , 0.0834884 ) @@ -4221,14 +6200,17 @@ colvars: ( -0.008383 , 0.0464138 , -0.0835108 ) colvars: ( -0.0186016 , 0.0668552 , -0.0355964 ) colvars: ( -0.0222711 , 0.0840595 , -0.0592566 ) colvars: ( -0.0243005 , 0.0928707 , -0.0694273 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 36. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 36. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 36, atoms_new_colvar_forces = { ( -6.87825515010302e-02 , 3.03551175854197e-01 , -4.02123591707848e-01 ), ( 1.39516159518603e-02 , 3.18209001221920e-02 , -2.40021075355466e-01 ), ( -4.30741931969209e-02 , 9.58131187992767e-02 , 8.43908110464439e-02 ), ( -9.74454677719412e-02 , 2.49896651123009e-01 , 6.33078221622214e-02 ), ( -1.73699557572936e-02 , 9.79928227747052e-02 , -1.71382115313688e-01 ), ( 7.10671728779809e-02 , -1.85053619004943e-01 , -3.73669781672519e-02 ), ( 8.46560683046808e-03 , -9.86698209726457e-02 , 2.54968457116350e-01 ), ( -4.17572287925473e-02 , 5.96014738190170e-02 , 1.93030343635103e-01 ), ( 6.64939874414992e-02 , -1.91924129005420e-01 , 3.50776228827208e-02 ), ( 1.13178124270782e-01 , -3.91734979956619e-01 , 2.77708435582395e-01 ), ( 2.42540016505370e-02 , -9.92689443102836e-02 , 9.65390072894102e-02 ), ( 2.64483115922368e-02 , -9.73909658951079e-02 , 6.02835162651832e-02 ), ( 1.21830809877307e-02 , -5.57474384223472e-02 , 7.28680948982734e-02 ), ( 1.23567667227087e-02 , -5.35903711954581e-02 , 6.16773865701317e-02 ), ( 5.34512949395847e-03 , -3.50605336726781e-02 , 7.58953439322042e-02 ), ( -8.85997764673843e-03 , 9.51947116101916e-03 , 7.55337438274853e-02 ), ( -2.19811885413010e-03 , -2.87995808817898e-03 , 4.04561704955643e-02 ), ( -5.88526593724566e-03 , 9.72531991195740e-03 , 3.60789200428813e-02 ), ( 2.70785417124687e-03 , -1.32566301520369e-02 , 1.97838389513108e-02 ), ( 9.23615813287942e-03 , -2.25432107077568e-02 , -2.64573206711712e-02 ), ( 8.82941764911573e-03 , -2.40931117783055e-02 , -1.47578476036868e-02 ), ( 6.76159384954824e-03 , -1.38680730198555e-02 , -3.02871414148130e-02 ), ( 1.51218095131350e-02 , -4.69300222271671e-02 , -1.79794353022244e-03 ), ( 2.77208071616533e-02 , -8.87078872996008e-02 , 7.79627322118805e-03 ), ( 1.43098597663197e-02 , -4.70098544163797e-02 , 9.06924461340023e-03 ), ( 1.42917926844773e-02 , -4.41588435488001e-02 , -2.50818581251333e-03 ), ( 9.23122439443106e-03 , -3.70775907849662e-02 , 3.38233725284600e-02 ), ( -1.09478835120119e-03 , -1.50664198922653e-02 , 7.66276922034176e-02 ), ( -3.90500816429111e-03 , 4.28528625123975e-03 , 3.29200157247979e-02 ), ( -5.97950807729433e-03 , 1.14030284170730e-02 , 3.03510423802199e-02 ), ( -7.39394176377097e-03 , 1.79949563178355e-02 , 2.13950536392084e-02 ), ( -1.63189362527715e-02 , 5.20555115448216e-02 , -3.90244624481999e-03 ), ( -9.72332312549996e-03 , 3.57401858757540e-02 , -2.18966122390077e-02 ), ( -1.37555195126383e-02 , 5.00244400005668e-02 , -2.87523394191009e-02 ), ( -1.87987996734087e-03 , 1.46958439822277e-02 , -3.64909585650040e-02 ), ( 1.08626211982598e-02 , -1.63434687790130e-02 , -7.32493095287909e-02 ), ( 4.54630977618069e-03 , -1.09000456952993e-03 , -5.44802162169457e-02 ), ( 3.56465799952970e-03 , 5.71884565694859e-03 , -6.99510120052419e-02 ), ( 7.23365133628510e-03 , -1.50553158520898e-02 , -3.14940893290122e-02 ), ( 1.31050916705081e-02 , -4.14742340010639e-02 , 1.76882071273220e-03 ), ( 5.27380256966284e-04 , 1.74973163386150e-03 , -1.40928889578658e-02 ), ( 4.65715758364314e-04 , 3.36837393393765e-03 , -1.99988030791925e-02 ), ( -6.58053681650212e-03 , 2.06913214588559e-02 , -3.31446169875402e-04 ), ( -2.07825151365776e-02 , 5.82009297448728e-02 , 2.85593613051498e-02 ), ( -1.90271656243260e-02 , 6.35436180091860e-02 , -1.63543335215463e-02 ), ( -2.27515526488475e-02 , 7.55598273573979e-02 , -1.78077907924695e-02 ), ( -1.66815106120319e-02 , 7.23904387415431e-02 , -8.34460512800944e-02 ), ( -1.97276671460812e-02 , 8.65124958483396e-02 , -1.02425344852602e-01 ), ( -8.38299757725755e-03 , 4.64137645103610e-02 , -8.35108075184974e-02 ), ( -1.86016314754188e-02 , 6.68552036549514e-02 , -3.55964346198361e-02 ), ( -2.43005014289642e-02 , 9.28706910473661e-02 , -6.94273071096894e-02 ) } +colvars: Step 36, atoms_new_colvar_forces = { ( -6.87825515010303e-02 , 3.03551175854197e-01 , -4.02123591707848e-01 ), ( 1.39516159518602e-02 , 3.18209001221919e-02 , -2.40021075355466e-01 ), ( -4.30741931969210e-02 , 9.58131187992768e-02 , 8.43908110464438e-02 ), ( -9.74454677719412e-02 , 2.49896651123009e-01 , 6.33078221622214e-02 ), ( -1.73699557572936e-02 , 9.79928227747052e-02 , -1.71382115313688e-01 ), ( 7.10671728779810e-02 , -1.85053619004943e-01 , -3.73669781672520e-02 ), ( 8.46560683046813e-03 , -9.86698209726457e-02 , 2.54968457116350e-01 ), ( -4.17572287925472e-02 , 5.96014738190170e-02 , 1.93030343635103e-01 ), ( 6.64939874414992e-02 , -1.91924129005421e-01 , 3.50776228827207e-02 ), ( 1.13178124270782e-01 , -3.91734979956620e-01 , 2.77708435582396e-01 ), ( 2.42540016505370e-02 , -9.92689443102836e-02 , 9.65390072894103e-02 ), ( 2.64483115922368e-02 , -9.73909658951079e-02 , 6.02835162651833e-02 ), ( 1.21830809877308e-02 , -5.57474384223472e-02 , 7.28680948982734e-02 ), ( 1.23567667227087e-02 , -5.35903711954581e-02 , 6.16773865701318e-02 ), ( 5.34512949395850e-03 , -3.50605336726781e-02 , 7.58953439322043e-02 ), ( -8.85997764673842e-03 , 9.51947116101915e-03 , 7.55337438274854e-02 ), ( -2.19811885413009e-03 , -2.87995808817898e-03 , 4.04561704955643e-02 ), ( -5.88526593724565e-03 , 9.72531991195741e-03 , 3.60789200428813e-02 ), ( 2.70785417124688e-03 , -1.32566301520370e-02 , 1.97838389513108e-02 ), ( 9.23615813287942e-03 , -2.25432107077569e-02 , -2.64573206711712e-02 ), ( 8.82941764911573e-03 , -2.40931117783055e-02 , -1.47578476036868e-02 ), ( 6.76159384954824e-03 , -1.38680730198555e-02 , -3.02871414148130e-02 ), ( 1.51218095131350e-02 , -4.69300222271671e-02 , -1.79794353022244e-03 ), ( 2.77208071616533e-02 , -8.87078872996009e-02 , 7.79627322118805e-03 ), ( 1.43098597663197e-02 , -4.70098544163797e-02 , 9.06924461340024e-03 ), ( 1.42917926844773e-02 , -4.41588435488001e-02 , -2.50818581251334e-03 ), ( 9.23122439443108e-03 , -3.70775907849662e-02 , 3.38233725284600e-02 ), ( -1.09478835120119e-03 , -1.50664198922653e-02 , 7.66276922034177e-02 ), ( -3.90500816429111e-03 , 4.28528625123975e-03 , 3.29200157247979e-02 ), ( -5.97950807729432e-03 , 1.14030284170730e-02 , 3.03510423802199e-02 ), ( -7.39394176377097e-03 , 1.79949563178355e-02 , 2.13950536392084e-02 ), ( -1.63189362527715e-02 , 5.20555115448216e-02 , -3.90244624481996e-03 ), ( -9.72332312549997e-03 , 3.57401858757540e-02 , -2.18966122390077e-02 ), ( -1.37555195126383e-02 , 5.00244400005668e-02 , -2.87523394191009e-02 ), ( -1.87987996734087e-03 , 1.46958439822277e-02 , -3.64909585650040e-02 ), ( 1.08626211982598e-02 , -1.63434687790130e-02 , -7.32493095287909e-02 ), ( 4.54630977618068e-03 , -1.09000456952993e-03 , -5.44802162169457e-02 ), ( 3.56465799952969e-03 , 5.71884565694859e-03 , -6.99510120052419e-02 ), ( 7.23365133628510e-03 , -1.50553158520898e-02 , -3.14940893290122e-02 ), ( 1.31050916705081e-02 , -4.14742340010639e-02 , 1.76882071273220e-03 ), ( 5.27380256966284e-04 , 1.74973163386151e-03 , -1.40928889578658e-02 ), ( 4.65715758364312e-04 , 3.36837393393763e-03 , -1.99988030791925e-02 ), ( -6.58053681650213e-03 , 2.06913214588559e-02 , -3.31446169875400e-04 ), ( -2.07825151365776e-02 , 5.82009297448728e-02 , 2.85593613051498e-02 ), ( -1.90271656243260e-02 , 6.35436180091860e-02 , -1.63543335215463e-02 ), ( -2.27515526488476e-02 , 7.55598273573979e-02 , -1.78077907924694e-02 ), ( -1.66815106120319e-02 , 7.23904387415432e-02 , -8.34460512800944e-02 ), ( -1.97276671460812e-02 , 8.65124958483397e-02 , -1.02425344852602e-01 ), ( -8.38299757725756e-03 , 4.64137645103610e-02 , -8.35108075184975e-02 ), ( -1.86016314754188e-02 , 6.68552036549514e-02 , -3.55964346198361e-02 ), ( -2.43005014289643e-02 , 9.28706910473661e-02 , -6.94273071096894e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 36, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4266,10 +6248,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 37, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 37, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 37, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 37, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 37, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 37, atoms_positions[size = 51] = { ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171618e-01 ), ( 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 ), ( 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 ), ( 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588425e-02 ), ( 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 ), ( 9.19169465945245e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 ), ( -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 ), ( -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 ), ( -3.66199545735369e+00 , 6.03753664064912e-02 , 5.45456574948843e+00 ), ( -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931395e+00 ), ( 8.24325423950952e+00 , 3.53606340058558e-02 , -6.74071896755363e-01 ), ( 7.01595064911502e+00 , -2.09226237248072e+00 , -8.23713639498106e-01 ), ( 6.10178478736824e+00 , -3.17827591276147e-01 , 8.15561834792713e-01 ), ( 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 ), ( 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 ), ( 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 ), ( 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 ), ( 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 ), ( 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757520e+00 ), ( 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 ), ( 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 ), ( 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 ), ( 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 ), ( 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 ), ( 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 ), ( 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 ), ( 2.01981272765407e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 ), ( 2.09593922434932e+00 , -1.09517162307367e+00 , 2.02627695012513e+00 ), ( 5.68648106130873e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 ), ( -6.10998899499221e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 ), ( 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 ), ( 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 ), ( -3.53783966258115e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 ), ( -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 ), ( -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 ), ( -7.78897366273469e-01 , 5.47909401918027e+00 , 2.48909074021991e+00 ), ( -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 ), ( -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 ), ( -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 ), ( -3.34173659956129e+00 , 9.09242156894626e-01 , 7.66376749024154e-01 ), ( -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 ), ( -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 ), ( -3.35601110578621e+00 , 7.08982263935928e-01 , 4.17614644200216e+00 ), ( -2.32477219663653e+00 , -2.67799335468043e-01 , 6.13612947330243e+00 ), ( -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 ), ( -5.35192634835997e+00 , 5.29009862298982e-01 , 7.17548197632397e+00 ), ( -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 ), ( -7.04702908508777e+00 , 4.30002272437193e+00 , 7.52014167082679e+00 ), ( -6.60462930316152e+00 , 3.17780650929997e+00 , 5.56735921475796e+00 ), ( -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 ), ( -4.00464293001051e+00 , 4.63648260149376e+00 , 7.28600629551503e+00 ) } +colvars: Step 37, atoms_positions[size = 51] = { ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 ), ( 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 ), ( 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 ), ( 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 ), ( 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 ), ( 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 ), ( -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 ), ( -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 ), ( -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 ), ( -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 ), ( 8.24325423950952e+00 , 3.53606340058551e-02 , -6.74071896755363e-01 ), ( 7.01595064911501e+00 , -2.09226237248072e+00 , -8.23713639498105e-01 ), ( 6.10178478736824e+00 , -3.17827591276146e-01 , 8.15561834792714e-01 ), ( 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 ), ( 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 ), ( 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 ), ( 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 ), ( 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 ), ( 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757519e+00 ), ( 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 ), ( 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 ), ( 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 ), ( 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 ), ( 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 ), ( 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 ), ( 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 ), ( 2.01981272765406e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 ), ( 2.09593922434932e+00 , -1.09517162307366e+00 , 2.02627695012513e+00 ), ( 5.68648106130872e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 ), ( -6.10998899499222e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 ), ( 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 ), ( 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 ), ( -3.53783966258116e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 ), ( -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 ), ( -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 ), ( -7.78897366273473e-01 , 5.47909401918027e+00 , 2.48909074021990e+00 ), ( -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 ), ( -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 ), ( -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 ), ( -3.34173659956129e+00 , 9.09242156894625e-01 , 7.66376749024157e-01 ), ( -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 ), ( -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 ), ( -3.35601110578621e+00 , 7.08982263935927e-01 , 4.17614644200216e+00 ), ( -2.32477219663652e+00 , -2.67799335468032e-01 , 6.13612947330242e+00 ), ( -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 ), ( -5.35192634835997e+00 , 5.29009862298980e-01 , 7.17548197632397e+00 ), ( -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 ), ( -7.04702908508777e+00 , 4.30002272437194e+00 , 7.52014167082679e+00 ), ( -6.60462930316152e+00 , 3.17780650929998e+00 , 5.56735921475797e+00 ), ( -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 ), ( -4.00464293001050e+00 , 4.63648260149376e+00 , 7.28600629551502e+00 ) } colvars: Step 37, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 37, atom_groups_ids[size = 0] = @@ -4288,15 +6270,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905548e-02 , -1.40858436164589e-02 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905549e-02 , -1.40858436164589e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.24325423950952e+00 , 3.53606340058551e-02 , -6.74071896755363e-01 , 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 7.01595064911501e+00 , -2.09226237248072e+00 , -8.23713639498105e-01 , 6.10178478736824e+00 , -3.17827591276146e-01 , 8.15561834792714e-01 , 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 , 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 , 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 , 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 , 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757519e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 , 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 , 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 , 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 , 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 , 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 , 2.01981272765406e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 2.09593922434932e+00 , -1.09517162307366e+00 , 2.02627695012513e+00 , 5.68648106130872e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 , -6.10998899499222e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 , 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 , -3.53783966258116e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 , -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 , -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -7.78897366273473e-01 , 5.47909401918027e+00 , 2.48909074021990e+00 , -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 , -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 , -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.34173659956129e+00 , 9.09242156894625e-01 , 7.66376749024157e-01 , -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 , -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 , -3.35601110578621e+00 , 7.08982263935927e-01 , 4.17614644200216e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -2.32477219663652e+00 , -2.67799335468032e-01 , 6.13612947330242e+00 , -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 , -5.35192634835997e+00 , 5.29009862298980e-01 , 7.17548197632397e+00 , -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 , -7.04702908508777e+00 , 4.30002272437194e+00 , 7.52014167082679e+00 , -6.60462930316152e+00 , 3.17780650929998e+00 , 5.56735921475797e+00 , -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 , -4.00464293001050e+00 , 4.63648260149376e+00 , 7.28600629551502e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905548e-02 , -1.40858436164589e-02 ). +colvars: Colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905549e-02 , -1.40858436164589e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.24325423950952e+00 , 3.53606340058551e-02 , -6.74071896755363e-01 , 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 7.01595064911501e+00 , -2.09226237248072e+00 , -8.23713639498105e-01 , 6.10178478736824e+00 , -3.17827591276146e-01 , 8.15561834792714e-01 , 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 , 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 , 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 , 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 , 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757519e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 , 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 , 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 , 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 , 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 , 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 , 2.01981272765406e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 2.09593922434932e+00 , -1.09517162307366e+00 , 2.02627695012513e+00 , 5.68648106130872e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 , -6.10998899499222e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 , 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 , -3.53783966258116e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 , -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 , -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -7.78897366273473e-01 , 5.47909401918027e+00 , 2.48909074021990e+00 , -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 , -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 , -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.34173659956129e+00 , 9.09242156894625e-01 , 7.66376749024157e-01 , -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 , -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 , -3.35601110578621e+00 , 7.08982263935927e-01 , 4.17614644200216e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -2.32477219663652e+00 , -2.67799335468032e-01 , 6.13612947330242e+00 , -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 , -5.35192634835997e+00 , 5.29009862298980e-01 , 7.17548197632397e+00 , -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 , -7.04702908508777e+00 , 4.30002272437194e+00 , 7.52014167082679e+00 , -6.60462930316152e+00 , 3.17780650929998e+00 , 5.56735921475797e+00 , -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 , -4.00464293001050e+00 , 4.63648260149376e+00 , 7.28600629551502e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4309,6 +6362,10 @@ colvars: Adding total bias energy: 11.5181 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4324,8 +6381,6 @@ colvars: ( 0.00581037 , -0.105151 , 0.315603 ) colvars: ( -0.0505867 , 0.0816238 , 0.215374 ) colvars: ( 0.0814022 , -0.236639 , 0.0275905 ) colvars: ( 0.135487 , -0.475891 , 0.337396 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242685 , -0.0992325 , 0.0965872 ) colvars: ( 0.0197404 , -0.0819204 , 0.0835444 ) @@ -4378,14 +6433,17 @@ colvars: ( -0.00837998 , 0.0463962 , -0.0835596 ) colvars: ( -0.0186179 , 0.0668371 , -0.0356468 ) colvars: ( -0.0222885 , 0.0840332 , -0.0593092 ) colvars: ( -0.0243192 , 0.0928383 , -0.0694669 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 37. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 37. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 37, atoms_new_colvar_forces = { ( -6.86992555484974e-02 , 3.03533865507726e-01 , -4.02549057467857e-01 ), ( 1.40856347083700e-02 , 3.16054533617281e-02 , -2.40108723882893e-01 ), ( -4.31377610411099e-02 , 9.58292762145927e-02 , 8.45772221147907e-02 ), ( -9.75869154560516e-02 , 2.50142296885573e-01 , 6.32383876309269e-02 ), ( -1.73276221003673e-02 , 9.79997153046434e-02 , -1.71639856633221e-01 ), ( 7.11709823308420e-02 , -1.85247971867427e-01 , -3.72684595182543e-02 ), ( 8.37449646162987e-03 , -9.85873004139697e-02 , 2.55249027610009e-01 ), ( -4.18999502863235e-02 , 5.98646644222401e-02 , 1.92995396989750e-01 ), ( 6.65453214330516e-02 , -1.91977552169553e-01 , 3.50417318547983e-02 ), ( 1.13198840831002e-01 , -3.91857648237532e-01 , 2.78086587467602e-01 ), ( 2.42685311116601e-02 , -9.92325269053165e-02 , 9.65872421316358e-02 ), ( 2.64701156863432e-02 , -9.73629786194261e-02 , 6.03536160863482e-02 ), ( 1.21863057138768e-02 , -5.57276902573276e-02 , 7.29140401008523e-02 ), ( 1.23620577888413e-02 , -5.35712074899439e-02 , 6.17139569187324e-02 ), ( 5.33950914573618e-03 , -3.50474741441835e-02 , 7.59433411582639e-02 ), ( -8.88281993356189e-03 , 9.51847849516835e-03 , 7.55785515708698e-02 ), ( -2.20759731463681e-03 , -2.87996413681205e-03 , 4.04933637879491e-02 ), ( -5.89828602420452e-03 , 9.72264454596837e-03 , 3.61036089633233e-02 ), ( 2.70697939545164e-03 , -1.32577794042574e-02 , 1.98338955000179e-02 ), ( 9.24941364417830e-03 , -2.25496043655818e-02 , -2.63902426068050e-02 ), ( 8.84119091067351e-03 , -2.40935956604268e-02 , -1.47161864940914e-02 ), ( 6.77327853075890e-03 , -1.38725010943118e-02 , -3.02535239169240e-02 ), ( 1.51393890116988e-02 , -4.69216812545930e-02 , -1.75516266427916e-03 ), ( 2.77524492898462e-02 , -8.86845708413805e-02 , 7.83766833850180e-03 ), ( 1.43255768269100e-02 , -4.69962060586814e-02 , 9.08675655639762e-03 ), ( 1.43093962067837e-02 , -4.41460571780060e-02 , -2.50001761113216e-03 ), ( 9.23731630260701e-03 , -3.70634757084186e-02 , 3.38363984449440e-02 ), ( -1.10699471847077e-03 , -1.50517238825784e-02 , 7.66243735456773e-02 ), ( -3.91421362763155e-03 , 4.28946728051717e-03 , 3.29098700792866e-02 ), ( -5.99053525305987e-03 , 1.14065895810092e-02 , 3.03281077571817e-02 ), ( -7.40598527053743e-03 , 1.79919911555435e-02 , 2.13931244285798e-02 ), ( -1.63384629373081e-02 , 5.20372766884958e-02 , -3.89721869762519e-03 ), ( -9.73183297611762e-03 , 3.57273056791311e-02 , -2.19055389368894e-02 ), ( -1.37676619415743e-02 , 5.00079066655861e-02 , -2.87728945664571e-02 ), ( -1.87701437763671e-03 , 1.46863241700003e-02 , -3.64889093585485e-02 ), ( 1.08859301674395e-02 , -1.63495717571680e-02 , -7.32330047742821e-02 ), ( 4.55998687637418e-03 , -1.09432736090071e-03 , -5.44924110293288e-02 ), ( 3.57956536940772e-03 , 5.71169649747299e-03 , -6.99712434611576e-02 ), ( 7.24739952063045e-03 , -1.50518827154552e-02 , -3.15090206351926e-02 ), ( 1.31215493743308e-02 , -4.14564908669138e-02 , 1.74314223554916e-03 ), ( 5.31212991272961e-04 , 1.75425920777903e-03 , -1.41362226136182e-02 ), ( 4.70616521599423e-04 , 3.37339310139416e-03 , -2.00531767539541e-02 ), ( -6.58732737457220e-03 , 2.06915304154358e-02 , -3.75933503541312e-04 ), ( -2.08104666769918e-02 , 5.81943213728344e-02 , 2.85028017920970e-02 ), ( -1.90464014201955e-02 , 6.35306924938405e-02 , -1.64163462385557e-02 ), ( -2.27747747072922e-02 , 7.55448881774991e-02 , -1.78830097269419e-02 ), ( -1.66885178805266e-02 , 7.23651669999104e-02 , -8.34994688828352e-02 ), ( -1.97355628115301e-02 , 8.64810282483968e-02 , -1.02483200962999e-01 ), ( -8.37997841556806e-03 , 4.63962179161769e-02 , -8.35596291533627e-02 ), ( -1.86179094057264e-02 , 6.68370515009343e-02 , -3.56468487901190e-02 ), ( -2.43191986518237e-02 , 9.28382805005676e-02 , -6.94669041832188e-02 ) } +colvars: Step 37, atoms_new_colvar_forces = { ( -6.86992555484975e-02 , 3.03533865507726e-01 , -4.02549057467857e-01 ), ( 1.40856347083699e-02 , 3.16054533617280e-02 , -2.40108723882893e-01 ), ( -4.31377610411099e-02 , 9.58292762145927e-02 , 8.45772221147907e-02 ), ( -9.75869154560515e-02 , 2.50142296885573e-01 , 6.32383876309269e-02 ), ( -1.73276221003674e-02 , 9.79997153046433e-02 , -1.71639856633221e-01 ), ( 7.11709823308419e-02 , -1.85247971867427e-01 , -3.72684595182543e-02 ), ( 8.37449646163001e-03 , -9.85873004139697e-02 , 2.55249027610008e-01 ), ( -4.18999502863234e-02 , 5.98646644222403e-02 , 1.92995396989750e-01 ), ( 6.65453214330516e-02 , -1.91977552169553e-01 , 3.50417318547981e-02 ), ( 1.13198840831002e-01 , -3.91857648237532e-01 , 2.78086587467602e-01 ), ( 2.42685311116601e-02 , -9.92325269053166e-02 , 9.65872421316359e-02 ), ( 2.64701156863432e-02 , -9.73629786194262e-02 , 6.03536160863482e-02 ), ( 1.21863057138768e-02 , -5.57276902573276e-02 , 7.29140401008524e-02 ), ( 1.23620577888413e-02 , -5.35712074899439e-02 , 6.17139569187325e-02 ), ( 5.33950914573622e-03 , -3.50474741441834e-02 , 7.59433411582640e-02 ), ( -8.88281993356185e-03 , 9.51847849516848e-03 , 7.55785515708699e-02 ), ( -2.20759731463679e-03 , -2.87996413681196e-03 , 4.04933637879492e-02 ), ( -5.89828602420450e-03 , 9.72264454596844e-03 , 3.61036089633234e-02 ), ( 2.70697939545163e-03 , -1.32577794042573e-02 , 1.98338955000179e-02 ), ( 9.24941364417825e-03 , -2.25496043655818e-02 , -2.63902426068051e-02 ), ( 8.84119091067348e-03 , -2.40935956604268e-02 , -1.47161864940915e-02 ), ( 6.77327853075886e-03 , -1.38725010943118e-02 , -3.02535239169240e-02 ), ( 1.51393890116988e-02 , -4.69216812545931e-02 , -1.75516266427920e-03 ), ( 2.77524492898462e-02 , -8.86845708413806e-02 , 7.83766833850178e-03 ), ( 1.43255768269100e-02 , -4.69962060586814e-02 , 9.08675655639763e-03 ), ( 1.43093962067837e-02 , -4.41460571780061e-02 , -2.50001761113216e-03 ), ( 9.23731630260703e-03 , -3.70634757084186e-02 , 3.38363984449441e-02 ), ( -1.10699471847071e-03 , -1.50517238825784e-02 , 7.66243735456774e-02 ), ( -3.91421362763153e-03 , 4.28946728051718e-03 , 3.29098700792867e-02 ), ( -5.99053525305984e-03 , 1.14065895810092e-02 , 3.03281077571817e-02 ), ( -7.40598527053741e-03 , 1.79919911555435e-02 , 2.13931244285798e-02 ), ( -1.63384629373081e-02 , 5.20372766884959e-02 , -3.89721869762521e-03 ), ( -9.73183297611764e-03 , 3.57273056791312e-02 , -2.19055389368894e-02 ), ( -1.37676619415743e-02 , 5.00079066655862e-02 , -2.87728945664571e-02 ), ( -1.87701437763674e-03 , 1.46863241700003e-02 , -3.64889093585485e-02 ), ( 1.08859301674394e-02 , -1.63495717571680e-02 , -7.32330047742822e-02 ), ( 4.55998687637413e-03 , -1.09432736090076e-03 , -5.44924110293288e-02 ), ( 3.57956536940767e-03 , 5.71169649747292e-03 , -6.99712434611576e-02 ), ( 7.24739952063043e-03 , -1.50518827154553e-02 , -3.15090206351926e-02 ), ( 1.31215493743308e-02 , -4.14564908669139e-02 , 1.74314223554922e-03 ), ( 5.31212991272958e-04 , 1.75425920777897e-03 , -1.41362226136182e-02 ), ( 4.70616521599421e-04 , 3.37339310139407e-03 , -2.00531767539541e-02 ), ( -6.58732737457219e-03 , 2.06915304154358e-02 , -3.75933503541254e-04 ), ( -2.08104666769917e-02 , 5.81943213728344e-02 , 2.85028017920971e-02 ), ( -1.90464014201955e-02 , 6.35306924938405e-02 , -1.64163462385557e-02 ), ( -2.27747747072921e-02 , 7.55448881774991e-02 , -1.78830097269419e-02 ), ( -1.66885178805266e-02 , 7.23651669999104e-02 , -8.34994688828353e-02 ), ( -1.97355628115302e-02 , 8.64810282483968e-02 , -1.02483200962999e-01 ), ( -8.37997841556812e-03 , 4.63962179161769e-02 , -8.35596291533627e-02 ), ( -1.86179094057264e-02 , 6.68370515009344e-02 , -3.56468487901189e-02 ), ( -2.43191986518237e-02 , 9.28382805005677e-02 , -6.94669041832188e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 37, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4423,10 +6481,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 38, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 38, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 38, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 38, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 38, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 38, atoms_positions[size = 51] = { ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114381e-01 ), ( 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 ), ( 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 ), ( 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556786e-02 ), ( 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975422e+00 ), ( 9.22097757526461e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 ), ( -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 ), ( -3.82716365577602e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 ), ( -3.66166853640507e+00 , 5.78854680676884e-02 , 5.44735153195077e+00 ), ( -4.79230652547135e+00 , 3.27021253565707e+00 , 7.18706754003824e+00 ), ( 8.23397334242518e+00 , 3.36629988416887e-02 , -6.69448059688789e-01 ), ( 7.02029295911994e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 ), ( 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545464e-01 ), ( 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 ), ( 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 ), ( 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 ), ( 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 ), ( 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522920e+00 ), ( 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 ), ( 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 ), ( 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 ), ( 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 ), ( 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868302e-01 ), ( 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 ), ( 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 ), ( 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 ), ( 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 ), ( 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 ), ( 5.67827189361794e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 ), ( -6.13967788582873e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 ), ( 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 ), ( 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 ), ( -3.51365065386000e-01 , 2.88588961715295e+00 , 4.91640875050460e+00 ), ( -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 ), ( -5.08771410005460e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 ), ( -7.81567996234711e-01 , 5.48701616412022e+00 , 2.48946663787883e+00 ), ( -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 ), ( -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 ), ( -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 ), ( -3.33868648611506e+00 , 9.16055538251035e-01 , 7.61631047253214e-01 ), ( -4.27757651872762e+00 , 1.01649290349519e+00 , 3.23714639246471e+00 ), ( -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 ), ( -3.35274399292602e+00 , 7.04100676066046e-01 , 4.17999176321870e+00 ), ( -2.31549361557950e+00 , -2.60750067046298e-01 , 6.13988294900187e+00 ), ( -4.48330176893684e+00 , 9.82575531416186e-01 , 6.42533908148497e+00 ), ( -5.35180750527742e+00 , 5.21809458288691e-01 , 7.17126620866168e+00 ), ( -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304484e+00 ), ( -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 ), ( -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 ), ( -4.12563405115866e+00 , 2.25335610553221e+00 , 6.43205928200358e+00 ), ( -4.00561105971608e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ) } +colvars: Step 38, atoms_positions[size = 51] = { ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 ), ( 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 ), ( 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 ), ( 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 ), ( 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 ), ( 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 ), ( -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 ), ( -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 ), ( -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 ), ( -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 ), ( 8.23397334242518e+00 , 3.36629988416880e-02 , -6.69448059688789e-01 ), ( 7.02029295911993e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 ), ( 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545465e-01 ), ( 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 ), ( 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 ), ( 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 ), ( 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 ), ( 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522921e+00 ), ( 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 ), ( 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 ), ( 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 ), ( 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 ), ( 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868301e-01 ), ( 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 ), ( 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 ), ( 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 ), ( 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 ), ( 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 ), ( 5.67827189361793e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 ), ( -6.13967788582874e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 ), ( 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 ), ( 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 ), ( -3.51365065386001e-01 , 2.88588961715295e+00 , 4.91640875050461e+00 ), ( -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 ), ( -5.08771410005461e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 ), ( -7.81567996234714e-01 , 5.48701616412022e+00 , 2.48946663787882e+00 ), ( -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 ), ( -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 ), ( -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 ), ( -3.33868648611506e+00 , 9.16055538251034e-01 , 7.61631047253218e-01 ), ( -4.27757651872762e+00 , 1.01649290349518e+00 , 3.23714639246471e+00 ), ( -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 ), ( -3.35274399292602e+00 , 7.04100676066045e-01 , 4.17999176321871e+00 ), ( -2.31549361557949e+00 , -2.60750067046287e-01 , 6.13988294900186e+00 ), ( -4.48330176893684e+00 , 9.82575531416185e-01 , 6.42533908148497e+00 ), ( -5.35180750527742e+00 , 5.21809458288690e-01 , 7.17126620866168e+00 ), ( -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304485e+00 ), ( -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 ), ( -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 ), ( -4.12563405115866e+00 , 2.25335610553220e+00 , 6.43205928200358e+00 ), ( -4.00561105971607e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ) } colvars: Step 38, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 38, atom_groups_ids[size = 0] = @@ -4443,17 +6501,88 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 38 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865609e-02 , 1.20819700460899e-02 , -1.38821562016640e-02 ). +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865608e-02 , 1.20819700460900e-02 , -1.38821562016639e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.23397334242518e+00 , 3.36629988416880e-02 , -6.69448059688789e-01 , 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 7.02029295911993e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 , 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545465e-01 , 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 , 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 , 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 , 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522921e+00 , 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 , 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 , 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 , 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868301e-01 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 , 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 , 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 , 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 , 5.67827189361793e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 , -6.13967788582874e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 , 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 , -3.51365065386001e-01 , 2.88588961715295e+00 , 4.91640875050461e+00 , -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 , -5.08771410005461e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -7.81567996234714e-01 , 5.48701616412022e+00 , 2.48946663787882e+00 , -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 , -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 , -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.33868648611506e+00 , 9.16055538251034e-01 , 7.61631047253218e-01 , -4.27757651872762e+00 , 1.01649290349518e+00 , 3.23714639246471e+00 , -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 , -3.35274399292602e+00 , 7.04100676066045e-01 , 4.17999176321871e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -2.31549361557949e+00 , -2.60750067046287e-01 , 6.13988294900186e+00 , -4.48330176893684e+00 , 9.82575531416185e-01 , 6.42533908148497e+00 , -5.35180750527742e+00 , 5.21809458288690e-01 , 7.17126620866168e+00 , -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304485e+00 , -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 , -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 , -4.12563405115866e+00 , 2.25335610553220e+00 , 6.43205928200358e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 , -4.00561105971607e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865609e-02 , 1.20819700460899e-02 , -1.38821562016640e-02 ). +colvars: Colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865608e-02 , 1.20819700460900e-02 , -1.38821562016639e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.23397334242518e+00 , 3.36629988416880e-02 , -6.69448059688789e-01 , 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 7.02029295911993e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 , 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545465e-01 , 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 , 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 , 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 , 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522921e+00 , 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 , 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 , 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 , 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868301e-01 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 , 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 , 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 , 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 , 5.67827189361793e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 , -6.13967788582874e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 , 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 , -3.51365065386001e-01 , 2.88588961715295e+00 , 4.91640875050461e+00 , -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 , -5.08771410005461e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -7.81567996234714e-01 , 5.48701616412022e+00 , 2.48946663787882e+00 , -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 , -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 , -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.33868648611506e+00 , 9.16055538251034e-01 , 7.61631047253218e-01 , -4.27757651872762e+00 , 1.01649290349518e+00 , 3.23714639246471e+00 , -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 , -3.35274399292602e+00 , 7.04100676066045e-01 , 4.17999176321871e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -2.31549361557949e+00 , -2.60750067046287e-01 , 6.13988294900186e+00 , -4.48330176893684e+00 , 9.82575531416185e-01 , 6.42533908148497e+00 , -5.35180750527742e+00 , 5.21809458288690e-01 , 7.17126620866168e+00 , -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304485e+00 , -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 , -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 , -4.12563405115866e+00 , 2.25335610553220e+00 , 6.43205928200358e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 , -4.00561105971607e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4466,6 +6595,10 @@ colvars: Adding total bias energy: 11.5217 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4481,8 +6614,6 @@ colvars: ( 0.0057215 , -0.105036 , 0.315906 ) colvars: ( -0.0507384 , 0.0819183 , 0.215358 ) colvars: ( 0.0814678 , -0.236681 , 0.0276068 ) colvars: ( 0.135538 , -0.475974 , 0.337859 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0242883 , -0.0991988 , 0.0966416 ) colvars: ( 0.0197551 , -0.0818928 , 0.083605 ) @@ -4535,14 +6666,17 @@ colvars: ( -0.00838046 , 0.0463758 , -0.083613 ) colvars: ( -0.0186358 , 0.0668199 , -0.0356982 ) colvars: ( -0.0223088 , 0.0840088 , -0.0593647 ) colvars: ( -0.024342 , 0.0928097 , -0.0695109 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 38. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 38. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 38, atoms_new_colvar_forces = { ( -6.86308206116251e-02 , 3.03483614991524e-01 , -4.03005467230188e-01 ), ( 1.42122004866687e-02 , 3.13538650225890e-02 , -2.40194902047227e-01 ), ( -4.31943237080591e-02 , 9.58453152835204e-02 , 8.47803175901869e-02 ), ( -9.77245156213514e-02 , 2.50405352501500e-01 , 6.31588211970295e-02 ), ( -1.72933931549215e-02 , 9.79973607673578e-02 , -1.71917156945550e-01 ), ( 7.12727321448884e-02 , -1.85456026954594e-01 , -3.71593100693835e-02 ), ( 8.29430983007023e-03 , -9.84834160035740e-02 , 2.55547810067643e-01 ), ( -4.20368158050724e-02 , 6.01617567264364e-02 , 1.92950990770399e-01 ), ( 6.65945023408876e-02 , -1.92024618939844e-01 , 3.50027046417249e-02 ), ( 1.13228932734361e-01 , -3.91964986992019e-01 , 2.78494124440071e-01 ), ( 2.42883201820208e-02 , -9.91987813394096e-02 , 9.66416199757184e-02 ), ( 2.64947648348943e-02 , -9.73364338961823e-02 , 6.04259622476607e-02 ), ( 1.21928076457344e-02 , -5.57068145202949e-02 , 7.29639460351480e-02 ), ( 1.23703282478627e-02 , -5.35520485838743e-02 , 6.17540627985405e-02 ), ( 5.33680830935799e-03 , -3.50306520250388e-02 , 7.59952094602463e-02 ), ( -8.90361352233686e-03 , 9.52588864838620e-03 , 7.56268806698402e-02 ), ( -2.21620231280117e-03 , -2.87498061072691e-03 , 4.05318787135928e-02 ), ( -5.91053580061553e-03 , 9.72490617764336e-03 , 3.61297622980792e-02 ), ( 2.70583315529539e-03 , -1.32544772276849e-02 , 1.98831553338981e-02 ), ( 9.25989089906256e-03 , -2.25524231939905e-02 , -2.63282702430853e-02 ), ( 8.85153296477523e-03 , -2.40929295219061e-02 , -1.46774587577451e-02 ), ( 6.78281666744161e-03 , -1.38760216221009e-02 , -3.02237522299002e-02 ), ( 1.51566055711864e-02 , -4.69141735790477e-02 , -1.71412442695696e-03 ), ( 2.77851147346442e-02 , -8.86665700485733e-02 , 7.87857868564020e-03 ), ( 1.43422027572354e-02 , -4.69856650191699e-02 , 9.10461085344261e-03 ), ( 1.43275767180269e-02 , -4.41374431611392e-02 , -2.49197110163824e-03 ), ( 9.24541543566428e-03 , -3.70509593640707e-02 , 3.38517921818639e-02 ), ( -1.11514134289475e-03 , -1.50363761218496e-02 , 7.66272962861233e-02 ), ( -3.92164379332093e-03 , 4.29421869707042e-03 , 3.29027198923366e-02 ), ( -5.99967910186779e-03 , 1.14100882546170e-02 , 3.03085239625797e-02 ), ( -7.41733786811938e-03 , 1.79915865282469e-02 , 2.13927487362460e-02 ), ( -1.63594388549170e-02 , 5.20252755586254e-02 , -3.89310930664072e-03 ), ( -9.74187732357990e-03 , 3.57167216706750e-02 , -2.19161002769431e-02 ), ( -1.37816216212824e-02 , 4.99938096396475e-02 , -2.87951941243782e-02 ), ( -1.87625613950849e-03 , 1.46773844030486e-02 , -3.64899362824451e-02 ), ( 1.09056209410314e-02 , -1.63583620058828e-02 , -7.32229830172713e-02 ), ( 4.57146300390369e-03 , -1.10195764427394e-03 , -5.45081993441415e-02 ), ( 3.59163170697867e-03 , 5.70061800575529e-03 , -6.99959399808052e-02 ), ( 7.26041751542734e-03 , -1.50528004946293e-02 , -3.15254859290255e-02 ), ( 1.31397398961161e-02 , -4.14460138981811e-02 , 1.71931122698228e-03 ), ( 5.35631856761167e-04 , 1.75395146515928e-03 , -1.41785278298944e-02 ), ( 4.76117787198403e-04 , 3.37239514763850e-03 , -2.01064513441219e-02 ), ( -6.59324679933046e-03 , 2.06893842474070e-02 , -4.18476613147334e-04 ), ( -2.08366128212283e-02 , 5.81893019564111e-02 , 2.84506088586252e-02 ), ( -1.90659163881719e-02 , 6.35178090703331e-02 , -1.64772486067613e-02 ), ( -2.27982067233440e-02 , 7.55299015632439e-02 , -1.79567088892806e-02 ), ( -1.66994361211408e-02 , 7.23394764221848e-02 , -8.35574744904818e-02 ), ( -1.97484391686671e-02 , 8.64495918792105e-02 , -1.02547043382609e-01 ), ( -8.38045756030608e-03 , 4.63758256138758e-02 , -8.36129911674441e-02 ), ( -1.86357970883621e-02 , 6.68198521875454e-02 , -3.56982452867784e-02 ), ( -2.43419891146704e-02 , 9.28096803384051e-02 , -6.95109079997762e-02 ) } +colvars: Step 38, atoms_new_colvar_forces = { ( -6.86308206116252e-02 , 3.03483614991524e-01 , -4.03005467230188e-01 ), ( 1.42122004866687e-02 , 3.13538650225891e-02 , -2.40194902047227e-01 ), ( -4.31943237080591e-02 , 9.58453152835205e-02 , 8.47803175901870e-02 ), ( -9.77245156213514e-02 , 2.50405352501500e-01 , 6.31588211970295e-02 ), ( -1.72933931549216e-02 , 9.79973607673579e-02 , -1.71917156945550e-01 ), ( 7.12727321448884e-02 , -1.85456026954594e-01 , -3.71593100693835e-02 ), ( 8.29430983007038e-03 , -9.84834160035740e-02 , 2.55547810067643e-01 ), ( -4.20368158050723e-02 , 6.01617567264364e-02 , 1.92950990770399e-01 ), ( 6.65945023408876e-02 , -1.92024618939844e-01 , 3.50027046417249e-02 ), ( 1.13228932734361e-01 , -3.91964986992019e-01 , 2.78494124440071e-01 ), ( 2.42883201820209e-02 , -9.91987813394095e-02 , 9.66416199757185e-02 ), ( 2.64947648348944e-02 , -9.73364338961822e-02 , 6.04259622476607e-02 ), ( 1.21928076457344e-02 , -5.57068145202949e-02 , 7.29639460351481e-02 ), ( 1.23703282478627e-02 , -5.35520485838742e-02 , 6.17540627985406e-02 ), ( 5.33680830935802e-03 , -3.50306520250387e-02 , 7.59952094602464e-02 ), ( -8.90361352233684e-03 , 9.52588864838625e-03 , 7.56268806698402e-02 ), ( -2.21620231280116e-03 , -2.87498061072686e-03 , 4.05318787135928e-02 ), ( -5.91053580061552e-03 , 9.72490617764340e-03 , 3.61297622980792e-02 ), ( 2.70583315529538e-03 , -1.32544772276848e-02 , 1.98831553338981e-02 ), ( 9.25989089906253e-03 , -2.25524231939904e-02 , -2.63282702430854e-02 ), ( 8.85153296477521e-03 , -2.40929295219061e-02 , -1.46774587577451e-02 ), ( 6.78281666744159e-03 , -1.38760216221009e-02 , -3.02237522299002e-02 ), ( 1.51566055711864e-02 , -4.69141735790476e-02 , -1.71412442695694e-03 ), ( 2.77851147346442e-02 , -8.86665700485733e-02 , 7.87857868564022e-03 ), ( 1.43422027572355e-02 , -4.69856650191699e-02 , 9.10461085344262e-03 ), ( 1.43275767180269e-02 , -4.41374431611392e-02 , -2.49197110163824e-03 ), ( 9.24541543566430e-03 , -3.70509593640707e-02 , 3.38517921818640e-02 ), ( -1.11514134289469e-03 , -1.50363761218496e-02 , 7.66272962861233e-02 ), ( -3.92164379332092e-03 , 4.29421869707043e-03 , 3.29027198923366e-02 ), ( -5.99967910186777e-03 , 1.14100882546170e-02 , 3.03085239625798e-02 ), ( -7.41733786811937e-03 , 1.79915865282469e-02 , 2.13927487362460e-02 ), ( -1.63594388549171e-02 , 5.20252755586254e-02 , -3.89310930664074e-03 ), ( -9.74187732357992e-03 , 3.57167216706750e-02 , -2.19161002769431e-02 ), ( -1.37816216212824e-02 , 4.99938096396475e-02 , -2.87951941243782e-02 ), ( -1.87625613950851e-03 , 1.46773844030486e-02 , -3.64899362824451e-02 ), ( 1.09056209410313e-02 , -1.63583620058829e-02 , -7.32229830172713e-02 ), ( 4.57146300390366e-03 , -1.10195764427398e-03 , -5.45081993441415e-02 ), ( 3.59163170697864e-03 , 5.70061800575523e-03 , -6.99959399808052e-02 ), ( 7.26041751542733e-03 , -1.50528004946293e-02 , -3.15254859290255e-02 ), ( 1.31397398961161e-02 , -4.14460138981812e-02 , 1.71931122698228e-03 ), ( 5.35631856761175e-04 , 1.75395146515923e-03 , -1.41785278298944e-02 ), ( 4.76117787198405e-04 , 3.37239514763842e-03 , -2.01064513441219e-02 ), ( -6.59324679933045e-03 , 2.06893842474070e-02 , -4.18476613147348e-04 ), ( -2.08366128212283e-02 , 5.81893019564110e-02 , 2.84506088586251e-02 ), ( -1.90659163881719e-02 , 6.35178090703330e-02 , -1.64772486067613e-02 ), ( -2.27982067233440e-02 , 7.55299015632438e-02 , -1.79567088892806e-02 ), ( -1.66994361211408e-02 , 7.23394764221847e-02 , -8.35574744904818e-02 ), ( -1.97484391686672e-02 , 8.64495918792104e-02 , -1.02547043382609e-01 ), ( -8.38045756030614e-03 , 4.63758256138757e-02 , -8.36129911674442e-02 ), ( -1.86357970883621e-02 , 6.68198521875454e-02 , -3.56982452867785e-02 ), ( -2.43419891146704e-02 , 9.28096803384051e-02 , -6.95109079997762e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 38, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4580,10 +6714,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 39, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 39, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 39, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 39, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 39, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 39, atoms_positions[size = 51] = { ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116680e-01 ), ( 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 ), ( 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 ), ( 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925346e-02 ), ( 1.30134291871750e+00 , 1.65124561639393e-01 , 1.66688264750347e+00 ), ( 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 ), ( -1.46198923284116e+00 , 4.48031715232442e+00 , 3.40319926113214e+00 ), ( -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 ), ( -3.66146058229158e+00 , 5.61986142826135e-02 , 5.44089379923338e+00 ), ( -4.78936447974314e+00 , 3.26644842590914e+00 , 7.18028305985000e+00 ), ( 8.22446419823708e+00 , 3.18649479383654e-02 , -6.64989816298089e-01 ), ( 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 ), ( 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254841e-01 ), ( 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 ), ( 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 ), ( 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 ), ( 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 ), ( 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 ), ( 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 ), ( 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 ), ( 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 ), ( 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991723e+00 ), ( 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 ), ( 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 ), ( 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528189e-01 ), ( 4.37681313203302e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 ), ( 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 ), ( 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 ), ( 5.67045576176349e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 ), ( -6.16431681139151e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 ), ( 1.29461765027047e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 ), ( 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 ), ( -3.48478472967696e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 ), ( -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 ), ( -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 ), ( -7.83422856191321e-01 , 5.49518347305934e+00 , 2.48952532366079e+00 ), ( -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 ), ( -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 ), ( -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 ), ( -3.33555341340174e+00 , 9.23051989092355e-01 , 7.57539942689168e-01 ), ( -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702990e+00 ), ( -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 ), ( -3.34976062208996e+00 , 6.99485565685802e-01 , 4.18343622948658e+00 ), ( -2.30616158940055e+00 , -2.54299022897341e-01 , 6.14408467519650e+00 ), ( -4.47912226138258e+00 , 9.89222211089517e-01 , 6.42454983767422e+00 ), ( -5.35161281557211e+00 , 5.14805563214697e-01 , 7.16688596353334e+00 ), ( -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 ), ( -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 ), ( -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 ), ( -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231195e+00 ), ( -4.00670158436285e+00 , 4.65485176981042e+00 , 7.28690738849569e+00 ) } +colvars: Step 39, atoms_positions[size = 51] = { ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 ), ( 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 ), ( 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 ), ( 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 ), ( 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 ), ( 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 ), ( -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 ), ( -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 ), ( -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 ), ( -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 ), ( 8.22446419823708e+00 , 3.18649479383647e-02 , -6.64989816298089e-01 ), ( 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 ), ( 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254842e-01 ), ( 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 ), ( 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 ), ( 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 ), ( 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 ), ( 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 ), ( 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 ), ( 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 ), ( 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 ), ( 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991724e+00 ), ( 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 ), ( 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 ), ( 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528188e-01 ), ( 4.37681313203301e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 ), ( 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 ), ( 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 ), ( 5.67045576176347e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 ), ( -6.16431681139152e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 ), ( 1.29461765027048e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 ), ( 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 ), ( -3.48478472967697e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 ), ( -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 ), ( -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 ), ( -7.83422856191325e-01 , 5.49518347305934e+00 , 2.48952532366078e+00 ), ( -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 ), ( -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 ), ( -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 ), ( -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 ), ( -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 ), ( -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 ), ( -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 ), ( -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 ), ( -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 ), ( -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 ), ( -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 ), ( -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 ), ( -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 ), ( -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 ), ( -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ) } colvars: Step 39, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 39, atom_groups_ids[size = 0] = @@ -4602,15 +6736,86 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. colvars: Colvar component no. 1 within colvar "one" has value ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.22446419823708e+00 , 3.18649479383647e-02 , -6.64989816298089e-01 , 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 , 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254842e-01 , 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 , 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 , 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 , 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 , 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 , 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 , 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991724e+00 , 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 , 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528188e-01 , 4.37681313203301e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 , 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 , 5.67045576176347e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 , -6.16431681139152e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 , 1.29461765027048e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 , -3.48478472967697e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 , -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 , -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -7.83422856191325e-01 , 5.49518347305934e+00 , 2.48952532366078e+00 , -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 , -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 , -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 , -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 , -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 , -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 , -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 , -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 , -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 , -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 , -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 , -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 , -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ). +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.22446419823708e+00 , 3.18649479383647e-02 , -6.64989816298089e-01 , 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 , 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254842e-01 , 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 , 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 , 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 , 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 , 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 , 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 , 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991724e+00 , 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 , 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528188e-01 , 4.37681313203301e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 , 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 , 5.67045576176347e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 , -6.16431681139152e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 , 1.29461765027048e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 , -3.48478472967697e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 , -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 , -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -7.83422856191325e-01 , 5.49518347305934e+00 , 2.48952532366078e+00 , -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 , -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 , -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 , -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 , -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 , -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 , -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 , -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 , -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 , -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 , -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 , -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 , -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4623,6 +6828,10 @@ colvars: Adding total bias energy: 11.5258 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4638,8 +6847,6 @@ colvars: ( 0.00564816 , -0.104898 , 0.316213 ) colvars: ( -0.0508777 , 0.0822372 , 0.215331 ) colvars: ( 0.0815265 , -0.236712 , 0.0276249 ) colvars: ( 0.135594 , -0.476027 , 0.338338 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243121 , -0.0991688 , 0.0967014 ) colvars: ( 0.0197729 , -0.0818665 , 0.0836688 ) @@ -4692,14 +6899,17 @@ colvars: ( -0.00838404 , 0.0463531 , -0.0836695 ) colvars: ( -0.0186545 , 0.0668045 , -0.0357494 ) colvars: ( -0.0223311 , 0.0839872 , -0.059422 ) colvars: ( -0.0243676 , 0.0927859 , -0.0695589 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 39. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 39. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 39, atoms_new_colvar_forces = { ( -6.85760792996511e-02 , 3.03391190372132e-01 , -4.03470465038437e-01 ), ( 1.43266319462628e-02 , 3.10765577955413e-02 , -2.40273727195948e-01 ), ( -4.32418115472582e-02 , 9.58623311770646e-02 , 8.49822855712108e-02 ), ( -9.78506393239423e-02 , 2.50668249779756e-01 , 6.30654919349158e-02 ), ( -1.72669714438694e-02 , 9.79803550809251e-02 , -1.72197348799224e-01 ), ( 7.13666644571403e-02 , -1.85663666663476e-01 , -3.70401934232006e-02 ), ( 8.22663282605443e-03 , -9.83576242859787e-02 , 2.55846331786987e-01 ), ( -4.21617012069782e-02 , 6.04769641875639e-02 , 1.92897427331650e-01 ), ( 6.66383033413407e-02 , -1.92060723280848e-01 , 3.49703055971520e-02 ), ( 1.13262969450724e-01 , -3.92040115424842e-01 , 2.78915680074420e-01 ), ( 2.43120615818260e-02 , -9.91687871383144e-02 , 9.67014422689911e-02 ), ( 2.65210286567995e-02 , -9.73126436762223e-02 , 6.04989195122588e-02 ), ( 1.22019876372007e-02 , -5.56854705073975e-02 , 7.30166371651342e-02 ), ( 1.23809460844627e-02 , -5.35335097256021e-02 , 6.17968896446734e-02 ), ( 5.33680866413092e-03 , -3.50104986769918e-02 , 7.60494168987403e-02 ), ( -8.92180929547350e-03 , 9.54178500425490e-03 , 7.56767473291031e-02 ), ( -2.22371115869817e-03 , -2.86513208581145e-03 , 4.05702084627808e-02 ), ( -5.92164461686849e-03 , 9.73218229005266e-03 , 3.61562278670125e-02 ), ( 2.70448252725674e-03 , -1.32471106341959e-02 , 1.99297111740999e-02 ), ( 9.26749253439040e-03 , -2.25524145633818e-02 , -2.62739003345519e-02 ), ( 8.86020893235893e-03 , -2.40916843932129e-02 , -1.46430826543643e-02 ), ( 6.79008106829284e-03 , -1.38790942151789e-02 , -3.01990451011923e-02 ), ( 1.51728533578124e-02 , -4.69082884526167e-02 , -1.67599335757655e-03 ), ( 2.78174735877192e-02 , -8.86550992426879e-02 , 7.91844579743056e-03 ), ( 1.43590192425672e-02 , -4.69788314968345e-02 , 9.12269597050372e-03 ), ( 1.43455946611162e-02 , -4.41335513916129e-02 , -2.48380726608012e-03 ), ( 9.25500305278820e-03 , -3.70404219689552e-02 , 3.38695002708129e-02 ), ( -1.11936165716947e-03 , -1.50202702602189e-02 , 7.66368011977586e-02 ), ( -3.92721222202764e-03 , 4.29975912649857e-03 , 3.28989332702641e-02 ), ( -6.00679980196902e-03 , 1.14138917306432e-02 , 3.02930976450661e-02 ), ( -7.42765119826021e-03 , 1.79940255100832e-02 , 2.13937723184561e-02 ), ( -1.63809278079067e-02 , 5.20200431521570e-02 , -3.89101834427693e-03 ), ( -9.75291630201696e-03 , 3.57088137252074e-02 , -2.19283949849110e-02 ), ( -1.37966814091787e-02 , 4.99827360070345e-02 , -2.88190408100287e-02 ), ( -1.87740684913841e-03 , 1.46690549469220e-02 , -3.64943197340017e-02 ), ( 1.09213485123973e-02 , -1.63703636169440e-02 , -7.32197132080785e-02 ), ( 4.58054909200228e-03 , -1.11301381598280e-03 , -5.45270632193023e-02 ), ( 3.60071564144867e-03 , 5.68556530723015e-03 , -7.00243396038003e-02 ), ( 7.27230082340127e-03 , -1.50582502822533e-02 , -3.15426687678145e-02 ), ( 1.31588021489714e-02 , -4.14431027325793e-02 , 1.69893986732976e-03 ), ( 5.40413457436416e-04 , 1.74904516444129e-03 , -1.42180257520665e-02 ), ( 4.81955385624926e-04 , 3.36568253909044e-03 , -2.01564103345881e-02 ), ( -6.59816426575166e-03 , 2.06853833091742e-02 , -4.57496077723121e-04 ), ( -2.08601693150008e-02 , 5.81869588982627e-02 , 2.84043742803996e-02 ), ( -1.90849481901457e-02 , 6.35059990249224e-02 , -1.65352950682017e-02 ), ( -2.28209467504911e-02 , 7.55161082636293e-02 , -1.80267509733149e-02 ), ( -1.67134328831536e-02 , 7.23142221324330e-02 , -8.36188006345148e-02 ), ( -1.97652753228754e-02 , 8.64191632927915e-02 , -1.02615606437546e-01 ), ( -8.38403595659010e-03 , 4.63531251980092e-02 , -8.36694766979938e-02 ), ( -1.86544506501744e-02 , 6.68045394632732e-02 , -3.57494057868076e-02 ), ( -2.43675801969378e-02 , 9.27859360530459e-02 , -6.95588936316066e-02 ) } +colvars: Step 39, atoms_new_colvar_forces = { ( -6.85760792996514e-02 , 3.03391190372132e-01 , -4.03470465038437e-01 ), ( 1.43266319462627e-02 , 3.10765577955413e-02 , -2.40273727195948e-01 ), ( -4.32418115472581e-02 , 9.58623311770647e-02 , 8.49822855712108e-02 ), ( -9.78506393239423e-02 , 2.50668249779756e-01 , 6.30654919349158e-02 ), ( -1.72669714438695e-02 , 9.79803550809251e-02 , -1.72197348799224e-01 ), ( 7.13666644571403e-02 , -1.85663666663477e-01 , -3.70401934232006e-02 ), ( 8.22663282605456e-03 , -9.83576242859786e-02 , 2.55846331786987e-01 ), ( -4.21617012069781e-02 , 6.04769641875639e-02 , 1.92897427331650e-01 ), ( 6.66383033413408e-02 , -1.92060723280848e-01 , 3.49703055971522e-02 ), ( 1.13262969450725e-01 , -3.92040115424842e-01 , 2.78915680074420e-01 ), ( 2.43120615818261e-02 , -9.91687871383143e-02 , 9.67014422689912e-02 ), ( 2.65210286567995e-02 , -9.73126436762223e-02 , 6.04989195122588e-02 ), ( 1.22019876372008e-02 , -5.56854705073975e-02 , 7.30166371651342e-02 ), ( 1.23809460844627e-02 , -5.35335097256021e-02 , 6.17968896446734e-02 ), ( 5.33680866413097e-03 , -3.50104986769917e-02 , 7.60494168987403e-02 ), ( -8.92180929547345e-03 , 9.54178500425501e-03 , 7.56767473291032e-02 ), ( -2.22371115869815e-03 , -2.86513208581138e-03 , 4.05702084627808e-02 ), ( -5.92164461686847e-03 , 9.73218229005274e-03 , 3.61562278670125e-02 ), ( 2.70448252725674e-03 , -1.32471106341959e-02 , 1.99297111740999e-02 ), ( 9.26749253439036e-03 , -2.25524145633818e-02 , -2.62739003345519e-02 ), ( 8.86020893235890e-03 , -2.40916843932129e-02 , -1.46430826543643e-02 ), ( 6.79008106829279e-03 , -1.38790942151789e-02 , -3.01990451011923e-02 ), ( 1.51728533578123e-02 , -4.69082884526167e-02 , -1.67599335757658e-03 ), ( 2.78174735877192e-02 , -8.86550992426879e-02 , 7.91844579743057e-03 ), ( 1.43590192425672e-02 , -4.69788314968345e-02 , 9.12269597050373e-03 ), ( 1.43455946611162e-02 , -4.41335513916129e-02 , -2.48380726608011e-03 ), ( 9.25500305278823e-03 , -3.70404219689551e-02 , 3.38695002708129e-02 ), ( -1.11936165716940e-03 , -1.50202702602189e-02 , 7.66368011977586e-02 ), ( -3.92721222202761e-03 , 4.29975912649859e-03 , 3.28989332702641e-02 ), ( -6.00679980196899e-03 , 1.14138917306432e-02 , 3.02930976450661e-02 ), ( -7.42765119826019e-03 , 1.79940255100833e-02 , 2.13937723184561e-02 ), ( -1.63809278079067e-02 , 5.20200431521571e-02 , -3.89101834427696e-03 ), ( -9.75291630201698e-03 , 3.57088137252074e-02 , -2.19283949849110e-02 ), ( -1.37966814091787e-02 , 4.99827360070345e-02 , -2.88190408100287e-02 ), ( -1.87740684913845e-03 , 1.46690549469220e-02 , -3.64943197340017e-02 ), ( 1.09213485123972e-02 , -1.63703636169440e-02 , -7.32197132080786e-02 ), ( 4.58054909200224e-03 , -1.11301381598286e-03 , -5.45270632193023e-02 ), ( 3.60071564144862e-03 , 5.68556530723009e-03 , -7.00243396038003e-02 ), ( 7.27230082340125e-03 , -1.50582502822534e-02 , -3.15426687678145e-02 ), ( 1.31588021489714e-02 , -4.14431027325794e-02 , 1.69893986732982e-03 ), ( 5.40413457436425e-04 , 1.74904516444122e-03 , -1.42180257520665e-02 ), ( 4.81955385624934e-04 , 3.36568253909036e-03 , -2.01564103345880e-02 ), ( -6.59816426575165e-03 , 2.06853833091742e-02 , -4.57496077723089e-04 ), ( -2.08601693150008e-02 , 5.81869588982627e-02 , 2.84043742803996e-02 ), ( -1.90849481901457e-02 , 6.35059990249224e-02 , -1.65352950682017e-02 ), ( -2.28209467504911e-02 , 7.55161082636293e-02 , -1.80267509733149e-02 ), ( -1.67134328831537e-02 , 7.23142221324330e-02 , -8.36188006345148e-02 ), ( -1.97652753228755e-02 , 8.64191632927915e-02 , -1.02615606437546e-01 ), ( -8.38403595659016e-03 , 4.63531251980092e-02 , -8.36694766979938e-02 ), ( -1.86544506501744e-02 , 6.68045394632732e-02 , -3.57494057868077e-02 ), ( -2.43675801969379e-02 , 9.27859360530459e-02 , -6.95588936316067e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 39, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4737,10 +6947,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 40, atoms_ids[size = 51] = { 3, 13, 23, 33, 43, 53, 63, 73, 83, 98, 0, 5, 9, 10, 11, 15, 19, 20, 21, 25, 29, 30, 31, 35, 39, 40, 41, 45, 49, 50, 51, 55, 59, 60, 61, 65, 69, 70, 71, 75, 79, 80, 81, 85, 89, 90, 91, 92, 93, 96, 100 } -colvars: Step 40, atoms_refcount[size = 51] = { 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 } +colvars: Step 40, atoms_refcount[size = 51] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } colvars: Step 40, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } colvars: Step 40, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } -colvars: Step 40, atoms_positions[size = 51] = { ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543952e-01 ), ( 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 ), ( 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 ), ( 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145887e-02 ), ( 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 ), ( 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 ), ( -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 ), ( -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 ), ( -3.66131282078092e+00 , 5.55259716682067e-02 , 5.43563780321032e+00 ), ( -4.78721531273729e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ), ( 8.21486247008991e+00 , 3.00039497048982e-02 , -6.60697462712691e-01 ), ( 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 ), ( 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528584e-01 ), ( 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 ), ( 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 ), ( 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 ), ( 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 ), ( 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896024e+00 ), ( 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 ), ( 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 ), ( 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 ), ( 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 ), ( 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 ), ( 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883072e+00 ), ( 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 ), ( 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 ), ( 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049652e+00 ), ( 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 ), ( 5.66268392317115e-01 , 6.44411030333317e-01 , 2.93545758947663e+00 ), ( -6.18281281150509e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 ), ( 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 ), ( 2.02515014278286e+00 , 2.79394318413906e+00 , 5.72833915031846e+00 ), ( -3.45150604495940e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 ), ( -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 ), ( -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 ), ( -7.84558308207992e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 ), ( -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 ), ( -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 ), ( -2.72175683744147e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 ), ( -3.33238449414696e+00 , 9.30098455178845e-01 , 7.54153994227607e-01 ), ( -4.27817669645113e+00 , 1.01230827582552e+00 , 3.22603647756983e+00 ), ( -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 ), ( -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427901e+00 ), ( -2.29703042167363e+00 , -2.48666237490765e-01 , 6.14849732461339e+00 ), ( -4.47429163821902e+00 , 9.93809554940078e-01 , 6.42347308377283e+00 ), ( -5.35121077038599e+00 , 5.08137902098546e-01 , 7.16226945729229e+00 ), ( -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781003e+00 ), ( -7.05853462677926e+00 , 4.28980729398598e+00 , 7.51013468005025e+00 ), ( -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 ), ( -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704306e+00 ), ( -4.00767500939248e+00 , 4.66160981547132e+00 , 7.28700289556107e+00 ) } +colvars: Step 40, atoms_positions[size = 51] = { ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 ), ( 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 ), ( 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 ), ( 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 ), ( 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 ), ( 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 ), ( -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 ), ( -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 ), ( -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 ), ( -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ), ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 ), ( 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 ), ( 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 ), ( 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 ), ( 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 ), ( 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 ), ( 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 ), ( 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 ), ( 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 ), ( 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 ), ( 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 ), ( 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 ), ( 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 ), ( 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 ), ( 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 ), ( 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 ), ( 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 ), ( 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 ), ( 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 ), ( -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 ), ( 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 ), ( 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 ), ( -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 ), ( -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 ), ( -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 ), ( -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 ), ( -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 ), ( -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 ), ( -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 ), ( -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 ), ( -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 ), ( -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 ), ( -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 ), ( -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 ), ( -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 ), ( -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 ), ( -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 ), ( -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 ), ( -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 ), ( -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 ), ( -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ) } colvars: Step 40, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 40, atom_groups_ids[size = 0] = @@ -4758,16 +6968,87 @@ colvars: Collective variables module, step no. 40 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629676e-02 , 1.15959419288222e-02 , -1.35102502789138e-02 ). +colvars: Colvar component no. 1 within colvar "main" has value ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629674e-02 , 1.15959419288222e-02 , -1.35102502789137e-02 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 , 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 , 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 , 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 , 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 , 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 , 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 , 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 , 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 , 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 , 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 , 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 , 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 , 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 , 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 , -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 , 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 , -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 , -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 , -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 , -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 , -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 , -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 , -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 , -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 , -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 , -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 , -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 , -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 , -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 , -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 , -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 , -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629676e-02 , 1.15959419288222e-02 , -1.35102502789138e-02 ). +colvars: Colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629674e-02 , 1.15959419288222e-02 , -1.35102502789137e-02 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 , 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 , 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 , 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 , 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 , 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 , 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 , 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 , 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 , 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 , 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 , 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 , 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 , 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 , 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 , -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 , 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 , -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 , -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 , -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 , -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 , -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 , -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 , -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 , -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 , -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 , -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 , -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 , -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 , -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 , -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 , -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 , -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ). +colvars: Done calculating colvar "fitting"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". @@ -4780,6 +7061,10 @@ colvars: Adding total bias energy: 11.53 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". @@ -4795,8 +7080,6 @@ colvars: ( 0.00559067 , -0.104738 , 0.316505 ) colvars: ( -0.0509985 , 0.082562 , 0.215293 ) colvars: ( 0.0815747 , -0.236729 , 0.0276524 ) colvars: ( 0.135649 , -0.476037 , 0.338813 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. colvars: Applying force on the fitting group of main group: colvars: ( 0.0243381 , -0.0991436 , 0.0967656 ) colvars: ( 0.0197924 , -0.0818427 , 0.0837345 ) @@ -4849,6 +7132,7 @@ colvars: ( -0.00839007 , 0.0463289 , -0.0837274 ) colvars: ( -0.0186729 , 0.066792 , -0.035799 ) colvars: ( -0.0223541 , 0.0839695 , -0.0594797 ) colvars: ( -0.0243944 , 0.092768 , -0.0696101 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 40. colvars: colvarmodule::write_traj_files() @@ -4859,8 +7143,10 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 40. colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". colvars: ---------------------------------------------------------------------- -colvars: Step 40, atoms_new_colvar_forces = { ( -6.85323667607085e-02 , 3.03250085633828e-01 , -4.03919244566743e-01 ), ( 1.44250120644039e-02 , 3.07866206325814e-02 , -2.40338909060198e-01 ), ( -4.32788268105407e-02 , 9.58815639835368e-02 , 8.51648417941772e-02 ), ( -9.79580001908215e-02 , 2.50912438003103e-01 , 6.29556416781234e-02 ), ( -1.72472401057155e-02 , 9.79440595116233e-02 , -1.72462588377445e-01 ), ( 7.14471883024387e-02 , -1.85855959156371e-01 , -3.69125172216922e-02 ), ( 8.17196163325179e-03 , -9.82110268157001e-02 , 2.56124884008761e-01 ), ( -4.22690273374395e-02 , 6.07920779777388e-02 , 1.92835186870276e-01 ), ( 6.66737009441522e-02 , -1.92081954588494e-01 , 3.49538806817385e-02 ), ( 1.13294551779845e-01 , -3.92067691417467e-01 , 2.79333500624614e-01 ), ( 2.43381070971489e-02 , -9.91435684382055e-02 , 9.67656042693870e-02 ), ( 2.65474804688020e-02 , -9.72928771737138e-02 , 6.05706743700988e-02 ), ( 1.22130220545263e-02 , -5.56644363052377e-02 , 7.30706999847849e-02 ), ( 1.23930794636728e-02 , -5.35162574221356e-02 , 6.18414015927799e-02 ), ( 5.33908232466113e-03 , -3.49877052428895e-02 , 7.61042263482980e-02 ), ( -8.93702422432012e-03 , 9.56574591985604e-03 , 7.57260345722720e-02 ), ( -2.22998076945108e-03 , -2.85083274124680e-03 , 4.06068065590374e-02 ), ( -5.93131133315950e-03 , 9.74426221995694e-03 , 3.61818108984666e-02 ), ( 2.70298600701359e-03 , -1.32362980851642e-02 , 1.99717264345225e-02 ), ( 9.27227028404926e-03 , -2.25504503061479e-02 , -2.62293277894644e-02 ), ( 8.86706074728804e-03 , -2.40904542112200e-02 , -1.46143142955973e-02 ), ( 6.79506980951520e-03 , -1.38821750859600e-02 , -3.01804053172093e-02 ), ( 1.51875404530745e-02 , -4.69047478317858e-02 , -1.64186260049467e-03 ), ( 2.78481343112598e-02 , -8.86510812523361e-02 , 7.95666205544641e-03 ), ( 1.43752539372569e-02 , -4.69761437538032e-02 , 9.14083867651916e-03 ), ( 1.43626830924914e-02 , -4.41347053823263e-02 , -2.47532915565276e-03 ), ( 9.26543336548817e-03 , -3.70321914229107e-02 , 3.38893091282548e-02 ), ( -1.12004885949660e-03 , -1.50034226484375e-02 , 7.66528774929137e-02 ), ( -3.93094451591357e-03 , 4.30623483933488e-03 , 3.28987164124701e-02 ), ( -6.01187124969791e-03 , 1.14183247352517e-02 , 3.02824521939553e-02 ), ( -7.43662755693067e-03 , 1.79994313113881e-02 , 2.13959799540316e-02 ), ( -1.64019199467728e-02 , 5.20217936348420e-02 , -3.89171641232288e-03 ), ( -9.76431618508571e-03 , 3.57038612670258e-02 , -2.19423983487685e-02 ), ( -1.38120095259618e-02 , 4.99751669683366e-02 , -2.88441005754843e-02 ), ( -1.88013590503811e-03 , 1.46613779011853e-02 , -3.65021572613942e-02 ), ( 1.09330016456256e-02 , -1.63858682409413e-02 , -7.32233385220953e-02 ), ( 4.58720889823015e-03 , -1.12738473805357e-03 , -5.45483074608205e-02 ), ( 3.60687333466525e-03 , 5.66676925795172e-03 , -7.00554557812025e-02 ), ( 7.28270763577972e-03 , -1.50681561528744e-02 , -3.15597043389583e-02 ), ( 1.31777917031141e-02 , -4.14476897041726e-02 , 1.68346700673696e-03 ), ( 5.45322168857217e-04 , 1.74002562910155e-03 , -1.42530289183739e-02 ), ( 4.87858268944159e-04 , 3.35386962129515e-03 , -2.02009403001517e-02 ), ( -6.60198593674321e-03 , 2.06801299134617e-02 , -4.91529279330384e-04 ), ( -2.08804561740570e-02 , 5.81882353586720e-02 , 2.83654816899834e-02 ), ( -1.91027000722412e-02 , 6.34962788800136e-02 , -1.65887744997137e-02 ), ( -2.28420590270769e-02 , 7.55047340022035e-02 , -1.80910514907058e-02 ), ( -1.67294107746415e-02 , 7.22903490015903e-02 , -8.36818944736092e-02 ), ( -1.97847172876338e-02 , 8.63908043813334e-02 , -1.02687251415262e-01 ), ( -8.39007040909995e-03 , 4.63288740292679e-02 , -8.37274147395396e-02 ), ( -1.86729126279069e-02 , 6.67920120077291e-02 , -3.57990212161275e-02 ), ( -2.43944182091028e-02 , 9.27679514953860e-02 , -6.96101218792903e-02 ) } +colvars: Step 40, atoms_new_colvar_forces = { ( -6.85323667607087e-02 , 3.03250085633828e-01 , -4.03919244566743e-01 ), ( 1.44250120644039e-02 , 3.07866206325814e-02 , -2.40338909060198e-01 ), ( -4.32788268105407e-02 , 9.58815639835369e-02 , 8.51648417941772e-02 ), ( -9.79580001908216e-02 , 2.50912438003103e-01 , 6.29556416781233e-02 ), ( -1.72472401057155e-02 , 9.79440595116233e-02 , -1.72462588377445e-01 ), ( 7.14471883024387e-02 , -1.85855959156371e-01 , -3.69125172216921e-02 ), ( 8.17196163325191e-03 , -9.82110268157001e-02 , 2.56124884008762e-01 ), ( -4.22690273374394e-02 , 6.07920779777388e-02 , 1.92835186870276e-01 ), ( 6.66737009441523e-02 , -1.92081954588494e-01 , 3.49538806817384e-02 ), ( 1.13294551779846e-01 , -3.92067691417467e-01 , 2.79333500624614e-01 ), ( 2.43381070971489e-02 , -9.91435684382055e-02 , 9.67656042693871e-02 ), ( 2.65474804688020e-02 , -9.72928771737139e-02 , 6.05706743700988e-02 ), ( 1.22130220545263e-02 , -5.56644363052378e-02 , 7.30706999847849e-02 ), ( 1.23930794636728e-02 , -5.35162574221356e-02 , 6.18414015927799e-02 ), ( 5.33908232466114e-03 , -3.49877052428895e-02 , 7.61042263482980e-02 ), ( -8.93702422432010e-03 , 9.56574591985604e-03 , 7.57260345722720e-02 ), ( -2.22998076945107e-03 , -2.85083274124681e-03 , 4.06068065590374e-02 ), ( -5.93131133315949e-03 , 9.74426221995694e-03 , 3.61818108984666e-02 ), ( 2.70298600701360e-03 , -1.32362980851642e-02 , 1.99717264345225e-02 ), ( 9.27227028404927e-03 , -2.25504503061480e-02 , -2.62293277894644e-02 ), ( 8.86706074728803e-03 , -2.40904542112200e-02 , -1.46143142955974e-02 ), ( 6.79506980951520e-03 , -1.38821750859600e-02 , -3.01804053172094e-02 ), ( 1.51875404530745e-02 , -4.69047478317859e-02 , -1.64186260049470e-03 ), ( 2.78481343112598e-02 , -8.86510812523362e-02 , 7.95666205544640e-03 ), ( 1.43752539372569e-02 , -4.69761437538033e-02 , 9.14083867651916e-03 ), ( 1.43626830924914e-02 , -4.41347053823264e-02 , -2.47532915565276e-03 ), ( 9.26543336548818e-03 , -3.70321914229108e-02 , 3.38893091282548e-02 ), ( -1.12004885949659e-03 , -1.50034226484375e-02 , 7.66528774929137e-02 ), ( -3.93094451591356e-03 , 4.30623483933488e-03 , 3.28987164124701e-02 ), ( -6.01187124969791e-03 , 1.14183247352518e-02 , 3.02824521939554e-02 ), ( -7.43662755693067e-03 , 1.79994313113881e-02 , 2.13959799540316e-02 ), ( -1.64019199467728e-02 , 5.20217936348420e-02 , -3.89171641232289e-03 ), ( -9.76431618508571e-03 , 3.57038612670259e-02 , -2.19423983487685e-02 ), ( -1.38120095259618e-02 , 4.99751669683367e-02 , -2.88441005754843e-02 ), ( -1.88013590503811e-03 , 1.46613779011853e-02 , -3.65021572613942e-02 ), ( 1.09330016456256e-02 , -1.63858682409413e-02 , -7.32233385220953e-02 ), ( 4.58720889823014e-03 , -1.12738473805356e-03 , -5.45483074608206e-02 ), ( 3.60687333466524e-03 , 5.66676925795172e-03 , -7.00554557812025e-02 ), ( 7.28270763577972e-03 , -1.50681561528744e-02 , -3.15597043389583e-02 ), ( 1.31777917031141e-02 , -4.14476897041726e-02 , 1.68346700673701e-03 ), ( 5.45322168857212e-04 , 1.74002562910157e-03 , -1.42530289183739e-02 ), ( 4.87858268944153e-04 , 3.35386962129516e-03 , -2.02009403001517e-02 ), ( -6.60198593674321e-03 , 2.06801299134617e-02 , -4.91529279330374e-04 ), ( -2.08804561740570e-02 , 5.81882353586720e-02 , 2.83654816899834e-02 ), ( -1.91027000722412e-02 , 6.34962788800136e-02 , -1.65887744997137e-02 ), ( -2.28420590270769e-02 , 7.55047340022036e-02 , -1.80910514907058e-02 ), ( -1.67294107746415e-02 , 7.22903490015903e-02 , -8.36818944736092e-02 ), ( -1.97847172876338e-02 , 8.63908043813335e-02 , -1.02687251415262e-01 ), ( -8.39007040909996e-03 , 4.63288740292679e-02 , -8.37274147395396e-02 ), ( -1.86729126279069e-02 , 6.67920120077291e-02 , -3.57990212161275e-02 ), ( -2.43944182091028e-02 , 9.27679514953860e-02 , -6.96101218792904e-02 ) } colvars: ---------------------------------------------------------------------- colvars: Step 40, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped index 28d381db9..05eb9d8b8 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,17 @@ configuration { colvar { name one - x ( 0.99973970766145 , 0.014266190562968 , 0.011595941928822 , -0.013510250278914 ) + x ( 0.99973970766145 , 0.014266190562967 , 0.011595941928822 , -0.013510250278914 ) +} + +colvar { + name main + x ( 6.8676208645464 , -0.61271733826672 , -0.47391111954395 , 6.0417423917699 , -0.2572065757875 , 3.280691671575 , 5.1246111101011 , 3.5063531103509 , 2.8331884221988 , 2.7427331318038 , 3.183939270326 , -0.098522041714588 , 1.299268032236 , 0.16207979639779 , 1.6709575658416 , 0.92364152112933 , 1.9975665777803 , 5.0731192588566 , -1.4675941518372 , 4.4813585508814 , 3.3973074276517 , -3.8283620698119 , 1.7699294118509 , 1.9801964665289 , -3.6613128207809 , 0.055525971668209 , 5.4356378032103 , -4.7872153127373 , 3.2636042470594 , 7.1751730326322 ) +} + +colvar { + name fitting + x ( 8.2148624700899 , 0.030003949704897 , -0.66069746271269 , 6.8676208645464 , -0.61271733826672 , -0.47391111954395 , 7.0302327289727 , -2.1065802455568 , -0.80413672843511 , 6.1059166071289 , -0.31420594476102 , 0.80450414252859 , 4.9009077589279 , -0.13778267203411 , 0.76612304317323 , 6.7529874091112 , -0.33024891439809 , 1.9771653633698 , 6.0417423917699 , -0.2572065757875 , 3.280691671575 , 7.0976664348158 , -0.36443719008101 , 4.4126033869916 , 5.2325979411613 , 1.0543652658116 , 3.345239990687 , 4.1096502105894 , 1.0076564480121 , 3.8336836889602 , 5.8085825883195 , 2.2431337878562 , 2.9523153959534 , 5.1246111101011 , 3.5063531103509 , 2.8331884221988 , 6.2444316302188 , 4.4076649760484 , 2.2727031062502 , 3.8681823242069 , 3.6105625251087 , 1.9922597257068 , 2.8664391562608 , 4.1512927538128 , 2.3986297766829 , 3.900402643639 , 3.1125094911486 , 0.79605361698408 , 2.7427331318038 , 3.183939270326 , -0.098522041714588 , 3.1502857891748 , 2.662780648907 , -1.5030953088307 , 1.6620934927936 , 2.3049571979405 , 0.47497903946509 , 0.44214209617904 , 2.6079434547308 , 0.40155618441789 , 2.0172699632204 , 1.1203884493605 , 1.0119885004965 , 1.299268032236 , 0.16207979639779 , 1.6709575658416 , 2.0998237962452 , -1.0951958530446 , 2.0131165512648 , 0.56626839231711 , 0.64441103033332 , 2.9354575894766 , -0.61828128115051 , 0.35845492398582 , 3.2232453783193 , 1.297658748413 , 1.443322963564 , 3.788554519119 , 0.92364152112933 , 1.9975665777803 , 5.0731192588566 , 2.0251501427829 , 2.7939431841391 , 5.7283391503185 , -0.34515060449594 , 2.8816108985945 , 4.916740331129 , -1.1133126917309 , 3.0740803793275 , 5.8967574266384 , -0.4981951970656 , 3.4448064301456 , 3.6924514397354 , -1.4675941518372 , 4.4813585508814 , 3.3973074276517 , -0.784558308208 , 5.5034619834142 , 2.4892899213029 , -2.7578640391705 , 3.9250471855758 , 2.7194020951498 , -3.7808515929938 , 4.6163616235847 , 2.7974905973992 , -2.7217568374415 , 2.6576894477977 , 2.333665549995 , -3.8283620698119 , 1.7699294118509 , 1.9801964665289 , -3.332384494147 , 0.93009845517884 , 0.75415399422761 , -4.2781766964511 , 1.0123082758255 , 3.2260364775698 , -5.404130077644 , 0.69496442496522 , 3.381616475444 , -3.3472467118183 , 0.69539921370932 , 4.186092874279 , -3.6613128207809 , 0.055525971668209 , 5.4356378032103 , -2.2970304216736 , -0.24866623749075 , 6.1484973246134 , -4.474291638219 , 0.99380955494008 , 6.4234730837728 , -5.351210770386 , 0.50813790209854 , 7.1622694572923 , -6.2601316351656 , 3.6007623232274 , 6.82644344781 , -7.0585346267793 , 4.289807293986 , 7.5101346800503 , -6.6052567178241 , 3.1849591257566 , 5.5759990068514 , -4.1350860238649 , 2.2571545644834 , 6.4351156570431 , -4.7872153127373 , 3.2636042470594 , 7.1751730326322 , -4.0076750093925 , 4.6616098154713 , 7.2870028955611 ) } restraint { diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj index cae2fd3bb..3b8b8dacc 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379277e-02 , -1.19157233149255e-02 ) ( -2.33415112386271e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) - 21 ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ) ( -2.29006853143000e-01 , 1.72135778158611e+01 , 1.72687267375248e+01 , 1.80464864475683e+01 ) - 22 ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072403e-02 , -1.24385326679425e-02 ) ( -2.25354457213011e-01 , 1.72171754135474e+01 , 1.72631618101901e+01 , 1.80562099325717e+01 ) - 23 ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ) ( -2.22544779088946e-01 , 1.72183237124724e+01 , 1.72567883292804e+01 , 1.80670193605806e+01 ) - 24 ( 9.99737489847089e-01 , 1.37893985756126e-02 , 1.27630697470619e-02 , -1.31113665114322e-02 ) ( -2.20603106002609e-01 , 1.72171554509598e+01 , 1.72500128724119e+01 , 1.80783704448867e+01 ) - 25 ( 9.99728636259111e-01 , 1.38933216876203e-02 , 1.29777530480417e-02 , -1.34613291247888e-02 ) ( -2.19486355870299e-01 , 1.72139646676619e+01 , 1.72432756028464e+01 , 1.80896940912098e+01 ) - 26 ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ) ( -2.19085878573173e-01 , 1.72091896600299e+01 , 1.72370208696570e+01 , 1.81004332960232e+01 ) - 27 ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ) ( -2.19239183005156e-01 , 1.72033736955944e+01 , 1.72316668936004e+01 , 1.81100807759075e+01 ) - 28 ( 9.99702390065719e-01 , 1.44141469092545e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ) ( -2.19748019832374e-01 , 1.71971104079588e+01 , 1.72275783419924e+01 , 1.81182129845822e+01 ) - 29 ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601430e-02 , -1.45578300084090e-02 ) ( -2.20399336095059e-01 , 1.71909839939957e+01 , 1.72250446125594e+01 , 1.81245164741949e+01 ) - 30 ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ) ( -2.20985728454130e-01 , 1.71855148115988e+01 , 1.72242650771018e+01 , 1.81288036297547e+01 ) - 31 ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250314e-02 , -1.47660205688039e-02 ) ( -2.21322757293946e-01 , 1.71811189756810e+01 , 1.72253411048109e+01 , 1.81310165171552e+01 ) - 32 ( 9.99688177857407e-01 , 1.49982495919956e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ) ( -2.21261370441172e-01 , 1.71780870762712e+01 , 1.72282738490838e+01 , 1.81312195438593e+01 ) - 33 ( 9.99690134322553e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ) ( -2.20694541572399e-01 , 1.71765830291102e+01 , 1.72329665905616e+01 , 1.81295834415202e+01 ) - 34 ( 9.99694127613340e-01 , 1.50525510111081e-02 , 1.30981148586897e-02 , -1.46120262321522e-02 ) ( -2.19558217033344e-01 , 1.71766598040325e+01 , 1.72392306187359e+01 , 1.81263642820461e+01 ) - 35 ( 9.99699846006243e-01 , 1.50116061858438e-02 , 1.28715966499478e-02 , -1.44634565196466e-02 ) ( -2.17827764309674e-01 , 1.71782851045968e+01 , 1.72467940429680e+01 , 1.81218814860652e+01 ) - 36 ( 9.99706901952671e-01 , 1.49283570956246e-02 , 1.26183883681986e-02 , -1.42839286474994e-02 ) ( -2.15512239618473e-01 , 1.71813676827162e+01 , 1.72553133391491e+01 , 1.81164979377424e+01 ) - 37 ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905548e-02 , -1.40858436164589e-02 ) ( -2.12649201856729e-01 , 1.71857754415149e+01 , 1.72643878203920e+01 , 1.81106036446139e+01 ) - 38 ( 9.99723286500429e-01 , 1.46513537865609e-02 , 1.20819700460899e-02 , -1.38821562016640e-02 ) ( -2.09302245721531e-01 , 1.71913399553369e+01 , 1.72735773588976e+01 , 1.81046024388439e+01 ) - 39 ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ) ( -2.05561935701077e-01 , 1.71978476772161e+01 , 1.72824235036234e+01 , 1.80988996968902e+01 ) - 40 ( 9.99739707661452e-01 , 1.42661905629676e-02 , 1.15959419288222e-02 , -1.35102502789138e-02 ) ( -2.01548974416543e-01 , 1.72050238188529e+01 , 1.72904735673894e+01 , 1.80938885690596e+01 ) +# step one fa_one main fitting + 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ) ( -2.33415112386265e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ) ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) + 21 ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ) ( -2.29006853143000e-01 , 1.72135778158611e+01 , 1.72687267375248e+01 , 1.80464864475683e+01 ) ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ) ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 , 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 , 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 , 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 , 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 , 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 , 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 , 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 , 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 , 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 , 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 , 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 , 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 , 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 , 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 , -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 , 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 , -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 , -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 , -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 , -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 , -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 , -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 , -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 , -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 , -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 , -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 , -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 , -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 , -6.96229704469881e+00 , 4.29845684597736e+00 , 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2.48952532366078e+00 , -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 , -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 , -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 , -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 , -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 , -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 , -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 , -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 , -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 , -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 , -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 , -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 , -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ) + 40 ( 9.99739707661452e-01 , 1.42661905629674e-02 , 1.15959419288222e-02 , -1.35102502789137e-02 ) ( -2.01548974416543e-01 , 1.72050238188529e+01 , 1.72904735673894e+01 , 1.80938885690596e+01 ) ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ) ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 , 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 , 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 , 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 , 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 , 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 , 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 , 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 , 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 , 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 , 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 , 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 , 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 , 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 , 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 , -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 , 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 , -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 , -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 , -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 , -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 , -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 , -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 , -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 , -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 , -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 , -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 , -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 , -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 , -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 , -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 , -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 , -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py new file mode 100644 index 000000000..ced91627c --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py @@ -0,0 +1,245 @@ +#!/usr/bin/env python3 +import torch +import re +import numpy as np + +torch.set_printoptions(precision=10) + +ref_main_group = torch.tensor( + [[6.3061, -1.592, -3.585], + [5.4031, -0.784, 0.045] , + [3.8061, 2.804, -0.129] , + [1.2441, 1.799, -2.726] , + [0.5861, -1.803, -1.516], + [-0.2169, -0.926, 2.133], + [-2.1679, 2.13, 1.258] , + [-4.4689, 0.434, -1.263], + [-4.8649, -2.25, 1.46] , + [-5.6269, 0.188, 4.323]], dtype=torch.float64) + +ref_fitting_group = torch.tensor( + [[5.69469, -1.80418, -5.22382] , + [6.37169, -1.08118, -4.10382] , + [6.61169, 0.365824, -4.58082] , + [5.62269, -1.09518, -2.77982] , + [4.39969, -0.986176, -2.72882] , + [6.36569, -1.21018, -1.66282] , + [5.83469, -1.37018, -0.318824] , + [7.00969, -1.45018, 0.678176] , + [4.84269, -0.296176, 0.126176] , + [3.77369, -0.596176, 0.648176] , + [5.15669, 0.991824, -0.113824] , + [4.27869, 2.10682, 0.190176] , + [5.03669, 3.42282, -0.0748235] , + [2.96669, 2.09282, -0.596824] , + [1.89969, 2.39182, -0.0678235] , + [3.01469, 1.69682, -1.88382] , + [1.84869, 1.57082, -2.73482] , + [2.30269, 1.40782, -4.19882] , + [0.962686, 0.399824, -2.31982] , + [-0.255314, 0.522824, -2.22882] , + [1.57569, -0.758176, -2.00882] , + [0.900686, -1.92218, -1.46882] , + [1.91969, -3.07218, -1.33582] , + [0.223686, -1.65518, -0.123824] , + [-0.930314, -2.01818, 0.0891765] , + [0.918686, -0.964176, 0.800176] , + [0.372686, -0.514176, 2.06618] , + [1.49069, 0.164824, 2.88418] , + [-0.814314, 0.435824, 1.92118] , + [-1.84631, 0.257824, 2.56118] , + [-0.707314, 1.45482, 1.04518] , + [-1.78431, 2.37982, 0.745176] , + [-1.24331, 3.48882, -0.178824] , + [-3.00931, 1.72082, 0.109176] , + [-4.14731, 2.02882, 0.455176] , + [-2.80331, 0.769824, -0.821824] , + [-3.86731, -0.00917647, -1.42282], + [-3.28731, -0.820176, -2.59882] , + [-4.57231, -0.946176, -0.440824] , + [-5.78931, -1.10018, -0.475824] , + [-3.81431, -1.58718, 0.469176] , + [-4.35131, -2.44718, 1.50418] , + [-3.19331, -3.25818, 2.12018] , + [-5.10031, -1.70118, 2.61018] , + [-6.15131, -2.13818, 3.07218] , + [-6.33131, 1.19882, 3.62918] , + [-7.08531, 1.74482, 4.44018] , + [-6.45431, 1.44382, 2.30618] , + [-4.56431, -0.557176, 3.07518] , + [-5.19131, 0.240824, 4.11318] , + [-4.10131, 1.05882, 4.83518]], dtype=torch.float64) + +# fitting_group = atom_positions +# main_group = atom_positions[[0, 1, 2, 3]] + + +def get_optimal_rotation(fitting_atoms: torch.tensor, reference_atoms: torch.tensor): + fitting_atoms_centered = fitting_atoms - fitting_atoms.mean(dim=0) + reference_atoms_centered = reference_atoms - reference_atoms.mean(dim=0) + mat_R = torch.linalg.matmul(fitting_atoms_centered.T, reference_atoms_centered) + F00 = mat_R[0][0] + mat_R[1][1] + mat_R[2][2] + F01 = mat_R[1][2] - mat_R[2][1] + F02 = mat_R[2][0] - mat_R[0][2] + F03 = mat_R[0][1] - mat_R[1][0] + F10 = F01 + F11 = mat_R[0][0] - mat_R[1][1] - mat_R[2][2] + F12 = mat_R[0][1] + mat_R[1][0] + F13 = mat_R[0][2] + mat_R[2][0] + F20 = F02 + F21 = F12 + F22 = -mat_R[0][0] + mat_R[1][1] - mat_R[2][2] + F23 = mat_R[1][2] + mat_R[2][1] + F30 = F03 + F31 = F13 + F32 = F23 + F33 = -mat_R[0][0] - mat_R[1][1] + mat_R[2][2] + row0 = torch.stack((F00, F01, F02, F03)) + row1 = torch.stack((F10, F11, F12, F13)) + row2 = torch.stack((F20, F21, F22, F23)) + row3 = torch.stack((F30, F31, F32, F33)) + F = torch.stack((row0, row1, row2, row3)) + w, v = torch.linalg.eigh(F) + q = v[:, -1] + R00 = q[0] * q[0] + q[1] * q[1] - q[2] * q[2] - q[3] * q[3] + R01 = 2.0 * (q[1] * q[2] - q[0] * q[3]) + R02 = 2.0 * (q[1] * q[3] + q[0] * q[2]) + R10 = 2.0 * (q[1] * q[2] + q[0] * q[3]) + R11 = q[0] * q[0] - q[1] * q[1] + q[2] * q[2] - q[3] * q[3] + R12 = 2.0 * (q[2] * q[3] - q[0] * q[1]) + R20 = 2.0 * (q[1] * q[3] - q[0] * q[2]) + R21 = 2.0 * (q[2] * q[3] + q[0] * q[1]) + R22 = q[0] * q[0] - q[1] * q[1] - q[2] * q[2] + q[3] * q[3] + row0 = torch.stack((R00, R01, R02)) + row1 = torch.stack((R10, R11, R12)) + row2 = torch.stack((R20, R21, R22)) + R = torch.stack((row0, row1, row2)) + return w, v, R + + +def test(force, main_group, fitting_group): + # Using all atoms as the fitting group + w, v, R = get_optimal_rotation(fitting_group, ref_fitting_group) + main_group_centered = main_group - main_group.mean(dim=0) + ref_main_group_centered = ref_main_group - ref_main_group.mean(dim=0) + # Rotate the main group + main_group_r = (R @ main_group_centered.T).T + # main_group_r.register_hook(set_grad(main_group_r)) + w2, v2, R2 = get_optimal_rotation(ref_main_group_centered, main_group_r) + q = v2[:, -1] + ref_quat = torch.tensor([1.0, 0.0, 0.0, 0.0], dtype=torch.float64) + q_inner_ref_quat = torch.sum(ref_quat * q) + if (q_inner_ref_quat > 0): + final_q = q + else: + final_q = -1.0 * q + # print('Orientation:\n', final_q) + # Force on q + # force = torch.tensor([3.40697e-06, -8.24548e-05, -5.71708e-05, 5.95895e-05], dtype=torch.float64) + # Apply force + # torch.sum(force * final_q).backward() + (force[0] * final_q[0]).backward(retain_graph=True) + (force[1] * final_q[1]).backward(retain_graph=True) + (force[2] * final_q[2]).backward(retain_graph=True) + (force[3] * final_q[3]).backward(retain_graph=True) + # print('main group force:\n', main_group.grad) + # print('main group (rotated) force:\n', main_group_r.grad) + # print('fitting group force:\n', fitting_group.grad) + return main_group.grad.cpu().detach().numpy(), fitting_group.grad.cpu().detach().numpy() + + +def read_data_from_traj(filename): + main_group_positions = [] + fitting_group_positions = [] + forces = [] + with open(filename, 'r') as f_input: + for line in f_input: + s = line.strip() + if s.startswith('#'): + # skip comment lines + continue + if len(s) > 0: + # skip empty lines + # match the data in parentheses + result = re.findall(r'\(([^)]+)\)', s) + # get the force applied on the orientation + forces.append(torch.tensor(list(map(float, result[1].split(','))), dtype=torch.float64)) + # get the main group position + tmp = np.array(list(map(float, result[2].split(',')))).reshape(-1, 3) + main_group_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + # get the fitting group position + tmp = np.array(list(map(float, result[3].split(',')))).reshape(-1, 3) + fitting_group_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + return forces, main_group_positions, fitting_group_positions + + +def scan_force_from_log(filename): + main_group_forces = [] + fitting_group_forces = [] + with open(filename, 'r') as f_input: + new_main_group_started = False + main_group_force = [] + new_fitting_group_started = False + fitting_group_force = [] + for line in f_input: + if new_main_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + main_group_force.append(list(map(float, result[0].split(',')))) + else: + new_main_group_started = False + main_group_forces.append(np.array(main_group_force)) + main_group_force = [] + if new_fitting_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + fitting_group_force.append(list(map(float, result[0].split(',')))) + else: + new_fitting_group_started = False + fitting_group_forces.append(np.array(fitting_group_force)) + fitting_group_force = [] + if line.startswith('colvars: Applying force on the fitting group of main group:'): + new_fitting_group_started = True + continue + if line.startswith('colvars: Applying force on main group'): + new_main_group_started = True + continue + return main_group_forces, fitting_group_forces + + +if __name__ == '__main__': + print('Compare AutoDiff/test.colvars.traj and AutoDiff/test.colvars.out') + # read positions from Colvars traj + forces, main_group_positions, fitting_group_positions = read_data_from_traj('AutoDiff/test.colvars.traj') + main_group_forces_pytorch = [] + fitting_group_forces_pytorch = [] + # calculate the forces by pytorch + for f, pm, pf in zip(forces, main_group_positions, fitting_group_positions): + f1, f2 = test(f, pm, pf) + main_group_forces_pytorch.append(f1) + fitting_group_forces_pytorch.append(f2) + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.colvars.out') + # compare the force (calculate the relative error) + for i in range(len(main_group_forces_colvars)): + error_main = np.mean(np.abs(main_group_forces_colvars[i] - main_group_forces_pytorch[i]) / np.abs(main_group_forces_colvars[i])) + error_fitting = np.mean(np.abs(fitting_group_forces_colvars[i] - fitting_group_forces_pytorch[i]) / np.abs(fitting_group_forces_colvars[i])) + print(f'Frame {i}: error of the main group forces {error_main:12.5e} , fitting group forces {error_fitting:12.5e}') + + # Do the same thing with the restart file + print('Compare AutoDiff/test.restart.colvars.traj and AutoDiff/test.restart.colvars.out') + forces, main_group_positions, fitting_group_positions = read_data_from_traj('AutoDiff/test.restart.colvars.traj') + main_group_forces_pytorch = [] + fitting_group_forces_pytorch = [] + # calculate the forces by pytorch + for f, pm, pf in zip(forces, main_group_positions, fitting_group_positions): + f1, f2 = test(f, pm, pf) + main_group_forces_pytorch.append(f1) + fitting_group_forces_pytorch.append(f2) + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.restart.colvars.out') + # compare the force (calculate the relative error) + for i in range(len(main_group_forces_colvars)): + error_main = np.mean(np.abs(main_group_forces_colvars[i] - main_group_forces_pytorch[i]) / np.abs(main_group_forces_colvars[i])) + error_fitting = np.mean(np.abs(fitting_group_forces_colvars[i] - fitting_group_forces_pytorch[i]) / np.abs(fitting_group_forces_colvars[i])) + print(f'Frame {i}: error of the main group forces {error_main:12.5e} , fitting group forces {error_fitting:12.5e}') diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in index 6ea85dcd3..68d8433c9 100644 --- a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in @@ -22,7 +22,25 @@ colvar { } refPositionsFile rmsd_atoms_refpos.xyz } -} +} + +colvar { + name main + cartesian { + atoms { + indexGroup RMSD_atoms + } + } +} + +colvar { + name fitting + cartesian { + atoms { + indexGroup heavy_atoms + } + } +} harmonic { colvars one From daca4bfcba99ee07a9186360b2a951def74ae0e4 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Sun, 6 Oct 2024 17:39:50 -0500 Subject: [PATCH 11/14] fix: fix the bug introduced in #541 This commit aims to fix the incorrect optimization introduced in commit adebdf61f492a3cdde659ba41b67523f48e152a5. --- src/colvaratoms.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 0b939cf34..917e0397a 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1251,7 +1251,7 @@ void cvm::atom_group::calc_fit_forces_impl( atom_grad += accessor_main(i); if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); } else { - if (B_ag_rotate) pos_orig = atoms[i].pos; + if (B_ag_rotate) pos_orig = rot_inv * atoms[i].pos; } if (B_ag_rotate) { // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i From b61dabdc48de26dc2c2609575767382fcea7040f Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 11 Oct 2024 16:20:25 -0500 Subject: [PATCH 12/14] test: update the test data after #724 --- .../AutoDiff/test.colvars.out | 9359 +++++++++++----- .../AutoDiff/test.colvars.state.stripped | 17 +- .../AutoDiff/test.colvars.traj | 44 +- .../AutoDiff/test.restart.colvars.out | 9422 ++++++++++++----- .../test.restart.colvars.state.stripped | 17 +- .../AutoDiff/test.restart.colvars.traj | 44 +- .../compare_with_pytorch.py | 262 + .../namd-version.txt | 4 +- .../test.in | 32 +- 9 files changed, 13693 insertions(+), 5508 deletions(-) create mode 100644 namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out index 315994e09..56e5917b5 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out @@ -5,6 +5,7 @@ colvars: as well as all other papers listed below for individual features used. colvars: This version was built with the C++11 standard or higher. colvars: Summary of compile-time features available in this build: colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Multiple replicas: enabled (replica number 1 of 1) colvars: - Lepton custom functions: available colvars: - Tcl interpreter: available colvars: Called colvarcript::init_commands() @@ -755,6 +756,7 @@ colvars: name one colvars: outputAppliedForce on colvars: width 0.5 colvars: distanceDir { +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -816,6 +818,7 @@ colvars: Looking for the keyword "distance" and its value. colvars: Keyword "distance" not found. colvars: Looking for the keyword "distanceDir" and its value. colvars: Keyword value = " +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -837,6 +840,7 @@ colvars: } colvars: ". colvars: Initializing a new "distanceDir" component, with configuration: colvars: +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -893,8 +897,10 @@ colvars: Keyword "forceNoPBC" not found. colvars: # forceNoPBC = off [default] colvars: DEPS: unnamed cvc of type "distanceDir" enabling "use_minimum-image_with_PBCs" colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword value = "off". +colvars: Looking for the keyword "scalable" and its value. colvars: Keyword "scalable" not found. -colvars: # scalable = on [default] +colvars: # scalable = off colvars: Done initializing cvc base object. colvars: Looking for the keyword "group1" and its value. colvars: Keyword value = " @@ -906,17 +912,6 @@ colvars: indexGroup heavy_atoms colvars: } colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: ". -colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" -colvars: scalable_calculation_of_centers_of_mass requires exclude explicit_gradient -colvars: scalable_calculation_of_centers_of_mass requires self scalable_calculation -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation" -colvars: scalable_calculation requires exclude explicit_gradient -colvars: DEPS: feature "scalable_calculation" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. -colvars: scalable_calculation_of_centers_of_mass requires self function_of_centers_of_mass -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "function_of_centers_of_mass" -colvars: DEPS: bumping ref_count to 1 -colvars: DEPS: feature "scalable_calculation_of_centers_of_mass" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. colvars: Initializing atom group "group1". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. @@ -1137,8 +1132,6 @@ colvars: indexGroup heavy_atoms colvars: } colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: ". -colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" colvars: Initializing atom group "group2". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. @@ -1198,29 +1191,1044 @@ colvars: Looking for the keyword "fittingGroup" and its value. colvars: Keyword value = " colvars: indexGroup heavy_atoms colvars: ". -colvars: Within atom group "group2": -colvars: Initializing atom group "fittingGroup". +colvars: Within atom group "group2": +colvars: Initializing atom group "fittingGroup". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group group2 enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: atom group "group2" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group group2 enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group group2 enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group group2 enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "group2". +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" +colvars: Configuration string for "group2": " +colvars: +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "oneSiteSystemForce" and its value. +colvars: Keyword "oneSiteSystemForce" not found. +colvars: # oneSiteSystemForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Looking for the keyword "oneSiteTotalForce" and its value. +colvars: Keyword "oneSiteTotalForce" not found. +colvars: # oneSiteTotalForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Configuration string for "distanceDir": " +colvars: +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group1 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group1" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group1 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group1 +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group1 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group1 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group1 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group1 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group1 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group1 +colvars: DEPS: colvar group1 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group1 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group1 testing "linear" +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group1". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group2" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group2 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group2" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group2 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group2 +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: feature "linear" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group2 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group2 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group2 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group2 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group2 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group2 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group2 +colvars: DEPS: colvar group2 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group2 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group2 testing "linear" +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group2". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting_group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. colvars: # name = "" [default] colvars: Looking for the keyword "centerToOrigin" and its value. colvars: Keyword "centerToOrigin" not found. colvars: # centerToOrigin = off [default] -colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms colvars: Looking for the keyword "centerReference" and its value. colvars: Keyword "centerReference" not found. -colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms colvars: Looking for the keyword "centerToReference" and its value. colvars: Keyword "centerToReference" not found. colvars: # centerToReference = off [default] -colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms colvars: Looking for the keyword "rotateReference" and its value. colvars: Keyword "rotateReference" not found. -colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms colvars: Looking for the keyword "rotateToReference" and its value. colvars: Keyword "rotateToReference" not found. colvars: # rotateToReference = off [default] -colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms colvars: Looking for the keyword "atomsOfGroup" and its value. colvars: Keyword "atomsOfGroup" not found. colvars: # atomsOfGroup = "" [default] @@ -1252,81 +2260,47 @@ colvars: # enableFitGradients = on [default] colvars: Looking for the keyword "printAtomIDs" and its value. colvars: Keyword "printAtomIDs" not found. colvars: # printAtomIDs = off [default] -colvars: Done initializing atom group "fittingGroup". -colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. -colvars: Configuration string for "fittingGroup": " -colvars: -colvars: indexGroup heavy_atoms -colvars: ". -colvars: DEPS: atom group group2 enabling "fitting_group" -colvars: DEPS: feature "fitting_group" in atom group group2 enabled, ref_count = 1. -colvars: Looking for the keyword "refPositions" and its value. -colvars: Keyword "refPositions" not found. -colvars: # refPositions = [default] -colvars: Looking for the keyword "refPositionsFile" and its value. -colvars: Keyword value = "heavy_atoms_refpos.xyz". -colvars: Looking for the keyword "refPositionsFile" and its value. -colvars: Keyword "refPositionsFile" not found. -colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" -colvars: Looking for the keyword "refPositionsCol" and its value. -colvars: Keyword "refPositionsCol" not found. -colvars: # refPositionsCol = "" [default] -colvars: Warning: atom group "group2" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. -colvars: Looking for the keyword "enableFitGradients" and its value. -colvars: Keyword "enableFitGradients" not found. -colvars: # enableFitGradients = on [default] -colvars: DEPS: atom group group2 enabling "fit_gradients" -colvars: fit_gradients requires self explicit_atom_gradient -colvars: DEPS: atom group group2 enabling "explicit_atom_gradient" -colvars: DEPS: feature "explicit_atom_gradient" in atom group group2 enabled, ref_count = 1. -colvars: DEPS: feature "fit_gradients" in atom group group2 enabled, ref_count = 1. -colvars: Looking for the keyword "printAtomIDs" and its value. -colvars: Keyword "printAtomIDs" not found. -colvars: # printAtomIDs = off [default] -colvars: Done initializing atom group "group2". -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" -colvars: Configuration string for "group2": " +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " colvars: -colvars: indexGroup group2 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: indexGroup heavy_atoms colvars: ". -colvars: Looking for the keyword "oneSiteSystemForce" and its value. -colvars: Keyword "oneSiteSystemForce" not found. -colvars: # oneSiteSystemForce = off [default] -colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" -colvars: Looking for the keyword "oneSiteTotalForce" and its value. -colvars: Keyword "oneSiteTotalForce" not found. -colvars: # oneSiteTotalForce = off [default] -colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" -colvars: Configuration string for "distanceDir": " -colvars: -colvars: group1 { -colvars: indexGroup group1 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz -colvars: } -colvars: group2 { -colvars: indexGroup group2 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms colvars: } colvars: ". -colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Done initializing a "cartesian" component, named "cartesian0001". colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. colvars: Looking for the keyword "distanceDir" and its value. colvars: Keyword "distanceDir" not found. colvars: Looking for the keyword "distanceInv" and its value. @@ -1394,42 +2368,40 @@ colvars: Looking for the keyword "customFunction" and its value. colvars: Keyword "customFunction" not found. colvars: Looking for the keyword "scriptedFunction" and its value. colvars: Keyword "scriptedFunction" not found. -colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. -colvars: DEPS: disabling feature "scalar" in colvar one -colvars: DEPS: colvar one enabling "linear" -colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. -colvars: DEPS: colvar one enabling "homogeneous" -colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. -colvars: DEPS: colvar one enabling "single_component" -colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting_group1 enabled, ref_count = 1. colvars: Looking for the keyword "timeStepFactor" and its value. colvars: Keyword "timeStepFactor" not found. colvars: # timeStepFactor = 1 [default] colvars: Looking for the keyword "width" and its value. -colvars: Keyword value = "0.5". -colvars: Looking for the keyword "width" and its value. colvars: Keyword "width" not found. -colvars: # width = 0.5 +colvars: # width = 1 [default] colvars: Looking for the keyword "hardLowerBoundary" and its value. colvars: Keyword "hardLowerBoundary" not found. colvars: # hardLowerBoundary = off [default] -colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting_group1 colvars: Looking for the keyword "hardUpperBoundary" and its value. colvars: Keyword "hardUpperBoundary" not found. colvars: # hardUpperBoundary = off [default] -colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting_group1 colvars: Looking for the keyword "expandBoundaries" and its value. colvars: Keyword "expandBoundaries" not found. colvars: # expandBoundaries = off [default] colvars: Looking for the keyword "extendedLagrangian" and its value. colvars: Keyword "extendedLagrangian" not found. colvars: # extendedLagrangian = off [default] -colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting_group1 colvars: Looking for the keyword "outputValue" and its value. colvars: Keyword "outputValue" not found. colvars: # outputValue = on [default] -colvars: DEPS: colvar one enabling "output_value" -colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting_group1 enabled, ref_count = 1. colvars: Looking for the keyword "outputVelocity" and its value. colvars: Keyword "outputVelocity" not found. colvars: # outputVelocity = off [default] @@ -1438,63 +2410,43 @@ colvars: Keyword "outputSystemForce" not found. colvars: Looking for the keyword "outputTotalForce" and its value. colvars: Keyword "outputTotalForce" not found. colvars: # outputTotalForce = off [default] -colvars: DEPS: disabling feature "output_total_force" in colvar one -colvars: Looking for the keyword "outputAppliedForce" and its value. -colvars: Keyword value = "on". +colvars: DEPS: disabling feature "output_total_force" in colvar fitting_group1 colvars: Looking for the keyword "outputAppliedForce" and its value. colvars: Keyword "outputAppliedForce" not found. -colvars: # outputAppliedForce = on -colvars: DEPS: colvar one enabling "output_applied_force" -colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting_group1 colvars: Looking for the keyword "subtractAppliedForce" and its value. colvars: Keyword "subtractAppliedForce" not found. colvars: # subtractAppliedForce = off [default] -colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one -colvars: DEPS: colvar one enabling "active" +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "active" colvars: active requires alt scalar -colvars: DEPS: colvar one testing "scalar" +colvars: DEPS: colvar fitting_group1 testing "scalar" colvars: active requires alt linear -colvars: DEPS: colvar one testing "linear" -colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: colvar fitting_group1 testing "linear" +colvars: DEPS: colvar fitting_group1 enabling "linear" colvars: DEPS: bumping ref_count to 1 -colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: DEPS: feature "active" in colvar fitting_group1 enabled, ref_count = 1. colvars: Looking for the keyword "runAve" and its value. colvars: Keyword "runAve" not found. colvars: # runAve = off [default] colvars: Looking for the keyword "corrFunc" and its value. colvars: Keyword "corrFunc" not found. colvars: # corrFunc = off [default] -colvars: Done initializing collective variable "one". +colvars: Done initializing collective variable "fitting_group1". colvars: Configuration string for "colvar": " colvars: -colvars: name one -colvars: outputAppliedForce on -colvars: width 0.5 -colvars: distanceDir { -colvars: group1 { -colvars: indexGroup group1 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz -colvars: } -colvars: group2 { -colvars: indexGroup group2 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms colvars: } colvars: } colvars: ". colvars: Looking for the keyword "colvar" and its value. colvars: Keyword "colvar" not found. colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. +colvars: Collective variables initialized, 4 in total. colvars: Initializing the collective variables biases. colvars: Looking for the keyword "abf" and its value. colvars: Keyword "abf" not found. @@ -1507,6 +2459,7 @@ colvars: Keyword value = " colvars: colvars one colvars: centers (1.0, 0.1, 0.2) colvars: forceConstant 10.0 +colvars: outputEnergy on colvars: ". colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. @@ -1524,8 +2477,10 @@ colvars: Keyword "stepZeroData" not found. colvars: # stepZeroData = off [default] colvars: DEPS: disabling feature "step_zero_data" in bias harmonic1 colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputEnergy" and its value. colvars: Keyword "outputEnergy" not found. -colvars: # outputEnergy = off [default] +colvars: # outputEnergy = on colvars: Looking for the keyword "outputFreq" and its value. colvars: Keyword "outputFreq" not found. colvars: # outputFreq = 10 [default] @@ -1615,9 +2570,9 @@ colvars: - Jacobian_derivative colvars: - total_force_from_one_group colvars: - debug_gradient colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - ON function_of_centers_of_mass +colvars: - scalable_calculation +colvars: - scalable_calculation_of_centers_of_mass colvars: - collect_atom_ids colvars: * child 1 colvars: Features of "atom group group1" (refcount) @@ -1690,6 +2645,7 @@ colvars: colvars: colvars one colvars: centers (1.0, 0.1, 0.2) colvars: forceConstant 10.0 +colvars: outputEnergy on colvars: ". colvars: Looking for the keyword "harmonic" and its value. colvars: Keyword "harmonic" not found. @@ -1716,6 +2672,7 @@ colvars: name one colvars: outputAppliedForce on colvars: width 0.5 colvars: distanceDir { +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -1735,11 +2692,36 @@ colvars: } colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: } colvars: } -colvars: } +colvars: } +colvars: colvar { +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } colvars: harmonic { colvars: colvars one colvars: centers (1.0, 0.1, 0.2) colvars: forceConstant 10.0 +colvars: outputEnergy on colvars: } colvars: ". colvars: ---------------------------------------------------------------------- @@ -1757,6 +2739,7 @@ colvars: - Colvars-NAMD interface: colvars: - Harmonic colvar bias implementation: colvars: - Moving frame of reference: colvars: - Optimal rotation via flexible fitting: +colvars: - cartesian colvar component: colvars: - distance colvar component: colvars: - distanceDir colvar component (derived from distance): colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 @@ -1774,6 +2757,9 @@ colvars: Current simulation parameters: initial step = 0, integration timestep = colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "group1":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "group2":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "fitting_group1":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: ---------------------------------------------------------------------- colvars: colvarproxy_namd, step no. 0 @@ -1783,7 +2769,7 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 0, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 0, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 0, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 0, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 0, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } colvars: Step 0, atoms_positions[size = 51] = { ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 ), ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 ), ( 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 ), ( 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ), ( 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 ), ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 ), ( 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 ), ( 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 ), ( 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 ), ( 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ), ( 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 ), ( 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 ), ( 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 ), ( 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 ), ( 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 ), ( 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 ), ( 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 ), ( 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 ), ( 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 ), ( 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 ), ( 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 ), ( 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 ), ( 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 ), ( 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 ), ( -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 ), ( 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 ), ( 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 ), ( 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 ), ( -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 ), ( -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 ), ( -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 ), ( -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 ), ( -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 ), ( -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 ), ( -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 ), ( -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 ), ( -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 ), ( -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 ), ( -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 ), ( -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 ), ( -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 ), ( -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 ), ( -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 ), ( -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 ), ( -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 ), ( -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 ), ( -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 ), ( -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 ), ( -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 ), ( -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ), ( -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) } @@ -1805,153 +2791,289 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". colvars: Colvar component no. 1 within colvar "one" has value ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ). +colvars: Calculating colvar components. colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. colvars: Colvar "one" has value ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.3141 , 1.79667 , -14.9057 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.8285 , 6.78285 , 13.5657 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.3141 , 1.79667 , -14.9057 ) to colvar "one". -colvars: Adding total bias energy: 45.892 +colvars: Adding biasing force ( 67.8285 , 6.78285 , 13.5657 ) to colvar "one". +colvars: Adding total bias energy: 59.0741 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.3141 , 1.79667 , -14.9057 ) +colvars: Force to be applied: ( 67.8285 , 6.78285 , 13.5657 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.83605 , -0.57345 , -1.60798 ) -colvars: ( -4.14691 , -0.491734 , -1.37884 ) -colvars: ( -4.14691 , -0.491734 , -1.37884 ) -colvars: ( -5.5238 , -0.655003 , -1.83666 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.24283 , -0.621686 , -1.74324 ) +colvars: ( -4.49572 , -0.533095 , -1.49482 ) +colvars: ( -4.49572 , -0.533095 , -1.49482 ) +colvars: ( -5.98843 , -0.710098 , -1.99115 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.904449 , 0.192195 , 0.652965 ) -colvars: ( 0.781455 , 0.264196 , 0.679172 ) -colvars: ( 0.767414 , 0.256567 , 0.660103 ) -colvars: ( 0.665192 , 0.266597 , 0.612546 ) -colvars: ( 0.652998 , 0.200174 , 0.512746 ) -colvars: ( 0.575103 , 0.345124 , 0.667639 ) -colvars: ( 0.463397 , 0.360776 , 0.622201 ) -colvars: ( 0.383597 , 0.459129 , 0.711085 ) -colvars: ( 0.380393 , 0.316766 , 0.510988 ) -colvars: ( 0.343708 , 0.275912 , 0.432042 ) -colvars: ( 0.352206 , 0.321644 , 0.500814 ) -colvars: ( 0.280154 , 0.279134 , 0.398279 ) -colvars: ( 0.254339 , 0.307672 , 0.422468 ) -colvars: ( 0.345014 , 0.180479 , 0.299985 ) -colvars: ( 0.284533 , 0.137844 , 0.204238 ) -colvars: ( 0.471912 , 0.141938 , 0.322704 ) -colvars: ( 0.547075 , 0.0496465 , 0.239467 ) -colvars: ( 0.681454 , 0.0269033 , 0.288679 ) -colvars: ( 0.553916 , 0.0184719 , 0.200189 ) -colvars: ( 0.53773 , -0.0463997 , 0.100148 ) -colvars: ( 0.573618 , 0.0668172 , 0.279343 ) -colvars: ( 0.56998 , 0.0514399 , 0.255748 ) -colvars: ( 0.605964 , 0.116347 , 0.367755 ) -colvars: ( 0.441227 , 0.0575265 , 0.186736 ) -colvars: ( 0.433486 , 0.00196018 , 0.10473 ) -colvars: ( 0.336494 , 0.12415 , 0.216447 ) -colvars: ( 0.207874 , 0.134227 , 0.15307 ) -colvars: ( 0.114014 , 0.220808 , 0.217104 ) -colvars: ( 0.180185 , 0.0603279 , 0.0335389 ) -colvars: ( 0.128667 , 0.0249964 , -0.0466463 ) -colvars: ( 0.216875 , 0.0336433 , 0.0184743 ) -colvars: ( 0.203893 , -0.0392063 , -0.0907449 ) -colvars: ( 0.242516 , -0.0437657 , -0.0738479 ) -colvars: ( 0.280911 , -0.125759 , -0.164876 ) -colvars: ( 0.235718 , -0.178415 , -0.265371 ) -colvars: ( 0.39894 , -0.141798 , -0.116172 ) -colvars: ( 0.478044 , -0.217851 , -0.174433 ) -colvars: ( 0.61295 , -0.221787 , -0.0987231 ) -colvars: ( 0.427261 , -0.221063 , -0.209465 ) -colvars: ( 0.432715 , -0.289069 , -0.300847 ) -colvars: ( 0.375506 , -0.146693 , -0.137089 ) -colvars: ( 0.317642 , -0.139121 , -0.161371 ) -colvars: ( 0.299087 , -0.0517292 , -0.0508885 ) -colvars: ( 0.190821 , -0.146631 , -0.248146 ) -colvars: ( 0.164689 , -0.187988 , -0.321443 ) -colvars: ( -0.0132844 , -0.191347 , -0.433224 ) -colvars: ( -0.106835 , -0.20819 , -0.512969 ) -colvars: ( 0.0914093 , -0.242821 , -0.441871 ) -colvars: ( 0.107821 , -0.105612 , -0.240998 ) -colvars: ( -0.0147712 , -0.108801 , -0.319215 ) -colvars: ( -0.105785 , -0.0274413 , -0.260735 ) +colvars: ( 0.980525 , 0.208361 , 0.707889 ) +colvars: ( 0.847187 , 0.286419 , 0.7363 ) +colvars: ( 0.831964 , 0.278148 , 0.715627 ) +colvars: ( 0.721144 , 0.289021 , 0.66407 ) +colvars: ( 0.707924 , 0.217011 , 0.555875 ) +colvars: ( 0.623477 , 0.374153 , 0.723797 ) +colvars: ( 0.502375 , 0.391122 , 0.674537 ) +colvars: ( 0.415863 , 0.497748 , 0.770897 ) +colvars: ( 0.41239 , 0.343411 , 0.553969 ) +colvars: ( 0.372619 , 0.29912 , 0.468382 ) +colvars: ( 0.381832 , 0.348698 , 0.54294 ) +colvars: ( 0.303719 , 0.302613 , 0.43178 ) +colvars: ( 0.275733 , 0.333551 , 0.458004 ) +colvars: ( 0.374035 , 0.19566 , 0.325218 ) +colvars: ( 0.308466 , 0.149439 , 0.221418 ) +colvars: ( 0.511606 , 0.153877 , 0.349848 ) +colvars: ( 0.593091 , 0.0538224 , 0.25961 ) +colvars: ( 0.738774 , 0.0291662 , 0.312961 ) +colvars: ( 0.600507 , 0.0200257 , 0.217028 ) +colvars: ( 0.582961 , -0.0503026 , 0.108571 ) +colvars: ( 0.621867 , 0.0724375 , 0.30284 ) +colvars: ( 0.617923 , 0.0557667 , 0.27726 ) +colvars: ( 0.656934 , 0.126134 , 0.398688 ) +colvars: ( 0.47834 , 0.0623652 , 0.202443 ) +colvars: ( 0.469948 , 0.00212506 , 0.113539 ) +colvars: ( 0.364797 , 0.134592 , 0.234653 ) +colvars: ( 0.225359 , 0.145517 , 0.165945 ) +colvars: ( 0.123604 , 0.239381 , 0.235366 ) +colvars: ( 0.195341 , 0.0654024 , 0.03636 ) +colvars: ( 0.13949 , 0.0270989 , -0.0505699 ) +colvars: ( 0.235117 , 0.0364732 , 0.0200283 ) +colvars: ( 0.221044 , -0.0425041 , -0.0983778 ) +colvars: ( 0.262915 , -0.0474471 , -0.0800596 ) +colvars: ( 0.30454 , -0.136337 , -0.178744 ) +colvars: ( 0.255545 , -0.193422 , -0.287693 ) +colvars: ( 0.432497 , -0.153726 , -0.125944 ) +colvars: ( 0.518254 , -0.236176 , -0.189105 ) +colvars: ( 0.664508 , -0.240442 , -0.107027 ) +colvars: ( 0.4632 , -0.239658 , -0.227084 ) +colvars: ( 0.469112 , -0.313383 , -0.326152 ) +colvars: ( 0.407091 , -0.159032 , -0.14862 ) +colvars: ( 0.34436 , -0.150822 , -0.174944 ) +colvars: ( 0.324244 , -0.0560804 , -0.055169 ) +colvars: ( 0.206872 , -0.158964 , -0.269019 ) +colvars: ( 0.178541 , -0.203801 , -0.348481 ) +colvars: ( -0.0144018 , -0.207442 , -0.469665 ) +colvars: ( -0.115821 , -0.225702 , -0.556117 ) +colvars: ( 0.0990981 , -0.263246 , -0.479038 ) +colvars: ( 0.11689 , -0.114495 , -0.26127 ) +colvars: ( -0.0160137 , -0.117953 , -0.346065 ) +colvars: ( -0.114683 , -0.0297495 , -0.282666 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.83605 , 0.57345 , 1.60798 ) -colvars: ( 4.14691 , 0.491734 , 1.37884 ) -colvars: ( 4.14691 , 0.491734 , 1.37884 ) -colvars: ( 5.5238 , 0.655003 , 1.83666 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.24283 , 0.621686 , 1.74324 ) +colvars: ( 4.49572 , 0.533095 , 1.49482 ) +colvars: ( 4.49572 , 0.533095 , 1.49482 ) +colvars: ( 5.98843 , 0.710098 , 1.99115 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.628624 , -0.0803095 , -0.404496 ) -colvars: ( -0.562979 , -0.162306 , -0.377749 ) -colvars: ( -0.517226 , -0.140683 , -0.3212 ) -colvars: ( -0.5184 , -0.190034 , -0.346132 ) -colvars: ( -0.50878 , -0.132262 , -0.30863 ) -colvars: ( -0.488908 , -0.281012 , -0.360168 ) -colvars: ( -0.450514 , -0.321339 , -0.340852 ) -colvars: ( -0.424599 , -0.427271 , -0.36569 ) -colvars: ( -0.387357 , -0.287046 , -0.260655 ) -colvars: ( -0.380307 , -0.262436 , -0.241701 ) -colvars: ( -0.340884 , -0.281609 , -0.211169 ) -colvars: ( -0.280874 , -0.245749 , -0.133392 ) -colvars: ( -0.235212 , -0.260495 , -0.094436 ) -colvars: ( -0.3036 , -0.143978 , -0.107338 ) -colvars: ( -0.270682 , -0.115574 , -0.0604717 ) -colvars: ( -0.362639 , -0.0868482 , -0.13939 ) -colvars: ( -0.392639 , 0.0101283 , -0.12298 ) -colvars: ( -0.448566 , 0.0577244 , -0.156481 ) -colvars: ( -0.426859 , 0.0248658 , -0.1504 ) -colvars: ( -0.415349 , 0.0805584 , -0.111992 ) -colvars: ( -0.467947 , -0.0281639 , -0.217356 ) -colvars: ( -0.49836 , -0.0296841 , -0.24876 ) -colvars: ( -0.546 , -0.0937884 , -0.327654 ) -colvars: ( -0.441259 , -0.0599455 , -0.205735 ) -colvars: ( -0.446751 , -0.0166987 , -0.190462 ) -colvars: ( -0.383423 , -0.133561 , -0.18283 ) -colvars: ( -0.321416 , -0.165078 , -0.13546 ) -colvars: ( -0.268688 , -0.25422 , -0.125177 ) -colvars: ( -0.282277 , -0.0936367 , -0.0616093 ) -colvars: ( -0.266256 , -0.0756726 , -0.0368075 ) -colvars: ( -0.267497 , -0.0492663 , -0.0253521 ) -colvars: ( -0.234777 , 0.0241484 , 0.042974 ) -colvars: ( -0.218877 , 0.0503727 , 0.0716291 ) -colvars: ( -0.280428 , 0.109829 , 0.0381639 ) -colvars: ( -0.2529 , 0.150602 , 0.0855471 ) -colvars: ( -0.352048 , 0.138136 , -0.0204457 ) -colvars: ( -0.402129 , 0.213447 , -0.034713 ) -colvars: ( -0.476749 , 0.236408 , -0.0989201 ) -colvars: ( -0.408333 , 0.193606 , -0.0505178 ) -colvars: ( -0.412792 , 0.253389 , -0.026247 ) -colvars: ( -0.408149 , 0.108199 , -0.0914308 ) -colvars: ( -0.409781 , 0.0781684 , -0.107528 ) -colvars: ( -0.427537 , -0.013667 , -0.169626 ) -colvars: ( -0.339772 , 0.0663524 , -0.0426067 ) -colvars: ( -0.340591 , 0.0920225 , -0.0310805 ) -colvars: ( -0.179083 , 0.0973929 , 0.134389 ) -colvars: ( -0.127239 , 0.098679 , 0.187293 ) -colvars: ( -0.211393 , 0.169106 , 0.136312 ) -colvars: ( -0.277077 , 0.025872 , 0.00114273 ) -colvars: ( -0.207386 , 0.0117805 , 0.064647 ) -colvars: ( -0.151761 , -0.0703734 , 0.0812133 ) +colvars: ( -0.6815 , -0.0870646 , -0.438519 ) +colvars: ( -0.610334 , -0.175958 , -0.409522 ) +colvars: ( -0.560732 , -0.152516 , -0.348217 ) +colvars: ( -0.562005 , -0.206019 , -0.375247 ) +colvars: ( -0.551575 , -0.143387 , -0.33459 ) +colvars: ( -0.530032 , -0.304649 , -0.390463 ) +colvars: ( -0.488409 , -0.348368 , -0.369523 ) +colvars: ( -0.460313 , -0.463211 , -0.39645 ) +colvars: ( -0.419939 , -0.311191 , -0.282579 ) +colvars: ( -0.412296 , -0.284511 , -0.262032 ) +colvars: ( -0.369557 , -0.305297 , -0.228931 ) +colvars: ( -0.3045 , -0.26642 , -0.144612 ) +colvars: ( -0.254997 , -0.282406 , -0.102379 ) +colvars: ( -0.329137 , -0.156089 , -0.116367 ) +colvars: ( -0.29345 , -0.125296 , -0.0655582 ) +colvars: ( -0.393142 , -0.0941533 , -0.151115 ) +colvars: ( -0.425665 , 0.0109803 , -0.133324 ) +colvars: ( -0.486297 , 0.0625799 , -0.169643 ) +colvars: ( -0.462764 , 0.0269574 , -0.163051 ) +colvars: ( -0.450285 , 0.0873345 , -0.121412 ) +colvars: ( -0.507307 , -0.0305329 , -0.235639 ) +colvars: ( -0.540279 , -0.032181 , -0.269684 ) +colvars: ( -0.591927 , -0.101677 , -0.355214 ) +colvars: ( -0.478375 , -0.0649877 , -0.22304 ) +colvars: ( -0.484329 , -0.0181032 , -0.206483 ) +colvars: ( -0.415674 , -0.144795 , -0.198208 ) +colvars: ( -0.348452 , -0.178964 , -0.146854 ) +colvars: ( -0.291288 , -0.275603 , -0.135706 ) +colvars: ( -0.30602 , -0.101513 , -0.0667915 ) +colvars: ( -0.288652 , -0.0820378 , -0.0399035 ) +colvars: ( -0.289997 , -0.0534103 , -0.0274846 ) +colvars: ( -0.254525 , 0.0261796 , 0.0465887 ) +colvars: ( -0.237288 , 0.0546097 , 0.0776541 ) +colvars: ( -0.304016 , 0.119067 , 0.041374 ) +colvars: ( -0.274172 , 0.16327 , 0.0927428 ) +colvars: ( -0.38166 , 0.149755 , -0.0221654 ) +colvars: ( -0.435953 , 0.231401 , -0.0376328 ) +colvars: ( -0.51685 , 0.256293 , -0.107241 ) +colvars: ( -0.44268 , 0.209891 , -0.0547671 ) +colvars: ( -0.447514 , 0.274703 , -0.0284547 ) +colvars: ( -0.44248 , 0.1173 , -0.0991214 ) +colvars: ( -0.44425 , 0.0847434 , -0.116572 ) +colvars: ( -0.463499 , -0.0148166 , -0.183894 ) +colvars: ( -0.368351 , 0.0719336 , -0.0461905 ) +colvars: ( -0.369239 , 0.0997629 , -0.0336948 ) +colvars: ( -0.194146 , 0.105585 , 0.145693 ) +colvars: ( -0.137942 , 0.106979 , 0.203047 ) +colvars: ( -0.229174 , 0.18333 , 0.147777 ) +colvars: ( -0.300383 , 0.0280482 , 0.00123885 ) +colvars: ( -0.22483 , 0.0127714 , 0.0700847 ) +colvars: ( -0.164527 , -0.0762928 , 0.0880445 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 0. colvars: colvarmodule::write_traj_files() @@ -1959,8 +3081,11 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: colvarmodule::end_of_step(), step = 0. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 0, atoms_new_colvar_forces = { ( -4.56022301351998e+00 , -4.61564888436068e-01 , -1.35951177988766e+00 ), ( -3.92843445711296e+00 , -3.89843112362469e-01 , -1.07742000515632e+00 ), ( -4.00011804015036e+00 , -4.15171281383325e-01 , -1.11243026024849e+00 ), ( -5.37958662474869e+00 , -5.87092156407929e-01 , -1.63254351293296e+00 ), ( 2.50188227787937e-01 , 1.15884548440611e-01 , 3.38902821897569e-01 ), ( 4.92224252104192e+00 , 6.37562353004536e-01 , 1.91545290434692e+00 ), ( 4.15979249713217e+00 , 5.31170028110173e-01 , 1.66019271046701e+00 ), ( -4.10013245486699e-02 , 3.18580111145642e-02 , 3.45394759111406e-01 ), ( 4.13994655920834e+00 , 5.21453476411363e-01 , 1.62917699767166e+00 ), ( 5.48720654003203e+00 , 6.68479365021477e-01 , 2.02700010370679e+00 ), ( 1.13228880308536e-02 , 4.00342907390078e-02 , 2.89645605122908e-01 ), ( -7.20125311565400e-04 , 3.33850914918679e-02 , 2.64887654827042e-01 ), ( 1.91272371136485e-02 , 4.71768859623820e-02 , 3.28032369661851e-01 ), ( 4.14145638066024e-02 , 3.65005871821940e-02 , 1.92646338795725e-01 ), ( 1.38509087206640e-02 , 2.22695518224478e-02 , 1.43766826482371e-01 ), ( 1.09272369395027e-01 , 5.50900822328472e-02 , 1.83313711879413e-01 ), ( 1.54435579943054e-01 , 5.97748101103748e-02 , 1.16487245422154e-01 ), ( 2.32887859519156e-01 , 8.46277010294356e-02 , 1.32198685408501e-01 ), ( 1.27056649533084e-01 , 4.33377389098029e-02 , 4.97892768769213e-02 ), ( 1.22381753985573e-01 , 3.41586847326240e-02 , -1.18445110129732e-02 ), ( 1.05671464855148e-01 , 3.86532894199961e-02 , 6.19869217567546e-02 ), ( 7.16203311743855e-02 , 2.17558192616861e-02 , 6.98849025123255e-03 ), ( 5.99640138968076e-02 , 2.25588560215600e-02 , 4.01011154373220e-02 ), ( -3.25542195704354e-05 , -2.41900197301183e-03 , -1.89984337550084e-02 ), ( -1.32647221593366e-02 , -1.47384674205409e-02 , -8.57328888562245e-02 ), ( -4.69295810825941e-02 , -9.41129292941427e-03 , 3.36169882557587e-02 ), ( -1.13541921192049e-01 , -3.08516894386112e-02 , 1.76094573558321e-02 ), ( -1.54674308412988e-01 , -3.34118168784681e-02 , 9.19268829537772e-02 ), ( -1.02091982823549e-01 , -3.33087248294972e-02 , -2.80703710993668e-02 ), ( -1.37588732745389e-01 , -5.06762598547442e-02 , -8.34537828360104e-02 ), ( -5.06218660559404e-02 , -1.56230283335258e-02 , -6.87781890768321e-03 ), ( -3.08839705592416e-02 , -1.50579525809766e-02 , -4.77709840365084e-02 ), ( 2.36395155405980e-02 , 6.60692129558478e-03 , -2.21885338022018e-03 ), ( 4.83354967454996e-04 , -1.59296729329767e-02 , -1.26712034451445e-01 ), ( -1.71815952692567e-02 , -2.78131275404488e-02 , -1.79824148452554e-01 ), ( 4.68922585797591e-02 , -3.66288751900909e-03 , -1.36617896790793e-01 ), ( 7.59151612564729e-02 , -4.40440718034790e-03 , -2.09145936861076e-01 ), ( 1.36201758070916e-01 , 1.46213983056402e-02 , -1.97643193338638e-01 ), ( 1.89282960943429e-02 , -2.74573869374166e-02 , -2.59983219655275e-01 ), ( 1.99223584509793e-02 , -3.56791693618768e-02 , -3.27093827759356e-01 ), ( -3.26432516920732e-02 , -3.84943911025121e-02 , -2.28519445694830e-01 ), ( -9.21394164551950e-02 , -6.09521307976269e-02 , -2.68898187169678e-01 ), ( -1.28449800819388e-01 , -6.53962493000429e-02 , -2.20514316951765e-01 ), ( -1.48950313055385e-01 , -8.02780675198336e-02 , -2.90752958515001e-01 ), ( -1.75902205718680e-01 , -9.59657763030266e-02 , -3.52523528143139e-01 ), ( -1.92367142029188e-01 , -9.39544201238159e-02 , -2.98835600202562e-01 ), ( -2.34073918659256e-01 , -1.09511474765624e-01 , -3.25676026667567e-01 ), ( -1.19983779327036e-01 , -7.37153221787298e-02 , -3.05559177101654e-01 ), ( -1.69256110911622e-01 , -7.97398200384644e-02 , -2.39855584707409e-01 ), ( -2.22157552370696e-01 , -9.70207445613183e-02 , -2.54568081838475e-01 ), ( -2.57546357186263e-01 , -9.78147696285256e-02 , -1.79521501278274e-01 ) } +colvars: Step 0, atoms_new_colvar_forces = { ( -4.94380109020736e+00 , -5.00388904640502e-01 , -1.47386559815863e+00 ), ( -4.25887034346859e+00 , -4.22634331302087e-01 , -1.16804598817012e+00 ), ( -4.33658351120613e+00 , -4.50092951033408e-01 , -1.20600109185253e+00 ), ( -5.83208455846301e+00 , -6.36474758865210e-01 , -1.76986309115155e+00 ), ( 2.71232531748555e-01 , 1.25632048086319e-01 , 3.67409255074628e-01 ), ( 5.33627146515550e+00 , 6.91190199802536e-01 , 2.07656909073876e+00 ), ( 4.50968880718936e+00 , 5.75848803067544e-01 , 1.79983797012281e+00 ), ( -4.44501052695659e-02 , 3.45377122156243e-02 , 3.74447254352333e-01 ), ( 4.48817355031418e+00 , 5.65314954451102e-01 , 1.76621340521082e+00 ), ( 5.94875680298447e+00 , 7.24707761830127e-01 , 2.19749895846013e+00 ), ( 1.22753001388897e-02 , 4.34017304887051e-02 , 3.14008822405178e-01 ), ( -7.80697849611267e-04 , 3.61932412570256e-02 , 2.87168384711426e-01 ), ( 2.07361033473052e-02 , 5.11451171492998e-02 , 3.55624446863570e-01 ), ( 4.48981036871490e-02 , 3.95707933953106e-02 , 2.08850570890745e-01 ), ( 1.50159624716962e-02 , 2.41427303559141e-02 , 1.55859612872436e-01 ), ( 1.18463692969193e-01 , 5.97239231052729e-02 , 1.98732940462020e-01 ), ( 1.67425756640778e-01 , 6.48027016473707e-02 , 1.26285440252794e-01 ), ( 2.52476962283068e-01 , 9.17460657890331e-02 , 1.43318430504137e-01 ), ( 1.37743878011550e-01 , 4.69830445208921e-02 , 5.39772464142627e-02 ), ( 1.32675758834949e-01 , 3.70319044311048e-02 , -1.28407988568328e-02 ), ( 1.14559902356933e-01 , 4.19045677827880e-02 , 6.72008825996200e-02 ), ( 7.76445955145584e-02 , 2.35857857533280e-02 , 7.57631932046199e-03 ), ( 6.50078200994428e-02 , 2.44563690553224e-02 , 4.34741760720458e-02 ), ( -3.52924814698841e-05 , -2.62247362813921e-03 , -2.05964658376968e-02 ), ( -1.43804694810325e-02 , -1.59781771824823e-02 , -9.29442152582067e-02 ), ( -5.08770104951550e-02 , -1.02029133458509e-02 , 3.64446437587760e-02 ), ( -1.23092373357461e-01 , -3.34467449133838e-02 , 1.90906572366346e-02 ), ( -1.67684565489913e-01 , -3.62222146197359e-02 , 9.96592102664404e-02 ), ( -1.10679336183364e-01 , -3.61104510979557e-02 , -3.04314790816462e-02 ), ( -1.49161855665883e-01 , -5.49388369767760e-02 , -9.04734047750292e-02 ), ( -5.48798679042043e-02 , -1.69371419508729e-02 , -7.45633898018655e-03 ), ( -3.34817413245006e-02 , -1.63245354811410e-02 , -5.17891871208446e-02 ), ( 2.56279270454741e-02 , 7.16265511734566e-03 , -2.40548975951840e-03 ), ( 5.24011831872395e-04 , -1.72695796190696e-02 , -1.37370276016371e-01 ), ( -1.86268060074735e-02 , -3.01525977674522e-02 , -1.94949856296420e-01 ), ( 5.08365486515878e-02 , -3.97098722060221e-03 , -1.48109358926904e-01 ), ( 8.23006804426702e-02 , -4.77487898187540e-03 , -2.26738014259551e-01 ), ( 1.47658217162366e-01 , 1.58512609294484e-02 , -2.14267730284841e-01 ), ( 2.05204286258686e-02 , -2.97669344400476e-02 , -2.81851418440884e-01 ), ( 2.15981054298106e-02 , -3.86802829304581e-02 , -3.54606960554895e-01 ), ( -3.53890024292071e-02 , -4.17323039104114e-02 , -2.47741104198243e-01 ), ( -9.98896207864740e-02 , -6.60790513521777e-02 , -2.91516258512565e-01 ), ( -1.39254212665718e-01 , -7.08969819297212e-02 , -2.39062632972191e-01 ), ( -1.61479102641855e-01 , -8.70305677041763e-02 , -3.15209319593768e-01 ), ( -1.90698023720256e-01 , -1.04037830628658e-01 , -3.82175651846584e-01 ), ( -2.08547889799338e-01 , -1.01857291465968e-01 , -3.23971823679259e-01 ), ( -2.53762785465945e-01 , -1.18722910421569e-01 , -3.53069902704324e-01 ), ( -1.30076081210408e-01 , -7.99158043524913e-02 , -3.31260946756196e-01 ), ( -1.83492900055176e-01 , -8.64470461357563e-02 , -2.60030769910419e-01 ), ( -2.40844087307098e-01 , -1.05181536366297e-01 , -2.75980792341469e-01 ), ( -2.79209582001028e-01 , -1.06042349967139e-01 , -1.94621752292357e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 0, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -1998,10 +3123,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 1, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 1, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 1, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 1, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 1, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 1, atoms_positions[size = 51] = { ( 8.42020860115927e+00 , 4.21991772440572e-02 , -7.45620320908196e-01 ), ( 7.00356168021470e+00 , -4.79961273240136e-01 , -6.79276268523547e-01 ), ( 6.23767829724485e+00 , -2.51247056733134e-01 , 6.26723013266982e-01 ), ( 5.02836760689927e+00 , -2.08045498598506e-01 , 6.39279949863210e-01 ), ( 7.03907190853467e+00 , -2.00682955930526e+00 , -1.03762126887887e+00 ), ( 6.90865762910286e+00 , -2.67402193238485e-01 , 1.77894374849930e+00 ), ( 6.18212607952751e+00 , -1.31162942641700e-01 , 3.03990487109687e+00 ), ( 7.19806650022761e+00 , -3.16977124704912e-01 , 4.30310525801892e+00 ), ( 5.30277106614921e+00 , 1.14009027458730e+00 , 3.26020429141508e+00 ), ( 4.09168799566628e+00 , 1.07931872502458e+00 , 3.60441862233567e+00 ), ( 5.87383598445601e+00 , 2.34423023509440e+00 , 2.94316659460719e+00 ), ( 5.23330840410800e+00 , 3.60157582019048e+00 , 2.87824077887178e+00 ), ( 6.32195899986517e+00 , 4.64361828650942e+00 , 2.47418830211963e+00 ), ( 3.90567262185191e+00 , 3.68544878849974e+00 , 2.03017213713226e+00 ), ( 2.93268290479868e+00 , 4.11879115223505e+00 , 2.57740403700341e+00 ), ( 3.81729626779150e+00 , 3.24363106424524e+00 , 7.83854251329338e-01 ), ( 2.65736293095857e+00 , 3.20810250854710e+00 , -6.18612205529565e-02 ), ( 3.04748223300176e+00 , 2.73697170209860e+00 , -1.57072865932818e+00 ), ( 1.65396529802342e+00 , 2.17247883063761e+00 , 5.62166269959855e-01 ), ( 4.23522803585828e-01 , 2.41894531818558e+00 , 5.75950510780766e-01 ), ( 1.99311747302112e+00 , 9.90200204878183e-01 , 1.06367245965403e+00 ), ( 1.11563866641463e+00 , 1.72485962153876e-02 , 1.68771527836420e+00 ), ( 2.01680432847577e+00 , -1.21223508026317e+00 , 2.02283227251816e+00 ), ( 4.93808100313684e-01 , 5.72993726796709e-01 , 3.01393255407714e+00 ), ( -6.88662684141346e-01 , 3.95917856413356e-01 , 3.20168916817509e+00 ), ( 1.26635423078224e+00 , 1.30187284743042e+00 , 3.82424713040866e+00 ), ( 8.02055999729061e-01 , 1.87550275041104e+00 , 5.08797241823521e+00 ), ( 2.07403821144199e+00 , 2.57688573350060e+00 , 5.62065001861050e+00 ), ( -3.48560203228005e-01 , 2.92052155004377e+00 , 4.98852924984934e+00 ), ( -1.18494600718505e+00 , 3.01232061184074e+00 , 5.89678764769942e+00 ), ( -3.82031855792474e-01 , 3.70595279193985e+00 , 3.87941565006141e+00 ), ( -1.45082110565174e+00 , 4.62175504315960e+00 , 3.53071333627421e+00 ), ( -7.75724398501387e-01 , 5.37503394369413e+00 , 2.40305640723820e+00 ), ( -2.70209506676955e+00 , 3.89870945597851e+00 , 2.94981388354107e+00 ), ( -3.85031566372397e+00 , 4.39752350986476e+00 , 2.87664301725662e+00 ), ( -2.54961285801488e+00 , 2.62499766609283e+00 , 2.51165344297249e+00 ), ( -3.73779778375935e+00 , 1.87724750734948e+00 , 2.08367054576034e+00 ), ( -3.40254393652096e+00 , 7.87407333184051e-01 , 1.02115029402814e+00 ), ( -4.34988393963124e+00 , 1.12609477459219e+00 , 3.21266592727085e+00 ), ( -5.52818384628272e+00 , 9.52475239449865e-01 , 3.35258498212062e+00 ), ( -3.48967721875033e+00 , 6.30398567215183e-01 , 4.18272134653624e+00 ), ( -3.74839312960716e+00 , 1.02522560825697e-01 , 5.46548357801744e+00 ), ( -2.45559644797203e+00 , -4.43402837804419e-01 , 6.12151759153573e+00 ), ( -4.45577146937068e+00 , 1.02426407947902e+00 , 6.42056265889269e+00 ), ( -5.32862086963481e+00 , 5.86032714410330e-01 , 7.17433883244170e+00 ), ( -6.29033006805714e+00 , 3.54932222936094e+00 , 6.69033999722774e+00 ), ( -6.93486349092612e+00 , 4.31932173934529e+00 , 7.41926550612646e+00 ), ( -6.77302656697589e+00 , 3.20630978062096e+00 , 5.49497885507638e+00 ), ( -4.07615678740045e+00 , 2.28779023613822e+00 , 6.46796989327310e+00 ), ( -4.91096621861803e+00 , 3.24745840702887e+00 , 7.21735263439854e+00 ), ( -4.05359762454723e+00 , 4.48287939172511e+00 , 7.26229858930884e+00 ) } +colvars: Step 1, atoms_positions[size = 51] = { ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 ), ( 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 ), ( 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 ), ( 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ), ( 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 ), ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 ), ( 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 ), ( 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 ), ( 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 ), ( 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ), ( 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 ), ( 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 ), ( 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 ), ( 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 ), ( 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 ), ( 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 ), ( 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 ), ( 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 ), ( 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 ), ( 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 ), ( 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 ), ( 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 ), ( 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 ), ( 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 ), ( -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 ), ( 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 ), ( 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 ), ( 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 ), ( -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 ), ( -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 ), ( -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 ), ( -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 ), ( -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 ), ( -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 ), ( -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 ), ( -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 ), ( -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 ), ( -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 ), ( -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 ), ( -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 ), ( -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 ), ( -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 ), ( -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 ), ( -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 ), ( -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 ), ( -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 ), ( -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 ), ( -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 ), ( -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 ), ( -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 ), ( -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ) } colvars: Step 1, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 1, atom_groups_ids[size = 0] = @@ -2018,163 +3143,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 1 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.39359239792396e-01 , 6.97253156444326e-03 , 9.40631006384071e-01 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ). +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.39355617493064e-01 , 6.97292683121385e-03 , 9.40632310293086e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 , 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 , 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 , 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 , 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 , 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 , 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 , 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 , 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 , 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 , 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 , 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 , 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 , 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 , 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 , 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 , -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 , 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 , 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 , 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 , -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 , -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 , -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 , -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 , -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 , -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 , -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 , -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 , -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 , -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 , -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 , -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 , -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 , -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 , -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 , -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 , -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 , -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 , -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 , -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 , -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 , -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 , -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.39359239792396e-01 , 6.97253156444326e-03 , 9.40631006384071e-01 ). +colvars: Colvar "one" has value ( -3.39355617493064e-01 , 6.97292683121385e-03 , 9.40632310293086e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 , 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 , 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 , 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 , 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 , 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 , 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 , 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 , 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 , 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 , 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 , 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 , 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 , 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 , 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 , 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 , -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 , 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 , 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 , 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 , -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 , -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 , -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 , -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 , -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 , -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 , -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 , -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 , -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 , -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 , -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 , -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 , -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 , -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 , -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 , -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 , -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 , -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 , -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 , -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 , -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 , -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 , -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.3052 , 1.81235 , -14.909 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.8087 , 6.78087 , 13.5617 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.3052 , 1.81235 , -14.909 ) to colvar "one". -colvars: Adding total bias energy: 45.8763 +colvars: Adding biasing force ( 67.8087 , 6.78087 , 13.5617 ) to colvar "one". +colvars: Adding total bias energy: 59.0466 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.3052 , 1.81235 , -14.909 ) +colvars: Force to be applied: ( 67.8087 , 6.78087 , 13.5617 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.83683 , -0.573221 , -1.60667 ) -colvars: ( -4.14758 , -0.491537 , -1.37772 ) -colvars: ( -4.14758 , -0.491537 , -1.37772 ) -colvars: ( -5.5247 , -0.654741 , -1.83516 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.24407 , -0.621478 , -1.74192 ) +colvars: ( -4.49679 , -0.532917 , -1.4937 ) +colvars: ( -4.49679 , -0.532917 , -1.4937 ) +colvars: ( -5.98986 , -0.709861 , -1.98965 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.903993 , 0.192289 , 0.652417 ) -colvars: ( 0.781088 , 0.264308 , 0.678501 ) -colvars: ( 0.76699 , 0.256656 , 0.659382 ) -colvars: ( 0.664952 , 0.266705 , 0.611922 ) -colvars: ( 0.652774 , 0.20025 , 0.512255 ) -colvars: ( 0.574956 , 0.345265 , 0.666906 ) -colvars: ( 0.463377 , 0.360922 , 0.621494 ) -colvars: ( 0.383656 , 0.459317 , 0.710222 ) -colvars: ( 0.380415 , 0.316875 , 0.510353 ) -colvars: ( 0.343791 , 0.276006 , 0.431519 ) -colvars: ( 0.352193 , 0.321737 , 0.50012 ) -colvars: ( 0.280168 , 0.279191 , 0.397647 ) -colvars: ( 0.254311 , 0.307723 , 0.421727 ) -colvars: ( 0.344972 , 0.180495 , 0.29952 ) -colvars: ( 0.284546 , 0.137834 , 0.203871 ) -colvars: ( 0.471756 , 0.141947 , 0.322278 ) -colvars: ( 0.546856 , 0.0496184 , 0.239198 ) -colvars: ( 0.681101 , 0.0268724 , 0.288403 ) -colvars: ( 0.553753 , 0.0184455 , 0.200036 ) -colvars: ( 0.537588 , -0.0464574 , 0.100124 ) -colvars: ( 0.573487 , 0.0668284 , 0.279141 ) -colvars: ( 0.569914 , 0.0514594 , 0.255635 ) -colvars: ( 0.605908 , 0.116412 , 0.367553 ) -colvars: ( 0.441286 , 0.0575401 , 0.186656 ) -colvars: ( 0.43358 , 0.00195342 , 0.104781 ) -colvars: ( 0.336623 , 0.12418 , 0.216247 ) -colvars: ( 0.208119 , 0.134251 , 0.152885 ) -colvars: ( 0.114315 , 0.220858 , 0.216757 ) -colvars: ( 0.180422 , 0.0603052 , 0.0334676 ) -colvars: ( 0.128974 , 0.0249581 , -0.0466157 ) -colvars: ( 0.217024 , 0.0335967 , 0.0183899 ) -colvars: ( 0.204019 , -0.0392982 , -0.0907238 ) -colvars: ( 0.242544 , -0.0438727 , -0.0738891 ) -colvars: ( 0.280998 , -0.125878 , -0.164685 ) -colvars: ( 0.235845 , -0.178563 , -0.265071 ) -colvars: ( 0.398949 , -0.141907 , -0.115956 ) -colvars: ( 0.478016 , -0.217981 , -0.174063 ) -colvars: ( 0.612818 , -0.221902 , -0.098366 ) -colvars: ( 0.427337 , -0.221184 , -0.209021 ) -colvars: ( 0.432801 , -0.289218 , -0.300262 ) -colvars: ( 0.375661 , -0.146774 , -0.136737 ) -colvars: ( 0.317902 , -0.139189 , -0.160966 ) -colvars: ( 0.299397 , -0.051749 , -0.0506101 ) -colvars: ( 0.191183 , -0.146717 , -0.247707 ) -colvars: ( 0.165106 , -0.188089 , -0.320888 ) -colvars: ( -0.0128421 , -0.1915 , -0.432746 ) -colvars: ( -0.106316 , -0.208362 , -0.512442 ) -colvars: ( 0.0917321 , -0.242996 , -0.441349 ) -colvars: ( 0.108209 , -0.105699 , -0.240659 ) -colvars: ( -0.0142897 , -0.108905 , -0.318854 ) -colvars: ( -0.105257 , -0.0275227 , -0.260534 ) +colvars: ( 0.980103 , 0.208479 , 0.707343 ) +colvars: ( 0.84685 , 0.286561 , 0.735623 ) +colvars: ( 0.831565 , 0.278265 , 0.714895 ) +colvars: ( 0.720936 , 0.28916 , 0.663439 ) +colvars: ( 0.707733 , 0.21711 , 0.555381 ) +colvars: ( 0.623363 , 0.374334 , 0.723051 ) +colvars: ( 0.502391 , 0.391309 , 0.673817 ) +colvars: ( 0.415958 , 0.497988 , 0.770015 ) +colvars: ( 0.412445 , 0.343553 , 0.553318 ) +colvars: ( 0.372737 , 0.299243 , 0.467848 ) +colvars: ( 0.381846 , 0.348825 , 0.542224 ) +colvars: ( 0.303758 , 0.302697 , 0.431124 ) +colvars: ( 0.275723 , 0.333631 , 0.457231 ) +colvars: ( 0.374017 , 0.195691 , 0.324736 ) +colvars: ( 0.308504 , 0.149439 , 0.221034 ) +colvars: ( 0.511475 , 0.153898 , 0.34941 ) +colvars: ( 0.592898 , 0.0537961 , 0.259335 ) +colvars: ( 0.738445 , 0.0291354 , 0.312683 ) +colvars: ( 0.600376 , 0.0199986 , 0.216876 ) +colvars: ( 0.58285 , -0.0503686 , 0.108553 ) +colvars: ( 0.621771 , 0.0724549 , 0.302641 ) +colvars: ( 0.617897 , 0.0557918 , 0.277156 ) +colvars: ( 0.656922 , 0.126213 , 0.398496 ) +colvars: ( 0.47844 , 0.0623842 , 0.202369 ) +colvars: ( 0.470085 , 0.00211752 , 0.113601 ) +colvars: ( 0.364965 , 0.134634 , 0.234452 ) +colvars: ( 0.225643 , 0.145553 , 0.165756 ) +colvars: ( 0.123941 , 0.239451 , 0.235005 ) +colvars: ( 0.195614 , 0.0653818 , 0.0362843 ) +colvars: ( 0.139834 , 0.0270587 , -0.0505412 ) +colvars: ( 0.235297 , 0.0364249 , 0.0199373 ) +colvars: ( 0.221197 , -0.0426071 , -0.0983626 ) +colvars: ( 0.262966 , -0.0475665 , -0.0801105 ) +colvars: ( 0.304657 , -0.136476 , -0.178551 ) +colvars: ( 0.255703 , -0.193597 , -0.287388 ) +colvars: ( 0.432539 , -0.153855 , -0.125719 ) +colvars: ( 0.518262 , -0.236333 , -0.188718 ) +colvars: ( 0.664413 , -0.240584 , -0.106649 ) +colvars: ( 0.463317 , -0.239806 , -0.226619 ) +colvars: ( 0.469241 , -0.313568 , -0.325542 ) +colvars: ( 0.40729 , -0.159132 , -0.14825 ) +colvars: ( 0.344669 , -0.150909 , -0.174519 ) +colvars: ( 0.324605 , -0.0561066 , -0.0548723 ) +colvars: ( 0.20728 , -0.159071 , -0.268562 ) +colvars: ( 0.179009 , -0.203925 , -0.347905 ) +colvars: ( -0.0139216 , -0.207624 , -0.46918 ) +colvars: ( -0.115265 , -0.225905 , -0.555586 ) +colvars: ( 0.0994568 , -0.263455 , -0.478507 ) +colvars: ( 0.117321 , -0.114598 , -0.260921 ) +colvars: ( -0.0154909 , -0.118075 , -0.345699 ) +colvars: ( -0.114117 , -0.029841 , -0.282469 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.83683 , 0.573221 , 1.60667 ) -colvars: ( 4.14758 , 0.491537 , 1.37772 ) -colvars: ( 4.14758 , 0.491537 , 1.37772 ) -colvars: ( 5.5247 , 0.654741 , 1.83516 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.24407 , 0.621478 , 1.74192 ) +colvars: ( 4.49679 , 0.532917 , 1.4937 ) +colvars: ( 4.49679 , 0.532917 , 1.4937 ) +colvars: ( 5.98986 , 0.709861 , 1.98965 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.628373 , -0.0803096 , -0.404156 ) -colvars: ( -0.562768 , -0.162435 , -0.377206 ) -colvars: ( -0.516859 , -0.140734 , -0.3205 ) -colvars: ( -0.518305 , -0.190229 , -0.34562 ) -colvars: ( -0.508681 , -0.132365 , -0.308245 ) -colvars: ( -0.488918 , -0.281371 , -0.359533 ) -colvars: ( -0.450653 , -0.321788 , -0.340237 ) -colvars: ( -0.42483 , -0.427905 , -0.364904 ) -colvars: ( -0.387449 , -0.287422 , -0.260022 ) -colvars: ( -0.380468 , -0.262789 , -0.241201 ) -colvars: ( -0.340853 , -0.28194 , -0.210376 ) -colvars: ( -0.280782 , -0.246001 , -0.132571 ) -colvars: ( -0.234992 , -0.260733 , -0.0934018 ) -colvars: ( -0.303441 , -0.144057 , -0.106704 ) -colvars: ( -0.270545 , -0.11561 , -0.0599066 ) -colvars: ( -0.362401 , -0.086826 , -0.138848 ) -colvars: ( -0.392337 , 0.0103139 , -0.122623 ) -colvars: ( -0.448151 , 0.0580048 , -0.156152 ) -colvars: ( -0.426686 , 0.0250386 , -0.150249 ) -colvars: ( -0.415174 , 0.0808204 , -0.111965 ) -colvars: ( -0.467892 , -0.0281086 , -0.217242 ) -colvars: ( -0.498444 , -0.0296691 , -0.248821 ) -colvars: ( -0.546188 , -0.0939051 , -0.327712 ) -colvars: ( -0.441439 , -0.0599934 , -0.205787 ) -colvars: ( -0.446978 , -0.0166911 , -0.190677 ) -colvars: ( -0.383628 , -0.133723 , -0.18269 ) -colvars: ( -0.321695 , -0.165299 , -0.135281 ) -colvars: ( -0.268983 , -0.254577 , -0.124763 ) -colvars: ( -0.282468 , -0.093719 , -0.0614744 ) -colvars: ( -0.266517 , -0.0757416 , -0.0367823 ) -colvars: ( -0.267531 , -0.0492391 , -0.0251369 ) -colvars: ( -0.234713 , 0.0243191 , 0.0431483 ) -colvars: ( -0.218644 , 0.0506275 , 0.0719412 ) -colvars: ( -0.280361 , 0.110129 , 0.0381004 ) -colvars: ( -0.252838 , 0.150968 , 0.0853995 ) -colvars: ( -0.351976 , 0.138471 , -0.0206253 ) -colvars: ( -0.402067 , 0.213892 , -0.0351229 ) -colvars: ( -0.476649 , 0.236888 , -0.0993991 ) -colvars: ( -0.408431 , 0.19398 , -0.0510639 ) -colvars: ( -0.412899 , 0.253854 , -0.026951 ) -colvars: ( -0.408376 , 0.108407 , -0.0919166 ) -colvars: ( -0.410166 , 0.0782913 , -0.10812 ) -colvars: ( -0.428039 , -0.0137189 , -0.170142 ) -colvars: ( -0.340193 , 0.0664573 , -0.0431592 ) -colvars: ( -0.341087 , 0.0921493 , -0.0317796 ) -colvars: ( -0.179362 , 0.0976022 , 0.134041 ) -colvars: ( -0.127545 , 0.0988906 , 0.186951 ) -colvars: ( -0.211539 , 0.169456 , 0.135918 ) -colvars: ( -0.277448 , 0.025934 , 0.000791771 ) -colvars: ( -0.207783 , 0.0118233 , 0.0643523 ) -colvars: ( -0.152155 , -0.0704514 , 0.0811613 ) +colvars: ( -0.681278 , -0.0870714 , -0.438179 ) +colvars: ( -0.610149 , -0.176111 , -0.408961 ) +colvars: ( -0.560375 , -0.152583 , -0.34748 ) +colvars: ( -0.561943 , -0.206245 , -0.374716 ) +colvars: ( -0.551508 , -0.143509 , -0.334194 ) +colvars: ( -0.530082 , -0.30506 , -0.3898 ) +colvars: ( -0.488596 , -0.34888 , -0.368879 ) +colvars: ( -0.460599 , -0.463931 , -0.395623 ) +colvars: ( -0.420071 , -0.31162 , -0.281911 ) +colvars: ( -0.412502 , -0.284913 , -0.261506 ) +colvars: ( -0.369551 , -0.305677 , -0.228086 ) +colvars: ( -0.304423 , -0.266712 , -0.14373 ) +colvars: ( -0.254778 , -0.282684 , -0.101263 ) +colvars: ( -0.328989 , -0.156186 , -0.115686 ) +colvars: ( -0.293324 , -0.125343 , -0.0649488 ) +colvars: ( -0.392913 , -0.0941361 , -0.150536 ) +colvars: ( -0.425369 , 0.0111821 , -0.132945 ) +colvars: ( -0.485882 , 0.062888 , -0.169297 ) +colvars: ( -0.46261 , 0.0271465 , -0.162897 ) +colvars: ( -0.450129 , 0.0876247 , -0.12139 ) +colvars: ( -0.507286 , -0.0304751 , -0.23553 ) +colvars: ( -0.54041 , -0.0321668 , -0.269768 ) +colvars: ( -0.592173 , -0.101811 , -0.355301 ) +colvars: ( -0.478606 , -0.0650441 , -0.223112 ) +colvars: ( -0.484612 , -0.018096 , -0.206729 ) +colvars: ( -0.415928 , -0.144981 , -0.198069 ) +colvars: ( -0.348781 , -0.179216 , -0.146669 ) +colvars: ( -0.291631 , -0.27601 , -0.135265 ) +colvars: ( -0.306251 , -0.101609 , -0.0666492 ) +colvars: ( -0.288957 , -0.0821179 , -0.0398784 ) +colvars: ( -0.290057 , -0.0533843 , -0.0272524 ) +colvars: ( -0.254475 , 0.0263669 , 0.0467815 ) +colvars: ( -0.237054 , 0.05489 , 0.0779985 ) +colvars: ( -0.303967 , 0.119401 , 0.0413084 ) +colvars: ( -0.274127 , 0.163678 , 0.0925894 ) +colvars: ( -0.381611 , 0.150129 , -0.0223614 ) +colvars: ( -0.435919 , 0.2319 , -0.0380797 ) +colvars: ( -0.51678 , 0.256832 , -0.107767 ) +colvars: ( -0.442818 , 0.210312 , -0.0553629 ) +colvars: ( -0.447663 , 0.275227 , -0.0292202 ) +colvars: ( -0.44276 , 0.117535 , -0.0996548 ) +colvars: ( -0.4447 , 0.0848834 , -0.117222 ) +colvars: ( -0.464078 , -0.0148733 , -0.184466 ) +colvars: ( -0.368836 , 0.0720531 , -0.0467928 ) +colvars: ( -0.369806 , 0.0999082 , -0.0344554 ) +colvars: ( -0.194465 , 0.10582 , 0.145326 ) +colvars: ( -0.138286 , 0.107217 , 0.20269 ) +colvars: ( -0.229351 , 0.183723 , 0.14736 ) +colvars: ( -0.300809 , 0.0281182 , 0.000858489 ) +colvars: ( -0.225279 , 0.0128195 , 0.06977 ) +colvars: ( -0.164968 , -0.076382 , 0.0879943 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 1. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 1. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 1, atoms_new_colvar_forces = { ( -4.56121296830658e+00 , -4.61241353827074e-01 , -1.35840638133783e+00 ), ( -3.92926416259046e+00 , -3.89663782249164e-01 , -1.07642270018368e+00 ), ( -4.00093646166547e+00 , -4.15060921777743e-01 , -1.11141506274544e+00 ), ( -5.38060802928969e+00 , -5.86855187741701e-01 , -1.63114963622738e+00 ), ( 2.50130489904713e-01 , 1.15921831227305e-01 , 3.38882353346319e-01 ), ( 4.92287015525418e+00 , 6.37114670971567e-01 , 1.91404037546853e+00 ), ( 4.16030699965575e+00 , 5.30670341810993e-01 , 1.65897480365853e+00 ), ( -4.11742060744669e-02 , 3.14122235304719e-02 , 3.45318167522374e-01 ), ( 4.14054924899995e+00 , 5.20990230072956e-01 , 1.62804834803012e+00 ), ( 5.48802414203826e+00 , 6.67957628124025e-01 , 2.02547787152414e+00 ), ( 1.13401367888580e-02 , 3.97968575512088e-02 , 2.89743590064456e-01 ), ( -6.13429998875925e-04 , 3.31904585487345e-02 , 2.65076285639856e-01 ), ( 1.93189132040426e-02 , 4.69906894317092e-02 , 3.28324792571684e-01 ), ( 4.15310107971116e-02 , 3.64372642432776e-02 , 1.92815524833123e-01 ), ( 1.40014331258611e-02 , 2.22243632771206e-02 , 1.43964433073201e-01 ), ( 1.09355673121523e-01 , 5.51208045376686e-02 , 1.83430053208428e-01 ), ( 1.54518940908901e-01 , 5.99322715671118e-02 , 1.16574711662165e-01 ), ( 2.32949880910387e-01 , 8.48772135203020e-02 , 1.32250608109155e-01 ), ( 1.27067186507369e-01 , 4.34840848401806e-02 , 4.97865198257480e-02 ), ( 1.22413872360718e-01 , 3.43629960831720e-02 , -1.18407958674590e-02 ), ( 1.05594346949082e-01 , 3.87197923562023e-02 , 6.18992448292895e-02 ), ( 7.14691535860895e-02 , 2.17903102851525e-02 , 6.81407061135675e-03 ), ( 5.97209641981943e-02 , 2.25071296417359e-02 , 3.98410799496707e-02 ), ( -1.53110558083924e-04 , -2.45333152116743e-03 , -1.91318682968406e-02 ), ( -1.33985293929014e-02 , -1.47376676480654e-02 , -8.58964055168903e-02 ), ( -4.70048825419079e-02 , -9.54275314410222e-03 , 3.35569101122025e-02 ), ( -1.13575193091344e-01 , -3.10487005981428e-02 , 1.76041991738181e-02 ), ( -1.54667891555866e-01 , -3.37194469106931e-02 , 9.19939515909655e-02 ), ( -1.02045936431039e-01 , -3.34138341929289e-02 , -2.80068672415610e-02 ), ( -1.37542540797621e-01 , -5.07835025888675e-02 , -8.33979922915723e-02 ), ( -5.05074127724774e-02 , -1.56424153031696e-02 , -6.74701525473648e-03 ), ( -3.06936455782306e-02 , -1.49790441228229e-02 , -4.75755526079221e-02 ), ( 2.39000305306330e-02 , 6.75481445114764e-03 , -1.94799258460876e-03 ), ( 6.37144587265381e-04 , -1.57489830272470e-02 , -1.26584734390641e-01 ), ( -1.69929924153842e-02 , -2.75956164402141e-02 , -1.79671034076676e-01 ), ( 4.69730059885827e-02 , -3.43618896392178e-03 , -1.36581244707262e-01 ), ( 7.59492983355819e-02 , -4.08946030671814e-03 , -2.09185780341426e-01 ), ( 1.36168129122491e-01 , 1.49856831637182e-02 , -1.97765073724213e-01 ), ( 1.89063730085664e-02 , -2.72042479706727e-02 , -2.60084439073423e-01 ), ( 1.99018506305078e-02 , -3.53633903280922e-02 , -3.27212801214469e-01 ), ( -3.27154388013418e-02 , -3.83669120876546e-02 , -2.28653734204113e-01 ), ( -9.22637240513290e-02 , -6.08979080427851e-02 , -2.69086145709003e-01 ), ( -1.28641601578139e-01 , -6.54678727585377e-02 , -2.20752217137649e-01 ), ( -1.49009988673130e-01 , -8.02600661059803e-02 , -2.90865913646557e-01 ), ( -1.75980595287395e-01 , -9.59396265372952e-02 , -3.52667928620230e-01 ), ( -1.92204196160349e-01 , -9.38979806873025e-02 , -2.98704791488973e-01 ), ( -2.33861549390566e-01 , -1.09471039414501e-01 , -3.25491120340965e-01 ), ( -1.19806713205189e-01 , -7.35403764057818e-02 , -3.05431270609309e-01 ), ( -1.69238240580481e-01 , -7.97645301640516e-02 , -2.39867247275705e-01 ), ( -2.22072836915525e-01 , -9.70814311455297e-02 , -2.54501227948042e-01 ), ( -2.57412102810795e-01 , -9.79740872238340e-02 , -1.79372920140549e-01 ) } +colvars: Step 1, atoms_new_colvar_forces = { ( -4.94524752703150e+00 , -5.00070478706819e-01 , -1.47275647312878e+00 ), ( -4.26009131684454e+00 , -4.22467159035450e-01 , -1.16703423693781e+00 ), ( -4.33779800471171e+00 , -4.50002583986641e-01 , -1.20497275307046e+00 ), ( -5.83363187452853e+00 , -6.36259583558461e-01 , -1.76846030974805e+00 ), ( 2.71190015483635e-01 , 1.25681762375493e-01 , 3.67414267382630e-01 ), ( 5.33735414735488e+00 , 6.90751295593571e-01 , 2.07517161763720e+00 ), ( 4.51058662070597e+00 , 5.75345653833406e-01 , 1.79863383269542e+00 ), ( -4.46408275205372e-02 , 3.40569702021636e-02 , 3.74391940973145e-01 ), ( 4.48916537934960e+00 , 5.64850532194998e-01 , 1.76510354545200e+00 ), ( 5.95009180286499e+00 , 7.24190384703997e-01 , 2.19598868309754e+00 ), ( 1.22949080365150e-02 , 4.31475303857823e-02 , 3.14138299966590e-01 ), ( -6.65082887394586e-04 , 3.59849096022542e-02 , 2.87394147806122e-01 ), ( 2.09454431592941e-02 , 5.09470381688317e-02 , 3.55967803435473e-01 ), ( 4.50276732595528e-02 , 3.95050702537192e-02 , 2.09049454974075e-01 ), ( 1.51802648863201e-02 , 2.40955261372282e-02 , 1.56085385382948e-01 ), ( 1.18562776981734e-01 , 5.97616492017114e-02 , 1.98873784794414e-01 ), ( 1.67528528090387e-01 , 6.49782066429318e-02 , 1.26389616432355e-01 ), ( 2.52562895437471e-01 , 9.20233604106910e-02 , 1.43385334010810e-01 ), ( 1.37765499890022e-01 , 4.71451801693997e-02 , 5.39782543565037e-02 ), ( 1.32720403241798e-01 , 3.72561466313631e-02 , -1.28377211574611e-02 ), ( 1.14484776500457e-01 , 4.19797663850426e-02 , 6.71108044658936e-02 ), ( 7.74864448064505e-02 , 2.36249234418552e-02 , 7.38778540003382e-03 ), ( 6.47491303559717e-02 , 2.44020990549570e-02 , 4.31954803199882e-02 ), ( -1.65996344847597e-04 , -2.65988605064772e-03 , -2.07426523928385e-02 ), ( -1.45266011426173e-02 , -1.59784925856758e-02 , -9.31283714811172e-02 ), ( -5.09624157039873e-02 , -1.03461898436014e-02 , 3.63822086561157e-02 ), ( -1.23137558839672e-01 , -3.36628074369859e-02 , 1.90863694359183e-02 ), ( -1.67690024220711e-01 , -3.65584088695555e-02 , 9.97392996339642e-02 ), ( -1.10637609383330e-01 , -3.62270759413579e-02 , -3.03648856269820e-02 ), ( -1.49122820034138e-01 , -5.50591676751083e-02 , -9.04196191188827e-02 ), ( -5.47598464287284e-02 , -1.69594129214750e-02 , -7.31508188067119e-03 ), ( -3.32778789705395e-02 , -1.62401947888544e-02 , -5.15811466436443e-02 ), ( 2.59122622261631e-02 , 7.32352281212509e-03 , -2.11201683056700e-03 ), ( 6.90782403088619e-04 , -1.70749634648680e-02 , -1.37242435415941e-01 ), ( -1.84237103006750e-02 , -2.99190152647431e-02 , -1.94798292468153e-01 ), ( 5.09278555322116e-02 , -3.72550751223835e-03 , -1.48080588220414e-01 ), ( 8.23437845427731e-02 , -4.43378522041665e-03 , -2.26797996663325e-01 ), ( 1.47632691579756e-01 , 1.62473698427204e-02 , -2.14415728561813e-01 ), ( 2.04981810854328e-02 , -2.94946983223998e-02 , -2.81982021639434e-01 ), ( 2.15774723237853e-02 , -3.83407955579049e-02 , -3.54762198175992e-01 ), ( -3.54698833919641e-02 , -4.15971863107600e-02 , -2.47905033768520e-01 ), ( -1.00031783639185e-01 , -6.60251552771045e-02 , -2.91741615166040e-01 ), ( -1.39472463045771e-01 , -7.09798775635357e-02 , -2.39338250043644e-01 ), ( -1.61555754569422e-01 , -8.70174905659755e-02 , -3.15355116544667e-01 ), ( -1.90797127483342e-01 , -1.04017177822925e-01 , -3.82360498044434e-01 ), ( -2.08386671206907e-01 , -1.01803638409611e-01 , -3.23853995585936e-01 ), ( -2.53551331972853e-01 , -1.18687855692914e-01 , -3.52895579795768e-01 ), ( -1.29893744126556e-01 , -7.97320503419824e-02 , -3.31146804351725e-01 ), ( -1.83487110521711e-01 , -8.64802309664682e-02 , -2.60062666463744e-01 ), ( -2.40770073694591e-01 , -1.05255110618706e-01 , -2.75928747265521e-01 ), ( -2.79084701552500e-01 , -1.06222917731058e-01 , -1.94475080116808e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 1, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2212,10 +3476,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 2, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 2, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 2, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 2, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 2, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 2, atoms_positions[size = 51] = { ( 8.41230217581484e+00 , 4.24326733536878e-02 , -7.47569490176025e-01 ), ( 7.00089513421555e+00 , -4.83663699546571e-01 , -6.72804704936553e-01 ), ( 6.24367623868857e+00 , -2.51597399688398e-01 , 6.35902751887321e-01 ), ( 5.02199310371592e+00 , -2.08647537136810e-01 , 6.45327524407029e-01 ), ( 7.03875423602966e+00 , -2.01024090894622e+00 , -1.03297768688768e+00 ), ( 6.90728101575796e+00 , -2.68409594185841e-01 , 1.78553096211824e+00 ), ( 6.17984674260531e+00 , -1.29067444864042e-01 , 3.04264192791274e+00 ), ( 7.19403104814050e+00 , -3.17368222969422e-01 , 4.30320854269290e+00 ), ( 5.30491583043216e+00 , 1.13376171120378e+00 , 3.26705018916841e+00 ), ( 4.08866819057517e+00 , 1.07659208744573e+00 , 3.60871383769025e+00 ), ( 5.87394211299741e+00 , 2.33800746103373e+00 , 2.95025840533623e+00 ), ( 5.23075710856745e+00 , 3.59958439514760e+00 , 2.87915965088407e+00 ), ( 6.32630915491025e+00 , 4.63549135662606e+00 , 2.47116449869166e+00 ), ( 3.90153079829527e+00 , 3.69481371251487e+00 , 2.02631829831871e+00 ), ( 2.92849868300238e+00 , 4.11702537266563e+00 , 2.57104338554592e+00 ), ( 3.81753045166978e+00 , 3.24384573133083e+00 , 7.83691308238158e-01 ), ( 2.66012692529136e+00 , 3.20111572487056e+00 , -6.86003878622946e-02 ), ( 3.04893081854912e+00 , 2.73309481829466e+00 , -1.57997395201901e+00 ), ( 1.64933960432362e+00 , 2.16482434474135e+00 , 5.69612675768092e-01 ), ( 4.24921990500371e-01 , 2.42605373880924e+00 , 5.70944354578611e-01 ), ( 1.98623149883073e+00 , 9.97645952529453e-01 , 1.06028397478289e+00 ), ( 1.12204224960049e+00 , 1.47142447093945e-02 , 1.68718091217601e+00 ), ( 2.01639805450803e+00 , -1.20568292550127e+00 , 2.02326698950649e+00 ), ( 4.98103216842537e-01 , 5.80679823587245e-01 , 3.01308846211547e+00 ), ( -6.84829676640720e-01 , 3.90833079255459e-01 , 3.19685945568519e+00 ), ( 1.27432015398850e+00 , 1.30473014901260e+00 , 3.82336698286764e+00 ), ( 8.08601410185370e-01 , 1.88137209556391e+00 , 5.08538325715984e+00 ), ( 2.07182119428108e+00 , 2.58031798980506e+00 , 5.62057423330987e+00 ), ( -3.51856598997225e-01 , 2.92077064179559e+00 , 4.98737393872034e+00 ), ( -1.18280182786636e+00 , 3.01570881875917e+00 , 5.89917061211271e+00 ), ( -3.87794274194742e-01 , 3.70427748455740e+00 , 3.87474110532419e+00 ), ( -1.45631640972632e+00 , 4.61459319965596e+00 , 3.53258775067119e+00 ), ( -7.71525256388986e-01 , 5.37658883982654e+00 , 2.40420584478656e+00 ), ( -2.70490428847905e+00 , 3.89833439606985e+00 , 2.94596721752849e+00 ), ( -3.85265652977568e+00 , 4.40316722845360e+00 , 2.87069810170517e+00 ), ( -2.55585210102612e+00 , 2.62089197346870e+00 , 2.50849831177278e+00 ), ( -3.73243894282155e+00 , 1.88635397507806e+00 , 2.08117958634558e+00 ), ( -3.40440145433502e+00 , 7.90661523283313e-01 , 1.01489749289712e+00 ), ( -4.34244223157238e+00 , 1.12117998375176e+00 , 3.21348381567827e+00 ), ( -5.52935798388581e+00 , 9.45031041354011e-01 , 3.35102684162587e+00 ), ( -3.48508740061830e+00 , 6.29273187233610e-01 , 4.17782066610908e+00 ), ( -3.75586810994823e+00 , 1.04520729936072e-01 , 5.46864564339515e+00 ), ( -2.44525456155645e+00 , -4.36565563433725e-01 , 6.12524646328179e+00 ), ( -4.45857770956377e+00 , 1.01874257320945e+00 , 6.41862259580145e+00 ), ( -5.32722304597339e+00 , 5.89222557864481e-01 , 7.17650762843785e+00 ), ( -6.29285957437603e+00 , 3.54731449624820e+00 , 6.69277829408017e+00 ), ( -6.92913918708456e+00 , 4.31545557739325e+00 , 7.41850538938275e+00 ), ( -6.76638490706359e+00 , 3.20728509611946e+00 , 5.49812757005705e+00 ), ( -4.07643470196769e+00 , 2.29036157014482e+00 , 6.47113725812446e+00 ), ( -4.91331138905739e+00 , 3.24680974286670e+00 , 7.21653939356896e+00 ), ( -4.05852930675624e+00 , 4.48539530316559e+00 , 7.26244311964441e+00 ) } +colvars: Step 2, atoms_positions[size = 51] = { ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 ), ( 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 ), ( 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 ), ( 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ), ( 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 ), ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 ), ( 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 ), ( 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 ), ( 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 ), ( 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ), ( 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 ), ( 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 ), ( 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 ), ( 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 ), ( 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 ), ( 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 ), ( 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 ), ( 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 ), ( 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 ), ( 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 ), ( 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 ), ( 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 ), ( 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 ), ( 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 ), ( -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 ), ( 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 ), ( 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 ), ( 2.07182033199839e+00 , 2.58031779371270e+00 , 5.62057469557046e+00 ), ( -3.51857196195411e-01 , 2.92077044604945e+00 , 4.98737377407843e+00 ), ( -1.18280243435512e+00 , 3.01570859553755e+00 , 5.89917024566929e+00 ), ( -3.87794524035796e-01 , 3.70427740475066e+00 , 3.87474106468534e+00 ), ( -1.45631659311092e+00 , 4.61459312113414e+00 , 3.53258748757127e+00 ), ( -7.71525128042554e-01 , 5.37658887799748e+00 , 2.40420582867879e+00 ), ( -2.70490428589622e+00 , 3.89833430415539e+00 , 2.94596647609308e+00 ), ( -3.85265660442606e+00 , 4.40316710638716e+00 , 2.87069731043829e+00 ), ( -2.55585188833545e+00 , 2.62089196733170e+00 , 2.50849763245218e+00 ), ( -3.73243849554280e+00 , 1.88635394790118e+00 , 2.08117836350766e+00 ), ( -3.40440071450160e+00 , 7.90661562036665e-01 , 1.01489640110740e+00 ), ( -4.34244212012249e+00 , 1.12117982289474e+00 , 3.21348229313481e+00 ), ( -5.52935789612539e+00 , 9.45030885109751e-01 , 3.35102540103283e+00 ), ( -3.48508756370938e+00 , 6.29272994238064e-01 , 4.17781951543363e+00 ), ( -3.75586862376688e+00 , 1.04520414973514e-01 , 5.46864407236529e+00 ), ( -2.44525530896877e+00 , -4.36565885647881e-01 , 6.12524526296224e+00 ), ( -4.45857858178953e+00 , 1.01874210402695e+00 , 6.41862089191568e+00 ), ( -5.32722382061257e+00 , 5.89222135203817e-01 , 7.17650607594958e+00 ), ( -6.29286070068146e+00 , 3.54731394746929e+00 , 6.69277654767522e+00 ), ( -6.92914021657276e+00 , 4.31545509454118e+00 , 7.41850395505831e+00 ), ( -6.76638550864120e+00 , 3.20728475580864e+00 , 5.49812607601866e+00 ), ( -4.07643555217667e+00 , 2.29036116971940e+00 , 6.47113605156518e+00 ), ( -4.91331270399169e+00 , 3.24680915830551e+00 , 7.21653797742536e+00 ), ( -4.05853070415384e+00 , 4.48539472961622e+00 , 7.26244219143046e+00 ) } colvars: Step 2, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 2, atom_groups_ids[size = 0] = @@ -2233,162 +3497,301 @@ colvars: Collective variables module, step no. 2 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ). +colvars: Calculating gradients of colvar "group1". colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.38680441300733e-01 , 6.30491679893380e-03 , 9.40880336017551e-01 ). +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.38665979440331e-01 , 6.30649599530219e-03 , 9.40885531017447e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 , 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 , 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 , 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 , 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 , 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 , 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 , 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 , 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 , 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 , 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 , 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 , 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 , 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 , 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 , 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 , -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 , 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 , 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 , 2.07182033199839e+00 , 2.58031779371270e+00 , 5.62057469557046e+00 , -3.51857196195411e-01 , 2.92077044604945e+00 , 4.98737377407843e+00 , -1.18280243435512e+00 , 3.01570859553755e+00 , 5.89917024566929e+00 , -3.87794524035796e-01 , 3.70427740475066e+00 , 3.87474106468534e+00 , -1.45631659311092e+00 , 4.61459312113414e+00 , 3.53258748757127e+00 , -7.71525128042554e-01 , 5.37658887799748e+00 , 2.40420582867879e+00 , -2.70490428589622e+00 , 3.89833430415539e+00 , 2.94596647609308e+00 , -3.85265660442606e+00 , 4.40316710638716e+00 , 2.87069731043829e+00 , -2.55585188833545e+00 , 2.62089196733170e+00 , 2.50849763245218e+00 , -3.73243849554280e+00 , 1.88635394790118e+00 , 2.08117836350766e+00 , -3.40440071450160e+00 , 7.90661562036665e-01 , 1.01489640110740e+00 , -4.34244212012249e+00 , 1.12117982289474e+00 , 3.21348229313481e+00 , -5.52935789612539e+00 , 9.45030885109751e-01 , 3.35102540103283e+00 , -3.48508756370938e+00 , 6.29272994238064e-01 , 4.17781951543363e+00 , -3.75586862376688e+00 , 1.04520414973514e-01 , 5.46864407236529e+00 , -2.44525530896877e+00 , -4.36565885647881e-01 , 6.12524526296224e+00 , -4.45857858178953e+00 , 1.01874210402695e+00 , 6.41862089191568e+00 , -5.32722382061257e+00 , 5.89222135203817e-01 , 7.17650607594958e+00 , -6.29286070068146e+00 , 3.54731394746929e+00 , 6.69277654767522e+00 , -6.92914021657276e+00 , 4.31545509454118e+00 , 7.41850395505831e+00 , -6.76638550864120e+00 , 3.20728475580864e+00 , 5.49812607601866e+00 , -4.07643555217667e+00 , 2.29036116971940e+00 , 6.47113605156518e+00 , -4.91331270399169e+00 , 3.24680915830551e+00 , 7.21653797742536e+00 , -4.05853070415384e+00 , 4.48539472961622e+00 , 7.26244219143046e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.38680441300733e-01 , 6.30491679893380e-03 , 9.40880336017551e-01 ). +colvars: Colvar "one" has value ( -3.38665979440331e-01 , 6.30649599530219e-03 , 9.40885531017447e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 , 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 , 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 , 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 , 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 , 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 , 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 , 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 , 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 , 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 , 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 , 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 , 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 , 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 , 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 , 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 , -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 , 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 , 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 , 2.07182033199839e+00 , 2.58031779371270e+00 , 5.62057469557046e+00 , -3.51857196195411e-01 , 2.92077044604945e+00 , 4.98737377407843e+00 , -1.18280243435512e+00 , 3.01570859553755e+00 , 5.89917024566929e+00 , -3.87794524035796e-01 , 3.70427740475066e+00 , 3.87474106468534e+00 , -1.45631659311092e+00 , 4.61459312113414e+00 , 3.53258748757127e+00 , -7.71525128042554e-01 , 5.37658887799748e+00 , 2.40420582867879e+00 , -2.70490428589622e+00 , 3.89833430415539e+00 , 2.94596647609308e+00 , -3.85265660442606e+00 , 4.40316710638716e+00 , 2.87069731043829e+00 , -2.55585188833545e+00 , 2.62089196733170e+00 , 2.50849763245218e+00 , -3.73243849554280e+00 , 1.88635394790118e+00 , 2.08117836350766e+00 , -3.40440071450160e+00 , 7.90661562036665e-01 , 1.01489640110740e+00 , -4.34244212012249e+00 , 1.12117982289474e+00 , 3.21348229313481e+00 , -5.52935789612539e+00 , 9.45030885109751e-01 , 3.35102540103283e+00 , -3.48508756370938e+00 , 6.29272994238064e-01 , 4.17781951543363e+00 , -3.75586862376688e+00 , 1.04520414973514e-01 , 5.46864407236529e+00 , -2.44525530896877e+00 , -4.36565885647881e-01 , 6.12524526296224e+00 , -4.45857858178953e+00 , 1.01874210402695e+00 , 6.41862089191568e+00 , -5.32722382061257e+00 , 5.89222135203817e-01 , 7.17650607594958e+00 , -6.29286070068146e+00 , 3.54731394746929e+00 , 6.69277654767522e+00 , -6.92914021657276e+00 , 4.31545509454118e+00 , 7.41850395505831e+00 , -6.76638550864120e+00 , 3.20728475580864e+00 , 5.49812607601866e+00 , -4.07643555217667e+00 , 2.29036116971940e+00 , 6.47113605156518e+00 , -4.91331270399169e+00 , 3.24680915830551e+00 , 7.21653797742536e+00 , -4.05853070415384e+00 , 4.48539472961622e+00 , 7.26244219143046e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.2916 , 1.8257 , -14.914 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.7758 , 6.77758 , 13.5552 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.2916 , 1.8257 , -14.914 ) to colvar "one". -colvars: Adding total bias energy: 45.8505 +colvars: Adding biasing force ( 67.7758 , 6.77758 , 13.5552 ) to colvar "one". +colvars: Adding total bias energy: 59.0009 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.2916 , 1.8257 , -14.914 ) +colvars: Force to be applied: ( 67.7758 , 6.77758 , 13.5552 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.83825 , -0.572725 , -1.60415 ) -colvars: ( -4.1488 , -0.491112 , -1.37556 ) -colvars: ( -4.1488 , -0.491112 , -1.37556 ) -colvars: ( -5.52632 , -0.654175 , -1.83229 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.24396 , -0.620729 , -1.73858 ) +colvars: ( -4.4967 , -0.532275 , -1.49083 ) +colvars: ( -4.4967 , -0.532275 , -1.49083 ) +colvars: ( -5.98973 , -0.709005 , -1.98583 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.903535 , 0.192419 , 0.651664 ) -colvars: ( 0.780731 , 0.264443 , 0.67763 ) -colvars: ( 0.766569 , 0.256779 , 0.658479 ) -colvars: ( 0.664736 , 0.266819 , 0.611113 ) -colvars: ( 0.652573 , 0.200335 , 0.511595 ) -colvars: ( 0.574848 , 0.345396 , 0.665979 ) -colvars: ( 0.463412 , 0.361039 , 0.620604 ) -colvars: ( 0.383782 , 0.459461 , 0.709164 ) -colvars: ( 0.380494 , 0.316955 , 0.509564 ) -colvars: ( 0.343936 , 0.276062 , 0.430853 ) -colvars: ( 0.352233 , 0.321808 , 0.499285 ) -colvars: ( 0.280237 , 0.279227 , 0.396903 ) -colvars: ( 0.254334 , 0.307761 , 0.420883 ) -colvars: ( 0.344972 , 0.180501 , 0.298957 ) -colvars: ( 0.284608 , 0.137811 , 0.203424 ) -colvars: ( 0.47163 , 0.141963 , 0.321743 ) -colvars: ( 0.546655 , 0.0496105 , 0.238828 ) -colvars: ( 0.680748 , 0.0268805 , 0.288013 ) -colvars: ( 0.553613 , 0.0184308 , 0.199777 ) -colvars: ( 0.537467 , -0.0465024 , 0.100013 ) -colvars: ( 0.573383 , 0.066842 , 0.278811 ) -colvars: ( 0.569881 , 0.0514707 , 0.255387 ) -colvars: ( 0.605891 , 0.116462 , 0.367187 ) -colvars: ( 0.441394 , 0.0575291 , 0.186457 ) -colvars: ( 0.433723 , 0.00191955 , 0.104723 ) -colvars: ( 0.336812 , 0.124174 , 0.215933 ) -colvars: ( 0.208438 , 0.134224 , 0.152605 ) -colvars: ( 0.1147 , 0.220846 , 0.216313 ) -colvars: ( 0.180728 , 0.0602387 , 0.0333285 ) -colvars: ( 0.129356 , 0.0248684 , -0.0466406 ) -colvars: ( 0.217231 , 0.0335218 , 0.0182484 ) -colvars: ( 0.204197 , -0.0394093 , -0.0907342 ) -colvars: ( 0.242613 , -0.0439831 , -0.0739554 ) -colvars: ( 0.281128 , -0.126008 , -0.164523 ) -colvars: ( 0.236018 , -0.178725 , -0.264779 ) -colvars: ( 0.398992 , -0.142018 , -0.115788 ) -colvars: ( 0.478014 , -0.218106 , -0.173742 ) -colvars: ( 0.612698 , -0.222 , -0.098081 ) -colvars: ( 0.42745 , -0.221316 , -0.208626 ) -colvars: ( 0.432923 , -0.289376 , -0.299715 ) -colvars: ( 0.375865 , -0.146882 , -0.136452 ) -colvars: ( 0.318224 , -0.139301 , -0.160631 ) -colvars: ( 0.299778 , -0.0518247 , -0.0504242 ) -colvars: ( 0.191617 , -0.146859 , -0.247312 ) -colvars: ( 0.165601 , -0.18825 , -0.32037 ) -colvars: ( -0.0123199 , -0.191709 , -0.432251 ) -colvars: ( -0.10571 , -0.208597 , -0.511879 ) -colvars: ( 0.0921189 , -0.243208 , -0.44081 ) -colvars: ( 0.108675 , -0.105843 , -0.240352 ) -colvars: ( -0.0137199 , -0.109076 , -0.318501 ) -colvars: ( -0.104631 , -0.0276806 , -0.260342 ) +colvars: ( 0.979291 , 0.208554 , 0.706289 ) +colvars: ( 0.84619 , 0.286615 , 0.734433 ) +colvars: ( 0.830841 , 0.27831 , 0.713677 ) +colvars: ( 0.720472 , 0.28919 , 0.66234 ) +colvars: ( 0.707289 , 0.217131 , 0.554478 ) +colvars: ( 0.623047 , 0.374354 , 0.721806 ) +colvars: ( 0.502269 , 0.391308 , 0.672626 ) +colvars: ( 0.415964 , 0.49798 , 0.76861 ) +colvars: ( 0.4124 , 0.343527 , 0.552278 ) +colvars: ( 0.372777 , 0.299206 , 0.466968 ) +colvars: ( 0.38177 , 0.348788 , 0.541138 ) +colvars: ( 0.303737 , 0.302636 , 0.430174 ) +colvars: ( 0.275662 , 0.333563 , 0.456164 ) +colvars: ( 0.3739 , 0.195634 , 0.324016 ) +colvars: ( 0.308474 , 0.149365 , 0.220475 ) +colvars: ( 0.511175 , 0.153865 , 0.348713 ) +colvars: ( 0.59249 , 0.0537709 , 0.258846 ) +colvars: ( 0.737825 , 0.0291363 , 0.312154 ) +colvars: ( 0.600032 , 0.0199766 , 0.216521 ) +colvars: ( 0.582532 , -0.0504006 , 0.108393 ) +colvars: ( 0.621459 , 0.0724462 , 0.30218 ) +colvars: ( 0.617665 , 0.0557857 , 0.276792 ) +colvars: ( 0.656694 , 0.126225 , 0.397964 ) +colvars: ( 0.478406 , 0.0623511 , 0.202083 ) +colvars: ( 0.470092 , 0.00207906 , 0.113497 ) +colvars: ( 0.365056 , 0.134583 , 0.234031 ) +colvars: ( 0.22592 , 0.145474 , 0.165395 ) +colvars: ( 0.124323 , 0.239359 , 0.234443 ) +colvars: ( 0.195886 , 0.0652868 , 0.0361188 ) +colvars: ( 0.140208 , 0.0269505 , -0.0505543 ) +colvars: ( 0.235449 , 0.0363307 , 0.0197749 ) +colvars: ( 0.221322 , -0.0427146 , -0.0983437 ) +colvars: ( 0.262958 , -0.0476711 , -0.0801578 ) +colvars: ( 0.304703 , -0.136573 , -0.178318 ) +colvars: ( 0.255811 , -0.19371 , -0.286979 ) +colvars: ( 0.432448 , -0.153926 , -0.125499 ) +colvars: ( 0.518095 , -0.236392 , -0.188311 ) +colvars: ( 0.664071 , -0.240612 , -0.106308 ) +colvars: ( 0.463292 , -0.239872 , -0.226121 ) +colvars: ( 0.469224 , -0.313638 , -0.324845 ) +colvars: ( 0.407383 , -0.159198 , -0.147896 ) +colvars: ( 0.34491 , -0.150983 , -0.174102 ) +colvars: ( 0.324918 , -0.0561727 , -0.0546567 ) +colvars: ( 0.207689 , -0.159174 , -0.268049 ) +colvars: ( 0.179492 , -0.204037 , -0.347232 ) +colvars: ( -0.0133458 , -0.207786 , -0.468491 ) +colvars: ( -0.114565 , -0.22609 , -0.554794 ) +colvars: ( 0.0998483 , -0.263602 , -0.477768 ) +colvars: ( 0.117794 , -0.11472 , -0.260506 ) +colvars: ( -0.0148628 , -0.118225 , -0.345206 ) +colvars: ( -0.113396 , -0.0300056 , -0.28217 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.83825 , 0.572725 , 1.60415 ) -colvars: ( 4.1488 , 0.491112 , 1.37556 ) -colvars: ( 4.1488 , 0.491112 , 1.37556 ) -colvars: ( 5.52632 , 0.654175 , 1.83229 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.24396 , 0.620729 , 1.73858 ) +colvars: ( 4.4967 , 0.532275 , 1.49083 ) +colvars: ( 4.4967 , 0.532275 , 1.49083 ) +colvars: ( 5.98973 , 0.709005 , 1.98583 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.628038 , -0.0803205 , -0.403541 ) -colvars: ( -0.562504 , -0.162549 , -0.376391 ) -colvars: ( -0.516435 , -0.140783 , -0.319547 ) -colvars: ( -0.518187 , -0.190392 , -0.344857 ) -colvars: ( -0.50856 , -0.132447 , -0.30764 ) -colvars: ( -0.488933 , -0.281669 , -0.358633 ) -colvars: ( -0.450828 , -0.322155 , -0.33937 ) -colvars: ( -0.42512 , -0.428424 , -0.363842 ) -colvars: ( -0.387594 , -0.287721 , -0.259182 ) -colvars: ( -0.380692 , -0.263066 , -0.240514 ) -colvars: ( -0.340876 , -0.282201 , -0.209392 ) -colvars: ( -0.280756 , -0.24619 , -0.131601 ) -colvars: ( -0.234841 , -0.26091 , -0.0922247 ) -colvars: ( -0.303329 , -0.144104 , -0.105948 ) -colvars: ( -0.270469 , -0.115615 , -0.0592513 ) -colvars: ( -0.362176 , -0.0867935 , -0.138171 ) -colvars: ( -0.392027 , 0.0104813 , -0.122151 ) -colvars: ( -0.447692 , 0.0582447 , -0.15569 ) -colvars: ( -0.426508 , 0.025196 , -0.149984 ) -colvars: ( -0.414997 , 0.0810551 , -0.111854 ) -colvars: ( -0.467834 , -0.0280515 , -0.216979 ) -colvars: ( -0.498531 , -0.0296447 , -0.24873 ) -colvars: ( -0.546374 , -0.0939945 , -0.327573 ) -colvars: ( -0.441655 , -0.0600148 , -0.205713 ) -colvars: ( -0.447244 , -0.016664 , -0.190785 ) -colvars: ( -0.383895 , -0.133835 , -0.182423 ) -colvars: ( -0.322068 , -0.165454 , -0.135001 ) -colvars: ( -0.269397 , -0.254844 , -0.124237 ) -colvars: ( -0.282755 , -0.0937551 , -0.0612828 ) -colvars: ( -0.266887 , -0.0757627 , -0.0367231 ) -colvars: ( -0.267647 , -0.0491851 , -0.024878 ) -colvars: ( -0.234727 , 0.0244956 , 0.0433257 ) -colvars: ( -0.218475 , 0.050872 , 0.0722516 ) -colvars: ( -0.280353 , 0.110411 , 0.0380266 ) -colvars: ( -0.252846 , 0.151309 , 0.0852086 ) -colvars: ( -0.351936 , 0.138778 , -0.0207893 ) -colvars: ( -0.402017 , 0.214287 , -0.0355247 ) -colvars: ( -0.47653 , 0.237306 , -0.0998371 ) -colvars: ( -0.408558 , 0.19432 , -0.0516044 ) -colvars: ( -0.413034 , 0.254271 , -0.0276744 ) -colvars: ( -0.408651 , 0.10861 , -0.092371 ) -colvars: ( -0.410618 , 0.0784253 , -0.108681 ) -colvars: ( -0.428619 , -0.0137323 , -0.170588 ) -colvars: ( -0.340712 , 0.0665832 , -0.0437158 ) -colvars: ( -0.341689 , 0.0922962 , -0.0325006 ) -colvars: ( -0.17978 , 0.0978275 , 0.133604 ) -colvars: ( -0.128013 , 0.0991234 , 0.186489 ) -colvars: ( -0.211793 , 0.169794 , 0.135432 ) -colvars: ( -0.277934 , 0.0260275 , 0.000425854 ) -colvars: ( -0.208326 , 0.0119073 , 0.0640095 ) -colvars: ( -0.152718 , -0.0704656 , 0.081068 ) +colvars: ( -0.680694 , -0.087056 , -0.437362 ) +colvars: ( -0.609666 , -0.176178 , -0.407936 ) +colvars: ( -0.559734 , -0.152587 , -0.346326 ) +colvars: ( -0.561635 , -0.206355 , -0.373758 ) +colvars: ( -0.551201 , -0.143552 , -0.333422 ) +colvars: ( -0.529929 , -0.305283 , -0.388688 ) +colvars: ( -0.48863 , -0.349163 , -0.367811 ) +colvars: ( -0.460769 , -0.464342 , -0.394334 ) +colvars: ( -0.420095 , -0.311842 , -0.280902 ) +colvars: ( -0.412615 , -0.28512 , -0.26067 ) +colvars: ( -0.36946 , -0.30586 , -0.226938 ) +colvars: ( -0.3043 , -0.26683 , -0.142626 ) +colvars: ( -0.254534 , -0.282784 , -0.0999484 ) +colvars: ( -0.328764 , -0.156185 , -0.114824 ) +colvars: ( -0.29315 , -0.125308 , -0.0642132 ) +colvars: ( -0.392544 , -0.0940704 , -0.149748 ) +colvars: ( -0.424897 , 0.0113595 , -0.132386 ) +colvars: ( -0.485227 , 0.0631266 , -0.168736 ) +colvars: ( -0.46227 , 0.0273082 , -0.162553 ) +colvars: ( -0.449793 , 0.0878505 , -0.121227 ) +colvars: ( -0.507061 , -0.0304032 , -0.235163 ) +colvars: ( -0.540332 , -0.0321297 , -0.269576 ) +colvars: ( -0.592186 , -0.101874 , -0.355028 ) +colvars: ( -0.478688 , -0.0650453 , -0.222954 ) +colvars: ( -0.484746 , -0.0180598 , -0.206775 ) +colvars: ( -0.416087 , -0.145054 , -0.197711 ) +colvars: ( -0.349077 , -0.179324 , -0.146314 ) +colvars: ( -0.291991 , -0.276207 , -0.134647 ) +colvars: ( -0.306468 , -0.101613 , -0.0664171 ) +colvars: ( -0.289271 , -0.0821123 , -0.0397993 ) +colvars: ( -0.290093 , -0.0533073 , -0.0269604 ) +colvars: ( -0.254412 , 0.0265505 , 0.0469599 ) +colvars: ( -0.236797 , 0.0551376 , 0.0783111 ) +colvars: ( -0.303863 , 0.119669 , 0.0412157 ) +colvars: ( -0.27405 , 0.163996 , 0.0923521 ) +colvars: ( -0.381446 , 0.150413 , -0.0225305 ) +colvars: ( -0.435726 , 0.232253 , -0.0385019 ) +colvars: ( -0.516485 , 0.257201 , -0.108205 ) +colvars: ( -0.442817 , 0.210612 , -0.0559301 ) +colvars: ( -0.447668 , 0.27559 , -0.0299949 ) +colvars: ( -0.442919 , 0.117717 , -0.100114 ) +colvars: ( -0.445052 , 0.0850025 , -0.117791 ) +colvars: ( -0.464562 , -0.0148811 , -0.184887 ) +colvars: ( -0.369286 , 0.0721681 , -0.0473807 ) +colvars: ( -0.370345 , 0.100037 , -0.0352261 ) +colvars: ( -0.194862 , 0.106032 , 0.144803 ) +colvars: ( -0.138755 , 0.107437 , 0.20212 ) +colvars: ( -0.229557 , 0.184032 , 0.146784 ) +colvars: ( -0.301245 , 0.0282123 , 0.000461777 ) +colvars: ( -0.225801 , 0.0129088 , 0.0693751 ) +colvars: ( -0.165531 , -0.0763699 , 0.0878645 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 2. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 2. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 2, atoms_new_colvar_forces = { ( -4.56275591432568e+00 , -4.60626201406985e-01 , -1.35602921553252e+00 ), ( -3.93057432356231e+00 , -3.89218540353453e-01 , -1.07432085574555e+00 ), ( -4.00225225577945e+00 , -4.14684542315428e-01 , -1.10930365840729e+00 ), ( -5.38231018573623e+00 , -5.86287786085435e-01 , -1.62833067766371e+00 ), ( 2.50133161932021e-01 , 1.15996383439220e-01 , 3.38932431945268e-01 ), ( 4.92416773946919e+00 , 6.36452457626012e-01 , 1.91149846005699e+00 ), ( 4.16138500265152e+00 , 5.29996299679700e-01 , 1.65679341661957e+00 ), ( -4.13386379963794e-02 , 3.10363702515917e-02 , 3.45321802947897e-01 ), ( 4.14170174373320e+00 , 5.20345366926022e-01 , 1.62594137310275e+00 ), ( 5.48956688633158e+00 , 6.67171491848512e-01 , 2.02262452634672e+00 ), ( 1.13572538101830e-02 , 3.96069067900944e-02 , 2.89892874903251e-01 ), ( -5.18992402491980e-04 , 3.30363442557886e-02 , 2.65302472716106e-01 ), ( 1.94934753306099e-02 , 4.68502764998364e-02 , 3.28657895366362e-01 ), ( 4.16436497949736e-02 , 3.63979047739679e-02 , 1.93008539238330e-01 ), ( 1.41385702217975e-02 , 2.21958752053348e-02 , 1.44173170879472e-01 ), ( 1.09453693916134e-01 , 5.51691320542270e-02 , 1.83572631283874e-01 ), ( 1.54627155519217e-01 , 6.00918449323470e-02 , 1.16676694421352e-01 ), ( 2.33056290670824e-01 , 8.51252625753025e-02 , 1.32322949487176e-01 ), ( 1.27104485771322e-01 , 4.36268377333083e-02 , 4.97931884745996e-02 ), ( 1.22469588881520e-01 , 3.45527297063639e-02 , -1.18411614465137e-02 ), ( 1.05548588130028e-01 , 3.87905064186184e-02 , 6.18318922172304e-02 ), ( 7.13498720750871e-02 , 2.18259599675757e-02 , 6.65707447147101e-03 ), ( 5.95169456640540e-02 , 2.24672160196834e-02 , 3.96137239089935e-02 ), ( -2.60767644603088e-04 , -2.48569559566528e-03 , -1.92565272867681e-02 ), ( -1.35207607822719e-02 , -1.47444722739935e-02 , -8.60621405897303e-02 ), ( -4.70825964826798e-02 , -9.66096510064252e-03 , 3.35101085101995e-02 ), ( -1.13630006285656e-01 , -3.12309114222545e-02 , 1.76042896158294e-02 ), ( -1.54696522040518e-01 , -3.39975897931801e-02 , 9.20754644045805e-02 ), ( -1.02027239087699e-01 , -3.35163749467409e-02 , -2.79542940474772e-02 ), ( -1.37531391006204e-01 , -5.08943593481360e-02 , -8.33636581276309e-02 ), ( -5.04163089596834e-02 , -1.56632782600083e-02 , -6.62965293435192e-03 ), ( -3.05302955123607e-02 , -1.49136379461020e-02 , -4.74085257795145e-02 ), ( 2.41379870386027e-02 , 6.88894780305944e-03 , -1.70374332627504e-03 ), ( 7.74988081106043e-04 , -1.55965123551653e-02 , -1.26496207176680e-01 ), ( -1.68277988227925e-02 , -2.74152433603144e-02 , -1.79570128967291e-01 ), ( 4.70558577979064e-02 , -3.24048717205680e-03 , -1.36577244444368e-01 ), ( 7.59971083401451e-02 , -3.81848829811693e-03 , -2.09266474286324e-01 ), ( 1.36168663308619e-01 , 1.53053615391257e-02 , -1.97918154817217e-01 ), ( 1.88916709109832e-02 , -2.69961088695052e-02 , -2.60230730369980e-01 ), ( 1.98888151078248e-02 , -3.51041763993108e-02 , -3.27389242672573e-01 ), ( -3.27865049719737e-02 , -3.82722054379483e-02 , -2.28822806188803e-01 ), ( -9.23943646511856e-02 , -6.08756444697767e-02 , -2.69311625873086e-01 ), ( -1.28840678665156e-01 , -6.55570021994047e-02 , -2.21012340430644e-01 ), ( -1.49095358557464e-01 , -8.02753353134499e-02 , -2.91027575172649e-01 ), ( -1.76088459354702e-01 , -9.59539844029730e-02 , -3.52870718355002e-01 ), ( -1.92100235430595e-01 , -9.38818108222520e-02 , -2.98647260389017e-01 ), ( -2.33722560153824e-01 , -1.09473757572936e-01 , -3.25389876174375e-01 ), ( -1.19674155785813e-01 , -7.34140642627520e-02 , -3.05378508384878e-01 ), ( -1.69258950149056e-01 , -7.98153405417789e-02 , -2.39926417106925e-01 ), ( -2.22045455872506e-01 , -9.71687672132796e-02 , -2.54491942785526e-01 ), ( -2.57348474469147e-01 , -9.81461925066468e-02 , -1.79273616435353e-01 ) } +colvars: Step 2, atoms_new_colvar_forces = { ( -4.94536484424471e+00 , -4.99230329339275e-01 , -1.46965138667428e+00 ), ( -4.26017169338647e+00 , -4.21837885497957e-01 , -1.16433344372845e+00 ), ( -4.33785972011736e+00 , -4.49439154598515e-01 , -1.20224951005482e+00 ), ( -5.83364162440807e+00 , -6.35425752643177e-01 , -1.76477374399873e+00 ), ( 2.71106477651610e-01 , 1.25722479883961e-01 , 3.67351443020935e-01 ), ( 5.33708059316313e+00 , 6.89799349662734e-01 , 2.07169601164356e+00 ), ( 4.51033556629133e+00 , 5.74419693366348e-01 , 1.79564555246299e+00 ), ( -4.48047999794275e-02 , 3.36388133054046e-02 , 3.74276559888785e-01 ), ( 4.48900187903556e+00 , 5.63959538908433e-01 , 1.76220658873513e+00 ), ( 5.94989167637375e+00 , 7.23091482993244e-01 , 2.19212860059994e+00 ), ( 1.23095353487825e-02 , 4.29279321141343e-02 , 3.14199957428508e-01 ), ( -5.62532568835983e-04 , 3.58064304664043e-02 , 2.87547664585458e-01 ), ( 2.11279362215647e-02 , 5.07786372071457e-02 , 3.56215326332885e-01 ), ( 4.51353870465388e-02 , 3.94498239469809e-02 , 2.09191993135665e-01 ), ( 1.53240403624194e-02 , 2.40569741006357e-02 , 1.56261841838829e-01 ), ( 1.18631213357434e-01 , 5.97949668988609e-02 , 1.98964911025173e-01 ), ( 1.67592406930671e-01 , 6.51304136706980e-02 , 1.26459852680159e-01 ), ( 2.52597717509630e-01 , 9.22628218633901e-02 , 1.43418033557420e-01 ), ( 1.37762014245814e-01 , 4.72848444314161e-02 , 5.39682796902565e-02 ), ( 1.32738485105735e-01 , 3.74498751149277e-02 , -1.28340241241104e-02 ), ( 1.14398700280755e-01 , 4.20430110654893e-02 , 6.70164300705228e-02 ), ( 7.73324842683294e-02 , 2.36560215455751e-02 , 7.21530116826130e-03 ), ( 6.45073992803266e-02 , 2.43510635340137e-02 , 4.29353375260687e-02 ), ( -2.82611138640421e-04 , -2.69411093985940e-03 , -2.08711298473133e-02 ), ( -1.46544324307763e-02 , -1.59807735460644e-02 , -9.32782921275177e-02 ), ( -5.10303929134580e-02 , -1.04709934114900e-02 , 3.63198957179338e-02 ), ( -1.23157715921451e-01 , -3.38495294483925e-02 , 1.90803829080292e-02 ), ( -1.67667609162110e-01 , -3.68481648406214e-02 , 9.97958424624752e-02 ), ( -1.10582086245515e-01 , -3.63266443574183e-02 , -3.02982381308109e-02 ), ( -1.49063210094619e-01 , -5.51617435820511e-02 , -9.03535974195620e-02 ), ( -5.46436650728548e-02 , -1.69766128267981e-02 , -7.18557018089740e-03 ), ( -3.30902501543696e-02 , -1.61641368762427e-02 , -5.13837073628916e-02 ), ( 2.61618773729005e-02 , 7.46654549545343e-03 , -1.84665973786238e-03 ), ( 8.39944953888894e-04 , -1.69042916182381e-02 , -1.37102762169889e-01 ), ( -1.82388158934780e-02 , -2.97140112926790e-02 , -1.94626862762827e-01 ), ( 5.10014130804014e-02 , -3.51224489192514e-03 , -1.48029058791080e-01 ), ( 8.23693559692558e-02 , -4.13873007770021e-03 , -2.26813159187842e-01 ), ( 1.47586222339250e-01 , 1.65886115570443e-02 , -2.14513279691095e-01 ), ( 2.04757191889185e-02 , -2.92597430710658e-02 , -2.82050682998041e-01 ), ( 2.15564734451574e-02 , -3.80476722220259e-02 , -3.54840336799863e-01 ), ( -3.55355903107537e-02 , -4.14812950402868e-02 , -2.48009242898295e-01 ), ( -1.00141474779805e-01 , -6.59799797980471e-02 , -2.91892981680507e-01 ), ( -1.39643749627078e-01 , -7.10538351169382e-02 , -2.39543859667753e-01 ), ( -1.61596777723409e-01 , -8.70062941269483e-02 , -3.15429800338440e-01 ), ( -1.90853207439237e-01 , -1.03999574012606e-01 , -3.82458396448231e-01 ), ( -2.08207591594682e-01 , -1.01753656038357e-01 , -3.23688440661073e-01 ), ( -2.53319897531783e-01 , -1.18652957765828e-01 , -3.52673399626206e-01 ), ( -1.29708690061578e-01 , -7.95697482525082e-02 , -3.30984091985120e-01 ), ( -1.83451072437040e-01 , -8.65077194601226e-02 , -2.60043906098063e-01 ), ( -2.40663663419215e-01 , -1.05316193775053e-01 , -2.75830749010938e-01 ), ( -2.78926800166438e-01 , -1.06375552664104e-01 , -1.94305492276471e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 2, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2426,10 +3829,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 3, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 3, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 3, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 3, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 3, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 3, atoms_positions[size = 51] = { ( 8.40432537347079e+00 , 4.27023523143084e-02 , -7.49794923258072e-01 ), ( 6.99827921913924e+00 , -4.88099279872046e-01 , -6.66623615895143e-01 ), ( 6.24916457435144e+00 , -2.53048519132688e-01 , 6.44402643797318e-01 ), ( 5.01528146738013e+00 , -2.08801464651714e-01 , 6.51168343880958e-01 ), ( 7.03895372542554e+00 , -2.01326453297722e+00 , -1.02798237640550e+00 ), ( 6.90599022218291e+00 , -2.69083020729788e-01 , 1.79259469596826e+00 ), ( 6.17819898214310e+00 , -1.26840925294146e-01 , 3.04742788378711e+00 ), ( 7.18887437910556e+00 , -3.18190833806877e-01 , 4.30239979123681e+00 ), ( 5.30617195835321e+00 , 1.12821582441797e+00 , 3.27354885186499e+00 ), ( 4.08708135560753e+00 , 1.07380406152037e+00 , 3.61286819362922e+00 ), ( 5.87428867854682e+00 , 2.33046793187875e+00 , 2.95718497242407e+00 ), ( 5.22756350482070e+00 , 3.59806525574326e+00 , 2.87989514418974e+00 ), ( 6.33004307020987e+00 , 4.62660812393183e+00 , 2.46802154801930e+00 ), ( 3.89875238684539e+00 , 3.70379061870336e+00 , 2.02347113410718e+00 ), ( 2.92333152941826e+00 , 4.11580387576656e+00 , 2.56498423514490e+00 ), ( 3.81870278458513e+00 , 3.24371694954947e+00 , 7.82492593993091e-01 ), ( 2.66310947197167e+00 , 3.19306357098013e+00 , -7.50220870549412e-02 ), ( 3.04938643337800e+00 , 2.72950976483335e+00 , -1.58743687892350e+00 ), ( 1.64232873722823e+00 , 2.15864496476834e+00 , 5.75792927917045e-01 ), ( 4.27089418257113e-01 , 2.43325458247010e+00 , 5.66066287421235e-01 ), ( 1.98044090530470e+00 , 1.00388484796073e+00 , 1.05723688588043e+00 ), ( 1.12901883607008e+00 , 1.29164702929013e-02 , 1.68724131837110e+00 ), ( 2.01590185879845e+00 , -1.19931648648901e+00 , 2.02325086478451e+00 ), ( 5.02873254555376e-01 , 5.87789153957021e-01 , 3.01035426063972e+00 ), ( -6.81444668247382e-01 , 3.85824447391906e-01 , 3.19254280514024e+00 ), ( 1.28185479878008e+00 , 1.30770660347493e+00 , 3.82341380909578e+00 ), ( 8.15487463448196e-01 , 1.88749925503596e+00 , 5.08218900980267e+00 ), ( 2.06839167547174e+00 , 2.58346656952317e+00 , 5.62073869300250e+00 ), ( -3.54751879904785e-01 , 2.92076574274276e+00 , 4.98648026571535e+00 ), ( -1.18059724189041e+00 , 3.01914654867617e+00 , 5.90115838004479e+00 ), ( -3.94242642986330e-01 , 3.70183887701549e+00 , 3.87005057704240e+00 ), ( -1.46136750440668e+00 , 4.60679196136818e+00 , 3.53446350406840e+00 ), ( -7.67375645143352e-01 , 5.37852585060086e+00 , 2.40557761823244e+00 ), ( -2.70861286210308e+00 , 3.89781603149094e+00 , 2.94244721299768e+00 ), ( -3.85397037061724e+00 , 4.40886783867621e+00 , 2.86514694670063e+00 ), ( -2.56238553987727e+00 , 2.61704026388775e+00 , 2.50463334676025e+00 ), ( -3.72731744273190e+00 , 1.89477473704136e+00 , 2.07834151690659e+00 ), ( -3.40648322734221e+00 , 7.94791140868560e-01 , 1.00822925596241e+00 ), ( -4.33411907667829e+00 , 1.11540771527026e+00 , 3.21619006920151e+00 ), ( -5.53124186056364e+00 , 9.37678491175850e-01 , 3.34931219584712e+00 ), ( -3.48029058481271e+00 , 6.29573843203298e-01 , 4.17165746663140e+00 ), ( -3.76293160038971e+00 , 1.04890509942572e-01 , 5.47218972935680e+00 ), ( -2.43524421545893e+00 , -4.28568742802307e-01 , 6.12917392570417e+00 ), ( -4.46137453930486e+00 , 1.01289730291090e+00 , 6.41730615543044e+00 ), ( -5.32588941289969e+00 , 5.92469724995526e-01 , 7.17853966797247e+00 ), ( -6.29516516770400e+00 , 3.54677363850763e+00 , 6.69521066423102e+00 ), ( -6.92401100227964e+00 , 4.31155236642489e+00 , 7.41786634158487e+00 ), ( -6.76023033797462e+00 , 3.20798202034655e+00 , 5.50142984649732e+00 ), ( -4.07780765935896e+00 , 2.29340417035688e+00 , 6.47431154141452e+00 ), ( -4.91395609424947e+00 , 3.24498075683916e+00 , 7.21568507981577e+00 ), ( -4.06366753987422e+00 , 4.48963350668488e+00 , 7.26344888853188e+00 ) } +colvars: Step 3, atoms_positions[size = 51] = { ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 ), ( 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 ), ( 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 ), ( 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ), ( 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 ), ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 ), ( 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 ), ( 7.18887438592740e+00 , -3.18190538896136e-01 , 4.30240438250701e+00 ), ( 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 ), ( 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ), ( 5.87428924915182e+00 , 2.33046858202937e+00 , 2.95718817842218e+00 ), ( 5.22756354085870e+00 , 3.59806563949040e+00 , 2.87989840364726e+00 ), ( 6.33004327971406e+00 , 4.62660866005681e+00 , 2.46802543565857e+00 ), ( 3.89875294604380e+00 , 3.70379107545018e+00 , 2.02347367014388e+00 ), ( 2.92333166283481e+00 , 4.11580409777728e+00 , 2.56498566370563e+00 ), ( 3.81870402884775e+00 , 3.24371757057811e+00 , 7.82494662400517e-01 ), ( 2.66311149915854e+00 , 3.19306435678778e+00 , -7.50205577463578e-02 ), ( 3.04938916927457e+00 , 2.72951079865366e+00 , -1.58743520554313e+00 ), ( 1.64233040103771e+00 , 2.15864553679670e+00 , 5.75793583272084e-01 ), ( 4.27090638049903e-01 , 2.43325492205922e+00 , 5.66066171000393e-01 ), ( 1.98044204554190e+00 , 1.00388530801315e+00 , 1.05723759401865e+00 ), ( 1.12901973159542e+00 , 1.29167416517915e-02 , 1.68724137458764e+00 ), ( 2.01590257389253e+00 , -1.19931623024337e+00 , 2.02325134846391e+00 ), ( 5.02873252997144e-01 , 5.87789122186409e-01 , 3.01035401048538e+00 ), ( -6.81444799066583e-01 , 3.85824301681720e-01 , 3.19254195491642e+00 ), ( 1.28185433712608e+00 , 1.30770649318966e+00 , 3.82341417641572e+00 ), ( 8.15485986974327e-01 , 1.88749888489650e+00 , 5.08218920724669e+00 ), ( 2.06838974384938e+00 , 2.58346613036847e+00 , 5.62073972587495e+00 ), ( -3.54753217917702e-01 , 2.92076530153912e+00 , 4.98647989495056e+00 ), ( -1.18059860901710e+00 , 3.01914604664074e+00 , 5.90115755916543e+00 ), ( -3.94243204894331e-01 , 3.70183869752321e+00 , 3.87005048430333e+00 ), ( -1.46136791229833e+00 , 4.60679178565910e+00 , 3.53446291377488e+00 ), ( -7.67375356843104e-01 , 5.37852593586357e+00 , 2.40557758311810e+00 ), ( -2.70861285809934e+00 , 3.89781582916249e+00 , 2.94244555060088e+00 ), ( -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 ), ( -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 ), ( -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 ), ( -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 ), ( -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 ), ( -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 ), ( -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 ), ( -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 ), ( -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 ), ( -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 ), ( -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 ), ( -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 ), ( -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 ), ( -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 ), ( -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 ), ( -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 ), ( -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ) } colvars: Step 3, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 3, atom_groups_ids[size = 0] = @@ -2446,163 +3849,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 3 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ). +colvars: Calculating gradients of colvar "group1". colvars: Calculating colvar "one", components 0 through 1. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.37759603496395e-01 , 5.75914840711148e-03 , 9.41214790818537e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.37727237769795e-01 , 5.76269013801485e-03 , 9.41226383114476e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 , 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 7.18887438592740e+00 , -3.18190538896136e-01 , 4.30240438250701e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 , 5.87428924915182e+00 , 2.33046858202937e+00 , 2.95718817842218e+00 , 5.22756354085870e+00 , 3.59806563949040e+00 , 2.87989840364726e+00 , 6.33004327971406e+00 , 4.62660866005681e+00 , 2.46802543565857e+00 , 3.89875294604380e+00 , 3.70379107545018e+00 , 2.02347367014388e+00 , 2.92333166283481e+00 , 4.11580409777728e+00 , 2.56498566370563e+00 , 3.81870402884775e+00 , 3.24371757057811e+00 , 7.82494662400517e-01 , 2.66311149915854e+00 , 3.19306435678778e+00 , -7.50205577463578e-02 , 3.04938916927457e+00 , 2.72951079865366e+00 , -1.58743520554313e+00 , 1.64233040103771e+00 , 2.15864553679670e+00 , 5.75793583272084e-01 , 4.27090638049903e-01 , 2.43325492205922e+00 , 5.66066171000393e-01 , 1.98044204554190e+00 , 1.00388530801315e+00 , 1.05723759401865e+00 , 1.12901973159542e+00 , 1.29167416517915e-02 , 1.68724137458764e+00 , 2.01590257389253e+00 , -1.19931623024337e+00 , 2.02325134846391e+00 , 5.02873252997144e-01 , 5.87789122186409e-01 , 3.01035401048538e+00 , -6.81444799066583e-01 , 3.85824301681720e-01 , 3.19254195491642e+00 , 1.28185433712608e+00 , 1.30770649318966e+00 , 3.82341417641572e+00 , 8.15485986974327e-01 , 1.88749888489650e+00 , 5.08218920724669e+00 , 2.06838974384938e+00 , 2.58346613036847e+00 , 5.62073972587495e+00 , -3.54753217917702e-01 , 2.92076530153912e+00 , 4.98647989495056e+00 , -1.18059860901710e+00 , 3.01914604664074e+00 , 5.90115755916543e+00 , -3.94243204894331e-01 , 3.70183869752321e+00 , 3.87005048430333e+00 , -1.46136791229833e+00 , 4.60679178565910e+00 , 3.53446291377488e+00 , -7.67375356843104e-01 , 5.37852593586357e+00 , 2.40557758311810e+00 , -2.70861285809934e+00 , 3.89781582916249e+00 , 2.94244555060088e+00 , -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 , -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 , -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 , -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 , -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 , -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 , -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 , -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 , -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 , -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 , -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 , -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 , -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 , -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 , -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 , -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 , -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.37759603496395e-01 , 5.75914840711148e-03 , 9.41214790818537e-01 ). +colvars: Colvar "one" has value ( -3.37727237769795e-01 , 5.76269013801485e-03 , 9.41226383114476e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 , 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 7.18887438592740e+00 , -3.18190538896136e-01 , 4.30240438250701e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 , 5.87428924915182e+00 , 2.33046858202937e+00 , 2.95718817842218e+00 , 5.22756354085870e+00 , 3.59806563949040e+00 , 2.87989840364726e+00 , 6.33004327971406e+00 , 4.62660866005681e+00 , 2.46802543565857e+00 , 3.89875294604380e+00 , 3.70379107545018e+00 , 2.02347367014388e+00 , 2.92333166283481e+00 , 4.11580409777728e+00 , 2.56498566370563e+00 , 3.81870402884775e+00 , 3.24371757057811e+00 , 7.82494662400517e-01 , 2.66311149915854e+00 , 3.19306435678778e+00 , -7.50205577463578e-02 , 3.04938916927457e+00 , 2.72951079865366e+00 , -1.58743520554313e+00 , 1.64233040103771e+00 , 2.15864553679670e+00 , 5.75793583272084e-01 , 4.27090638049903e-01 , 2.43325492205922e+00 , 5.66066171000393e-01 , 1.98044204554190e+00 , 1.00388530801315e+00 , 1.05723759401865e+00 , 1.12901973159542e+00 , 1.29167416517915e-02 , 1.68724137458764e+00 , 2.01590257389253e+00 , -1.19931623024337e+00 , 2.02325134846391e+00 , 5.02873252997144e-01 , 5.87789122186409e-01 , 3.01035401048538e+00 , -6.81444799066583e-01 , 3.85824301681720e-01 , 3.19254195491642e+00 , 1.28185433712608e+00 , 1.30770649318966e+00 , 3.82341417641572e+00 , 8.15485986974327e-01 , 1.88749888489650e+00 , 5.08218920724669e+00 , 2.06838974384938e+00 , 2.58346613036847e+00 , 5.62073972587495e+00 , -3.54753217917702e-01 , 2.92076530153912e+00 , 4.98647989495056e+00 , -1.18059860901710e+00 , 3.01914604664074e+00 , 5.90115755916543e+00 , -3.94243204894331e-01 , 3.70183869752321e+00 , 3.87005048430333e+00 , -1.46136791229833e+00 , 4.60679178565910e+00 , 3.53446291377488e+00 , -7.67375356843104e-01 , 5.37852593586357e+00 , 2.40557758311810e+00 , -2.70861285809934e+00 , 3.89781582916249e+00 , 2.94244555060088e+00 , -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 , -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 , -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 , -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 , -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 , -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 , -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 , -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 , -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 , -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 , -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 , -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 , -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 , -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 , -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 , -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 , -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.2732 , 1.83662 , -14.9207 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.7293 , 6.77293 , 13.5459 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.2732 , 1.83662 , -14.9207 ) to colvar "one". -colvars: Adding total bias energy: 45.8141 +colvars: Adding biasing force ( 67.7293 , 6.77293 , 13.5459 ) to colvar "one". +colvars: Adding total bias energy: 58.9364 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.2732 , 1.83662 , -14.9207 ) +colvars: Force to be applied: ( 67.7293 , 6.77293 , 13.5459 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.84033 , -0.571928 , -1.60039 ) -colvars: ( -4.15058 , -0.490428 , -1.37234 ) -colvars: ( -4.15058 , -0.490428 , -1.37234 ) -colvars: ( -5.52869 , -0.653265 , -1.82799 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.24245 , -0.619393 , -1.73315 ) +colvars: ( -4.4954 , -0.531129 , -1.48618 ) +colvars: ( -4.4954 , -0.531129 , -1.48618 ) +colvars: ( -5.988 , -0.70748 , -1.97963 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.903074 , 0.192581 , 0.6507 ) -colvars: ( 0.780384 , 0.264594 , 0.676557 ) -colvars: ( 0.766151 , 0.256931 , 0.65739 ) -colvars: ( 0.664546 , 0.266933 , 0.610115 ) -colvars: ( 0.652397 , 0.200421 , 0.510762 ) -colvars: ( 0.57478 , 0.345509 , 0.664858 ) -colvars: ( 0.463502 , 0.36112 , 0.619527 ) -colvars: ( 0.383978 , 0.459551 , 0.707907 ) -colvars: ( 0.380632 , 0.316998 , 0.508619 ) -colvars: ( 0.344144 , 0.276077 , 0.430041 ) -colvars: ( 0.352328 , 0.321851 , 0.498309 ) -colvars: ( 0.280362 , 0.279236 , 0.396046 ) -colvars: ( 0.254409 , 0.307779 , 0.419935 ) -colvars: ( 0.345018 , 0.180496 , 0.298293 ) -colvars: ( 0.284718 , 0.137772 , 0.202897 ) -colvars: ( 0.471532 , 0.141983 , 0.321097 ) -colvars: ( 0.54647 , 0.0496204 , 0.238356 ) -colvars: ( 0.680396 , 0.0269253 , 0.287507 ) -colvars: ( 0.553494 , 0.0184252 , 0.19941 ) -colvars: ( 0.537367 , -0.0465365 , 0.09981 ) -colvars: ( 0.573307 , 0.0668544 , 0.278348 ) -colvars: ( 0.569884 , 0.05147 , 0.254999 ) -colvars: ( 0.605913 , 0.116491 , 0.366652 ) -colvars: ( 0.441552 , 0.0574899 , 0.186135 ) -colvars: ( 0.433918 , 0.00185543 , 0.104552 ) -colvars: ( 0.337063 , 0.124129 , 0.215504 ) -colvars: ( 0.208832 , 0.134142 , 0.152227 ) -colvars: ( 0.115172 , 0.22077 , 0.21577 ) -colvars: ( 0.181105 , 0.0601262 , 0.0331193 ) -colvars: ( 0.129816 , 0.024725 , -0.0467234 ) -colvars: ( 0.217497 , 0.0334169 , 0.0180474 ) -colvars: ( 0.204427 , -0.0395403 , -0.0907781 ) -colvars: ( 0.242723 , -0.0440971 , -0.0740483 ) -colvars: ( 0.281303 , -0.126149 , -0.164391 ) -colvars: ( 0.236237 , -0.178898 , -0.264498 ) -colvars: ( 0.399068 , -0.142132 , -0.115671 ) -colvars: ( 0.478039 , -0.218225 , -0.173473 ) -colvars: ( 0.612593 , -0.222081 , -0.0978724 ) -colvars: ( 0.427601 , -0.221458 , -0.208287 ) -colvars: ( 0.433081 , -0.289542 , -0.29921 ) -colvars: ( 0.37612 , -0.147017 , -0.136236 ) -colvars: ( 0.31861 , -0.139457 , -0.160368 ) -colvars: ( 0.300234 , -0.0519593 , -0.0503347 ) -colvars: ( 0.192127 , -0.147055 , -0.246965 ) -colvars: ( 0.166176 , -0.188473 , -0.319892 ) -colvars: ( -0.0117145 , -0.191974 , -0.431741 ) -colvars: ( -0.105012 , -0.208896 , -0.51128 ) -colvars: ( 0.0925722 , -0.243456 , -0.440256 ) -colvars: ( 0.109222 , -0.106045 , -0.240081 ) -colvars: ( -0.0130582 , -0.109316 , -0.318161 ) -colvars: ( -0.103904 , -0.0279159 , -0.260159 ) +colvars: ( 0.978076 , 0.208579 , 0.704715 ) +colvars: ( 0.845198 , 0.286571 , 0.73272 ) +colvars: ( 0.829782 , 0.278273 , 0.711963 ) +colvars: ( 0.719742 , 0.289103 , 0.660762 ) +colvars: ( 0.706584 , 0.217067 , 0.55316 ) +colvars: ( 0.622523 , 0.374202 , 0.72005 ) +colvars: ( 0.502006 , 0.391108 , 0.670955 ) +colvars: ( 0.415878 , 0.497712 , 0.766674 ) +colvars: ( 0.412254 , 0.343321 , 0.550839 ) +colvars: ( 0.372736 , 0.299001 , 0.465737 ) +colvars: ( 0.381599 , 0.348578 , 0.539675 ) +colvars: ( 0.303656 , 0.302424 , 0.428922 ) +colvars: ( 0.275547 , 0.333338 , 0.454796 ) +colvars: ( 0.37368 , 0.195485 , 0.323053 ) +colvars: ( 0.308374 , 0.149212 , 0.219736 ) +colvars: ( 0.5107 , 0.153775 , 0.347749 ) +colvars: ( 0.59186 , 0.0537435 , 0.258138 ) +colvars: ( 0.736906 , 0.0291659 , 0.31137 ) +colvars: ( 0.599468 , 0.0199567 , 0.215958 ) +colvars: ( 0.582001 , -0.0504 , 0.108088 ) +colvars: ( 0.620927 , 0.0724069 , 0.301449 ) +colvars: ( 0.617221 , 0.0557437 , 0.27616 ) +colvars: ( 0.656243 , 0.126163 , 0.397082 ) +colvars: ( 0.478233 , 0.0622615 , 0.201579 ) +colvars: ( 0.469965 , 0.00200631 , 0.113222 ) +colvars: ( 0.365068 , 0.134434 , 0.233387 ) +colvars: ( 0.226189 , 0.145276 , 0.164857 ) +colvars: ( 0.124752 , 0.239097 , 0.233677 ) +colvars: ( 0.196159 , 0.0651142 , 0.0358609 ) +colvars: ( 0.140611 , 0.026772 , -0.050611 ) +colvars: ( 0.235571 , 0.0361886 , 0.0195385 ) +colvars: ( 0.221416 , -0.0428267 , -0.0983218 ) +colvars: ( 0.262891 , -0.0477602 , -0.0802021 ) +colvars: ( 0.304675 , -0.136627 , -0.178048 ) +colvars: ( 0.255867 , -0.193758 , -0.286466 ) +colvars: ( 0.43222 , -0.153936 , -0.125284 ) +colvars: ( 0.517748 , -0.236348 , -0.187886 ) +colvars: ( 0.663475 , -0.240523 , -0.106009 ) +colvars: ( 0.463123 , -0.239851 , -0.225591 ) +colvars: ( 0.469058 , -0.313589 , -0.324064 ) +colvars: ( 0.407368 , -0.15923 , -0.147559 ) +colvars: ( 0.345084 , -0.151044 , -0.173694 ) +colvars: ( 0.325182 , -0.0562811 , -0.0545258 ) +colvars: ( 0.208097 , -0.159275 , -0.26748 ) +colvars: ( 0.179992 , -0.204133 , -0.346463 ) +colvars: ( -0.0126718 , -0.207924 , -0.467596 ) +colvars: ( -0.113717 , -0.226252 , -0.553737 ) +colvars: ( 0.100274 , -0.26368 , -0.476817 ) +colvars: ( 0.118308 , -0.114859 , -0.260023 ) +colvars: ( -0.0141262 , -0.118403 , -0.344586 ) +colvars: ( -0.112516 , -0.0302437 , -0.281767 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.84033 , 0.571928 , 1.60039 ) -colvars: ( 4.15058 , 0.490428 , 1.37234 ) -colvars: ( 4.15058 , 0.490428 , 1.37234 ) -colvars: ( 5.52869 , 0.653265 , 1.82799 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.24245 , 0.619393 , 1.73315 ) +colvars: ( 4.4954 , 0.531129 , 1.48618 ) +colvars: ( 4.4954 , 0.531129 , 1.48618 ) +colvars: ( 5.988 , 0.70748 , 1.97963 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.627615 , -0.0803386 , -0.402643 ) -colvars: ( -0.562184 , -0.162644 , -0.375296 ) -colvars: ( -0.515953 , -0.140825 , -0.318333 ) -colvars: ( -0.518047 , -0.190518 , -0.343837 ) -colvars: ( -0.508418 , -0.132507 , -0.306808 ) -colvars: ( -0.488952 , -0.281898 , -0.357461 ) -colvars: ( -0.451039 , -0.322432 , -0.338247 ) -colvars: ( -0.425473 , -0.428821 , -0.362499 ) -colvars: ( -0.387791 , -0.287939 , -0.258132 ) -colvars: ( -0.38098 , -0.263262 , -0.239637 ) -colvars: ( -0.340955 , -0.282387 , -0.208214 ) -colvars: ( -0.2808 , -0.246314 , -0.130479 ) -colvars: ( -0.23476 , -0.261025 , -0.0909025 ) -colvars: ( -0.303266 , -0.144114 , -0.105067 ) -colvars: ( -0.270457 , -0.115588 , -0.0585038 ) -colvars: ( -0.361966 , -0.0867489 , -0.137354 ) -colvars: ( -0.39171 , 0.0106314 , -0.121561 ) -colvars: ( -0.447187 , 0.0584443 , -0.155089 ) -colvars: ( -0.426325 , 0.0253396 , -0.1496 ) -colvars: ( -0.414817 , 0.0812633 , -0.111655 ) -colvars: ( -0.467772 , -0.0279898 , -0.216562 ) -colvars: ( -0.49862 , -0.0296075 , -0.24848 ) -colvars: ( -0.54656 , -0.0940514 , -0.327231 ) -colvars: ( -0.441907 , -0.0600057 , -0.205507 ) -colvars: ( -0.447549 , -0.0166137 , -0.190782 ) -colvars: ( -0.384226 , -0.133894 , -0.182027 ) -colvars: ( -0.322539 , -0.16554 , -0.134618 ) -colvars: ( -0.269934 , -0.255015 , -0.123599 ) -colvars: ( -0.283142 , -0.0937417 , -0.061033 ) -colvars: ( -0.267372 , -0.0757326 , -0.036629 ) -colvars: ( -0.267846 , -0.0491024 , -0.0245742 ) -colvars: ( -0.234822 , 0.0246784 , 0.0435066 ) -colvars: ( -0.218371 , 0.0511056 , 0.0725609 ) -colvars: ( -0.280406 , 0.110676 , 0.0379434 ) -colvars: ( -0.252924 , 0.151626 , 0.0849745 ) -colvars: ( -0.351927 , 0.139056 , -0.0209354 ) -colvars: ( -0.401979 , 0.214633 , -0.0359157 ) -colvars: ( -0.476388 , 0.237661 , -0.10023 ) -colvars: ( -0.408716 , 0.194626 , -0.0521367 ) -colvars: ( -0.413196 , 0.254641 , -0.0284146 ) -colvars: ( -0.408976 , 0.108808 , -0.0927914 ) -colvars: ( -0.411141 , 0.0785735 , -0.109209 ) -colvars: ( -0.429281 , -0.0137024 , -0.170961 ) -colvars: ( -0.341333 , 0.0667333 , -0.0442755 ) -colvars: ( -0.342402 , 0.0924665 , -0.0332427 ) -colvars: ( -0.180342 , 0.0980697 , 0.133075 ) -colvars: ( -0.128647 , 0.099378 , 0.185903 ) -colvars: ( -0.212159 , 0.170121 , 0.134852 ) -colvars: ( -0.278541 , 0.026155 , 4.52214e-05 ) -colvars: ( -0.209019 , 0.0120352 , 0.0636175 ) -colvars: ( -0.153454 , -0.070413 , 0.080932 ) +colvars: ( -0.679737 , -0.0870137 , -0.436053 ) +colvars: ( -0.608874 , -0.176153 , -0.406435 ) +colvars: ( -0.558802 , -0.152523 , -0.344743 ) +colvars: ( -0.561074 , -0.20634 , -0.372365 ) +colvars: ( -0.550646 , -0.143511 , -0.332264 ) +colvars: ( -0.529565 , -0.305307 , -0.387119 ) +colvars: ( -0.488507 , -0.349205 , -0.36631 ) +colvars: ( -0.46082 , -0.464428 , -0.392574 ) +colvars: ( -0.420008 , -0.311847 , -0.279546 ) +colvars: ( -0.412632 , -0.285121 , -0.259518 ) +colvars: ( -0.36928 , -0.305836 , -0.225483 ) +colvars: ( -0.30413 , -0.266767 , -0.141296 ) +colvars: ( -0.254266 , -0.2827 , -0.0984329 ) +colvars: ( -0.32846 , -0.156081 , -0.113777 ) +colvars: ( -0.292928 , -0.125186 , -0.0633496 ) +colvars: ( -0.392032 , -0.0939533 , -0.148744 ) +colvars: ( -0.424245 , 0.0115129 , -0.131642 ) +colvars: ( -0.484326 , 0.0632946 , -0.167953 ) +colvars: ( -0.461736 , 0.0274434 , -0.16201 ) +colvars: ( -0.449272 , 0.0880112 , -0.120917 ) +colvars: ( -0.506626 , -0.0303141 , -0.23453 ) +colvars: ( -0.540038 , -0.0320652 , -0.2691 ) +colvars: ( -0.591959 , -0.10186 , -0.354386 ) +colvars: ( -0.478618 , -0.0649862 , -0.22256 ) +colvars: ( -0.484728 , -0.0179905 , -0.206614 ) +colvars: ( -0.416148 , -0.14501 , -0.197129 ) +colvars: ( -0.349341 , -0.179282 , -0.145785 ) +colvars: ( -0.292369 , -0.276187 , -0.13385 ) +colvars: ( -0.306671 , -0.101522 , -0.0660933 ) +colvars: ( -0.289593 , -0.0820165 , -0.039665 ) +colvars: ( -0.290103 , -0.0531769 , -0.0266075 ) +colvars: ( -0.254336 , 0.0267304 , 0.0471237 ) +colvars: ( -0.236516 , 0.0553508 , 0.078591 ) +colvars: ( -0.303704 , 0.119869 , 0.0410966 ) +colvars: ( -0.27394 , 0.16422 , 0.0920304 ) +colvars: ( -0.381163 , 0.150604 , -0.0226701 ) +colvars: ( -0.43537 , 0.232458 , -0.0388958 ) +colvars: ( -0.515956 , 0.257397 , -0.108549 ) +colvars: ( -0.442669 , 0.21079 , -0.0564647 ) +colvars: ( -0.447522 , 0.275789 , -0.0307751 ) +colvars: ( -0.442953 , 0.117847 , -0.100493 ) +colvars: ( -0.4453 , 0.0851032 , -0.118274 ) +colvars: ( -0.464948 , -0.0148347 , -0.185152 ) +colvars: ( -0.369698 , 0.0722808 , -0.0479517 ) +colvars: ( -0.370856 , 0.100152 , -0.0360047 ) +colvars: ( -0.195338 , 0.10622 , 0.14412 ) +colvars: ( -0.139351 , 0.107638 , 0.201333 ) +colvars: ( -0.229794 , 0.184253 , 0.146045 ) +colvars: ( -0.301692 , 0.0283331 , 4.94566e-05 ) +colvars: ( -0.226397 , 0.0130417 , 0.0688985 ) +colvars: ( -0.166219 , -0.0762527 , 0.0876522 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 3. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 3. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 3, atoms_new_colvar_forces = { ( -4.56487061011886e+00 , -4.59685831895255e-01 , -1.35233694819707e+00 ), ( -3.93238146654361e+00 , -3.88478641659634e-01 , -1.07107701968183e+00 ), ( -4.00408244135132e+00 , -4.14012759563741e-01 , -1.10605930645938e+00 ), ( -5.38471609876755e+00 , -5.85350253472914e-01 , -1.62403928539813e+00 ), ( 2.50197518083188e-01 , 1.16105599315324e-01 , 3.39056906872779e-01 ), ( 4.92615705354908e+00 , 6.35538871221162e-01 , 1.90779136990955e+00 ), ( 4.16304480640670e+00 , 5.29116839520988e-01 , 1.65361772228232e+00 ), ( -4.14949383727183e-02 , 3.07305285718129e-02 , 3.45408411279225e-01 ), ( 4.14342185132284e+00 , 5.19487842965588e-01 , 1.62282443813380e+00 ), ( 5.49185857422559e+00 , 6.66080075257598e-01 , 2.01839684326895e+00 ), ( 1.13735276396146e-02 , 3.94637412988196e-02 , 2.90095116759329e-01 ), ( -4.37980711462616e-04 , 3.29219895556979e-02 , 2.65567142933957e-01 ), ( 1.96493372913084e-02 , 4.67544004734959e-02 , 3.29032608954994e-01 ), ( 4.17517513185083e-02 , 3.63815161495367e-02 , 1.93226093065388e-01 ), ( 1.42613454118347e-02 , 2.21833393193577e-02 , 1.44393101146810e-01 ), ( 1.09566380540977e-01 , 5.52336030720906e-02 , 1.83742711865076e-01 ), ( 1.54760666636931e-01 , 6.02518219830255e-02 , 1.16794349329711e-01 ), ( 2.33208169185079e-01 , 8.53695062893084e-02 , 1.32417563596404e-01 ), ( 1.27169303485221e-01 , 4.37648180459563e-02 , 4.98102976435282e-02 ), ( 1.22549673285161e-01 , 3.47268139157361e-02 , -1.18451040129114e-02 ), ( 1.05535179110596e-01 , 3.88646125237500e-02 , 6.17863190148528e-02 ), ( 7.12637190605996e-02 , 2.18625136619909e-02 , 6.51885003976191e-03 ), ( 5.93534652820759e-02 , 2.24391092563474e-02 , 3.94210417867065e-02 ), ( -3.54900192036711e-04 , -2.51577365533177e-03 , -1.93718318195105e-02 ), ( -1.36306602564206e-02 , -1.47582898551569e-02 , -8.62299095607836e-02 ), ( -4.71627870611054e-02 , -9.76542623030544e-03 , 3.34769198330712e-02 ), ( -1.13707074495827e-01 , -3.13973323221215e-02 , 1.76093197346190e-02 ), ( -1.54761587457910e-01 , -3.42451509648487e-02 , 9.21709637097256e-02 ), ( -1.02036789446135e-01 , -3.36155506237409e-02 , -2.79137093293044e-02 ), ( -1.37556306244541e-01 , -5.10076308736129e-02 , -8.33523807337776e-02 ), ( -5.03494574316361e-02 , -1.56854513186011e-02 , -6.52673962942850e-03 ), ( -3.03949427132665e-02 , -1.48618314992314e-02 , -4.72714612957865e-02 ), ( 2.43523124840560e-02 , 7.00851641007569e-03 , -1.48746276996539e-03 ), ( 8.96461779929136e-04 , -1.54723804513230e-02 , -1.26448067123199e-01 ), ( -1.66866040324639e-02 , -2.72719594462136e-02 , -1.79523664908714e-01 ), ( 4.71411047327051e-02 , -3.07609723793698e-03 , -1.36606863263470e-01 ), ( 7.60594961592974e-02 , -3.59179757849404e-03 , -2.09388962054148e-01 ), ( 1.36205003469239e-01 , 1.55797619110987e-02 , -1.98102552728792e-01 ), ( 1.88850720429327e-02 , -2.68325710041684e-02 , -2.60423364304162e-01 ), ( 1.98842994345018e-02 , -3.49010102631597e-02 , -3.27624815446407e-01 ), ( -3.28557809917819e-02 , -3.82093859713364e-02 , -2.29027780483115e-01 ), ( -9.25307546435023e-02 , -6.08837585106190e-02 , -2.69576051073301e-01 ), ( -1.29046508739680e-01 , -6.56616889443625e-02 , -2.21295666946355e-01 ), ( -1.49206511158328e-01 , -8.03219299582977e-02 , -2.91240214591351e-01 ), ( -1.76225841867150e-01 , -9.60065163528050e-02 , -3.53134587891629e-01 ), ( -1.92056714839460e-01 , -9.39041113894416e-02 , -2.98666867374924e-01 ), ( -2.33658882296404e-01 , -1.09517546841951e-01 , -3.25376851383054e-01 ), ( -1.19587084081475e-01 , -7.33352095500071e-02 , -3.05404423424871e-01 ), ( -1.69318973902053e-01 , -7.98904179788683e-02 , -2.40035638596806e-01 ), ( -2.22076815170801e-01 , -9.72806075816354e-02 , -2.54543565760879e-01 ), ( -2.57357559050462e-01 , -9.83289077236454e-02 , -1.79226994917502e-01 ) } +colvars: Step 3, atoms_new_colvar_forces = { ( -4.94411184671079e+00 , -4.97827513445736e-01 , -1.46449135037820e+00 ), ( -4.25907640521865e+00 , -4.20711456786056e-01 , -1.15989394156424e+00 ), ( -4.33673317769691e+00 , -4.48366501363439e-01 , -1.19778202100695e+00 ), ( -5.83206630045447e+00 , -6.33924119977363e-01 , -1.75873742632449e+00 ), ( 2.70980020612708e-01 , 1.25749755944837e-01 , 3.67220461302410e-01 ), ( 5.33540843769253e+00 , 6.88287635230181e-01 , 2.06608439293031e+00 ), ( 4.50889974963906e+00 , 5.73031757721403e-01 , 1.79082311728939e+00 ), ( -4.49416315065174e-02 , 3.32833456980806e-02 , 3.74099563837129e-01 ), ( 4.48764679167200e+00 , 5.62602923523582e-01 , 1.75747196273388e+00 ), ( 5.94810856283136e+00 , 7.21359809854066e-01 , 2.18585209845762e+00 ), ( 1.23182431151496e-02 , 4.27418719254232e-02 , 3.14191620291453e-01 ), ( -4.74416193415428e-04 , 3.56567177610567e-02 , 2.87626199467661e-01 ), ( 2.12814041388975e-02 , 5.06380997492398e-02 , 3.56363328527525e-01 ), ( 4.52197772755877e-02 , 3.94035396542006e-02 , 2.09276201599730e-01 ), ( 1.54458868355712e-02 , 2.40259994114552e-02 , 1.56386914327082e-01 ), ( 1.18667398254240e-01 , 5.98215048345298e-02 , 1.99005120483717e-01 ), ( 1.67615720865544e-01 , 6.52564920828010e-02 , 1.26495754888538e-01 ), ( 2.52579421928450e-01 , 9.24605005403267e-02 , 1.43416723091599e-01 ), ( 1.37732531939567e-01 , 4.74000180514384e-02 , 5.39477638410795e-02 ), ( 1.32729168872771e-01 , 3.76112537757227e-02 , -1.28290054297651e-02 ), ( 1.14301418742866e-01 , 4.20928208462876e-02 , 6.69186082022440e-02 ), ( 7.71832550686790e-02 , 2.36784766810483e-02 , 7.06042771512738e-03 ), ( 6.42837202712789e-02 , 2.43030078484564e-02 , 4.26956614103106e-02 ), ( -3.84329372512093e-04 , -2.72472916439909e-03 , -2.09808707804465e-02 ), ( -1.47628235207854e-02 , -1.59841739107175e-02 , -9.33924543843910e-02 ), ( -5.10803034919172e-02 , -1.05765153684527e-02 , 3.62576862219569e-02 ), ( -1.23152065175043e-01 , -3.40052163812419e-02 , 1.90720230464335e-02 ), ( -1.67616763767845e-01 , -3.70895287307892e-02 , 9.98270398312682e-02 ), ( -1.10512426265833e-01 , -3.64077329425433e-02 , -3.02323805237733e-02 ), ( -1.48982346206602e-01 , -5.52444650887813e-02 , -9.02760252414938e-02 ), ( -5.45317489037881e-02 , -1.69883324043285e-02 , -7.06894903341551e-03 ), ( -3.29197549988429e-02 , -1.60963474146286e-02 , -5.11981358015210e-02 ), ( 2.63750143131919e-02 , 7.59060243351772e-03 , -1.61115692641367e-03 ), ( 9.70867813391729e-04 , -1.67576633972936e-02 , -1.36951455760848e-01 ), ( -1.80727359462569e-02 , -2.95373785036137e-02 , -1.94435756236881e-01 ), ( 5.10568221807806e-02 , -3.33172246149266e-03 , -1.47954036182704e-01 ), ( 8.23773230277767e-02 , -3.89030474462265e-03 , -2.26781689509279e-01 ), ( 1.47518804880217e-01 , 1.68736913838752e-02 , -2.14557736824648e-01 ), ( 2.04537680097125e-02 , -2.90615161904835e-02 , -2.82055200722617e-01 ), ( 2.15359977798839e-02 , -3.78001826957295e-02 , -3.54838685488566e-01 ), ( -3.55848857133958e-02 , -4.13832707320046e-02 , -2.48051749485939e-01 ), ( -1.00216698830745e-01 , -6.59410279588554e-02 , -2.91968109753298e-01 ), ( -1.39765584367239e-01 , -7.11157696196284e-02 , -2.39677324262951e-01 ), ( -1.61600215592381e-01 , -8.69937885828269e-02 , -3.15431833916719e-01 ), ( -1.90863879034194e-01 , -1.03981201565893e-01 , -3.82467406313103e-01 ), ( -2.08009834583172e-01 , -1.01704171955603e-01 , -3.23475504908314e-01 ), ( -2.53067678027391e-01 , -1.18614509952742e-01 , -3.52404165644519e-01 ), ( -1.29520566963423e-01 , -7.94267978023419e-02 , -3.30772706408666e-01 ), ( -1.83383340883908e-01 , -8.65264099464878e-02 , -2.59974038061368e-01 ), ( -2.40523504544333e-01 , -1.05361075555689e-01 , -2.75687099588435e-01 ), ( -2.78734843790854e-01 , -1.06496400307745e-01 , -1.94114453032528e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 3, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2640,10 +4182,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 4, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 4, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 4, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 4, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 4, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 4, atoms_positions[size = 51] = { ( 8.39630587064579e+00 , 4.29943465782394e-02 , -7.52199108723305e-01 ), ( 6.99593233779914e+00 , -4.93189643592685e-01 , -6.60809448212279e-01 ), ( 6.25334620052430e+00 , -2.55576423048625e-01 , 6.52134952756242e-01 ), ( 5.00863481394510e+00 , -2.08509189081610e-01 , 6.56823873951176e-01 ), ( 7.03960944147393e+00 , -2.01594374016989e+00 , -1.02263212502426e+00 ), ( 6.90486605359888e+00 , -2.69474731448735e-01 , 1.79995455816582e+00 ), ( 6.17721298300845e+00 , -1.24592364672657e-01 , 3.05436709893728e+00 ), ( 7.18263050000036e+00 , -3.19480526235659e-01 , 4.30079231053380e+00 ), ( 5.30638862165417e+00 , 1.12357846240288e+00 , 3.27971835376572e+00 ), ( 4.08699891438005e+00 , 1.07094504461034e+00 , 3.61687655216301e+00 ), ( 5.87480603087758e+00 , 2.32183540838686e+00 , 2.96384694642444e+00 ), ( 5.22401915265732e+00 , 3.59700412458860e+00 , 2.88057747926707e+00 ), ( 6.33313533401084e+00 , 4.61702887256776e+00 , 2.46480269594214e+00 ), ( 3.89738305245604e+00 , 3.71211781175670e+00 , 2.02161270713417e+00 ), ( 2.91712091159561e+00 , 4.11519986001302e+00 , 2.55927131780976e+00 ), ( 3.82085076072587e+00 , 3.24332122198801e+00 , 7.80298010083329e-01 ), ( 2.66609412663421e+00 , 3.18393292087782e+00 , -8.09732098745300e-02 ), ( 3.04893607098911e+00 , 2.72636467572710e+00 , -1.59291650460730e+00 ), ( 1.63335066410015e+00 , 2.15440563920939e+00 , 5.80232627280548e-01 ), ( 4.29818984818214e-01 , 2.44050626812841e+00 , 5.61388467671019e-01 ), ( 1.97583065645857e+00 , 1.00857630417830e+00 , 1.05487824551291e+00 ), ( 1.13634226071496e+00 , 1.23089593893438e-02 , 1.68772194611812e+00 ), ( 2.01544817887602e+00 , -1.19309537116505e+00 , 2.02278050366493e+00 ), ( 5.08048336175847e-01 , 5.94101137645552e-01 , 3.00574686454125e+00 ), ( -6.78412934869142e-01 , 3.80967717896477e-01 , 3.18874653147992e+00 ), ( 1.28890187333229e+00 , 1.31089121022321e+00 , 3.82435149915531e+00 ), ( 8.22534449637726e-01 , 1.89379486709480e+00 , 5.07838479055152e+00 ), ( 2.06389289096600e+00 , 2.58645934212356e+00 , 5.62114574845432e+00 ), ( -3.57121046548542e-01 , 2.92054171335235e+00 , 4.98576532871696e+00 ), ( -1.17836314763820e+00 , 3.02261193921792e+00 , 5.90276985343399e+00 ), ( -4.01301426275823e-01 , 3.69849913582816e+00 , 3.86545359028066e+00 ), ( -1.46590819015392e+00 , 4.59865726720223e+00 , 3.53615951568706e+00 ), ( -7.63234155976260e-01 , 5.38072815661016e+00 , 2.40731489624795e+00 ), ( -2.71331069827867e+00 , 3.89707543976032e+00 , 2.93922599438776e+00 ), ( -3.85425520137104e+00 , 4.41458103160539e+00 , 2.85997009027781e+00 ), ( -2.56891327231543e+00 , 2.61382709061189e+00 , 2.50018343044392e+00 ), ( -3.72280990264342e+00 , 1.90196009531901e+00 , 2.07499763501250e+00 ), ( -3.40868018825125e+00 , 7.99802390159160e-01 , 1.00115989809505e+00 ), ( -4.32545326123900e+00 , 1.10899602039969e+00 , 3.22040107072979e+00 ), ( -5.53351212628670e+00 , 9.30424355623366e-01 , 3.34744388032221e+00 ), ( -3.47526168876013e+00 , 6.31186970943236e-01 , 4.16470822933633e+00 ), ( -3.76916025366485e+00 , 1.03561979531401e-01 , 5.47575484720759e+00 ), ( -2.42579310007635e+00 , -4.19509630099199e-01 , 6.13327791685099e+00 ), ( -4.46410471486241e+00 , 1.00719118603773e+00 , 6.41671194409057e+00 ), ( -5.32471233100479e+00 , 5.95667181679337e-01 , 7.18047936707207e+00 ), ( -6.29683336764235e+00 , 3.54744147510084e+00 , 6.69753385518659e+00 ), ( -6.91965812216361e+00 , 4.30777659601339e+00 , 7.41750168295901e+00 ), ( -6.75473038539063e+00 , 3.20844432219158e+00 , 5.50482636834567e+00 ), ( -4.08019852473436e+00 , 2.29656195202179e+00 , 6.47727219430328e+00 ), ( -4.91287960219249e+00 , 3.24198162568352e+00 , 7.21486613348559e+00 ), ( -4.06885052697904e+00 , 4.49555549485688e+00 , 7.26530725052506e+00 ) } +colvars: Step 4, atoms_positions[size = 51] = { ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 ), ( 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 ), ( 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 ), ( 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ), ( 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 ), ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 ), ( 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 ), ( 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 ), ( 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 ), ( 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ), ( 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 ), ( 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 ), ( 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 ), ( 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 ), ( 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 ), ( 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 ), ( 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 ), ( 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 ), ( 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 ), ( 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 ), ( 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 ), ( 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 ), ( 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 ), ( 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 ), ( -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 ), ( 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 ), ( 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 ), ( 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 ), ( -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 ), ( -1.17836558276957e+00 , 3.02261104816295e+00 , 5.90276840372370e+00 ), ( -4.01302424179341e-01 , 3.69849881712387e+00 , 3.86545342166451e+00 ), ( -1.46590890439991e+00 , 4.59865695705450e+00 , 3.53615846971960e+00 ), ( -7.63233646113516e-01 , 5.38072830628868e+00 , 2.40731483544891e+00 ), ( -2.71331069598888e+00 , 3.89707509031229e+00 , 2.93922305454171e+00 ), ( -3.85425548868909e+00 , 4.41458054455749e+00 , 2.85996693260786e+00 ), ( -2.56891242118530e+00 , 2.61382706053113e+00 , 2.50018071521494e+00 ), ( -3.72280812663129e+00 , 1.90195999542730e+00 , 2.07499278897672e+00 ), ( -3.40867725952187e+00 , 7.99802561950416e-01 , 1.00115557235893e+00 ), ( -4.32545280821172e+00 , 1.10899537342912e+00 , 3.22039502470298e+00 ), ( -5.53351177439246e+00 , 9.30423737330286e-01 , 3.34743812026931e+00 ), ( -3.47526232399215e+00 , 6.31186205193408e-01 , 4.16470361442067e+00 ), ( -3.76916231092019e+00 , 1.03560723559009e-01 , 5.47574864057925e+00 ), ( -2.42579604390000e+00 , -4.19510894178595e-01 , 6.13327314251220e+00 ), ( -4.46410817799216e+00 , 1.00718933605956e+00 , 6.41670516158355e+00 ), ( -5.32471542662051e+00 , 5.95665490335250e-01 , 7.18047316154811e+00 ), ( -6.29683784304267e+00 , 3.54743931376085e+00 , 6.69752696916196e+00 ), ( -6.91966222332481e+00 , 4.30777465539821e+00 , 7.41749594212074e+00 ), ( -6.75473280268310e+00 , 3.20844297878927e+00 , 5.50482041882141e+00 ), ( -4.08020191955437e+00 , 2.29656035348140e+00 , 6.47726737906147e+00 ), ( -4.91288479652016e+00 , 3.24197930773862e+00 , 7.21486048527815e+00 ), ( -4.06885606267348e+00 , 4.49555323945452e+00 , 7.26530353283818e+00 ) } colvars: Step 4, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 4, atom_groups_ids[size = 0] = @@ -2661,162 +4203,301 @@ colvars: Collective variables module, step no. 4 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.36592560477046e-01 , 5.33466425476265e-03 , 9.41635274184647e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 , 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 , 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 , 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 , 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 , 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 , 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 , 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 , 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 , 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 , 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 , 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 , 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 , 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 , 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 , 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 , -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 , 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 , 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 , 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 , -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 , -1.17836558276957e+00 , 3.02261104816295e+00 , 5.90276840372370e+00 , -4.01302424179341e-01 , 3.69849881712387e+00 , 3.86545342166451e+00 , -1.46590890439991e+00 , 4.59865695705450e+00 , 3.53615846971960e+00 , -7.63233646113516e-01 , 5.38072830628868e+00 , 2.40731483544891e+00 , -2.71331069598888e+00 , 3.89707509031229e+00 , 2.93922305454171e+00 , -3.85425548868909e+00 , 4.41458054455749e+00 , 2.85996693260786e+00 , -2.56891242118530e+00 , 2.61382706053113e+00 , 2.50018071521494e+00 , -3.72280812663129e+00 , 1.90195999542730e+00 , 2.07499278897672e+00 , -3.40867725952187e+00 , 7.99802561950416e-01 , 1.00115557235893e+00 , -4.32545280821172e+00 , 1.10899537342912e+00 , 3.22039502470298e+00 , -5.53351177439246e+00 , 9.30423737330286e-01 , 3.34743812026931e+00 , -3.47526232399215e+00 , 6.31186205193408e-01 , 4.16470361442067e+00 , -3.76916231092019e+00 , 1.03560723559009e-01 , 5.47574864057925e+00 , -2.42579604390000e+00 , -4.19510894178595e-01 , 6.13327314251220e+00 , -4.46410817799216e+00 , 1.00718933605956e+00 , 6.41670516158355e+00 , -5.32471542662051e+00 , 5.95665490335250e-01 , 7.18047316154811e+00 , -6.29683784304267e+00 , 3.54743931376085e+00 , 6.69752696916196e+00 , -6.91966222332481e+00 , 4.30777465539821e+00 , 7.41749594212074e+00 , -6.75473280268310e+00 , 3.20844297878927e+00 , 5.50482041882141e+00 , -4.08020191955437e+00 , 2.29656035348140e+00 , 6.47726737906147e+00 , -4.91288479652016e+00 , 3.24197930773862e+00 , 7.21486048527815e+00 , -4.06885606267348e+00 , 4.49555323945452e+00 , 7.26530353283818e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.36535507777281e-01 , 5.34093077602620e-03 , 9.41655630505937e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.36592560477046e-01 , 5.33466425476265e-03 , 9.41635274184647e-01 ). +colvars: Colvar "one" has value ( -3.36535507777281e-01 , 5.34093077602620e-03 , 9.41655630505937e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 , 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 , 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 , 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 , 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 , 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 , 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 , 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 , 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 , 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 , 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 , 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 , 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 , 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 , 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 , 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 , -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 , 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 , 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 , 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 , -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 , -1.17836558276957e+00 , 3.02261104816295e+00 , 5.90276840372370e+00 , -4.01302424179341e-01 , 3.69849881712387e+00 , 3.86545342166451e+00 , -1.46590890439991e+00 , 4.59865695705450e+00 , 3.53615846971960e+00 , -7.63233646113516e-01 , 5.38072830628868e+00 , 2.40731483544891e+00 , -2.71331069598888e+00 , 3.89707509031229e+00 , 2.93922305454171e+00 , -3.85425548868909e+00 , 4.41458054455749e+00 , 2.85996693260786e+00 , -2.56891242118530e+00 , 2.61382706053113e+00 , 2.50018071521494e+00 , -3.72280812663129e+00 , 1.90195999542730e+00 , 2.07499278897672e+00 , -3.40867725952187e+00 , 7.99802561950416e-01 , 1.00115557235893e+00 , -4.32545280821172e+00 , 1.10899537342912e+00 , 3.22039502470298e+00 , -5.53351177439246e+00 , 9.30423737330286e-01 , 3.34743812026931e+00 , -3.47526232399215e+00 , 6.31186205193408e-01 , 4.16470361442067e+00 , -3.76916231092019e+00 , 1.03560723559009e-01 , 5.47574864057925e+00 , -2.42579604390000e+00 , -4.19510894178595e-01 , 6.13327314251220e+00 , -4.46410817799216e+00 , 1.00718933605956e+00 , 6.41670516158355e+00 , -5.32471542662051e+00 , 5.95665490335250e-01 , 7.18047316154811e+00 , -6.29683784304267e+00 , 3.54743931376085e+00 , 6.69752696916196e+00 , -6.91966222332481e+00 , 4.30777465539821e+00 , 7.41749594212074e+00 , -6.75473280268310e+00 , 3.20844297878927e+00 , 5.50482041882141e+00 , -4.08020191955437e+00 , 2.29656035348140e+00 , 6.47726737906147e+00 , -4.91288479652016e+00 , 3.24197930773862e+00 , 7.21486048527815e+00 , -4.06885606267348e+00 , 4.49555323945452e+00 , 7.26530353283818e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.2499 , 1.84511 , -14.9291 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.6692 , 6.76692 , 13.5338 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.2499 , 1.84511 , -14.9291 ) to colvar "one". -colvars: Adding total bias energy: 45.7669 +colvars: Adding biasing force ( 67.6692 , 6.76692 , 13.5338 ) to colvar "one". +colvars: Adding total bias energy: 58.8527 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.2499 , 1.84511 , -14.9291 ) +colvars: Force to be applied: ( 67.6692 , 6.76692 , 13.5338 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.84306 , -0.570804 , -1.59539 ) -colvars: ( -4.15292 , -0.489465 , -1.36805 ) -colvars: ( -4.15292 , -0.489465 , -1.36805 ) -colvars: ( -5.53182 , -0.651981 , -1.82228 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.23957 , -0.61745 , -1.72566 ) +colvars: ( -4.49293 , -0.529463 , -1.47975 ) +colvars: ( -4.49293 , -0.529463 , -1.47975 ) +colvars: ( -5.98471 , -0.705261 , -1.97107 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.902607 , 0.192767 , 0.649526 ) -colvars: ( 0.780045 , 0.264756 , 0.67528 ) -colvars: ( 0.765734 , 0.257105 , 0.656115 ) -colvars: ( 0.664379 , 0.267042 , 0.608928 ) -colvars: ( 0.652243 , 0.200504 , 0.509757 ) -colvars: ( 0.574751 , 0.345598 , 0.663541 ) -colvars: ( 0.463648 , 0.36116 , 0.618264 ) -colvars: ( 0.384243 , 0.459583 , 0.706454 ) -colvars: ( 0.380828 , 0.317001 , 0.507517 ) -colvars: ( 0.344416 , 0.276046 , 0.429083 ) -colvars: ( 0.352477 , 0.321861 , 0.497191 ) -colvars: ( 0.280541 , 0.279216 , 0.395076 ) -colvars: ( 0.254535 , 0.307776 , 0.418884 ) -colvars: ( 0.345106 , 0.180475 , 0.297529 ) -colvars: ( 0.284877 , 0.137714 , 0.202288 ) -colvars: ( 0.471463 , 0.142003 , 0.320337 ) -colvars: ( 0.546302 , 0.0496451 , 0.237779 ) -colvars: ( 0.680042 , 0.0270031 , 0.286884 ) -colvars: ( 0.553398 , 0.018426 , 0.198934 ) -colvars: ( 0.537287 , -0.0465617 , 0.099515 ) -colvars: ( 0.573259 , 0.0668623 , 0.277753 ) -colvars: ( 0.569922 , 0.0514542 , 0.254472 ) -colvars: ( 0.605975 , 0.116495 , 0.365948 ) -colvars: ( 0.441761 , 0.0574199 , 0.185692 ) -colvars: ( 0.434165 , 0.00175912 , 0.104268 ) -colvars: ( 0.337376 , 0.124041 , 0.214957 ) -colvars: ( 0.209303 , 0.134004 , 0.15175 ) -colvars: ( 0.115732 , 0.220625 , 0.21513 ) -colvars: ( 0.181554 , 0.0599665 , 0.0328395 ) -colvars: ( 0.130354 , 0.0245276 , -0.0468646 ) -colvars: ( 0.217823 , 0.0332811 , 0.0177865 ) -colvars: ( 0.204712 , -0.0396912 , -0.0908564 ) -colvars: ( 0.242875 , -0.044215 , -0.0741694 ) -colvars: ( 0.281522 , -0.126301 , -0.164292 ) -colvars: ( 0.236504 , -0.179083 , -0.26423 ) -colvars: ( 0.39918 , -0.142248 , -0.115607 ) -colvars: ( 0.47809 , -0.21834 , -0.173259 ) -colvars: ( 0.612502 , -0.222146 , -0.0977414 ) -colvars: ( 0.427791 , -0.221611 , -0.208003 ) -colvars: ( 0.433276 , -0.289716 , -0.298749 ) -colvars: ( 0.376428 , -0.147181 , -0.136092 ) -colvars: ( 0.319062 , -0.139658 , -0.160177 ) -colvars: ( 0.300766 , -0.0521534 , -0.0503418 ) -colvars: ( 0.192714 , -0.147306 , -0.246666 ) -colvars: ( 0.166833 , -0.188756 , -0.319455 ) -colvars: ( -0.0110242 , -0.192291 , -0.431218 ) -colvars: ( -0.104221 , -0.209253 , -0.510647 ) -colvars: ( 0.0930934 , -0.243737 , -0.439689 ) -colvars: ( 0.109852 , -0.106305 , -0.239846 ) -colvars: ( -0.0123028 , -0.109622 , -0.317833 ) -colvars: ( -0.103074 , -0.0282269 , -0.259987 ) +colvars: ( 0.976464 , 0.208547 , 0.702628 ) +colvars: ( 0.843878 , 0.286424 , 0.730489 ) +colvars: ( 0.828394 , 0.278149 , 0.70976 ) +colvars: ( 0.718751 , 0.288893 , 0.658711 ) +colvars: ( 0.705622 , 0.216911 , 0.551429 ) +colvars: ( 0.621792 , 0.373873 , 0.717791 ) +colvars: ( 0.501603 , 0.390705 , 0.668811 ) +colvars: ( 0.415703 , 0.497178 , 0.764213 ) +colvars: ( 0.412007 , 0.342932 , 0.549009 ) +colvars: ( 0.372617 , 0.298625 , 0.464159 ) +colvars: ( 0.381335 , 0.348192 , 0.53784 ) +colvars: ( 0.303514 , 0.302058 , 0.427375 ) +colvars: ( 0.275379 , 0.332955 , 0.453133 ) +colvars: ( 0.373359 , 0.19524 , 0.32185 ) +colvars: ( 0.308203 , 0.148979 , 0.21882 ) +colvars: ( 0.510051 , 0.153623 , 0.346523 ) +colvars: ( 0.591012 , 0.0537111 , 0.257212 ) +colvars: ( 0.73569 , 0.0292204 , 0.310332 ) +colvars: ( 0.59869 , 0.0199359 , 0.215188 ) +colvars: ( 0.581261 , -0.050369 , 0.107638 ) +colvars: ( 0.620177 , 0.0723336 , 0.300452 ) +colvars: ( 0.616569 , 0.0556627 , 0.275264 ) +colvars: ( 0.655572 , 0.126024 , 0.395856 ) +colvars: ( 0.477925 , 0.062113 , 0.20086 ) +colvars: ( 0.469708 , 0.0018974 , 0.112776 ) +colvars: ( 0.365002 , 0.134183 , 0.23252 ) +colvars: ( 0.226453 , 0.144958 , 0.164145 ) +colvars: ( 0.125227 , 0.238664 , 0.23271 ) +colvars: ( 0.196432 , 0.0648636 , 0.0355108 ) +colvars: ( 0.141045 , 0.0265233 , -0.050712 ) +colvars: ( 0.235666 , 0.0359979 , 0.0192281 ) +colvars: ( 0.221481 , -0.0429434 , -0.0982988 ) +colvars: ( 0.262764 , -0.0478342 , -0.0802453 ) +colvars: ( 0.304575 , -0.136638 , -0.177742 ) +colvars: ( 0.255874 , -0.193739 , -0.285853 ) +colvars: ( 0.431857 , -0.153888 , -0.125077 ) +colvars: ( 0.517223 , -0.236204 , -0.187445 ) +colvars: ( 0.662629 , -0.240319 , -0.105754 ) +colvars: ( 0.462811 , -0.239746 , -0.225032 ) +colvars: ( 0.468745 , -0.313423 , -0.323201 ) +colvars: ( 0.407248 , -0.159229 , -0.147241 ) +colvars: ( 0.345191 , -0.151094 , -0.173297 ) +colvars: ( 0.3254 , -0.0564323 , -0.0544799 ) +colvars: ( 0.208508 , -0.159371 , -0.266858 ) +colvars: ( 0.180511 , -0.204213 , -0.3456 ) +colvars: ( -0.0118988 , -0.208037 , -0.466498 ) +colvars: ( -0.112719 , -0.226389 , -0.552422 ) +colvars: ( 0.100734 , -0.263689 , -0.475662 ) +colvars: ( 0.118867 , -0.115016 , -0.259477 ) +colvars: ( -0.0132805 , -0.118606 , -0.343842 ) +colvars: ( -0.111477 , -0.0305532 , -0.281262 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.84306 , 0.570804 , 1.59539 ) -colvars: ( 4.15292 , 0.489465 , 1.36805 ) -colvars: ( 4.15292 , 0.489465 , 1.36805 ) -colvars: ( 5.53182 , 0.651981 , 1.82228 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.23957 , 0.61745 , 1.72566 ) +colvars: ( 4.49293 , 0.529463 , 1.47975 ) +colvars: ( 4.49293 , 0.529463 , 1.47975 ) +colvars: ( 5.98471 , 0.705261 , 1.97107 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.627104 , -0.0803608 , -0.401461 ) -colvars: ( -0.561809 , -0.162717 , -0.373921 ) -colvars: ( -0.515412 , -0.14086 , -0.31686 ) -colvars: ( -0.517883 , -0.190604 , -0.34256 ) -colvars: ( -0.508255 , -0.13254 , -0.305749 ) -colvars: ( -0.488975 , -0.282057 , -0.356018 ) -colvars: ( -0.451287 , -0.322617 , -0.336868 ) -colvars: ( -0.425887 , -0.429092 , -0.360877 ) -colvars: ( -0.388043 , -0.288072 , -0.256872 ) -colvars: ( -0.381332 , -0.263374 , -0.238572 ) -colvars: ( -0.341089 , -0.282497 , -0.206842 ) -colvars: ( -0.280912 , -0.246372 , -0.129207 ) -colvars: ( -0.234749 , -0.261076 , -0.0894365 ) -colvars: ( -0.303251 , -0.144089 , -0.104062 ) -colvars: ( -0.270507 , -0.115529 , -0.0576641 ) -colvars: ( -0.36177 , -0.086691 , -0.136397 ) -colvars: ( -0.391384 , 0.0107654 , -0.120851 ) -colvars: ( -0.446637 , 0.0586049 , -0.154349 ) -colvars: ( -0.426137 , 0.0254712 , -0.149096 ) -colvars: ( -0.414634 , 0.0814467 , -0.111367 ) -colvars: ( -0.467706 , -0.0279212 , -0.21599 ) -colvars: ( -0.498712 , -0.0295545 , -0.248072 ) -colvars: ( -0.546745 , -0.0940725 , -0.326685 ) -colvars: ( -0.442197 , -0.0599633 , -0.20517 ) -colvars: ( -0.447893 , -0.0165373 , -0.190668 ) -colvars: ( -0.384622 , -0.133898 , -0.1815 ) -colvars: ( -0.323109 , -0.165552 , -0.134132 ) -colvars: ( -0.270594 , -0.255088 , -0.12285 ) -colvars: ( -0.283628 , -0.0936773 , -0.0607249 ) -colvars: ( -0.26797 , -0.0756497 , -0.0364999 ) -colvars: ( -0.26813 , -0.0489899 , -0.024225 ) -colvars: ( -0.234999 , 0.0248681 , 0.0436921 ) -colvars: ( -0.218332 , 0.0513285 , 0.0728703 ) -colvars: ( -0.28052 , 0.110925 , 0.0378527 ) -colvars: ( -0.253073 , 0.151919 , 0.0846994 ) -colvars: ( -0.351951 , 0.139306 , -0.0210618 ) -colvars: ( -0.401953 , 0.214932 , -0.0362933 ) -colvars: ( -0.476225 , 0.237957 , -0.100575 ) -colvars: ( -0.408904 , 0.1949 , -0.0526585 ) -colvars: ( -0.413387 , 0.254965 , -0.0291688 ) -colvars: ( -0.409351 , 0.109005 , -0.0931761 ) -colvars: ( -0.411734 , 0.0787388 , -0.109701 ) -colvars: ( -0.430024 , -0.0136259 , -0.17126 ) -colvars: ( -0.342057 , 0.0669099 , -0.0448369 ) -colvars: ( -0.343224 , 0.0926625 , -0.0340042 ) -colvars: ( -0.181048 , 0.0983297 , 0.132455 ) -colvars: ( -0.129447 , 0.0996551 , 0.185195 ) -colvars: ( -0.212637 , 0.170437 , 0.134181 ) -colvars: ( -0.279269 , 0.0263186 , -0.000349039 ) -colvars: ( -0.209862 , 0.0122083 , 0.0631773 ) -colvars: ( -0.154364 , -0.0702927 , 0.0807534 ) +colvars: ( -0.678413 , -0.0869414 , -0.434258 ) +colvars: ( -0.607779 , -0.176034 , -0.404464 ) +colvars: ( -0.557584 , -0.152389 , -0.342737 ) +colvars: ( -0.560265 , -0.206199 , -0.370541 ) +colvars: ( -0.549849 , -0.143384 , -0.330724 ) +colvars: ( -0.528996 , -0.305131 , -0.385097 ) +colvars: ( -0.488229 , -0.349007 , -0.364383 ) +colvars: ( -0.460755 , -0.464191 , -0.390352 ) +colvars: ( -0.419812 , -0.311635 , -0.277848 ) +colvars: ( -0.412554 , -0.284915 , -0.258055 ) +colvars: ( -0.369014 , -0.305605 , -0.223727 ) +colvars: ( -0.303915 , -0.266524 , -0.139746 ) +colvars: ( -0.253974 , -0.282433 , -0.0967209 ) +colvars: ( -0.328079 , -0.155876 , -0.112548 ) +colvars: ( -0.292658 , -0.124978 , -0.0623596 ) +colvars: ( -0.39138 , -0.093784 , -0.147528 ) +colvars: ( -0.423414 , 0.0116438 , -0.130714 ) +colvars: ( -0.483183 , 0.063394 , -0.166949 ) +colvars: ( -0.461013 , 0.027554 , -0.161271 ) +colvars: ( -0.448569 , 0.0881091 , -0.12046 ) +colvars: ( -0.505985 , -0.0302053 , -0.233634 ) +colvars: ( -0.53953 , -0.0319706 , -0.26834 ) +colvars: ( -0.591494 , -0.101766 , -0.353379 ) +colvars: ( -0.478396 , -0.0648645 , -0.221932 ) +colvars: ( -0.48456 , -0.0178852 , -0.206247 ) +colvars: ( -0.416114 , -0.144846 , -0.196325 ) +colvars: ( -0.349574 , -0.179088 , -0.145085 ) +colvars: ( -0.292765 , -0.275947 , -0.132877 ) +colvars: ( -0.306861 , -0.101333 , -0.0656787 ) +colvars: ( -0.289925 , -0.0818295 , -0.0394757 ) +colvars: ( -0.29009 , -0.0529923 , -0.0261937 ) +colvars: ( -0.254247 , 0.0269071 , 0.0472739 ) +colvars: ( -0.236212 , 0.0555298 , 0.0788397 ) +colvars: ( -0.303491 , 0.120004 , 0.0409534 ) +colvars: ( -0.273799 , 0.164352 , 0.0916275 ) +colvars: ( -0.380763 , 0.150705 , -0.022778 ) +colvars: ( -0.434854 , 0.232517 , -0.0392581 ) +colvars: ( -0.515198 , 0.257423 , -0.108795 ) +colvars: ( -0.442378 , 0.210849 , -0.0569636 ) +colvars: ( -0.447228 , 0.275828 , -0.0315567 ) +colvars: ( -0.442866 , 0.117928 , -0.100792 ) +colvars: ( -0.445448 , 0.0851888 , -0.11867 ) +colvars: ( -0.465238 , -0.0147308 , -0.185259 ) +colvars: ( -0.370074 , 0.0723941 , -0.0485041 ) +colvars: ( -0.371339 , 0.100255 , -0.0367886 ) +colvars: ( -0.195894 , 0.106385 , 0.143282 ) +colvars: ( -0.140075 , 0.10782 , 0.200332 ) +colvars: ( -0.230063 , 0.184389 , 0.145148 ) +colvars: ( -0.30215 , 0.0284824 , -0.000376771 ) +colvars: ( -0.227069 , 0.0132196 , 0.0683424 ) +colvars: ( -0.167032 , -0.0760299 , 0.0873589 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 4. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 4. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 4, atoms_new_colvar_forces = { ( -4.56755970043401e+00 , -4.58398711848707e-01 , -1.34732300742556e+00 ), ( -3.93468791836226e+00 , -3.87426465624286e-01 , -1.06668606236787e+00 ), ( -4.00642888403167e+00 , -4.13027385595220e-01 , -1.10167706048978e+00 ), ( -5.38782761704673e+00 , -5.84016677733107e-01 , -1.61826841698039e+00 ), ( 2.50321504886440e-01 , 1.16245295489213e-01 , 3.39255398975650e-01 ), ( 4.92883736981228e+00 , 6.34345651122820e-01 , 1.90291170887934e+00 ), ( 4.16528605368736e+00 , 5.28007727220982e-01 , 1.64944100269517e+00 ), ( -4.16437368020444e-02 , 3.04913040696692e-02 , 3.45576187807646e-01 ), ( 4.14570946719244e+00 , 5.18393800215361e-01 , 1.61869086476715e+00 ), ( 5.49489950751797e+00 , 6.64653134297239e-01 , 2.01278646669079e+00 ), ( 1.13883455696422e-02 , 3.93643843013007e-02 , 2.90349004028925e-01 ), ( -3.70807556216823e-04 , 3.28447072483438e-02 , 2.65869032407028e-01 ), ( 1.97859397429609e-02 , 4.66996762106549e-02 , 3.29447457923400e-01 ), ( 4.18548301059438e-02 , 3.63860215155832e-02 , 1.93467465381695e-01 ), ( 1.43695494209841e-02 , 2.21852577237395e-02 , 1.44623595784099e-01 ), ( 1.09692872721714e-01 , 5.53120347165737e-02 , 1.83939950194680e-01 ), ( 1.54918505135066e-01 , 6.04105659645602e-02 , 1.16927864882144e-01 ), ( 2.33404078254006e-01 , 8.56079164497673e-02 , 1.32534946989211e-01 ), ( 1.27260876156989e-01 , 4.38971456075600e-02 , 4.98382262109091e-02 ), ( 1.22653529168925e-01 , 3.48850093387145e-02 , -1.18519795553965e-02 ), ( 1.05553360591133e-01 , 3.89411671411217e-02 , 6.17627536192067e-02 ), ( 7.12101521699346e-02 , 2.18996851388409e-02 , 6.39972885720105e-03 ), ( 5.92298878883137e-02 , 2.24222184028202e-02 , 3.92631636924738e-02 ), ( -4.35588411519083e-04 , -2.54337581643551e-03 , -1.94776782216607e-02 ), ( -1.37281194031207e-02 , -1.47782136067391e-02 , -8.63993568512332e-02 ), ( -4.72453442307985e-02 , -9.85634197974009e-03 , 3.34569676626325e-02 ), ( -1.13805860803223e-01 , -3.15478085997175e-02 , 1.76186612653798e-02 ), ( -1.54862439390776e-01 , -3.44626087716927e-02 , 9.22792674757840e-02 ), ( -1.02073944256152e-01 , -3.37107738130019e-02 , -2.78854802297323e-02 ), ( -1.37616345424722e-01 , -5.11220622448815e-02 , -8.33644381165563e-02 ), ( -5.03064636035201e-02 , -1.57087122606304e-02 , -6.43850145005012e-03 ), ( -3.02871431291500e-02 , -1.48230430191508e-02 , -4.71643061872050e-02 ), ( 2.45431398711071e-02 , 7.11348030937944e-03 , -1.29905709631239e-03 ), ( 1.00196235262762e-03 , -1.53752966528304e-02 , -1.26439733331159e-01 ), ( -1.65687790100254e-02 , -2.71638812066232e-02 , -1.79530900424476e-01 ), ( 4.72288447177213e-02 , -2.94176658105896e-03 , -1.36669240405971e-01 ), ( 7.61365023631097e-02 , -3.40748521546808e-03 , -2.09551895307170e-01 ), ( 1.36276780675960e-01 , 1.58104907876680e-02 , -1.98316673595567e-01 ), ( 1.88869653133905e-02 , -2.67110483526931e-02 , -2.60661022091157e-01 ), ( 1.98888205232494e-02 , -3.47506266933952e-02 , -3.27917879997113e-01 ), ( -3.29227145289210e-02 , -3.81760368618233e-02 , -2.29267730012848e-01 ), ( -9.26719967181926e-02 , -6.09192490450635e-02 , -2.69878585659409e-01 ), ( -1.29258162337561e-01 , -6.57793184853189e-02 , -2.21601756566605e-01 ), ( -1.49342140870217e-01 , -8.03964576088819e-02 , -2.91503175829467e-01 ), ( -1.76391190701122e-01 , -9.60931232258814e-02 , -3.53458718354442e-01 ), ( -1.92071864528452e-01 , -9.39612737579393e-02 , -2.98763154821138e-01 ), ( -2.33668423067563e-01 , -1.09598401532826e-01 , -3.25451669556599e-01 ), ( -1.19544086295381e-01 , -7.33003482140267e-02 , -3.05508177947573e-01 ), ( -1.69416922526762e-01 , -7.99868253862246e-02 , -2.40194602873481e-01 ), ( -2.22165149877229e-01 , -9.74137079021122e-02 , -2.54655982572481e-01 ), ( -2.57437502491945e-01 , -9.85196456364392e-02 , -1.79233471872105e-01 ) } +colvars: Step 4, atoms_new_colvar_forces = { ( -4.94151873108853e+00 , -4.95844394742801e-01 , -1.45728843242111e+00 ), ( -4.25683152929605e+00 , -4.19073570429103e-01 , -1.15372614016457e+00 ), ( -4.33444438845863e+00 , -4.46769799211681e-01 , -1.19158111943272e+00 ), ( -5.82894022039823e+00 , -6.31733357552042e-01 , -1.75036623073903e+00 ), ( 2.70809952346392e-01 , 1.25759659929497e-01 , 3.67022957097078e-01 ), ( 5.33236665680773e+00 , 6.86192275166386e-01 , 2.05835151414738e+00 ), ( 4.50630396391752e+00 , 5.71161364447410e-01 , 1.78417888002817e+00 ), ( -4.50521064735852e-02 , 3.29873596199127e-02 , 3.73861120665321e-01 ), ( 4.48512499842786e+00 , 5.60760529967644e-01 , 1.75091180485056e+00 ), ( 5.94477590622766e+00 , 7.18969977626746e-01 , 2.17717508972119e+00 ), ( 1.23204279884955e-02 , 4.25864921143228e-02 , 3.14113516873341e-01 ), ( -4.01260714282592e-04 , 3.55331586591927e-02 , 2.87629810528536e-01 ), ( 2.14052148191664e-02 , 5.05221201997225e-02 , 3.56411931734833e-01 ), ( 4.52804785364694e-02 , 3.93641970626369e-02 , 2.09302312339995e-01 ), ( 1.55455475389473e-02 , 2.40011187840913e-02 , 1.56460619817514e-01 ), ( 1.18670986750850e-01 , 5.98391688943326e-02 , 1.98995041694911e-01 ), ( 1.67598272749677e-01 , 6.53548826711292e-02 , 1.26498155048923e-01 ), ( 2.52507784367427e-01 , 9.26144883813088e-02 , 1.43382693002266e-01 ), ( 1.37676970832130e-01 , 4.74898849057159e-02 , 5.39174198038382e-02 ), ( 1.32692507809491e-01 , 3.77400726622781e-02 , -1.28220381118743e-02 ), ( 1.14192795160641e-01 , 4.21283427876479e-02 , 6.68180303148438e-02 ), ( 7.70387094492635e-02 , 2.36920825383860e-02 , 6.92370981846402e-03 ), ( 6.40779472015232e-02 , 2.42574612242072e-02 , 4.24770456540305e-02 ), ( -4.71146217026763e-04 , -2.75151840879517e-03 , -2.10717675375920e-02 ), ( -1.48516349236037e-02 , -1.59877827070383e-02 , -9.34708518249164e-02 ), ( -5.11122474941834e-02 , -1.06629392444262e-02 , 3.61954208352342e-02 ), ( -1.23120670979236e-01 , -3.41297369124331e-02 , 1.90607158308125e-02 ), ( -1.67537703748154e-01 , -3.72829997464116e-02 , 9.98321014309942e-02 ), ( -1.10428572677273e-01 , -3.64698190250280e-02 , -3.01679323445352e-02 ), ( -1.48880060390512e-01 , -5.53061782201492e-02 , -9.01877507098243e-02 ), ( -5.44240578645827e-02 , -1.69944092753382e-02 , -6.96561227952253e-03 ), ( -3.27662421073514e-02 , -1.60363396419879e-02 , -5.10248197226018e-02 ), ( 2.65517574135329e-02 , 7.69557423923618e-03 , -1.40564014935160e-03 ), ( 1.08386285815548e-03 , -1.66338922359559e-02 , -1.36788746907841e-01 ), ( -1.79250392762637e-02 , -2.93873777960727e-02 , -1.94225368128489e-01 ), ( 5.10944014416220e-02 , -3.18275430613568e-03 , -1.47855432047221e-01 ), ( 8.23681479943154e-02 , -3.68667686980284e-03 , -2.26703340912932e-01 ), ( 1.47430866801357e-01 , 1.71041949493687e-02 , -2.14548450271599e-01 ), ( 2.04328717296331e-02 , -2.88975256565817e-02 , -2.81995614928140e-01 ), ( 2.15167314441352e-02 , -3.75951838175833e-02 , -3.54757322940780e-01 ), ( -3.56173143482683e-02 , -4.13007796309533e-02 , -2.48032804522046e-01 ), ( -1.00256939903858e-01 , -6.59054030137752e-02 , -2.91967548149587e-01 ), ( -1.39837578616564e-01 , -7.11631415690601e-02 , -2.39739292495174e-01 ), ( -1.61565496181255e-01 , -8.69767375581534e-02 , -3.15362153547064e-01 ), ( -1.90828449787856e-01 , -1.03958146781982e-01 , -3.82388631261111e-01 ), ( -2.07792752897369e-01 , -1.01651827484115e-01 , -3.23216587535757e-01 ), ( -2.52793961676474e-01 , -1.18568799618888e-01 , -3.52089570352585e-01 ), ( -1.29328698069343e-01 , -7.92999657404734e-02 , -3.30513670981765e-01 ), ( -1.83283431592216e-01 , -8.65335336324582e-02 , -2.59854154010991e-01 ), ( -2.40349070486967e-01 , -1.05386727914137e-01 , -2.75499254537413e-01 ), ( -2.78508454946323e-01 , -1.06583088087811e-01 , -1.93903612270080e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 4, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2854,10 +4535,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 5, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 5, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 5, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 5, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 5, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 5, atoms_positions[size = 51] = { ( 8.38826312441025e+00 , 4.32888237930165e-02 , -7.54675773037975e-01 ), ( 6.99401820014457e+00 , -4.98814692882301e-01 , -6.55412617370388e-01 ), ( 6.25553939543217e+00 , -2.59136807844394e-01 , 6.59061145245593e-01 ), ( 5.00241331038846e+00 , -2.07780021618727e-01 , 6.62310517785252e-01 ), ( 7.04065218160799e+00 , -2.01833631588376e+00 , -1.01694795435808e+00 ), ( 6.90394945934699e+00 , -2.69627423956689e-01 , 1.80743544886632e+00 ), ( 6.17687930822337e+00 , -1.22440873196289e-01 , 3.06343563573041e+00 ), ( 7.17537831251022e+00 , -3.21243267443331e-01 , 4.29853733458758e+00 ), ( 5.30553815329920e+00 , 1.11989718325646e+00 , 3.28558165082311e+00 ), ( 4.08841558874180e+00 , 1.06801273878407e+00 , 3.62074729123617e+00 ), ( 5.87539437014727e+00 , 2.31240698981955e+00 , 2.97013979692365e+00 ), ( 5.22045553148862e+00 , 3.59633905368878e+00 , 2.88134102962379e+00 ), ( 6.33556785019079e+00 , 4.60686978260033e+00 , 2.46153202451686e+00 ), ( 3.89733815963180e+00 , 3.71958256211498e+00 , 2.02068427507450e+00 ), ( 2.90986815591977e+00 , 4.11525632332891e+00 , 2.55392464879702e+00 ), ( 3.82401942445680e+00 , 3.24274539244656e+00 , 7.77213156482582e-01 ), ( 2.66882752044054e+00 , 3.17373646269596e+00 , -8.63455684056099e-02 ), ( 3.04771552949509e+00 , 2.72378753594042e+00 , -1.59629639528942e+00 ), ( 1.62300085673154e+00 , 2.15239258201508e+00 , 5.82562684490643e-01 ), ( 4.32822116349314e-01 , 2.44779921445653e+00 , 5.56964352470077e-01 ), ( 1.97245902367590e+00 , 1.01153179605837e+00 , 1.05347444161927e+00 ), ( 1.14378127395772e+00 , 1.32526980536757e-02 , 1.68846421958047e+00 ), ( 2.01515457557546e+00 , -1.18697461776164e+00 , 2.02187446643857e+00 ), ( 5.13510131564253e-01 , 5.99454131544490e-01 , 2.99941530739477e+00 ), ( -6.75608864846344e-01 , 3.76333381606639e-01 , 3.18545385099906e+00 ), ( 1.29542211863670e+00 , 1.31432351581721e+00 , 3.82604713879422e+00 ), ( 8.29534604581958e-01 , 1.90018079264796e+00 , 5.07401854513477e+00 ), ( 2.05856363564941e+00 , 2.58942602120153e+00 , 5.62179434951341e+00 ), ( -3.58859976297028e-01 , 2.92014631902862e+00 , 4.98512722536177e+00 ), ( -1.17612766767868e+00 , 3.02608003185974e+00 , 5.90402944495260e+00 ), ( -4.08861565874776e-01 , 3.69412626548260e+00 , 3.86107612713235e+00 ), ( -1.46993085000088e+00 , 4.59050357313592e+00 , 3.53748159806234e+00 ), ( -7.59061023216564e-01 , 5.38308591896450e+00 , 2.40952232961719e+00 ), ( -2.71897816168511e+00 , 3.89602914930668e+00 , 2.93626552401718e+00 ), ( -3.85356068716273e+00 , 4.42028349637097e+00 , 2.85514810456908e+00 ), ( -2.57516889268564e+00 , 2.61161662691592e+00 , 2.49527974380284e+00 ), ( -3.71923442891987e+00 , 1.90738900127391e+00 , 2.07104008103557e+00 ), ( -3.41086464468343e+00 , 8.05652926698358e-01 , 9.93708353839769e-01 ), ( -4.31703059699794e+00 , 1.10221203230376e+00 , 3.22564085779991e+00 ), ( -5.53582774533983e+00 , 9.23270006620592e-01 , 3.34544140351197e+00 ), ( -3.46995064414351e+00 , 6.33935530671426e-01 , 4.15753540802055e+00 ), ( -3.77419317548219e+00 , 1.00549858819052e-01 , 5.47895461462770e+00 ), ( -2.41708481082698e+00 , -4.09546097586824e-01 , 6.13752475430754e+00 ), ( -4.46669955995532e+00 , 1.00204957729110e+00 , 6.41689844970049e+00 ), ( -5.32378814837926e+00 , 5.98706771018336e-01 , 7.18237841153734e+00 ), ( -6.29749438766859e+00 , 3.54903428818487e+00 , 6.69965967371175e+00 ), ( -6.91624074182789e+00 , 4.30429019871442e+00 , 7.41755872782235e+00 ), ( -6.75003990259343e+00 , 3.20870922124133e+00 , 5.50823685204315e+00 ), ( -4.08349342960840e+00 , 2.29945882106867e+00 , 6.47979179303521e+00 ), ( -4.91012602716345e+00 , 3.23790127696191e+00 , 7.21413892695397e+00 ), ( -4.07391902579364e+00 , 4.50301961064101e+00 , 7.26796867056682e+00 ) } +colvars: Step 5, atoms_positions[size = 51] = { ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 ), ( 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 ), ( 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 ), ( 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 ), ( 7.04065873224138e+00 , -2.01833296981288e+00 , -1.01693732833577e+00 ), ( 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 ), ( 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 ), ( 7.17538034267917e+00 , -3.21242762016170e-01 , 4.29855168076096e+00 ), ( 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 ), ( 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 ), ( 5.87539806276546e+00 , 2.31240985061275e+00 , 2.97014834098906e+00 ), ( 5.22045541044482e+00 , 3.59634000902379e+00 , 2.88135009450921e+00 ), ( 6.33556840963606e+00 , 4.60687122456596e+00 , 2.46154267623522e+00 ), ( 3.89733976249443e+00 , 3.71958370766481e+00 , 2.02069126404248e+00 ), ( 2.90986850355711e+00 , 4.11525694547682e+00 , 2.55392862424380e+00 ), ( 3.82402284814097e+00 , 3.24274713169095e+00 , 7.77218893145038e-01 ), ( 2.66883306741140e+00 , 3.17373864836739e+00 , -8.63413721619713e-02 ), ( 3.04772299627009e+00 , 2.72379039269836e+00 , -1.59629179777349e+00 ), ( 1.62300540102769e+00 , 2.15239416279852e+00 , 5.82564492602534e-01 ), ( 4.32825535551040e-01 , 2.44780015548533e+00 , 5.56964034822003e-01 ), ( 1.97246218522001e+00 , 1.01153306857404e+00 , 1.05347641473001e+00 ), ( 1.14378372746903e+00 , 1.32534609583773e-02 , 1.68846439706830e+00 ), ( 2.01515655210737e+00 , -1.18697389770786e+00 , 2.02187581765090e+00 ), ( 5.13510127632644e-01 , 5.99454044877085e-01 , 2.99941462155069e+00 ), ( -6.75609219672412e-01 , 3.76332979525036e-01 , 3.18545149481743e+00 ), ( 1.29542103087650e+00 , 1.31432316768908e+00 , 3.82604811682509e+00 ), ( 8.29530569093443e-01 , 1.90017975542296e+00 , 5.07401910024172e+00 ), ( 2.05855836566831e+00 , 2.58942481763467e+00 , 5.62179715274072e+00 ), ( -3.58863638717831e-01 , 2.92014509118021e+00 , 4.98512619418679e+00 ), ( -1.17613148004942e+00 , 3.02607864337171e+00 , 5.90402719946517e+00 ), ( -4.08863122404988e-01 , 3.69412576843576e+00 , 3.86107585574595e+00 ), ( -1.46993194559316e+00 , 4.59050309281920e+00 , 3.53747996998097e+00 ), ( -7.59060233310232e-01 , 5.38308614886267e+00 , 2.40952223666742e+00 ), ( -2.71897816745416e+00 , 3.89602862252007e+00 , 2.93626096222774e+00 ), ( -3.85356112454900e+00 , 4.42028273573898e+00 , 2.85514318192395e+00 ), ( -2.57516756309611e+00 , 2.61161657288815e+00 , 2.49527550724508e+00 ), ( -3.71923167479111e+00 , 1.90738885494446e+00 , 2.07103256252133e+00 ), ( -3.41086011185269e+00 , 8.05653207893339e-01 , 9.93701643727931e-01 ), ( -4.31702988150970e+00 , 1.10221101723040e+00 , 3.22563146928878e+00 ), ( -5.53582719469801e+00 , 9.23269046977417e-01 , 3.34543241383312e+00 ), ( -3.46995162329921e+00 , 6.33934339046132e-01 , 4.15752819281306e+00 ), ( -3.77419638808229e+00 , 1.00547898851902e-01 , 5.47894501126548e+00 ), ( -2.41708935603261e+00 , -4.09548047162091e-01 , 6.13751734042486e+00 ), ( -4.46670493814301e+00 , 1.00204671894782e+00 , 6.41688790074973e+00 ), ( -5.32379297742663e+00 , 5.98704129809046e-01 , 7.18236872886878e+00 ), ( -6.29750134152972e+00 , 3.54903094952594e+00 , 6.69964903296575e+00 ), ( -6.91624712767947e+00 , 4.30428715900772e+00 , 7.41754976068118e+00 ), ( -6.75004367444995e+00 , 3.20870713576147e+00 , 5.50822758656231e+00 ), ( -4.08349872089577e+00 , 2.29945633007041e+00 , 6.47978428488058e+00 ), ( -4.91013406314155e+00 , 3.23789768567445e+00 , 7.21413013421060e+00 ), ( -4.07392760517108e+00 , 4.50301612731662e+00 , 7.26796286445452e+00 ) } colvars: Step 5, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 5, atom_groups_ids[size = 0] = @@ -2875,162 +4556,301 @@ colvars: Collective variables module, step no. 5 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.35182699996778e-01 , 5.02452781962055e-03 , 9.42139751705160e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.35094576448585e-01 , 5.03425973663854e-03 , 9.42171046606532e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 7.04065873224138e+00 , -2.01833296981288e+00 , -1.01693732833577e+00 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 , 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 7.17538034267917e+00 , -3.21242762016170e-01 , 4.29855168076096e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 , 5.87539806276546e+00 , 2.31240985061275e+00 , 2.97014834098906e+00 , 5.22045541044482e+00 , 3.59634000902379e+00 , 2.88135009450921e+00 , 6.33556840963606e+00 , 4.60687122456596e+00 , 2.46154267623522e+00 , 3.89733976249443e+00 , 3.71958370766481e+00 , 2.02069126404248e+00 , 2.90986850355711e+00 , 4.11525694547682e+00 , 2.55392862424380e+00 , 3.82402284814097e+00 , 3.24274713169095e+00 , 7.77218893145038e-01 , 2.66883306741140e+00 , 3.17373864836739e+00 , -8.63413721619713e-02 , 3.04772299627009e+00 , 2.72379039269836e+00 , -1.59629179777349e+00 , 1.62300540102769e+00 , 2.15239416279852e+00 , 5.82564492602534e-01 , 4.32825535551040e-01 , 2.44780015548533e+00 , 5.56964034822003e-01 , 1.97246218522001e+00 , 1.01153306857404e+00 , 1.05347641473001e+00 , 1.14378372746903e+00 , 1.32534609583773e-02 , 1.68846439706830e+00 , 2.01515655210737e+00 , -1.18697389770786e+00 , 2.02187581765090e+00 , 5.13510127632644e-01 , 5.99454044877085e-01 , 2.99941462155069e+00 , -6.75609219672412e-01 , 3.76332979525036e-01 , 3.18545149481743e+00 , 1.29542103087650e+00 , 1.31432316768908e+00 , 3.82604811682509e+00 , 8.29530569093443e-01 , 1.90017975542296e+00 , 5.07401910024172e+00 , 2.05855836566831e+00 , 2.58942481763467e+00 , 5.62179715274072e+00 , -3.58863638717831e-01 , 2.92014509118021e+00 , 4.98512619418679e+00 , -1.17613148004942e+00 , 3.02607864337171e+00 , 5.90402719946517e+00 , -4.08863122404988e-01 , 3.69412576843576e+00 , 3.86107585574595e+00 , -1.46993194559316e+00 , 4.59050309281920e+00 , 3.53747996998097e+00 , -7.59060233310232e-01 , 5.38308614886267e+00 , 2.40952223666742e+00 , -2.71897816745416e+00 , 3.89602862252007e+00 , 2.93626096222774e+00 , -3.85356112454900e+00 , 4.42028273573898e+00 , 2.85514318192395e+00 , -2.57516756309611e+00 , 2.61161657288815e+00 , 2.49527550724508e+00 , -3.71923167479111e+00 , 1.90738885494446e+00 , 2.07103256252133e+00 , -3.41086011185269e+00 , 8.05653207893339e-01 , 9.93701643727931e-01 , -4.31702988150970e+00 , 1.10221101723040e+00 , 3.22563146928878e+00 , -5.53582719469801e+00 , 9.23269046977417e-01 , 3.34543241383312e+00 , -3.46995162329921e+00 , 6.33934339046132e-01 , 4.15752819281306e+00 , -3.77419638808229e+00 , 1.00547898851902e-01 , 5.47894501126548e+00 , -2.41708935603261e+00 , -4.09548047162091e-01 , 6.13751734042486e+00 , -4.46670493814301e+00 , 1.00204671894782e+00 , 6.41688790074973e+00 , -5.32379297742663e+00 , 5.98704129809046e-01 , 7.18236872886878e+00 , -6.29750134152972e+00 , 3.54903094952594e+00 , 6.69964903296575e+00 , -6.91624712767947e+00 , 4.30428715900772e+00 , 7.41754976068118e+00 , -6.75004367444995e+00 , 3.20870713576147e+00 , 5.50822758656231e+00 , -4.08349872089577e+00 , 2.29945633007041e+00 , 6.47978428488058e+00 , -4.91013406314155e+00 , 3.23789768567445e+00 , 7.21413013421060e+00 , -4.07392760517108e+00 , 4.50301612731662e+00 , 7.26796286445452e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.35182699996778e-01 , 5.02452781962055e-03 , 9.42139751705160e-01 ). +colvars: Colvar "one" has value ( -3.35094576448585e-01 , 5.03425973663854e-03 , 9.42171046606532e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 7.04065873224138e+00 , -2.01833296981288e+00 , -1.01693732833577e+00 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 , 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 7.17538034267917e+00 , -3.21242762016170e-01 , 4.29855168076096e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 , 5.87539806276546e+00 , 2.31240985061275e+00 , 2.97014834098906e+00 , 5.22045541044482e+00 , 3.59634000902379e+00 , 2.88135009450921e+00 , 6.33556840963606e+00 , 4.60687122456596e+00 , 2.46154267623522e+00 , 3.89733976249443e+00 , 3.71958370766481e+00 , 2.02069126404248e+00 , 2.90986850355711e+00 , 4.11525694547682e+00 , 2.55392862424380e+00 , 3.82402284814097e+00 , 3.24274713169095e+00 , 7.77218893145038e-01 , 2.66883306741140e+00 , 3.17373864836739e+00 , -8.63413721619713e-02 , 3.04772299627009e+00 , 2.72379039269836e+00 , -1.59629179777349e+00 , 1.62300540102769e+00 , 2.15239416279852e+00 , 5.82564492602534e-01 , 4.32825535551040e-01 , 2.44780015548533e+00 , 5.56964034822003e-01 , 1.97246218522001e+00 , 1.01153306857404e+00 , 1.05347641473001e+00 , 1.14378372746903e+00 , 1.32534609583773e-02 , 1.68846439706830e+00 , 2.01515655210737e+00 , -1.18697389770786e+00 , 2.02187581765090e+00 , 5.13510127632644e-01 , 5.99454044877085e-01 , 2.99941462155069e+00 , -6.75609219672412e-01 , 3.76332979525036e-01 , 3.18545149481743e+00 , 1.29542103087650e+00 , 1.31432316768908e+00 , 3.82604811682509e+00 , 8.29530569093443e-01 , 1.90017975542296e+00 , 5.07401910024172e+00 , 2.05855836566831e+00 , 2.58942481763467e+00 , 5.62179715274072e+00 , -3.58863638717831e-01 , 2.92014509118021e+00 , 4.98512619418679e+00 , -1.17613148004942e+00 , 3.02607864337171e+00 , 5.90402719946517e+00 , -4.08863122404988e-01 , 3.69412576843576e+00 , 3.86107585574595e+00 , -1.46993194559316e+00 , 4.59050309281920e+00 , 3.53747996998097e+00 , -7.59060233310232e-01 , 5.38308614886267e+00 , 2.40952223666742e+00 , -2.71897816745416e+00 , 3.89602862252007e+00 , 2.93626096222774e+00 , -3.85356112454900e+00 , 4.42028273573898e+00 , 2.85514318192395e+00 , -2.57516756309611e+00 , 2.61161657288815e+00 , 2.49527550724508e+00 , -3.71923167479111e+00 , 1.90738885494446e+00 , 2.07103256252133e+00 , -3.41086011185269e+00 , 8.05653207893339e-01 , 9.93701643727931e-01 , -4.31702988150970e+00 , 1.10221101723040e+00 , 3.22563146928878e+00 , -5.53582719469801e+00 , 9.23269046977417e-01 , 3.34543241383312e+00 , -3.46995162329921e+00 , 6.33934339046132e-01 , 4.15752819281306e+00 , -3.77419638808229e+00 , 1.00547898851902e-01 , 5.47894501126548e+00 , -2.41708935603261e+00 , -4.09548047162091e-01 , 6.13751734042486e+00 , -4.46670493814301e+00 , 1.00204671894782e+00 , 6.41688790074973e+00 , -5.32379297742663e+00 , 5.98704129809046e-01 , 7.18236872886878e+00 , -6.29750134152972e+00 , 3.54903094952594e+00 , 6.69964903296575e+00 , -6.91624712767947e+00 , 4.30428715900772e+00 , 7.41754976068118e+00 , -6.75004367444995e+00 , 3.20870713576147e+00 , 5.50822758656231e+00 , -4.08349872089577e+00 , 2.29945633007041e+00 , 6.47978428488058e+00 , -4.91013406314155e+00 , 3.23789768567445e+00 , 7.21413013421060e+00 , -4.07392760517108e+00 , 4.50301612731662e+00 , 7.26796286445452e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.2217 , 1.85131 , -14.9392 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.5957 , 6.75957 , 13.5191 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.2217 , 1.85131 , -14.9392 ) to colvar "one". -colvars: Adding total bias energy: 45.7091 +colvars: Adding biasing force ( 67.5957 , 6.75957 , 13.5191 ) to colvar "one". +colvars: Adding total bias energy: 58.7504 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.2217 , 1.85131 , -14.9392 ) +colvars: Force to be applied: ( 67.5957 , 6.75957 , 13.5191 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.84643 , -0.569343 , -1.58917 ) -colvars: ( -4.15581 , -0.488211 , -1.36271 ) -colvars: ( -4.15581 , -0.488211 , -1.36271 ) -colvars: ( -5.53566 , -0.650312 , -1.81517 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.23542 , -0.614906 , -1.71618 ) +colvars: ( -4.48937 , -0.527282 , -1.47163 ) +colvars: ( -4.48937 , -0.527282 , -1.47163 ) +colvars: ( -5.97997 , -0.702355 , -1.96025 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.90213 , 0.19297 , 0.648149 ) -colvars: ( 0.779712 , 0.264921 , 0.673806 ) -colvars: ( 0.765315 , 0.257295 , 0.654659 ) -colvars: ( 0.664234 , 0.267138 , 0.607557 ) -colvars: ( 0.652109 , 0.20058 , 0.508584 ) -colvars: ( 0.574758 , 0.345658 , 0.662034 ) -colvars: ( 0.463847 , 0.361153 , 0.61682 ) -colvars: ( 0.384576 , 0.459552 , 0.704808 ) -colvars: ( 0.38108 , 0.31696 , 0.506263 ) -colvars: ( 0.344749 , 0.275966 , 0.427983 ) -colvars: ( 0.352677 , 0.321836 , 0.495935 ) -colvars: ( 0.280774 , 0.279164 , 0.393995 ) -colvars: ( 0.25471 , 0.307747 , 0.417731 ) -colvars: ( 0.345236 , 0.180437 , 0.296666 ) -colvars: ( 0.285082 , 0.137636 , 0.201598 ) -colvars: ( 0.471419 , 0.142021 , 0.319468 ) -colvars: ( 0.546147 , 0.0496815 , 0.237101 ) -colvars: ( 0.679683 , 0.0271096 , 0.286145 ) -colvars: ( 0.55332 , 0.0184306 , 0.198352 ) -colvars: ( 0.537227 , -0.0465799 , 0.0991299 ) -colvars: ( 0.573237 , 0.0668629 , 0.277029 ) -colvars: ( 0.569993 , 0.0514208 , 0.253808 ) -colvars: ( 0.606074 , 0.116471 , 0.365081 ) -colvars: ( 0.442019 , 0.057318 , 0.18513 ) -colvars: ( 0.434463 , 0.00163008 , 0.103875 ) -colvars: ( 0.33775 , 0.12391 , 0.214297 ) -colvars: ( 0.20985 , 0.13381 , 0.151178 ) -colvars: ( 0.116377 , 0.220413 , 0.214393 ) -colvars: ( 0.182074 , 0.0597604 , 0.0324908 ) -colvars: ( 0.13097 , 0.0242779 , -0.0470627 ) -colvars: ( 0.218208 , 0.0331147 , 0.0174665 ) -colvars: ( 0.205048 , -0.0398613 , -0.0909691 ) -colvars: ( 0.243066 , -0.0443367 , -0.0743187 ) -colvars: ( 0.281785 , -0.126462 , -0.164225 ) -colvars: ( 0.236816 , -0.179277 , -0.263975 ) -colvars: ( 0.399324 , -0.142366 , -0.115595 ) -colvars: ( 0.478166 , -0.218449 , -0.173096 ) -colvars: ( 0.612422 , -0.222196 , -0.0976857 ) -colvars: ( 0.42802 , -0.221774 , -0.207772 ) -colvars: ( 0.433508 , -0.289896 , -0.29833 ) -colvars: ( 0.376788 , -0.147371 , -0.136015 ) -colvars: ( 0.319579 , -0.139901 , -0.160058 ) -colvars: ( 0.301373 , -0.0524053 , -0.050442 ) -colvars: ( 0.193379 , -0.147609 , -0.246415 ) -colvars: ( 0.167573 , -0.189094 , -0.319056 ) -colvars: ( -0.0102493 , -0.192656 , -0.430682 ) -colvars: ( -0.103337 , -0.209665 , -0.509981 ) -colvars: ( 0.093682 , -0.244047 , -0.439109 ) -colvars: ( 0.110564 , -0.10662 , -0.239645 ) -colvars: ( -0.0114541 , -0.109991 , -0.317518 ) -colvars: ( -0.10214 , -0.0286097 , -0.259825 ) +colvars: ( 0.974477 , 0.208456 , 0.700053 ) +colvars: ( 0.842247 , 0.286172 , 0.727769 ) +colvars: ( 0.826692 , 0.277938 , 0.707092 ) +colvars: ( 0.717514 , 0.288561 , 0.656212 ) +colvars: ( 0.704417 , 0.216666 , 0.549309 ) +colvars: ( 0.620868 , 0.373372 , 0.715055 ) +colvars: ( 0.501069 , 0.390104 , 0.666218 ) +colvars: ( 0.415445 , 0.496388 , 0.761257 ) +colvars: ( 0.411666 , 0.342367 , 0.546806 ) +colvars: ( 0.372425 , 0.298083 , 0.462251 ) +colvars: ( 0.380984 , 0.347635 , 0.535653 ) +colvars: ( 0.303316 , 0.301542 , 0.425547 ) +colvars: ( 0.275161 , 0.332419 , 0.451189 ) +colvars: ( 0.372944 , 0.194902 , 0.320418 ) +colvars: ( 0.307968 , 0.148668 , 0.217734 ) +colvars: ( 0.50924 , 0.153411 , 0.345046 ) +colvars: ( 0.589957 , 0.0536714 , 0.256079 ) +colvars: ( 0.734195 , 0.0292958 , 0.309051 ) +colvars: ( 0.597707 , 0.019912 , 0.214221 ) +colvars: ( 0.580324 , -0.0503113 , 0.107049 ) +colvars: ( 0.619223 , 0.0722252 , 0.2992 ) +colvars: ( 0.615722 , 0.0555417 , 0.274116 ) +colvars: ( 0.654697 , 0.125806 , 0.394302 ) +colvars: ( 0.477491 , 0.0619063 , 0.199936 ) +colvars: ( 0.46933 , 0.00175207 , 0.112168 ) +colvars: ( 0.364865 , 0.133835 , 0.231442 ) +colvars: ( 0.226714 , 0.144524 , 0.163267 ) +colvars: ( 0.125749 , 0.238068 , 0.23155 ) +colvars: ( 0.19671 , 0.0645378 , 0.0350719 ) +colvars: ( 0.141511 , 0.0262074 , -0.0508564 ) +colvars: ( 0.235737 , 0.0357602 , 0.018846 ) +colvars: ( 0.22152 , -0.0430649 , -0.0982764 ) +colvars: ( 0.262582 , -0.0478942 , -0.0802893 ) +colvars: ( 0.304408 , -0.136607 , -0.177405 ) +colvars: ( 0.255835 , -0.193658 , -0.285147 ) +colvars: ( 0.431369 , -0.153783 , -0.124881 ) +colvars: ( 0.516531 , -0.235964 , -0.186992 ) +colvars: ( 0.661548 , -0.240008 , -0.105542 ) +colvars: ( 0.462368 , -0.239561 , -0.224449 ) +colvars: ( 0.468296 , -0.313145 , -0.322263 ) +colvars: ( 0.407032 , -0.159197 , -0.146943 ) +colvars: ( 0.34524 , -0.151134 , -0.172914 ) +colvars: ( 0.325577 , -0.0566256 , -0.0545162 ) +colvars: ( 0.208925 , -0.159463 , -0.266188 ) +colvars: ( 0.181052 , -0.204277 , -0.344651 ) +colvars: ( -0.0110289 , -0.208124 , -0.465212 ) +colvars: ( -0.111578 , -0.2265 , -0.550864 ) +colvars: ( 0.101231 , -0.26363 , -0.474315 ) +colvars: ( 0.119471 , -0.115188 , -0.258873 ) +colvars: ( -0.0123278 , -0.118833 , -0.342983 ) +colvars: ( -0.110283 , -0.0309296 , -0.280664 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.84643 , 0.569343 , 1.58917 ) -colvars: ( 4.15581 , 0.488211 , 1.36271 ) -colvars: ( 4.15581 , 0.488211 , 1.36271 ) -colvars: ( 5.53566 , 0.650312 , 1.81517 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.23542 , 0.614906 , 1.71618 ) +colvars: ( 4.48937 , 0.527282 , 1.47163 ) +colvars: ( 4.48937 , 0.527282 , 1.47163 ) +colvars: ( 5.97997 , 0.702355 , 1.96025 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.626509 , -0.0803844 , -0.400005 ) -colvars: ( -0.56138 , -0.162767 , -0.372276 ) -colvars: ( -0.514815 , -0.140885 , -0.315136 ) -colvars: ( -0.517698 , -0.19065 , -0.341035 ) -colvars: ( -0.508071 , -0.132545 , -0.304472 ) -colvars: ( -0.489004 , -0.282145 , -0.354315 ) -colvars: ( -0.451571 , -0.322711 , -0.335245 ) -colvars: ( -0.426362 , -0.42924 , -0.358989 ) -colvars: ( -0.388347 , -0.288123 , -0.25541 ) -colvars: ( -0.381747 , -0.263404 , -0.237326 ) -colvars: ( -0.341276 , -0.282532 , -0.205284 ) -colvars: ( -0.281091 , -0.246364 , -0.12779 ) -colvars: ( -0.234806 , -0.261066 , -0.0878318 ) -colvars: ( -0.303283 , -0.144028 , -0.102935 ) -colvars: ( -0.270618 , -0.115437 , -0.0567348 ) -colvars: ( -0.361587 , -0.086619 , -0.135305 ) -colvars: ( -0.391049 , 0.0108852 , -0.120025 ) -colvars: ( -0.446043 , 0.0587294 , -0.153471 ) -colvars: ( -0.425943 , 0.0255928 , -0.148475 ) -colvars: ( -0.414448 , 0.081608 , -0.110991 ) -colvars: ( -0.467636 , -0.0278437 , -0.215269 ) -colvars: ( -0.498806 , -0.0294836 , -0.247509 ) -colvars: ( -0.546931 , -0.0940559 , -0.325943 ) -colvars: ( -0.442522 , -0.0598865 , -0.204704 ) -colvars: ( -0.448276 , -0.0164332 , -0.190445 ) -colvars: ( -0.38508 , -0.133845 , -0.180848 ) -colvars: ( -0.323774 , -0.165494 , -0.133546 ) -colvars: ( -0.271374 , -0.255066 , -0.121994 ) -colvars: ( -0.284211 , -0.0935622 , -0.06036 ) -colvars: ( -0.268679 , -0.0755144 , -0.0363361 ) -colvars: ( -0.268493 , -0.0488475 , -0.0238308 ) -colvars: ( -0.235253 , 0.0250653 , 0.0438838 ) -colvars: ( -0.218354 , 0.0515414 , 0.0731819 ) -colvars: ( -0.280692 , 0.11116 , 0.0377568 ) -colvars: ( -0.253289 , 0.15219 , 0.0843872 ) -colvars: ( -0.352005 , 0.139532 , -0.0211668 ) -colvars: ( -0.401939 , 0.215188 , -0.0366553 ) -colvars: ( -0.476041 , 0.238197 , -0.100872 ) -colvars: ( -0.409123 , 0.195147 , -0.0531677 ) -colvars: ( -0.413605 , 0.255249 , -0.0299338 ) -colvars: ( -0.409775 , 0.109203 , -0.0935246 ) -colvars: ( -0.412396 , 0.0789234 , -0.110159 ) -colvars: ( -0.430848 , -0.0135015 , -0.171487 ) -colvars: ( -0.342879 , 0.0671146 , -0.0453985 ) -colvars: ( -0.344154 , 0.0928863 , -0.0347829 ) -colvars: ( -0.181891 , 0.0986082 , 0.131751 ) -colvars: ( -0.130408 , 0.0999549 , 0.184372 ) -colvars: ( -0.213223 , 0.170743 , 0.133424 ) -colvars: ( -0.280113 , 0.0265189 , -0.000755106 ) -colvars: ( -0.210852 , 0.0124267 , 0.0626921 ) -colvars: ( -0.155442 , -0.0701059 , 0.0805347 ) +colvars: ( -0.676743 , -0.0868383 , -0.432001 ) +colvars: ( -0.606398 , -0.175823 , -0.402048 ) +colvars: ( -0.556095 , -0.152189 , -0.340329 ) +colvars: ( -0.559222 , -0.205937 , -0.368308 ) +colvars: ( -0.548823 , -0.143174 , -0.328821 ) +colvars: ( -0.528234 , -0.304763 , -0.382648 ) +colvars: ( -0.487808 , -0.348577 , -0.362053 ) +colvars: ( -0.460583 , -0.463644 , -0.387694 ) +colvars: ( -0.419516 , -0.311215 , -0.275827 ) +colvars: ( -0.412391 , -0.284513 , -0.256299 ) +colvars: ( -0.368669 , -0.305178 , -0.221684 ) +colvars: ( -0.303659 , -0.266111 , -0.137985 ) +colvars: ( -0.253661 , -0.281993 , -0.0948231 ) +colvars: ( -0.327626 , -0.155573 , -0.111145 ) +colvars: ( -0.292344 , -0.124687 , -0.0612491 ) +colvars: ( -0.390597 , -0.0935645 , -0.146109 ) +colvars: ( -0.422416 , 0.0117541 , -0.12961 ) +colvars: ( -0.481811 , 0.0634295 , -0.165733 ) +colvars: ( -0.460111 , 0.027643 , -0.160343 ) +colvars: ( -0.447695 , 0.0881492 , -0.119861 ) +colvars: ( -0.50515 , -0.0300757 , -0.232485 ) +colvars: ( -0.538824 , -0.0318446 , -0.267311 ) +colvars: ( -0.590808 , -0.101593 , -0.352023 ) +colvars: ( -0.478035 , -0.0646808 , -0.22108 ) +colvars: ( -0.484252 , -0.0177428 , -0.205684 ) +colvars: ( -0.415992 , -0.144566 , -0.19531 ) +colvars: ( -0.349778 , -0.178748 , -0.144221 ) +colvars: ( -0.293181 , -0.275499 , -0.131738 ) +colvars: ( -0.307041 , -0.101051 , -0.0651772 ) +colvars: ( -0.290268 , -0.0815542 , -0.0392334 ) +colvars: ( -0.290057 , -0.0527551 , -0.0257211 ) +colvars: ( -0.254149 , 0.0270817 , 0.0474133 ) +colvars: ( -0.235888 , 0.0556767 , 0.0790609 ) +colvars: ( -0.303228 , 0.120077 , 0.0407899 ) +colvars: ( -0.273629 , 0.164398 , 0.0911506 ) +colvars: ( -0.380254 , 0.150721 , -0.0228531 ) +colvars: ( -0.434188 , 0.232441 , -0.0395872 ) +colvars: ( -0.514225 , 0.257292 , -0.108945 ) +colvars: ( -0.441955 , 0.210798 , -0.0574257 ) +colvars: ( -0.446797 , 0.275718 , -0.0323361 ) +colvars: ( -0.442665 , 0.117966 , -0.101012 ) +colvars: ( -0.445504 , 0.0852636 , -0.118981 ) +colvars: ( -0.465439 , -0.0145686 , -0.185217 ) +colvars: ( -0.370419 , 0.0725111 , -0.0490366 ) +colvars: ( -0.3718 , 0.100351 , -0.0375754 ) +colvars: ( -0.196527 , 0.106531 , 0.142298 ) +colvars: ( -0.140921 , 0.107988 , 0.199132 ) +colvars: ( -0.230363 , 0.184445 , 0.144105 ) +colvars: ( -0.302623 , 0.0286614 , -0.000814407 ) +colvars: ( -0.227813 , 0.0134423 , 0.0677126 ) +colvars: ( -0.167965 , -0.0757054 , 0.0869896 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 5. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 5. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 5, atoms_new_colvar_forces = { ( -4.57080684447655e+00 , -4.56757474205258e-01 , -1.34102307171331e+00 ), ( -3.93747933215641e+00 , -3.86057338789111e-01 , -1.06117980046159e+00 ), ( -4.00927585857282e+00 , -4.11723324486918e-01 , -1.09618838089752e+00 ), ( -5.39162219427185e+00 , -5.82277485042152e-01 , -1.61105752315784e+00 ), ( 2.50499884075726e-01 , 1.16409947280580e-01 , 3.39523401748820e-01 ), ( 4.93218264419087e+00 , 6.32855477223542e-01 , 1.89688596676198e+00 ), ( 4.16808727784256e+00 , 5.26653504109717e-01 , 1.64428538084388e+00 ), ( -4.17860487363991e-02 , 3.03117103968229e-02 , 3.45818921212498e-01 ), ( 4.14854415606074e+00 , 5.17048519073003e-01 , 1.61356370786374e+00 ), ( 5.49866324358008e+00 , 6.62873647003371e-01 , 2.00582619307530e+00 ), ( 1.14012440143183e-02 , 3.93035748419776e-02 , 2.90650467510932e-01 ), ( -3.17040350262143e-04 , 3.27998909670149e-02 , 2.66204944764889e-01 ), ( 1.99039043264463e-02 , 4.66806301700874e-02 , 3.29898912273345e-01 ), ( 4.19527538390151e-02 , 3.64083238256336e-02 , 1.93730700466022e-01 ), ( 1.44638449731704e-02 , 2.21994295576479e-02 , 1.44863533841288e-01 ), ( 1.09831626893484e-01 , 5.54016538627385e-02 , 1.84162532551469e-01 ), ( 1.55098431698864e-01 , 6.05666978079027e-02 , 1.17076539039485e-01 ), ( 2.33640235017002e-01 , 8.58390448148273e-02 , 1.32674281012204e-01 ), ( 1.27377000149962e-01 , 4.40233800636930e-02 , 4.98767088688037e-02 ), ( 1.22779275317610e-01 , 3.50280548828395e-02 , -1.18610391719648e-02 ), ( 1.05600645114430e-01 , 3.90191934872285e-02 , 6.17601479328360e-02 ), ( 7.11868109790795e-02 , 2.19371933538081e-02 , 6.29890121668214e-03 ), ( 5.91433406710006e-02 , 2.24153630278143e-02 , 3.91381972993816e-02 ), ( -5.03685952378485e-04 , -2.56847520689389e-03 , -1.95745320550648e-02 ), ( -1.38137677312026e-02 , -1.48030671154608e-02 , -8.65701004571590e-02 ), ( -4.73300457103983e-02 , -9.93470162873675e-03 , 3.34491547077175e-02 ), ( -1.13924654194938e-01 , -3.16831573457569e-02 , 1.76315017947849e-02 ), ( -1.54996461323862e-01 , -3.46521916242989e-02 , 9.23985997100513e-02 ), ( -1.02136551133698e-01 , -3.38017646487173e-02 , -2.78692317279842e-02 ), ( -1.37708661800939e-01 , -5.12364765932485e-02 , -8.33987592573597e-02 ), ( -5.02856010121193e-02 , -1.57328062474774e-02 , -6.36429116155157e-03 ), ( -3.02049049275266e-02 , -1.47959889480401e-02 , -4.70852908917164e-02 ), ( 2.47119619522573e-02 , 7.20466392188440e-03 , -1.13681819999997e-03 ), ( 1.09277549907982e-03 , -1.53025068800609e-02 , -1.26468416302199e-01 ), ( -1.64724043297200e-02 , -2.70872431561396e-02 , -1.79588114525385e-01 ), ( 4.73190353632281e-02 , -2.83458982824220e-03 , -1.36761747937318e-01 ), ( 7.62273370426887e-02 , -3.26132908138688e-03 , -2.09751788637767e-01 ), ( 1.36381644721633e-01 , 1.60015897261400e-02 , -1.98557429325506e-01 ), ( 1.88972130932885e-02 , -2.66267328650469e-02 , -2.60940000748580e-01 ), ( 1.99023246462202e-02 , -3.46469713197062e-02 , -3.28263746013194e-01 ), ( -3.29869544103972e-02 , -3.81682488079819e-02 , -2.29539878144585e-01 ), ( -9.28170291224147e-02 , -6.09778122526505e-02 , -2.70216370990327e-01 ), ( -1.29474503398891e-01 , -6.59067902809915e-02 , -2.21928981664928e-01 ), ( -1.49499695039101e-01 , -8.04942388469761e-02 , -2.91813060961600e-01 ), ( -1.76581536684527e-01 , -9.62081310288704e-02 , -3.53839012520408e-01 ), ( -1.92140739724632e-01 , -9.40480253856186e-02 , -2.98931372311928e-01 ), ( -2.33745114138208e-01 , -1.09710568743338e-01 , -3.25609015287589e-01 ), ( -1.19541366284067e-01 , -7.33037889823187e-02 , -3.05684612691047e-01 ), ( -1.69549392593515e-01 , -8.01006867640513e-02 , -2.40400237740579e-01 ), ( -2.22305627275974e-01 , -9.75639286307687e-02 , -2.54825659835956e-01 ), ( -2.57582595709948e-01 , -9.87156446620556e-02 , -1.79290409704149e-01 ) } +colvars: Step 5, atoms_new_colvar_forces = { ( -4.93768494226984e+00 , -4.93288890120217e-01 , -1.44813121666665e+00 ), ( -4.25352244045865e+00 , -4.16932622912841e-01 , -1.14590509214404e+00 ), ( -4.33107906543258e+00 , -4.44657599180775e-01 , -1.18372237480152e+00 ), ( -5.82437716510441e+00 , -6.28862714358498e-01 , -1.73976202698154e+00 ), ( 2.70597007471361e-01 , 1.25749083418850e-01 , 3.66762712094374e-01 ), ( 5.32805357607444e+00 , 6.83514841741323e-01 , 2.04859034711696e+00 ), ( 4.50263191825848e+00 , 5.68808850993012e-01 , 1.77579237717863e+00 ), ( -4.51382818778515e-02 , 3.27442119592583e-02 , 3.73563356008317e-01 ), ( 4.48152078257820e+00 , 5.58433238338579e-01 , 1.74260582654412e+00 ), ( 5.94000610865309e+00 , 7.15925282711389e-01 , 2.16620236805264e+00 ), ( 1.23158819761253e-02 , 4.24571519063832e-02 , 3.13968587103605e-01 ), ( -3.42648006105506e-04 , 3.54316380041383e-02 , 2.87561707841683e-01 ), ( 2.15004642581194e-02 , 5.04259784843997e-02 , 3.56365547326197e-01 ), ( 4.53183625143250e-02 , 3.93293574566300e-02 , 2.09273044603217e-01 ), ( 1.56240373387013e-02 , 2.39805029931352e-02 , 1.56485320228507e-01 ), ( 1.18643062750990e-01 , 5.98463107270278e-02 , 1.98937335082845e-01 ), ( 1.67541539661773e-01 , 6.54255296348837e-02 , 1.26469225808406e-01 ), ( 2.52384616803299e-01 , 9.27252495603290e-02 , 1.43318408152354e-01 ), ( 1.37596176637766e-01 , 4.75550056436365e-02 , 5.38782333859945e-02 ), ( 1.32629566187619e-01 , 3.78379244128352e-02 , -1.28126143201877e-02 ), ( 1.14072860060252e-01 , 4.21494678827976e-02 , 6.67151860121063e-02 ), ( 7.68981766913132e-02 , 2.36970776153220e-02 , 6.80453237339584e-03 ), ( 6.38885969511801e-02 , 2.42137378221992e-02 , 4.22785885005952e-02 ), ( -5.43938299810420e-04 , -2.77449159653712e-03 , -2.11447458474619e-02 ), ( -1.49218348929824e-02 , -1.59906824553589e-02 , -9.35151814964226e-02 ), ( -5.11271463814839e-02 , -1.07315298382845e-02 , 3.61327974958587e-02 ), ( -1.23064556176147e-01 , -3.42246880068121e-02 , 1.90460325794582e-02 ), ( -1.67431531351463e-01 , -3.74317405334914e-02 , 9.98114173401053e-02 ), ( -1.10330813486318e-01 , -3.65134029501701e-02 , -3.01052348849448e-02 ), ( -1.48756794797632e-01 , -5.53468429960343e-02 , -9.00897716356312e-02 ), ( -5.43200581784176e-02 , -1.69949591558956e-02 , -6.87509706350081e-03 ), ( -3.26284208685158e-02 , -1.59831328795033e-02 , -5.08631551834695e-02 ), ( 2.66942179180675e-02 , 7.78245929666979e-03 , -1.22844473176587e-03 ), ( 1.18026594086185e-03 , -1.65304508485450e-02 , -1.36614909479677e-01 ), ( -1.77941700646179e-02 , -2.92606942760620e-02 , -1.93996331615999e-01 ), ( 5.11152593622973e-02 , -3.06235115996423e-03 , -1.47733904656736e-01 ), ( 8.23428845352939e-02 , -3.52346953015942e-03 , -2.26579657776115e-01 ), ( 1.47323334991899e-01 , 1.72847684719611e-02 , -2.14487061656851e-01 ), ( 2.04133605463603e-02 , -2.87633124040187e-02 , -2.81874503252225e-01 ), ( 2.14991172292727e-02 , -3.74270878535857e-02 , -3.54599462106207e-01 ), ( -3.56333073901528e-02 , -4.12305732399287e-02 , -2.47955170408784e-01 ), ( -1.00263354533243e-01 , -6.58699640719693e-02 , -2.91894976071863e-01 ), ( -1.39861702854053e-01 , -7.11941852439772e-02 , -2.39733518258875e-01 ), ( -1.61493635100085e-01 , -8.69520689517708e-02 , -3.15224448305118e-01 ), ( -1.90748165374756e-01 , -1.03926651134371e-01 , -3.82226565007153e-01 ), ( -2.07555968566540e-01 , -1.01593274904900e-01 , -3.22914235361790e-01 ), ( -2.52498236898942e-01 , -1.18512344933050e-01 , -3.51732259815879e-01 ), ( -1.29132112882627e-01 , -7.91849803206830e-02 , -3.30209259457896e-01 ), ( -1.83151985289478e-01 , -8.65268695798549e-02 , -2.59687044895439e-01 ), ( -2.40140828851289e-01 , -1.05391069455491e-01 , -2.75269918588568e-01 ), ( -2.78248070003092e-01 , -1.06635024182009e-01 , -1.93674768357050e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 5, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3068,10 +4888,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 6, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 6, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 6, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 6, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 6, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 6, atoms_positions[size = 51] = { ( 8.38021201992906e+00 , 4.35622795205877e-02 , -7.57115549324088e-01 ), ( 6.99262075636104e+00 , -5.04815880767098e-01 , -6.50451452925487e-01 ), ( 6.25524799500166e+00 , -2.63667412648881e-01 , 6.65189730502905e-01 ), ( 4.99690128414275e+00 , -2.06630997050247e-01 , 6.67638995185915e-01 ), ( 7.04200716597089e+00 , -2.02050994511587e+00 , -1.01097403828471e+00 ), ( 6.90323517761355e+00 , -2.69573324907610e-01 , 1.81488311154711e+00 ), ( 6.17714731650717e+00 , -1.20515781462237e-01 , 3.07447537163275e+00 ), ( 7.16724113885896e+00 , -3.23458232146617e-01 , 4.29582213736862e+00 ), ( 5.30371594464467e+00 , 1.11714457836753e+00 , 3.29116469814723e+00 ), ( 4.09124849388116e+00 , 1.06501228412928e+00 , 3.62450262691055e+00 ), ( 5.87592866731547e+00 , 2.30253352539849e+00 , 2.97596071644480e+00 ), ( 5.21721389427611e+00 , 3.59596879390688e+00 , 2.88231338201453e+00 ), ( 6.33732766261078e+00 , 4.59629301054931e+00 , 2.45820200815087e+00 ), ( 3.89841652616976e+00 , 3.72602361681020e+00 , 2.02059671909465e+00 ), ( 2.90163811499207e+00 , 4.11598602240834e+00 , 2.54893878749135e+00 ), ( 3.82824919667602e+00 , 3.24208207942299e+00 , 7.73397951419180e-01 ), ( 2.67104733587927e+00 , 3.16251592386761e+00 , -9.10789941855962e-02 ), ( 3.04589936923495e+00 , 2.72187283946001e+00 , -1.59753742891037e+00 ), ( 1.61199981524947e+00 , 2.15269245744589e+00 , 5.82542052598303e-01 ), ( 4.35751799960440e-01 , 2.45515498134900e+00 , 5.52825511508801e-01 ), ( 1.97036780896963e+00 , 1.01273359174694e+00 , 1.05319136812280e+00 ), ( 1.15110250994451e+00 , 1.59855514824167e-02 , 1.68932967303409e+00 ), ( 2.01511729620419e+00 , -1.18091189184246e+00 , 2.02057383850610e+00 ), ( 5.19105471671030e-01 , 6.03751819725599e-01 , 2.99163240110414e+00 ), ( -6.72886335070202e-01 , 3.71984468858815e-01 , 3.18262593486689e+00 ), ( 1.30139050900177e+00 , 1.31799183325441e+00 , 3.82827802807958e+00 ), ( 8.36262416995475e-01 , 1.90659178940060e+00 , 5.06918797411790e+00 ), ( 2.05272790066819e+00 , 2.59249147938586e+00 , 5.62268788668921e+00 ), ( -3.59893314125172e-01 , 2.91963533099828e+00 , 4.98445769700446e+00 ), ( -1.17391249997732e+00 , 3.02952357363619e+00 , 5.90496283539945e+00 ), ( -4.16789831385964e-01 , 3.68860637085030e+00 , 3.85705143789314e+00 ), ( -1.47348624273045e+00 , 4.58263341198187e+00 , 3.53823008437198e+00 ), ( -7.54821420980561e-01 , 5.38550361473275e+00 , 2.41225635423488e+00 ), ( -2.72548455940354e+00 , 3.89460562853851e+00 , 2.93352283387009e+00 ), ( -3.85198517324324e+00 , 4.42597164355928e+00 , 2.85066191943228e+00 ), ( -2.58094023964050e+00 , 2.61071842582377e+00 , 2.49004794895700e+00 ), ( -3.71683196204322e+00 , 1.91061848615932e+00 , 2.06642203885726e+00 ), ( -3.41290123558981e+00 , 8.12251625818482e-01 , 9.85897670341821e-01 ), ( -4.30943088113364e+00 , 1.09535078280136e+00 , 3.23137618348510e+00 ), ( -5.53785685645807e+00 , 9.16210965946274e-01 , 3.34334002368099e+00 ), ( -3.46429849587187e+00 , 6.37594506320484e-01 , 4.15073901356801e+00 ), ( -3.77774838928890e+00 , 9.59601976211820e-02 , 5.48141661971274e+00 ), ( -2.40925846838727e+00 , -3.98892124368813e-01 , 6.14186628363733e+00 ), ( -4.46908183155242e+00 , 9.97824625721238e-01 , 6.41787423491210e+00 ), ( -5.32321128737128e+00 , 6.01484903984397e-01 , 7.18429115422948e+00 ), ( -6.29685375196358e+00 , 3.55127290010162e+00 , 6.70152734031360e+00 ), ( -6.91388693893618e+00 , 4.30123660545722e+00 , 7.41816638381674e+00 ), ( -6.74629264999051e+00 , 3.20880368173676e+00 , 5.51156283491087e+00 ), ( -4.08754871373955e+00 , 2.30173173767669e+00 , 6.48165063911067e+00 ), ( -4.90580092458475e+00 , 3.23290383832168e+00 , 7.21354073589404e+00 ), ( -4.07873592871374e+00 , 4.51178543035802e+00 , 7.27132768660334e+00 ) } +colvars: Step 6, atoms_positions[size = 51] = { ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 ), ( 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 ), ( 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 ), ( 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 ), ( 7.04201555099061e+00 , -2.02050568202986e+00 , -1.01095918508983e+00 ), ( 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 ), ( 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 ), ( 7.16724600547698e+00 , -3.23457816615841e-01 , 4.29584430367597e+00 ), ( 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 ), ( 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 ), ( 5.87593597617318e+00 , 2.30253862916233e+00 , 2.97597265646037e+00 ), ( 5.21721353076129e+00 , 3.59597007511603e+00 , 2.88232644638125e+00 ), ( 6.33732844472895e+00 , 4.59629505881425e+00 , 2.45821720058526e+00 ), ( 3.89841886989411e+00 , 3.72602515256593e+00 , 2.02060672375480e+00 ), ( 2.90163859561185e+00 , 4.11598692141058e+00 , 2.54894451315239e+00 ), ( 3.82825409784994e+00 , 3.24208459259053e+00 , 7.73406194586500e-01 ), ( 2.67105524123482e+00 , 3.16251906451889e+00 , -9.10730059314331e-02 ), ( 3.04590999511220e+00 , 2.72187692027414e+00 , -1.59753086769456e+00 ), ( 1.61200628352592e+00 , 2.15269472340813e+00 , 5.82544644062388e-01 ), ( 4.35756748777557e-01 , 2.45515633198171e+00 , 5.52825059613988e-01 ), ( 1.97037235331458e+00 , 1.01273541810539e+00 , 1.05319421577032e+00 ), ( 1.15110600864534e+00 , 1.59866561905923e-02 , 1.68932994796430e+00 ), ( 2.01512013916619e+00 , -1.18091084465548e+00 , 2.02057579533244e+00 ), ( 5.19105469798803e-01 , 6.03751696402325e-01 , 2.99163142287312e+00 ), ( -6.72886836516355e-01 , 3.71983893027156e-01 , 3.18262255084290e+00 ), ( 1.30138914203718e+00 , 1.31799129123245e+00 , 3.82827939703354e+00 ), ( 8.36256674898712e-01 , 1.90659029059265e+00 , 5.06918877544204e+00 ), ( 2.05272041220510e+00 , 2.59248976061916e+00 , 5.62269186133449e+00 ), ( -3.59898534695024e-01 , 2.91963356273390e+00 , 4.98445621212317e+00 ), ( -1.17391800038070e+00 , 3.02952158168549e+00 , 5.90495963634345e+00 ), ( -4.16792067248368e-01 , 3.68860565679751e+00 , 3.85705103294777e+00 ), ( -1.47348778711130e+00 , 4.58263272771055e+00 , 3.53822775040597e+00 ), ( -7.54820296625674e-01 , 5.38550393877410e+00 , 2.41225622261323e+00 ), ( -2.72548458263952e+00 , 3.89460490153238e+00 , 2.93351632047225e+00 ), ( -3.85198578444575e+00 , 4.42597054842895e+00 , 2.85065485184329e+00 ), ( -2.58093832643556e+00 , 2.61071833644784e+00 , 2.49004186169887e+00 ), ( -3.71682803626518e+00 , 1.91061829197026e+00 , 2.06641130275165e+00 ), ( -3.41289478688424e+00 , 8.12252048203337e-01 , 9.85888091499494e-01 ), ( -4.30942983875831e+00 , 1.09534931485942e+00 , 3.23136276915903e+00 ), ( -5.53785606211609e+00 , 9.16209594457123e-01 , 3.34332710128568e+00 ), ( -3.46429988873949e+00 , 6.37592796519501e-01 , 4.15072862341052e+00 ), ( -3.77775300960228e+00 , 9.59573757368899e-02 , 5.48140295359406e+00 ), ( -2.40926491947795e+00 , -3.98894890699091e-01 , 6.14185569677671e+00 ), ( -4.46908951835721e+00 , 9.97820565764761e-01 , 6.41785913641396e+00 ), ( -5.32321822477403e+00 , 6.01481105198029e-01 , 7.18427723959524e+00 ), ( -6.29686369435140e+00 , 3.55126815673210e+00 , 6.70151222217351e+00 ), ( -6.91389609509752e+00 , 4.30123221834033e+00 , 7.41815348169977e+00 ), ( -6.74629806351582e+00 , 3.20880069721169e+00 , 5.51154954373544e+00 ), ( -4.08755630619893e+00 , 2.30172816421519e+00 , 6.48163985555273e+00 ), ( -4.90581235595044e+00 , 3.23289872377110e+00 , 7.21352814018328e+00 ), ( -4.07874815839021e+00 , 4.51178048034416e+00 , 7.27131933992993e+00 ) } colvars: Step 6, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 6, atom_groups_ids[size = 0] = @@ -3089,162 +4909,301 @@ colvars: Collective variables module, step no. 6 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.33541437426750e-01 , 4.81523415673580e-03 , 9.42723142306008e-01 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.33416359589612e-01 , 4.82914602417237e-03 , 9.42767315145518e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 7.04201555099061e+00 , -2.02050568202986e+00 , -1.01095918508983e+00 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 , 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 7.16724600547698e+00 , -3.23457816615841e-01 , 4.29584430367597e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 , 5.87593597617318e+00 , 2.30253862916233e+00 , 2.97597265646037e+00 , 5.21721353076129e+00 , 3.59597007511603e+00 , 2.88232644638125e+00 , 6.33732844472895e+00 , 4.59629505881425e+00 , 2.45821720058526e+00 , 3.89841886989411e+00 , 3.72602515256593e+00 , 2.02060672375480e+00 , 2.90163859561185e+00 , 4.11598692141058e+00 , 2.54894451315239e+00 , 3.82825409784994e+00 , 3.24208459259053e+00 , 7.73406194586500e-01 , 2.67105524123482e+00 , 3.16251906451889e+00 , -9.10730059314331e-02 , 3.04590999511220e+00 , 2.72187692027414e+00 , -1.59753086769456e+00 , 1.61200628352592e+00 , 2.15269472340813e+00 , 5.82544644062388e-01 , 4.35756748777557e-01 , 2.45515633198171e+00 , 5.52825059613988e-01 , 1.97037235331458e+00 , 1.01273541810539e+00 , 1.05319421577032e+00 , 1.15110600864534e+00 , 1.59866561905923e-02 , 1.68932994796430e+00 , 2.01512013916619e+00 , -1.18091084465548e+00 , 2.02057579533244e+00 , 5.19105469798803e-01 , 6.03751696402325e-01 , 2.99163142287312e+00 , -6.72886836516355e-01 , 3.71983893027156e-01 , 3.18262255084290e+00 , 1.30138914203718e+00 , 1.31799129123245e+00 , 3.82827939703354e+00 , 8.36256674898712e-01 , 1.90659029059265e+00 , 5.06918877544204e+00 , 2.05272041220510e+00 , 2.59248976061916e+00 , 5.62269186133449e+00 , -3.59898534695024e-01 , 2.91963356273390e+00 , 4.98445621212317e+00 , -1.17391800038070e+00 , 3.02952158168549e+00 , 5.90495963634345e+00 , -4.16792067248368e-01 , 3.68860565679751e+00 , 3.85705103294777e+00 , -1.47348778711130e+00 , 4.58263272771055e+00 , 3.53822775040597e+00 , -7.54820296625674e-01 , 5.38550393877410e+00 , 2.41225622261323e+00 , -2.72548458263952e+00 , 3.89460490153238e+00 , 2.93351632047225e+00 , -3.85198578444575e+00 , 4.42597054842895e+00 , 2.85065485184329e+00 , -2.58093832643556e+00 , 2.61071833644784e+00 , 2.49004186169887e+00 , -3.71682803626518e+00 , 1.91061829197026e+00 , 2.06641130275165e+00 , -3.41289478688424e+00 , 8.12252048203337e-01 , 9.85888091499494e-01 , -4.30942983875831e+00 , 1.09534931485942e+00 , 3.23136276915903e+00 , -5.53785606211609e+00 , 9.16209594457123e-01 , 3.34332710128568e+00 , -3.46429988873949e+00 , 6.37592796519501e-01 , 4.15072862341052e+00 , -3.77775300960228e+00 , 9.59573757368899e-02 , 5.48140295359406e+00 , -2.40926491947795e+00 , -3.98894890699091e-01 , 6.14185569677671e+00 , -4.46908951835721e+00 , 9.97820565764761e-01 , 6.41785913641396e+00 , -5.32321822477403e+00 , 6.01481105198029e-01 , 7.18427723959524e+00 , -6.29686369435140e+00 , 3.55126815673210e+00 , 6.70151222217351e+00 , -6.91389609509752e+00 , 4.30123221834033e+00 , 7.41815348169977e+00 , -6.74629806351582e+00 , 3.20880069721169e+00 , 5.51154954373544e+00 , -4.08755630619893e+00 , 2.30172816421519e+00 , 6.48163985555273e+00 , -4.90581235595044e+00 , 3.23289872377110e+00 , 7.21352814018328e+00 , -4.07874815839021e+00 , 4.51178048034416e+00 , 7.27131933992993e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.33541437426750e-01 , 4.81523415673580e-03 , 9.42723142306008e-01 ). +colvars: Colvar "one" has value ( -3.33416359589612e-01 , 4.82914602417237e-03 , 9.42767315145518e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 7.04201555099061e+00 , -2.02050568202986e+00 , -1.01095918508983e+00 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 , 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 7.16724600547698e+00 , -3.23457816615841e-01 , 4.29584430367597e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 , 5.87593597617318e+00 , 2.30253862916233e+00 , 2.97597265646037e+00 , 5.21721353076129e+00 , 3.59597007511603e+00 , 2.88232644638125e+00 , 6.33732844472895e+00 , 4.59629505881425e+00 , 2.45821720058526e+00 , 3.89841886989411e+00 , 3.72602515256593e+00 , 2.02060672375480e+00 , 2.90163859561185e+00 , 4.11598692141058e+00 , 2.54894451315239e+00 , 3.82825409784994e+00 , 3.24208459259053e+00 , 7.73406194586500e-01 , 2.67105524123482e+00 , 3.16251906451889e+00 , -9.10730059314331e-02 , 3.04590999511220e+00 , 2.72187692027414e+00 , -1.59753086769456e+00 , 1.61200628352592e+00 , 2.15269472340813e+00 , 5.82544644062388e-01 , 4.35756748777557e-01 , 2.45515633198171e+00 , 5.52825059613988e-01 , 1.97037235331458e+00 , 1.01273541810539e+00 , 1.05319421577032e+00 , 1.15110600864534e+00 , 1.59866561905923e-02 , 1.68932994796430e+00 , 2.01512013916619e+00 , -1.18091084465548e+00 , 2.02057579533244e+00 , 5.19105469798803e-01 , 6.03751696402325e-01 , 2.99163142287312e+00 , -6.72886836516355e-01 , 3.71983893027156e-01 , 3.18262255084290e+00 , 1.30138914203718e+00 , 1.31799129123245e+00 , 3.82827939703354e+00 , 8.36256674898712e-01 , 1.90659029059265e+00 , 5.06918877544204e+00 , 2.05272041220510e+00 , 2.59248976061916e+00 , 5.62269186133449e+00 , -3.59898534695024e-01 , 2.91963356273390e+00 , 4.98445621212317e+00 , -1.17391800038070e+00 , 3.02952158168549e+00 , 5.90495963634345e+00 , -4.16792067248368e-01 , 3.68860565679751e+00 , 3.85705103294777e+00 , -1.47348778711130e+00 , 4.58263272771055e+00 , 3.53822775040597e+00 , -7.54820296625674e-01 , 5.38550393877410e+00 , 2.41225622261323e+00 , -2.72548458263952e+00 , 3.89460490153238e+00 , 2.93351632047225e+00 , -3.85198578444575e+00 , 4.42597054842895e+00 , 2.85065485184329e+00 , -2.58093832643556e+00 , 2.61071833644784e+00 , 2.49004186169887e+00 , -3.71682803626518e+00 , 1.91061829197026e+00 , 2.06641130275165e+00 , -3.41289478688424e+00 , 8.12252048203337e-01 , 9.85888091499494e-01 , -4.30942983875831e+00 , 1.09534931485942e+00 , 3.23136276915903e+00 , -5.53785606211609e+00 , 9.16209594457123e-01 , 3.34332710128568e+00 , -3.46429988873949e+00 , 6.37592796519501e-01 , 4.15072862341052e+00 , -3.77775300960228e+00 , 9.59573757368899e-02 , 5.48140295359406e+00 , -2.40926491947795e+00 , -3.98894890699091e-01 , 6.14185569677671e+00 , -4.46908951835721e+00 , 9.97820565764761e-01 , 6.41785913641396e+00 , -5.32321822477403e+00 , 6.01481105198029e-01 , 7.18427723959524e+00 , -6.29686369435140e+00 , 3.55126815673210e+00 , 6.70151222217351e+00 , -6.91389609509752e+00 , 4.30123221834033e+00 , 7.41815348169977e+00 , -6.74629806351582e+00 , 3.20880069721169e+00 , 5.51154954373544e+00 , -4.08755630619893e+00 , 2.30172816421519e+00 , 6.48163985555273e+00 , -4.90581235595044e+00 , 3.23289872377110e+00 , 7.21352814018328e+00 , -4.07874815839021e+00 , 4.51178048034416e+00 , 7.27131933992993e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.1888 , 1.8555 , -14.9509 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.5097 , 6.75097 , 13.5019 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.1888 , 1.8555 , -14.9509 ) to colvar "one". -colvars: Adding total bias energy: 45.6413 +colvars: Adding biasing force ( 67.5097 , 6.75097 , 13.5019 ) to colvar "one". +colvars: Adding total bias energy: 58.6303 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.1888 , 1.8555 , -14.9509 ) +colvars: Force to be applied: ( 67.5097 , 6.75097 , 13.5019 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.85038 , -0.567546 , -1.5818 ) -colvars: ( -4.1592 , -0.486671 , -1.35639 ) -colvars: ( -4.1592 , -0.486671 , -1.35639 ) -colvars: ( -5.54018 , -0.648259 , -1.80676 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.23016 , -0.611795 , -1.7049 ) +colvars: ( -4.48486 , -0.524614 , -1.46195 ) +colvars: ( -4.48486 , -0.524614 , -1.46195 ) +colvars: ( -5.97397 , -0.698801 , -1.94736 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.901641 , 0.193183 , 0.646578 ) -colvars: ( 0.779379 , 0.265084 , 0.672145 ) -colvars: ( 0.764888 , 0.257493 , 0.653031 ) -colvars: ( 0.664104 , 0.267219 , 0.606012 ) -colvars: ( 0.651991 , 0.200643 , 0.507252 ) -colvars: ( 0.574797 , 0.345684 , 0.660348 ) -colvars: ( 0.464093 , 0.361099 , 0.615206 ) -colvars: ( 0.384969 , 0.459456 , 0.702981 ) -colvars: ( 0.381382 , 0.316874 , 0.504866 ) -colvars: ( 0.345139 , 0.275836 , 0.426748 ) -colvars: ( 0.352924 , 0.321772 , 0.494547 ) -colvars: ( 0.281055 , 0.279078 , 0.392807 ) -colvars: ( 0.25493 , 0.30769 , 0.416479 ) -colvars: ( 0.345404 , 0.180378 , 0.295708 ) -colvars: ( 0.285329 , 0.137537 , 0.200832 ) -colvars: ( 0.471397 , 0.142033 , 0.318494 ) -colvars: ( 0.546003 , 0.0497262 , 0.236327 ) -colvars: ( 0.679318 , 0.0272402 , 0.285298 ) -colvars: ( 0.553258 , 0.0184365 , 0.197669 ) -colvars: ( 0.537182 , -0.0465929 , 0.0986598 ) -colvars: ( 0.573236 , 0.0668538 , 0.276184 ) -colvars: ( 0.570093 , 0.0513687 , 0.253018 ) -colvars: ( 0.606206 , 0.116419 , 0.364061 ) -colvars: ( 0.442321 , 0.0571844 , 0.184457 ) -colvars: ( 0.434807 , 0.00146932 , 0.103379 ) -colvars: ( 0.33818 , 0.123737 , 0.213531 ) -colvars: ( 0.210467 , 0.133562 , 0.150515 ) -colvars: ( 0.117104 , 0.220136 , 0.213566 ) -colvars: ( 0.182661 , 0.0595102 , 0.0320774 ) -colvars: ( 0.131661 , 0.0239791 , -0.047314 ) -colvars: ( 0.218647 , 0.0329188 , 0.0170909 ) -colvars: ( 0.205434 , -0.0400493 , -0.0911145 ) -colvars: ( 0.243294 , -0.0444622 , -0.0744956 ) -colvars: ( 0.282088 , -0.126633 , -0.164188 ) -colvars: ( 0.237173 , -0.179479 , -0.263732 ) -colvars: ( 0.3995 , -0.142487 , -0.115631 ) -colvars: ( 0.478266 , -0.218552 , -0.172983 ) -colvars: ( 0.612353 , -0.22223 , -0.0977002 ) -colvars: ( 0.428284 , -0.221944 , -0.207592 ) -colvars: ( 0.433774 , -0.290079 , -0.297949 ) -colvars: ( 0.377195 , -0.147585 , -0.136002 ) -colvars: ( 0.320158 , -0.140183 , -0.160003 ) -colvars: ( 0.302051 , -0.0527111 , -0.0506283 ) -colvars: ( 0.194117 , -0.147958 , -0.246205 ) -colvars: ( 0.168392 , -0.189483 , -0.318693 ) -colvars: ( -0.00939214 , -0.193064 , -0.430133 ) -colvars: ( -0.102361 , -0.210124 , -0.509284 ) -colvars: ( 0.094336 , -0.244381 , -0.438516 ) -colvars: ( 0.111355 , -0.106983 , -0.239476 ) -colvars: ( -0.0105149 , -0.110415 , -0.317213 ) -colvars: ( -0.101108 , -0.0290579 , -0.259673 ) +colvars: ( 0.972151 , 0.208306 , 0.697037 ) +colvars: ( 0.840336 , 0.285822 , 0.724605 ) +colvars: ( 0.824708 , 0.277643 , 0.704003 ) +colvars: ( 0.716055 , 0.288116 , 0.653307 ) +colvars: ( 0.702995 , 0.216335 , 0.546834 ) +colvars: ( 0.619771 , 0.372709 , 0.711888 ) +colvars: ( 0.50042 , 0.38932 , 0.66322 ) +colvars: ( 0.415115 , 0.495361 , 0.757852 ) +colvars: ( 0.411244 , 0.341637 , 0.544266 ) +colvars: ( 0.37217 , 0.297387 , 0.460046 ) +colvars: ( 0.380558 , 0.346921 , 0.533146 ) +colvars: ( 0.30307 , 0.300889 , 0.423463 ) +colvars: ( 0.2749 , 0.331741 , 0.448989 ) +colvars: ( 0.372446 , 0.194478 , 0.318779 ) +colvars: ( 0.307677 , 0.148284 , 0.216494 ) +colvars: ( 0.508283 , 0.153141 , 0.343342 ) +colvars: ( 0.588718 , 0.053623 , 0.254756 ) +colvars: ( 0.732448 , 0.0293876 , 0.30755 ) +colvars: ( 0.596544 , 0.0198831 , 0.213074 ) +colvars: ( 0.579211 , -0.0502308 , 0.106332 ) +colvars: ( 0.618086 , 0.0720823 , 0.297718 ) +colvars: ( 0.614701 , 0.0553818 , 0.272738 ) +colvars: ( 0.653639 , 0.125515 , 0.392451 ) +colvars: ( 0.476947 , 0.0616445 , 0.198823 ) +colvars: ( 0.468846 , 0.00157184 , 0.111411 ) +colvars: ( 0.364667 , 0.133395 , 0.230172 ) +colvars: ( 0.226976 , 0.143982 , 0.162237 ) +colvars: ( 0.126317 , 0.23732 , 0.230216 ) +colvars: ( 0.196994 , 0.0641426 , 0.0345513 ) +colvars: ( 0.14201 , 0.0258295 , -0.0510417 ) +colvars: ( 0.235788 , 0.0354787 , 0.0183974 ) +colvars: ( 0.221539 , -0.043191 , -0.0982568 ) +colvars: ( 0.262353 , -0.0479419 , -0.0803363 ) +colvars: ( 0.304184 , -0.13654 , -0.177041 ) +colvars: ( 0.255758 , -0.19352 , -0.28436 ) +colvars: ( 0.430771 , -0.153629 , -0.124695 ) +colvars: ( 0.515693 , -0.235639 , -0.186531 ) +colvars: ( 0.660258 , -0.239599 , -0.105372 ) +colvars: ( 0.461809 , -0.239303 , -0.223846 ) +colvars: ( 0.467728 , -0.312765 , -0.321262 ) +colvars: ( 0.406732 , -0.159138 , -0.146666 ) +colvars: ( 0.345241 , -0.151164 , -0.172544 ) +colvars: ( 0.325723 , -0.0568582 , -0.0546286 ) +colvars: ( 0.209352 , -0.159552 , -0.265476 ) +colvars: ( 0.181617 , -0.204328 , -0.343627 ) +colvars: ( -0.0100666 , -0.208187 , -0.463758 ) +colvars: ( -0.110301 , -0.226585 , -0.54909 ) +colvars: ( 0.101764 , -0.263508 , -0.472797 ) +colvars: ( 0.120119 , -0.115375 , -0.258217 ) +colvars: ( -0.0112737 , -0.119081 , -0.342021 ) +colvars: ( -0.108947 , -0.0313666 , -0.279983 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.85038 , 0.567546 , 1.5818 ) -colvars: ( 4.1592 , 0.486671 , 1.35639 ) -colvars: ( 4.1592 , 0.486671 , 1.35639 ) -colvars: ( 5.54018 , 0.648259 , 1.80676 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.23016 , 0.611795 , 1.7049 ) +colvars: ( 4.48486 , 0.524614 , 1.46195 ) +colvars: ( 4.48486 , 0.524614 , 1.46195 ) +colvars: ( 5.97397 , 0.698801 , 1.94736 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.625835 , -0.0804071 , -0.398294 ) -colvars: ( -0.560902 , -0.162793 , -0.37038 ) -colvars: ( -0.514164 , -0.1409 , -0.313178 ) -colvars: ( -0.517493 , -0.190657 , -0.339281 ) -colvars: ( -0.507867 , -0.132524 , -0.302991 ) -colvars: ( -0.489037 , -0.282167 , -0.352372 ) -colvars: ( -0.451889 , -0.322721 , -0.333395 ) -colvars: ( -0.426892 , -0.429274 , -0.356855 ) -colvars: ( -0.388699 , -0.288097 , -0.253762 ) -colvars: ( -0.38222 , -0.263357 , -0.235911 ) -colvars: ( -0.341512 , -0.282498 , -0.203554 ) -colvars: ( -0.28133 , -0.246297 , -0.126237 ) -colvars: ( -0.234925 , -0.261 , -0.0860976 ) -colvars: ( -0.303358 , -0.143934 , -0.101695 ) -colvars: ( -0.270783 , -0.115314 , -0.0557208 ) -colvars: ( -0.361416 , -0.0865334 , -0.134086 ) -colvars: ( -0.390706 , 0.0109931 , -0.119088 ) -colvars: ( -0.445407 , 0.0588221 , -0.152464 ) -colvars: ( -0.425744 , 0.0257071 , -0.147744 ) -colvars: ( -0.414259 , 0.0817507 , -0.110531 ) -colvars: ( -0.467563 , -0.027756 , -0.214408 ) -colvars: ( -0.498903 , -0.0293939 , -0.246804 ) -colvars: ( -0.547117 , -0.0940021 , -0.325019 ) -colvars: ( -0.442882 , -0.0597757 , -0.20412 ) -colvars: ( -0.448696 , -0.0163008 , -0.190121 ) -colvars: ( -0.385596 , -0.133739 , -0.180079 ) -colvars: ( -0.324528 , -0.165367 , -0.132869 ) -colvars: ( -0.272264 , -0.254954 , -0.121039 ) -colvars: ( -0.284882 , -0.0933989 , -0.0599412 ) -colvars: ( -0.269489 , -0.075329 , -0.036139 ) -colvars: ( -0.268931 , -0.0486762 , -0.0233934 ) -colvars: ( -0.235578 , 0.0252706 , 0.0440836 ) -colvars: ( -0.218432 , 0.0517461 , 0.0734982 ) -colvars: ( -0.280917 , 0.111383 , 0.0376588 ) -colvars: ( -0.253567 , 0.152443 , 0.0840435 ) -colvars: ( -0.352088 , 0.139737 , -0.0212495 ) -colvars: ( -0.401936 , 0.215405 , -0.0370002 ) -colvars: ( -0.475837 , 0.23839 , -0.10112 ) -colvars: ( -0.409369 , 0.195371 , -0.0536629 ) -colvars: ( -0.413849 , 0.255498 , -0.0307062 ) -colvars: ( -0.410244 , 0.109405 , -0.0938378 ) -colvars: ( -0.413122 , 0.0791291 , -0.110582 ) -colvars: ( -0.431746 , -0.0133296 , -0.171647 ) -colvars: ( -0.343793 , 0.0673481 , -0.0459587 ) -colvars: ( -0.345184 , 0.0931388 , -0.035576 ) -colvars: ( -0.182863 , 0.0989059 , 0.13097 ) -colvars: ( -0.131518 , 0.100277 , 0.183445 ) -colvars: ( -0.213909 , 0.171044 , 0.132591 ) -colvars: ( -0.281066 , 0.0267554 , -0.00117054 ) -colvars: ( -0.211976 , 0.0126889 , 0.0621667 ) -colvars: ( -0.156676 , -0.0698563 , 0.0802804 ) +colvars: ( -0.674764 , -0.0867058 , -0.429325 ) +colvars: ( -0.604763 , -0.175528 , -0.399227 ) +colvars: ( -0.554365 , -0.151927 , -0.337557 ) +colvars: ( -0.557971 , -0.205564 , -0.365705 ) +colvars: ( -0.547594 , -0.142886 , -0.326589 ) +colvars: ( -0.527301 , -0.304222 , -0.379813 ) +colvars: ( -0.48726 , -0.347939 , -0.359358 ) +colvars: ( -0.460318 , -0.462817 , -0.384642 ) +colvars: ( -0.419132 , -0.310607 , -0.273513 ) +colvars: ( -0.412152 , -0.283931 , -0.254276 ) +colvars: ( -0.368253 , -0.304574 , -0.219383 ) +colvars: ( -0.303367 , -0.265542 , -0.136035 ) +colvars: ( -0.25333 , -0.281398 , -0.0927564 ) +colvars: ( -0.32711 , -0.155181 , -0.109585 ) +colvars: ( -0.291993 , -0.124322 , -0.060028 ) +colvars: ( -0.389697 , -0.0932992 , -0.144505 ) +colvars: ( -0.421269 , 0.011847 , -0.128343 ) +colvars: ( -0.480234 , 0.0634082 , -0.164322 ) +colvars: ( -0.459052 , 0.0277143 , -0.159243 ) +colvars: ( -0.446669 , 0.088139 , -0.119132 ) +colvars: ( -0.504144 , -0.0299254 , -0.231108 ) +colvars: ( -0.537941 , -0.0316877 , -0.266037 ) +colvars: ( -0.589927 , -0.101344 , -0.350353 ) +colvars: ( -0.477551 , -0.0644384 , -0.220025 ) +colvars: ( -0.483822 , -0.0175638 , -0.20494 ) +colvars: ( -0.415794 , -0.14418 , -0.194103 ) +colvars: ( -0.349962 , -0.178275 , -0.14321 ) +colvars: ( -0.293618 , -0.274862 , -0.130449 ) +colvars: ( -0.307214 , -0.100683 , -0.0645956 ) +colvars: ( -0.290623 , -0.0811972 , -0.0389415 ) +colvars: ( -0.290007 , -0.0524691 , -0.0251934 ) +colvars: ( -0.254043 , 0.0272558 , 0.0475453 ) +colvars: ( -0.235547 , 0.0557954 , 0.0792603 ) +colvars: ( -0.302922 , 0.120097 , 0.040611 ) +colvars: ( -0.273436 , 0.164368 , 0.0906101 ) +colvars: ( -0.37965 , 0.150664 , -0.0228955 ) +colvars: ( -0.43339 , 0.232245 , -0.0398829 ) +colvars: ( -0.51306 , 0.257022 , -0.109006 ) +colvars: ( -0.441414 , 0.210651 , -0.0578512 ) +colvars: ( -0.446245 , 0.275478 , -0.0331099 ) +colvars: ( -0.442366 , 0.117969 , -0.101158 ) +colvars: ( -0.44548 , 0.0853325 , -0.119214 ) +colvars: ( -0.465566 , -0.0143499 , -0.185038 ) +colvars: ( -0.370739 , 0.072635 , -0.0495491 ) +colvars: ( -0.372244 , 0.100444 , -0.0383625 ) +colvars: ( -0.197233 , 0.106661 , 0.141186 ) +colvars: ( -0.141879 , 0.108143 , 0.197754 ) +colvars: ( -0.230694 , 0.184432 , 0.142934 ) +colvars: ( -0.30311 , 0.0288702 , -0.00126033 ) +colvars: ( -0.228627 , 0.0137081 , 0.0670182 ) +colvars: ( -0.169008 , -0.075287 , 0.0865533 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 6. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 6. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 6, atoms_new_colvar_forces = { ( -4.57457590091407e+00 , -4.54769792276199e-01 , -1.33351707855332e+00 ), ( -3.94072400108378e+00 , -3.84380271113976e-01 , -1.05462859139149e+00 ), ( -4.01258945124985e+00 , -4.10109375456033e-01 , -1.08966275115916e+00 ), ( -5.39605214643696e+00 , -5.80140582968099e-01 , -1.60249485637283e+00 ), ( 2.50724548660147e-01 , 1.16592979696714e-01 , 3.39852632993541e-01 ), ( 4.93614108413631e+00 , 6.31063238128868e-01 , 1.88977701154470e+00 ), ( 4.17140544998400e+00 , 5.25048525480392e-01 , 1.63820398799561e+00 ), ( -4.19233568377603e-02 , 3.01812045108948e-02 , 3.46126386938239e-01 ), ( 4.15188469720697e+00 , 5.15447446166591e-01 , 1.60749792277893e+00 ), ( 5.50309595182518e+00 , 6.60739122455141e-01 , 1.99759268427134e+00 ), ( 1.14119430284726e-02 , 3.92738611795704e-02 , 2.90993062355441e-01 ), ( -2.75358202559972e-04 , 3.27811062718754e-02 , 2.66570139588651e-01 ), ( 2.00051288091696e-02 , 4.66898393156434e-02 , 3.30381886686014e-01 ), ( 4.20458379946161e-02 , 3.64444128073375e-02 , 1.94012894368770e-01 ), ( 1.45458339541725e-02 , 2.22230271631906e-02 , 1.45111545271329e-01 ), ( 1.09980586478823e-01 , 5.54992517679401e-02 , 1.84407419045777e-01 ), ( 1.55297160248552e-01 , 6.07192690646057e-02 , 1.17238922544312e-01 ), ( 2.33910828741050e-01 , 8.60622613534296e-02 , 1.32833565871435e-01 ), ( 1.27514196804622e-01 , 4.41436407988194e-02 , 4.99248708458485e-02 ), ( 1.22923907696598e-01 , 3.51577700283853e-02 , -1.18714649727845e-02 ), ( 1.05672931481030e-01 , 3.90977730899397e-02 , 6.17761989815965e-02 ), ( 7.11895650300886e-02 , 2.19747986094425e-02 , 6.21434578213198e-03 ), ( 5.90887226343063e-02 , 2.24167941881323e-02 , 3.90421673496766e-02 ), ( -5.60854668515354e-04 , -2.59123290819695e-03 , -1.96635008192578e-02 ), ( -1.38890313213493e-02 , -1.48314610215812e-02 , -8.67418934573790e-02 ), ( -4.74166351608394e-02 , -1.00023195858622e-02 , 3.34516895036507e-02 ), ( -1.14060720473267e-01 , -3.18052610494058e-02 , 1.76468853341181e-02 ), ( -1.55159256123518e-01 , -3.48179780444641e-02 , 9.25267549914819e-02 ), ( -1.02221065357800e-01 , -3.38886349648099e-02 , -2.78638372939027e-02 ), ( -1.37828667250468e-01 , -5.13499038997308e-02 , -8.34529773880383e-02 ), ( -5.02838432334893e-02 , -1.57574706892050e-02 , -6.30253794941990e-03 ), ( -3.01446766030854e-02 , -1.47786917641173e-02 , -4.70309076154132e-02 ), ( 2.48617336337160e-02 , 7.28381713931851e-03 , -9.97329476770725e-04 ), ( 1.17111278742887e-03 , -1.52498038272826e-02 , -1.26529222394273e-01 ), ( -1.63942486188990e-02 , -2.70364317515549e-02 , -1.79688761882733e-01 ), ( 4.74115681131560e-02 , -2.74999557612118e-03 , -1.36880149751937e-01 ), ( 7.63304734857032e-02 , -3.14677873538044e-03 , -2.09983299662943e-01 ), ( 1.36515415149144e-01 , 1.61595861306180e-02 , -1.98820545958617e-01 ), ( 1.89151549537173e-02 , -2.65726554723585e-02 , -2.61254566381825e-01 ), ( 1.99241892300920e-02 , -3.45812794293266e-02 , -3.28655113023876e-01 ), ( -3.30484240030184e-02 , -3.81807226834966e-02 , -2.29839916874141e-01 ), ( -9.29647904685690e-02 , -6.10540128733924e-02 , -2.70584900912252e-01 ), ( -1.29694415948701e-01 , -6.60407161880313e-02 , -2.22274856383424e-01 ), ( -1.49675593189720e-01 , -8.06095207714782e-02 , -2.92164093126229e-01 ), ( -1.76792755195341e-01 , -9.63445469293042e-02 , -3.54268538508474e-01 ), ( -1.92255432658238e-01 , -9.41576450489818e-02 , -2.99162749866294e-01 ), ( -2.33879163494353e-01 , -1.09846797309254e-01 , -3.25838911485061e-01 ), ( -1.19572861011783e-01 , -7.33377688046537e-02 , -3.05924542942689e-01 ), ( -1.69711186872272e-01 , -8.02273904813037e-02 , -2.40646967816807e-01 ), ( -2.22490615695736e-01 , -9.77264749791153e-02 , -2.55045883517791e-01 ), ( -2.57783569993132e-01 , -9.89142087441336e-02 , -1.79392228103473e-01 ) } +colvars: Step 6, atoms_new_colvar_forces = { ( -4.93277292055766e+00 , -4.90194513271413e-01 , -1.43718383333350e+00 ), ( -4.24928844495011e+00 , -4.14319730328549e-01 , -1.13656961900244e+00 ), ( -4.32677727761942e+00 , -4.42061894343978e-01 , -1.17434520382541e+00 ), ( -5.81856326291688e+00 , -6.25352159657104e-01 , -1.72711250346991e+00 ), ( 2.70343425805526e-01 , 1.25715952073241e-01 , 3.66445668373938e-01 ), ( 5.32263066066988e+00 , 6.80282678401000e-01 , 2.03697104157011e+00 ), ( 4.49802088896574e+00 , 5.65995619089272e-01 , 1.76580945083832e+00 ), ( -4.52035265146508e-02 , 3.25438648520574e-02 , 3.73210410765344e-01 ), ( 4.47697249662949e+00 , 5.55643205079631e-01 , 1.73270046685604e+00 ), ( 5.93398341449267e+00 , 7.12257975911161e-01 , 2.15312644673420e+00 ), ( 1.23048167143113e-02 , 4.23475122450560e-02 , 3.13762582844874e-01 ), ( -2.97171646727656e-04 , 3.53466248661184e-02 , 2.87428385601990e-01 ), ( 2.15700519999917e-02 , 5.03436675814751e-02 , 3.56233058093854e-01 ), ( 4.53355923905861e-02 , 3.92962552243516e-02 , 2.09193704051278e-01 ), ( 1.56836952509605e-02 , 2.39620465464446e-02 , 1.56465827499981e-01 ), ( 1.18586204326617e-01 , 5.98418472976366e-02 , 1.98836754857717e-01 ), ( 1.67448748047038e-01 , 6.54700065207059e-02 , 1.26412506316467e-01 ), ( 2.52213861342067e-01 , 9.27957885803099e-02 , 1.43227506416146e-01 ), ( 1.37491966621685e-01 , 4.75973997241057e-02 , 5.38314454658977e-02 ), ( 1.32542463896655e-01 , 3.79082711831248e-02 , -1.28003734385221e-02 ), ( 1.13941825729200e-01 , 4.21568906295997e-02 , 6.66103202097719e-02 ), ( 7.67603445059466e-02 , 2.36941602198378e-02 , 6.70103940096495e-03 ), ( 6.37128045711135e-02 , 2.41709392214954e-02 , 4.20977889768344e-02 ), ( -6.04497053169673e-04 , -2.79392161927046e-03 , -2.12018202273477e-02 ), ( -1.49755440332211e-02 , -1.59920005743246e-02 , -9.35289229831404e-02 ), ( -5.11267753565900e-02 , -1.07846615639152e-02 , 3.60693662718652e-02 ), ( -1.22985744019474e-01 , -3.42934558425949e-02 , 1.90277168373195e-02 ), ( -1.67300274843786e-01 , -3.75416338873689e-02 , 9.97666384062255e-02 ), ( -1.10219801322070e-01 , -3.65400619460836e-02 , -3.00443107593338e-02 ), ( -1.48613635269094e-01 , -5.53676205887283e-02 , -8.99832027239536e-02 ), ( -5.42187072697088e-02 , -1.69903857255689e-02 , -6.79602414139265e-03 ), ( -3.25038224479355e-02 , -1.59352502622686e-02 , -5.07114756277418e-02 ), ( 2.68066106451045e-02 , 7.85342832467995e-03 , -1.07601146900668e-03 ), ( 1.26247108743466e-03 , -1.64434790416789e-02 , -1.36430240369820e-01 ), ( -1.76774126169826e-02 , -2.91524626528663e-02 , -1.93749495888178e-01 ), ( 5.11213223315123e-02 , -2.96571820449221e-03 , -1.47590885938418e-01 ), ( 8.23031978551875e-02 , -3.39377031822058e-03 , -2.26414054631252e-01 ), ( 1.47197656354189e-01 , 1.74231335128101e-02 , -2.14377625068559e-01 ), ( 2.03953358800427e-02 , -2.86525120856640e-02 , -2.81697082376507e-01 ), ( 2.14833367169718e-02 , -3.72879411012616e-02 , -3.54371573849421e-01 ), ( -3.56342243788104e-02 , -4.11685773495180e-02 , -2.47824216738292e-01 ), ( -1.00238847665071e-01 , -6.58314657400450e-02 , -2.91757315536222e-01 ), ( -1.39842388910251e-01 , -7.12080659211185e-02 , -2.39666973315091e-01 ), ( -1.61387312507324e-01 , -8.69170398054735e-02 , -3.15025236157483e-01 ), ( -1.90626303123439e-01 , -1.03883309669788e-01 , -3.81989187490294e-01 ), ( -2.07299403741781e-01 , -1.01525330995274e-01 , -3.22572117774458e-01 ), ( -2.52180223912891e-01 , -1.18442069433478e-01 , -3.51335784780881e-01 ), ( -1.28929552893268e-01 , -7.90766459788611e-02 , -3.29862989467372e-01 ), ( -1.82990827114357e-01 , -8.65048942820909e-02 , -2.59477222294974e-01 ), ( -2.39900299630396e-01 , -1.05373135934358e-01 , -2.75003028614189e-01 ), ( -2.77954990514854e-01 , -1.06653558958758e-01 , -1.93429795096022e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 6, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3282,10 +5241,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 7, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 7, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 7, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 7, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 7, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 7, atoms_positions[size = 51] = { ( 8.37216689789659e+00 , 4.37901021565677e-02 , -7.59411723254822e-01 ), ( 6.99173054907958e+00 , -5.11003354462312e-01 , -6.45907471420836e-01 ), ( 6.25221119267448e+00 , -2.69091534483833e-01 , 6.70571886292195e-01 ), ( 4.99228195304877e+00 , -2.05086330889782e-01 , 6.72814098426171e-01 ), ( 7.04359599190517e+00 , -2.02253704031353e+00 , -1.00477459978557e+00 ), ( 6.90267241837949e+00 , -2.69335919735951e-01 , 1.82217587835446e+00 ), ( 6.17792876764567e+00 , -1.18953323080614e-01 , 3.08719841013444e+00 ), ( 7.15838402043010e+00 , -3.26081341049786e-01 , 4.29286456775614e+00 ), ( 5.30112870328665e+00 , 1.11522696219995e+00 , 3.29649468447787e+00 ), ( 4.09534266970237e+00 , 1.06195563949245e+00 , 3.62817802468735e+00 ), ( 5.87626839767972e+00 , 2.29259571261726e+00 , 2.98121564432398e+00 ), ( 5.21461288512338e+00 , 3.59576583004550e+00 , 2.88360626769294e+00 ), ( 6.33840920834483e+00 , 4.58549358015512e+00 , 2.45476724732243e+00 ), ( 3.90032408292894e+00 , 3.73133036989772e+00 , 2.02124029549192e+00 ), ( 2.89255588836865e+00 , 4.11737318509602e+00 , 2.54428457609364e+00 ), ( 3.83356219454626e+00 , 3.24142387567202e+00 , 7.69050780996117e-01 ), ( 2.67251421064126e+00 , 3.15034569878916e+00 , -9.51577527267812e-02 ), ( 3.04368512113888e+00 , 2.72066769781539e+00 , -1.59666941033504e+00 ), ( 1.60112724258352e+00 , 2.15518793050311e+00 , 5.80068295548032e-01 ), ( 4.38233270168014e-01 , 2.46262153981858e+00 , 5.48981598165023e-01 ), ( 1.96958751120776e+00 , 1.01234128829259e+00 , 1.05408371514749e+00 ), ( 1.15807522608227e+00 , 2.06027233883888e-02 , 1.69020068061949e+00 ), ( 2.01540564756394e+00 , -1.17487324590962e+00 , 2.01894159981868e+00 ), ( 5.24663007784567e-01 , 6.06965819914373e-01 , 2.98277643258594e+00 ), ( -6.70090969972222e-01 , 3.67974474617330e-01 , 3.18020553481106e+00 ), ( 1.30679036128140e+00 , 1.32183633270117e+00 , 3.83074757279869e+00 ), ( 8.42488195596810e-01 , 1.91297572203268e+00 , 5.06403148238549e+00 ), ( 2.04677603931843e+00 , 2.59577348740326e+00 , 5.62384342827763e+00 ), ( -3.60180939664793e-01 , 2.91906679253784e+00 , 4.98365594086841e+00 ), ( -1.17172989361066e+00 , 3.03291389730550e+00 , 5.90559291049596e+00 ), ( -4.24939831007310e-01 , 3.68185624142305e+00 , 3.85350870437035e+00 ), ( -1.47667593349521e+00 , 4.57531737478610e+00 , 3.53820703004744e+00 ), ( -7.50487409870848e-01 , 5.38790604517640e+00 , 2.41552088477231e+00 ), ( -2.73259917625150e+00 , 3.89276123730311e+00 , 2.93095501406970e+00 ), ( -3.84966840439603e+00 , 4.43165783486031e+00 , 2.84649266920355e+00 ), ( -2.58608181826962e+00 , 2.61135617881768e+00 , 2.48459688257362e+00 ), ( -3.71575716909455e+00 , 1.91132912833534e+00 , 2.06115901113227e+00 ), ( -3.41465732316873e+00 , 8.19462590483590e-01 , 9.77757428708235e-01 ), ( -4.30317407348321e+00 , 1.08871154582173e+00 , 3.23705656315551e+00 ), ( -5.53930318891123e+00 , 9.09237161496671e-01 , 3.34118827929819e+00 ), ( -3.45825224147659e+00 , 6.41909647597761e-01 , 4.14490520440339e+00 ), ( -3.77963526796013e+00 , 8.99923158144878e-02 , 5.48281966476050e+00 ), ( -2.40241084597597e+00 , -3.87809119227215e-01 , 6.14623871747730e+00 ), ( -4.47116968586997e+00 , 9.94765591923464e-01 , 6.41959234942850e+00 ), ( -5.32306816356207e+00 , 6.03907780412336e-01 , 7.18626963175422e+00 ), ( -6.29471935298229e+00 , 3.55391001295303e+00 , 6.70311288498439e+00 ), ( -6.91268166174429e+00 , 4.29872678709487e+00 , 7.41942409497783e+00 ), ( -6.74358894487107e+00 , 3.20874084258452e+00 , 5.51469129648207e+00 ), ( -4.09219714159797e+00 , 2.30306276865046e+00 , 6.48264861014977e+00 ), ( -4.90006546259677e+00 , 3.22721863105854e+00 , 7.21309658831055e+00 ), ( -4.08320233912291e+00 , 4.52152873527003e+00 , 7.27521294593529e+00 ) } +colvars: Step 7, atoms_positions[size = 51] = { ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 ), ( 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 ), ( 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 ), ( 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 ), ( 7.04360578585032e+00 , -2.02253210321486e+00 , -1.00475508697818e+00 ), ( 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 ), ( 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 ), ( 7.15839369415653e+00 , -3.26081276239317e-01 , 4.29289707258867e+00 ), ( 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 ), ( 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 ), ( 5.87628142275448e+00 , 2.29260416098295e+00 , 2.98123131140797e+00 ), ( 5.21461212463495e+00 , 3.59576743915649e+00 , 2.88362406780732e+00 ), ( 6.33841023238199e+00 , 4.58549633824642e+00 , 2.45478769693888e+00 ), ( 3.90032731528937e+00 , 3.73133228488110e+00 , 2.02125381715923e+00 ), ( 2.89255651494714e+00 , 4.11737441114465e+00 , 2.54429236626012e+00 ), ( 3.83356882425037e+00 , 3.24142730507447e+00 , 7.69061966445767e-01 ), ( 2.67252484262143e+00 , 3.15034995420553e+00 , -9.51496895508225e-02 ), ( 3.04369939118193e+00 , 2.72067318755565e+00 , -1.59666058085304e+00 ), ( 1.60113592967078e+00 , 2.15519099674224e+00 , 5.80071804456076e-01 ), ( 4.38240041119901e-01 , 2.46262336976879e+00 , 5.48980991334079e-01 ), ( 1.96959368088953e+00 , 1.01234376536455e+00 , 1.05408760152221e+00 ), ( 1.15807993418597e+00 , 2.06042343395636e-02 , 1.69020108367558e+00 ), ( 2.01540951886049e+00 , -1.17487180030149e+00 , 2.01894428622946e+00 ), ( 5.24663015581007e-01 , 6.06965654388053e-01 , 2.98277511565960e+00 ), ( -6.70091636820477e-01 , 3.67973696398877e-01 , 3.18020094552207e+00 ), ( 1.30678882139017e+00 , 1.32183553100694e+00 , 3.83074937761609e+00 ), ( 8.42480492065935e-01 , 1.91297367485748e+00 , 5.06403257253622e+00 ), ( 2.04676600763386e+00 , 2.59577116983262e+00 , 5.62384874446350e+00 ), ( -3.60187962065452e-01 , 2.91906438707605e+00 , 4.98365392120015e+00 ), ( -1.17173739380431e+00 , 3.03291119872267e+00 , 5.90558861048476e+00 ), ( -4.24942864299879e-01 , 3.68185527221630e+00 , 3.85350813056666e+00 ), ( -1.47667798663298e+00 , 4.57531645519427e+00 , 3.53820386981816e+00 ), ( -7.50485901509571e-01 , 5.38790647509149e+00 , 2.41552070759660e+00 ), ( -2.73259922857375e+00 , 3.89276029477454e+00 , 2.93094623652956e+00 ), ( -3.84966920894560e+00 , 4.43165634430076e+00 , 2.84648308433646e+00 ), ( -2.58607921786046e+00 , 2.61135604056535e+00 , 2.48458862212576e+00 ), ( -3.71575189353043e+00 , 1.91132888948723e+00 , 2.06114453689343e+00 ), ( -3.41464867152714e+00 , 8.19463186795656e-01 , 9.77744520824400e-01 ), ( -4.30317263798616e+00 , 1.08870954003847e+00 , 3.23703847428725e+00 ), ( -5.53930210531588e+00 , 9.09235310273094e-01 , 3.34117073165080e+00 ), ( -3.45825411873271e+00 , 6.41907326842739e-01 , 4.14489107139214e+00 ), ( -3.77964154389490e+00 , 8.99884693047571e-02 , 5.48280131463119e+00 ), ( -2.40241948018949e+00 , -3.87812824665575e-01 , 6.14622445774217e+00 ), ( -4.47118005780455e+00 , 9.94760153779481e-01 , 6.41957195336128e+00 ), ( -5.32307757703637e+00 , 6.03902619770999e-01 , 7.18625074294096e+00 ), ( -6.29473276809766e+00 , 3.55390365365507e+00 , 6.70309262515356e+00 ), ( -6.91269406186489e+00 , 4.29872080475097e+00 , 7.41940655795881e+00 ), ( -6.74359627925831e+00 , 3.20873680426871e+00 , 5.51467328326202e+00 ), ( -4.09220742797595e+00 , 2.30305792852368e+00 , 6.48263397793547e+00 ), ( -4.90008080100881e+00 , 3.22721176264580e+00 , 7.21307955904248e+00 ), ( -4.08321878774328e+00 , 4.52152209517614e+00 , 7.27520162172180e+00 ) } colvars: Step 7, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 7, atom_groups_ids[size = 0] = @@ -3303,162 +5262,301 @@ colvars: Collective variables module, step no. 7 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.31688046920632e-01 , 4.68707413595258e-03 , 9.43377480580293e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.31520710742130e-01 , 4.70585069947745e-03 , 9.43436205219106e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 7.04360578585032e+00 , -2.02253210321486e+00 , -1.00475508697818e+00 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 , 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 7.15839369415653e+00 , -3.26081276239317e-01 , 4.29289707258867e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 , 5.87628142275448e+00 , 2.29260416098295e+00 , 2.98123131140797e+00 , 5.21461212463495e+00 , 3.59576743915649e+00 , 2.88362406780732e+00 , 6.33841023238199e+00 , 4.58549633824642e+00 , 2.45478769693888e+00 , 3.90032731528937e+00 , 3.73133228488110e+00 , 2.02125381715923e+00 , 2.89255651494714e+00 , 4.11737441114465e+00 , 2.54429236626012e+00 , 3.83356882425037e+00 , 3.24142730507447e+00 , 7.69061966445767e-01 , 2.67252484262143e+00 , 3.15034995420553e+00 , -9.51496895508225e-02 , 3.04369939118193e+00 , 2.72067318755565e+00 , -1.59666058085304e+00 , 1.60113592967078e+00 , 2.15519099674224e+00 , 5.80071804456076e-01 , 4.38240041119901e-01 , 2.46262336976879e+00 , 5.48980991334079e-01 , 1.96959368088953e+00 , 1.01234376536455e+00 , 1.05408760152221e+00 , 1.15807993418597e+00 , 2.06042343395636e-02 , 1.69020108367558e+00 , 2.01540951886049e+00 , -1.17487180030149e+00 , 2.01894428622946e+00 , 5.24663015581007e-01 , 6.06965654388053e-01 , 2.98277511565960e+00 , -6.70091636820477e-01 , 3.67973696398877e-01 , 3.18020094552207e+00 , 1.30678882139017e+00 , 1.32183553100694e+00 , 3.83074937761609e+00 , 8.42480492065935e-01 , 1.91297367485748e+00 , 5.06403257253622e+00 , 2.04676600763386e+00 , 2.59577116983262e+00 , 5.62384874446350e+00 , -3.60187962065452e-01 , 2.91906438707605e+00 , 4.98365392120015e+00 , -1.17173739380431e+00 , 3.03291119872267e+00 , 5.90558861048476e+00 , -4.24942864299879e-01 , 3.68185527221630e+00 , 3.85350813056666e+00 , -1.47667798663298e+00 , 4.57531645519427e+00 , 3.53820386981816e+00 , -7.50485901509571e-01 , 5.38790647509149e+00 , 2.41552070759660e+00 , -2.73259922857375e+00 , 3.89276029477454e+00 , 2.93094623652956e+00 , -3.84966920894560e+00 , 4.43165634430076e+00 , 2.84648308433646e+00 , -2.58607921786046e+00 , 2.61135604056535e+00 , 2.48458862212576e+00 , -3.71575189353043e+00 , 1.91132888948723e+00 , 2.06114453689343e+00 , -3.41464867152714e+00 , 8.19463186795656e-01 , 9.77744520824400e-01 , -4.30317263798616e+00 , 1.08870954003847e+00 , 3.23703847428725e+00 , -5.53930210531588e+00 , 9.09235310273094e-01 , 3.34117073165080e+00 , -3.45825411873271e+00 , 6.41907326842739e-01 , 4.14489107139214e+00 , -3.77964154389490e+00 , 8.99884693047571e-02 , 5.48280131463119e+00 , -2.40241948018949e+00 , -3.87812824665575e-01 , 6.14622445774217e+00 , -4.47118005780455e+00 , 9.94760153779481e-01 , 6.41957195336128e+00 , -5.32307757703637e+00 , 6.03902619770999e-01 , 7.18625074294096e+00 , -6.29473276809766e+00 , 3.55390365365507e+00 , 6.70309262515356e+00 , -6.91269406186489e+00 , 4.29872080475097e+00 , 7.41940655795881e+00 , -6.74359627925831e+00 , 3.20873680426871e+00 , 5.51467328326202e+00 , -4.09220742797595e+00 , 2.30305792852368e+00 , 6.48263397793547e+00 , -4.90008080100881e+00 , 3.22721176264580e+00 , 7.21307955904248e+00 , -4.08321878774328e+00 , 4.52152209517614e+00 , 7.27520162172180e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.31688046920632e-01 , 4.68707413595258e-03 , 9.43377480580293e-01 ). +colvars: Colvar "one" has value ( -3.31520710742130e-01 , 4.70585069947745e-03 , 9.43436205219106e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 7.04360578585032e+00 , -2.02253210321486e+00 , -1.00475508697818e+00 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 , 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 7.15839369415653e+00 , -3.26081276239317e-01 , 4.29289707258867e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 , 5.87628142275448e+00 , 2.29260416098295e+00 , 2.98123131140797e+00 , 5.21461212463495e+00 , 3.59576743915649e+00 , 2.88362406780732e+00 , 6.33841023238199e+00 , 4.58549633824642e+00 , 2.45478769693888e+00 , 3.90032731528937e+00 , 3.73133228488110e+00 , 2.02125381715923e+00 , 2.89255651494714e+00 , 4.11737441114465e+00 , 2.54429236626012e+00 , 3.83356882425037e+00 , 3.24142730507447e+00 , 7.69061966445767e-01 , 2.67252484262143e+00 , 3.15034995420553e+00 , -9.51496895508225e-02 , 3.04369939118193e+00 , 2.72067318755565e+00 , -1.59666058085304e+00 , 1.60113592967078e+00 , 2.15519099674224e+00 , 5.80071804456076e-01 , 4.38240041119901e-01 , 2.46262336976879e+00 , 5.48980991334079e-01 , 1.96959368088953e+00 , 1.01234376536455e+00 , 1.05408760152221e+00 , 1.15807993418597e+00 , 2.06042343395636e-02 , 1.69020108367558e+00 , 2.01540951886049e+00 , -1.17487180030149e+00 , 2.01894428622946e+00 , 5.24663015581007e-01 , 6.06965654388053e-01 , 2.98277511565960e+00 , -6.70091636820477e-01 , 3.67973696398877e-01 , 3.18020094552207e+00 , 1.30678882139017e+00 , 1.32183553100694e+00 , 3.83074937761609e+00 , 8.42480492065935e-01 , 1.91297367485748e+00 , 5.06403257253622e+00 , 2.04676600763386e+00 , 2.59577116983262e+00 , 5.62384874446350e+00 , -3.60187962065452e-01 , 2.91906438707605e+00 , 4.98365392120015e+00 , -1.17173739380431e+00 , 3.03291119872267e+00 , 5.90558861048476e+00 , -4.24942864299879e-01 , 3.68185527221630e+00 , 3.85350813056666e+00 , -1.47667798663298e+00 , 4.57531645519427e+00 , 3.53820386981816e+00 , -7.50485901509571e-01 , 5.38790647509149e+00 , 2.41552070759660e+00 , -2.73259922857375e+00 , 3.89276029477454e+00 , 2.93094623652956e+00 , -3.84966920894560e+00 , 4.43165634430076e+00 , 2.84648308433646e+00 , -2.58607921786046e+00 , 2.61135604056535e+00 , 2.48458862212576e+00 , -3.71575189353043e+00 , 1.91132888948723e+00 , 2.06114453689343e+00 , -3.41464867152714e+00 , 8.19463186795656e-01 , 9.77744520824400e-01 , -4.30317263798616e+00 , 1.08870954003847e+00 , 3.23703847428725e+00 , -5.53930210531588e+00 , 9.09235310273094e-01 , 3.34117073165080e+00 , -3.45825411873271e+00 , 6.41907326842739e-01 , 4.14489107139214e+00 , -3.77964154389490e+00 , 8.99884693047571e-02 , 5.48280131463119e+00 , -2.40241948018949e+00 , -3.87812824665575e-01 , 6.14622445774217e+00 , -4.47118005780455e+00 , 9.94760153779481e-01 , 6.41957195336128e+00 , -5.32307757703637e+00 , 6.03902619770999e-01 , 7.18625074294096e+00 , -6.29473276809766e+00 , 3.55390365365507e+00 , 6.70309262515356e+00 , -6.91269406186489e+00 , 4.29872080475097e+00 , 7.41940655795881e+00 , -6.74359627925831e+00 , 3.20873680426871e+00 , 5.51467328326202e+00 , -4.09220742797595e+00 , 2.30305792852368e+00 , 6.48263397793547e+00 , -4.90008080100881e+00 , 3.22721176264580e+00 , 7.21307955904248e+00 , -4.08321878774328e+00 , 4.52152209517614e+00 , 7.27520162172180e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.1518 , 1.85806 , -14.9639 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.4123 , 6.74123 , 13.4825 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.1518 , 1.85806 , -14.9639 ) to colvar "one". -colvars: Adding total bias energy: 45.5643 +colvars: Adding biasing force ( 67.4123 , 6.74123 , 13.4825 ) to colvar "one". +colvars: Adding total bias energy: 58.4943 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.1518 , 1.85806 , -14.9639 ) +colvars: Force to be applied: ( 67.4123 , 6.74123 , 13.4825 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.85485 , -0.565432 , -1.5734 ) -colvars: ( -4.16303 , -0.484858 , -1.34919 ) -colvars: ( -4.16303 , -0.484858 , -1.34919 ) -colvars: ( -5.54528 , -0.645845 , -1.79716 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.22401 , -0.608175 , -1.69203 ) +colvars: ( -4.47959 , -0.52151 , -1.45092 ) +colvars: ( -4.47959 , -0.52151 , -1.45092 ) +colvars: ( -5.96694 , -0.694666 , -1.93266 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.901133 , 0.193401 , 0.644831 ) -colvars: ( 0.779041 , 0.265239 , 0.670314 ) -colvars: ( 0.76445 , 0.257694 , 0.651244 ) -colvars: ( 0.663985 , 0.267279 , 0.604309 ) -colvars: ( 0.651883 , 0.200691 , 0.505776 ) -colvars: ( 0.574859 , 0.345676 , 0.658498 ) -colvars: ( 0.46438 , 0.360995 , 0.613435 ) -colvars: ( 0.385415 , 0.459294 , 0.700988 ) -colvars: ( 0.381729 , 0.316741 , 0.503336 ) -colvars: ( 0.345579 , 0.275658 , 0.425392 ) -colvars: ( 0.353211 , 0.321669 , 0.493039 ) -colvars: ( 0.281378 , 0.278957 , 0.391523 ) -colvars: ( 0.255188 , 0.307604 , 0.415137 ) -colvars: ( 0.345603 , 0.180299 , 0.294663 ) -colvars: ( 0.285614 , 0.137417 , 0.199996 ) -colvars: ( 0.471392 , 0.142036 , 0.317424 ) -colvars: ( 0.545865 , 0.049776 , 0.235465 ) -colvars: ( 0.678942 , 0.0273897 , 0.284351 ) -colvars: ( 0.553209 , 0.018442 , 0.196895 ) -colvars: ( 0.53715 , -0.0466022 , 0.098113 ) -colvars: ( 0.573252 , 0.0668338 , 0.275229 ) -colvars: ( 0.570216 , 0.0512977 , 0.252113 ) -colvars: ( 0.606365 , 0.116338 , 0.362902 ) -colvars: ( 0.442663 , 0.0570208 , 0.183683 ) -colvars: ( 0.435193 , 0.00127931 , 0.102791 ) -colvars: ( 0.33866 , 0.123523 , 0.212668 ) -colvars: ( 0.211149 , 0.133263 , 0.149772 ) -colvars: ( 0.117906 , 0.219797 , 0.212656 ) -colvars: ( 0.183309 , 0.0592197 , 0.0316057 ) -colvars: ( 0.13242 , 0.0236363 , -0.0476128 ) -colvars: ( 0.219137 , 0.0326958 , 0.0166649 ) -colvars: ( 0.205864 , -0.0402532 , -0.0912891 ) -colvars: ( 0.243556 , -0.044591 , -0.0746975 ) -colvars: ( 0.282429 , -0.126809 , -0.164177 ) -colvars: ( 0.237569 , -0.179685 , -0.263499 ) -colvars: ( 0.399702 , -0.142608 , -0.115709 ) -colvars: ( 0.478385 , -0.218648 , -0.172912 ) -colvars: ( 0.61229 , -0.22225 , -0.0977766 ) -colvars: ( 0.42858 , -0.222118 , -0.207454 ) -colvars: ( 0.43407 , -0.290263 , -0.2976 ) -colvars: ( 0.377647 , -0.14782 , -0.136044 ) -colvars: ( 0.320792 , -0.140498 , -0.160004 ) -colvars: ( 0.302795 , -0.0530645 , -0.0508904 ) -colvars: ( 0.194924 , -0.148346 , -0.246032 ) -colvars: ( 0.169284 , -0.189914 , -0.318358 ) -colvars: ( -0.00845748 , -0.193505 , -0.42957 ) -colvars: ( -0.1013 , -0.210621 , -0.508556 ) -colvars: ( 0.0950515 , -0.244734 , -0.437909 ) -colvars: ( 0.112219 , -0.107388 , -0.239335 ) -colvars: ( -0.00949102 , -0.110888 , -0.316915 ) -colvars: ( -0.099982 , -0.0295633 , -0.259527 ) +colvars: ( 0.969539 , 0.208103 , 0.693641 ) +colvars: ( 0.838189 , 0.285384 , 0.72106 ) +colvars: ( 0.822485 , 0.277273 , 0.700551 ) +colvars: ( 0.714411 , 0.287569 , 0.650053 ) +colvars: ( 0.701391 , 0.215928 , 0.544054 ) +colvars: ( 0.618529 , 0.371905 , 0.70835 ) +colvars: ( 0.499675 , 0.388375 , 0.659873 ) +colvars: ( 0.414726 , 0.494126 , 0.754062 ) +colvars: ( 0.410754 , 0.340762 , 0.541435 ) +colvars: ( 0.371865 , 0.296557 , 0.457583 ) +colvars: ( 0.380069 , 0.346068 , 0.530364 ) +colvars: ( 0.302786 , 0.300114 , 0.42116 ) +colvars: ( 0.274604 , 0.330939 , 0.446571 ) +colvars: ( 0.371879 , 0.193977 , 0.316959 ) +colvars: ( 0.307341 , 0.147836 , 0.215119 ) +colvars: ( 0.507205 , 0.15282 , 0.341441 ) +colvars: ( 0.587324 , 0.0535654 , 0.253269 ) +colvars: ( 0.730489 , 0.0294919 , 0.305857 ) +colvars: ( 0.595229 , 0.0198484 , 0.211771 ) +colvars: ( 0.577952 , -0.0501319 , 0.105502 ) +colvars: ( 0.616797 , 0.0719077 , 0.296035 ) +colvars: ( 0.613536 , 0.0551863 , 0.271162 ) +colvars: ( 0.65243 , 0.125158 , 0.390343 ) +colvars: ( 0.476312 , 0.0613334 , 0.197549 ) +colvars: ( 0.468277 , 0.00135988 , 0.110525 ) +colvars: ( 0.364422 , 0.132876 , 0.228735 ) +colvars: ( 0.227244 , 0.143346 , 0.161076 ) +colvars: ( 0.12693 , 0.236441 , 0.22873 ) +colvars: ( 0.197289 , 0.0636863 , 0.0339587 ) +colvars: ( 0.142542 , 0.0253974 , -0.051264 ) +colvars: ( 0.235828 , 0.0351586 , 0.0178898 ) +colvars: ( 0.221545 , -0.0433218 , -0.0982416 ) +colvars: ( 0.262089 , -0.0479795 , -0.0803878 ) +colvars: ( 0.303916 , -0.136442 , -0.176658 ) +colvars: ( 0.255654 , -0.193332 , -0.283505 ) +colvars: ( 0.430083 , -0.153433 , -0.124522 ) +colvars: ( 0.514734 , -0.23524 , -0.186065 ) +colvars: ( 0.658793 , -0.239108 , -0.105241 ) +colvars: ( 0.461157 , -0.238983 , -0.223229 ) +colvars: ( 0.467064 , -0.312298 , -0.320208 ) +colvars: ( 0.406366 , -0.159055 , -0.146409 ) +colvars: ( 0.345206 , -0.151188 , -0.172188 ) +colvars: ( 0.325848 , -0.0571261 , -0.0548084 ) +colvars: ( 0.209793 , -0.159639 , -0.264731 ) +colvars: ( 0.182211 , -0.204366 , -0.34254 ) +colvars: ( -0.00901934 , -0.208228 , -0.462163 ) +colvars: ( -0.108902 , -0.226648 , -0.547132 ) +colvars: ( 0.102335 , -0.263333 , -0.471135 ) +colvars: ( 0.120813 , -0.115575 , -0.25752 ) +colvars: ( -0.0101266 , -0.119347 , -0.340975 ) +colvars: ( -0.107481 , -0.0318559 , -0.279233 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.85485 , 0.565432 , 1.5734 ) -colvars: ( 4.16303 , 0.484858 , 1.34919 ) -colvars: ( 4.16303 , 0.484858 , 1.34919 ) -colvars: ( 5.54528 , 0.645845 , 1.79716 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.22401 , 0.608175 , 1.69203 ) +colvars: ( 4.47959 , 0.52151 , 1.45092 ) +colvars: ( 4.47959 , 0.52151 , 1.45092 ) +colvars: ( 5.96694 , 0.694666 , 1.93266 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.625093 , -0.0804276 , -0.396358 ) -colvars: ( -0.560381 , -0.162799 , -0.368263 ) -colvars: ( -0.513465 , -0.140907 , -0.311013 ) -colvars: ( -0.51727 , -0.190629 , -0.337324 ) -colvars: ( -0.507647 , -0.132478 , -0.30133 ) -colvars: ( -0.489074 , -0.282131 , -0.350216 ) -colvars: ( -0.452237 , -0.322655 , -0.331346 ) -colvars: ( -0.427473 , -0.429208 , -0.354503 ) -colvars: ( -0.389093 , -0.288003 , -0.251948 ) -colvars: ( -0.382743 , -0.263241 , -0.234348 ) -colvars: ( -0.341791 , -0.282403 , -0.20167 ) -colvars: ( -0.281622 , -0.246177 , -0.124564 ) -colvars: ( -0.235095 , -0.260886 , -0.084247 ) -colvars: ( -0.303468 , -0.14381 , -0.100353 ) -colvars: ( -0.270996 , -0.115164 , -0.05463 ) -colvars: ( -0.361254 , -0.0864348 , -0.132753 ) -colvars: ( -0.390355 , 0.0110919 , -0.118052 ) -colvars: ( -0.444733 , 0.0588882 , -0.151341 ) -colvars: ( -0.425541 , 0.0258167 , -0.146914 ) -colvars: ( -0.414066 , 0.0818792 , -0.109995 ) -colvars: ( -0.467487 , -0.0276577 , -0.213421 ) -colvars: ( -0.499004 , -0.0292854 , -0.24597 ) -colvars: ( -0.547306 , -0.0939133 , -0.323933 ) -colvars: ( -0.443272 , -0.0596328 , -0.203429 ) -colvars: ( -0.449149 , -0.0161412 , -0.189706 ) -colvars: ( -0.386164 , -0.133585 , -0.179206 ) -colvars: ( -0.325359 , -0.16518 , -0.132108 ) -colvars: ( -0.273251 , -0.254763 , -0.119995 ) -colvars: ( -0.285632 , -0.0931916 , -0.0594732 ) -colvars: ( -0.27039 , -0.075098 , -0.0359107 ) -colvars: ( -0.269434 , -0.0484783 , -0.0229157 ) -colvars: ( -0.235966 , 0.0254846 , 0.0442931 ) -colvars: ( -0.218559 , 0.0519446 , 0.0738219 ) -colvars: ( -0.281189 , 0.111598 , 0.0375617 ) -colvars: ( -0.253899 , 0.152681 , 0.0836751 ) -colvars: ( -0.352196 , 0.139926 , -0.0213099 ) -colvars: ( -0.401942 , 0.215593 , -0.0373274 ) -colvars: ( -0.475618 , 0.238543 , -0.101324 ) -colvars: ( -0.40964 , 0.195579 , -0.0541433 ) -colvars: ( -0.414117 , 0.25572 , -0.0314825 ) -colvars: ( -0.410754 , 0.109613 , -0.0941181 ) -colvars: ( -0.413907 , 0.0793564 , -0.110974 ) -colvars: ( -0.432712 , -0.0131131 , -0.171746 ) -colvars: ( -0.34479 , 0.0676101 , -0.0465161 ) -colvars: ( -0.346304 , 0.0934199 , -0.0363803 ) -colvars: ( -0.183948 , 0.0992229 , 0.130125 ) -colvars: ( -0.132758 , 0.100623 , 0.182429 ) -colvars: ( -0.214682 , 0.171341 , 0.131694 ) -colvars: ( -0.282114 , 0.0270264 , -0.00159238 ) -colvars: ( -0.213219 , 0.012992 , 0.061608 ) -colvars: ( -0.158046 , -0.0695496 , 0.0799967 ) +colvars: ( -0.672527 , -0.0865473 , -0.42629 ) +colvars: ( -0.602916 , -0.175161 , -0.39606 ) +colvars: ( -0.552432 , -0.151613 , -0.334472 ) +colvars: ( -0.556549 , -0.205096 , -0.362785 ) +colvars: ( -0.546196 , -0.142532 , -0.324075 ) +colvars: ( -0.526227 , -0.303532 , -0.376647 ) +colvars: ( -0.48661 , -0.347122 , -0.356352 ) +colvars: ( -0.459978 , -0.461752 , -0.381254 ) +colvars: ( -0.418678 , -0.309839 , -0.270948 ) +colvars: ( -0.411853 , -0.283195 , -0.252025 ) +colvars: ( -0.367782 , -0.303818 , -0.21686 ) +colvars: ( -0.303048 , -0.264843 , -0.13392 ) +colvars: ( -0.252986 , -0.280671 , -0.0905431 ) +colvars: ( -0.326543 , -0.154715 , -0.107887 ) +colvars: ( -0.291613 , -0.123893 , -0.0587098 ) +colvars: ( -0.3887 , -0.0929944 , -0.142741 ) +colvars: ( -0.419999 , 0.0119261 , -0.126936 ) +colvars: ( -0.478487 , 0.0633397 , -0.162743 ) +colvars: ( -0.457862 , 0.0277721 , -0.157992 ) +colvars: ( -0.445518 , 0.0880883 , -0.118288 ) +colvars: ( -0.502997 , -0.0297556 , -0.229532 ) +colvars: ( -0.536913 , -0.0315019 , -0.264552 ) +colvars: ( -0.588884 , -0.10103 , -0.348412 ) +colvars: ( -0.476968 , -0.0641437 , -0.218795 ) +colvars: ( -0.483293 , -0.0173508 , -0.204042 ) +colvars: ( -0.415536 , -0.143701 , -0.192731 ) +colvars: ( -0.350131 , -0.177687 , -0.14207 ) +colvars: ( -0.294076 , -0.274062 , -0.12903 ) +colvars: ( -0.307385 , -0.100239 , -0.0639435 ) +colvars: ( -0.290994 , -0.0807683 , -0.0386053 ) +colvars: ( -0.289947 , -0.05214 , -0.0246159 ) +colvars: ( -0.253934 , 0.027431 , 0.0476745 ) +colvars: ( -0.235193 , 0.0558913 , 0.0794448 ) +colvars: ( -0.302582 , 0.120074 , 0.0404226 ) +colvars: ( -0.273225 , 0.164276 , 0.0900191 ) +colvars: ( -0.378968 , 0.150547 , -0.0229066 ) +colvars: ( -0.432483 , 0.231952 , -0.0401464 ) +colvars: ( -0.511737 , 0.256637 , -0.108986 ) +colvars: ( -0.440778 , 0.210426 , -0.0582424 ) +colvars: ( -0.445595 , 0.275131 , -0.0338755 ) +colvars: ( -0.441988 , 0.117945 , -0.101239 ) +colvars: ( -0.445394 , 0.085401 , -0.119376 ) +colvars: ( -0.465634 , -0.0140789 , -0.184741 ) +colvars: ( -0.371044 , 0.0727693 , -0.0500422 ) +colvars: ( -0.372679 , 0.100541 , -0.0391477 ) +colvars: ( -0.198004 , 0.106783 , 0.139968 ) +colvars: ( -0.142938 , 0.108293 , 0.196227 ) +colvars: ( -0.231054 , 0.184364 , 0.141655 ) +colvars: ( -0.303616 , 0.029108 , -0.00171098 ) +colvars: ( -0.229503 , 0.0140142 , 0.0662712 ) +colvars: ( -0.170151 , -0.0747861 , 0.0860621 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 7. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 7. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 7, atoms_new_colvar_forces = { ( -4.57881203862854e+00 , -4.52458345793086e-01 , -1.32492776682226e+00 ), ( -3.94437384767086e+00 , -3.82417843017137e-01 , -1.04713994835495e+00 ), ( -4.01631867516224e+00 , -4.08208157242501e-01 , -1.08220634144740e+00 ), ( -5.40104624412911e+00 , -5.77631414378630e-01 , -1.59271593308303e+00 ), ( 2.50984966528159e-01 , 1.16787110595548e-01 , 3.40231544502879e-01 ), ( 4.94063698000285e+00 , 6.28976582484485e-01 , 1.88168352904184e+00 ), ( 4.17517745135057e+00 , 5.23197450817813e-01 , 1.63128052240920e+00 ), ( -4.20576341559172e-02 , 3.00860374184086e-02 , 3.46484923582174e-01 ), ( 4.15567049794573e+00 , 5.13596645883970e-01 , 1.60057985982117e+00 ), ( 5.50811824623009e+00 , 6.58262060591907e-01 , 1.98820557210076e+00 ), ( 1.14203592291789e-02 , 3.92658818748587e-02 , 2.91368412510501e-01 ), ( -2.43584894888960e-04 , 3.27803392663165e-02 , 2.66958721176205e-01 ), ( 2.00927636844206e-02 , 4.67182343113446e-02 , 3.30890207317210e-01 ), ( 4.21348827655389e-02 , 3.64895436103206e-02 , 1.94310464858261e-01 ), ( 1.46180376589936e-02 , 2.22527232081962e-02 , 1.45366201047434e-01 ), ( 1.10137344647507e-01 , 5.56013586772384e-02 , 1.84670598380992e-01 ), ( 1.55510598512366e-01 , 6.08678727783858e-02 , 1.17412964942392e-01 ), ( 2.34208401915362e-01 , 8.62778847570254e-02 , 1.33009786672209e-01 ), ( 1.27667927087642e-01 , 4.42586584499522e-02 , 4.99812886998157e-02 ), ( 1.23083500300451e-01 , 3.52770442088739e-02 , -1.18824088660680e-02 ), ( 1.05764707525599e-01 , 3.91761163391697e-02 , 6.18074492802734e-02 ), ( 7.12126795258260e-02 , 2.20123250534493e-02 , 6.14286387951918e-03 ), ( 5.90588761872212e-02 , 2.24242570234704e-02 , 3.89691217501037e-02 ), ( -6.09530360472066e-04 , -2.61200572806048e-03 , -1.97463383138328e-02 ), ( -1.39561171330660e-02 , -1.48618650562138e-02 , -8.69147276533931e-02 ), ( -4.75048814931489e-02 , -1.00617973682600e-02 , 3.34621595037623e-02 ), ( -1.14210487647717e-01 , -3.19170509843065e-02 , 1.76637592968527e-02 ), ( -1.55344913649278e-01 , -3.49658124342954e-02 , 9.26612570797246e-02 ), ( -1.02322737878863e-01 , -3.39719229125203e-02 , -2.78674605719969e-02 ), ( -1.37970280897008e-01 , -5.14616706976876e-02 , -8.35235536373673e-02 ), ( -5.02969831431410e-02 , -1.57824537127487e-02 , -6.25077624580102e-03 ), ( -3.01014536880143e-02 , -1.47685444530168e-02 , -4.69960206071053e-02 ), ( 2.49968386091572e-02 , 7.35359067746522e-03 , -8.75526166746188e-04 ), ( 1.24006954608552e-03 , -1.52116641400138e-02 , -1.26615382461637e-01 ), ( -1.63298505474880e-02 , -2.70041779785319e-02 , -1.79823789126329e-01 ), ( 4.75063265139463e-02 , -2.68188527752566e-03 , -1.37018835573269e-01 ), ( 7.64437698499632e-02 , -3.05515994060623e-03 , -2.10239569080751e-01 ), ( 1.36672325487755e-01 , 1.62933078486417e-02 , -1.99100878528603e-01 ), ( 1.89396477903299e-02 , -2.65399369148128e-02 , -2.61597355036449e-01 ), ( 1.99532646554350e-02 , -3.45423922930599e-02 , -3.29082575762017e-01 ), ( -3.31073554508113e-02 , -3.82069868180719e-02 , -2.30162342620894e-01 ), ( -9.31143410004120e-02 , -6.11415380356488e-02 , -2.70978402664321e-01 ), ( -1.29916968755332e-01 , -6.61776222449396e-02 , -2.22636324356853e-01 ), ( -1.49865463946659e-01 , -8.07357596419478e-02 , -2.92548538421674e-01 ), ( -1.77019843655578e-01 , -9.64944012637901e-02 , -3.54738040576786e-01 ), ( -1.92405447073281e-01 , -9.42822745455138e-02 , -2.99444973862644e-01 ), ( -2.34057515354482e-01 , -1.09998681358580e-01 , -3.26127242550109e-01 ), ( -1.19630494885950e-01 , -7.33927701270712e-02 , -3.06215255951226e-01 ), ( -1.69895608366100e-01 , -8.03618298557150e-02 , -2.40927071349435e-01 ), ( -2.22710088160625e-01 , -9.78961594255737e-02 , -2.55307146559071e-01 ), ( -2.58028075821192e-01 , -9.91129022369759e-02 , -1.79530681601258e-01 ) } +colvars: Step 7, atoms_new_colvar_forces = { ( -4.92699883197614e+00 , -4.86618724078052e-01 , -1.42467913094181e+00 ), ( -4.24431483555213e+00 , -4.11287219671329e-01 , -1.12591650522093e+00 ), ( -4.32172548846806e+00 , -4.39036591639196e-01 , -1.16364704256842e+00 ), ( -5.81174639582869e+00 , -6.21270459094370e-01 , -1.71268334398654e+00 ), ( 2.70052898658315e-01 , 1.25659362376525e-01 , 3.66079747178291e-01 ), ( 5.31631328128861e+00 , 6.76547546607386e-01 , 2.02373389034186e+00 ), ( 4.49265382843113e+00 , 5.62763039892953e-01 , 1.75443622150832e+00 ), ( -4.52524431744932e-02 , 3.23732624357328e-02 , 3.72808324782638e-01 ), ( 4.47166464129130e+00 , 5.52432741893097e-01 , 1.72140285504558e+00 ), ( 5.92695336328533e+00 , 7.08027654029380e-01 , 2.13821958782846e+00 ), ( 1.22878489801734e-02 , 4.22497951376943e-02 , 3.13503913694177e-01 ), ( -2.62484217107173e-04 , 3.52714054790649e-02 , 2.87239453324821e-01 ), ( 2.16185923554538e-02 , 5.02681587839578e-02 , 3.56027588063913e-01 ), ( 4.53355603635980e-02 , 3.92619305021430e-02 , 2.09072043074313e-01 ), ( 1.57281166857478e-02 , 2.39434706755070e-02 , 1.56409280914787e-01 ), ( 1.18504415282576e-01 , 5.98253385749289e-02 , 1.98700017301344e-01 ), ( 1.67324793120046e-01 , 6.54914977375688e-02 , 1.26332799629771e-01 ), ( 2.52001495399523e-01 , 9.28315906323536e-02 , 1.43114686396074e-01 ), ( 1.37367087737100e-01 , 4.76204952545460e-02 , 5.37785095330312e-02 ), ( 1.32434327972042e-01 , 3.79563375141697e-02 , -1.27851195363125e-02 ), ( 1.13800086301131e-01 , 4.21520983496086e-02 , 6.65034147195922e-02 ), ( 7.66233001267707e-02 , 2.36844621949030e-02 , 6.61017092669614e-03 ), ( 6.35464049324757e-02 , 2.41279804304955e-02 , 4.19305974577354e-02 ), ( -6.55479027328432e-04 , -2.81034241410720e-03 , -2.12460458791061e-02 ), ( -1.50159753928555e-02 , -1.59909609765167e-02 , -9.35172506680649e-02 ), ( -5.11137193793151e-02 , -1.08257415609619e-02 , 3.60045413260593e-02 ), ( -1.22887211874929e-01 , -3.43411097624845e-02 , 1.90056983032946e-02 ), ( -1.67146847611439e-01 , -3.76210820417883e-02 , 9.97006441348429e-02 ), ( -1.10096542309538e-01 , -3.65524061995518e-02 , -2.99848532408046e-02 ), ( -1.48452289187343e-01 , -5.53708545005314e-02 , -8.98692329159941e-02 ), ( -5.41184858954967e-02 , -1.69813649118323e-02 , -6.72612538257950e-03 ), ( -3.23888681510061e-02 , -1.58907664148986e-02 , -5.05670848859939e-02 ), ( 2.68951404023747e-02 , 7.91176868470593e-03 , -9.42971094339551e-04 ), ( 1.33386914111683e-03 , -1.63679234867106e-02 , -1.36235044052652e-01 ), ( -1.75709611069120e-02 , -2.90564481287763e-02 , -1.93485892842965e-01 ), ( 5.11152898928713e-02 , -2.88642876811310e-03 , -1.47428542727451e-01 ), ( 8.22513316859267e-02 , -3.28838801100539e-03 , -2.26211728774532e-01 ), ( 1.47055774923415e-01 , 1.75298052307391e-02 , -2.14226510447514e-01 ), ( 2.03786775835960e-02 , -2.85571087585229e-02 , -2.81471070714635e-01 ), ( 2.14693175798356e-02 , -3.71677411212247e-02 , -3.54083216026652e-01 ), ( -3.56223109084824e-02 , -4.11100708189845e-02 , -2.47647777397812e-01 ), ( -1.00187991162661e-01 , -6.57867228273436e-02 , -2.91564544866084e-01 ), ( -1.39786410977202e-01 , -7.12049629450578e-02 , -2.39549659977143e-01 ), ( -1.61250801320601e-01 , -8.68693877612319e-02 , -3.14773680781064e-01 ), ( -1.90468083862388e-01 , -1.03825257324807e-01 , -3.81687741360248e-01 ), ( -2.07023287438830e-01 , -1.01445134203992e-01 , -3.22194905697269e-01 ), ( -2.51839889257839e-01 , -1.18355459820924e-01 , -3.50904477214909e-01 ), ( -1.28719504995320e-01 , -7.89690629367549e-02 , -3.29479510394179e-01 ), ( -1.82802921447344e-01 , -8.64668811244112e-02 , -2.59230783675944e-01 ), ( -2.39630021885021e-01 , -1.05333163037167e-01 , -2.74703626973197e-01 ), ( -2.77631361011988e-01 , -1.06641978076813e-01 , -1.93170565240454e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 7, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3496,10 +5594,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 8, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 8, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 8, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 8, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 8, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 8, atoms_positions[size = 51] = { ( 8.36414562955246e+00 , 4.39491520117101e-02 , -7.61465752784014e-01 ), ( 6.99124365928816e+00 , -5.17168081148215e-01 , -6.41722339118265e-01 ), ( 6.24642810472991e+00 , -2.75322333841344e-01 , 6.75295340628177e-01 ), ( 4.98862323934973e+00 , -2.03175910272633e-01 , 6.77834882121448e-01 ), ( 7.04533790569600e+00 , -2.02448926271327e+00 , -9.98429050453915e-01 ), ( 6.90217139512517e+00 , -2.68933690729307e-01 , 1.82923166797993e+00 ), ( 6.17910591250209e+00 , -1.17889565169931e-01 , 3.10120127862239e+00 ), ( 7.14900881728461e+00 , -3.29048642728293e-01 , 4.28990368612928e+00 ), ( 5.29807241339890e+00 , 1.11399743146709e+00 , 3.30159846251327e+00 ), ( 4.10048248387142e+00 , 1.05886027048216e+00 , 3.63182068564134e+00 ), ( 5.87627128395544e+00 , 2.28297783431676e+00 , 2.98582534532623e+00 ), ( 5.21291751013209e+00 , 3.59559249648075e+00 , 2.88530813891945e+00 ), ( 6.33882055167443e+00 , 4.57468564952785e+00 , 2.45114548842214e+00 ), ( 3.90270476849195e+00 , 3.73543946966959e+00 , 2.02249299328080e+00 ), ( 2.88279899651480e+00 , 4.11937654924065e+00 , 2.53991298785212e+00 ), ( 3.83994916640648e+00 , 3.24085633863087e+00 , 7.64389773024474e-01 ), ( 2.67304378296441e+00 , 3.13733741515520e+00 , -9.86014610419304e-02 ), ( 3.04127619585192e+00 , 2.72015813917021e+00 , -1.59378650427401e+00 ), ( 1.59114910455646e+00 , 2.15957060798836e+00 , 5.75176375064758e-01 ), ( 4.39898768954398e-01 , 2.47026507927626e+00 , 5.45423000782526e-01 ), ( 1.97013573003170e+00 , 1.01068491768257e+00 , 1.05609300283235e+00 ), ( 1.16447767483790e+00 , 2.70492508108200e-02 , 1.69098108917443e+00 ), ( 2.01605815135543e+00 , -1.16883679388384e+00 , 2.01706039103549e+00 ), ( 5.30011373102028e-01 , 6.09134564598044e-01 , 2.97330411338839e+00 ), ( -6.67073156924597e-01 , 3.64345499449882e-01 , 3.17812208143694e+00 ), ( 1.31160615660600e+00 , 1.32575664901383e+00 , 3.83310879776563e+00 ), ( 8.47993750313544e-01 , 1.91929252820542e+00 , 5.05871476478534e+00 ), ( 2.04113716352292e+00 , 2.59938327267694e+00 , 5.62529864458867e+00 ), ( -3.59722350522117e-01 , 2.91849518036233e+00 , 4.98264198214745e+00 ), ( -1.16958058346025e+00 , 3.03622187083803e+00 , 5.90593641611715e+00 ), ( -4.33163554736300e-01 , 3.67383514574877e+00 , 3.85056023167338e+00 ), ( -1.47963774811415e+00 , 4.56877579992782e+00 , 3.53722432686352e+00 ), ( -7.46039498319265e-01 , 5.39024221562592e+00 , 2.41926953184947e+00 ), ( -2.74001310166305e+00 , 3.89049424798704e+00 , 2.92852320403613e+00 ), ( -3.84678053760197e+00 , 4.43736504431714e+00 , 2.84262148699286e+00 ), ( -2.59051894955208e+00 , 2.61364284712942e+00 , 2.47900930243999e+00 ), ( -3.71607674693391e+00 , 1.90935976894779e+00 , 2.05532296722771e+00 ), ( -3.41601193968398e+00 , 8.27113019808494e-01 , 9.69328172836758e-01 ), ( -4.29867066960749e+00 , 1.08257393526329e+00 , 3.24215630625605e+00 ), ( -5.53992972413454e+00 , 9.02333823848470e-01 , 3.33904409628711e+00 ), ( -3.45177678617437e+00 , 6.46618658489588e-01 , 4.14055635132178e+00 ), ( -3.77976112126359e+00 , 8.29345963562324e-02 , 5.48292537427215e+00 ), ( -2.39659991009518e+00 , -3.76593461979270e-01 , 6.15056380343767e+00 ), ( -4.47288185649612e+00 , 9.92997842083107e-01 , 6.42195032275813e+00 ), ( -5.32343113024443e+00 , 6.05896370513471e-01 , 7.18835870483030e+00 ), ( -6.29102177553357e+00 , 3.55675183621645e+00 , 6.70443456787512e+00 ), ( -6.91265869085218e+00 , 4.29682881912548e+00 , 7.42139316651740e+00 ), ( -6.74198079214409e+00 , 3.20851726934949e+00 , 5.51749927782646e+00 ), ( -4.09725344014070e+00 , 2.30320690324963e+00 , 6.48261488982570e+00 ), ( -4.89312829848055e+00 , 3.22112397688395e+00 , 7.21282981111052e+00 ), ( -4.08726624310037e+00 , 4.53186400797260e+00 , 7.27938796196023e+00 ) } +colvars: Step 8, atoms_positions[size = 51] = { ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 ), ( 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 ), ( 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 ), ( 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 ), ( 7.04534836653206e+00 , -2.02448407054308e+00 , -9.98404589097309e-01 ), ( 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 ), ( 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 ), ( 7.14902591067445e+00 , -3.29049307138878e-01 , 4.28994950397455e+00 ), ( 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 ), ( 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 ), ( 5.87629272107495e+00 , 2.28299099600567e+00 , 2.98584493482321e+00 ), ( 5.21291617904918e+00 , 3.59559442159943e+00 , 2.88533141464119e+00 ), ( 6.33882182249135e+00 , 4.57468922568852e+00 , 2.45117186603165e+00 ), ( 3.90270903183939e+00 , 3.73544171710473e+00 , 2.02251051274607e+00 ), ( 2.88279978105576e+00 , 4.11937815033797e+00 , 2.53992315236496e+00 ), ( 3.83995777165251e+00 , 3.24086082368063e+00 , 7.64404324467284e-01 ), ( 2.67305748498782e+00 , 3.13734293346480e+00 , -9.85910588833170e-02 ), ( 3.04129456288167e+00 , 2.72016520151402e+00 , -1.59377513008085e+00 ), ( 1.59116028395355e+00 , 2.15957458460487e+00 , 5.75180933236148e-01 ), ( 4.39907657454557e-01 , 2.47026745569223e+00 , 5.45422219368124e-01 ), ( 1.97014376172849e+00 , 1.01068814224053e+00 , 1.05609809458750e+00 ), ( 1.16448374596575e+00 , 2.70512316447285e-02 , 1.69098165565567e+00 ), ( 2.01606322025152e+00 , -1.16883486837498e+00 , 2.01706394316924e+00 ), ( 5.30011405833675e-01 , 6.09134351990563e-01 , 2.97330241396327e+00 ), ( -6.67074004134921e-01 , 3.64344491997748e-01 , 3.17811611541346e+00 ), ( 1.31160462125396e+00 , 1.32575550905386e+00 , 3.83311107606156e+00 ), ( 8.47983856956386e-01 , 1.91928984360101e+00 , 5.05871618317316e+00 ), ( 2.04112429756780e+00 , 2.59938027721393e+00 , 5.62530545703922e+00 ), ( -3.59731401881105e-01 , 2.91849204256345e+00 , 4.98263934846755e+00 ), ( -1.16959039530870e+00 , 3.03621836564236e+00 , 5.90593087889633e+00 ), ( -4.33167500245590e-01 , 3.67383388380730e+00 , 3.85055944875870e+00 ), ( -1.47964036329859e+00 , 4.56877461658980e+00 , 3.53722022403730e+00 ), ( -7.46037561806663e-01 , 5.39024276065731e+00 , 2.41926930155664e+00 ), ( -2.74001319544020e+00 , 3.89049308176989e+00 , 2.92851186870193e+00 ), ( -3.84678155103800e+00 , 4.43736309769519e+00 , 2.84260902125762e+00 ), ( -2.59051556066129e+00 , 2.61364264511348e+00 , 2.47899855467404e+00 ), ( -3.71606996116065e+00 , 1.90935949382654e+00 , 2.05530426056400e+00 ), ( -3.41600082364528e+00 , 8.27113821984746e-01 , 9.69311501518656e-01 ), ( -4.29866877430971e+00 , 1.08257130745408e+00 , 3.24213293255095e+00 ), ( -5.53992830490405e+00 , 9.02331427755674e-01 , 3.33902124343832e+00 ), ( -3.45177922141792e+00 , 6.46615632694836e-01 , 4.14053791760893e+00 ), ( -3.77976929413120e+00 , 8.29295553901299e-02 , 5.48290176368017e+00 ), ( -2.39661097592831e+00 , -3.76598220818232e-01 , 6.15054540772288e+00 ), ( -4.47289527207232e+00 , 9.92990867028161e-01 , 6.42192392244427e+00 ), ( -5.32344337905715e+00 , 6.05889648480862e-01 , 7.18833411462202e+00 ), ( -6.29103911668904e+00 , 3.55674366561199e+00 , 6.70440856281332e+00 ), ( -6.91267479614233e+00 , 4.29682099619191e+00 , 7.42137030682990e+00 ), ( -6.74199032214353e+00 , 3.20851202494557e+00 , 5.51747586064245e+00 ), ( -4.09726679864892e+00 , 2.30320061945396e+00 , 6.48259584656277e+00 ), ( -4.89314801165446e+00 , 3.22111514411689e+00 , 7.21280775033448e+00 ), ( -4.08728743975958e+00 , 4.53185546978033e+00 , 7.27937324449132e+00 ) } colvars: Step 8, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 8, atom_groups_ids[size = 0] = @@ -3517,162 +5615,301 @@ colvars: Collective variables module, step no. 8 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.29649003636170e-01 , 4.61519105247550e-03 , 9.44092280666053e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 7.04534836653206e+00 , -2.02448407054308e+00 , -9.98404589097309e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 , 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 7.14902591067445e+00 , -3.29049307138878e-01 , 4.28994950397455e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 , 5.87629272107495e+00 , 2.28299099600567e+00 , 2.98584493482321e+00 , 5.21291617904918e+00 , 3.59559442159943e+00 , 2.88533141464119e+00 , 6.33882182249135e+00 , 4.57468922568852e+00 , 2.45117186603165e+00 , 3.90270903183939e+00 , 3.73544171710473e+00 , 2.02251051274607e+00 , 2.88279978105576e+00 , 4.11937815033797e+00 , 2.53992315236496e+00 , 3.83995777165251e+00 , 3.24086082368063e+00 , 7.64404324467284e-01 , 2.67305748498782e+00 , 3.13734293346480e+00 , -9.85910588833170e-02 , 3.04129456288167e+00 , 2.72016520151402e+00 , -1.59377513008085e+00 , 1.59116028395355e+00 , 2.15957458460487e+00 , 5.75180933236148e-01 , 4.39907657454557e-01 , 2.47026745569223e+00 , 5.45422219368124e-01 , 1.97014376172849e+00 , 1.01068814224053e+00 , 1.05609809458750e+00 , 1.16448374596575e+00 , 2.70512316447285e-02 , 1.69098165565567e+00 , 2.01606322025152e+00 , -1.16883486837498e+00 , 2.01706394316924e+00 , 5.30011405833675e-01 , 6.09134351990563e-01 , 2.97330241396327e+00 , -6.67074004134921e-01 , 3.64344491997748e-01 , 3.17811611541346e+00 , 1.31160462125396e+00 , 1.32575550905386e+00 , 3.83311107606156e+00 , 8.47983856956386e-01 , 1.91928984360101e+00 , 5.05871618317316e+00 , 2.04112429756780e+00 , 2.59938027721393e+00 , 5.62530545703922e+00 , -3.59731401881105e-01 , 2.91849204256345e+00 , 4.98263934846755e+00 , -1.16959039530870e+00 , 3.03621836564236e+00 , 5.90593087889633e+00 , -4.33167500245590e-01 , 3.67383388380730e+00 , 3.85055944875870e+00 , -1.47964036329859e+00 , 4.56877461658980e+00 , 3.53722022403730e+00 , -7.46037561806663e-01 , 5.39024276065731e+00 , 2.41926930155664e+00 , -2.74001319544020e+00 , 3.89049308176989e+00 , 2.92851186870193e+00 , -3.84678155103800e+00 , 4.43736309769519e+00 , 2.84260902125762e+00 , -2.59051556066129e+00 , 2.61364264511348e+00 , 2.47899855467404e+00 , -3.71606996116065e+00 , 1.90935949382654e+00 , 2.05530426056400e+00 , -3.41600082364528e+00 , 8.27113821984746e-01 , 9.69311501518656e-01 , -4.29866877430971e+00 , 1.08257130745408e+00 , 3.24213293255095e+00 , -5.53992830490405e+00 , 9.02331427755674e-01 , 3.33902124343832e+00 , -3.45177922141792e+00 , 6.46615632694836e-01 , 4.14053791760893e+00 , -3.77976929413120e+00 , 8.29295553901299e-02 , 5.48290176368017e+00 , -2.39661097592831e+00 , -3.76598220818232e-01 , 6.15054540772288e+00 , -4.47289527207232e+00 , 9.92990867028161e-01 , 6.42192392244427e+00 , -5.32344337905715e+00 , 6.05889648480862e-01 , 7.18833411462202e+00 , -6.29103911668904e+00 , 3.55674366561199e+00 , 6.70440856281332e+00 , -6.91267479614233e+00 , 4.29682099619191e+00 , 7.42137030682990e+00 , -6.74199032214353e+00 , 3.20851202494557e+00 , 5.51747586064245e+00 , -4.09726679864892e+00 , 2.30320061945396e+00 , 6.48259584656277e+00 , -4.89314801165446e+00 , 3.22111514411689e+00 , 7.21280775033448e+00 , -4.08728743975958e+00 , 4.53185546978033e+00 , 7.27937324449132e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.29434737593730e-01 , 4.63948372091272e-03 , 9.44166949674343e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.29649003636170e-01 , 4.61519105247550e-03 , 9.44092280666053e-01 ). +colvars: Colvar "one" has value ( -3.29434737593730e-01 , 4.63948372091272e-03 , 9.44166949674343e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 7.04534836653206e+00 , -2.02448407054308e+00 , -9.98404589097309e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 , 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 7.14902591067445e+00 , -3.29049307138878e-01 , 4.28994950397455e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 , 5.87629272107495e+00 , 2.28299099600567e+00 , 2.98584493482321e+00 , 5.21291617904918e+00 , 3.59559442159943e+00 , 2.88533141464119e+00 , 6.33882182249135e+00 , 4.57468922568852e+00 , 2.45117186603165e+00 , 3.90270903183939e+00 , 3.73544171710473e+00 , 2.02251051274607e+00 , 2.88279978105576e+00 , 4.11937815033797e+00 , 2.53992315236496e+00 , 3.83995777165251e+00 , 3.24086082368063e+00 , 7.64404324467284e-01 , 2.67305748498782e+00 , 3.13734293346480e+00 , -9.85910588833170e-02 , 3.04129456288167e+00 , 2.72016520151402e+00 , -1.59377513008085e+00 , 1.59116028395355e+00 , 2.15957458460487e+00 , 5.75180933236148e-01 , 4.39907657454557e-01 , 2.47026745569223e+00 , 5.45422219368124e-01 , 1.97014376172849e+00 , 1.01068814224053e+00 , 1.05609809458750e+00 , 1.16448374596575e+00 , 2.70512316447285e-02 , 1.69098165565567e+00 , 2.01606322025152e+00 , -1.16883486837498e+00 , 2.01706394316924e+00 , 5.30011405833675e-01 , 6.09134351990563e-01 , 2.97330241396327e+00 , -6.67074004134921e-01 , 3.64344491997748e-01 , 3.17811611541346e+00 , 1.31160462125396e+00 , 1.32575550905386e+00 , 3.83311107606156e+00 , 8.47983856956386e-01 , 1.91928984360101e+00 , 5.05871618317316e+00 , 2.04112429756780e+00 , 2.59938027721393e+00 , 5.62530545703922e+00 , -3.59731401881105e-01 , 2.91849204256345e+00 , 4.98263934846755e+00 , -1.16959039530870e+00 , 3.03621836564236e+00 , 5.90593087889633e+00 , -4.33167500245590e-01 , 3.67383388380730e+00 , 3.85055944875870e+00 , -1.47964036329859e+00 , 4.56877461658980e+00 , 3.53722022403730e+00 , -7.46037561806663e-01 , 5.39024276065731e+00 , 2.41926930155664e+00 , -2.74001319544020e+00 , 3.89049308176989e+00 , 2.92851186870193e+00 , -3.84678155103800e+00 , 4.43736309769519e+00 , 2.84260902125762e+00 , -2.59051556066129e+00 , 2.61364264511348e+00 , 2.47899855467404e+00 , -3.71606996116065e+00 , 1.90935949382654e+00 , 2.05530426056400e+00 , -3.41600082364528e+00 , 8.27113821984746e-01 , 9.69311501518656e-01 , -4.29866877430971e+00 , 1.08257130745408e+00 , 3.24213293255095e+00 , -5.53992830490405e+00 , 9.02331427755674e-01 , 3.33902124343832e+00 , -3.45177922141792e+00 , 6.46615632694836e-01 , 4.14053791760893e+00 , -3.77976929413120e+00 , 8.29295553901299e-02 , 5.48290176368017e+00 , -2.39661097592831e+00 , -3.76598220818232e-01 , 6.15054540772288e+00 , -4.47289527207232e+00 , 9.92990867028161e-01 , 6.42192392244427e+00 , -5.32344337905715e+00 , 6.05889648480862e-01 , 7.18833411462202e+00 , -6.29103911668904e+00 , 3.55674366561199e+00 , 6.70440856281332e+00 , -6.91267479614233e+00 , 4.29682099619191e+00 , 7.42137030682990e+00 , -6.74199032214353e+00 , 3.20851202494557e+00 , 5.51747586064245e+00 , -4.09726679864892e+00 , 2.30320061945396e+00 , 6.48259584656277e+00 , -4.89314801165446e+00 , 3.22111514411689e+00 , 7.21280775033448e+00 , -4.08728743975958e+00 , 4.53185546978033e+00 , 7.27937324449132e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.111 , 1.8595 , -14.9782 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.3053 , 6.73053 , 13.4611 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.111 , 1.8595 , -14.9782 ) to colvar "one". -colvars: Adding total bias energy: 45.4794 +colvars: Adding biasing force ( 67.3053 , 6.73053 , 13.4611 ) to colvar "one". +colvars: Adding total bias energy: 58.3443 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.111 , 1.8595 , -14.9782 ) +colvars: Force to be applied: ( 67.3053 , 6.73053 , 13.4611 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.85975 , -0.563033 , -1.56411 ) -colvars: ( -4.16724 , -0.4828 , -1.34123 ) -colvars: ( -4.16724 , -0.4828 , -1.34123 ) -colvars: ( -5.55088 , -0.643104 , -1.78655 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.21723 , -0.604127 , -1.67788 ) +colvars: ( -4.47377 , -0.518039 , -1.43878 ) +colvars: ( -4.47377 , -0.518039 , -1.43878 ) +colvars: ( -5.9592 , -0.690043 , -1.9165 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.900602 , 0.193618 , 0.642932 ) -colvars: ( 0.778693 , 0.265381 , 0.668333 ) -colvars: ( 0.763996 , 0.25789 , 0.649319 ) -colvars: ( 0.66387 , 0.267317 , 0.602466 ) -colvars: ( 0.651779 , 0.200723 , 0.504174 ) -colvars: ( 0.574938 , 0.34563 , 0.656504 ) -colvars: ( 0.464696 , 0.360843 , 0.611528 ) -colvars: ( 0.385903 , 0.45907 , 0.69885 ) -colvars: ( 0.38211 , 0.316565 , 0.501691 ) -colvars: ( 0.346059 , 0.275434 , 0.423928 ) -colvars: ( 0.353531 , 0.321527 , 0.491424 ) -colvars: ( 0.281737 , 0.278802 , 0.390152 ) -colvars: ( 0.255478 , 0.307487 , 0.413714 ) -colvars: ( 0.345829 , 0.180199 , 0.293543 ) -colvars: ( 0.285931 , 0.137275 , 0.199098 ) -colvars: ( 0.471399 , 0.142029 , 0.316269 ) -colvars: ( 0.54573 , 0.0498282 , 0.234525 ) -colvars: ( 0.678552 , 0.0275533 , 0.283317 ) -colvars: ( 0.553166 , 0.0184456 , 0.196043 ) -colvars: ( 0.537125 , -0.0466086 , 0.0975006 ) -colvars: ( 0.573279 , 0.0668023 , 0.274178 ) -colvars: ( 0.570357 , 0.0512089 , 0.251109 ) -colvars: ( 0.606542 , 0.116229 , 0.361625 ) -colvars: ( 0.443036 , 0.0568301 , 0.182823 ) -colvars: ( 0.435612 , 0.00106392 , 0.102126 ) -colvars: ( 0.339181 , 0.123273 , 0.211722 ) -colvars: ( 0.211886 , 0.13292 , 0.148958 ) -colvars: ( 0.118772 , 0.219404 , 0.211675 ) -colvars: ( 0.184011 , 0.0588939 , 0.0310843 ) -colvars: ( 0.133238 , 0.0232558 , -0.0479516 ) -colvars: ( 0.21967 , 0.0324492 , 0.0161958 ) -colvars: ( 0.206335 , -0.0404701 , -0.0914884 ) -colvars: ( 0.243847 , -0.0447225 , -0.0749207 ) -colvars: ( 0.282803 , -0.12699 , -0.164187 ) -colvars: ( 0.238002 , -0.179893 , -0.263272 ) -colvars: ( 0.399927 , -0.142728 , -0.115822 ) -colvars: ( 0.47852 , -0.218735 , -0.172876 ) -colvars: ( 0.612231 , -0.222255 , -0.0979043 ) -colvars: ( 0.428902 , -0.222294 , -0.207351 ) -colvars: ( 0.434393 , -0.290442 , -0.297276 ) -colvars: ( 0.378135 , -0.14807 , -0.136132 ) -colvars: ( 0.321476 , -0.140839 , -0.160051 ) -colvars: ( 0.303594 , -0.0534576 , -0.0512158 ) -colvars: ( 0.195792 , -0.148765 , -0.245888 ) -colvars: ( 0.170242 , -0.190378 , -0.318045 ) -colvars: ( -0.00745225 , -0.193973 , -0.428992 ) -colvars: ( -0.100159 , -0.211147 , -0.507799 ) -colvars: ( 0.095823 , -0.245098 , -0.437288 ) -colvars: ( 0.113148 , -0.107827 , -0.239214 ) -colvars: ( -0.00839075 , -0.111399 , -0.316622 ) -colvars: ( -0.0987717 , -0.030116 , -0.259386 ) +colvars: ( 0.966702 , 0.207855 , 0.689941 ) +colvars: ( 0.835857 , 0.284872 , 0.717209 ) +colvars: ( 0.820076 , 0.27684 , 0.696811 ) +colvars: ( 0.712623 , 0.286937 , 0.64652 ) +colvars: ( 0.699645 , 0.215457 , 0.54103 ) +colvars: ( 0.617177 , 0.370983 , 0.704515 ) +colvars: ( 0.49886 , 0.387298 , 0.656246 ) +colvars: ( 0.414295 , 0.49272 , 0.749964 ) +colvars: ( 0.410217 , 0.339769 , 0.538373 ) +colvars: ( 0.371526 , 0.295616 , 0.454914 ) +colvars: ( 0.379536 , 0.345101 , 0.527362 ) +colvars: ( 0.302476 , 0.299241 , 0.41868 ) +colvars: ( 0.274287 , 0.330036 , 0.443976 ) +colvars: ( 0.371263 , 0.193413 , 0.314995 ) +colvars: ( 0.306976 , 0.147336 , 0.213636 ) +colvars: ( 0.506035 , 0.152456 , 0.339381 ) +colvars: ( 0.585811 , 0.0534993 , 0.251649 ) +colvars: ( 0.728365 , 0.029605 , 0.304011 ) +colvars: ( 0.593799 , 0.0198077 , 0.21034 ) +colvars: ( 0.576581 , -0.0500194 , 0.104582 ) +colvars: ( 0.615392 , 0.071706 , 0.294192 ) +colvars: ( 0.612262 , 0.0549605 , 0.269426 ) +colvars: ( 0.651105 , 0.124746 , 0.388028 ) +colvars: ( 0.475612 , 0.0609809 , 0.196143 ) +colvars: ( 0.467646 , 0.00112084 , 0.109533 ) +colvars: ( 0.364145 , 0.132289 , 0.227163 ) +colvars: ( 0.227522 , 0.142632 , 0.159808 ) +colvars: ( 0.127583 , 0.235453 , 0.227123 ) +colvars: ( 0.197599 , 0.0631797 , 0.0333066 ) +colvars: ( 0.143108 , 0.0249203 , -0.051518 ) +colvars: ( 0.235865 , 0.0348063 , 0.0173332 ) +colvars: ( 0.221547 , -0.043457 , -0.098232 ) +colvars: ( 0.261801 , -0.0480094 , -0.080445 ) +colvars: ( 0.30362 , -0.136319 , -0.176261 ) +colvars: ( 0.255535 , -0.193105 , -0.2826 ) +colvars: ( 0.42933 , -0.153203 , -0.124361 ) +colvars: ( 0.513685 , -0.234782 , -0.185599 ) +colvars: ( 0.657196 , -0.23855 , -0.105143 ) +colvars: ( 0.460437 , -0.238614 , -0.222603 ) +colvars: ( 0.46633 , -0.311761 , -0.319115 ) +colvars: ( 0.405955 , -0.158956 , -0.146171 ) +colvars: ( 0.345149 , -0.151207 , -0.171847 ) +colvars: ( 0.325963 , -0.0574239 , -0.0550448 ) +colvars: ( 0.210253 , -0.159724 , -0.263964 ) +colvars: ( 0.182834 , -0.204395 , -0.341407 ) +colvars: ( -0.00789679 , -0.208252 , -0.460458 ) +colvars: ( -0.107399 , -0.226693 , -0.545031 ) +colvars: ( 0.102943 , -0.263114 , -0.469362 ) +colvars: ( 0.121549 , -0.115786 , -0.256793 ) +colvars: ( -0.00889815 , -0.119629 , -0.339863 ) +colvars: ( -0.105904 , -0.0323883 , -0.27843 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.85975 , 0.563033 , 1.56411 ) -colvars: ( 4.16724 , 0.4828 , 1.34123 ) -colvars: ( 4.16724 , 0.4828 , 1.34123 ) -colvars: ( 5.55088 , 0.643104 , 1.78655 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.21723 , 0.604127 , 1.67788 ) +colvars: ( 4.47377 , 0.518039 , 1.43878 ) +colvars: ( 4.47377 , 0.518039 , 1.43878 ) +colvars: ( 5.9592 , 0.690043 , 1.9165 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.624295 , -0.0804454 , -0.394233 ) -colvars: ( -0.559823 , -0.162786 , -0.365959 ) -colvars: ( -0.512727 , -0.140905 , -0.308673 ) -colvars: ( -0.517032 , -0.190572 , -0.335196 ) -colvars: ( -0.507413 , -0.132411 , -0.299518 ) -colvars: ( -0.489115 , -0.282047 , -0.347882 ) -colvars: ( -0.452609 , -0.322528 , -0.329129 ) -colvars: ( -0.428094 , -0.42906 , -0.351971 ) -colvars: ( -0.389522 , -0.287852 , -0.249995 ) -colvars: ( -0.383309 , -0.263068 , -0.23266 ) -colvars: ( -0.342104 , -0.282258 , -0.199657 ) -colvars: ( -0.281955 , -0.246013 , -0.122788 ) -colvars: ( -0.235307 , -0.260731 , -0.0822969 ) -colvars: ( -0.303608 , -0.14366 , -0.0989237 ) -colvars: ( -0.271247 , -0.114991 , -0.0534722 ) -colvars: ( -0.3611 , -0.0863248 , -0.131322 ) -colvars: ( -0.389996 , 0.0111844 , -0.116929 ) -colvars: ( -0.444028 , 0.0589339 , -0.150118 ) -colvars: ( -0.425333 , 0.0259242 , -0.145999 ) -colvars: ( -0.413872 , 0.0819983 , -0.109394 ) -colvars: ( -0.467409 , -0.0275487 , -0.212329 ) -colvars: ( -0.499108 , -0.0291592 , -0.245029 ) -colvars: ( -0.547497 , -0.0937937 , -0.322713 ) -colvars: ( -0.443689 , -0.0594615 , -0.202649 ) -colvars: ( -0.44963 , -0.0159566 , -0.189215 ) -colvars: ( -0.386776 , -0.133389 , -0.178244 ) -colvars: ( -0.326256 , -0.164942 , -0.131277 ) -colvars: ( -0.274318 , -0.254507 , -0.118875 ) -colvars: ( -0.286446 , -0.0929464 , -0.0589619 ) -colvars: ( -0.271365 , -0.0748273 , -0.0356544 ) -colvars: ( -0.26999 , -0.0482567 , -0.0224016 ) -colvars: ( -0.236404 , 0.0257076 , 0.0445142 ) -colvars: ( -0.218724 , 0.0521399 , 0.0741557 ) -colvars: ( -0.281499 , 0.111808 , 0.0374689 ) -colvars: ( -0.254276 , 0.152911 , 0.08329 ) -colvars: ( -0.352323 , 0.140105 , -0.0213487 ) -colvars: ( -0.401956 , 0.215759 , -0.0376367 ) -colvars: ( -0.475385 , 0.238669 , -0.101488 ) -colvars: ( -0.409933 , 0.195776 , -0.0546091 ) -colvars: ( -0.414405 , 0.255925 , -0.0322594 ) -colvars: ( -0.411299 , 0.10983 , -0.094369 ) -colvars: ( -0.414741 , 0.0796053 , -0.111339 ) -colvars: ( -0.433735 , -0.0128565 , -0.171794 ) -colvars: ( -0.345856 , 0.0678991 , -0.0470693 ) -colvars: ( -0.347499 , 0.0937285 , -0.0371919 ) -colvars: ( -0.185126 , 0.0995592 , 0.129229 ) -colvars: ( -0.134105 , 0.10099 , 0.181342 ) -colvars: ( -0.215528 , 0.17164 , 0.130747 ) -colvars: ( -0.283243 , 0.0273287 , -0.00201727 ) -colvars: ( -0.214561 , 0.0133318 , 0.0610243 ) -colvars: ( -0.15953 , -0.0691937 , 0.0796911 ) +colvars: ( -0.670093 , -0.0863681 , -0.422968 ) +colvars: ( -0.600907 , -0.17474 , -0.392618 ) +colvars: ( -0.550346 , -0.151261 , -0.331136 ) +colvars: ( -0.554996 , -0.204553 , -0.359612 ) +colvars: ( -0.544672 , -0.142126 , -0.321336 ) +colvars: ( -0.525048 , -0.302727 , -0.373217 ) +colvars: ( -0.485884 , -0.346166 , -0.353099 ) +colvars: ( -0.459586 , -0.460503 , -0.3776 ) +colvars: ( -0.418173 , -0.308946 , -0.268184 ) +colvars: ( -0.411513 , -0.28234 , -0.249592 ) +colvars: ( -0.36727 , -0.302945 , -0.214159 ) +colvars: ( -0.302712 , -0.264042 , -0.131673 ) +colvars: ( -0.252634 , -0.279844 , -0.0882105 ) +colvars: ( -0.325941 , -0.154189 , -0.106077 ) +colvars: ( -0.291214 , -0.123413 , -0.0573111 ) +colvars: ( -0.387632 , -0.0926585 , -0.140846 ) +colvars: ( -0.418635 , 0.0119953 , -0.125413 ) +colvars: ( -0.47661 , 0.0632353 , -0.161025 ) +colvars: ( -0.456573 , 0.0278213 , -0.156619 ) +colvars: ( -0.444272 , 0.0880081 , -0.117349 ) +colvars: ( -0.501743 , -0.0295687 , -0.227797 ) +colvars: ( -0.535778 , -0.0312911 , -0.262898 ) +colvars: ( -0.587721 , -0.100663 , -0.346256 ) +colvars: ( -0.476312 , -0.0638054 , -0.217424 ) +colvars: ( -0.482693 , -0.0171078 , -0.203019 ) +colvars: ( -0.415236 , -0.143148 , -0.191226 ) +colvars: ( -0.350295 , -0.177006 , -0.140827 ) +colvars: ( -0.294558 , -0.273134 , -0.127506 ) +colvars: ( -0.307561 , -0.0997336 , -0.0632329 ) +colvars: ( -0.291383 , -0.0802803 , -0.0382311 ) +colvars: ( -0.289882 , -0.0517751 , -0.0239956 ) +colvars: ( -0.253826 , 0.0276095 , 0.0478056 ) +colvars: ( -0.234833 , 0.0559711 , 0.0796225 ) +colvars: ( -0.302221 , 0.120021 , 0.0402311 ) +colvars: ( -0.273005 , 0.16414 , 0.0893929 ) +colvars: ( -0.378229 , 0.150387 , -0.0228888 ) +colvars: ( -0.431495 , 0.231586 , -0.0403806 ) +colvars: ( -0.510296 , 0.256168 , -0.108899 ) +colvars: ( -0.440074 , 0.210147 , -0.058603 ) +colvars: ( -0.444874 , 0.274706 , -0.0346312 ) +colvars: ( -0.441555 , 0.117906 , -0.101264 ) +colvars: ( -0.445266 , 0.0854742 , -0.119482 ) +colvars: ( -0.465665 , -0.0137622 , -0.184349 ) +colvars: ( -0.371343 , 0.0729169 , -0.0505175 ) +colvars: ( -0.373114 , 0.100645 , -0.039929 ) +colvars: ( -0.198831 , 0.106902 , 0.138669 ) +colvars: ( -0.144079 , 0.108443 , 0.194588 ) +colvars: ( -0.231443 , 0.184258 , 0.140297 ) +colvars: ( -0.304141 , 0.0293729 , -0.00216246 ) +colvars: ( -0.230435 , 0.0143563 , 0.0654858 ) +colvars: ( -0.171376 , -0.074217 , 0.0855308 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 8. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 8. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 8, atoms_new_colvar_forces = { ( -4.58344434885704e+00 , -4.49860158678809e-01 , -1.31541615237951e+00 ), ( -3.94836672387277e+00 , -3.80205458682773e-01 , -1.03885454368685e+00 ), ( -4.02039792462075e+00 , -4.06055353329953e-01 , -1.07395808320483e+00 ), ( -5.40651315208959e+00 , -5.74792210794058e-01 , -1.58189861696530e+00 ), ( 2.51268730056784e-01 , 1.16984740749356e-01 , 3.40645929350380e-01 ), ( 4.94557440742433e+00 , 6.26616067403621e-01 , 1.87273677478185e+00 ), ( 4.17932315036328e+00 , 5.21115482468212e-01 , 1.62362651306334e+00 ), ( -4.21912554978746e-02 , 3.00100291342354e-02 , 3.46878154095955e-01 ), ( 4.15982453800690e+00 , 5.11512963645720e-01 , 1.59292438489359e+00 ), ( 5.51362904246052e+00 , 6.55469922523709e-01 , 1.97782338151619e+00 ), ( 1.14265985695535e-02 , 3.92688940204443e-02 , 2.91766646742411e-01 ), ( -2.18814736665685e-04 , 3.27884520916616e-02 , 2.67363940426838e-01 ), ( 2.01710328789859e-02 , 4.67556153602492e-02 , 3.31416923897180e-01 ), ( 4.22211241168671e-02 , 3.65385046560910e-02 , 1.94619332477587e-01 ), ( 1.46837581712214e-02 , 2.22848815686842e-02 , 1.45626079920616e-01 ), ( 1.10299267126576e-01 , 5.57044334535554e-02 , 1.84947293564009e-01 ), ( 1.55734063950428e-01 , 6.10126566180705e-02 , 1.17596118387542e-01 ), ( 2.34524245568810e-01 , 8.64871478696009e-02 , 1.33199069265361e-01 ), ( 1.27832833023067e-01 , 4.43697239750103e-02 , 5.00440650162387e-02 ), ( 1.23253416627463e-01 , 3.53896649196837e-02 , -1.18930374930429e-02 ), ( 1.05869341764032e-01 , 3.92535967111143e-02 , 6.18494720302165e-02 ), ( 7.12491199655274e-02 , 2.20496609093494e-02 , 6.08025480232838e-03 ), ( 5.90449651647699e-02 , 2.24351068203813e-02 , 3.89114551921695e-02 ), ( -6.52793404475660e-04 , -2.63132930808936e-03 , -1.98253468619322e-02 ), ( -1.40178933589912e-02 , -1.48926970356135e-02 , -8.70888270975484e-02 ), ( -4.75945938876590e-02 , -1.01163750495041e-02 , 3.34776604677360e-02 ), ( -1.14369738689893e-01 , -3.20223336783406e-02 , 1.76810302294982e-02 ), ( -1.55546331266055e-01 , -3.51029627420427e-02 , 9.27994864871048e-02 ), ( -1.02435867973602e-01 , -3.40525533251060e-02 , -2.78776543776639e-02 ), ( -1.38126250865608e-01 , -5.15714260733037e-02 , -8.36059651088255e-02 ), ( -5.03198562699047e-02 , -1.58075213240080e-02 , -6.20578071133937e-03 ), ( -3.00690419058648e-02 , -1.47624501626466e-02 , -4.69741442118032e-02 ), ( 2.51228587554857e-02 , 7.41739157852034e-03 , -7.64972945065112e-04 ), ( 1.30346671309423e-03 , -1.51815562046862e-02 , -1.26718612931018e-01 ), ( -1.62737474331351e-02 , -2.69819613950322e-02 , -1.79982117012514e-01 ), ( 4.76031994387484e-02 , -2.62297912456652e-03 , -1.37171117397487e-01 ), ( 7.65645931911323e-02 , -2.97616953392221e-03 , -2.10512579582090e-01 ), ( 1.36845339987936e-01 , 1.64133730704317e-02 , -1.99392676538652e-01 ), ( 1.89691374920026e-02 , -2.65182912392013e-02 , -2.61959755448783e-01 ), ( 1.99879490737617e-02 , -3.45173894265902e-02 , -3.29535113440665e-01 ), ( -3.31642689686467e-02 , -3.82397618534294e-02 , -2.30500739735148e-01 ), ( -9.32649038958296e-02 , -6.12335498914378e-02 , -2.71390132170575e-01 ), ( -1.30141459289913e-01 , -6.63141399704378e-02 , -2.23009909093778e-01 ), ( -1.50064368321367e-01 , -8.08659803519194e-02 , -2.92957107313791e-01 ), ( -1.77257176407694e-01 , -9.66491859286723e-02 , -3.55236419133693e-01 ), ( -1.92578245837911e-01 , -9.44133429746729e-02 , -2.99762839292360e-01 ), ( -2.34264533059651e-01 , -1.10157110915457e-01 , -3.26456503527616e-01 ), ( -1.19704597095965e-01 , -7.34580441687327e-02 , -3.06541184157487e-01 ), ( -1.70094809091255e-01 , -8.04986777869762e-02 , -2.41231085210268e-01 ), ( -2.22952147964946e-01 , -9.80676749608512e-02 , -2.55597650901597e-01 ), ( -2.58301335228226e-01 , -9.93096636368683e-02 , -1.79695298676914e-01 ) } +colvars: Step 8, atoms_new_colvar_forces = { ( -4.92062102276460e+00 , -4.82640086402408e-01 , -1.41090709788162e+00 ), ( -4.23882300605358e+00 , -4.07905998443878e-01 , -1.11419071648431e+00 ), ( -4.31614662308449e+00 , -4.35654787495289e-01 , -1.15187353857763e+00 ), ( -5.80422300642920e+00 , -6.16711741355150e-01 , -1.69680505101877e+00 ), ( 2.69730415475049e-01 , 1.25579660928816e-01 , 3.65674486085080e-01 ), ( 5.30935930421059e+00 , 6.72383167042985e-01 , 2.00917749325564e+00 ), ( 4.48674966182718e+00 , 5.59170530438994e-01 , 1.74192893872839e+00 ), ( -4.52906298257705e-02 , 3.22171503858267e-02 , 3.72364783352675e-01 ), ( 4.46581806624927e+00 , 5.48862333806290e-01 , 1.70897058867861e+00 ), ( 5.91920974857694e+00 , 7.03318412070536e-01 , 2.12182035960104e+00 ), ( 1.22659525918241e-02 , 4.21552798374245e-02 , 3.13203231438047e-01 ), ( -2.35449825619849e-04 , 3.51985139700656e-02 , 2.87007138398798e-01 ), ( 2.16521316420076e-02 , 5.01918575449373e-02 , 3.55765812291965e-01 ), ( 4.53226913390948e-02 , 3.92234256799797e-02 , 2.08917853504543e-01 ), ( 1.57619387743165e-02 , 2.39224751759000e-02 , 1.56324760053555e-01 ), ( 1.18402915597713e-01 , 5.97970291228929e-02 , 1.98535455383764e-01 ), ( 1.67175995244537e-01 , 6.54946140811529e-02 , 1.26235922817558e-01 ), ( 2.51755249276545e-01 , 9.28402975914267e-02 , 1.42985471270553e-01 ), ( 1.37225093985104e-01 , 4.76289236613890e-02 , 5.37210230860738e-02 ), ( 1.32309149368861e-01 , 3.79887911644722e-02 , -1.27668340774620e-02 ), ( 1.13648225863308e-01 , 4.21372838913594e-02 , 6.63942130256543e-02 ), ( 7.64846659166681e-02 , 2.36694781705501e-02 , 6.52785402352585e-03 ), ( 6.33841952374116e-02 , 2.40836554961314e-02 , 4.17716779614807e-02 ), ( -7.00248608696719e-04 , -2.82451954875375e-03 , -2.12813385831128e-02 ), ( -1.50472452036515e-02 , -1.59869396997441e-02 , -9.34867470803088e-02 ), ( -5.10912382790079e-02 , -1.08590004350120e-02 , 3.59376467537308e-02 ), ( -1.22772754211688e-01 , -3.43740921663118e-02 , 1.89801000449557e-02 ), ( -1.66974932373970e-01 , -3.76804871495528e-02 , 9.96173937663538e-02 ), ( -1.09962368821707e-01 , -3.65539210011210e-02 , -2.99262571378577e-02 ), ( -1.48275025635186e-01 , -5.53599330649248e-02 , -8.97490845489287e-02 ), ( -5.40175037301750e-02 , -1.69688024866761e-02 , -6.66238588198451e-03 ), ( -3.22790874989935e-02 , -1.58474256704186e-02 , -5.04264386623485e-02 ), ( 2.69676448462849e-02 , 7.96168744989820e-03 , -8.22472164126120e-04 ), ( 1.39865524379135e-03 , -1.62978531419949e-02 , -1.36029656644145e-01 ), ( -1.74701394458462e-02 , -2.89654373170617e-02 , -1.93206735091724e-01 ), ( 5.11004986260297e-02 , -2.81682533688396e-03 , -1.47249689247549e-01 ), ( 8.21900123767041e-02 , -3.19642828593120e-03 , -2.25979411403335e-01 ), ( 1.46900072719255e-01 , 1.76174357491722e-02 , -2.14042077672817e-01 ), ( 2.03630711473856e-02 , -2.84679434628290e-02 , -2.81206304273171e-01 ), ( 2.14567618961489e-02 , -3.70550714493615e-02 , -3.53746559626665e-01 ), ( -3.56005649721288e-02 , -4.10499915429206e-02 , -2.47435750153755e-01 ), ( -1.00116770630907e-01 , -6.57328263410535e-02 , -2.91329182539394e-01 ), ( -1.39702517366954e-01 , -7.11860778591733e-02 , -2.39394078165158e-01 ), ( -1.61089749065314e-01 , -8.68074914211787e-02 , -3.14481134001435e-01 ), ( -1.90280403524510e-01 , -1.03750370890082e-01 , -3.81336169015597e-01 ), ( -2.06728189061952e-01 , -1.01350338916010e-01 , -3.21788092155524e-01 ), ( -2.51477506982419e-01 , -1.18250740234853e-01 , -3.50443301704092e-01 ), ( -1.28500313421132e-01 , -7.88560071267686e-02 , -3.29064425604893e-01 ), ( -1.82592240115323e-01 , -8.64129621561250e-02 , -2.58955125406175e-01 ), ( -2.39333463508562e-01 , -1.05272589551821e-01 , -2.74377645288446e-01 ), ( -2.77280117590632e-01 , -1.06605313306912e-01 , -1.92898903429652e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 8, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3710,10 +5947,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 9, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 9, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 9, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 9, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 9, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 9, atoms_positions[size = 51] = { ( 8.35617328958012e+00 , 4.40201111550499e-02 , -7.63192151632155e-01 ), ( 6.99097240602844e+00 , -5.23098682154020e-01 , -6.37797836607381e-01 ), ( 6.23815514520239e+00 , -2.82267287807500e-01 , 6.79477069875679e-01 ), ( 4.98587590394737e+00 , -2.00932986909559e-01 , 6.82695304324461e-01 ), ( 7.04715049340700e+00 , -2.02643209091800e+00 , -9.92025769775599e-01 ), ( 6.90161384614784e+00 , -2.68384744323356e-01 , 1.83601037032123e+00 ), ( 6.18054212321817e+00 , -1.17450447738679e-01 , 3.11598783394613e+00 ), ( 7.13934721123654e+00 , -3.32279104868168e-01 , 4.28718687453315e+00 ), ( 5.29490234909104e+00 , 1.11327202908185e+00 , 3.30650130783058e+00 ), ( 4.10640776207485e+00 , 1.05574731323172e+00 , 3.63548712960390e+00 ), ( 5.87580925869317e+00 , 2.27404129461307e+00 , 2.98972979204815e+00 ), ( 5.21231284290999e+00 , 3.59531799564475e+00 , 2.88747776096073e+00 ), ( 6.33859155764595e+00 , 4.56408994671179e+00 , 2.44722573395776e+00 ), ( 3.90517545640542e+00 , 3.73832953430805e+00 , 2.02422730802836e+00 ), ( 2.87258579891551e+00 , 4.12193333072030e+00 , 2.53576047562773e+00 ), ( 3.84735886677987e+00 , 3.24045019666927e+00 , 7.59633277859372e-01 ), ( 2.67253480373983e+00 , 3.12364501480597e+00 , -1.01452792510276e-01 ), ( 3.03886841154488e+00 , 2.72025863545469e+00 , -1.58904877234166e+00 ), ( 1.58274495770850e+00 , 2.16537127625444e+00 , 5.68027596240243e-01 ), ( 4.40423296023978e-01 , 2.47815927412273e+00 , 5.42125148164896e-01 ), ( 1.97200939263015e+00 , 1.00824310186052e+00 , 1.05905375799457e+00 ), ( 1.17010508599150e+00 , 3.51247468335211e-02 , 1.69159923058915e+00 ), ( 2.01708154865540e+00 , -1.16279420424218e+00 , 2.01502857453269e+00 ), ( 5.34997050289972e-01 , 6.10358356760984e-01 , 2.96371694185010e+00 ), ( -6.63700711229056e-01 , 3.61126800954301e-01 , 3.17629794481568e+00 ), ( 1.31581740276896e+00 , 1.32962342021575e+00 , 3.83499332809479e+00 ), ( 8.52588626285425e-01 , 1.92551209086982e+00 , 5.05341516621813e+00 ), ( 2.03624439154334e+00 , 2.60342652482486e+00 , 5.62711318893577e+00 ), ( -3.58558490625571e-01 , 2.91796618389863e+00 , 4.98136792635613e+00 ), ( -1.16745295221365e+00 , 3.03941892019623e+00 , 5.90600181805091e+00 ), ( -4.41322306075072e-01 , 3.66455474655012e+00 , 3.84828838059791e+00 ), ( -1.48252578938067e+00 , 4.56316356375946e+00 , 3.53511400940353e+00 ), ( -7.41468959412178e-01 , 5.39248644752632e+00 , 2.42341400340784e+00 ), ( -2.74736893011247e+00 , 3.88785555416379e+00 , 2.92619479610957e+00 ), ( -3.84350855686151e+00 , 4.44312079852304e+00 , 2.83902955175231e+00 ), ( -2.59424505987070e+00 , 2.61756475163911e+00 , 2.47333619260125e+00 ), ( -3.71777271979420e+00 , 1.90472692667774e+00 , 2.04903238796236e+00 ), ( -3.41686265392583e+00 , 8.35004039841956e-01 , 9.60666142566565e-01 ), ( -4.29618105174137e+00 , 1.07717611171578e+00 , 3.24621515370550e+00 ), ( -5.53957738113770e+00 , 8.95482826704819e-01 , 3.33696988539247e+00 ), ( -3.44486334884249e+00 , 6.51473089862034e-01 , 4.13810663291588e+00 ), ( -3.77813050514537e+00 , 7.51531857860098e-02 , 5.48160152246266e+00 ), ( -2.39184882813385e+00 , -3.65561141921903e-01 , 6.15475234122969e+00 ), ( -4.47414411182857e+00 , 9.92512844121139e-01 , 6.42479652659573e+00 ), ( -5.32435262549222e+00 , 6.07391462923434e-01 , 7.19059188262768e+00 ), ( -6.28582600349913e+00 , 3.55967174203309e+00 , 6.70555358996822e+00 ), ( -6.91379627624659e+00 , 4.29556210374275e+00 , 7.42409134891773e+00 ), ( -6.74145689380113e+00 , 3.20811190368739e+00 , 5.51986027101593e+00 ), ( -4.10251973193467e+00 , 2.30201306228987e+00 , 6.48141691185082e+00 ), ( -4.88523547828012e+00 , 3.21492618966655e+00 , 7.21277338851064e+00 ), ( -4.09092078104340e+00 , 4.54237014762350e+00 , 7.28356625152157e+00 ) } +colvars: Step 9, atoms_positions[size = 51] = { ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 ), ( 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 ), ( 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 ), ( 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 ), ( 7.04716055156384e+00 , -2.02642724541937e+00 , -9.91996217526734e-01 ), ( 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 ), ( 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 ), ( 7.13937501148286e+00 , -3.32281007196666e-01 , 4.28724944051132e+00 ), ( 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 ), ( 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 ), ( 5.87584240605616e+00 , 2.27406079439535e+00 , 2.98975335414505e+00 ), ( 5.21231076724505e+00 , 3.59532021733656e+00 , 2.88750725412396e+00 ), ( 6.33859306036526e+00 , 4.56409445599567e+00 , 2.44725866444525e+00 ), ( 3.90518088129681e+00 , 3.73833202821970e+00 , 2.02424928541876e+00 ), ( 2.87258675504871e+00 , 4.12193535116982e+00 , 2.53577331855110e+00 ), ( 3.84736969212799e+00 , 3.24045587181967e+00 , 7.59651605650163e-01 ), ( 2.67255189423094e+00 , 3.12365193022208e+00 , -1.01439806041565e-01 ), ( 3.03889129974584e+00 , 2.72026741320911e+00 , -1.58903460828758e+00 ), ( 1.58275888302685e+00 , 2.16537626786957e+00 , 5.68033334049131e-01 ), ( 4.40434598356364e-01 , 2.47816226156406e+00 , 5.42124173255944e-01 ), ( 1.97201951582835e+00 , 1.00824717188618e+00 , 1.05906022437336e+00 ), ( 1.17011266336580e+00 , 3.51272591235100e-02 , 1.69160000001138e+00 ), ( 2.01708799463464e+00 , -1.16279170265369e+00 , 2.01503314553798e+00 ), ( 5.34997134557080e-01 , 6.10358093113758e-01 , 2.96371481860032e+00 ), ( -6.63701749479078e-01 , 3.61125539662574e-01 , 3.17629043775601e+00 ), ( 1.31581612316446e+00 , 1.32962185090911e+00 , 3.83499611283094e+00 ), ( 8.52576343402521e-01 , 1.92550867614467e+00 , 5.05341694767528e+00 ), ( 2.03622843302767e+00 , 2.60342277714730e+00 , 5.62712163754377e+00 ), ( -3.58569781342234e-01 , 2.91796222083163e+00 , 4.98136460221299e+00 ), ( -1.16746538661149e+00 , 3.03941451175296e+00 , 5.90599491867180e+00 ), ( -4.41327274576360e-01 , 3.66455315494170e+00 , 3.84828734308887e+00 ), ( -1.48252901462828e+00 , 4.56316209173146e+00 , 3.53510885209680e+00 ), ( -7.41466556365248e-01 , 5.39248711418538e+00 , 2.42341371144279e+00 ), ( -2.74736907658648e+00 , 3.88785416209683e+00 , 2.92618062941570e+00 ), ( -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 ), ( -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 ), ( -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 ), ( -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 ), ( -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 ), ( -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 ), ( -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 ), ( -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 ), ( -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 ), ( -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 ), ( -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 ), ( -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 ), ( -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 ), ( -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 ), ( -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 ), ( -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 ), ( -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ) } colvars: Step 9, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 9, atom_groups_ids[size = 0] = @@ -3731,162 +5968,301 @@ colvars: Collective variables module, step no. 9 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.27191798357385e-01 , 4.60173684513572e-03 , 9.44946745116183e-01 ). +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.27457007407554e-01 , 4.57131359996204e-03 , 9.44855021361299e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 ). colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating gradients of colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 7.04716055156384e+00 , -2.02642724541937e+00 , -9.91996217526734e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 , 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 7.13937501148286e+00 , -3.32281007196666e-01 , 4.28724944051132e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 , 5.87584240605616e+00 , 2.27406079439535e+00 , 2.98975335414505e+00 , 5.21231076724505e+00 , 3.59532021733656e+00 , 2.88750725412396e+00 , 6.33859306036526e+00 , 4.56409445599567e+00 , 2.44725866444525e+00 , 3.90518088129681e+00 , 3.73833202821970e+00 , 2.02424928541876e+00 , 2.87258675504871e+00 , 4.12193535116982e+00 , 2.53577331855110e+00 , 3.84736969212799e+00 , 3.24045587181967e+00 , 7.59651605650163e-01 , 2.67255189423094e+00 , 3.12365193022208e+00 , -1.01439806041565e-01 , 3.03889129974584e+00 , 2.72026741320911e+00 , -1.58903460828758e+00 , 1.58275888302685e+00 , 2.16537626786957e+00 , 5.68033334049131e-01 , 4.40434598356364e-01 , 2.47816226156406e+00 , 5.42124173255944e-01 , 1.97201951582835e+00 , 1.00824717188618e+00 , 1.05906022437336e+00 , 1.17011266336580e+00 , 3.51272591235100e-02 , 1.69160000001138e+00 , 2.01708799463464e+00 , -1.16279170265369e+00 , 2.01503314553798e+00 , 5.34997134557080e-01 , 6.10358093113758e-01 , 2.96371481860032e+00 , -6.63701749479078e-01 , 3.61125539662574e-01 , 3.17629043775601e+00 , 1.31581612316446e+00 , 1.32962185090911e+00 , 3.83499611283094e+00 , 8.52576343402521e-01 , 1.92550867614467e+00 , 5.05341694767528e+00 , 2.03622843302767e+00 , 2.60342277714730e+00 , 5.62712163754377e+00 , -3.58569781342234e-01 , 2.91796222083163e+00 , 4.98136460221299e+00 , -1.16746538661149e+00 , 3.03941451175296e+00 , 5.90599491867180e+00 , -4.41327274576360e-01 , 3.66455315494170e+00 , 3.84828734308887e+00 , -1.48252901462828e+00 , 4.56316209173146e+00 , 3.53510885209680e+00 , -7.41466556365248e-01 , 5.39248711418538e+00 , 2.42341371144279e+00 , -2.74736907658648e+00 , 3.88785416209683e+00 , 2.92618062941570e+00 , -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 , -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 , -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 , -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 , -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 , -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 , -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 , -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 , -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 , -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 , -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 , -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 , -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 , -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 , -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 , -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 , -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.27457007407554e-01 , 4.57131359996204e-03 , 9.44855021361299e-01 ). +colvars: Colvar "one" has value ( -3.27191798357385e-01 , 4.60173684513572e-03 , 9.44946745116183e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 7.04716055156384e+00 , -2.02642724541937e+00 , -9.91996217526734e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 , 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 7.13937501148286e+00 , -3.32281007196666e-01 , 4.28724944051132e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 , 5.87584240605616e+00 , 2.27406079439535e+00 , 2.98975335414505e+00 , 5.21231076724505e+00 , 3.59532021733656e+00 , 2.88750725412396e+00 , 6.33859306036526e+00 , 4.56409445599567e+00 , 2.44725866444525e+00 , 3.90518088129681e+00 , 3.73833202821970e+00 , 2.02424928541876e+00 , 2.87258675504871e+00 , 4.12193535116982e+00 , 2.53577331855110e+00 , 3.84736969212799e+00 , 3.24045587181967e+00 , 7.59651605650163e-01 , 2.67255189423094e+00 , 3.12365193022208e+00 , -1.01439806041565e-01 , 3.03889129974584e+00 , 2.72026741320911e+00 , -1.58903460828758e+00 , 1.58275888302685e+00 , 2.16537626786957e+00 , 5.68033334049131e-01 , 4.40434598356364e-01 , 2.47816226156406e+00 , 5.42124173255944e-01 , 1.97201951582835e+00 , 1.00824717188618e+00 , 1.05906022437336e+00 , 1.17011266336580e+00 , 3.51272591235100e-02 , 1.69160000001138e+00 , 2.01708799463464e+00 , -1.16279170265369e+00 , 2.01503314553798e+00 , 5.34997134557080e-01 , 6.10358093113758e-01 , 2.96371481860032e+00 , -6.63701749479078e-01 , 3.61125539662574e-01 , 3.17629043775601e+00 , 1.31581612316446e+00 , 1.32962185090911e+00 , 3.83499611283094e+00 , 8.52576343402521e-01 , 1.92550867614467e+00 , 5.05341694767528e+00 , 2.03622843302767e+00 , 2.60342277714730e+00 , 5.62712163754377e+00 , -3.58569781342234e-01 , 2.91796222083163e+00 , 4.98136460221299e+00 , -1.16746538661149e+00 , 3.03941451175296e+00 , 5.90599491867180e+00 , -4.41327274576360e-01 , 3.66455315494170e+00 , 3.84828734308887e+00 , -1.48252901462828e+00 , 4.56316209173146e+00 , 3.53510885209680e+00 , -7.41466556365248e-01 , 5.39248711418538e+00 , 2.42341371144279e+00 , -2.74736907658648e+00 , 3.88785416209683e+00 , 2.92618062941570e+00 , -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 , -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 , -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 , -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 , -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 , -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 , -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 , -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 , -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 , -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 , -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 , -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 , -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 , -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 , -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 , -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 , -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.0671 , 1.86037 , -14.9935 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.1907 , 6.71907 , 13.4381 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.0671 , 1.86037 , -14.9935 ) to colvar "one". -colvars: Adding total bias energy: 45.3881 +colvars: Adding biasing force ( 67.1907 , 6.71907 , 13.4381 ) to colvar "one". +colvars: Adding total bias energy: 58.1833 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.0671 , 1.86037 , -14.9935 ) +colvars: Force to be applied: ( 67.1907 , 6.71907 , 13.4381 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.86498 , -0.560393 , -1.55412 ) -colvars: ( -4.17172 , -0.480537 , -1.33265 ) -colvars: ( -4.17172 , -0.480537 , -1.33265 ) -colvars: ( -5.55685 , -0.640089 , -1.77513 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.21011 , -0.599752 , -1.66278 ) +colvars: ( -4.46767 , -0.514287 , -1.42583 ) +colvars: ( -4.46767 , -0.514287 , -1.42583 ) +colvars: ( -5.95106 , -0.685045 , -1.89925 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.900044 , 0.193828 , 0.640905 ) -colvars: ( 0.778327 , 0.265507 , 0.666228 ) -colvars: ( 0.763521 , 0.258077 , 0.647278 ) -colvars: ( 0.663751 , 0.267332 , 0.600509 ) -colvars: ( 0.651672 , 0.200736 , 0.502468 ) -colvars: ( 0.575024 , 0.345549 , 0.65439 ) -colvars: ( 0.465033 , 0.360647 , 0.609507 ) -colvars: ( 0.386421 , 0.458787 , 0.696589 ) -colvars: ( 0.382517 , 0.316347 , 0.49995 ) -colvars: ( 0.34657 , 0.275169 , 0.422376 ) -colvars: ( 0.353873 , 0.321348 , 0.48972 ) -colvars: ( 0.282122 , 0.278613 , 0.388708 ) -colvars: ( 0.255793 , 0.30734 , 0.412222 ) -colvars: ( 0.346074 , 0.180078 , 0.292359 ) -colvars: ( 0.286273 , 0.137115 , 0.19815 ) -colvars: ( 0.471413 , 0.142011 , 0.315046 ) -colvars: ( 0.545593 , 0.0498805 , 0.233524 ) -colvars: ( 0.678147 , 0.0277263 , 0.282213 ) -colvars: ( 0.553125 , 0.0184466 , 0.195126 ) -colvars: ( 0.537104 , -0.0466127 , 0.0968358 ) -colvars: ( 0.57331 , 0.0667599 , 0.273051 ) -colvars: ( 0.570507 , 0.0511046 , 0.250025 ) -colvars: ( 0.60673 , 0.116096 , 0.36025 ) -colvars: ( 0.443432 , 0.0566168 , 0.181895 ) -colvars: ( 0.436056 , 0.000828193 , 0.101399 ) -colvars: ( 0.339734 , 0.122991 , 0.210709 ) -colvars: ( 0.212668 , 0.132538 , 0.148088 ) -colvars: ( 0.11969 , 0.218962 , 0.210635 ) -colvars: ( 0.184756 , 0.0585392 , 0.0305233 ) -colvars: ( 0.134107 , 0.0228453 , -0.0483214 ) -colvars: ( 0.220239 , 0.032183 , 0.0156924 ) -colvars: ( 0.206839 , -0.0406968 , -0.0917063 ) -colvars: ( 0.244163 , -0.0448557 , -0.0751602 ) -colvars: ( 0.283203 , -0.127172 , -0.164213 ) -colvars: ( 0.238465 , -0.180099 , -0.263048 ) -colvars: ( 0.400169 , -0.142845 , -0.115962 ) -colvars: ( 0.478667 , -0.218813 , -0.172864 ) -colvars: ( 0.612171 , -0.222246 , -0.0980705 ) -colvars: ( 0.429245 , -0.222467 , -0.207272 ) -colvars: ( 0.434736 , -0.290614 , -0.296967 ) -colvars: ( 0.378652 , -0.148329 , -0.136253 ) -colvars: ( 0.322198 , -0.141198 , -0.160132 ) -colvars: ( 0.304437 , -0.0538809 , -0.0515897 ) -colvars: ( 0.196709 , -0.149206 , -0.245763 ) -colvars: ( 0.171254 , -0.190863 , -0.317744 ) -colvars: ( -0.00638552 , -0.194456 , -0.428398 ) -colvars: ( -0.0989486 , -0.211691 , -0.507013 ) -colvars: ( 0.0966431 , -0.245467 , -0.436651 ) -colvars: ( 0.114132 , -0.108291 , -0.239107 ) -colvars: ( -0.00722485 , -0.111939 , -0.316329 ) -colvars: ( -0.0974884 , -0.030705 , -0.259247 ) +colvars: ( 0.963712 , 0.207573 , 0.686021 ) +colvars: ( 0.833401 , 0.284306 , 0.713138 ) +colvars: ( 0.81754 , 0.276361 , 0.692862 ) +colvars: ( 0.710739 , 0.286244 , 0.642785 ) +colvars: ( 0.697806 , 0.214939 , 0.537829 ) +colvars: ( 0.615751 , 0.369975 , 0.700468 ) +colvars: ( 0.498 , 0.386123 , 0.652419 ) +colvars: ( 0.413841 , 0.491188 , 0.745646 ) +colvars: ( 0.409652 , 0.338688 , 0.535144 ) +colvars: ( 0.37117 , 0.294592 , 0.452096 ) +colvars: ( 0.378978 , 0.344049 , 0.524202 ) +colvars: ( 0.302155 , 0.298293 , 0.416074 ) +colvars: ( 0.273959 , 0.329057 , 0.441256 ) +colvars: ( 0.37062 , 0.192802 , 0.312926 ) +colvars: ( 0.306596 , 0.146796 , 0.212074 ) +colvars: ( 0.504807 , 0.152059 , 0.337208 ) +colvars: ( 0.584222 , 0.0534264 , 0.249932 ) +colvars: ( 0.726131 , 0.0297241 , 0.302052 ) +colvars: ( 0.592294 , 0.0197618 , 0.208817 ) +colvars: ( 0.57514 , -0.0498975 , 0.103594 ) +colvars: ( 0.613911 , 0.0714834 , 0.29223 ) +colvars: ( 0.610919 , 0.0547113 , 0.267572 ) +colvars: ( 0.649707 , 0.124292 , 0.385563 ) +colvars: ( 0.474873 , 0.0605968 , 0.19464 ) +colvars: ( 0.466979 , 0.000860634 , 0.108462 ) +colvars: ( 0.363854 , 0.131653 , 0.225493 ) +colvars: ( 0.227816 , 0.141861 , 0.158461 ) +colvars: ( 0.128273 , 0.234386 , 0.225427 ) +colvars: ( 0.197927 , 0.0626348 , 0.0326096 ) +colvars: ( 0.143705 , 0.0244091 , -0.0517976 ) +colvars: ( 0.235907 , 0.0344294 , 0.0167392 ) +colvars: ( 0.221554 , -0.0435962 , -0.0982291 ) +colvars: ( 0.261505 , -0.0480343 , -0.0805084 ) +colvars: ( 0.303312 , -0.136178 , -0.175857 ) +colvars: ( 0.255414 , -0.19285 , -0.281661 ) +colvars: ( 0.428539 , -0.15295 , -0.124212 ) +colvars: ( 0.512582 , -0.234282 , -0.185136 ) +colvars: ( 0.655513 , -0.237945 , -0.105074 ) +colvars: ( 0.459679 , -0.238211 , -0.221976 ) +colvars: ( 0.465557 , -0.311174 , -0.318 ) +colvars: ( 0.40552 , -0.158845 , -0.145951 ) +colvars: ( 0.345088 , -0.151225 , -0.17152 ) +colvars: ( 0.32608 , -0.0577453 , -0.0553256 ) +colvars: ( 0.210737 , -0.159811 , -0.263183 ) +colvars: ( 0.183488 , -0.20442 , -0.340246 ) +colvars: ( -0.00671073 , -0.208265 , -0.458678 ) +colvars: ( -0.10581 , -0.226727 , -0.542833 ) +colvars: ( 0.103587 , -0.262864 , -0.467513 ) +colvars: ( 0.122325 , -0.116007 , -0.256048 ) +colvars: ( -0.00760195 , -0.119923 , -0.338709 ) +colvars: ( -0.104241 , -0.0329536 , -0.277592 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.86498 , 0.560393 , 1.55412 ) -colvars: ( 4.17172 , 0.480537 , 1.33265 ) -colvars: ( 4.17172 , 0.480537 , 1.33265 ) -colvars: ( 5.55685 , 0.640089 , 1.77513 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.21011 , 0.599752 , 1.66278 ) +colvars: ( 4.46767 , 0.514287 , 1.42583 ) +colvars: ( 4.46767 , 0.514287 , 1.42583 ) +colvars: ( 5.95106 , 0.685045 , 1.89925 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.623455 , -0.0804608 , -0.391963 ) -colvars: ( -0.559239 , -0.16276 , -0.363513 ) -colvars: ( -0.511959 , -0.140899 , -0.306199 ) -colvars: ( -0.516784 , -0.190494 , -0.332938 ) -colvars: ( -0.50717 , -0.132327 , -0.297589 ) -colvars: ( -0.489159 , -0.281927 , -0.345411 ) -colvars: ( -0.453001 , -0.322355 , -0.326785 ) -colvars: ( -0.428748 , -0.428851 , -0.349301 ) -colvars: ( -0.389977 , -0.28766 , -0.247935 ) -colvars: ( -0.383908 , -0.262853 , -0.230874 ) -colvars: ( -0.342442 , -0.282076 , -0.197543 ) -colvars: ( -0.28232 , -0.245818 , -0.12093 ) -colvars: ( -0.235548 , -0.260548 , -0.0802672 ) -colvars: ( -0.303768 , -0.143492 , -0.0974243 ) -colvars: ( -0.271526 , -0.114799 , -0.05226 ) -colvars: ( -0.360949 , -0.0862058 , -0.129814 ) -colvars: ( -0.38963 , 0.0112737 , -0.115738 ) -colvars: ( -0.443298 , 0.0589657 , -0.148816 ) -colvars: ( -0.425122 , 0.026032 , -0.145015 ) -colvars: ( -0.413675 , 0.0821126 , -0.108738 ) -colvars: ( -0.467331 , -0.0274302 , -0.211154 ) -colvars: ( -0.499216 , -0.0290179 , -0.244004 ) -colvars: ( -0.547693 , -0.0936495 , -0.321389 ) -colvars: ( -0.444126 , -0.0592667 , -0.201798 ) -colvars: ( -0.450134 , -0.0157506 , -0.188663 ) -colvars: ( -0.38742 , -0.133161 , -0.177214 ) -colvars: ( -0.327201 , -0.164664 , -0.13039 ) -colvars: ( -0.275446 , -0.2542 , -0.117696 ) -colvars: ( -0.28731 , -0.0926709 , -0.0584148 ) -colvars: ( -0.272396 , -0.0745244 , -0.0353736 ) -colvars: ( -0.270586 , -0.0480154 , -0.0218562 ) -colvars: ( -0.236879 , 0.0259398 , 0.0447484 ) -colvars: ( -0.218916 , 0.0523348 , 0.0745018 ) -colvars: ( -0.281838 , 0.112019 , 0.0373833 ) -colvars: ( -0.254685 , 0.153138 , 0.0828963 ) -colvars: ( -0.352467 , 0.14028 , -0.0213675 ) -colvars: ( -0.401977 , 0.215914 , -0.0379292 ) -colvars: ( -0.475144 , 0.238777 , -0.101619 ) -colvars: ( -0.410244 , 0.195971 , -0.0550606 ) -colvars: ( -0.41471 , 0.256121 , -0.0330337 ) -colvars: ( -0.411872 , 0.110058 , -0.0945951 ) -colvars: ( -0.415614 , 0.0798746 , -0.11168 ) -colvars: ( -0.434804 , -0.0125662 , -0.171802 ) -colvars: ( -0.346976 , 0.0682126 , -0.0476167 ) -colvars: ( -0.348753 , 0.0940626 , -0.0380068 ) -colvars: ( -0.186374 , 0.0999143 , 0.128299 ) -colvars: ( -0.135534 , 0.101378 , 0.180206 ) -colvars: ( -0.216428 , 0.171944 , 0.129766 ) -colvars: ( -0.284433 , 0.0276585 , -0.00244153 ) -colvars: ( -0.215979 , 0.0137028 , 0.0604248 ) -colvars: ( -0.161099 , -0.0687978 , 0.0793727 ) +colvars: ( -0.66753 , -0.0861754 , -0.419444 ) +colvars: ( -0.598793 , -0.174281 , -0.388979 ) +colvars: ( -0.548158 , -0.150883 , -0.327622 ) +colvars: ( -0.553361 , -0.203962 , -0.35626 ) +colvars: ( -0.543067 , -0.141684 , -0.318436 ) +colvars: ( -0.523804 , -0.301845 , -0.369602 ) +colvars: ( -0.485115 , -0.345117 , -0.34967 ) +colvars: ( -0.459165 , -0.459129 , -0.373757 ) +colvars: ( -0.41764 , -0.307967 , -0.265277 ) +colvars: ( -0.411152 , -0.281402 , -0.247028 ) +colvars: ( -0.366738 , -0.301994 , -0.211329 ) +colvars: ( -0.302367 , -0.263173 , -0.129328 ) +colvars: ( -0.252281 , -0.27895 , -0.085789 ) +colvars: ( -0.325318 , -0.153624 , -0.104184 ) +colvars: ( -0.290805 , -0.122899 , -0.055851 ) +colvars: ( -0.386519 , -0.0923014 , -0.138855 ) +colvars: ( -0.417212 , 0.0120587 , -0.123804 ) +colvars: ( -0.474647 , 0.063107 , -0.159207 ) +colvars: ( -0.455224 , 0.0278664 , -0.155157 ) +colvars: ( -0.442968 , 0.0879107 , -0.116339 ) +colvars: ( -0.500424 , -0.0293682 , -0.225948 ) +colvars: ( -0.534577 , -0.0310604 , -0.261123 ) +colvars: ( -0.586486 , -0.100256 , -0.343948 ) +colvars: ( -0.475616 , -0.0634342 , -0.215952 ) +colvars: ( -0.482053 , -0.0168402 , -0.201907 ) +colvars: ( -0.414917 , -0.142542 , -0.189625 ) +colvars: ( -0.350463 , -0.176261 , -0.139509 ) +colvars: ( -0.295062 , -0.272117 , -0.125905 ) +colvars: ( -0.307746 , -0.0991835 , -0.0624773 ) +colvars: ( -0.29179 , -0.0797481 , -0.0378264 ) +colvars: ( -0.289821 , -0.0513831 , -0.0233405 ) +colvars: ( -0.253724 , 0.0277934 , 0.0479436 ) +colvars: ( -0.234472 , 0.0560423 , 0.0798017 ) +colvars: ( -0.30185 , 0.119951 , 0.0400426 ) +colvars: ( -0.272784 , 0.163978 , 0.0887478 ) +colvars: ( -0.377458 , 0.150201 , -0.022846 ) +colvars: ( -0.430459 , 0.231176 , -0.0405895 ) +colvars: ( -0.508779 , 0.255645 , -0.10876 ) +colvars: ( -0.439331 , 0.209835 , -0.0589382 ) +colvars: ( -0.444112 , 0.274236 , -0.0353756 ) +colvars: ( -0.441093 , 0.117862 , -0.101249 ) +colvars: ( -0.44512 , 0.0855573 , -0.119545 ) +colvars: ( -0.465681 , -0.0134083 , -0.183889 ) +colvars: ( -0.371648 , 0.0730804 , -0.0509772 ) +colvars: ( -0.37356 , 0.100763 , -0.0407045 ) +colvars: ( -0.199704 , 0.107026 , 0.13732 ) +colvars: ( -0.145284 , 0.1086 , 0.192875 ) +colvars: ( -0.231857 , 0.184133 , 0.138889 ) +colvars: ( -0.304689 , 0.0296625 , -0.00261076 ) +colvars: ( -0.231413 , 0.0147291 , 0.0646776 ) +colvars: ( -0.172664 , -0.0735964 , 0.0849759 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 9. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 9. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 9, atoms_new_colvar_forces = { ( -4.58838939552603e+00 , -4.47025406485466e-01 , -1.30517458629373e+00 ), ( -3.95262953610289e+00 , -3.77790051392105e-01 , -1.02994016022491e+00 ), ( -4.02475028214488e+00 , -4.03698360924690e-01 , -1.06508371318764e+00 ), ( -5.41234607372141e+00 , -5.71680551513149e-01 , -1.57025556500880e+00 ), ( 2.51562216889713e-01 , 1.17178376118225e-01 , 3.41079617991009e-01 ), ( 4.95084225672090e+00 , 6.24014982972654e-01 , 1.86309528259453e+00 ), ( 4.18374962124968e+00 , 5.18828422240018e-01 , 1.61537684187741e+00 ), ( -4.23267784255257e-02 , 2.99357634345412e-02 , 3.47287849172900e-01 ), ( 4.16425737827149e+00 , 5.09223970527797e-01 , 1.58467017776851e+00 ), ( 5.51951081381373e+00 , 6.52404708008969e-01 , 1.96663701025769e+00 ), ( 1.14309374908305e-02 , 3.92715412937946e-02 , 2.92176818157258e-01 ), ( -1.97626284989816e-04 , 3.27958376982011e-02 , 2.67778399480675e-01 ), ( 2.02449020889785e-02 , 4.67913698494855e-02 , 3.31954452118544e-01 ), ( 4.23060999561829e-02 , 3.65859673557188e-02 , 1.94935003509608e-01 ), ( 1.47468199500804e-02 , 2.23158061441952e-02 , 1.45889702940907e-01 ), ( 1.10463574728554e-01 , 5.58050595088237e-02 , 1.85232110153984e-01 ), ( 1.55962471079082e-01 , 6.11542297307415e-02 , 1.17785392145717e-01 ), ( 2.34848803626830e-01 , 8.66919870393438e-02 , 1.33396818480500e-01 ), ( 1.28003003150382e-01 , 4.44785301151353e-02 , 5.01109143233972e-02 ), ( 1.23428526411529e-01 , 3.54999806743200e-02 , -1.19025851190753e-02 ), ( 1.05979465254891e-01 , 3.93297450713575e-02 , 6.18971412911153e-02 ), ( 7.12909988965698e-02 , 2.20867361726002e-02 , 6.02163646700365e-03 ), ( 5.90370670778059e-02 , 2.24464791202778e-02 , 3.88604569920168e-02 ), ( -6.94140731715032e-04 , -2.64987447240094e-03 , -1.99031728324598e-02 ), ( -1.40776635980440e-02 , -1.49224245825257e-02 , -8.72645246846075e-02 ), ( -4.76855873423211e-02 , -1.01696705013155e-02 , 3.34949842275970e-02 ), ( -1.14533806333947e-01 , -3.21254569734481e-02 , 1.76976299207021e-02 ), ( -1.55755579574356e-01 , -3.52375175545587e-02 , 9.29387757429661e-02 ), ( -1.02554119821961e-01 , -3.41317207071895e-02 , -2.78915169926651e-02 ), ( -1.38288549138629e-01 , -5.16790984770918e-02 , -8.36949556710445e-02 ), ( -5.03466708133782e-02 , -1.58324531341675e-02 , -6.16381064425375e-03 ), ( -3.00404839183512e-02 , -1.47570375988996e-02 , -4.69578936620170e-02 ), ( 2.52461364857733e-02 , 7.47911462853162e-03 , -6.58367711261681e-04 ), ( 1.36556717716091e-03 , -1.51524177235188e-02 , -1.26829611284271e-01 ), ( -1.62198623073919e-02 , -2.69606235091154e-02 , -1.80151290106232e-01 ), ( 4.77020405271442e-02 , -2.56536827973369e-03 , -1.37329588016078e-01 ), ( 7.66899354199569e-02 , -2.89865855484989e-03 , -2.10793530067861e-01 ), ( 1.37026533235403e-01 , 1.65313564537396e-02 , -1.99689795007217e-01 ), ( 1.90017538023108e-02 , -2.64967761920840e-02 , -2.62332266474575e-01 ), ( 2.00262856142383e-02 , -3.44925295012664e-02 , -3.30000554065977e-01 ), ( -3.32199011481871e-02 , -3.82714658780087e-02 , -2.30848003170492e-01 ), ( -9.34158282033889e-02 , -6.13231263029747e-02 , -2.71812571879274e-01 ), ( -1.30367333523874e-01 , -6.64471755188303e-02 , -2.23391713824821e-01 ), ( -1.50267012108277e-01 , -8.09932006274197e-02 , -2.93379324869338e-01 ), ( -1.77498740239768e-01 , -9.68003745367784e-02 , -3.55751166841283e-01 ), ( -1.92759980965373e-01 , -9.45420930354249e-02 , -3.00099074615717e-01 ), ( -2.34482915509898e-01 , -1.10312817777597e-01 , -3.26806772145153e-01 ), ( -1.19784494264076e-01 , -7.35223318744086e-02 , -3.06884751428479e-01 ), ( -1.70300196712858e-01 , -8.06326849680640e-02 , -2.41548251140115e-01 ), ( -2.23203680393268e-01 , -9.82358675590512e-02 , -2.55903918425207e-01 ), ( -2.58586970064436e-01 , -9.95028280023367e-02 , -1.79873980219490e-01 ) } +colvars: Step 9, atoms_new_colvar_forces = { ( -4.91392645926424e+00 , -4.78354531687070e-01 , -1.39619988059762e+00 ), ( -4.23305884780525e+00 , -4.04262063894514e-01 , -1.10167278383500e+00 ), ( -4.31028839697398e+00 , -4.32005112276300e-01 , -1.13930590856027e+00 ), ( -5.79632262732491e+00 , -6.11790903768499e-01 , -1.67985596207422e+00 ), ( 2.69382053999768e-01 , 1.25478466987595e-01 , 3.65240538808074e-01 ), ( 5.30205583008023e+00 , 6.67881948967973e-01 , 1.99364353829785e+00 ), ( 4.48055204292375e+00 , 5.55293047410926e-01 , 1.72858092947742e+00 ), ( -4.53242727510913e-02 , 3.20593150676229e-02 , 3.71888776093524e-01 ), ( 4.45967856098579e+00 , 5.45008042861195e-01 , 1.69569854356309e+00 ), ( 5.91107943140383e+00 , 6.98235090240089e-01 , 2.10431632234368e+00 ), ( 1.22403891305727e-02 , 4.20550206168737e-02 , 3.12872795008926e-01 ), ( -2.12391322996941e-04 , 3.51203463737099e-02 , 2.86745499073317e-01 ), ( 2.16776872887153e-02 , 5.01072337327672e-02 , 3.55466855085267e-01 ), ( 4.53021258186663e-02 , 3.91780386785694e-02 , 2.08742319671006e-01 ), ( 1.57904867750500e-02 , 2.38969326720686e-02 , 1.56222654966668e-01 ), ( 1.18287811551815e-01 , 5.97578523001544e-02 , 1.98352484870876e-01 ), ( 1.67009717114514e-01 , 6.54850482940890e-02 , 1.26128324451353e-01 ), ( 2.51484170048454e-01 , 9.28311309487453e-02 , 1.42845864193466e-01 ), ( 1.37070160525086e-01 , 4.76281665264511e-02 , 5.36606379111071e-02 ), ( 1.32171559729858e-01 , 3.80132223916730e-02 , -1.27456875581090e-02 ), ( 1.13487049449578e-01 , 4.21151863718765e-02 , 6.62822948290591e-02 ), ( 7.63418376715962e-02 , 2.36509551170928e-02 , 6.44934673773689e-03 ), ( 6.32203858685036e-02 , 2.40367443921425e-02 , 4.16148852737993e-02 ), ( -7.42614556335675e-04 , -2.83738966827861e-03 , -2.13121661541531e-02 ), ( -1.50740598991539e-02 , -1.59795212905273e-02 , -9.34449304075277e-02 ), ( -5.10630458821023e-02 , -1.08891564905611e-02 , 3.58680014850378e-02 ), ( -1.22646768338075e-01 , -3.43997144551907e-02 , 1.89512433421106e-02 ), ( -1.66788805970042e-01 , -3.77314303498387e-02 , 9.95216766404465e-02 ), ( -1.09818909430557e-01 , -3.65487013332218e-02 , -2.98676931507554e-02 ), ( -1.48084597629049e-01 , -5.53390393636705e-02 , -8.96239836590932e-02 ), ( -5.39136842169272e-02 , -1.69537682150749e-02 , -6.60130000650828e-03 ), ( -3.21694905209136e-02 , -1.58028299577319e-02 , -5.02854795889152e-02 ), ( 2.70329980947698e-02 , 8.00797613028162e-03 , -7.06751342333167e-04 ), ( 1.46150130702782e-03 , -1.62269426707087e-02 , -1.35814526781097e-01 ), ( -1.73697791017358e-02 , -2.88718298453524e-02 , -1.92913469723319e-01 ), ( 5.10806956956508e-02 , -2.74863623601343e-03 , -1.47057670884840e-01 ), ( 8.21222916884362e-02 , -3.10617064293883e-03 , -2.25724988678412e-01 ), ( 1.46733283375062e-01 , 1.76998043841258e-02 , -2.13834152603038e-01 ), ( 2.03480472695023e-02 , -2.83754617248093e-02 , -2.80914143807489e-01 ), ( 2.14451854438670e-02 , -3.69380339824519e-02 , -3.53375659821508e-01 ), ( -3.55725250144994e-02 , -4.09833596594847e-02 , -2.47199471705149e-01 ), ( -1.00032182737161e-01 , -6.56674034689093e-02 , -2.91065479520581e-01 ), ( -1.39600838208372e-01 , -7.11535661152981e-02 , -2.39214377766981e-01 ), ( -1.60910842962379e-01 , -8.67305353722443e-02 , -3.14160443699850e-01 ), ( -1.90071419859278e-01 , -1.03657481132018e-01 , -3.80950258633566e-01 ), ( -2.06415112665146e-01 , -1.01239344797800e-01 , -3.21357793188336e-01 ), ( -2.51093806299783e-01 , -1.18127062642584e-01 , -3.49957723265751e-01 ), ( -1.28270395442697e-01 , -7.87314622598084e-02 , -3.28624089938550e-01 ), ( -1.82363573694134e-01 , -8.63441521289618e-02 , -2.58658535128284e-01 ), ( -2.39014910464563e-01 , -1.05193984024581e-01 , -2.74031630992006e-01 ), ( -2.76904944904725e-01 , -1.06549981011579e-01 , -1.92616589050566e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 9, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3924,10 +6300,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 10, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 10, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 10, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 10, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 10, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 10, atoms_positions[size = 51] = { ( 8.34828490212455e+00 , 4.39894433023356e-02 , -7.64522375820389e-01 ), ( 6.99066540503349e+00 , -5.28601023906280e-01 , -6.34000486864719e-01 ), ( 6.22787719172293e+00 , -2.89831996815122e-01 , 6.83255367663832e-01 ), ( 4.98388392467191e+00 , -1.98391484362259e-01 , 6.87385272656312e-01 ), ( 7.04895001260948e+00 , -2.02841985382283e+00 , -9.85655084473563e-01 ), ( 6.90086556455800e+00 , -2.67711113006922e-01 , 1.84251244929543e+00 ), ( 6.18209256661512e+00 , -1.17740826747379e-01 , 3.13099931567514e+00 ), ( 7.12965186159977e+00 , -3.35676864764050e-01 , 4.28495453374987e+00 ), ( 5.29199820865372e+00 , 1.11284754163302e+00 , 3.31122615081410e+00 ), ( 4.11283309435019e+00 , 1.05263945814561e+00 , 3.63923997924621e+00 ), ( 5.87478417221971e+00 , 2.26610006058109e+00 , 2.99289064644132e+00 ), ( 5.21288515405497e+00 , 3.59483387029529e+00 , 2.89013831118651e+00 ), ( 6.33778100011006e+00 , 4.55392283929975e+00 , 2.44288214950251e+00 ), ( 3.90736158670035e+00 , 3.74001471462344e+00 , 2.02631562061012e+00 ), ( 2.86216126640952e+00 , 4.12496378479377e+00 , 2.53175509803549e+00 ), ( 3.85569108363366e+00 , 3.24025358116369e+00 , 7.54981812605449e-01 ), ( 2.67098973829651e+00 , 3.10946892730785e+00 , -1.03764678446356e-01 ), ( 3.03664326320571e+00 , 2.72080972454192e+00 , -1.58268844848001e+00 ), ( 1.57644296541130e+00 , 2.17200559816706e+00 , 5.58891174795041e-01 ), ( 4.39558011672441e-01 , 2.48637330476707e+00 , 5.39053206581799e-01 ), ( 1.97517386223124e+00 , 1.00560560902377e+00 , 1.06270749861102e+00 ), ( 1.17477948121920e+00 , 4.45000157290994e-02 , 1.69201394519546e+00 ), ( 2.01845353772129e+00 , -1.15675025686559e+00 , 2.01295487579453e+00 ), ( 5.39499967580355e-01 , 6.10790411480097e-01 , 2.95452398667484e+00 ), ( -6.59870110540155e-01 , 3.58333963239616e-01 , 3.17465537308870e+00 ), ( 1.31939556510853e+00 , 1.33329287373207e+00 , 3.83604298766876e+00 ), ( 8.56125141777084e-01 , 1.93161115115897e+00 , 5.04830601042540e+00 ), ( 2.03249704322438e+00 , 2.60800253069114e+00 , 5.62936319970994e+00 ), ( -3.56770742758726e-01 , 2.91751267018339e+00 , 4.97982558507318e+00 ), ( -1.16532359861227e+00 , 3.04247810993894e+00 , 5.90578872487953e+00 ), ( -4.49296030429180e-01 , 3.65408615124073e+00 , 3.84673383894858e+00 ), ( -1.48548772780184e+00 , 4.55855948345671e+00 , 3.53174132461905e+00 ), ( -7.36781504246551e-01 , 5.39463649316501e+00 , 2.42783688629379e+00 ), ( -2.75429472876099e+00 , 3.88495472413804e+00 , 2.92394328126824e+00 ), ( -3.84004154165180e+00 , 4.44895112862008e+00 , 2.83569853222850e+00 ), ( -2.59731427225162e+00 , 2.62297631579534e+00 , 2.46759561069813e+00 ), ( -3.72074920442391e+00 , 1.89762696393657e+00 , 2.04244110775780e+00 ), ( -3.41713011421728e+00 , 8.42923170279376e-01 , 9.51846315365505e-01 ), ( -4.29578789041755e+00 , 1.07269722121539e+00 , 3.24887402230753e+00 ), ( -5.53817683691649e+00 , 8.88664207121781e-01 , 3.33502724950635e+00 ), ( -3.43753460573195e+00 , 6.56258582345316e-01 , 4.13782656979711e+00 ), ( -3.77483687997640e+00 , 6.70731232223418e-02 , 5.47883543248952e+00 ), ( -2.38814976257285e+00 , -3.55030569804516e-01 , 6.15870945269310e+00 ), ( -4.47489688972547e+00 , 9.93170557498753e-01 , 6.42794280092462e+00 ), ( -5.32585979374457e+00 , 6.08358684041427e-01 , 7.19298823114831e+00 ), ( -6.27933301187145e+00 , 3.56261466069330e+00 , 6.70656970156401e+00 ), ( -6.91601696318481e+00 , 4.29489682897800e+00 , 7.42749128910578e+00 ), ( -6.74193048548450e+00 , 3.20748748801981e+00 , 5.52165326494754e+00 ), ( -4.10779169319408e+00 , 2.29943673434181e+00 , 6.47896963556771e+00 ), ( -4.87665888157469e+00 , 3.20893642721787e+00 , 7.21297894686708e+00 ), ( -4.09419104402405e+00 , 4.55261536958934e+00 , 7.28744062529414e+00 ) } +colvars: Step 10, atoms_positions[size = 51] = { ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 ), ( 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 ), ( 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 ), ( 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ), ( 7.04895826785284e+00 , -2.02841613924265e+00 , -9.85620442392675e-01 ), ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 ), ( 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 ), ( 7.12969433751879e+00 , -3.35680652336380e-01 , 4.28503772503019e+00 ), ( 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 ), ( 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ), ( 5.87483291148707e+00 , 2.26612775399137e+00 , 2.99291808497733e+00 ), ( 5.21288218233115e+00 , 3.59483636987744e+00 , 2.89017476261959e+00 ), ( 6.33778269382874e+00 , 4.55392840471158e+00 , 2.44292221389244e+00 ), ( 3.90736828557834e+00 , 3.74001732699088e+00 , 2.02634249627287e+00 ), ( 2.86216241234034e+00 , 4.12496626340601e+00 , 2.53177091658216e+00 ), ( 3.85570437251192e+00 , 3.24026057383498e+00 , 7.55004313381073e-01 ), ( 2.67101051130264e+00 , 3.10947735928082e+00 , -1.03748879769602e-01 ), ( 3.03667107279091e+00 , 2.72082034295573e+00 , -1.58267128144666e+00 ), ( 1.57645987327715e+00 , 2.17201170366100e+00 , 5.58898221912687e-01 ), ( 4.39572022444068e-01 , 2.48637696550970e+00 , 5.39052019817798e-01 ), ( 1.97518629797634e+00 , 1.00561062528445e+00 , 1.06271551157552e+00 ), ( 1.17478869838474e+00 , 4.45031176098170e-02 , 1.69201496031117e+00 ), ( 2.01846155214988e+00 , -1.15674706353646e+00 , 2.01296064067269e+00 ), ( 5.39500145364343e-01 , 6.10790093980941e-01 , 2.95452140096997e+00 ), ( -6.59871345662798e-01 , 3.58332426277972e-01 , 3.17464616891419e+00 ), ( 1.31939486528605e+00 , 1.33329077272868e+00 , 3.83604631037267e+00 ), ( 8.56110299823718e-01 , 1.93160690859167e+00 , 5.04830818361770e+00 ), ( 2.03247776335589e+00 , 2.60799796092075e+00 , 5.62937340995863e+00 ), ( -3.56784467007829e-01 , 2.91750779164715e+00 , 4.97982149780186e+00 ), ( -1.16533896424590e+00 , 3.04247270492991e+00 , 5.90578034932131e+00 ), ( -4.49302128018119e-01 , 3.65408419381410e+00 , 3.84673249600533e+00 ), ( -1.48549160764506e+00 , 4.55855770175891e+00 , 3.53173500540108e+00 ), ( -7.36778602155233e-01 , 5.39463728504328e+00 , 2.42783652284936e+00 ), ( -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 ), ( -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 ), ( -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 ), ( -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 ), ( -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 ), ( -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 ), ( -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 ), ( -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 ), ( -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 ), ( -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 ), ( -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 ), ( -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 ), ( -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 ), ( -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 ), ( -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 ), ( -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 ), ( -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 ), ( -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ) } colvars: Step 10, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 10, atom_groups_ids[size = 0] = @@ -3945,154 +6321,290 @@ colvars: Collective variables module, step no. 10 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.25149814022648e-01 , 4.52596031009924e-03 , 9.45651687527870e-01 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.24830306441272e-01 , 4.56308785799901e-03 , 9.45761307226337e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 7.04895826785284e+00 , -2.02841613924265e+00 , -9.85620442392675e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 , 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 7.12969433751879e+00 , -3.35680652336380e-01 , 4.28503772503019e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 , 5.87483291148707e+00 , 2.26612775399137e+00 , 2.99291808497733e+00 , 5.21288218233115e+00 , 3.59483636987744e+00 , 2.89017476261959e+00 , 6.33778269382874e+00 , 4.55392840471158e+00 , 2.44292221389244e+00 , 3.90736828557834e+00 , 3.74001732699088e+00 , 2.02634249627287e+00 , 2.86216241234034e+00 , 4.12496626340601e+00 , 2.53177091658216e+00 , 3.85570437251192e+00 , 3.24026057383498e+00 , 7.55004313381073e-01 , 2.67101051130264e+00 , 3.10947735928082e+00 , -1.03748879769602e-01 , 3.03667107279091e+00 , 2.72082034295573e+00 , -1.58267128144666e+00 , 1.57645987327715e+00 , 2.17201170366100e+00 , 5.58898221912687e-01 , 4.39572022444068e-01 , 2.48637696550970e+00 , 5.39052019817798e-01 , 1.97518629797634e+00 , 1.00561062528445e+00 , 1.06271551157552e+00 , 1.17478869838474e+00 , 4.45031176098170e-02 , 1.69201496031117e+00 , 2.01846155214988e+00 , -1.15674706353646e+00 , 2.01296064067269e+00 , 5.39500145364343e-01 , 6.10790093980941e-01 , 2.95452140096997e+00 , -6.59871345662798e-01 , 3.58332426277972e-01 , 3.17464616891419e+00 , 1.31939486528605e+00 , 1.33329077272868e+00 , 3.83604631037267e+00 , 8.56110299823718e-01 , 1.93160690859167e+00 , 5.04830818361770e+00 , 2.03247776335589e+00 , 2.60799796092075e+00 , 5.62937340995863e+00 , -3.56784467007829e-01 , 2.91750779164715e+00 , 4.97982149780186e+00 , -1.16533896424590e+00 , 3.04247270492991e+00 , 5.90578034932131e+00 , -4.49302128018119e-01 , 3.65408419381410e+00 , 3.84673249600533e+00 , -1.48549160764506e+00 , 4.55855770175891e+00 , 3.53173500540108e+00 , -7.36778602155233e-01 , 5.39463728504328e+00 , 2.42783652284936e+00 , -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 , -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 , -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 , -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 , -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 , -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 , -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 , -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 , -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 , -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 , -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 , -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 , -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 , -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 , -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 , -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 , -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 , -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.25149814022648e-01 , 4.52596031009924e-03 , 9.45651687527870e-01 ). +colvars: Colvar "one" has value ( -3.24830306441272e-01 , 4.56308785799901e-03 , 9.45761307226337e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 7.04895826785284e+00 , -2.02841613924265e+00 , -9.85620442392675e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 , 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 7.12969433751879e+00 , -3.35680652336380e-01 , 4.28503772503019e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 , 5.87483291148707e+00 , 2.26612775399137e+00 , 2.99291808497733e+00 , 5.21288218233115e+00 , 3.59483636987744e+00 , 2.89017476261959e+00 , 6.33778269382874e+00 , 4.55392840471158e+00 , 2.44292221389244e+00 , 3.90736828557834e+00 , 3.74001732699088e+00 , 2.02634249627287e+00 , 2.86216241234034e+00 , 4.12496626340601e+00 , 2.53177091658216e+00 , 3.85570437251192e+00 , 3.24026057383498e+00 , 7.55004313381073e-01 , 2.67101051130264e+00 , 3.10947735928082e+00 , -1.03748879769602e-01 , 3.03667107279091e+00 , 2.72082034295573e+00 , -1.58267128144666e+00 , 1.57645987327715e+00 , 2.17201170366100e+00 , 5.58898221912687e-01 , 4.39572022444068e-01 , 2.48637696550970e+00 , 5.39052019817798e-01 , 1.97518629797634e+00 , 1.00561062528445e+00 , 1.06271551157552e+00 , 1.17478869838474e+00 , 4.45031176098170e-02 , 1.69201496031117e+00 , 2.01846155214988e+00 , -1.15674706353646e+00 , 2.01296064067269e+00 , 5.39500145364343e-01 , 6.10790093980941e-01 , 2.95452140096997e+00 , -6.59871345662798e-01 , 3.58332426277972e-01 , 3.17464616891419e+00 , 1.31939486528605e+00 , 1.33329077272868e+00 , 3.83604631037267e+00 , 8.56110299823718e-01 , 1.93160690859167e+00 , 5.04830818361770e+00 , 2.03247776335589e+00 , 2.60799796092075e+00 , 5.62937340995863e+00 , -3.56784467007829e-01 , 2.91750779164715e+00 , 4.97982149780186e+00 , -1.16533896424590e+00 , 3.04247270492991e+00 , 5.90578034932131e+00 , -4.49302128018119e-01 , 3.65408419381410e+00 , 3.84673249600533e+00 , -1.48549160764506e+00 , 4.55855770175891e+00 , 3.53173500540108e+00 , -7.36778602155233e-01 , 5.39463728504328e+00 , 2.42783652284936e+00 , -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 , -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 , -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 , -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 , -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 , -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 , -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 , -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 , -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 , -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 , -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 , -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 , -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 , -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 , -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 , -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 , -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 , -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 26.021 , 1.86128 , -15.0094 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 67.0705 , 6.70705 , 13.4141 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 26.021 , 1.86128 , -15.0094 ) to colvar "one". -colvars: Adding total bias energy: 45.292 +colvars: Adding biasing force ( 67.0705 , 6.70705 , 13.4141 ) to colvar "one". +colvars: Adding total bias energy: 58.0141 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 26.021 , 1.86128 , -15.0094 ) +colvars: Force to be applied: ( 67.0705 , 6.70705 , 13.4141 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.87042 , -0.557571 , -1.5436 ) -colvars: ( -4.17638 , -0.478117 , -1.32364 ) -colvars: ( -4.17638 , -0.478117 , -1.32364 ) -colvars: ( -5.56306 , -0.636865 , -1.76313 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.20295 , -0.595163 , -1.64708 ) +colvars: ( -4.46153 , -0.510352 , -1.41237 ) +colvars: ( -4.46153 , -0.510352 , -1.41237 ) +colvars: ( -5.94288 , -0.679804 , -1.88132 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.899454 , 0.19403 , 0.638783 ) -colvars: ( 0.77794 , 0.265616 , 0.664028 ) -colvars: ( 0.763022 , 0.258252 , 0.645148 ) -colvars: ( 0.663621 , 0.267325 , 0.598464 ) -colvars: ( 0.651555 , 0.200731 , 0.500683 ) -colvars: ( 0.575107 , 0.345435 , 0.652183 ) -colvars: ( 0.46538 , 0.360411 , 0.607398 ) -colvars: ( 0.386955 , 0.458454 , 0.694233 ) -colvars: ( 0.382938 , 0.316093 , 0.498135 ) -colvars: ( 0.3471 , 0.274869 , 0.420757 ) -colvars: ( 0.35423 , 0.321135 , 0.487947 ) -colvars: ( 0.282525 , 0.278396 , 0.387209 ) -colvars: ( 0.256124 , 0.307164 , 0.410675 ) -colvars: ( 0.346331 , 0.179938 , 0.291127 ) -colvars: ( 0.286632 , 0.136937 , 0.197162 ) -colvars: ( 0.471428 , 0.141981 , 0.313769 ) -colvars: ( 0.545451 , 0.0499312 , 0.232476 ) -colvars: ( 0.677724 , 0.0279046 , 0.281056 ) -colvars: ( 0.553082 , 0.0184449 , 0.194164 ) -colvars: ( 0.537081 , -0.0466146 , 0.0961337 ) -colvars: ( 0.57334 , 0.0667081 , 0.271866 ) -colvars: ( 0.570659 , 0.0509882 , 0.248884 ) -colvars: ( 0.606919 , 0.115944 , 0.358803 ) -colvars: ( 0.443841 , 0.0563863 , 0.180916 ) -colvars: ( 0.436516 , 0.000578149 , 0.100627 ) -colvars: ( 0.340309 , 0.122685 , 0.209646 ) -colvars: ( 0.213482 , 0.132128 , 0.147176 ) -colvars: ( 0.120648 , 0.218483 , 0.209551 ) -colvars: ( 0.185534 , 0.058163 , 0.0299343 ) -colvars: ( 0.135015 , 0.0224134 , -0.0487122 ) -colvars: ( 0.220834 , 0.0319022 , 0.0151648 ) -colvars: ( 0.207368 , -0.04093 , -0.0919361 ) -colvars: ( 0.244498 , -0.0449898 , -0.0754104 ) -colvars: ( 0.283624 , -0.127352 , -0.164246 ) -colvars: ( 0.238953 , -0.1803 , -0.262821 ) -colvars: ( 0.400423 , -0.142958 , -0.116118 ) -colvars: ( 0.47882 , -0.218878 , -0.172867 ) -colvars: ( 0.612106 , -0.222221 , -0.0982612 ) -colvars: ( 0.429603 , -0.222634 , -0.207206 ) -colvars: ( 0.435093 , -0.290774 , -0.296664 ) -colvars: ( 0.37919 , -0.148593 , -0.136395 ) -colvars: ( 0.322948 , -0.141566 , -0.160234 ) -colvars: ( 0.305312 , -0.054324 , -0.0519959 ) -colvars: ( 0.197664 , -0.149658 , -0.245647 ) -colvars: ( 0.172308 , -0.191359 , -0.317448 ) -colvars: ( -0.0052684 , -0.194948 , -0.427787 ) -colvars: ( -0.09768 , -0.212243 , -0.506201 ) -colvars: ( 0.0975032 , -0.245834 , -0.435996 ) -colvars: ( 0.11516 , -0.10877 , -0.239006 ) -colvars: ( -0.00600621 , -0.112495 , -0.316031 ) -colvars: ( -0.0961462 , -0.0313186 , -0.259104 ) +colvars: ( 0.960645 , 0.20727 , 0.681975 ) +colvars: ( 0.830884 , 0.283707 , 0.70894 ) +colvars: ( 0.814942 , 0.275855 , 0.688794 ) +colvars: ( 0.708811 , 0.285512 , 0.638933 ) +colvars: ( 0.695925 , 0.214392 , 0.534525 ) +colvars: ( 0.614294 , 0.368914 , 0.696296 ) +colvars: ( 0.497125 , 0.384887 , 0.648476 ) +colvars: ( 0.413383 , 0.48958 , 0.7412 ) +colvars: ( 0.409082 , 0.337554 , 0.531817 ) +colvars: ( 0.370815 , 0.293518 , 0.44919 ) +colvars: ( 0.378416 , 0.342947 , 0.52095 ) +colvars: ( 0.301837 , 0.297301 , 0.413393 ) +colvars: ( 0.273635 , 0.328033 , 0.438462 ) +colvars: ( 0.369971 , 0.192162 , 0.310795 ) +colvars: ( 0.306219 , 0.146232 , 0.210464 ) +colvars: ( 0.503556 , 0.151643 , 0.334966 ) +colvars: ( 0.5826 , 0.0533491 , 0.248158 ) +colvars: ( 0.723846 , 0.029847 , 0.300027 ) +colvars: ( 0.590758 , 0.0197121 , 0.207238 ) +colvars: ( 0.57367 , -0.0497709 , 0.102563 ) +colvars: ( 0.6124 , 0.0712476 , 0.290198 ) +colvars: ( 0.609547 , 0.0544469 , 0.265647 ) +colvars: ( 0.648277 , 0.123812 , 0.383008 ) +colvars: ( 0.474125 , 0.0601924 , 0.193077 ) +colvars: ( 0.466305 , 0.000586045 , 0.107342 ) +colvars: ( 0.363565 , 0.130986 , 0.223763 ) +colvars: ( 0.228131 , 0.141053 , 0.157065 ) +colvars: ( 0.128996 , 0.233268 , 0.223677 ) +colvars: ( 0.198279 , 0.0620654 , 0.0318832 ) +colvars: ( 0.144334 , 0.0238752 , -0.0520959 ) +colvars: ( 0.235965 , 0.0340363 , 0.0161204 ) +colvars: ( 0.221577 , -0.0437392 , -0.0982334 ) +colvars: ( 0.261215 , -0.0480571 , -0.0805785 ) +colvars: ( 0.30301 , -0.136029 , -0.175454 ) +colvars: ( 0.255306 , -0.19258 , -0.280708 ) +colvars: ( 0.427739 , -0.152684 , -0.124074 ) +colvars: ( 0.51146 , -0.233759 , -0.184679 ) +colvars: ( 0.653794 , -0.237313 , -0.105025 ) +colvars: ( 0.458912 , -0.237788 , -0.221353 ) +colvars: ( 0.464775 , -0.310559 , -0.316877 ) +colvars: ( 0.405086 , -0.158729 , -0.145745 ) +colvars: ( 0.345036 , -0.151244 , -0.171207 ) +colvars: ( 0.326212 , -0.0580833 , -0.0556372 ) +colvars: ( 0.211248 , -0.159901 , -0.262401 ) +colvars: ( 0.184175 , -0.204445 , -0.339074 ) +colvars: ( -0.00547473 , -0.208274 , -0.45686 ) +colvars: ( -0.10416 , -0.226756 , -0.540583 ) +colvars: ( 0.104265 , -0.262599 , -0.465626 ) +colvars: ( 0.123138 , -0.116236 , -0.255298 ) +colvars: ( -0.00625371 , -0.120228 , -0.337536 ) +colvars: ( -0.102514 , -0.0335414 , -0.27674 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.87042 , 0.557571 , 1.5436 ) -colvars: ( 4.17638 , 0.478117 , 1.32364 ) -colvars: ( 4.17638 , 0.478117 , 1.32364 ) -colvars: ( 5.56306 , 0.636865 , 1.76313 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.20295 , 0.595163 , 1.64708 ) +colvars: ( 4.46153 , 0.510352 , 1.41237 ) +colvars: ( 4.46153 , 0.510352 , 1.41237 ) +colvars: ( 5.94288 , 0.679804 , 1.88132 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.622591 , -0.0804752 , -0.389597 ) -colvars: ( -0.558639 , -0.162727 , -0.360972 ) -colvars: ( -0.511171 , -0.140891 , -0.303633 ) -colvars: ( -0.51653 , -0.190403 , -0.330592 ) -colvars: ( -0.506921 , -0.132233 , -0.295581 ) -colvars: ( -0.489206 , -0.281787 , -0.342849 ) -colvars: ( -0.453406 , -0.322155 , -0.324354 ) -colvars: ( -0.429422 , -0.428608 , -0.346538 ) -colvars: ( -0.390449 , -0.287442 , -0.245802 ) -colvars: ( -0.384527 , -0.262612 , -0.229023 ) -colvars: ( -0.342796 , -0.281873 , -0.19536 ) -colvars: ( -0.282702 , -0.245603 , -0.119014 ) -colvars: ( -0.235805 , -0.260349 , -0.0781804 ) -colvars: ( -0.30394 , -0.143311 , -0.0958746 ) -colvars: ( -0.271821 , -0.114595 , -0.051007 ) -colvars: ( -0.360801 , -0.0860808 , -0.12825 ) -colvars: ( -0.38926 , 0.0113623 , -0.114498 ) -colvars: ( -0.442551 , 0.0589901 , -0.147458 ) -colvars: ( -0.42491 , 0.0261421 , -0.143984 ) -colvars: ( -0.413477 , 0.0822271 , -0.108044 ) -colvars: ( -0.467252 , -0.0273039 , -0.209921 ) -colvars: ( -0.499328 , -0.0288647 , -0.242922 ) -colvars: ( -0.547894 , -0.0934882 , -0.319996 ) -colvars: ( -0.444578 , -0.0590547 , -0.200899 ) -colvars: ( -0.450654 , -0.0155278 , -0.188069 ) -colvars: ( -0.388087 , -0.13291 , -0.176135 ) -colvars: ( -0.328179 , -0.164359 , -0.129464 ) -colvars: ( -0.276612 , -0.253861 , -0.116474 ) -colvars: ( -0.288205 , -0.0923737 , -0.0578402 ) -colvars: ( -0.273463 , -0.0741982 , -0.0350726 ) -colvars: ( -0.271206 , -0.0477593 , -0.0212858 ) -colvars: ( -0.237377 , 0.0261811 , 0.0449965 ) -colvars: ( -0.219124 , 0.0525326 , 0.0748622 ) -colvars: ( -0.282193 , 0.112235 , 0.0373077 ) -colvars: ( -0.255115 , 0.153369 , 0.0825029 ) -colvars: ( -0.35262 , 0.140457 , -0.0213685 ) -colvars: ( -0.402003 , 0.216067 , -0.0382063 ) -colvars: ( -0.474899 , 0.23888 , -0.101725 ) -colvars: ( -0.410567 , 0.196169 , -0.0554991 ) -colvars: ( -0.415027 , 0.256319 , -0.0338025 ) -colvars: ( -0.412465 , 0.110298 , -0.0948017 ) -colvars: ( -0.416514 , 0.0801623 , -0.112004 ) -colvars: ( -0.435906 , -0.0122501 , -0.171781 ) -colvars: ( -0.348132 , 0.0685475 , -0.048157 ) -colvars: ( -0.350046 , 0.0944194 , -0.0388206 ) -colvars: ( -0.187668 , 0.100287 , 0.127352 ) -colvars: ( -0.137015 , 0.101786 , 0.179044 ) -colvars: ( -0.217362 , 0.172259 , 0.128769 ) -colvars: ( -0.285663 , 0.0280107 , -0.00286133 ) -colvars: ( -0.217445 , 0.014099 , 0.0598197 ) -colvars: ( -0.162722 , -0.0683725 , 0.0790507 ) +colvars: ( -0.664913 , -0.0859778 , -0.415805 ) +colvars: ( -0.596637 , -0.173807 , -0.38523 ) +colvars: ( -0.545927 , -0.150496 , -0.324005 ) +colvars: ( -0.551694 , -0.203347 , -0.352805 ) +colvars: ( -0.541432 , -0.141225 , -0.315444 ) +colvars: ( -0.522538 , -0.300927 , -0.365881 ) +colvars: ( -0.484335 , -0.344022 , -0.346143 ) +colvars: ( -0.458742 , -0.457696 , -0.36981 ) +colvars: ( -0.417104 , -0.306948 , -0.262287 ) +colvars: ( -0.410792 , -0.280424 , -0.24439 ) +colvars: ( -0.366203 , -0.301006 , -0.208424 ) +colvars: ( -0.302027 , -0.262272 , -0.126923 ) +colvars: ( -0.251932 , -0.278026 , -0.0833115 ) +colvars: ( -0.324691 , -0.153039 , -0.102238 ) +colvars: ( -0.290399 , -0.122366 , -0.0543501 ) +colvars: ( -0.38539 , -0.091934 , -0.136805 ) +colvars: ( -0.415766 , 0.01212 , -0.122141 ) +colvars: ( -0.472648 , 0.0629672 , -0.157325 ) +colvars: ( -0.453851 , 0.027912 , -0.153639 ) +colvars: ( -0.441643 , 0.0878083 , -0.115285 ) +colvars: ( -0.499083 , -0.0291587 , -0.224031 ) +colvars: ( -0.533355 , -0.0308162 , -0.259278 ) +colvars: ( -0.585228 , -0.0998259 , -0.341555 ) +colvars: ( -0.474911 , -0.0630423 , -0.21442 ) +colvars: ( -0.481406 , -0.0165546 , -0.200741 ) +colvars: ( -0.414598 , -0.141907 , -0.187968 ) +colvars: ( -0.350645 , -0.175478 , -0.138145 ) +colvars: ( -0.295589 , -0.271054 , -0.124258 ) +colvars: ( -0.307947 , -0.0986065 , -0.0616914 ) +colvars: ( -0.292218 , -0.0791881 , -0.0373993 ) +colvars: ( -0.28977 , -0.0509737 , -0.0226596 ) +colvars: ( -0.253632 , 0.0279845 , 0.0480933 ) +colvars: ( -0.234115 , 0.0561127 , 0.0799906 ) +colvars: ( -0.301483 , 0.11988 , 0.0398636 ) +colvars: ( -0.272571 , 0.163811 , 0.0881004 ) +colvars: ( -0.37668 , 0.15001 , -0.0227826 ) +colvars: ( -0.429409 , 0.230753 , -0.0407782 ) +colvars: ( -0.507236 , 0.255104 , -0.108588 ) +colvars: ( -0.438579 , 0.209517 , -0.0592538 ) +colvars: ( -0.443341 , 0.273754 , -0.0361082 ) +colvars: ( -0.440628 , 0.117823 , -0.101205 ) +colvars: ( -0.444978 , 0.0856549 , -0.119581 ) +colvars: ( -0.465704 , -0.013027 , -0.183388 ) +colvars: ( -0.37197 , 0.0732619 , -0.0514237 ) +colvars: ( -0.374025 , 0.100898 , -0.0414726 ) +colvars: ( -0.200611 , 0.107163 , 0.13595 ) +colvars: ( -0.146531 , 0.108771 , 0.19113 ) +colvars: ( -0.232294 , 0.184008 , 0.137461 ) +colvars: ( -0.30526 , 0.0299734 , -0.00305187 ) +colvars: ( -0.232426 , 0.0151267 , 0.0638633 ) +colvars: ( -0.173996 , -0.0729419 , 0.0844146 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 10. colvars: colvarmodule::write_traj_files() @@ -4103,8 +6615,11 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 10. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 10, atoms_new_colvar_forces = { ( -4.59355517748052e+00 , -4.44015582373764e-01 , -1.29441814405527e+00 ), ( -3.95708173849547e+00 , -3.75228180486825e-01 , -1.02058421403536e+00 ), ( -4.02929122398260e+00 , -4.01194296213209e-01 , -1.05576841054788e+00 ), ( -5.41842798778098e+00 , -5.68367125599078e-01 , -1.55802487116354e+00 ), ( 2.51851372887664e-01 , 1.17361051476457e-01 , 3.41515291608866e-01 ), ( 4.95632002040441e+00 , 6.21218647463185e-01 , 1.85293826133283e+00 ), ( 4.18835600817839e+00 , 5.16372339342320e-01 , 1.60668415040966e+00 ), ( -4.24666245193869e-02 , 2.98460525351839e-02 , 3.47694943353193e-01 ), ( 4.16887175490274e+00 , 5.06767494651288e-01 , 1.57597385144500e+00 ), ( 5.52563560582053e+00 , 6.49121921402458e-01 , 1.95486160530762e+00 ), ( 1.14338044971929e-02 , 3.92627685380244e-02 , 2.92587354077863e-01 ), ( -1.76353895908199e-04 , 3.27931934186928e-02 , 2.68194224423467e-01 ), ( 2.03196459775179e-02 , 4.68153052057464e-02 , 3.32494641046370e-01 ), ( 4.23914640979515e-02 , 3.66268781596063e-02 , 1.95252610481756e-01 ), ( 1.48112287820190e-02 , 2.23420181197107e-02 , 1.46155393268324e-01 ), ( 1.10627414805206e-01 , 5.59001320634085e-02 , 1.85519171104405e-01 ), ( 1.56190520271940e-01 , 6.12934875812506e-02 , 1.17977390525700e-01 ), ( 2.35172116741031e-01 , 8.68947006454514e-02 , 1.33597866154505e-01 ), ( 1.28172272983708e-01 , 4.45869353089523e-02 , 5.01792661929765e-02 ), ( 1.23603441351940e-01 , 3.56124503587407e-02 , -1.19104122689279e-02 ), ( 1.06087434773844e-01 , 3.94042136454398e-02 , 6.19449742594518e-02 ), ( 7.13301364336489e-02 , 2.21234866110346e-02 , 5.96187343917060e-03 ), ( 5.90249315729242e-02 , 2.24554982023740e-02 , 3.88070281089110e-02 ), ( -7.37185733114432e-04 , -2.66838208090871e-03 , -1.99825276030163e-02 ), ( -1.41388668208941e-02 , -1.49496680985678e-02 , -8.74420666668334e-02 ), ( -4.77776168715920e-02 , -1.02253422823412e-02 , 3.35108529817474e-02 ), ( -1.14697783246846e-01 , -3.22308661056235e-02 , 1.77125899747320e-02 ), ( -1.55964318524189e-01 , -3.53776095124567e-02 , 9.30764924170915e-02 ), ( -1.02670899719694e-01 , -3.42107177704016e-02 , -2.79058955250904e-02 ), ( -1.38448839720594e-01 , -5.17848001772567e-02 , -8.37848463015384e-02 ), ( -5.03714226955432e-02 , -1.58570314938234e-02 , -6.12093541209686e-03 ), ( -3.00086115625056e-02 , -1.47489284659867e-02 , -4.69395684412112e-02 ), ( 2.53731877118849e-02 , 7.54278441208116e-03 , -5.48209286519691e-04 ), ( 1.43069654691069e-03 , -1.51172445636054e-02 , -1.26938667375671e-01 ), ( -1.61620144077224e-02 , -2.69311168224513e-02 , -1.80318274271151e-01 ), ( 4.78025904146258e-02 , -2.50120185002350e-03 , -1.37486543738285e-01 ), ( 7.68165274518192e-02 , -2.81160123981145e-03 , -2.11073250310744e-01 ), ( 1.37207528057790e-01 , 1.66587451843357e-02 , -1.99985892888856e-01 ), ( 1.90354178595755e-02 , -2.64646968483361e-02 , -2.62704873731052e-01 ), ( 2.00660700555651e-02 , -3.44543827886409e-02 , -3.30466067975266e-01 ), ( -3.32751058238674e-02 , -3.82948005392128e-02 , -2.31196550790619e-01 ), ( -9.35665127547106e-02 , -6.14037431164247e-02 , -2.72237598425034e-01 ), ( -1.30594036332267e-01 , -6.65740465220482e-02 , -2.23777346184272e-01 ), ( -1.50467976632238e-01 , -8.11108803068862e-02 , -2.93803922833369e-01 ), ( -1.77738387046901e-01 , -9.69399751611738e-02 , -3.56268826708945e-01 ), ( -1.92936389879557e-01 , -9.46601609724783e-02 , -3.00435337930446e-01 ), ( -2.34694823424672e-01 , -1.10456969420736e-01 , -3.27156893105670e-01 ), ( -1.19859255162479e-01 , -7.35747042567381e-02 , -3.07227390840892e-01 ), ( -1.70502911342417e-01 , -8.07589792449124e-02 , -2.41867029203612e-01 ), ( -2.23451131897684e-01 , -9.83959930751030e-02 , -2.56211521024765e-01 ), ( -2.58867996826473e-01 , -9.96910769369178e-02 , -1.80053743267714e-01 ) } +colvars: Step 10, atoms_new_colvar_forces = { ( -4.90721521818644e+00 , -4.73870786712652e-01 , -1.38091477818025e+00 ), ( -4.22727947915419e+00 , -4.00452243715495e-01 , -1.08866450508672e+00 ), ( -4.30440996742968e+00 , -4.28187255104780e-01 , -1.12624661622607e+00 ), ( -5.78839020894122e+00 , -6.06637961847330e-01 , -1.66224301649813e+00 ), ( 2.69014751613858e-01 , 1.25358618238813e-01 , 3.64789105177912e-01 ), ( 5.29470412581475e+00 , 6.63150876426976e-01 , 1.97749961084672e+00 ), ( 4.47431659059565e+00 , 5.51217931478780e-01 , 1.71470785458333e+00 ), ( -4.53596158039452e-02 , 3.18840627601026e-02 , 3.71390215390095e-01 ), ( 4.45350387722105e+00 , 5.40958244259191e-01 , 1.68190394486273e+00 ), ( 5.90290505873046e+00 , 6.92898590570129e-01 , 2.08612444512667e+00 ), ( 1.22126331866665e-02 , 4.19406780340398e-02 , 3.12525703172802e-01 ), ( -1.89394613707761e-04 , 3.50298648912931e-02 , 2.86469456014899e-01 ), ( 2.17026752784405e-02 , 5.00075282522233e-02 , 3.55150927912739e-01 ), ( 4.52793272988443e-02 , 3.91235906882275e-02 , 2.08557220462046e-01 ), ( 1.58193300286871e-02 , 2.38650932441996e-02 , 1.56113879996155e-01 ), ( 1.18165693090680e-01 , 5.97093876394846e-02 , 1.98160954730796e-01 ), ( 1.66833895016226e-01 , 6.54691100847247e-02 , 1.26016621253944e-01 ), ( 2.51198093154190e-01 , 9.28141306260056e-02 , 1.42701941432096e-01 ), ( 1.36906860890021e-01 , 4.76240982493063e-02 , 5.35989609398464e-02 ), ( 1.32026557753796e-01 , 3.80374903598184e-02 , -1.27220490949054e-02 ), ( 1.13317635725557e-01 , 4.20888774190430e-02 , 6.61671896305862e-02 ), ( 7.61922963739712e-02 , 2.36307558005545e-02 , 6.36968734366083e-03 ), ( 6.30491839407602e-02 , 2.39861444751687e-02 , 4.14538911418829e-02 ), ( -7.86494290214823e-04 , -2.84997613756573e-03 , -2.13431538111226e-02 ), ( -1.51013213602507e-02 , -1.59685447206908e-02 , -9.33996609892180e-02 ), ( -5.10330310243135e-02 , -1.09209992052759e-02 , 3.57950318514191e-02 ), ( -1.22513991104271e-01 , -3.44255258188375e-02 , 1.89196500716248e-02 ), ( -1.66593126748012e-01 , -3.77856611671253e-02 , 9.94187969247893e-02 ), ( -1.09668061787916e-01 , -3.65411120110773e-02 , -2.98082150050602e-02 ), ( -1.47884159951637e-01 , -5.53128169067022e-02 , -8.94951448539763e-02 ), ( -5.38050059720047e-02 , -1.69374144538034e-02 , -6.53920598676141e-03 ), ( -3.20550484318294e-02 , -1.57546688528021e-02 , -5.01400797346093e-02 ), ( 2.71003511424442e-02 , 8.05558174944536e-03 , -5.87867940786607e-04 ), ( 1.52713215699579e-03 , -1.61490539427529e-02 , -1.35590342281533e-01 ), ( -1.72647112458419e-02 , -2.87683438518996e-02 , -1.92607880448279e-01 ), ( 5.10597482439506e-02 , -2.67372040503736e-03 , -1.46856235504666e-01 ), ( 8.20513443320531e-02 , -3.00612150775692e-03 , -2.25457045193199e-01 ), ( 1.46558386589924e-01 , 1.77905963189787e-02 , -2.13613377753834e-01 ), ( 2.03330229305949e-02 , -2.82705894952819e-02 , -2.80606754848932e-01 ), ( 2.14339555948247e-02 , -3.68053410607088e-02 , -3.52985572218408e-01 ), ( -3.55420123674877e-02 , -4.09057515777496e-02 , -2.46950953915162e-01 ), ( -9.99417416209531e-02 , -6.55888745871515e-02 , -2.90788430582709e-01 ), ( -1.39492151096945e-01 , -7.11103908817001e-02 , -2.39025312091656e-01 ), ( -1.60721409442294e-01 , -8.66386440202250e-02 , -3.13825121559050e-01 ), ( -1.89850057174861e-01 , -1.03546550046362e-01 , -3.80546615670789e-01 ), ( -2.06085649306466e-01 , -1.01111515874264e-01 , -3.20910555605155e-01 ), ( -2.50690197418701e-01 , -1.17984671586598e-01 , -3.49453608696638e-01 ), ( -1.28028542025109e-01 , -7.85902187842150e-02 , -3.28165409791750e-01 ), ( -1.82122317573020e-01 , -8.62623196497184e-02 , -2.58349718696580e-01 ), ( -2.38679358248130e-01 , -1.05100891525063e-01 , -2.73672453172879e-01 ), ( -2.76510254384952e-01 , -1.06483286115883e-01 , -1.92325407427920e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 10, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4142,10 +6657,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 11, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 11, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 11, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 11, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 11, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 11, atoms_positions[size = 51] = { ( 8.34052672881583e+00 , 4.38508509545042e-02 , -7.65407392242128e-01 ), ( 6.99003358745559e+00 , -5.33517344223640e-01 , -6.30171873135856e-01 ), ( 6.21625615191044e+00 , -2.97922534055335e-01 , 6.86781779786704e-01 ), ( 4.98240576208412e+00 , -1.95583496296942e-01 , 6.91891998399505e-01 ), ( 7.05065161917571e+00 , -2.03049166569140e+00 , -9.79402107372247e-01 ), ( 6.89978919361934e+00 , -2.66941748921589e-01 , 1.84877477574450e+00 ), ( 6.18361273865802e+00 , -1.18834935336737e-01 , 3.14564946586988e+00 ), ( 7.12018607770449e+00 , -3.39133444194479e-01 , 4.28342409989501e+00 ), ( 5.28972774565670e+00 , 1.11251939790860e+00 , 3.31579332456398e+00 ), ( 4.11946856705428e+00 , 1.04955885047178e+00 , 3.64314414480319e+00 ), ( 5.87314062584667e+00 , 2.25939982092709e+00 , 2.99529215588447e+00 ), ( 5.21461221236525e+00 , 3.59406567754698e+00 , 2.89327208680642e+00 ), ( 6.33647971926123e+00 , 4.54438634602907e+00 , 2.43799153373710e+00 ), ( 3.90893018123439e+00 , 3.74053771608229e+00 , 2.02863443162684e+00 ), ( 2.85178143029123e+00 , 4.12837607322095e+00 , 2.52782271173447e+00 ), ( 3.86479385176451e+00 , 3.24028536473171e+00 , 7.50603483927780e-01 ), ( 2.66852534664435e+00 , 3.09505731900435e+00 , -1.05589370912802e-01 ), ( 3.03476771861854e+00 , 2.72158829630843e+00 , -1.57501570121844e+00 ), ( 1.57256907379180e+00 , 2.17883113470269e+00 , 5.48121120390495e-01 ), ( 4.37157985028312e-01 , 2.49496004378577e+00 , 5.36166029002277e-01 ), ( 1.97955365004857e+00 , 1.00342201375213e+00 , 1.06672437926646e+00 ), ( 1.17836136809065e+00 , 5.47447152221373e-02 , 1.69222191033390e+00 ), ( 2.02012954087636e+00 , -1.15072095948188e+00 , 2.01095221725133e+00 ), ( 5.43445055480431e-01 , 6.10623986654365e-01 , 2.94620431664111e+00 ), ( -6.55515370594273e-01 , 3.55968869687285e-01 , 3.17312349336380e+00 ), ( 1.32230512468366e+00 , 1.33662322216111e+00 , 3.83594085279798e+00 ), ( 8.58510581431592e-01 , 1.93756947490075e+00 , 5.04354275866483e+00 ), ( 2.03022561426183e+00 , 2.61320004550326e+00 , 5.63213006966011e+00 ), ( -3.54477007570914e-01 , 2.91715217679086e+00 , 4.97804937059007e+00 ), ( -1.16315933060431e+00 , 3.04537524561224e+00 , 5.90528903163306e+00 ), ( -4.56990337670391e-01 , 3.64256325723145e+00 , 3.84588691845218e+00 ), ( -1.48864258329021e+00 , 4.55496162424248e+00 , 3.52701983361952e+00 ), ( -7.32001928779663e-01 , 5.39670861979645e+00 , 2.43240618541534e+00 ), ( -2.76043849975506e+00 , 3.88196022461464e+00 , 2.92174554398755e+00 ), ( -3.83655630145068e+00 , 4.45487516920878e+00 , 2.83261139928302e+00 ), ( -2.59983145788163e+00 , 2.62960630289858e+00 , 2.46177627650691e+00 ), ( -3.72484225979729e+00 , 1.88842135467647e+00 , 2.03572771512213e+00 ), ( -3.41676046733324e+00 , 8.50656873830850e-01 , 9.42962055798462e-01 ), ( -4.29738453201457e+00 , 1.06924562870131e+00 , 3.24990257230490e+00 ), ( -5.53575216260335e+00 , 8.81857604131008e-01 , 3.33327200415026e+00 ), ( -3.42984743988176e+00 , 6.60811055660684e-01 , 4.13981911095222e+00 ), ( -3.77004771139532e+00 , 5.91521031988681e-02 , 5.47473677954351e+00 ), ( -2.38546708128188e+00 , -3.45304623138144e-01 , 6.16234065583497e+00 ), ( -4.47510333484871e+00 , 9.94714080794383e-01 , 6.43118179611945e+00 ), ( -5.32795009589764e+00 , 6.08792548504162e-01 , 7.19555040150092e+00 ), ( -6.27187030467191e+00 , 3.56559208374733e+00 , 6.70761174381335e+00 ), ( -6.91919188498955e+00 , 4.29475861302874e+00 , 7.43152309603963e+00 ), ( -6.74323318420630e+00 , 3.20659487665074e+00 , 5.52277473089573e+00 ), ( -4.11286614873520e+00 , 2.29554357073650e+00 , 6.47524521982787e+00 ), ( -4.86768391437572e+00 , 3.20344925316398e+00 , 7.21352022461795e+00 ), ( -4.09711095439933e+00 , 4.56217863115927e+00 , 7.29072155849984e+00 ) } +colvars: Step 11, atoms_positions[size = 51] = { ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 ), ( 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 ), ( 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 ), ( 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 ), ( 7.05065634311566e+00 , -2.03049004075621e+00 , -9.79362510556569e-01 ), ( 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 ), ( 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 ), ( 7.12024786069621e+00 , -3.39139905946113e-01 , 4.28353219426788e+00 ), ( 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 ), ( 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 ), ( 5.87320938131017e+00 , 2.25943775728641e+00 , 2.99532323655327e+00 ), ( 5.21460824073739e+00 , 3.59406844683129e+00 , 2.89331623199200e+00 ), ( 6.33648153033934e+00 , 4.54439309911936e+00 , 2.43803927314067e+00 ), ( 3.90893824316231e+00 , 3.74054027462900e+00 , 2.02866662801620e+00 ), ( 2.85178279175922e+00 , 4.12837904124339e+00 , 2.52784179556043e+00 ), ( 3.86480984721616e+00 , 3.24029379334385e+00 , 7.50630541184627e-01 ), ( 2.66855007312622e+00 , 3.09506737302471e+00 , -1.05570547346993e-01 ), ( 3.03480083010960e+00 , 2.72160086873890e+00 , -1.57499534729745e+00 ), ( 1.57258918789361e+00 , 2.17883844709657e+00 , 5.48129606098152e-01 ), ( 4.37174994281082e-01 , 2.49496443849042e+00 , 5.36164612719916e-01 ), ( 1.97956860962535e+00 , 1.00342808156705e+00 , 1.06673411380361e+00 ), ( 1.17837235004353e+00 , 5.47484601953032e-02 , 1.69222321530186e+00 ), ( 2.02013932698568e+00 , -1.15071693488931e+00 , 2.01095937665247e+00 ), ( 5.43445388214036e-01 , 6.10623613737296e-01 , 2.94620123320234e+00 ), ( -6.55516802788368e-01 , 3.55967038646797e-01 , 3.17311244502176e+00 ), ( 1.32230539727642e+00 , 1.33662047778142e+00 , 3.83594474675778e+00 ), ( 8.58493041787829e-01 , 1.93756430053514e+00 , 5.04354534429340e+00 ), ( 2.03020280879893e+00 , 2.61319458720498e+00 , 5.63214215280723e+00 ), ( -3.54493344367681e-01 , 2.91714629572789e+00 , 4.97804445234563e+00 ), ( -1.16317793575365e+00 , 3.04536875480708e+00 , 5.90527907810562e+00 ), ( -4.56997665157424e-01 , 3.64256089882158e+00 , 3.84588521388551e+00 ), ( -1.48864716069633e+00 , 4.55495951618193e+00 , 3.52701224906812e+00 ), ( -7.31998500857074e-01 , 5.39670953743225e+00 , 2.43240573927225e+00 ), ( -2.76043877081303e+00 , 3.88195838914561e+00 , 2.92172497691190e+00 ), ( -3.83655800207824e+00 , 4.45487150145009e+00 , 2.83258820678848e+00 ), ( -2.59982512815912e+00 , 2.62960582150409e+00 , 2.46175627757411e+00 ), ( -3.72483017568435e+00 , 1.88842108509526e+00 , 2.03569362921275e+00 ), ( -3.41674062596946e+00 , 8.50658448856212e-01 , 9.42931751107171e-01 ), ( -4.29738088737320e+00 , 1.06924065433557e+00 , 3.24986009184129e+00 ), ( -5.53574944736067e+00 , 8.81853210644467e-01 , 3.33322930420472e+00 ), ( -3.42985203154369e+00 , 6.60805330089051e-01 , 4.13978457976856e+00 ), ( -3.77006292042066e+00 , 5.91423770166127e-02 , 5.47469431926495e+00 ), ( -2.38548666440762e+00 , -3.45313164861201e-01 , 6.16230742959650e+00 ), ( -4.47512784749258e+00 , 9.94701715919259e-01 , 6.43113361680443e+00 ), ( -5.32797291281713e+00 , 6.08780004872583e-01 , 7.19550451845062e+00 ), ( -6.27190177315000e+00 , 3.56557744419283e+00 , 6.70756545526345e+00 ), ( -6.91922175772896e+00 , 4.29474385581630e+00 , 7.43148031565427e+00 ), ( -6.74325099782148e+00 , 3.20658513246779e+00 , 5.52273116069913e+00 ), ( -4.11289081713227e+00 , 2.29553198796951e+00 , 6.47520971040690e+00 ), ( -4.86771915066433e+00 , 3.20343344496405e+00 , 7.21347983898504e+00 ), ( -4.09714919691758e+00 , 4.56216329369550e+00 , 7.29069443330947e+00 ) } colvars: Step 11, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 11, atom_groups_ids[size = 0] = @@ -4163,162 +6678,301 @@ colvars: Collective variables module, step no. 11 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.22768924320888e-01 , 4.45076971931406e-03 , 9.46467332844427e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.22392395713355e-01 , 4.49513088585881e-03 , 9.46595445258703e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 7.05065634311566e+00 , -2.03049004075621e+00 , -9.79362510556569e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 , 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 7.12024786069621e+00 , -3.39139905946113e-01 , 4.28353219426788e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 , 5.87320938131017e+00 , 2.25943775728641e+00 , 2.99532323655327e+00 , 5.21460824073739e+00 , 3.59406844683129e+00 , 2.89331623199200e+00 , 6.33648153033934e+00 , 4.54439309911936e+00 , 2.43803927314067e+00 , 3.90893824316231e+00 , 3.74054027462900e+00 , 2.02866662801620e+00 , 2.85178279175922e+00 , 4.12837904124339e+00 , 2.52784179556043e+00 , 3.86480984721616e+00 , 3.24029379334385e+00 , 7.50630541184627e-01 , 2.66855007312622e+00 , 3.09506737302471e+00 , -1.05570547346993e-01 , 3.03480083010960e+00 , 2.72160086873890e+00 , -1.57499534729745e+00 , 1.57258918789361e+00 , 2.17883844709657e+00 , 5.48129606098152e-01 , 4.37174994281082e-01 , 2.49496443849042e+00 , 5.36164612719916e-01 , 1.97956860962535e+00 , 1.00342808156705e+00 , 1.06673411380361e+00 , 1.17837235004353e+00 , 5.47484601953032e-02 , 1.69222321530186e+00 , 2.02013932698568e+00 , -1.15071693488931e+00 , 2.01095937665247e+00 , 5.43445388214036e-01 , 6.10623613737296e-01 , 2.94620123320234e+00 , -6.55516802788368e-01 , 3.55967038646797e-01 , 3.17311244502176e+00 , 1.32230539727642e+00 , 1.33662047778142e+00 , 3.83594474675778e+00 , 8.58493041787829e-01 , 1.93756430053514e+00 , 5.04354534429340e+00 , 2.03020280879893e+00 , 2.61319458720498e+00 , 5.63214215280723e+00 , -3.54493344367681e-01 , 2.91714629572789e+00 , 4.97804445234563e+00 , -1.16317793575365e+00 , 3.04536875480708e+00 , 5.90527907810562e+00 , -4.56997665157424e-01 , 3.64256089882158e+00 , 3.84588521388551e+00 , -1.48864716069633e+00 , 4.55495951618193e+00 , 3.52701224906812e+00 , -7.31998500857074e-01 , 5.39670953743225e+00 , 2.43240573927225e+00 , -2.76043877081303e+00 , 3.88195838914561e+00 , 2.92172497691190e+00 , -3.83655800207824e+00 , 4.45487150145009e+00 , 2.83258820678848e+00 , -2.59982512815912e+00 , 2.62960582150409e+00 , 2.46175627757411e+00 , -3.72483017568435e+00 , 1.88842108509526e+00 , 2.03569362921275e+00 , -3.41674062596946e+00 , 8.50658448856212e-01 , 9.42931751107171e-01 , -4.29738088737320e+00 , 1.06924065433557e+00 , 3.24986009184129e+00 , -5.53574944736067e+00 , 8.81853210644467e-01 , 3.33322930420472e+00 , -3.42985203154369e+00 , 6.60805330089051e-01 , 4.13978457976856e+00 , -3.77006292042066e+00 , 5.91423770166127e-02 , 5.47469431926495e+00 , -2.38548666440762e+00 , -3.45313164861201e-01 , 6.16230742959650e+00 , -4.47512784749258e+00 , 9.94701715919259e-01 , 6.43113361680443e+00 , -5.32797291281713e+00 , 6.08780004872583e-01 , 7.19550451845062e+00 , -6.27190177315000e+00 , 3.56557744419283e+00 , 6.70756545526345e+00 , -6.91922175772896e+00 , 4.29474385581630e+00 , 7.43148031565427e+00 , -6.74325099782148e+00 , 3.20658513246779e+00 , 5.52273116069913e+00 , -4.11289081713227e+00 , 2.29553198796951e+00 , 6.47520971040690e+00 , -4.86771915066433e+00 , 3.20343344496405e+00 , 7.21347983898504e+00 , -4.09714919691758e+00 , 4.56216329369550e+00 , 7.29069443330947e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.22768924320888e-01 , 4.45076971931406e-03 , 9.46467332844427e-01 ). +colvars: Colvar "one" has value ( -3.22392395713355e-01 , 4.49513088585881e-03 , 9.46595445258703e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 7.05065634311566e+00 , -2.03049004075621e+00 , -9.79362510556569e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 , 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 7.12024786069621e+00 , -3.39139905946113e-01 , 4.28353219426788e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 , 5.87320938131017e+00 , 2.25943775728641e+00 , 2.99532323655327e+00 , 5.21460824073739e+00 , 3.59406844683129e+00 , 2.89331623199200e+00 , 6.33648153033934e+00 , 4.54439309911936e+00 , 2.43803927314067e+00 , 3.90893824316231e+00 , 3.74054027462900e+00 , 2.02866662801620e+00 , 2.85178279175922e+00 , 4.12837904124339e+00 , 2.52784179556043e+00 , 3.86480984721616e+00 , 3.24029379334385e+00 , 7.50630541184627e-01 , 2.66855007312622e+00 , 3.09506737302471e+00 , -1.05570547346993e-01 , 3.03480083010960e+00 , 2.72160086873890e+00 , -1.57499534729745e+00 , 1.57258918789361e+00 , 2.17883844709657e+00 , 5.48129606098152e-01 , 4.37174994281082e-01 , 2.49496443849042e+00 , 5.36164612719916e-01 , 1.97956860962535e+00 , 1.00342808156705e+00 , 1.06673411380361e+00 , 1.17837235004353e+00 , 5.47484601953032e-02 , 1.69222321530186e+00 , 2.02013932698568e+00 , -1.15071693488931e+00 , 2.01095937665247e+00 , 5.43445388214036e-01 , 6.10623613737296e-01 , 2.94620123320234e+00 , -6.55516802788368e-01 , 3.55967038646797e-01 , 3.17311244502176e+00 , 1.32230539727642e+00 , 1.33662047778142e+00 , 3.83594474675778e+00 , 8.58493041787829e-01 , 1.93756430053514e+00 , 5.04354534429340e+00 , 2.03020280879893e+00 , 2.61319458720498e+00 , 5.63214215280723e+00 , -3.54493344367681e-01 , 2.91714629572789e+00 , 4.97804445234563e+00 , -1.16317793575365e+00 , 3.04536875480708e+00 , 5.90527907810562e+00 , -4.56997665157424e-01 , 3.64256089882158e+00 , 3.84588521388551e+00 , -1.48864716069633e+00 , 4.55495951618193e+00 , 3.52701224906812e+00 , -7.31998500857074e-01 , 5.39670953743225e+00 , 2.43240573927225e+00 , -2.76043877081303e+00 , 3.88195838914561e+00 , 2.92172497691190e+00 , -3.83655800207824e+00 , 4.45487150145009e+00 , 2.83258820678848e+00 , -2.59982512815912e+00 , 2.62960582150409e+00 , 2.46175627757411e+00 , -3.72483017568435e+00 , 1.88842108509526e+00 , 2.03569362921275e+00 , -3.41674062596946e+00 , 8.50658448856212e-01 , 9.42931751107171e-01 , -4.29738088737320e+00 , 1.06924065433557e+00 , 3.24986009184129e+00 , -5.53574944736067e+00 , 8.81853210644467e-01 , 3.33322930420472e+00 , -3.42985203154369e+00 , 6.60805330089051e-01 , 4.13978457976856e+00 , -3.77006292042066e+00 , 5.91423770166127e-02 , 5.47469431926495e+00 , -2.38548666440762e+00 , -3.45313164861201e-01 , 6.16230742959650e+00 , -4.47512784749258e+00 , 9.94701715919259e-01 , 6.43113361680443e+00 , -5.32797291281713e+00 , 6.08780004872583e-01 , 7.19550451845062e+00 , -6.27190177315000e+00 , 3.56557744419283e+00 , 6.70756545526345e+00 , -6.91922175772896e+00 , 4.29474385581630e+00 , 7.43148031565427e+00 , -6.74325099782148e+00 , 3.20658513246779e+00 , 5.52273116069913e+00 , -4.11289081713227e+00 , 2.29553198796951e+00 , 6.47520971040690e+00 , -4.86771915066433e+00 , 3.20343344496405e+00 , 7.21347983898504e+00 , -4.09714919691758e+00 , 4.56216329369550e+00 , 7.29069443330947e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.9734 , 1.86278 , -15.0257 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.9473 , 6.69473 , 13.3895 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.9734 , 1.86278 , -15.0257 ) to colvar "one". -colvars: Adding total bias energy: 45.193 +colvars: Adding biasing force ( 66.9473 , 6.69473 , 13.3895 ) to colvar "one". +colvars: Adding total bias energy: 57.84 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.9734 , 1.86278 , -15.0257 ) +colvars: Force to be applied: ( 66.9473 , 6.69473 , 13.3895 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.87596 , -0.554631 , -1.53279 ) -colvars: ( -4.18113 , -0.475596 , -1.31437 ) -colvars: ( -4.18113 , -0.475596 , -1.31437 ) -colvars: ( -5.56939 , -0.633508 , -1.75077 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.19605 , -0.590483 , -1.63117 ) +colvars: ( -4.45561 , -0.506339 , -1.39873 ) +colvars: ( -4.45561 , -0.506339 , -1.39873 ) +colvars: ( -5.935 , -0.674459 , -1.86314 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.898831 , 0.194221 , 0.636598 ) -colvars: ( 0.777528 , 0.265708 , 0.661764 ) -colvars: ( 0.762497 , 0.258412 , 0.642958 ) -colvars: ( 0.663476 , 0.267298 , 0.596359 ) -colvars: ( 0.651424 , 0.200712 , 0.498847 ) -colvars: ( 0.575181 , 0.345294 , 0.649914 ) -colvars: ( 0.465725 , 0.360144 , 0.60523 ) -colvars: ( 0.387493 , 0.458082 , 0.691812 ) -colvars: ( 0.383363 , 0.315812 , 0.49627 ) -colvars: ( 0.347637 , 0.274542 , 0.419092 ) -colvars: ( 0.354591 , 0.320896 , 0.486126 ) -colvars: ( 0.282937 , 0.278156 , 0.38567 ) -colvars: ( 0.256465 , 0.306965 , 0.409089 ) -colvars: ( 0.346593 , 0.179783 , 0.289863 ) -colvars: ( 0.287 , 0.136747 , 0.19615 ) -colvars: ( 0.471439 , 0.14194 , 0.312458 ) -colvars: ( 0.5453 , 0.049979 , 0.231398 ) -colvars: ( 0.677282 , 0.0280841 , 0.279865 ) -colvars: ( 0.553031 , 0.0184407 , 0.193172 ) -colvars: ( 0.537052 , -0.0466147 , 0.0954103 ) -colvars: ( 0.573362 , 0.0666491 , 0.270647 ) -colvars: ( 0.570804 , 0.0508636 , 0.247707 ) -colvars: ( 0.6071 , 0.115778 , 0.357313 ) -colvars: ( 0.444254 , 0.0561451 , 0.179908 ) -colvars: ( 0.43698 , 0.000320414 , 0.0998317 ) -colvars: ( 0.340894 , 0.122362 , 0.208552 ) -colvars: ( 0.214315 , 0.131698 , 0.146239 ) -colvars: ( 0.121631 , 0.217978 , 0.208438 ) -colvars: ( 0.186333 , 0.0577736 , 0.0293293 ) -colvars: ( 0.135947 , 0.0219692 , -0.0491135 ) -colvars: ( 0.221447 , 0.0316125 , 0.0146235 ) -colvars: ( 0.207915 , -0.041166 , -0.0921709 ) -colvars: ( 0.244846 , -0.0451237 , -0.0756655 ) -colvars: ( 0.284058 , -0.127529 , -0.164281 ) -colvars: ( 0.239458 , -0.180494 , -0.262588 ) -colvars: ( 0.400683 , -0.143065 , -0.11628 ) -colvars: ( 0.478975 , -0.218933 , -0.172873 ) -colvars: ( 0.612034 , -0.222183 , -0.0984613 ) -colvars: ( 0.429966 , -0.222791 , -0.207142 ) -colvars: ( 0.435457 , -0.29092 , -0.296356 ) -colvars: ( 0.379738 , -0.148854 , -0.136544 ) -colvars: ( 0.323715 , -0.141935 , -0.160342 ) -colvars: ( 0.306205 , -0.0547758 , -0.0524171 ) -colvars: ( 0.198645 , -0.150113 , -0.245531 ) -colvars: ( 0.173391 , -0.191856 , -0.317147 ) -colvars: ( -0.00411391 , -0.195438 , -0.427159 ) -colvars: ( -0.0963675 , -0.212793 , -0.505365 ) -colvars: ( 0.0983927 , -0.246193 , -0.435323 ) -colvars: ( 0.116217 , -0.109253 , -0.238903 ) -colvars: ( -0.0047496 , -0.113057 , -0.315725 ) -colvars: ( -0.094761 , -0.0319444 , -0.258956 ) +colvars: ( 0.957579 , 0.206963 , 0.677893 ) +colvars: ( 0.82837 , 0.2831 , 0.704709 ) +colvars: ( 0.812345 , 0.275342 , 0.684693 ) +colvars: ( 0.70689 , 0.28477 , 0.63505 ) +colvars: ( 0.694052 , 0.213836 , 0.531192 ) +colvars: ( 0.612848 , 0.367838 , 0.692092 ) +colvars: ( 0.496265 , 0.383633 , 0.6445 ) +colvars: ( 0.412941 , 0.487947 , 0.736719 ) +colvars: ( 0.408528 , 0.336402 , 0.528462 ) +colvars: ( 0.370478 , 0.292427 , 0.446259 ) +colvars: ( 0.377869 , 0.341828 , 0.517672 ) +colvars: ( 0.301538 , 0.296295 , 0.410691 ) +colvars: ( 0.273329 , 0.326996 , 0.435649 ) +colvars: ( 0.369338 , 0.191513 , 0.308646 ) +colvars: ( 0.305861 , 0.145659 , 0.208839 ) +colvars: ( 0.502318 , 0.151221 , 0.332704 ) +colvars: ( 0.580989 , 0.0532704 , 0.246365 ) +colvars: ( 0.721568 , 0.0299716 , 0.297982 ) +colvars: ( 0.589235 , 0.0196607 , 0.205639 ) +colvars: ( 0.572214 , -0.0496437 , 0.101516 ) +colvars: ( 0.610902 , 0.0710068 , 0.288144 ) +colvars: ( 0.60819 , 0.0541764 , 0.263699 ) +colvars: ( 0.646861 , 0.123322 , 0.380426 ) +colvars: ( 0.473395 , 0.0597794 , 0.191494 ) +colvars: ( 0.465651 , 0.000304383 , 0.106202 ) +colvars: ( 0.363298 , 0.130306 , 0.222012 ) +colvars: ( 0.228471 , 0.14023 , 0.155652 ) +colvars: ( 0.129745 , 0.232132 , 0.221908 ) +colvars: ( 0.198656 , 0.0614855 , 0.0311433 ) +colvars: ( 0.144991 , 0.0233311 , -0.0524055 ) +colvars: ( 0.236047 , 0.033636 , 0.0154899 ) +colvars: ( 0.221623 , -0.0438856 , -0.0982455 ) +colvars: ( 0.260948 , -0.0480808 , -0.0806554 ) +colvars: ( 0.302731 , -0.135879 , -0.175058 ) +colvars: ( 0.255222 , -0.192307 , -0.279759 ) +colvars: ( 0.42696 , -0.152416 , -0.123946 ) +colvars: ( 0.510357 , -0.23323 , -0.184232 ) +colvars: ( 0.65209 , -0.236675 , -0.10499 ) +colvars: ( 0.458167 , -0.237362 , -0.22074 ) +colvars: ( 0.464016 , -0.309939 , -0.315763 ) +colvars: ( 0.404675 , -0.158615 , -0.145553 ) +colvars: ( 0.345011 , -0.151267 , -0.170907 ) +colvars: ( 0.326371 , -0.0584309 , -0.0559652 ) +colvars: ( 0.211789 , -0.159996 , -0.261629 ) +colvars: ( 0.184894 , -0.204475 , -0.33791 ) +colvars: ( -0.00420391 , -0.208287 , -0.455043 ) +colvars: ( -0.102471 , -0.226789 , -0.538331 ) +colvars: ( 0.104975 , -0.262332 , -0.463739 ) +colvars: ( 0.123982 , -0.116472 , -0.254555 ) +colvars: ( -0.00487049 , -0.12054 , -0.336366 ) +colvars: ( -0.100751 , -0.0341408 , -0.275891 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.87596 , 0.554631 , 1.53279 ) -colvars: ( 4.18113 , 0.475596 , 1.31437 ) -colvars: ( 4.18113 , 0.475596 , 1.31437 ) -colvars: ( 5.56939 , 0.633508 , 1.75077 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.19605 , 0.590483 , 1.63117 ) +colvars: ( 4.45561 , 0.506339 , 1.39873 ) +colvars: ( 4.45561 , 0.506339 , 1.39873 ) +colvars: ( 5.935 , 0.674459 , 1.86314 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.621718 , -0.0804909 , -0.387185 ) -colvars: ( -0.558034 , -0.162695 , -0.358385 ) -colvars: ( -0.510374 , -0.140885 , -0.301022 ) -colvars: ( -0.516275 , -0.190309 , -0.328203 ) -colvars: ( -0.506671 , -0.132137 , -0.293534 ) -colvars: ( -0.489255 , -0.281642 , -0.340244 ) -colvars: ( -0.453819 , -0.321948 , -0.321882 ) -colvars: ( -0.430106 , -0.428356 , -0.343732 ) -colvars: ( -0.390929 , -0.287218 , -0.243631 ) -colvars: ( -0.385156 , -0.262361 , -0.227137 ) -colvars: ( -0.343155 , -0.281664 , -0.19314 ) -colvars: ( -0.283089 , -0.245383 , -0.117066 ) -colvars: ( -0.236064 , -0.260146 , -0.0760604 ) -colvars: ( -0.304114 , -0.143126 , -0.0942955 ) -colvars: ( -0.272119 , -0.114386 , -0.0497285 ) -colvars: ( -0.360651 , -0.0859532 , -0.126655 ) -colvars: ( -0.388887 , 0.0114524 , -0.113229 ) -colvars: ( -0.441797 , 0.0590135 , -0.146069 ) -colvars: ( -0.424697 , 0.026256 , -0.142926 ) -colvars: ( -0.413279 , 0.0823459 , -0.107326 ) -colvars: ( -0.467176 , -0.0271723 , -0.208659 ) -colvars: ( -0.499446 , -0.0287038 , -0.241811 ) -colvars: ( -0.548101 , -0.0933183 , -0.31857 ) -colvars: ( -0.445039 , -0.0588327 , -0.199974 ) -colvars: ( -0.451185 , -0.0152937 , -0.187453 ) -colvars: ( -0.388764 , -0.132649 , -0.17503 ) -colvars: ( -0.329172 , -0.16404 , -0.128514 ) -colvars: ( -0.277795 , -0.253509 , -0.115228 ) -colvars: ( -0.289112 , -0.0920643 , -0.0572469 ) -colvars: ( -0.274546 , -0.0738579 , -0.0347564 ) -colvars: ( -0.271835 , -0.0474935 , -0.0206969 ) -colvars: ( -0.237882 , 0.026431 , 0.0452591 ) -colvars: ( -0.219335 , 0.0527359 , 0.075238 ) -colvars: ( -0.282555 , 0.112459 , 0.0372444 ) -colvars: ( -0.255552 , 0.153609 , 0.0821179 ) -colvars: ( -0.352778 , 0.140641 , -0.0213547 ) -colvars: ( -0.402034 , 0.216228 , -0.0384702 ) -colvars: ( -0.474654 , 0.238989 , -0.101813 ) -colvars: ( -0.410898 , 0.196379 , -0.055926 ) -colvars: ( -0.415352 , 0.256529 , -0.0345629 ) -colvars: ( -0.413069 , 0.11055 , -0.0949945 ) -colvars: ( -0.417431 , 0.0804657 , -0.112315 ) -colvars: ( -0.437026 , -0.0119167 , -0.171745 ) -colvars: ( -0.349307 , 0.0688996 , -0.0486888 ) -colvars: ( -0.351361 , 0.0947951 , -0.0396287 ) -colvars: ( -0.18898 , 0.100677 , 0.126406 ) -colvars: ( -0.138516 , 0.102211 , 0.177879 ) -colvars: ( -0.218311 , 0.172588 , 0.127773 ) -colvars: ( -0.286911 , 0.0283797 , -0.00327288 ) -colvars: ( -0.218932 , 0.0145134 , 0.0592193 ) -colvars: ( -0.164367 , -0.0679289 , 0.0787349 ) +colvars: ( -0.662314 , -0.0857846 , -0.412142 ) +colvars: ( -0.594498 , -0.17334 , -0.381457 ) +colvars: ( -0.543709 , -0.150118 , -0.320362 ) +colvars: ( -0.550047 , -0.202737 , -0.349328 ) +colvars: ( -0.539817 , -0.140768 , -0.31243 ) +colvars: ( -0.521292 , -0.300015 , -0.362138 ) +colvars: ( -0.483578 , -0.342932 , -0.342594 ) +colvars: ( -0.458343 , -0.45627 , -0.36584 ) +colvars: ( -0.416589 , -0.305932 , -0.259277 ) +colvars: ( -0.410453 , -0.279445 , -0.241731 ) +colvars: ( -0.365685 , -0.300023 , -0.205497 ) +colvars: ( -0.3017 , -0.261374 , -0.124497 ) +colvars: ( -0.251594 , -0.277108 , -0.0808113 ) +colvars: ( -0.324079 , -0.152455 , -0.100272 ) +colvars: ( -0.290007 , -0.121833 , -0.0528296 ) +colvars: ( -0.384275 , -0.0915677 , -0.134734 ) +colvars: ( -0.414332 , 0.0121828 , -0.120458 ) +colvars: ( -0.470661 , 0.0628277 , -0.155422 ) +colvars: ( -0.452495 , 0.0279618 , -0.152102 ) +colvars: ( -0.440334 , 0.0877128 , -0.114213 ) +colvars: ( -0.49776 , -0.0289453 , -0.222095 ) +colvars: ( -0.532156 , -0.0305656 , -0.257415 ) +colvars: ( -0.583996 , -0.0993912 , -0.339143 ) +colvars: ( -0.47423 , -0.0626427 , -0.212872 ) +colvars: ( -0.480784 , -0.0162585 , -0.19956 ) +colvars: ( -0.414303 , -0.141265 , -0.186294 ) +colvars: ( -0.35085 , -0.174689 , -0.136766 ) +colvars: ( -0.296138 , -0.269986 , -0.122594 ) +colvars: ( -0.308168 , -0.0980209 , -0.0608902 ) +colvars: ( -0.292668 , -0.0786171 , -0.0369583 ) +colvars: ( -0.289736 , -0.0505569 , -0.0219625 ) +colvars: ( -0.253555 , 0.0281846 , 0.048259 ) +colvars: ( -0.233769 , 0.0561899 , 0.080197 ) +colvars: ( -0.301131 , 0.11982 , 0.0396995 ) +colvars: ( -0.272372 , 0.163659 , 0.0874669 ) +colvars: ( -0.375918 , 0.149831 , -0.0227038 ) +colvars: ( -0.428377 , 0.230344 , -0.0409524 ) +colvars: ( -0.505712 , 0.254577 , -0.108401 ) +colvars: ( -0.437849 , 0.209216 , -0.0595566 ) +colvars: ( -0.442594 , 0.273292 , -0.0368289 ) +colvars: ( -0.440188 , 0.117802 , -0.101149 ) +colvars: ( -0.444864 , 0.0857708 , -0.119606 ) +colvars: ( -0.465758 , -0.0126292 , -0.182876 ) +colvars: ( -0.372318 , 0.073463 , -0.05186 ) +colvars: ( -0.374519 , 0.101056 , -0.0422317 ) +colvars: ( -0.201538 , 0.10732 , 0.13459 ) +colvars: ( -0.147798 , 0.108964 , 0.189393 ) +colvars: ( -0.23275 , 0.183904 , 0.136043 ) +colvars: ( -0.305856 , 0.0303019 , -0.00348203 ) +colvars: ( -0.233462 , 0.0155426 , 0.0630591 ) +colvars: ( -0.17535 , -0.072272 , 0.0838643 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 11. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 11. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 11, atoms_new_colvar_forces = { ( -4.59884513447972e+00 , -4.40900820867944e-01 , -1.28337506853621e+00 ), ( -3.96163887115342e+00 , -3.72583406983679e-01 , -1.01098544233917e+00 ), ( -4.03393239834945e+00 , -3.98607267392641e-01 , -1.04620861900968e+00 ), ( -5.42463701602936e+00 , -5.64932512498923e-01 , -1.54545968977434e+00 ), ( 2.52122600767734e-01 , 1.17526712350953e-01 , 3.41935437795740e-01 ), ( 4.96188382968194e+00 , 6.18282820313522e-01 , 1.84245832108118e+00 ), ( 4.19303858656264e+00 , 5.13792492554205e-01 , 1.59771267574707e+00 ), ( -4.26127345682579e-02 , 2.97254133625255e-02 , 3.48080688600381e-01 ), ( 4.17356734697521e+00 , 5.04190403647140e-01 , 1.56700347347154e+00 ), ( 5.53187126614492e+00 , 6.45688546426307e-01 , 1.94272759159626e+00 ), ( 1.14357699440463e-02 , 3.92327263640231e-02 , 2.92986597107914e-01 ), ( -1.51372103148639e-04 , 3.27722799696802e-02 , 2.68603304469462e-01 ), ( 2.04003955970579e-02 , 4.68184559794554e-02 , 3.33028914310537e-01 ), ( 4.24787983461165e-02 , 3.66568305659243e-02 , 1.95566998128986e-01 ), ( 1.48808118778211e-02 , 2.23605158788987e-02 , 1.46421157206805e-01 ), ( 1.10787960062394e-01 , 5.59870178408550e-02 , 1.85802306159689e-01 ), ( 1.56412927814132e-01 , 6.14314039279574e-02 , 1.18168388061017e-01 ), ( 2.35484338777458e-01 , 8.70975640996397e-02 , 1.33796672484103e-01 ), ( 1.28334568769220e-01 , 4.46967062211768e-02 , 5.02463943210389e-02 ), ( 1.23772787025132e-01 , 3.57311716871498e-02 , -1.19160624079119e-02 ), ( 1.06185848120741e-01 , 3.94767284527993e-02 , 6.19875167770056e-02 ), ( 7.13586731729734e-02 , 2.21598185424610e-02 , 5.89604027723398e-03 ), ( 5.89988047881739e-02 , 2.24594945422259e-02 , 3.87424590980556e-02 ), ( -7.85336772361367e-04 , -2.68758796431411e-03 , -2.00658935725362e-02 ), ( -1.42047598250104e-02 , -1.49732891714304e-02 , -8.76214225949302e-02 ), ( -4.78703133974230e-02 , -1.02867402626420e-02 , 3.35221731945086e-02 ), ( -1.14856764966572e-01 , -3.23426402810121e-02 , 1.77251173079882e-02 ), ( -1.56164265820016e-01 , -3.55306178344022e-02 , 9.32101362088979e-02 ), ( -1.02779777673893e-01 , -3.42907513475975e-02 , -2.79176158306193e-02 ), ( -1.38599004907390e-01 , -5.18887123716195e-02 , -8.38698931274176e-02 ), ( -5.03883490752813e-02 , -1.58810317266450e-02 , -6.07338679726589e-03 ), ( -2.99666445512997e-02 , -1.47350139960092e-02 , -4.69117871334710e-02 ), ( 2.55100756206192e-02 , 7.61217337109285e-03 , -4.27509143430649e-04 ), ( 1.50283291200376e-03 , -1.50696887306304e-02 , -1.27036342323648e-01 ), ( -1.60944744697057e-02 , -2.68852617720362e-02 , -1.80470346539109e-01 ), ( 4.79043970101733e-02 , -2.42338409384135e-03 , -1.37634460798546e-01 ), ( 7.69409680429476e-02 , -2.70507328915792e-03 , -2.11342681785463e-01 ), ( 1.37379981564062e-01 , 1.68058816156087e-02 , -2.00274676521168e-01 ), ( 1.90679535935423e-02 , -2.64125042132309e-02 , -2.63067504258520e-01 ), ( 2.01049607196809e-02 , -3.43909572427850e-02 , -3.30918761131843e-01 ), ( -3.33307589809503e-02 , -3.83033210706806e-02 , -2.31538599588535e-01 ), ( -9.37163462636916e-02 , -6.14697262270893e-02 , -2.72656723612530e-01 ), ( -1.30820877143099e-01 , -6.66925790424657e-02 , -2.24161892236045e-01 ), ( -1.50661997623523e-01 , -8.12133363018726e-02 , -2.94219328629125e-01 ), ( -1.77970142126282e-01 , -9.70610417104104e-02 , -3.56775566209909e-01 ), ( -1.93093795451497e-01 , -9.47601328613884e-02 , -3.00753355593030e-01 ), ( -2.34883133458497e-01 , -1.10581736122046e-01 , -3.27485825976173e-01 ), ( -1.19918516908678e-01 , -7.36053910619497e-02 , -3.07550702818950e-01 ), ( -1.70694370259342e-01 , -8.08733348585255e-02 , -2.42175707234071e-01 ), ( -2.23681388006602e-01 , -9.85439408538684e-02 , -2.56505928004477e-01 ), ( -2.59127939526269e-01 , -9.98733555627645e-02 , -1.80221569877279e-01 ) } +colvars: Step 11, atoms_new_colvar_forces = { ( -4.90078343283082e+00 , -4.69304939716054e-01 , -1.36541654232102e+00 ), ( -4.22173864945088e+00 , -3.96579211311637e-01 , -1.07547405982912e+00 ), ( -4.29876725746840e+00 , -4.24306744780342e-01 , -1.11300446941000e+00 ), ( -5.78076668885247e+00 , -6.01391375743044e-01 , -1.64438175232614e+00 ), ( 2.68636078315130e-01 , 1.25224014736973e-01 , 3.64331369994507e-01 ), ( 5.28760305095590e+00 , 6.58306388945491e-01 , 1.96112134983409e+00 ), ( 4.46829684153746e+00 , 5.47040898538111e-01 , 1.70063240131138e+00 ), ( -4.54023956339813e-02 , 3.16776544920516e-02 , 3.70879550465582e-01 ), ( 4.44754945706128e+00 , 5.36809513694409e-01 , 1.66791086412683e+00 ), ( 5.89502605346830e+00 , 6.87440092337066e-01 , 2.06767076232209e+00 ), ( 1.21843034227425e-02 , 4.18052959825408e-02 , 3.12175108656937e-01 ), ( -1.62618102043321e-04 , 3.49212496434206e-02 , 2.86193795220697e-01 ), ( 2.17343226901442e-02 , 4.98873878221798e-02 , 3.54837926670121e-01 ), ( 4.52596785697127e-02 , 3.90586460782221e-02 , 2.08374109794610e-01 ), ( 1.58538228914107e-02 , 2.38257529877301e-02 , 1.56009062475107e-01 ), ( 1.18043219659774e-01 , 5.96537616383347e-02 , 1.97970486543308e-01 ), ( 1.66656553754429e-01 , 6.54532082555734e-02 , 1.25907131884304e-01 ), ( 2.50907095860839e-01 , 9.27993251652997e-02 , 1.42559451292976e-01 ), ( 1.36739936503245e-01 , 4.76224964818958e-02 , 5.35374623532944e-02 ), ( 1.31879223673249e-01 , 3.80690478972656e-02 , -1.26964879861136e-02 ), ( 1.13141394409887e-01 , 4.20615216140231e-02 , 6.60485051673235e-02 ), ( 7.60339342339692e-02 , 2.36107162974138e-02 , 6.28416739353432e-03 ), ( 6.28654041122315e-02 , 2.39309972060159e-02 , 4.12828419792915e-02 ), ( -8.35563968785369e-04 , -2.86329479710402e-03 , -2.13786742540487e-02 ), ( -1.51337174937063e-02 , -1.59541245139078e-02 , -9.33585281143269e-02 ), ( -5.10049654171213e-02 , -1.09589661405002e-02 , 3.57183867004734e-02 ), ( -1.22379223950270e-01 , -3.44586629208166e-02 , 1.88860376509928e-02 ), ( -1.66392710395628e-01 , -3.78540757063262e-02 , 9.93142380172693e-02 ), ( -1.09511965645556e-01 , -3.65354269878942e-02 , -2.97468795261682e-02 ), ( -1.47677186588062e-01 , -5.52859983018182e-02 , -8.93637689973341e-02 ), ( -5.36897552770025e-02 , -1.69208906193615e-02 , -6.47263810149609e-03 ), ( -3.19311971427954e-02 , -1.57009459162498e-02 , -4.99865053421004e-02 ), ( 2.71783388133797e-02 , 8.10915997456257e-03 , -4.58466748998743e-04 ), ( 1.59987902378828e-03 , -1.60588035212056e-02 , -1.35358167121535e-01 ), ( -1.71502863079521e-02 , -2.86486967752420e-02 , -1.92292202522445e-01 ), ( 5.10413359017399e-02 , -2.58480080072415e-03 , -1.46649401714235e-01 ), ( 8.19802503728982e-02 , -2.88604582924412e-03 , -2.25184391896305e-01 ), ( 1.46378492350565e-01 , 1.79021935732166e-02 , -2.13390534719039e-01 ), ( 2.03173362292667e-02 , -2.81455653081005e-02 , -2.80296367683953e-01 ), ( 2.14223207336109e-02 , -3.66473521516703e-02 , -3.52591445070795e-01 ), ( -3.55128696236089e-02 , -4.08137237993783e-02 , -2.46702100673147e-01 ), ( -9.98529723625791e-02 , -6.54966394007973e-02 , -2.90512763082388e-01 ), ( -1.39387121834031e-01 , -7.10601043642288e-02 , -2.38841167077406e-01 ), ( -1.60529005762194e-01 , -8.65329339682001e-02 , -3.13488499661599e-01 ), ( -1.89625501057259e-01 , -1.03418749868344e-01 , -3.80141619715457e-01 ), ( -2.05742146333561e-01 , -1.00967320951149e-01 , -3.20453183152707e-01 ), ( -2.50269018572833e-01 , -1.17824980701032e-01 , -3.48937154277653e-01 ), ( -1.27774241837926e-01 , -7.84284067810070e-02 , -3.27695656311434e-01 ), ( -1.81874256847324e-01 , -8.61700864243677e-02 , -2.58037329988097e-01 ), ( -2.38332407520861e-01 , -1.04997600001132e-01 , -2.73307023037450e-01 ), ( -2.76101168267298e-01 , -1.06412855260919e-01 , -1.92027229192213e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 11, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4356,10 +7010,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 12, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 12, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 12, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 12, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 12, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 12, atoms_positions[size = 51] = { ( 8.33295571895662e+00 , 4.36061656045469e-02 , -7.65818806317456e-01 ), ( 6.98877846778014e+00 , -5.37741483712509e-01 , -6.26144120316792e-01 ), ( 6.20406265157318e+00 , -3.06445668968316e-01 , 6.90213293377312e-01 ), ( 4.98114405786721e+00 , -1.92537607642435e-01 , 6.96201523086720e-01 ), ( 7.05216970222226e+00 , -2.03266865864220e+00 , -9.73340123141853e-01 ), ( 6.89825599504267e+00 , -2.66113724750723e-01 , 1.85486440943486e+00 ), ( 6.18496365955545e+00 , -1.20770477430784e-01 , 3.15936212167099e+00 ), ( 7.11121253656082e+00 , -3.42530652917635e-01 , 4.28277545291277e+00 ), ( 5.28841220037515e+00 , 1.11209820607442e+00 , 3.32022070845398e+00 ), ( 4.12604012509779e+00 , 1.04652528783029e+00 , 3.64726274554401e+00 ), ( 5.87087372721693e+00 , 2.25410236808351e+00 , 2.99694107228310e+00 ), ( 5.21736348697982e+00 , 3.59297928625683e+00 , 2.89681673047679e+00 ), ( 6.33480788548696e+00 , 4.53565809183101e+00 , 2.43245136361519e+00 ), ( 3.90961739436181e+00 , 3.73996287366647e+00 , 2.03106767909737e+00 ), ( 2.84169790894118e+00 , 4.13207118883219e+00 , 2.52389262293396e+00 ), ( 3.87446485100083e+00 , 3.24053076273417e+00 , 7.46624285597141e-01 ), ( 2.66537195679257e+00 , 3.08070250699176e+00 , -1.06970825269599e-01 ), ( 3.03339709044189e+00 , 2.72233175202439e+00 , -1.56641643435355e+00 ), ( 1.57121526890728e+00 , 2.18520968208356e+00 , 5.36130647529653e-01 ), ( 4.33201316981108e-01 , 2.50394567657911e+00 , 5.33418648401908e-01 ), ( 1.98502933817818e+00 , 1.00234124743323e+00 , 1.07073191094727e+00 ), ( 1.18076254581051e+00 , 6.53645310955235e-02 , 1.69226266857951e+00 ), ( 2.02205290769318e+00 , -1.14473097002340e+00 , 2.00913153765872e+00 ), ( 5.46808386891470e-01 , 6.10076055254844e-01 , 2.93917233454231e+00 ), ( -6.50613837447251e-01 , 3.54020578335481e-01 , 3.17164471336799e+00 ), ( 1.32450853334442e+00 , 1.33949134166068e+00 , 3.83443885250890e+00 ), ( 8.59715275247287e-01 , 1.94336563984750e+00 , 5.03925228208658e+00 ), ( 2.02966514880358e+00 , 2.61908990284665e+00 , 5.63548641588938e+00 ), ( -3.51825069730810e-01 , 2.91688608723441e+00 , 4.97611389187533e+00 ), ( -1.16092050531517e+00 , 3.04808993560574e+00 , 5.90448975522759e+00 ), ( -4.64340852385915e-01 , 3.63018167649035e+00 , 3.84568329380056e+00 ), ( -1.49206207655392e+00 , 4.55228924756019e+00 , 3.52092650506299e+00 ), ( -7.27178460610727e-01 , 5.39873008902098e+00 , 2.43698904581802e+00 ), ( -2.76549961074677e+00 , 3.87909298094911e+00 , 2.91957687931561e+00 ), ( -3.83320500718966e+00 , 4.46090103812986e+00 , 2.82975353569123e+00 ), ( -2.60194127387236e+00 , 2.63707560012780e+00 , 2.45584524632627e+00 ), ( -3.72983316266672e+00 , 1.87760732537601e+00 , 2.02908581185006e+00 ), ( -3.41572625315696e+00 , 8.58001699944253e-01 , 9.34120452580659e-01 ), ( -4.30068086593182e+00 , 1.06685373748620e+00 , 3.24921589040063e+00 ), ( -5.53241571682040e+00 , 8.75043424747895e-01 , 3.33175013181537e+00 ), ( -3.42189417280314e+00 , 6.65026977550348e-01 , 4.14400913502875e+00 ), ( -3.76398547140368e+00 , 5.18481619405909e-02 , 5.46953003321335e+00 ), ( -2.38373988627510e+00 , -3.36652890873889e-01 , 6.16555774885334e+00 ), ( -4.47475638623978e+00 , 9.96794401766116e-01 , 6.43430594146024e+00 ), ( -5.33058868219778e+00 , 6.08717875327609e-01 , 7.19826346543950e+00 ), ( -6.26387125422770e+00 , 3.56866870710881e+00 , 6.70882368927237e+00 ), ( -6.92314946980549e+00 , 4.29503765079163e+00 , 7.43608083062516e+00 ), ( -6.74511748440753e+00 , 3.20538001822847e+00 , 5.52315269871824e+00 ), ( -4.11755045843843e+00 , 2.29050371691807e+00 , 6.47028156112260e+00 ), ( -4.85859726047702e+00 , 3.19872694766136e+00 , 7.21448858099587e+00 ), ( -4.09969496157519e+00 , 4.57066698467727e+00 , 7.29317571082817e+00 ) } +colvars: Step 12, atoms_positions[size = 51] = { ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 ), ( 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 ), ( 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 ), ( 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 ), ( 7.05216884472931e+00 , -2.03267024040295e+00 , -9.73295825255848e-01 ), ( 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 ), ( 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 ), ( 7.11129887748832e+00 , -3.42540715561059e-01 , 4.28291306597860e+00 ), ( 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 ), ( 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 ), ( 5.87096740802154e+00 , 2.25415274518504e+00 , 2.99697544006320e+00 ), ( 5.21735848461560e+00 , 3.59298233811180e+00 , 2.89686929389489e+00 ), ( 6.33480970096802e+00 , 4.53566617377819e+00 , 2.43250728524615e+00 ), ( 3.90962688169957e+00 , 3.73996516051568e+00 , 2.03110560361885e+00 ), ( 2.84169952185721e+00 , 4.13207466760969e+00 , 2.52391525387548e+00 ), ( 3.87448379573895e+00 , 3.24054073488516e+00 , 7.46656271121759e-01 ), ( 2.66540088662928e+00 , 3.08071427694430e+00 , -1.06948776577169e-01 ), ( 3.03343586756372e+00 , 2.72234638656259e+00 , -1.56639273202783e+00 ), ( 1.57123880468663e+00 , 2.18521828854670e+00 , 5.36140700280098e-01 ), ( 4.33221607223244e-01 , 2.50395086530901e+00 , 5.33416986325957e-01 ), ( 1.98504702243356e+00 , 1.00234847816603e+00 , 1.07074354564732e+00 ), ( 1.18077541027169e+00 , 6.53689673177442e-02 , 1.69226430609757e+00 ), ( 2.02206467836376e+00 , -1.14472594761737e+00 , 2.00914031973690e+00 ), ( 5.46808959195410e-01 , 6.10075626469495e-01 , 2.93916872266926e+00 ), ( -6.50615460135450e-01 , 3.54018439017094e-01 , 3.17163168329279e+00 ), ( 1.32451023183092e+00 , 1.33948783531163e+00 , 3.83444335546463e+00 ), ( 8.59694930478069e-01 , 1.94335942266418e+00 , 5.03925529093421e+00 ), ( 2.02963863244139e+00 , 2.61908349136240e+00 , 5.63550046903603e+00 ), ( -3.51844184523290e-01 , 2.91687912000407e+00 , 4.97610808070261e+00 ), ( -1.16094265390643e+00 , 3.04808227265965e+00 , 5.90447813097405e+00 ), ( -4.64349504781026e-01 , 3.63017888319001e+00 , 3.84568116619849e+00 ), ( -1.49206739475396e+00 , 4.55228680080772e+00 , 3.52091755495627e+00 ), ( -7.27174485366121e-01 , 5.39873112983284e+00 , 2.43698850432327e+00 ), ( -2.76549994203998e+00 , 3.87909092947422e+00 , 2.91955278431552e+00 ), ( -3.83320694871914e+00 , 4.46089668565823e+00 , 2.82972610602657e+00 ), ( -2.60193378324243e+00 , 2.63707500181704e+00 , 2.45582159900282e+00 ), ( -3.72981911892557e+00 , 1.87760712012116e+00 , 2.02904580470210e+00 ), ( -3.41570312436543e+00 , 8.58003564587794e-01 , 9.34084900309542e-01 ), ( -4.30067653974697e+00 , 1.06684783467702e+00 , 3.24916609074616e+00 ), ( -5.53241246992859e+00 , 8.75038253548931e-01 , 3.33169955912849e+00 ), ( -3.42189965148397e+00 , 6.65020150722877e-01 , 4.14396823941459e+00 ), ( -3.76400342980764e+00 , 5.18364871068631e-02 , 5.46948036416195e+00 ), ( -2.38376264792475e+00 , -3.36662883499113e-01 , 6.16551886812340e+00 ), ( -4.47478519017763e+00 , 9.96780026303595e-01 , 6.43424940827949e+00 ), ( -5.33061567930435e+00 , 6.08703030602428e-01 , 7.19820914998331e+00 ), ( -6.26390807988011e+00 , 3.56865160210561e+00 , 6.70876978233037e+00 ), ( -6.92318478431468e+00 , 4.29502014255646e+00 , 7.43603016595229e+00 ), ( -6.74513867300062e+00 , 3.20536849185209e+00 , 5.52310114289021e+00 ), ( -4.11757953139702e+00 , 2.29049008233997e+00 , 6.47023954517971e+00 ), ( -4.85863836232743e+00 , 3.19870850025164e+00 , 7.21444112192501e+00 ), ( -4.09973971458373e+00 , 4.57064905249189e+00 , 7.29314379280119e+00 ) } colvars: Step 12, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 12, atom_groups_ids[size = 0] = @@ -4377,162 +7031,301 @@ colvars: Collective variables module, step no. 12 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.20358118183599e-01 , 4.32056543368708e-03 , 9.47286656101624e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.19922434142702e-01 , 4.37264221813040e-03 , 9.47433647350695e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". colvars: Calculating fit gradients. +colvars: Done calculating colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 7.05216884472931e+00 , -2.03267024040295e+00 , -9.73295825255848e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 , 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 7.11129887748832e+00 , -3.42540715561059e-01 , 4.28291306597860e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 , 5.87096740802154e+00 , 2.25415274518504e+00 , 2.99697544006320e+00 , 5.21735848461560e+00 , 3.59298233811180e+00 , 2.89686929389489e+00 , 6.33480970096802e+00 , 4.53566617377819e+00 , 2.43250728524615e+00 , 3.90962688169957e+00 , 3.73996516051568e+00 , 2.03110560361885e+00 , 2.84169952185721e+00 , 4.13207466760969e+00 , 2.52391525387548e+00 , 3.87448379573895e+00 , 3.24054073488516e+00 , 7.46656271121759e-01 , 2.66540088662928e+00 , 3.08071427694430e+00 , -1.06948776577169e-01 , 3.03343586756372e+00 , 2.72234638656259e+00 , -1.56639273202783e+00 , 1.57123880468663e+00 , 2.18521828854670e+00 , 5.36140700280098e-01 , 4.33221607223244e-01 , 2.50395086530901e+00 , 5.33416986325957e-01 , 1.98504702243356e+00 , 1.00234847816603e+00 , 1.07074354564732e+00 , 1.18077541027169e+00 , 6.53689673177442e-02 , 1.69226430609757e+00 , 2.02206467836376e+00 , -1.14472594761737e+00 , 2.00914031973690e+00 , 5.46808959195410e-01 , 6.10075626469495e-01 , 2.93916872266926e+00 , -6.50615460135450e-01 , 3.54018439017094e-01 , 3.17163168329279e+00 , 1.32451023183092e+00 , 1.33948783531163e+00 , 3.83444335546463e+00 , 8.59694930478069e-01 , 1.94335942266418e+00 , 5.03925529093421e+00 , 2.02963863244139e+00 , 2.61908349136240e+00 , 5.63550046903603e+00 , -3.51844184523290e-01 , 2.91687912000407e+00 , 4.97610808070261e+00 , -1.16094265390643e+00 , 3.04808227265965e+00 , 5.90447813097405e+00 , -4.64349504781026e-01 , 3.63017888319001e+00 , 3.84568116619849e+00 , -1.49206739475396e+00 , 4.55228680080772e+00 , 3.52091755495627e+00 , -7.27174485366121e-01 , 5.39873112983284e+00 , 2.43698850432327e+00 , -2.76549994203998e+00 , 3.87909092947422e+00 , 2.91955278431552e+00 , -3.83320694871914e+00 , 4.46089668565823e+00 , 2.82972610602657e+00 , -2.60193378324243e+00 , 2.63707500181704e+00 , 2.45582159900282e+00 , -3.72981911892557e+00 , 1.87760712012116e+00 , 2.02904580470210e+00 , -3.41570312436543e+00 , 8.58003564587794e-01 , 9.34084900309542e-01 , -4.30067653974697e+00 , 1.06684783467702e+00 , 3.24916609074616e+00 , -5.53241246992859e+00 , 8.75038253548931e-01 , 3.33169955912849e+00 , -3.42189965148397e+00 , 6.65020150722877e-01 , 4.14396823941459e+00 , -3.76400342980764e+00 , 5.18364871068631e-02 , 5.46948036416195e+00 , -2.38376264792475e+00 , -3.36662883499113e-01 , 6.16551886812340e+00 , -4.47478519017763e+00 , 9.96780026303595e-01 , 6.43424940827949e+00 , -5.33061567930435e+00 , 6.08703030602428e-01 , 7.19820914998331e+00 , -6.26390807988011e+00 , 3.56865160210561e+00 , 6.70876978233037e+00 , -6.92318478431468e+00 , 4.29502014255646e+00 , 7.43603016595229e+00 , -6.74513867300062e+00 , 3.20536849185209e+00 , 5.52310114289021e+00 , -4.11757953139702e+00 , 2.29049008233997e+00 , 6.47023954517971e+00 , -4.85863836232743e+00 , 3.19870850025164e+00 , 7.21444112192501e+00 , -4.09973971458373e+00 , 4.57064905249189e+00 , 7.29314379280119e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.20358118183599e-01 , 4.32056543368708e-03 , 9.47286656101624e-01 ). +colvars: Colvar "one" has value ( -3.19922434142702e-01 , 4.37264221813040e-03 , 9.47433647350695e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 7.05216884472931e+00 , -2.03267024040295e+00 , -9.73295825255848e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 , 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 7.11129887748832e+00 , -3.42540715561059e-01 , 4.28291306597860e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 , 5.87096740802154e+00 , 2.25415274518504e+00 , 2.99697544006320e+00 , 5.21735848461560e+00 , 3.59298233811180e+00 , 2.89686929389489e+00 , 6.33480970096802e+00 , 4.53566617377819e+00 , 2.43250728524615e+00 , 3.90962688169957e+00 , 3.73996516051568e+00 , 2.03110560361885e+00 , 2.84169952185721e+00 , 4.13207466760969e+00 , 2.52391525387548e+00 , 3.87448379573895e+00 , 3.24054073488516e+00 , 7.46656271121759e-01 , 2.66540088662928e+00 , 3.08071427694430e+00 , -1.06948776577169e-01 , 3.03343586756372e+00 , 2.72234638656259e+00 , -1.56639273202783e+00 , 1.57123880468663e+00 , 2.18521828854670e+00 , 5.36140700280098e-01 , 4.33221607223244e-01 , 2.50395086530901e+00 , 5.33416986325957e-01 , 1.98504702243356e+00 , 1.00234847816603e+00 , 1.07074354564732e+00 , 1.18077541027169e+00 , 6.53689673177442e-02 , 1.69226430609757e+00 , 2.02206467836376e+00 , -1.14472594761737e+00 , 2.00914031973690e+00 , 5.46808959195410e-01 , 6.10075626469495e-01 , 2.93916872266926e+00 , -6.50615460135450e-01 , 3.54018439017094e-01 , 3.17163168329279e+00 , 1.32451023183092e+00 , 1.33948783531163e+00 , 3.83444335546463e+00 , 8.59694930478069e-01 , 1.94335942266418e+00 , 5.03925529093421e+00 , 2.02963863244139e+00 , 2.61908349136240e+00 , 5.63550046903603e+00 , -3.51844184523290e-01 , 2.91687912000407e+00 , 4.97610808070261e+00 , -1.16094265390643e+00 , 3.04808227265965e+00 , 5.90447813097405e+00 , -4.64349504781026e-01 , 3.63017888319001e+00 , 3.84568116619849e+00 , -1.49206739475396e+00 , 4.55228680080772e+00 , 3.52091755495627e+00 , -7.27174485366121e-01 , 5.39873112983284e+00 , 2.43698850432327e+00 , -2.76549994203998e+00 , 3.87909092947422e+00 , 2.91955278431552e+00 , -3.83320694871914e+00 , 4.46089668565823e+00 , 2.82972610602657e+00 , -2.60193378324243e+00 , 2.63707500181704e+00 , 2.45582159900282e+00 , -3.72981911892557e+00 , 1.87760712012116e+00 , 2.02904580470210e+00 , -3.41570312436543e+00 , 8.58003564587794e-01 , 9.34084900309542e-01 , -4.30067653974697e+00 , 1.06684783467702e+00 , 3.24916609074616e+00 , -5.53241246992859e+00 , 8.75038253548931e-01 , 3.33169955912849e+00 , -3.42189965148397e+00 , 6.65020150722877e-01 , 4.14396823941459e+00 , -3.76400342980764e+00 , 5.18364871068631e-02 , 5.46948036416195e+00 , -2.38376264792475e+00 , -3.36662883499113e-01 , 6.16551886812340e+00 , -4.47478519017763e+00 , 9.96780026303595e-01 , 6.43424940827949e+00 , -5.33061567930435e+00 , 6.08703030602428e-01 , 7.19820914998331e+00 , -6.26390807988011e+00 , 3.56865160210561e+00 , 6.70876978233037e+00 , -6.92318478431468e+00 , 4.29502014255646e+00 , 7.43603016595229e+00 , -6.74513867300062e+00 , 3.20536849185209e+00 , 5.52310114289021e+00 , -4.11757953139702e+00 , 2.29049008233997e+00 , 6.47023954517971e+00 , -4.85863836232743e+00 , 3.19870850025164e+00 , 7.21444112192501e+00 , -4.09973971458373e+00 , 4.57064905249189e+00 , 7.29314379280119e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.9252 , 1.86539 , -15.0421 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.8232 , 6.68232 , 13.3646 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.9252 , 1.86539 , -15.0421 ) to colvar "one". -colvars: Adding total bias energy: 45.093 +colvars: Adding biasing force ( 66.8232 , 6.68232 , 13.3646 ) to colvar "one". +colvars: Adding total bias energy: 57.6644 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.9252 , 1.86539 , -15.0421 ) +colvars: Force to be applied: ( 66.8232 , 6.68232 , 13.3646 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.88148 , -0.551647 , -1.52188 ) -colvars: ( -4.18587 , -0.473038 , -1.30501 ) -colvars: ( -4.18587 , -0.473038 , -1.30501 ) -colvars: ( -5.5757 , -0.6301 , -1.73832 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.18969 , -0.585835 , -1.61538 ) +colvars: ( -4.45016 , -0.502354 , -1.38519 ) +colvars: ( -4.45016 , -0.502354 , -1.38519 ) +colvars: ( -5.92774 , -0.66915 , -1.84512 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.898175 , 0.194402 , 0.634384 ) -colvars: ( 0.777089 , 0.265785 , 0.65947 ) -colvars: ( 0.761945 , 0.258557 , 0.640737 ) -colvars: ( 0.663309 , 0.267255 , 0.594227 ) -colvars: ( 0.651274 , 0.200681 , 0.496986 ) -colvars: ( 0.575238 , 0.345133 , 0.647614 ) -colvars: ( 0.466059 , 0.359857 , 0.603032 ) -colvars: ( 0.388024 , 0.457683 , 0.689357 ) -colvars: ( 0.383782 , 0.315512 , 0.494379 ) -colvars: ( 0.348171 , 0.274199 , 0.417406 ) -colvars: ( 0.354946 , 0.320639 , 0.48428 ) -colvars: ( 0.283349 , 0.277898 , 0.38411 ) -colvars: ( 0.256805 , 0.306747 , 0.40748 ) -colvars: ( 0.346853 , 0.179616 , 0.288582 ) -colvars: ( 0.28737 , 0.136547 , 0.195125 ) -colvars: ( 0.471441 , 0.141891 , 0.31113 ) -colvars: ( 0.545137 , 0.0500229 , 0.230307 ) -colvars: ( 0.676822 , 0.028261 , 0.278661 ) -colvars: ( 0.552969 , 0.0184345 , 0.192171 ) -colvars: ( 0.537014 , -0.0466133 , 0.0946818 ) -colvars: ( 0.573371 , 0.0665855 , 0.269414 ) -colvars: ( 0.570938 , 0.0507356 , 0.246519 ) -colvars: ( 0.607267 , 0.115605 , 0.355806 ) -colvars: ( 0.444661 , 0.0558999 , 0.178891 ) -colvars: ( 0.437441 , 6.18542e-05 , 0.0990312 ) -colvars: ( 0.341478 , 0.122032 , 0.207448 ) -colvars: ( 0.215155 , 0.131259 , 0.145293 ) -colvars: ( 0.122623 , 0.217459 , 0.207313 ) -colvars: ( 0.18714 , 0.0573797 , 0.0287208 ) -colvars: ( 0.136892 , 0.0215226 , -0.0495148 ) -colvars: ( 0.222066 , 0.0313196 , 0.014079 ) -colvars: ( 0.20847 , -0.0414012 , -0.0924042 ) -colvars: ( 0.245199 , -0.0452568 , -0.0759201 ) -colvars: ( 0.284498 , -0.1277 , -0.164309 ) -colvars: ( 0.239971 , -0.18068 , -0.262345 ) -colvars: ( 0.400942 , -0.143165 , -0.116437 ) -colvars: ( 0.479126 , -0.218976 , -0.17287 ) -colvars: ( 0.611952 , -0.222134 , -0.0986562 ) -colvars: ( 0.43033 , -0.222938 , -0.207068 ) -colvars: ( 0.435822 , -0.291051 , -0.296034 ) -colvars: ( 0.380288 , -0.149108 , -0.136687 ) -colvars: ( 0.324486 , -0.142298 , -0.160443 ) -colvars: ( 0.307103 , -0.0552255 , -0.0528358 ) -colvars: ( 0.199638 , -0.15056 , -0.245403 ) -colvars: ( 0.174487 , -0.192344 , -0.316831 ) -colvars: ( -0.0029368 , -0.195918 , -0.426513 ) -colvars: ( -0.0950272 , -0.213334 , -0.504508 ) -colvars: ( 0.0992999 , -0.246541 , -0.434632 ) -colvars: ( 0.117289 , -0.109732 , -0.23879 ) -colvars: ( -0.00347128 , -0.113615 , -0.315407 ) -colvars: ( -0.0933505 , -0.0325701 , -0.2588 ) +colvars: ( 0.954588 , 0.206666 , 0.673866 ) +colvars: ( 0.825922 , 0.282508 , 0.700532 ) +colvars: ( 0.809815 , 0.274843 , 0.680647 ) +colvars: ( 0.705027 , 0.284043 , 0.631216 ) +colvars: ( 0.692237 , 0.213291 , 0.527901 ) +colvars: ( 0.611451 , 0.366782 , 0.687941 ) +colvars: ( 0.495446 , 0.382401 , 0.640575 ) +colvars: ( 0.412534 , 0.486343 , 0.732296 ) +colvars: ( 0.408012 , 0.33527 , 0.525148 ) +colvars: ( 0.370176 , 0.291353 , 0.443362 ) +colvars: ( 0.377358 , 0.340729 , 0.514434 ) +colvars: ( 0.301269 , 0.295306 , 0.40802 ) +colvars: ( 0.273051 , 0.325976 , 0.432867 ) +colvars: ( 0.368743 , 0.190875 , 0.30652 ) +colvars: ( 0.305537 , 0.145094 , 0.207228 ) +colvars: ( 0.501127 , 0.150807 , 0.330468 ) +colvars: ( 0.579432 , 0.0531935 , 0.244591 ) +colvars: ( 0.719352 , 0.0300962 , 0.29596 ) +colvars: ( 0.587767 , 0.0196095 , 0.204058 ) +colvars: ( 0.570812 , -0.0495204 , 0.100478 ) +colvars: ( 0.609458 , 0.0707695 , 0.286113 ) +colvars: ( 0.606887 , 0.0539088 , 0.261773 ) +colvars: ( 0.645501 , 0.12284 , 0.377875 ) +colvars: ( 0.47271 , 0.0593701 , 0.189927 ) +colvars: ( 0.465042 , 2.30471e-05 , 0.105072 ) +colvars: ( 0.363068 , 0.129634 , 0.220279 ) +colvars: ( 0.228839 , 0.139417 , 0.154251 ) +colvars: ( 0.130515 , 0.23101 , 0.220157 ) +colvars: ( 0.199061 , 0.0609095 , 0.0304057 ) +colvars: ( 0.145672 , 0.0227888 , -0.0527192 ) +colvars: ( 0.236159 , 0.0332374 , 0.01486 ) +colvars: ( 0.221701 , -0.044035 , -0.0982658 ) +colvars: ( 0.260714 , -0.0481082 , -0.0807397 ) +colvars: ( 0.302489 , -0.135737 , -0.174675 ) +colvars: ( 0.255174 , -0.192046 , -0.278831 ) +colvars: ( 0.426226 , -0.152157 , -0.123826 ) +colvars: ( 0.509307 , -0.232715 , -0.183798 ) +colvars: ( 0.650449 , -0.236051 , -0.10496 ) +colvars: ( 0.45747 , -0.23695 , -0.220141 ) +colvars: ( 0.463307 , -0.309337 , -0.314669 ) +colvars: ( 0.404308 , -0.158511 , -0.145369 ) +colvars: ( 0.345026 , -0.151299 , -0.170617 ) +colvars: ( 0.326567 , -0.0587806 , -0.0562952 ) +colvars: ( 0.212362 , -0.1601 , -0.260874 ) +colvars: ( 0.185643 , -0.204516 , -0.33677 ) +colvars: ( -0.00291463 , -0.208311 , -0.45326 ) +colvars: ( -0.10077 , -0.226834 , -0.53612 ) +colvars: ( 0.105712 , -0.26208 , -0.461887 ) +colvars: ( 0.124851 , -0.116714 , -0.253832 ) +colvars: ( -0.00347029 , -0.120859 , -0.335222 ) +colvars: ( -0.0989785 , -0.0347412 , -0.275065 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.88148 , 0.551647 , 1.52188 ) -colvars: ( 4.18587 , 0.473038 , 1.30501 ) -colvars: ( 4.18587 , 0.473038 , 1.30501 ) -colvars: ( 5.5757 , 0.6301 , 1.73832 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.18969 , 0.585835 , 1.61538 ) +colvars: ( 4.45016 , 0.502354 , 1.38519 ) +colvars: ( 4.45016 , 0.502354 , 1.38519 ) +colvars: ( 5.92774 , 0.66915 , 1.84512 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.620856 , -0.0805104 , -0.384779 ) -colvars: ( -0.557435 , -0.16267 , -0.355802 ) -colvars: ( -0.509582 , -0.140887 , -0.298413 ) -colvars: ( -0.516025 , -0.190223 , -0.325817 ) -colvars: ( -0.506426 , -0.132044 , -0.291488 ) -colvars: ( -0.489307 , -0.281509 , -0.337642 ) -colvars: ( -0.454232 , -0.321754 , -0.319413 ) -colvars: ( -0.43079 , -0.428122 , -0.340929 ) -colvars: ( -0.391406 , -0.287004 , -0.241461 ) -colvars: ( -0.385783 , -0.262119 , -0.22525 ) -colvars: ( -0.343509 , -0.281465 , -0.190917 ) -colvars: ( -0.283468 , -0.245172 , -0.115112 ) -colvars: ( -0.236314 , -0.259953 , -0.0739318 ) -colvars: ( -0.304283 , -0.142944 , -0.0927086 ) -colvars: ( -0.272411 , -0.114178 , -0.0484402 ) -colvars: ( -0.360499 , -0.0858269 , -0.125054 ) -colvars: ( -0.388512 , 0.011546 , -0.111953 ) -colvars: ( -0.441045 , 0.0590415 , -0.144673 ) -colvars: ( -0.424485 , 0.0263748 , -0.141862 ) -colvars: ( -0.413083 , 0.0824728 , -0.106601 ) -colvars: ( -0.467103 , -0.0270385 , -0.207394 ) -colvars: ( -0.499569 , -0.0285401 , -0.240699 ) -colvars: ( -0.548316 , -0.0931488 , -0.317147 ) -colvars: ( -0.445503 , -0.058608 , -0.199046 ) -colvars: ( -0.45172 , -0.0150543 , -0.186833 ) -colvars: ( -0.389442 , -0.132388 , -0.173921 ) -colvars: ( -0.330161 , -0.163724 , -0.127559 ) -colvars: ( -0.278971 , -0.253162 , -0.113975 ) -colvars: ( -0.290015 , -0.0917525 , -0.0566445 ) -colvars: ( -0.275624 , -0.0735136 , -0.0344299 ) -colvars: ( -0.272459 , -0.0472238 , -0.0200969 ) -colvars: ( -0.238379 , 0.0266885 , 0.0455361 ) -colvars: ( -0.219538 , 0.0529473 , 0.0756297 ) -colvars: ( -0.282913 , 0.112695 , 0.0371953 ) -colvars: ( -0.255983 , 0.153863 , 0.0817491 ) -colvars: ( -0.352935 , 0.140839 , -0.0213295 ) -colvars: ( -0.402066 , 0.216405 , -0.0387233 ) -colvars: ( -0.474416 , 0.239115 , -0.101894 ) -colvars: ( -0.411233 , 0.196605 , -0.056343 ) -colvars: ( -0.415681 , 0.256758 , -0.0353124 ) -colvars: ( -0.413676 , 0.110816 , -0.0951795 ) -colvars: ( -0.418351 , 0.0807814 , -0.112619 ) -colvars: ( -0.43815 , -0.0115757 , -0.171704 ) -colvars: ( -0.350482 , 0.0692644 , -0.049211 ) -colvars: ( -0.352675 , 0.0951855 , -0.0404267 ) -colvars: ( -0.190283 , 0.101082 , 0.125477 ) -colvars: ( -0.140005 , 0.102653 , 0.176734 ) -colvars: ( -0.219253 , 0.172934 , 0.126795 ) -colvars: ( -0.288156 , 0.0287593 , -0.00367274 ) -colvars: ( -0.220411 , 0.0149384 , 0.0586334 ) -colvars: ( -0.166001 , -0.0674787 , 0.0784344 ) +colvars: ( -0.659805 , -0.0856054 , -0.408542 ) +colvars: ( -0.592436 , -0.1729 , -0.377742 ) +colvars: ( -0.541561 , -0.149764 , -0.316769 ) +colvars: ( -0.548468 , -0.202158 , -0.345904 ) +colvars: ( -0.538268 , -0.140332 , -0.309462 ) +colvars: ( -0.520108 , -0.299149 , -0.35845 ) +colvars: ( -0.482874 , -0.341894 , -0.339097 ) +colvars: ( -0.457991 , -0.454914 , -0.361929 ) +colvars: ( -0.416115 , -0.304962 , -0.256305 ) +colvars: ( -0.410156 , -0.278508 , -0.239107 ) +colvars: ( -0.365201 , -0.299085 , -0.2026 ) +colvars: ( -0.301398 , -0.260515 , -0.122087 ) +colvars: ( -0.251272 , -0.276233 , -0.0783211 ) +colvars: ( -0.323495 , -0.151892 , -0.0983161 ) +colvars: ( -0.289638 , -0.121315 , -0.0513105 ) +colvars: ( -0.3832 , -0.0912138 , -0.132678 ) +colvars: ( -0.412946 , 0.0122499 , -0.118786 ) +colvars: ( -0.468731 , 0.0626997 , -0.153536 ) +colvars: ( -0.451193 , 0.0280191 , -0.15058 ) +colvars: ( -0.439077 , 0.0876347 , -0.113148 ) +colvars: ( -0.496498 , -0.0287334 , -0.220187 ) +colvars: ( -0.531022 , -0.0303162 , -0.255585 ) +colvars: ( -0.582836 , -0.0989689 , -0.336778 ) +colvars: ( -0.473603 , -0.0622484 , -0.211349 ) +colvars: ( -0.480218 , -0.0159597 , -0.198401 ) +colvars: ( -0.41405 , -0.140641 , -0.184641 ) +colvars: ( -0.351087 , -0.173922 , -0.135399 ) +colvars: ( -0.296707 , -0.268956 , -0.120943 ) +colvars: ( -0.308414 , -0.097445 , -0.0600886 ) +colvars: ( -0.29314 , -0.0780518 , -0.0365119 ) +colvars: ( -0.289726 , -0.0501427 , -0.0212587 ) +colvars: ( -0.253496 , 0.0283949 , 0.048444 ) +colvars: ( -0.23344 , 0.0562809 , 0.0804273 ) +colvars: ( -0.300806 , 0.119785 , 0.0395552 ) +colvars: ( -0.272196 , 0.163538 , 0.0868623 ) +colvars: ( -0.375197 , 0.149681 , -0.0226153 ) +colvars: ( -0.427395 , 0.229978 , -0.0411181 ) +colvars: ( -0.504252 , 0.254095 , -0.108216 ) +colvars: ( -0.43717 , 0.208956 , -0.0598532 ) +colvars: ( -0.441898 , 0.27288 , -0.0375383 ) +colvars: ( -0.439797 , 0.117805 , -0.101095 ) +colvars: ( -0.444799 , 0.085908 , -0.119635 ) +colvars: ( -0.465863 , -0.0122259 , -0.18238 ) +colvars: ( -0.372703 , 0.0736841 , -0.0522888 ) +colvars: ( -0.37505 , 0.101239 , -0.0429806 ) +colvars: ( -0.202473 , 0.107503 , 0.133268 ) +colvars: ( -0.149063 , 0.109183 , 0.187705 ) +colvars: ( -0.23322 , 0.183837 , 0.134665 ) +colvars: ( -0.306477 , 0.0306434 , -0.00389796 ) +colvars: ( -0.23451 , 0.01597 , 0.0622802 ) +colvars: ( -0.176705 , -0.0716049 , 0.083341 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 12. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 12. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 12, atoms_new_colvar_forces = { ( -4.60416200301848e+00 , -4.37756284700426e-01 , -1.27227691754553e+00 ), ( -3.96621596863790e+00 , -3.69922931911158e-01 , -1.00134529679591e+00 ), ( -4.03858528774981e+00 , -3.96004927783702e-01 , -1.03660358798177e+00 ), ( -5.43085162563976e+00 , -5.61462924506829e-01 , -1.53281752140938e+00 ), ( 2.52363689247368e-01 , 1.17670511959752e-01 , 3.42323432777615e-01 ), ( 4.96741230845689e+00 , 6.15270971905017e-01 , 1.83185400807489e+00 ), ( 4.19769564488300e+00 , 5.11141221197853e-01 , 1.58863191712320e+00 ), ( -4.27662929355598e-02 , 2.95612670755830e-02 , 3.48427877676948e-01 ), ( 4.17824538855081e+00 , 5.01546377407413e-01 , 1.55793193781718e+00 ), ( 5.53808746651970e+00 , 6.42179756465880e-01 , 1.93047144887531e+00 ), ( 1.14375417566049e-02 , 3.91734938130505e-02 , 2.93363468353129e-01 ), ( -1.19347846750439e-04 , 3.27265206291947e-02 , 2.68997676509169e-01 ), ( 2.04917499010411e-02 , 4.67937133134244e-02 , 3.33548614846786e-01 ), ( 4.25694709662555e-02 , 3.66723510925716e-02 , 1.95872932010920e-01 ), ( 1.49589089809564e-02 , 2.23689698419174e-02 , 1.46684679808794e-01 ), ( 1.10942559946892e-01 , 5.60636699505158e-02 , 1.86075351427912e-01 ), ( 1.56624720330733e-01 , 6.15688485861727e-02 , 1.18354490821199e-01 ), ( 2.35776330104741e-01 , 8.73025032542672e-02 , 1.33987616003798e-01 ), ( 1.28484285779145e-01 , 4.48093035207972e-02 , 5.03095763111477e-02 ), ( 1.23931515695198e-01 , 3.58594939211851e-02 , -1.19193045247740e-02 ), ( 1.06268060132023e-01 , 3.95470517957588e-02 , 6.20197301896569e-02 ), ( 7.13696518171053e-02 , 2.21955893176192e-02 , 5.81983461485280e-03 ), ( 5.89501894578733e-02 , 2.24561960891333e-02 , 3.86591357010410e-02 ), ( -8.41514629004392e-04 , -2.70815266962117e-03 , -2.01552831428085e-02 ), ( -1.42781456312115e-02 , -1.49924494423558e-02 , -8.78021804497830e-02 ), ( -4.79631559915603e-02 , -1.03566167906717e-02 , 3.35262719064853e-02 ), ( -1.15006131967528e-01 , -3.24641122952530e-02 , 1.77346578863561e-02 ), ( -1.56347702432740e-01 , -3.57025213484728e-02 , 9.33374664950721e-02 ), ( -1.02874919178057e-01 , -3.43727930989843e-02 , -2.79237118241520e-02 ), ( -1.38731690028093e-01 , -5.19909893725838e-02 , -8.39446687419543e-02 ), ( -5.03923572669588e-02 , -1.59042210930658e-02 , -6.01787372405616e-03 ), ( -2.99087347311788e-02 , -1.47126907452013e-02 , -4.68680712295294e-02 ), ( 2.56618747965985e-02 , 7.69047263856128e-03 , -2.90404569400160e-04 ), ( 1.58524766448676e-03 , -1.50045503741583e-02 , -1.27114139759477e-01 ), ( -1.60124616049861e-02 , -2.68163680344020e-02 , -1.80595986281854e-01 ), ( 4.80067747608525e-02 , -2.32614238032083e-03 , -1.37766493033706e-01 ), ( 7.70598843276784e-02 , -2.57104270572023e-03 , -2.11593424546662e-01 ), ( 1.37536095785058e-01 , 1.69811113976544e-02 , -2.00550226781543e-01 ), ( 1.90971989338418e-02 , -2.63325143667982e-02 , -2.63410591662629e-01 ), ( 2.01405894558621e-02 , -3.42926000685874e-02 , -3.31346404967134e-01 ), ( -3.33876932201316e-02 , -3.82918851108436e-02 , -2.31866561651735e-01 ), ( -9.38647083066095e-02 , -6.15165982123629e-02 , -2.73061494078509e-01 ), ( -1.31046987776956e-01 , -6.68011620217128e-02 , -2.24540057378766e-01 ), ( -1.50844297938520e-01 , -8.12960617680461e-02 , -2.94614300476024e-01 ), ( -1.78188578549210e-01 , -9.71580672763863e-02 , -3.57257930575860e-01 ), ( -1.93220098418491e-01 , -9.48359932665020e-02 , -3.01036128669544e-01 ), ( -2.35032678802051e-01 , -1.10680750129854e-01 , -3.27774055228857e-01 ), ( -1.19953280936978e-01 , -7.36064528570606e-02 , -3.07837674488556e-01 ), ( -1.70866846813936e-01 , -8.09723802475359e-02 , -2.42463108076809e-01 ), ( -2.23882676752656e-01 , -9.86764076408371e-02 , -2.56773434825889e-01 ), ( -2.59351961445597e-01 , -1.00048802953869e-01 , -1.80365290808875e-01 ) } +colvars: Step 12, atoms_new_colvar_forces = { ( -4.89490574889113e+00 , -4.64774252641731e-01 , -1.35006023160969e+00 ), ( -4.21667171666565e+00 , -3.92745935728585e-01 , -1.06240156560237e+00 ), ( -4.29359785587889e+00 , -4.20469184921439e-01 , -1.09988016615827e+00 ), ( -5.77376897192617e+00 , -5.96190549932710e-01 , -1.62667691433255e+00 ), ( 2.68254009642205e-01 , 1.25079351029727e-01 , 3.63878023447364e-01 ), ( 5.28103187483856e+00 , 6.53468241162387e-01 , 1.94487516194241e+00 ), ( 4.46272966411243e+00 , 5.42861093800513e-01 , 1.68666944573490e+00 ), ( -4.54573561845573e-02 , 3.14293983525731e-02 , 3.70367397645178e-01 ), ( 4.44205365781094e+00 , 5.32661605360381e-01 , 1.65403521844747e+00 ), ( 5.88775893813820e+00 , 6.81994156523306e-01 , 2.04937066321476e+00 ), ( 1.21571008088405e-02 , 4.16438537525102e-02 , 3.11833525414787e-01 ), ( -1.28558119093569e-04 , 3.47903538534744e-02 , 2.85932299166015e-01 ), ( 2.17791621243190e-02 , 4.97432814457449e-02 , 3.54546217085878e-01 ), ( 4.52481308887325e-02 , 3.89826259618592e-02 , 2.08203610691296e-01 ), ( 1.58987103728810e-02 , 2.37783431230710e-02 , 1.55917845951448e-01 ), ( 1.17926751938918e-01 , 5.95934911655521e-02 , 1.97789911765121e-01 ), ( 1.66485372508838e-01 , 6.54433615727072e-02 , 1.25805491016107e-01 ), ( 2.50621000683816e-01 , 9.27959688237679e-02 , 1.42423490979841e-01 ), ( 1.36574083657088e-01 , 4.76286029298191e-02 , 5.34774085413792e-02 ), ( 1.31734460156563e-01 , 3.81143676165490e-02 , -1.26697582429871e-02 ), ( 1.12960101651388e-01 , 4.20361460399759e-02 , 6.59260414106081e-02 ), ( 7.58653239458306e-02 , 2.35925197995797e-02 , 6.18873743058740e-03 ), ( 6.26649822284892e-02 , 2.38707788780387e-02 , 4.10969144218748e-02 ), ( -8.92959680793504e-04 , -2.87826672277569e-03 , -2.14225009843340e-02 ), ( -1.51753706219444e-02 , -1.59366362085343e-02 , -9.33283264047111e-02 ), ( -5.09822485294129e-02 , -1.10067941638486e-02 , 3.56380243051370e-02 ), ( -1.22247083974906e-01 , -3.45052996690010e-02 , 1.88512984490016e-02 ), ( -1.66192319555690e-01 , -3.79458769336318e-02 , 9.92133503535462e-02 ), ( -1.09352966810302e-01 , -3.65355087010639e-02 , -2.96828571144716e-02 ), ( -1.47467382472801e-01 , -5.52630536494705e-02 , -8.92310488465498e-02 ), ( -5.35667351986572e-02 , -1.69052661733132e-02 , -6.39862819504183e-03 ), ( -3.17942629359031e-02 , -1.56401522438041e-02 , -4.98218056743984e-02 ), ( 2.72743998191535e-02 , 8.17269516888103e-03 , -3.12415826215579e-04 ), ( 1.68329897527458e-03 , -1.59519978436565e-02 , -1.35119541705500e-01 ), ( -1.70228143957742e-02 , -2.85081164231803e-02 , -1.91969200515544e-01 ), ( 5.10286830970168e-02 , -2.47603852696932e-03 , -1.46441326330843e-01 ), ( 8.19118009903109e-02 , -2.73776863389308e-03 , -2.24915635454790e-01 ), ( 1.46196725947246e-01 , 1.80447162321154e-02 , -2.13175934601129e-01 ), ( 2.03002750710456e-02 , -2.79945513141760e-02 , -2.79994622801097e-01 ), ( 2.14094345429477e-02 , -3.64568337373448e-02 , -3.52207715795593e-01 ), ( -3.54887320110356e-02 , -4.07050867573193e-02 , -2.46464027267080e-01 ), ( -9.97729655908142e-02 , -6.53911315690126e-02 , -2.90252067443280e-01 ), ( -1.39295638967675e-01 , -7.10065750701262e-02 , -2.38674851929840e-01 ), ( -1.60341051122720e-01 , -8.64154448082740e-02 , -3.13163006600101e-01 ), ( -1.89406743056207e-01 , -1.03276392503134e-01 , -3.79750528934929e-01 ), ( -2.05387826104413e-01 , -1.00808334778545e-01 , -3.19992579801541e-01 ), ( -2.49833715710703e-01 , -1.17650508088223e-01 , -3.48414816503726e-01 ), ( -1.27507941145204e-01 , -7.82438307878345e-02 , -3.27222287886911e-01 ), ( -1.81625360124679e-01 , -8.60706461792183e-02 , -2.57729569122441e-01 ), ( -2.37980145706232e-01 , -1.04888838911070e-01 , -2.72942057278126e-01 ), ( -2.75683472569685e-01 , -1.06346078970650e-01 , -1.91724088450644e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 12, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4570,10 +7363,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 13, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 13, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 13, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 13, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 13, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 13, atoms_positions[size = 51] = { ( 8.32563668862924e+00 , 4.32657320564243e-02 , -7.65748447617707e-01 ), ( 6.98661919936763e+00 , -5.41227563033319e-01 , -6.21758543748275e-01 ), ( 6.19209801346542e+00 , -3.15306580245825e-01 , 6.93705052961330e-01 ), ( 4.97978049326016e+00 , -1.89278595719519e-01 , 7.00300270066944e-01 ), ( 7.05341851019372e+00 , -2.03495284782903e+00 , -9.67525140668200e-01 ), ( 6.89615579853863e+00 , -2.65271694396097e-01 , 1.86087063899170e+00 ), ( 6.18601376492217e+00 , -1.23547653691593e-01 , 3.17160838459325e+00 ), ( 7.10298170551818e+00 , -3.45744813901811e-01 , 4.28313968504903e+00 ), ( 5.28829647670455e+00 , 1.11142363892930e+00 , 3.32452399627943e+00 ), ( 4.13230788771988e+00 , 1.04355492143894e+00 , 3.65165316687648e+00 ), ( 5.86803046994690e+00 , 2.25027637895970e+00 , 2.99786612839834e+00 ), ( 5.22090995318872e+00 , 3.59158121811476e+00 , 2.90066447440529e+00 ), ( 6.33290598194421e+00 , 4.52788068981783e+00 , 2.42619501232639e+00 ), ( 3.90924832418276e+00 , 3.73836971419749e+00 , 2.03350920492794e+00 ), ( 2.83214384561086e+00 , 4.13594770995655e+00 , 2.51990224649253e+00 ), ( 3.88445670732267e+00 , 3.24094017599406e+00 , 7.43123862429219e-01 ), ( 2.66186122446235e+00 , 3.06673144525553e+00 , -1.07940780309680e-01 ), ( 3.03267628080236e+00 , 2.72277183365063e+00 , -1.55733631745110e+00 ), ( 1.57223017446702e+00 , 2.19056819808818e+00 , 5.23365936649474e-01 ), ( 4.27797343425988e-01 , 2.51332171791790e+00 , 5.30763201286296e-01 ), ( 1.99144319024645e+00 , 1.00294925032535e+00 , 1.07434901335352e+00 ), ( 1.18195814860052e+00 , 7.58451142980359e-02 , 1.69221730557218e+00 ), ( 2.02416703905804e+00 , -1.13881127834980e+00 , 2.00759640101040e+00 ), ( 5.49617185678168e-01 , 6.09368571473590e-01 , 2.93374885372882e+00 ), ( -6.45188447181623e-01 , 3.52467064801428e-01 , 3.17017989878665e+00 ), ( 1.32597370357311e+00 , 1.34180807118143e+00 , 3.83137967123143e+00 ), ( 8.59775872582345e-01 , 1.94897297063648e+00 , 5.03552588557840e+00 ), ( 2.03094018947012e+00 , 2.62571564767449e+00 , 5.63948259151190e+00 ), ( -3.48983674247370e-01 , 2.91670045601694e+00 , 4.97412630730138e+00 ), ( -1.15856527598334e+00 , 3.05060646151493e+00 , 5.90337715179325e+00 ), ( -4.71314783134488e-01 , 3.61719276093745e+00 , 3.84600498612597e+00 ), ( -1.49575782198763e+00 , 4.55039130986648e+00 , 3.51351392910702e+00 ), ( -7.22385227454294e-01 , 5.40073011168207e+00 , 2.44146282214525e+00 ), ( -2.76925428816865e+00 , 3.87661302285524e+00 , 2.91740443128944e+00 ), ( -3.83010584362955e+00 , 4.46702339232755e+00 , 2.82711386484213e+00 ), ( -2.60381690422610e+00 , 2.64492564216005e+00 , 2.44975836915772e+00 ), ( -3.73546535960365e+00 , 1.86577767106548e+00 , 2.02271438672350e+00 ), ( -3.41402649543479e+00 , 8.64772982443447e-01 , 9.25433492011849e-01 ), ( -4.30522658520302e+00 , 1.06547933586241e+00 , 3.24687854450203e+00 ), ( -5.52835461462766e+00 , 8.68203672679641e-01 , 3.33049508088187e+00 ), ( -3.41380267786763e+00 , 6.68866823699580e-01 , 4.15014754048846e+00 ), ( -3.75690767903950e+00 , 4.55839844889497e-02 , 5.46353760075140e+00 ), ( -2.38288396029947e+00 , -3.29295031220147e-01 , 6.16828366291920e+00 ), ( -4.47388340590213e+00 , 9.99001790413945e-01 , 6.43712437824932e+00 ), ( -5.33370829992695e+00 , 6.08187134023306e-01 , 7.20109423386675e+00 ), ( -6.25584413419192e+00 , 3.57194274168611e+00 , 6.71034737659518e+00 ), ( -6.92768822243289e+00 , 4.29560122448252e+00 , 7.44103235347024e+00 ), ( -6.74726924123469e+00 , 3.20379273004767e+00 , 5.52276082551144e+00 ), ( -4.12167346184729e+00 , 2.28457680469545e+00 , 6.46418689653973e+00 ), ( -4.84967541764903e+00 , 3.19499187486762e+00 , 7.21597988933476e+00 ), ( -4.10191196539783e+00 , 4.57773057696201e+00 , 7.29465500401028e+00 ) } +colvars: Step 13, atoms_positions[size = 51] = { ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 ), ( 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 ), ( 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 ), ( 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 ), ( 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 ), ( 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 ), ( 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 ), ( 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 ), ( 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 ), ( 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 ), ( 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 ), ( 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 ), ( 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 ), ( 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 ), ( 2.83214575810826e+00 , 4.13595170834672e+00 , 2.51992869876098e+00 ), ( 3.88447884319767e+00 , 3.24095178677905e+00 , 7.43161138393898e-01 ), ( 2.66189458936046e+00 , 3.06674501687041e+00 , -1.07915315664321e-01 ), ( 3.03272107178712e+00 , 2.72278863903895e+00 , -1.55730911754205e+00 ), ( 1.57225734397424e+00 , 2.19057818008372e+00 , 5.23377682763401e-01 ), ( 4.27821186858660e-01 , 2.51332776145223e+00 , 5.30761279881784e-01 ), ( 1.99146378967290e+00 , 1.00295776233815e+00 , 1.07436273138212e+00 ), ( 1.18197300708239e+00 , 7.58502845988991e-02 , 1.69221931299880e+00 ), ( 2.02418101326422e+00 , -1.13880506272946e+00 , 2.00760706123916e+00 ), ( 5.49618108438383e-01 , 6.09368087019359e-01 , 2.93374468907765e+00 ), ( -6.45190245409923e-01 , 3.52464608156817e-01 , 3.17016475896813e+00 ), ( 1.32597733453506e+00 , 1.34180367960609e+00 , 3.83138482698476e+00 ), ( 8.59752646405481e-01 , 1.94896559215968e+00 , 5.03552931652643e+00 ), ( 2.03090979027595e+00 , 2.62570821811796e+00 , 5.63949869801013e+00 ), ( -3.49005720764981e-01 , 2.91669232246480e+00 , 4.97411954802775e+00 ), ( -1.15859126627669e+00 , 3.05059754241338e+00 , 5.90336377131071e+00 ), ( -4.71324849253532e-01 , 3.61718950042861e+00 , 3.84600236908586e+00 ), ( -1.49576392608207e+00 , 4.55038851624654e+00 , 3.51350351544032e+00 ), ( -7.22380687986103e-01 , 5.40073126999859e+00 , 2.44146217134017e+00 ), ( -2.76925466861065e+00 , 3.87661075599847e+00 , 2.91737661568981e+00 ), ( -3.83010802920451e+00 , 4.46701830454351e+00 , 2.82708188305086e+00 ), ( -2.60380816777968e+00 , 2.64492492063907e+00 , 2.44973080554366e+00 ), ( -3.73544928409753e+00 , 1.86577757211119e+00 , 2.02266810954733e+00 ), ( -3.41399991375659e+00 , 8.64775140375181e-01 , 9.25392368021579e-01 ), ( -4.30522154846684e+00 , 1.06547244135007e+00 , 3.24682101086543e+00 ), ( -5.52835078590118e+00 , 8.68197671934854e-01 , 3.33043603374501e+00 ), ( -3.41380912283504e+00 , 6.68858792934437e-01 , 4.15009982032347e+00 ), ( -3.75692856388351e+00 , 4.55701681879979e-02 , 5.46348028888173e+00 ), ( -2.38291005376584e+00 , -3.29306560614546e-01 , 6.16823880404895e+00 ), ( -4.47391676453799e+00 , 9.98985309012160e-01 , 6.43705901718938e+00 ), ( -5.33373979385291e+00 , 6.08169813898481e-01 , 7.20103084854860e+00 ), ( -6.25588657480039e+00 , 3.57192302949498e+00 , 6.71028547717466e+00 ), ( -6.92772939382645e+00 , 4.29558076535878e+00 , 7.44097322494073e+00 ), ( -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 ), ( -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 ), ( -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 ), ( -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ) } colvars: Step 13, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 13, atom_groups_ids[size = 0] = @@ -4591,162 +7384,301 @@ colvars: Collective variables module, step no. 13 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.17961771860725e-01 , 4.11480979755661e-03 , 9.48094604971212e-01 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.17465326396842e-01 , 4.17503558318963e-03 , 9.48260689691198e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 , 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 , 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 , 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 , 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 , 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 , 2.83214575810826e+00 , 4.13595170834672e+00 , 2.51992869876098e+00 , 3.88447884319767e+00 , 3.24095178677905e+00 , 7.43161138393898e-01 , 2.66189458936046e+00 , 3.06674501687041e+00 , -1.07915315664321e-01 , 3.03272107178712e+00 , 2.72278863903895e+00 , -1.55730911754205e+00 , 1.57225734397424e+00 , 2.19057818008372e+00 , 5.23377682763401e-01 , 4.27821186858660e-01 , 2.51332776145223e+00 , 5.30761279881784e-01 , 1.99146378967290e+00 , 1.00295776233815e+00 , 1.07436273138212e+00 , 1.18197300708239e+00 , 7.58502845988991e-02 , 1.69221931299880e+00 , 2.02418101326422e+00 , -1.13880506272946e+00 , 2.00760706123916e+00 , 5.49618108438383e-01 , 6.09368087019359e-01 , 2.93374468907765e+00 , -6.45190245409923e-01 , 3.52464608156817e-01 , 3.17016475896813e+00 , 1.32597733453506e+00 , 1.34180367960609e+00 , 3.83138482698476e+00 , 8.59752646405481e-01 , 1.94896559215968e+00 , 5.03552931652643e+00 , 2.03090979027595e+00 , 2.62570821811796e+00 , 5.63949869801013e+00 , -3.49005720764981e-01 , 2.91669232246480e+00 , 4.97411954802775e+00 , -1.15859126627669e+00 , 3.05059754241338e+00 , 5.90336377131071e+00 , -4.71324849253532e-01 , 3.61718950042861e+00 , 3.84600236908586e+00 , -1.49576392608207e+00 , 4.55038851624654e+00 , 3.51350351544032e+00 , -7.22380687986103e-01 , 5.40073126999859e+00 , 2.44146217134017e+00 , -2.76925466861065e+00 , 3.87661075599847e+00 , 2.91737661568981e+00 , -3.83010802920451e+00 , 4.46701830454351e+00 , 2.82708188305086e+00 , -2.60380816777968e+00 , 2.64492492063907e+00 , 2.44973080554366e+00 , -3.73544928409753e+00 , 1.86577757211119e+00 , 2.02266810954733e+00 , -3.41399991375659e+00 , 8.64775140375181e-01 , 9.25392368021579e-01 , -4.30522154846684e+00 , 1.06547244135007e+00 , 3.24682101086543e+00 , -5.52835078590118e+00 , 8.68197671934854e-01 , 3.33043603374501e+00 , -3.41380912283504e+00 , 6.68858792934437e-01 , 4.15009982032347e+00 , -3.75692856388351e+00 , 4.55701681879979e-02 , 5.46348028888173e+00 , -2.38291005376584e+00 , -3.29306560614546e-01 , 6.16823880404895e+00 , -4.47391676453799e+00 , 9.98985309012160e-01 , 6.43705901718938e+00 , -5.33373979385291e+00 , 6.08169813898481e-01 , 7.20103084854860e+00 , -6.25588657480039e+00 , 3.57192302949498e+00 , 6.71028547717466e+00 , -6.92772939382645e+00 , 4.29558076535878e+00 , 7.44097322494073e+00 , -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 , -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 , -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 , -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.17961771860725e-01 , 4.11480979755661e-03 , 9.48094604971212e-01 ). +colvars: Colvar "one" has value ( -3.17465326396842e-01 , 4.17503558318963e-03 , 9.48260689691198e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 , 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 , 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 , 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 , 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 , 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 , 2.83214575810826e+00 , 4.13595170834672e+00 , 2.51992869876098e+00 , 3.88447884319767e+00 , 3.24095178677905e+00 , 7.43161138393898e-01 , 2.66189458936046e+00 , 3.06674501687041e+00 , -1.07915315664321e-01 , 3.03272107178712e+00 , 2.72278863903895e+00 , -1.55730911754205e+00 , 1.57225734397424e+00 , 2.19057818008372e+00 , 5.23377682763401e-01 , 4.27821186858660e-01 , 2.51332776145223e+00 , 5.30761279881784e-01 , 1.99146378967290e+00 , 1.00295776233815e+00 , 1.07436273138212e+00 , 1.18197300708239e+00 , 7.58502845988991e-02 , 1.69221931299880e+00 , 2.02418101326422e+00 , -1.13880506272946e+00 , 2.00760706123916e+00 , 5.49618108438383e-01 , 6.09368087019359e-01 , 2.93374468907765e+00 , -6.45190245409923e-01 , 3.52464608156817e-01 , 3.17016475896813e+00 , 1.32597733453506e+00 , 1.34180367960609e+00 , 3.83138482698476e+00 , 8.59752646405481e-01 , 1.94896559215968e+00 , 5.03552931652643e+00 , 2.03090979027595e+00 , 2.62570821811796e+00 , 5.63949869801013e+00 , -3.49005720764981e-01 , 2.91669232246480e+00 , 4.97411954802775e+00 , -1.15859126627669e+00 , 3.05059754241338e+00 , 5.90336377131071e+00 , -4.71324849253532e-01 , 3.61718950042861e+00 , 3.84600236908586e+00 , -1.49576392608207e+00 , 4.55038851624654e+00 , 3.51350351544032e+00 , -7.22380687986103e-01 , 5.40073126999859e+00 , 2.44146217134017e+00 , -2.76925466861065e+00 , 3.87661075599847e+00 , 2.91737661568981e+00 , -3.83010802920451e+00 , 4.46701830454351e+00 , 2.82708188305086e+00 , -2.60380816777968e+00 , 2.64492492063907e+00 , 2.44973080554366e+00 , -3.73544928409753e+00 , 1.86577757211119e+00 , 2.02266810954733e+00 , -3.41399991375659e+00 , 8.64775140375181e-01 , 9.25392368021579e-01 , -4.30522154846684e+00 , 1.06547244135007e+00 , 3.24682101086543e+00 , -5.52835078590118e+00 , 8.68197671934854e-01 , 3.33043603374501e+00 , -3.41380912283504e+00 , 6.68858792934437e-01 , 4.15009982032347e+00 , -3.75692856388351e+00 , 4.55701681879979e-02 , 5.46348028888173e+00 , -2.38291005376584e+00 , -3.29306560614546e-01 , 6.16823880404895e+00 , -4.47391676453799e+00 , 9.98985309012160e-01 , 6.43705901718938e+00 , -5.33373979385291e+00 , 6.08169813898481e-01 , 7.20103084854860e+00 , -6.25588657480039e+00 , 3.57192302949498e+00 , 6.71028547717466e+00 , -6.92772939382645e+00 , 4.29558076535878e+00 , 7.44097322494073e+00 , -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 , -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 , -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 , -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.8772 , 1.8695 , -15.0583 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.7009 , 6.67009 , 13.3402 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.8772 , 1.8695 , -15.0583 ) to colvar "one". -colvars: Adding total bias energy: 44.9939 +colvars: Adding biasing force ( 66.7009 , 6.67009 , 13.3402 ) to colvar "one". +colvars: Adding total bias energy: 57.4906 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.8772 , 1.8695 , -15.0583 ) +colvars: Force to be applied: ( 66.7009 , 6.67009 , 13.3402 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.88688 , -0.548692 , -1.5111 ) -colvars: ( -4.1905 , -0.470504 , -1.29577 ) -colvars: ( -4.1905 , -0.470504 , -1.29577 ) -colvars: ( -5.58187 , -0.626724 , -1.726 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.18411 , -0.581337 , -1.60007 ) +colvars: ( -4.44538 , -0.498496 , -1.37206 ) +colvars: ( -4.44538 , -0.498496 , -1.37206 ) +colvars: ( -5.92137 , -0.664012 , -1.82762 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.897491 , 0.194571 , 0.632175 ) -colvars: ( 0.776624 , 0.26585 , 0.657177 ) -colvars: ( 0.761369 , 0.258688 , 0.638515 ) -colvars: ( 0.66312 , 0.267203 , 0.592097 ) -colvars: ( 0.651102 , 0.200643 , 0.49513 ) -colvars: ( 0.575274 , 0.344962 , 0.645314 ) -colvars: ( 0.466374 , 0.359562 , 0.600835 ) -colvars: ( 0.388536 , 0.457275 , 0.6869 ) -colvars: ( 0.384187 , 0.315206 , 0.492489 ) -colvars: ( 0.348691 , 0.273852 , 0.415723 ) -colvars: ( 0.355289 , 0.320372 , 0.482431 ) -colvars: ( 0.283751 , 0.277633 , 0.382546 ) -colvars: ( 0.257138 , 0.306519 , 0.405865 ) -colvars: ( 0.347103 , 0.179444 , 0.287301 ) -colvars: ( 0.287733 , 0.136344 , 0.194101 ) -colvars: ( 0.47143 , 0.141834 , 0.309803 ) -colvars: ( 0.544961 , 0.0500621 , 0.229222 ) -colvars: ( 0.676344 , 0.0284316 , 0.277462 ) -colvars: ( 0.552893 , 0.0184267 , 0.191179 ) -colvars: ( 0.536964 , -0.0466112 , 0.0939638 ) -colvars: ( 0.573364 , 0.0665204 , 0.26819 ) -colvars: ( 0.571056 , 0.0506088 , 0.245343 ) -colvars: ( 0.607413 , 0.115433 , 0.354311 ) -colvars: ( 0.445056 , 0.0556579 , 0.177886 ) -colvars: ( 0.43789 , -0.000190828 , 0.0982455 ) -colvars: ( 0.342052 , 0.121703 , 0.206352 ) -colvars: ( 0.215988 , 0.130824 , 0.144355 ) -colvars: ( 0.123611 , 0.216942 , 0.206191 ) -colvars: ( 0.187944 , 0.0569904 , 0.0281205 ) -colvars: ( 0.137835 , 0.0210832 , -0.0499059 ) -colvars: ( 0.222682 , 0.0310296 , 0.0135415 ) -colvars: ( 0.209024 , -0.0416324 , -0.0926299 ) -colvars: ( 0.245552 , -0.0453886 , -0.0761696 ) -colvars: ( 0.284935 , -0.127864 , -0.164326 ) -colvars: ( 0.240484 , -0.180857 , -0.262089 ) -colvars: ( 0.401195 , -0.143259 , -0.11658 ) -colvars: ( 0.479269 , -0.219011 , -0.17285 ) -colvars: ( 0.611857 , -0.222077 , -0.0988319 ) -colvars: ( 0.430686 , -0.223072 , -0.206973 ) -colvars: ( 0.43618 , -0.291168 , -0.295689 ) -colvars: ( 0.380831 , -0.14935 , -0.136811 ) -colvars: ( 0.325251 , -0.142647 , -0.160522 ) -colvars: ( 0.307992 , -0.0556623 , -0.0532347 ) -colvars: ( 0.200628 , -0.150992 , -0.245256 ) -colvars: ( 0.175582 , -0.192813 , -0.316493 ) -colvars: ( -0.00175316 , -0.196383 , -0.425851 ) -colvars: ( -0.0936769 , -0.213857 , -0.503636 ) -colvars: ( 0.100212 , -0.246873 , -0.433924 ) -colvars: ( 0.118362 , -0.110197 , -0.238661 ) -colvars: ( -0.00218851 , -0.114158 , -0.315073 ) -colvars: ( -0.0919338 , -0.0331834 , -0.258632 ) +colvars: ( 0.951742 , 0.206395 , 0.669976 ) +colvars: ( 0.823598 , 0.281953 , 0.696495 ) +colvars: ( 0.807407 , 0.274379 , 0.676732 ) +colvars: ( 0.703269 , 0.283357 , 0.627508 ) +colvars: ( 0.690526 , 0.212778 , 0.524718 ) +colvars: ( 0.610142 , 0.365782 , 0.683925 ) +colvars: ( 0.494697 , 0.381231 , 0.636776 ) +colvars: ( 0.412181 , 0.484819 , 0.728013 ) +colvars: ( 0.407552 , 0.334192 , 0.521938 ) +colvars: ( 0.369926 , 0.290328 , 0.440556 ) +colvars: ( 0.3769 , 0.339683 , 0.511294 ) +colvars: ( 0.301044 , 0.294362 , 0.405425 ) +colvars: ( 0.272813 , 0.325005 , 0.430163 ) +colvars: ( 0.368204 , 0.190265 , 0.304454 ) +colvars: ( 0.305259 , 0.144552 , 0.205661 ) +colvars: ( 0.500013 , 0.150414 , 0.328299 ) +colvars: ( 0.577965 , 0.0531211 , 0.242872 ) +colvars: ( 0.717251 , 0.0302189 , 0.294003 ) +colvars: ( 0.58639 , 0.0195602 , 0.202526 ) +colvars: ( 0.5695 , -0.0494051 , 0.0994725 ) +colvars: ( 0.608107 , 0.0705437 , 0.284148 ) +colvars: ( 0.605676 , 0.0536527 , 0.259913 ) +colvars: ( 0.644236 , 0.12238 , 0.375411 ) +colvars: ( 0.472096 , 0.058976 , 0.188411 ) +colvars: ( 0.464503 , -0.000250906 , 0.103981 ) +colvars: ( 0.36289 , 0.128989 , 0.2186 ) +colvars: ( 0.229238 , 0.138634 , 0.15289 ) +colvars: ( 0.131299 , 0.229934 , 0.218453 ) +colvars: ( 0.199494 , 0.0603511 , 0.0296852 ) +colvars: ( 0.146374 , 0.0222602 , -0.0530299 ) +colvars: ( 0.236307 , 0.0328493 , 0.0142427 ) +colvars: ( 0.221815 , -0.0441871 , -0.0982948 ) +colvars: ( 0.260524 , -0.0481423 , -0.0808319 ) +colvars: ( 0.302298 , -0.135613 , -0.174311 ) +colvars: ( 0.255169 , -0.19181 , -0.277941 ) +colvars: ( 0.425561 , -0.151919 , -0.123714 ) +colvars: ( 0.508339 , -0.232233 , -0.183377 ) +colvars: ( 0.648912 , -0.235461 , -0.104928 ) +colvars: ( 0.456848 , -0.236568 , -0.219562 ) +colvars: ( 0.462673 , -0.308775 , -0.31361 ) +colvars: ( 0.404004 , -0.158421 , -0.14519 ) +colvars: ( 0.345093 , -0.151342 , -0.170336 ) +colvars: ( 0.32681 , -0.0591255 , -0.0566127 ) +colvars: ( 0.212966 , -0.160214 , -0.260146 ) +colvars: ( 0.186419 , -0.204572 , -0.335668 ) +colvars: ( -0.00162404 , -0.208354 , -0.451546 ) +colvars: ( -0.0990831 , -0.226899 , -0.533993 ) +colvars: ( 0.106468 , -0.261859 , -0.460104 ) +colvars: ( 0.125739 , -0.116961 , -0.253137 ) +colvars: ( -0.00207154 , -0.121181 , -0.334124 ) +colvars: ( -0.0972232 , -0.035332 , -0.274277 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.88688 , 0.548692 , 1.5111 ) -colvars: ( 4.1905 , 0.470504 , 1.29577 ) -colvars: ( 4.1905 , 0.470504 , 1.29577 ) -colvars: ( 5.58187 , 0.626724 , 1.726 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.18411 , 0.581337 , 1.60007 ) +colvars: ( 4.44538 , 0.498496 , 1.37206 ) +colvars: ( 4.44538 , 0.498496 , 1.37206 ) +colvars: ( 5.92137 , 0.664012 , 1.82762 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.620021 , -0.0805364 , -0.382427 ) -colvars: ( -0.556854 , -0.16266 , -0.353271 ) -colvars: ( -0.508805 , -0.140899 , -0.29585 ) -colvars: ( -0.515785 , -0.190154 , -0.323478 ) -colvars: ( -0.50619 , -0.131963 , -0.289483 ) -colvars: ( -0.489363 , -0.281404 , -0.335089 ) -colvars: ( -0.454642 , -0.321591 , -0.316991 ) -colvars: ( -0.431464 , -0.427931 , -0.338178 ) -colvars: ( -0.391874 , -0.286817 , -0.239325 ) -colvars: ( -0.386398 , -0.261902 , -0.223394 ) -colvars: ( -0.34385 , -0.281293 , -0.188723 ) -colvars: ( -0.283828 , -0.244982 , -0.113176 ) -colvars: ( -0.23654 , -0.259782 , -0.071819 ) -colvars: ( -0.304438 , -0.142773 , -0.0911351 ) -colvars: ( -0.272685 , -0.113978 , -0.0471576 ) -colvars: ( -0.360342 , -0.0857058 , -0.123471 ) -colvars: ( -0.388139 , 0.0116444 , -0.11069 ) -colvars: ( -0.440304 , 0.0590793 , -0.143297 ) -colvars: ( -0.424277 , 0.0264991 , -0.140813 ) -colvars: ( -0.412889 , 0.082611 , -0.105884 ) -colvars: ( -0.467035 , -0.0269055 , -0.206153 ) -colvars: ( -0.499698 , -0.0283782 , -0.239613 ) -colvars: ( -0.548541 , -0.0929887 , -0.31576 ) -colvars: ( -0.445964 , -0.0583885 , -0.198138 ) -colvars: ( -0.452252 , -0.0148158 , -0.186229 ) -colvars: ( -0.390108 , -0.13214 , -0.172831 ) -colvars: ( -0.33113 , -0.163422 , -0.126614 ) -colvars: ( -0.280119 , -0.25284 , -0.112734 ) -colvars: ( -0.290895 , -0.0914479 , -0.0560422 ) -colvars: ( -0.276676 , -0.0731749 , -0.0340985 ) -colvars: ( -0.273061 , -0.046956 , -0.0194933 ) -colvars: ( -0.238855 , 0.0269524 , 0.0458266 ) -colvars: ( -0.219719 , 0.0531687 , 0.076037 ) -colvars: ( -0.283255 , 0.112946 , 0.0371613 ) -colvars: ( -0.256396 , 0.154137 , 0.0814032 ) -colvars: ( -0.353086 , 0.141053 , -0.0212965 ) -colvars: ( -0.402098 , 0.216607 , -0.0389684 ) -colvars: ( -0.474188 , 0.239268 , -0.101976 ) -colvars: ( -0.411565 , 0.196853 , -0.0567524 ) -colvars: ( -0.416009 , 0.257016 , -0.0360491 ) -colvars: ( -0.414277 , 0.111093 , -0.0953628 ) -colvars: ( -0.419262 , 0.0811054 , -0.112922 ) -colvars: ( -0.439264 , -0.0112365 , -0.171672 ) -colvars: ( -0.351638 , 0.0696366 , -0.0497227 ) -colvars: ( -0.353971 , 0.0955855 , -0.041211 ) -colvars: ( -0.191552 , 0.1015 , 0.124582 ) -colvars: ( -0.141454 , 0.103108 , 0.175631 ) -colvars: ( -0.220168 , 0.173301 , 0.12585 ) -colvars: ( -0.289376 , 0.029143 , -0.00405802 ) -colvars: ( -0.221857 , 0.0153666 , 0.0580709 ) -colvars: ( -0.167594 , -0.0670334 , 0.0781573 ) +colvars: ( -0.657448 , -0.0854485 , -0.405083 ) +colvars: ( -0.590503 , -0.172507 , -0.374162 ) +colvars: ( -0.53953 , -0.149449 , -0.313293 ) +colvars: ( -0.546999 , -0.201635 , -0.342603 ) +colvars: ( -0.536827 , -0.139934 , -0.306601 ) +colvars: ( -0.519022 , -0.298367 , -0.354892 ) +colvars: ( -0.482251 , -0.340952 , -0.335722 ) +colvars: ( -0.457708 , -0.453687 , -0.358149 ) +colvars: ( -0.415704 , -0.304077 , -0.253425 ) +colvars: ( -0.409917 , -0.277649 , -0.236567 ) +colvars: ( -0.364767 , -0.298229 , -0.199781 ) +colvars: ( -0.301128 , -0.259727 , -0.119728 ) +colvars: ( -0.250971 , -0.275431 , -0.0758715 ) +colvars: ( -0.322955 , -0.151369 , -0.0963992 ) +colvars: ( -0.289302 , -0.120829 , -0.0498127 ) +colvars: ( -0.382191 , -0.0908824 , -0.130672 ) +colvars: ( -0.411638 , 0.0123237 , -0.117155 ) +colvars: ( -0.466902 , 0.0625931 , -0.151704 ) +colvars: ( -0.449976 , 0.0280866 , -0.149107 ) +colvars: ( -0.437903 , 0.0875837 , -0.112115 ) +colvars: ( -0.495331 , -0.0285283 , -0.218348 ) +colvars: ( -0.52999 , -0.0300751 , -0.253833 ) +colvars: ( -0.581791 , -0.0985751 , -0.334519 ) +colvars: ( -0.473057 , -0.0618716 , -0.209889 ) +colvars: ( -0.479733 , -0.0156658 , -0.197295 ) +colvars: ( -0.413857 , -0.140057 , -0.183046 ) +colvars: ( -0.35136 , -0.173204 , -0.134073 ) +colvars: ( -0.297295 , -0.268002 , -0.119332 ) +colvars: ( -0.308688 , -0.0968957 , -0.0593007 ) +colvars: ( -0.293633 , -0.0775081 , -0.0360683 ) +colvars: ( -0.289743 , -0.0497408 , -0.0205576 ) +colvars: ( -0.253457 , 0.0286157 , 0.0486508 ) +colvars: ( -0.23313 , 0.0563915 , 0.0806867 ) +colvars: ( -0.300518 , 0.119787 , 0.0394344 ) +colvars: ( -0.272049 , 0.163467 , 0.0862993 ) +colvars: ( -0.374537 , 0.149575 , -0.0225226 ) +colvars: ( -0.426491 , 0.229678 , -0.0412815 ) +colvars: ( -0.502895 , 0.253687 , -0.108051 ) +colvars: ( -0.436566 , 0.208754 , -0.0601502 ) +colvars: ( -0.441279 , 0.272545 , -0.0382371 ) +colvars: ( -0.439477 , 0.117842 , -0.101056 ) +colvars: ( -0.444801 , 0.0860681 , -0.119682 ) +colvars: ( -0.466036 , -0.0118282 , -0.181925 ) +colvars: ( -0.373131 , 0.0739249 , -0.0527134 ) +colvars: ( -0.375622 , 0.101449 , -0.0437187 ) +colvars: ( -0.203403 , 0.107717 , 0.13201 ) +colvars: ( -0.150306 , 0.109435 , 0.186099 ) +colvars: ( -0.233699 , 0.183823 , 0.133351 ) +colvars: ( -0.30712 , 0.0309932 , -0.00429714 ) +colvars: ( -0.235557 , 0.0164018 , 0.0615402 ) +colvars: ( -0.17804 , -0.0709576 , 0.082859 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 13. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 13. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 13, atoms_new_colvar_forces = { ( -4.60941152857979e+00 , -4.34657732283577e-01 , -1.26134882081779e+00 ), ( -3.97073083473694e+00 , -3.67313651566339e-01 , -9.91859389363031e-01 ), ( -4.04316472548736e+00 , -3.93454487430930e-01 , -1.02714696681659e+00 ), ( -5.43695557364111e+00 , -5.58045088291464e-01 , -1.52034955209816e+00 ), ( 2.52564673419413e-01 , 1.17788991033556e-01 , 3.42664670190256e-01 ), ( 4.97279195956864e+00 , 6.12250390674802e-01 , 1.82132229160582e+00 ), ( 4.20223194665849e+00 , 5.08474736142992e-01 , 1.57961024511043e+00 ), ( -4.29276074776823e-02 , 2.93446213700490e-02 , 3.48722012915199e-01 ), ( 4.18281293288223e+00 , 4.98892623958362e-01 , 1.54893034738508e+00 ), ( 5.54416128143707e+00 , 6.38674358062218e-01 , 1.91832647544192e+00 ), ( 1.14399585720751e-02 , 3.90794787476342e-02 , 2.93708226731225e-01 ), ( -7.74227782932568e-05 , 3.26513237297457e-02 , 2.69370076729104e-01 ), ( 2.05975207283844e-02 , 4.67361566095524e-02 , 3.34045608643490e-01 ), ( 4.26645761142326e-02 , 3.66710482458952e-02 , 1.96165462885331e-01 ), ( 1.50481746260900e-02 , 2.23658164168660e-02 , 1.46943492053965e-01 ), ( 1.11088946090217e-01 , 5.61286874900876e-02 , 1.86332573791074e-01 ), ( 1.56821586267231e-01 , 6.17064835141191e-02 , 1.18531904330075e-01 ), ( 2.36040288827892e-01 , 8.75109152017895e-02 , 1.34165376638010e-01 ), ( 1.28616670071091e-01 , 4.49257663790903e-02 , 5.03662776739318e-02 ), ( 1.24075243198848e-01 , 3.59998038770147e-02 , -1.19201499422995e-02 ), ( 1.06328632335919e-01 , 3.96149728507969e-02 , 6.20373291991009e-02 ), ( 7.13574773389903e-02 , 2.22306139835790e-02 , 5.72986097930586e-03 ), ( 5.88724090671617e-02 , 2.24438607366800e-02 , 3.85510442010033e-02 ), ( -9.07964480255985e-04 , -2.73061051878320e-03 , -2.02521081487401e-02 ), ( -1.43612030032016e-02 , -1.50066306082719e-02 , -8.79835825452684e-02 ), ( -4.80555049049832e-02 , -1.04369604238727e-02 , 3.35210763573743e-02 ), ( -1.15141857182860e-01 , -3.25976579414282e-02 , 1.77409353727871e-02 ), ( -1.56507975530757e-01 , -3.58975451284672e-02 , 9.34566598098229e-02 ), ( -1.02951477208506e-01 , -3.44575047755011e-02 , -2.79216233723472e-02 ), ( -1.38840804626506e-01 , -5.20917148981355e-02 , -8.40044277638193e-02 ), ( -5.03793616759529e-02 , -1.59263713413516e-02 , -5.95179953464081e-03 ), ( -2.98303562581878e-02 , -1.46800115534475e-02 , -4.68032765683968e-02 ), ( 2.58323416427286e-02 , 7.78008423467155e-03 , -1.32545044126964e-04 ), ( 1.68027528414161e-03 , -1.49180664151575e-02 , -1.27165078361497e-01 ), ( -1.59124803691898e-02 , -2.67195990972143e-02 , -1.80685652304989e-01 ), ( 4.81088347348926e-02 , -2.20534914566670e-03 , -1.37876936909011e-01 ), ( 7.71701297516348e-02 , -2.40380998444134e-03 , -2.11818312120294e-01 ), ( 1.37669110328292e-01 , 1.71903182358169e-02 , -2.00807409614685e-01 ), ( 1.91211137365860e-02 , -2.62193053405430e-02 , -2.63725732867441e-01 ), ( 2.01706741704832e-02 , -3.41524960997568e-02 , -3.31738275345898e-01 ), ( -3.34466762409990e-02 , -3.82568962355038e-02 , -2.32173567232608e-01 ), ( -9.40110524129654e-02 , -6.15412620828612e-02 , -2.73444075319582e-01 ), ( -1.31271417989929e-01 , -6.68987632847314e-02 , -2.24906537274629e-01 ), ( -1.51010948978680e-01 , -8.13559030288523e-02 , -2.94978697112032e-01 ), ( -1.78389231192939e-01 , -9.72272014198814e-02 , -3.57703764515572e-01 ), ( -1.93305620802337e-01 , -9.48833976742998e-02 , -3.01269082478313e-01 ), ( -2.35131299405755e-01 , -1.10749390328410e-01 , -3.28004908137406e-01 ), ( -1.19956549612358e-01 , -7.35721764200462e-02 , -3.08073831054048e-01 ), ( -1.71014019022640e-01 , -8.10537214557247e-02 , -2.42719349761469e-01 ), ( -2.24045387087126e-01 , -9.87910106647013e-02 , -2.57002091063096e-01 ), ( -2.59527876165445e-01 , -1.00216736055959e-01 , -1.80474404556519e-01 ) } +colvars: Step 13, atoms_new_colvar_forces = { ( -4.88981896196504e+00 , -4.60390551723254e-01 , -1.33517556811277e+00 ), ( -4.21228162928695e+00 , -3.89049902129704e-01 , -1.04972585545871e+00 ), ( -4.28910692410658e+00 , -4.16774313998016e-01 , -1.08715306920586e+00 ), ( -5.76767119194412e+00 , -5.91167953139013e-01 , -1.60950471137606e+00 ), ( 2.67876680524958e-01 , 1.24929752216452e-01 , 3.63438904895691e-01 ), ( 5.27523399227998e+00 , 6.48752607816794e-01 , 1.92910237707154e+00 ), ( 4.45782140789246e+00 , 5.38775378359889e-01 , 1.67311243783968e+00 ), ( -4.55279460566612e-02 , 3.11321705147235e-02 , 3.69864187073456e-01 ), ( 4.43722378982507e+00 , 5.28611708271286e-01 , 1.64057106278070e+00 ), ( 5.88137875686962e+00 , 6.76691019162951e-01 , 2.03161084176304e+00 ), ( 1.21327495420109e-02 , 4.14534690353304e-02 , 3.11512309172057e-01 ), ( -8.42319167825289e-05 , 3.46348595636129e-02 , 2.85697126200144e-01 ), ( 2.18426861463246e-02 , 4.95735984439514e-02 , 3.54291786058363e-01 ), ( 4.52489567860466e-02 , 3.88957799718568e-02 , 2.08054927761938e-01 ), ( 1.59578651818409e-02 , 2.37229136416288e-02 , 1.55848419325201e-01 ), ( 1.17822071543679e-01 , 5.95312822654525e-02 , 1.97626888946625e-01 ), ( 1.66327351419946e-01 , 6.54448163200975e-02 , 1.25716406855178e-01 ), ( 2.50348975389216e-01 , 9.28119703385379e-02 , 1.42298313485828e-01 ), ( 1.36413773283859e-01 , 4.76468082553589e-02 , 5.34198309692146e-02 ), ( 1.31596787808496e-01 , 3.81785730709885e-02 , -1.26427591612700e-02 ), ( 1.12775883922173e-01 , 4.20154527965672e-02 , 6.57998608481610e-02 ), ( 7.56858654316191e-02 , 2.35776056205410e-02 , 6.08026662443523e-03 ), ( 6.24452792462686e-02 , 2.38053309565956e-02 , 4.08926522131212e-02 ), ( -9.61086682672252e-04 , -2.89565406751356e-03 , -2.14775907665281e-02 ), ( -1.52296050911035e-02 , -1.59166635104930e-02 , -9.33147102978675e-02 ), ( -5.09677319010105e-02 , -1.10673114533446e-02 , 3.55542436727819e-02 ), ( -1.22121809149347e-01 , -3.45702970881061e-02 , 1.88164571166034e-02 ), ( -1.65996483973189e-01 , -3.80680744946709e-02 , 9.91210968432649e-02 ), ( -1.09193558771200e-01 , -3.65445810195318e-02 , -2.96155108704943e-02 ), ( -1.47258577096358e-01 , -5.52479126945070e-02 , -8.90981727184671e-02 ), ( -5.34353811403274e-02 , -1.68914730059245e-02 , -6.31489749812243e-03 ), ( -3.16417197793630e-02 , -1.55713484237388e-02 , -4.96440396384484e-02 ), ( 2.73943373716786e-02 , 8.24926005665480e-03 , -1.45188845464467e-04 ), ( 1.77994020406858e-03 , -1.58258443290363e-02 , -1.34876499903599e-01 ), ( -1.68798291810008e-02 , -2.83435715816595e-02 , -1.91642157004365e-01 ), ( 5.10243811266533e-02 , -2.34333172226778e-03 , -1.46236166494363e-01 ), ( 8.18483615665809e-02 , -2.55558445760179e-03 , -2.24658827699174e-01 ), ( 1.46016120702545e-01 , 1.82255016213926e-02 , -2.12978949787339e-01 ), ( 2.02811035476966e-02 , -2.78138914247876e-02 , -2.79712078538106e-01 ), ( 2.13943829889179e-02 , -3.62292780674321e-02 , -3.51847504541956e-01 ), ( -3.54728586973324e-02 , -4.05789606437091e-02 , -2.46246573978784e-01 ), ( -9.97080491558552e-02 , -6.52737100745764e-02 , -2.90018194421679e-01 ), ( -1.39226336381453e-01 , -7.09536931282848e-02 , -2.38537296583322e-01 ), ( -1.60164526816236e-01 , -8.62889353775075e-02 , -3.12859657823101e-01 ), ( -1.89202213571486e-01 , -1.03122691420405e-01 , -3.79386850276111e-01 ), ( -2.05026780807315e-01 , -1.00637069523100e-01 , -3.19535591632303e-01 ), ( -2.49388860668061e-01 , -1.17464648436431e-01 , -3.47893206719193e-01 ), ( -1.27231151927321e-01 , -7.80360159431520e-02 , -3.26752761726856e-01 ), ( -1.81381579036729e-01 , -8.59675133319940e-02 , -2.57433890746736e-01 ), ( -2.37628983834062e-01 , -1.04779438973798e-01 , -2.72583892963877e-01 ), ( -2.75263491664155e-01 , -1.06289643117102e-01 , -1.91418222726097e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 13, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4784,10 +7716,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 14, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 14, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 14, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 14, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 14, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 14, atoms_positions[size = 51] = { ( 8.31863750519705e+00 , 4.28481966305417e-02 , -7.65206741939643e-01 ), ( 6.98331590064913e+00 , -5.43991075653974e-01 , -6.16884455522366e-01 ), ( 6.18111442627412e+00 , -3.24404099978712e-01 , 6.97403733346897e-01 ), ( 4.97801206783498e+00 , -1.85828863818795e-01 , 7.04176494016022e-01 ), ( 7.05431325902464e+00 , -2.03732785898560e+00 , -9.61992064451894e-01 ), ( 6.89340484043793e+00 , -2.64466142941914e-01 , 1.86689532454778e+00 ), ( 6.18663853782403e+00 , -1.27133089111293e-01 , 3.18194056005567e+00 ), ( 7.09572082235899e+00 , -3.48652736844465e-01 , 4.28459267746327e+00 ), ( 5.28952645252616e+00 , 1.11037466441903e+00 , 3.32871674110496e+00 ), ( 4.13808099528070e+00 , 1.04065956594520e+00 , 3.65636369414770e+00 ), ( 5.86470469300440e+00 , 2.24789547729248e+00 , 2.99811719126949e+00 ), ( 5.22494219944958e+00 , 3.58991350029252e+00 , 2.90466592388533e+00 ), ( 6.33092062020958e+00 , 4.52115114886205e+00 , 2.41920114776961e+00 ), ( 3.90774768740196e+00 , 3.73584735239143e+00 , 2.03586437430797e+00 ), ( 2.82332237875758e+00 , 4.13990616960905e+00 , 2.51580050247276e+00 ), ( 3.89448587872994e+00 , 3.24143183651133e+00 , 7.40136563845258e-01 ), ( 2.65840305240840e+00 , 3.05349047909279e+00 , -1.08518046424564e-01 ), ( 3.03273633519467e+00 , 2.72266970420083e+00 , -1.54825072249137e+00 ), ( 1.57523337633800e+00 , 2.19445215623750e+00 , 5.10280557617337e-01 ), ( 4.21182621729726e-01 , 2.52304005585736e+00 , 5.28148743679193e-01 ), ( 1.99861255663857e+00 , 1.00571244570487e+00 , 1.07722229584875e+00 ), ( 1.18199531938308e+00 , 8.56985360570121e-02 , 1.69219813070834e+00 ), ( 2.02642714277573e+00 , -1.13299810631360e+00 , 2.00643889685938e+00 ), ( 5.51943737918944e-01 , 6.08708944595558e-01 , 2.93014012300699e+00 ), ( -6.39306298584151e-01 , 3.51277656962935e-01 , 3.16871182423111e+00 ), ( 1.32668201217350e+00 , 1.34353055777980e+00 , 3.82671156457060e+00 ), ( 8.58793759228554e-01 , 1.95435624128480e+00 , 5.03241615749648e+00 ), ( 2.03406101961544e+00 , 2.63308418324986e+00 , 5.64413623984418e+00 ), ( -3.46131928142968e-01 , 2.91656829817748e+00 , 4.97221412870430e+00 ), ( -1.15605456019786e+00 , 3.05291443243522e+00 , 5.90194179828644e+00 ), ( -4.77909747478039e-01 , 3.60389260342203e+00 , 3.84668661004553e+00 ), ( -1.49967549984600e+00 , 4.54906058839603e+00 , 3.50491675486485e+00 ), ( -7.17721575937902e-01 , 5.40273099800795e+00 , 2.44572269188412e+00 ), ( -2.77157313701106e+00 , 3.87479971881634e+00 , 2.91518005527361e+00 ), ( -3.82733748016690e+00 , 4.47322294191850e+00 , 2.82468573954751e+00 ), ( -2.60564839500708e+00 , 2.65265533898342e+00 , 2.44347184607968e+00 ), ( -3.74146458335978e+00 , 1.85357453515159e+00 , 2.01680732864283e+00 ), ( -3.41168661134235e+00 , 8.70810771691938e-01 , 9.17006250189225e-01 ), ( -4.31045011776362e+00 , 1.06501267850850e+00 , 3.24309556219264e+00 ), ( -5.52380999153781e+00 , 8.61322541413432e-01 , 3.32952655005222e+00 ), ( -3.40573488210103e+00 , 6.72351857022020e-01 , 4.15783018513658e+00 ), ( -3.74908880178937e+00 , 4.07118213772935e-02 , 5.45715542794465e+00 ), ( -2.38279341493287e+00 , -3.23386240057656e-01 , 6.17045574130615e+00 ), ( -4.47254737130439e+00 , 1.00090046845871e+00 , 6.43947533768169e+00 ), ( -5.33721208135359e+00 , 6.07273663880178e-01 , 7.20399112266022e+00 ), ( -6.24833293180304e+00 , 3.57552261214592e+00 , 6.71230379498847e+00 ), ( -6.93259262162092e+00 , 4.29630801696207e+00 , 7.44623149775835e+00 ), ( -6.74932958271965e+00 , 3.20179591103569e+00 , 5.52162953840506e+00 ), ( -4.12509679092533e+00 , 2.27808818570299e+00 , 6.45713772268763e+00 ), ( -4.84117444611746e+00 , 3.19242576639085e+00 , 7.21807501097597e+00 ), ( -4.10366948633281e+00 , 4.58307875841315e+00 , 7.29510970661580e+00 ) } +colvars: Step 14, atoms_positions[size = 51] = { ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 ), ( 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 ), ( 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 ), ( 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ), ( 7.05429385254313e+00 , -2.03733971095845e+00 , -9.61939487520703e-01 ), ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 ), ( 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 ), ( 7.09587417768813e+00 , -3.48673267580415e-01 , 4.28480410351882e+00 ), ( 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 ), ( 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 ), ( 5.86486454274355e+00 , 2.24797767579896e+00 , 2.99815671646628e+00 ), ( 5.22493545201210e+00 , 3.58991729210236e+00 , 2.90473741736489e+00 ), ( 6.33092192081317e+00 , 4.52116236648895e+00 , 2.41927485778368e+00 ), ( 3.90776010512297e+00 , 3.73584825978615e+00 , 2.03591493688509e+00 ), ( 2.82332465249931e+00 , 4.13991068119476e+00 , 2.51583104327529e+00 ), ( 3.89451144592941e+00 , 3.24144516682814e+00 , 7.40179485370264e-01 ), ( 2.65844106989744e+00 , 3.05350593383516e+00 , -1.08488981331887e-01 ), ( 3.03278747309343e+00 , 2.72268879368398e+00 , -1.54821987670355e+00 ), ( 1.57526439270054e+00 , 2.19446358993994e+00 , 5.10294119197168e-01 ), ( 4.21210277979123e-01 , 2.52304701718955e+00 , 5.28146554175524e-01 ), ( 1.99863625271151e+00 , 1.00572236418968e+00 , 1.07723828604057e+00 ), ( 1.18201227767348e+00 , 8.57044788501173e-02 , 1.69220053554445e+00 ), ( 2.02644354157259e+00 , -1.13299047266892e+00 , 2.00645171537107e+00 ), ( 5.51945150516580e-01 , 6.08708404493696e-01 , 2.93013538978696e+00 ), ( -6.39308246883680e-01 , 3.51274880191373e-01 , 3.16869445588155e+00 ), ( 1.32668812244549e+00 , 1.34352515560620e+00 , 3.82671742359831e+00 ), ( 8.58767606428859e-01 , 1.95434757556696e+00 , 5.03241999566417e+00 ), ( 2.03402657414422e+00 , 2.63307566831980e+00 , 5.64415447011505e+00 ), ( -3.46157050289023e-01 , 2.91655892147137e+00 , 4.97220637353131e+00 ), ( -1.15608468363693e+00 , 3.05290417480726e+00 , 5.90192658127788e+00 ), ( -4.77921309709439e-01 , 3.60388884533245e+00 , 3.84668343251162e+00 ), ( -1.49968243814569e+00 , 4.54905744339707e+00 , 3.50490478092210e+00 ), ( -7.17716458963084e-01 , 5.40273226525777e+00 , 2.44572191675940e+00 ), ( -2.77157354783216e+00 , 3.87479723188297e+00 , 2.91514834348317e+00 ), ( -3.82733991171425e+00 , 4.47321707177170e+00 , 2.82464889913065e+00 ), ( -2.60563833123193e+00 , 2.65265449319031e+00 , 2.44344010564801e+00 ), ( -3.74144641201036e+00 , 1.85357458698069e+00 , 2.01675445782806e+00 ), ( -3.41165642068151e+00 , 8.70813218294187e-01 , 9.16959236491071e-01 ), ( -4.31044435731333e+00 , 1.06500473684454e+00 , 3.24302990936214e+00 ), ( -5.52380553228657e+00 , 8.61315661384654e-01 , 3.32945844168612e+00 ), ( -3.40574236242845e+00 , 6.72342519459051e-01 , 4.15777520505137e+00 ), ( -3.74911277543839e+00 , 4.06956805094106e-02 , 5.45709004439605e+00 ), ( -2.38282299687553e+00 , -3.23399386002607e-01 , 6.17040458948034e+00 ), ( -4.47258552805660e+00 , 1.00088178449150e+00 , 6.43940071021629e+00 ), ( -5.33724838402981e+00 , 6.07253695391686e-01 , 7.20391804672296e+00 ), ( -6.24838121141889e+00 , 3.57550015605705e+00 , 6.71223354327823e+00 ), ( -6.93264006079421e+00 , 4.29628442025119e+00 , 7.44616335288087e+00 ), ( -6.74935856072400e+00 , 3.20178040778415e+00 , 5.52156016554329e+00 ), ( -4.12513552072745e+00 , 2.27807008788324e+00 , 6.45708129476173e+00 ), ( -4.84122820244433e+00 , 3.19240161416128e+00 , 7.21801211044439e+00 ), ( -4.10372836840617e+00 , 4.58305518886815e+00 , 7.29506732137016e+00 ) } colvars: Step 14, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 14, atom_groups_ids[size = 0] = @@ -4805,162 +7737,301 @@ colvars: Collective variables module, step no. 14 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.15622953688594e-01 , 3.81824775894985e-03 , 9.48877005775216e-01 ). +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.15064599275101e-01 , 3.88700842418579e-03 , 9.49062268478276e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 7.05429385254313e+00 , -2.03733971095845e+00 , -9.61939487520703e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 , 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 7.09587417768813e+00 , -3.48673267580415e-01 , 4.28480410351882e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 , 5.86486454274355e+00 , 2.24797767579896e+00 , 2.99815671646628e+00 , 5.22493545201210e+00 , 3.58991729210236e+00 , 2.90473741736489e+00 , 6.33092192081317e+00 , 4.52116236648895e+00 , 2.41927485778368e+00 , 3.90776010512297e+00 , 3.73584825978615e+00 , 2.03591493688509e+00 , 2.82332465249931e+00 , 4.13991068119476e+00 , 2.51583104327529e+00 , 3.89451144592941e+00 , 3.24144516682814e+00 , 7.40179485370264e-01 , 2.65844106989744e+00 , 3.05350593383516e+00 , -1.08488981331887e-01 , 3.03278747309343e+00 , 2.72268879368398e+00 , -1.54821987670355e+00 , 1.57526439270054e+00 , 2.19446358993994e+00 , 5.10294119197168e-01 , 4.21210277979123e-01 , 2.52304701718955e+00 , 5.28146554175524e-01 , 1.99863625271151e+00 , 1.00572236418968e+00 , 1.07723828604057e+00 , 1.18201227767348e+00 , 8.57044788501173e-02 , 1.69220053554445e+00 , 2.02644354157259e+00 , -1.13299047266892e+00 , 2.00645171537107e+00 , 5.51945150516580e-01 , 6.08708404493696e-01 , 2.93013538978696e+00 , -6.39308246883680e-01 , 3.51274880191373e-01 , 3.16869445588155e+00 , 1.32668812244549e+00 , 1.34352515560620e+00 , 3.82671742359831e+00 , 8.58767606428859e-01 , 1.95434757556696e+00 , 5.03241999566417e+00 , 2.03402657414422e+00 , 2.63307566831980e+00 , 5.64415447011505e+00 , -3.46157050289023e-01 , 2.91655892147137e+00 , 4.97220637353131e+00 , -1.15608468363693e+00 , 3.05290417480726e+00 , 5.90192658127788e+00 , -4.77921309709439e-01 , 3.60388884533245e+00 , 3.84668343251162e+00 , -1.49968243814569e+00 , 4.54905744339707e+00 , 3.50490478092210e+00 , -7.17716458963084e-01 , 5.40273226525777e+00 , 2.44572191675940e+00 , -2.77157354783216e+00 , 3.87479723188297e+00 , 2.91514834348317e+00 , -3.82733991171425e+00 , 4.47321707177170e+00 , 2.82464889913065e+00 , -2.60563833123193e+00 , 2.65265449319031e+00 , 2.44344010564801e+00 , -3.74144641201036e+00 , 1.85357458698069e+00 , 2.01675445782806e+00 , -3.41165642068151e+00 , 8.70813218294187e-01 , 9.16959236491071e-01 , -4.31044435731333e+00 , 1.06500473684454e+00 , 3.24302990936214e+00 , -5.52380553228657e+00 , 8.61315661384654e-01 , 3.32945844168612e+00 , -3.40574236242845e+00 , 6.72342519459051e-01 , 4.15777520505137e+00 , -3.74911277543839e+00 , 4.06956805094106e-02 , 5.45709004439605e+00 , -2.38282299687553e+00 , -3.23399386002607e-01 , 6.17040458948034e+00 , -4.47258552805660e+00 , 1.00088178449150e+00 , 6.43940071021629e+00 , -5.33724838402981e+00 , 6.07253695391686e-01 , 7.20391804672296e+00 , -6.24838121141889e+00 , 3.57550015605705e+00 , 6.71223354327823e+00 , -6.93264006079421e+00 , 4.29628442025119e+00 , 7.44616335288087e+00 , -6.74935856072400e+00 , 3.20178040778415e+00 , 5.52156016554329e+00 , -4.12513552072745e+00 , 2.27807008788324e+00 , 6.45708129476173e+00 , -4.84122820244433e+00 , 3.19240161416128e+00 , 7.21801211044439e+00 , -4.10372836840617e+00 , 4.58305518886815e+00 , 7.29506732137016e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.15622953688594e-01 , 3.81824775894985e-03 , 9.48877005775216e-01 ). +colvars: Colvar "one" has value ( -3.15064599275101e-01 , 3.88700842418579e-03 , 9.49062268478276e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 7.05429385254313e+00 , -2.03733971095845e+00 , -9.61939487520703e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 , 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 7.09587417768813e+00 , -3.48673267580415e-01 , 4.28480410351882e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 , 5.86486454274355e+00 , 2.24797767579896e+00 , 2.99815671646628e+00 , 5.22493545201210e+00 , 3.58991729210236e+00 , 2.90473741736489e+00 , 6.33092192081317e+00 , 4.52116236648895e+00 , 2.41927485778368e+00 , 3.90776010512297e+00 , 3.73584825978615e+00 , 2.03591493688509e+00 , 2.82332465249931e+00 , 4.13991068119476e+00 , 2.51583104327529e+00 , 3.89451144592941e+00 , 3.24144516682814e+00 , 7.40179485370264e-01 , 2.65844106989744e+00 , 3.05350593383516e+00 , -1.08488981331887e-01 , 3.03278747309343e+00 , 2.72268879368398e+00 , -1.54821987670355e+00 , 1.57526439270054e+00 , 2.19446358993994e+00 , 5.10294119197168e-01 , 4.21210277979123e-01 , 2.52304701718955e+00 , 5.28146554175524e-01 , 1.99863625271151e+00 , 1.00572236418968e+00 , 1.07723828604057e+00 , 1.18201227767348e+00 , 8.57044788501173e-02 , 1.69220053554445e+00 , 2.02644354157259e+00 , -1.13299047266892e+00 , 2.00645171537107e+00 , 5.51945150516580e-01 , 6.08708404493696e-01 , 2.93013538978696e+00 , -6.39308246883680e-01 , 3.51274880191373e-01 , 3.16869445588155e+00 , 1.32668812244549e+00 , 1.34352515560620e+00 , 3.82671742359831e+00 , 8.58767606428859e-01 , 1.95434757556696e+00 , 5.03241999566417e+00 , 2.03402657414422e+00 , 2.63307566831980e+00 , 5.64415447011505e+00 , -3.46157050289023e-01 , 2.91655892147137e+00 , 4.97220637353131e+00 , -1.15608468363693e+00 , 3.05290417480726e+00 , 5.90192658127788e+00 , -4.77921309709439e-01 , 3.60388884533245e+00 , 3.84668343251162e+00 , -1.49968243814569e+00 , 4.54905744339707e+00 , 3.50490478092210e+00 , -7.17716458963084e-01 , 5.40273226525777e+00 , 2.44572191675940e+00 , -2.77157354783216e+00 , 3.87479723188297e+00 , 2.91514834348317e+00 , -3.82733991171425e+00 , 4.47321707177170e+00 , 2.82464889913065e+00 , -2.60563833123193e+00 , 2.65265449319031e+00 , 2.44344010564801e+00 , -3.74144641201036e+00 , 1.85357458698069e+00 , 2.01675445782806e+00 , -3.41165642068151e+00 , 8.70813218294187e-01 , 9.16959236491071e-01 , -4.31044435731333e+00 , 1.06500473684454e+00 , 3.24302990936214e+00 , -5.52380553228657e+00 , 8.61315661384654e-01 , 3.32945844168612e+00 , -3.40574236242845e+00 , 6.72342519459051e-01 , 4.15777520505137e+00 , -3.74911277543839e+00 , 4.06956805094106e-02 , 5.45709004439605e+00 , -2.38282299687553e+00 , -3.23399386002607e-01 , 6.17040458948034e+00 , -4.47258552805660e+00 , 1.00088178449150e+00 , 6.43940071021629e+00 , -5.33724838402981e+00 , 6.07253695391686e-01 , 7.20391804672296e+00 , -6.24838121141889e+00 , 3.57550015605705e+00 , 6.71223354327823e+00 , -6.93264006079421e+00 , 4.29628442025119e+00 , 7.44616335288087e+00 , -6.74935856072400e+00 , 3.20178040778415e+00 , 5.52156016554329e+00 , -4.12513552072745e+00 , 2.27807008788324e+00 , 6.45708129476173e+00 , -4.84122820244433e+00 , 3.19240161416128e+00 , 7.21801211044439e+00 , -4.10372836840617e+00 , 4.58305518886815e+00 , 7.29506732137016e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.8305 , 1.87544 , -15.0739 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.5823 , 6.65823 , 13.3165 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.8305 , 1.87544 , -15.0739 ) to colvar "one". -colvars: Adding total bias energy: 44.8977 +colvars: Adding biasing force ( 66.5823 , 6.65823 , 13.3165 ) to colvar "one". +colvars: Adding total bias energy: 57.3219 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.8305 , 1.87544 , -15.0739 ) +colvars: Force to be applied: ( 66.5823 , 6.65823 , 13.3165 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.89206 , -0.545836 , -1.50063 ) -colvars: ( -4.19494 , -0.468054 , -1.28679 ) -colvars: ( -4.19494 , -0.468054 , -1.28679 ) -colvars: ( -5.58778 , -0.623462 , -1.71405 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17951 , -0.577094 , -1.58552 ) +colvars: ( -4.44143 , -0.494858 , -1.35958 ) +colvars: ( -4.44143 , -0.494858 , -1.35958 ) +colvars: ( -5.91612 , -0.659165 , -1.811 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.896784 , 0.19473 , 0.630006 ) -colvars: ( 0.776135 , 0.265906 , 0.65492 ) -colvars: ( 0.760773 , 0.258807 , 0.636322 ) -colvars: ( 0.662908 , 0.267148 , 0.589999 ) -colvars: ( 0.650909 , 0.200601 , 0.493307 ) -colvars: ( 0.575285 , 0.34479 , 0.643047 ) -colvars: ( 0.466665 , 0.359272 , 0.598669 ) -colvars: ( 0.389022 , 0.456875 , 0.684472 ) -colvars: ( 0.384569 , 0.314904 , 0.490624 ) -colvars: ( 0.349191 , 0.273513 , 0.414065 ) -colvars: ( 0.355613 , 0.320107 , 0.480602 ) -colvars: ( 0.284136 , 0.277369 , 0.380998 ) -colvars: ( 0.257454 , 0.306288 , 0.404258 ) -colvars: ( 0.347337 , 0.179272 , 0.286035 ) -colvars: ( 0.288081 , 0.136142 , 0.193091 ) -colvars: ( 0.471404 , 0.141775 , 0.308496 ) -colvars: ( 0.54477 , 0.0500958 , 0.228158 ) -colvars: ( 0.675852 , 0.028592 , 0.276287 ) -colvars: ( 0.552801 , 0.0184175 , 0.190212 ) -colvars: ( 0.536899 , -0.0466095 , 0.0932708 ) -colvars: ( 0.573338 , 0.0664566 , 0.266997 ) -colvars: ( 0.571153 , 0.0504875 , 0.244202 ) -colvars: ( 0.607537 , 0.115267 , 0.352857 ) -colvars: ( 0.445431 , 0.0554257 , 0.176913 ) -colvars: ( 0.43832 , -0.000431498 , 0.0974928 ) -colvars: ( 0.342606 , 0.121386 , 0.205283 ) -colvars: ( 0.216802 , 0.130404 , 0.143441 ) -colvars: ( 0.124579 , 0.21644 , 0.205088 ) -colvars: ( 0.188731 , 0.0566147 , 0.0275399 ) -colvars: ( 0.138762 , 0.0206604 , -0.0502775 ) -colvars: ( 0.223283 , 0.0307484 , 0.0130203 ) -colvars: ( 0.209567 , -0.0418568 , -0.0928429 ) -colvars: ( 0.245894 , -0.0455188 , -0.07641 ) -colvars: ( 0.285361 , -0.128022 , -0.164327 ) -colvars: ( 0.240987 , -0.181025 , -0.261818 ) -colvars: ( 0.401435 , -0.143347 , -0.116702 ) -colvars: ( 0.479399 , -0.21904 , -0.172803 ) -colvars: ( 0.611748 , -0.222018 , -0.0989759 ) -colvars: ( 0.431028 , -0.223196 , -0.20685 ) -colvars: ( 0.436525 , -0.291273 , -0.295315 ) -colvars: ( 0.381357 , -0.149578 , -0.136904 ) -colvars: ( 0.325998 , -0.142976 , -0.160569 ) -colvars: ( 0.308862 , -0.0560768 , -0.0535979 ) -colvars: ( 0.201602 , -0.151402 , -0.24508 ) -colvars: ( 0.176661 , -0.193256 , -0.316125 ) -colvars: ( -0.000579805 , -0.196827 , -0.425176 ) -colvars: ( -0.0923356 , -0.214357 , -0.502753 ) -colvars: ( 0.101114 , -0.247189 , -0.433201 ) -colvars: ( 0.11942 , -0.11064 , -0.23851 ) -colvars: ( -0.000918935 , -0.114676 , -0.314722 ) -colvars: ( -0.0905301 , -0.0337725 , -0.258451 ) +colvars: ( 0.949101 , 0.206161 , 0.666297 ) +colvars: ( 0.821447 , 0.281457 , 0.692669 ) +colvars: ( 0.805171 , 0.273966 , 0.673017 ) +colvars: ( 0.701654 , 0.282736 , 0.623993 ) +colvars: ( 0.688957 , 0.212312 , 0.521702 ) +colvars: ( 0.608953 , 0.36487 , 0.680115 ) +colvars: ( 0.494037 , 0.380158 , 0.633169 ) +colvars: ( 0.411895 , 0.483418 , 0.723944 ) +colvars: ( 0.407164 , 0.3332 , 0.518885 ) +colvars: ( 0.369738 , 0.289383 , 0.437888 ) +colvars: ( 0.376509 , 0.33872 , 0.508304 ) +colvars: ( 0.30087 , 0.293491 , 0.402949 ) +colvars: ( 0.272622 , 0.324109 , 0.427578 ) +colvars: ( 0.367734 , 0.189701 , 0.302483 ) +colvars: ( 0.305038 , 0.144047 , 0.204161 ) +colvars: ( 0.499001 , 0.150052 , 0.326234 ) +colvars: ( 0.576622 , 0.0530556 , 0.241236 ) +colvars: ( 0.715306 , 0.0303374 , 0.292145 ) +colvars: ( 0.585136 , 0.0195142 , 0.201074 ) +colvars: ( 0.568308 , -0.049302 , 0.0985199 ) +colvars: ( 0.606881 , 0.0703363 , 0.282289 ) +colvars: ( 0.604586 , 0.0534159 , 0.258156 ) +colvars: ( 0.643099 , 0.121959 , 0.373085 ) +colvars: ( 0.471571 , 0.0586073 , 0.186978 ) +colvars: ( 0.464052 , -0.000511152 , 0.102952 ) +colvars: ( 0.362775 , 0.128388 , 0.217006 ) +colvars: ( 0.229669 , 0.137901 , 0.151594 ) +colvars: ( 0.13209 , 0.22893 , 0.216827 ) +colvars: ( 0.199955 , 0.0598229 , 0.0289948 ) +colvars: ( 0.14709 , 0.0217562 , -0.053331 ) +colvars: ( 0.236494 , 0.0324794 , 0.0136481 ) +colvars: ( 0.221967 , -0.0443413 , -0.0983329 ) +colvars: ( 0.260385 , -0.0481855 , -0.0809328 ) +colvars: ( 0.302165 , -0.135512 , -0.173971 ) +colvars: ( 0.255213 , -0.19161 , -0.277103 ) +colvars: ( 0.424983 , -0.15171 , -0.123607 ) +colvars: ( 0.507479 , -0.2318 , -0.182973 ) +colvars: ( 0.647514 , -0.234925 , -0.104887 ) +colvars: ( 0.456317 , -0.23623 , -0.219004 ) +colvars: ( 0.462135 , -0.308273 , -0.312596 ) +colvars: ( 0.403777 , -0.158353 , -0.145014 ) +colvars: ( 0.345221 , -0.151398 , -0.17006 ) +colvars: ( 0.327105 , -0.059459 , -0.0569043 ) +colvars: ( 0.2136 , -0.160341 , -0.259451 ) +colvars: ( 0.187219 , -0.204648 , -0.334616 ) +colvars: ( -0.000349529 , -0.208422 , -0.449926 ) +colvars: ( -0.0974344 , -0.226991 , -0.531985 ) +colvars: ( 0.107237 , -0.26168 , -0.458417 ) +colvars: ( 0.126636 , -0.11721 , -0.252479 ) +colvars: ( -0.000692436 , -0.121505 , -0.333088 ) +colvars: ( -0.0955107 , -0.0359033 , -0.273542 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.89206 , 0.545836 , 1.50063 ) -colvars: ( 4.19494 , 0.468054 , 1.28679 ) -colvars: ( 4.19494 , 0.468054 , 1.28679 ) -colvars: ( 5.58778 , 0.623462 , 1.71405 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17951 , 0.577094 , 1.58552 ) +colvars: ( 4.44143 , 0.494858 , 1.35958 ) +colvars: ( 4.44143 , 0.494858 , 1.35958 ) +colvars: ( 5.91612 , 0.659165 , 1.811 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.61923 , -0.0805709 , -0.380173 ) -colvars: ( -0.556302 , -0.16267 , -0.350836 ) -colvars: ( -0.508054 , -0.140927 , -0.293375 ) -colvars: ( -0.51556 , -0.190112 , -0.321226 ) -colvars: ( -0.50597 , -0.1319 , -0.287552 ) -colvars: ( -0.489423 , -0.281339 , -0.332629 ) -colvars: ( -0.455043 , -0.321477 , -0.314653 ) -colvars: ( -0.432118 , -0.427804 , -0.33552 ) -colvars: ( -0.392323 , -0.286673 , -0.237256 ) -colvars: ( -0.386991 , -0.261726 , -0.221596 ) -colvars: ( -0.344169 , -0.28116 , -0.186589 ) -colvars: ( -0.284159 , -0.244825 , -0.111283 ) -colvars: ( -0.236734 , -0.259645 , -0.0697447 ) -colvars: ( -0.304572 , -0.14262 , -0.0895949 ) -colvars: ( -0.272931 , -0.113792 , -0.0458956 ) -colvars: ( -0.360178 , -0.0855932 , -0.121927 ) -colvars: ( -0.38777 , 0.0117489 , -0.109461 ) -colvars: ( -0.439582 , 0.0591317 , -0.141962 ) -colvars: ( -0.424073 , 0.0266292 , -0.139798 ) -colvars: ( -0.412699 , 0.082763 , -0.10519 ) -colvars: ( -0.466974 , -0.0267763 , -0.20496 ) -colvars: ( -0.499834 , -0.0282228 , -0.238578 ) -colvars: ( -0.548776 , -0.092846 , -0.314443 ) -colvars: ( -0.446417 , -0.058181 , -0.19727 ) -colvars: ( -0.452775 , -0.0145841 , -0.185658 ) -colvars: ( -0.390753 , -0.131915 , -0.171778 ) -colvars: ( -0.332063 , -0.163149 , -0.125697 ) -colvars: ( -0.281219 , -0.252558 , -0.111522 ) -colvars: ( -0.291737 , -0.0911599 , -0.0554493 ) -colvars: ( -0.277684 , -0.0728513 , -0.0337679 ) -colvars: ( -0.273629 , -0.0466957 , -0.0188936 ) -colvars: ( -0.239295 , 0.027221 , 0.0461291 ) -colvars: ( -0.219871 , 0.0534014 , 0.0764588 ) -colvars: ( -0.283572 , 0.113214 , 0.0371428 ) -colvars: ( -0.256779 , 0.154433 , 0.0810857 ) -colvars: ( -0.353225 , 0.141288 , -0.0212597 ) -colvars: ( -0.40213 , 0.21684 , -0.0392086 ) -colvars: ( -0.473974 , 0.239455 , -0.102066 ) -colvars: ( -0.41189 , 0.197126 , -0.0571564 ) -colvars: ( -0.416332 , 0.257307 , -0.0367715 ) -colvars: ( -0.414866 , 0.111382 , -0.0955503 ) -colvars: ( -0.420153 , 0.0814335 , -0.113229 ) -colvars: ( -0.440355 , -0.0109082 , -0.171659 ) -colvars: ( -0.352761 , 0.0700109 , -0.0502238 ) -colvars: ( -0.35523 , 0.0959901 , -0.0419782 ) -colvars: ( -0.192764 , 0.101927 , 0.123735 ) -colvars: ( -0.142835 , 0.103572 , 0.174587 ) -colvars: ( -0.221038 , 0.17369 , 0.124953 ) -colvars: ( -0.290551 , 0.0295241 , -0.00442667 ) -colvars: ( -0.223244 , 0.0157899 , 0.0575392 ) -colvars: ( -0.169117 , -0.0666042 , 0.0779103 ) +colvars: ( -0.655297 , -0.0853211 , -0.401835 ) +colvars: ( -0.588743 , -0.172177 , -0.370783 ) +colvars: ( -0.537659 , -0.149185 , -0.309994 ) +colvars: ( -0.545678 , -0.201188 , -0.339484 ) +colvars: ( -0.535531 , -0.139589 , -0.303901 ) +colvars: ( -0.518063 , -0.297699 , -0.351524 ) +colvars: ( -0.481732 , -0.340143 , -0.332526 ) +colvars: ( -0.457511 , -0.452636 , -0.354564 ) +colvars: ( -0.415371 , -0.30331 , -0.250686 ) +colvars: ( -0.40975 , -0.276899 , -0.234153 ) +colvars: ( -0.364396 , -0.297487 , -0.197082 ) +colvars: ( -0.300897 , -0.259037 , -0.11745 ) +colvars: ( -0.250693 , -0.27473 , -0.0734898 ) +colvars: ( -0.322469 , -0.150902 , -0.0945471 ) +colvars: ( -0.289003 , -0.120387 , -0.048354 ) +colvars: ( -0.381267 , -0.0905823 , -0.128746 ) +colvars: ( -0.410433 , 0.0124063 , -0.115593 ) +colvars: ( -0.465207 , 0.0625162 , -0.149958 ) +colvars: ( -0.448873 , 0.0281663 , -0.147709 ) +colvars: ( -0.436838 , 0.0875673 , -0.111136 ) +colvars: ( -0.49429 , -0.0283346 , -0.216618 ) +colvars: ( -0.529091 , -0.0298488 , -0.252199 ) +colvars: ( -0.580894 , -0.0982238 , -0.332417 ) +colvars: ( -0.472613 , -0.0615233 , -0.208524 ) +colvars: ( -0.479351 , -0.0153838 , -0.196274 ) +colvars: ( -0.413738 , -0.139531 , -0.181539 ) +colvars: ( -0.351676 , -0.172558 , -0.132811 ) +colvars: ( -0.297899 , -0.267155 , -0.117785 ) +colvars: ( -0.308991 , -0.096388 , -0.0585392 ) +colvars: ( -0.294145 , -0.077 , -0.0356353 ) +colvars: ( -0.28979 , -0.0493597 , -0.019868 ) +colvars: ( -0.25344 , 0.0288471 , 0.0488806 ) +colvars: ( -0.232843 , 0.0565264 , 0.0809789 ) +colvars: ( -0.300274 , 0.119833 , 0.0393395 ) +colvars: ( -0.271933 , 0.163456 , 0.0857883 ) +colvars: ( -0.373953 , 0.149526 , -0.0224313 ) +colvars: ( -0.425687 , 0.229464 , -0.0414481 ) +colvars: ( -0.501675 , 0.253374 , -0.107921 ) +colvars: ( -0.436058 , 0.208628 , -0.0604538 ) +colvars: ( -0.440758 , 0.27231 , -0.0389264 ) +colvars: ( -0.439245 , 0.117917 , -0.101044 ) +colvars: ( -0.444884 , 0.0862516 , -0.119761 ) +colvars: ( -0.466291 , -0.011446 , -0.181533 ) +colvars: ( -0.373606 , 0.074184 , -0.0531369 ) +colvars: ( -0.376239 , 0.101686 , -0.0444456 ) +colvars: ( -0.204314 , 0.107965 , 0.130837 ) +colvars: ( -0.151506 , 0.10972 , 0.184606 ) +colvars: ( -0.234183 , 0.183874 , 0.132123 ) +colvars: ( -0.307785 , 0.0313461 , -0.004678 ) +colvars: ( -0.236593 , 0.0168307 , 0.0608499 ) +colvars: ( -0.179337 , -0.0703459 , 0.0824296 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 14. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 14. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 14, atoms_new_colvar_forces = { ( -4.61450602640700e+00 , -4.31676671528701e-01 , -1.25080020984094e+00 ), ( -3.97510716789020e+00 , -3.64817999724983e-01 , -9.82709320886759e-01 ), ( -4.04759222147279e+00 , -3.91018565422788e-01 , -1.01801876556222e+00 ), ( -5.44284249213996e+00 , -5.54760749370383e-01 , -1.50829039988538e+00 ), ( 2.52718512476039e-01 , 1.17880134339312e-01 , 3.42947612228118e-01 ), ( 4.97792183217986e+00 , 6.09287478385831e-01 , 1.81105109336112e+00 ), ( 4.20656257158341e+00 , 5.05849087254249e-01 , 1.57080852302660e+00 ), ( -4.30961886988918e-02 , 2.90701294203428e-02 , 3.48952279642574e-01 ), ( 4.18718659982550e+00 , 4.96285825796295e-01 , 1.54016151029299e+00 ), ( 5.54998211663514e+00 , 6.35249374838715e-01 , 1.90651372157920e+00 ), ( 1.14439721104215e-02 , 3.89474388950308e-02 , 2.94013247420377e-01 ), ( -2.33043535206590e-05 , 3.25440834054942e-02 , 2.69714613993296e-01 ), ( 2.07206469285749e-02 , 4.66430442639520e-02 , 3.34513106278825e-01 ), ( 4.27649656650401e-02 , 3.66516084532864e-02 , 1.96440421996249e-01 ), ( 1.51505234874290e-02 , 2.23502413638598e-02 , 1.47195309119272e-01 ), ( 1.11225470706758e-01 , 5.61813219637322e-02 , 1.86569185231302e-01 ), ( 1.57000249590496e-01 , 6.18447669604415e-02 , 1.18697289349362e-01 ), ( 2.36270351339931e-01 , 8.77236833964157e-02 , 1.34325378589763e-01 ), ( 1.28728160579330e-01 , 4.50467234393944e-02 , 5.04143418874738e-02 ), ( 1.24200576225722e-01 , 3.61535273370629e-02 , -1.19188382213505e-02 ), ( 1.06363656214637e-01 , 3.96803352031447e-02 , 6.20370267648966e-02 ), ( 7.13181889830789e-02 , 2.22647003640655e-02 , 5.62373875832980e-03 ), ( 5.87608872439214e-02 , 2.24213311806150e-02 , 3.84139966468095e-02 ), ( -9.86194847365840e-04 , -2.75534766873105e-03 , -2.03571868396717e-02 ), ( -1.44554464500086e-02 , -1.50156162722387e-02 , -8.81647134780060e-02 ), ( -4.81467006225004e-02 , -1.05289818277412e-02 , 3.35052098907826e-02 ), ( -1.15260808893536e-01 , -3.27446961034470e-02 , 1.77439571372890e-02 ), ( -1.56639945765975e-01 , -3.61181651663380e-02 , 9.35664818984968e-02 ), ( -1.03005895219810e-01 , -3.45452566823875e-02 , -2.79093368579001e-02 ), ( -1.38921916680910e-01 , -5.21909275820709e-02 , -8.40454132348312e-02 ), ( -5.03464794637534e-02 , -1.59472851414498e-02 , -5.87334630048160e-03 ), ( -2.97284772667758e-02 , -1.46357287018351e-02 , -4.67138061700371e-02 ), ( 2.60238542554710e-02 , 7.88257179222090e-03 , 4.88175185451301e-05 ), ( 1.78925796517954e-03 , -1.48079508047937e-02 , -1.27184088935109e-01 ), ( -1.57924347793951e-02 , -2.65920248764480e-02 , -1.80732343935604e-01 ), ( 4.82095954510571e-02 , -2.05854545221507e-03 , -1.37961606606668e-01 ), ( 7.72690086426210e-02 , -2.20002645233214e-03 , -2.12011950998016e-01 ), ( 1.37773726264281e-01 , 1.74369239463660e-02 , -2.01042331311657e-01 ), ( 1.91378798360463e-02 , -2.60697326981438e-02 , -2.64006370760446e-01 ), ( 2.01931304241948e-02 , -3.39666890545063e-02 , -3.32086015852685e-01 ), ( -3.35084346251156e-02 , -3.81963108192040e-02 , -2.32454068643556e-01 ), ( -9.41550647483956e-02 , -6.15420054768978e-02 , -2.73797973221259e-01 ), ( -1.31493369474420e-01 , -6.69849192020118e-02 , -2.25256601586974e-01 ), ( -1.51159216019756e-01 , -8.13910821533683e-02 , -2.95304308607336e-01 ), ( -1.78568999425414e-01 , -9.72662760378736e-02 , -3.58103215110623e-01 ), ( -1.93343679105279e-01 , -9.48997421716479e-02 , -3.01441021178621e-01 ), ( -2.35170551634876e-01 , -1.10784866676663e-01 , -3.28165619370478e-01 ), ( -1.19923703529548e-01 , -7.34991426099793e-02 , -3.08248179504989e-01 ), ( -1.71131416290035e-01 , -8.11159771046006e-02 , -2.42936577336104e-01 ), ( -2.24162693429279e-01 , -9.88863405666131e-02 , -2.57182521268237e-01 ), ( -2.59646905379640e-01 , -1.00376708649434e-01 , -1.80540731105742e-01 ) } +colvars: Step 14, atoms_new_colvar_forces = { ( -4.88570851171614e+00 , -4.56253773604222e-01 , -1.32105352356695e+00 ), ( -4.20872734720022e+00 , -3.85577613582362e-01 , -1.03769308681141e+00 ), ( -4.28545554283310e+00 , -4.13310422094279e-01 , -1.07506981499262e+00 ), ( -5.76268914269491e+00 , -5.86441559791649e-01 , -1.59319752412968e+00 ), ( 2.67512102221459e-01 , 1.24780358318433e-01 , 3.63022771990672e-01 ), ( 5.27040311425189e+00 , 6.44265037876371e-01 , 1.91410551223546e+00 ), ( 4.45373613235302e+00 , 5.34872338551382e-01 , 1.66022158070880e+00 ), ( -4.56162545283365e-02 , 3.07822880510977e-02 , 3.69379816749984e-01 ), ( 4.43322433359100e+00 , 5.24748477029104e-01 , 1.62777876693457e+00 ), ( 5.87610342295328e+00 , 6.71648743826014e-01 , 2.01473368668632e+00 ), ( 1.21129363114962e-02 , 4.12332214763805e-02 , 3.11221341098453e-01 ), ( -2.72594888404143e-05 , 3.44541115508831e-02 , 2.85498488619319e-01 ), ( 2.19292006304853e-02 , 4.93784141234822e-02 , 3.54087834954247e-01 ), ( 4.52656312081194e-02 , 3.87990197041604e-02 , 2.07935621960817e-01 ), ( 1.60341902337049e-02 , 2.36600144308958e-02 , 1.55807321364653e-01 ), ( 1.17734207293443e-01 , 5.94698107445170e-02 , 1.97487731813883e-01 ), ( 1.66188600935006e-01 , 6.54618221384618e-02 , 1.25643584368926e-01 ), ( 2.50099248022815e-01 , 9.28535899253148e-02 , 1.42187278413497e-01 ), ( 1.36263108376236e-01 , 4.76805032052302e-02 , 5.33655307421763e-02 ), ( 1.31470207380580e-01 , 3.82653253584018e-02 , -1.26164721125454e-02 ), ( 1.12591132066163e-01 , 4.20016978708232e-02 , 6.56702954911367e-02 ), ( 7.54957736633364e-02 , 2.35671232324818e-02 , 5.95661542695908e-03 ), ( 6.22051143747376e-02 , 2.37348216717266e-02 , 4.06680244553650e-02 ), ( -1.04156663180405e-03 , -2.91602931812204e-03 , -2.15460267798273e-02 ), ( -1.52988657110378e-02 , -1.58949153969860e-02 , -9.33220667363659e-02 ), ( -5.09636443969827e-02 , -1.11423999111707e-02 , 3.54676473714911e-02 ), ( -1.22007129997978e-01 , -3.46571012622777e-02 , 1.87826057448190e-02 ), ( -1.65809356973343e-01 , -3.82253925041095e-02 , 9.90418747629360e-02 ), ( -1.09036292463458e-01 , -3.65651253925265e-02 , -2.95444296338051e-02 ), ( -1.47054589715852e-01 , -5.52437965616422e-02 , -8.89663143807316e-02 ), ( -5.32957551050355e-02 , -1.68802731208616e-02 , -6.21990813741620e-03 ), ( -3.14722294827953e-02 , -1.54941403179506e-02 , -4.94522956387948e-02 ), ( 2.75421871166536e-02 , 8.34095154176619e-03 , 4.60709069004805e-05 ), ( 1.89129609959227e-03 , -1.56789060797776e-02 , -1.34631476306283e-01 ), ( -1.67201223624295e-02 , -2.81536860558904e-02 , -1.91314740817814e-01 ), ( 5.10303260942475e-02 , -2.18429606248802e-03 , -1.46037931519005e-01 ), ( 8.17918095188016e-02 , -2.33621650666099e-03 , -2.24421210018944e-01 ), ( 1.45839520074683e-01 , 1.84490934142702e-02 , -2.12807721141153e-01 ), ( 2.02590891265704e-02 , -2.76019791361587e-02 , -2.79457910987898e-01 ), ( 2.13762196086749e-02 , -3.59627343913501e-02 , -3.51522240654599e-01 ), ( -3.54680361374518e-02 , -4.04356042436027e-02 , -2.46058050575770e-01 ), ( -9.96636026791784e-02 , -6.51464009076693e-02 , -2.89820968951444e-01 ), ( -1.39186349422021e-01 , -7.09050939470902e-02 , -2.38437216008359e-01 ), ( -1.60005755834681e-01 , -8.61565706229697e-02 , -3.12587792726267e-01 ), ( -1.89019516974402e-01 , -1.02961385390356e-01 , -3.79062016598802e-01 ), ( -2.04663798434532e-01 , -1.00456653359914e-01 , -3.19088822976699e-01 ), ( -2.48939950746201e-01 , -1.17271305621107e-01 , -3.47378913111159e-01 ), ( -1.26946357370064e-01 , -7.78059529956875e-02 , -3.26294311463582e-01 ), ( -1.81148646425748e-01 , -8.58642323381825e-02 , -2.57156829928261e-01 ), ( -2.37285425767131e-01 , -1.04673994747542e-01 , -2.72238343238541e-01 ), ( -2.74847852412318e-01 , -1.06249208776591e-01 , -1.91112042856661e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 14, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4998,10 +8069,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 15, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 15, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 15, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 15, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 15, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 15, atoms_positions[size = 51] = { ( 8.31202261101125e+00 , 4.23796498118627e-02 , -7.64220071348988e-01 ), ( 6.97868795425818e+00 , -5.46103079445024e-01 , -6.11435181462593e-01 ), ( 6.17174118946339e+00 , -3.33624037573884e-01 , 7.01441582404698e-01 ), ( 4.97558495509138e+00 , -1.82211620719155e-01 , 7.07821553822601e-01 ), ( 7.05477187719790e+00 , -2.03976160973846e+00 , -9.56752700471823e-01 ), ( 6.88995159388955e+00 , -2.63751198225184e-01 , 1.87304167781028e+00 ), ( 6.18671941704904e+00 , -1.31467336757217e-01 , 3.19002055929260e+00 ), ( 7.08962428732410e+00 , -3.51139370372955e-01 , 4.28715408570870e+00 ), ( 5.29213514706219e+00 , 1.10887550309795e+00 , 3.33280986530589e+00 ), ( 4.14322790696180e+00 , 1.03784659138943e+00 , 3.66143109773539e+00 ), ( 5.86102669669466e+00 , 2.24684402162226e+00 , 2.99776379726542e+00 ), ( 5.22909465861429e+00 , 3.58804430388609e+00 , 2.90863920936324e+00 ), ( 6.32898758184422e+00 , 4.51551188683693e+00 , 2.41149544875236e+00 ), ( 3.90514082551049e+00 , 3.73248991539767e+00 , 2.03805080994276e+00 ), ( 2.81539843557420e+00 , 4.14385283470926e+00 , 2.51154985284035e+00 ), ( 3.90424485220926e+00 , 3.24189820908485e+00 , 7.37657034667304e-01 ), ( 2.65545318874566e+00 , 3.04132589384411e+00 , -1.08710069237004e-01 ), ( 3.03368637956660e+00 , 2.72184315385574e+00 , -1.53962636118920e+00 ), ( 1.57965283747802e+00 , 2.19656656186226e+00 , 4.97311505574982e-01 ), ( 4.13704665071233e-01 , 2.53301138784715e+00 , 5.25520790241601e-01 ), ( 2.00634706157258e+00 , 1.01093312800957e+00 , 1.07906058097648e+00 ), ( 1.18099612919785e+00 , 9.45069292926887e-02 , 1.69232947207939e+00 ), ( 2.02880908859515e+00 , -1.12733354866967e+00 , 2.00573693563177e+00 ), ( 5.53894018990116e-01 , 6.08271704663100e-01 , 2.92842622488218e+00 ), ( -6.33073749600056e-01 , 3.50415897877268e-01 , 3.16724657244207e+00 ), ( 1.32663479222770e+00 , 1.34467036890182e+00 , 3.82049540489378e+00 ), ( 8.56929113872508e-01 , 1.95946974867600e+00 , 5.02993732399448e+00 ), ( 2.03892826349660e+00 , 2.64115851607595e+00 , 5.64942613997402e+00 ), ( -3.43447816689619e-01 , 2.91645304024642e+00 , 4.97050972356219e+00 ), ( -1.15335724926495e+00 , 3.05500913433501e+00 , 5.90018402580842e+00 ), ( -4.84149940425839e-01 , 3.59060643176087e+00 , 3.84752616033055e+00 ), ( -1.50369609083765e+00 , 4.54805191745859e+00 , 3.49535023676454e+00 ), ( -7.13307749595086e-01 , 5.40474157759740e+00 , 2.44968592586854e+00 ), ( -2.77242957381128e+00 , 3.87392695363197e+00 , 2.91283382403749e+00 ), ( -3.82493765258508e+00 , 4.47946797763180e+00 , 2.82246734035799e+00 ), ( -2.60763007564851e+00 , 2.65976302871916e+00 , 2.43695328704627e+00 ), ( -3.74756066920069e+00 , 1.84164211135460e+00 , 2.01154163700279e+00 ), ( -3.40875828845985e+00 , 8.75983615192798e-01 , 9.08924061424964e-01 ), ( -4.31570991431919e+00 , 1.06528805904774e+00 , 3.23819136175682e+00 ), ( -5.51905109064995e+00 , 8.54387005753863e-01 , 3.32885063175874e+00 ), ( -3.39788230390646e+00 , 6.75555119521035e-01 , 4.16653064719874e+00 ), ( -3.74080565954384e+00 , 3.74836151898684e-02 , 5.45082325228767e+00 ), ( -2.38334247335428e+00 , -3.19005874588463e-01 , 6.17202715964624e+00 ), ( -4.47084459574025e+00 , 1.00206439945020e+00 , 6.44123375865510e+00 ), ( -5.34097893028944e+00 , 6.06062255611571e-01 , 7.20688505094935e+00 ), ( -6.24187316663723e+00 , 3.57950307162747e+00 , 6.71477529448104e+00 ), ( -6.93765081932641e+00 , 4.29702260556012e+00 , 7.45153130375767e+00 ), ( -6.75092365959200e+00 , 3.19937371474768e+00 , 5.51985142036843e+00 ), ( -4.12772439963364e+00 , 2.27139866060630e+00 , 6.44936894039559e+00 ), ( -4.83332103117952e+00 , 3.19117184751636e+00 , 7.22081853615269e+00 ), ( -4.10481403887107e+00 , 4.58650030551778e+00 , 7.29458450809990e+00 ) } +colvars: Step 15, atoms_positions[size = 51] = { ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 ), ( 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 ), ( 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 ), ( 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 ), ( 7.05473892361697e+00 , -2.03978069585531e+00 , -9.56696656116159e-01 ), ( 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 ), ( 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 ), ( 7.08982096830755e+00 , -3.51166956940753e-01 , 4.28741001920924e+00 ), ( 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 ), ( 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 ), ( 5.86122840089223e+00 , 2.24694565302836e+00 , 2.99780509390531e+00 ), ( 5.22908745139920e+00 , 3.58804864345765e+00 , 2.90872115379629e+00 ), ( 6.32898826127183e+00 , 4.51552495482869e+00 , 2.41157873756936e+00 ), ( 3.90515470301220e+00 , 3.73248962779382e+00 , 2.03810827469954e+00 ), ( 2.81540114626890e+00 , 4.14385783489665e+00 , 2.51158474333925e+00 ), ( 3.90427408855215e+00 , 3.24191332378665e+00 , 7.37705952617010e-01 ), ( 2.65549606729918e+00 , 3.04134331251243e+00 , -1.08677222532784e-01 ), ( 3.03374418258581e+00 , 2.72186464645366e+00 , -1.53959171143427e+00 ), ( 1.57968791847728e+00 , 2.19657951904758e+00 , 4.97326997898410e-01 ), ( 4.13736379675307e-01 , 2.53301933374089e+00 , 5.25518331164459e-01 ), ( 2.00637403029016e+00 , 1.01094458268083e+00 , 1.07907903832468e+00 ), ( 1.18101528704331e+00 , 9.45136804738401e-02 , 1.69233228752184e+00 ), ( 2.02882813167391e+00 , -1.12732424294064e+00 , 2.00575221268911e+00 ), ( 5.53896090649999e-01 , 6.08271107573916e-01 , 2.92842091817883e+00 ), ( -6.33075809288131e-01 , 3.50412805654254e-01 , 3.16722686530329e+00 ), ( 1.32664395338748e+00 , 1.34466383120341e+00 , 3.82050202372060e+00 ), ( 8.56900020281219e-01 , 1.95945966251021e+00 , 5.02994153920588e+00 ), ( 2.03888961235672e+00 , 2.64114884413221e+00 , 5.64944655306628e+00 ), ( -3.43476150263057e-01 , 2.91644234646218e+00 , 4.97050093225404e+00 ), ( -1.15339178958262e+00 , 3.05499745666966e+00 , 5.90016689498669e+00 ), ( -4.84163074687500e-01 , 3.59060214801384e+00 , 3.84752234703474e+00 ), ( -1.50370391596201e+00 , 4.54804841951908e+00 , 3.49533660645804e+00 ), ( -7.13302044273382e-01 , 5.40474294273752e+00 , 2.44968501069186e+00 ), ( -2.77242998921563e+00 , 3.87392423478275e+00 , 2.91279805481020e+00 ), ( -3.82494033075986e+00 , 4.47946128165195e+00 , 2.82242534232936e+00 ), ( -2.60761860638666e+00 , 2.65976206398845e+00 , 2.43691711549907e+00 ), ( -3.74754034078466e+00 , 1.84164235626245e+00 , 2.01148186853148e+00 ), ( -3.40872433891289e+00 , 8.75986337224676e-01 , 9.08870838393818e-01 ), ( -4.31570343382940e+00 , 1.06527902394077e+00 , 3.23811722831961e+00 ), ( -5.51904595554738e+00 , 8.54379198401675e-01 , 3.32877288881578e+00 ), ( -3.39789087362984e+00 , 6.75544372858960e-01 , 4.16646799533518e+00 ), ( -3.74083287107551e+00 , 3.74649832889368e-02 , 5.45074936620928e+00 ), ( -2.38337571287417e+00 , -3.19020711104221e-01 , 6.17196940319086e+00 ), ( -4.47088777474719e+00 , 1.00204341019923e+00 , 6.44114945541213e+00 ), ( -5.34102035078252e+00 , 6.06039466412292e-01 , 7.20680167942385e+00 ), ( -6.24192748330466e+00 , 3.57947773859450e+00 , 6.71469633163971e+00 ), ( -6.93770493403295e+00 , 4.29699569742557e+00 , 7.45145361667983e+00 ), ( -6.75095708241872e+00 , 3.19935601312637e+00 , 5.51977222423106e+00 ), ( -4.12776835616795e+00 , 2.27137817021339e+00 , 6.44930464900907e+00 ), ( -4.83338156729211e+00 , 3.19114462708207e+00 , 7.22074730215993e+00 ), ( -4.10488051315969e+00 , 4.58647369597667e+00 , 7.29453646157747e+00 ) } colvars: Step 15, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 15, atom_groups_ids[size = 0] = @@ -5019,162 +8090,301 @@ colvars: Collective variables module, step no. 15 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.13381355030095e-01 , 3.42072155991049e-03 , 9.49621200786667e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.12760327150548e-01 , 3.49835932914566e-03 , 9.49825636231559e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 7.05473892361697e+00 , -2.03978069585531e+00 , -9.56696656116159e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 , 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 7.08982096830755e+00 , -3.51166956940753e-01 , 4.28741001920924e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 , 5.86122840089223e+00 , 2.24694565302836e+00 , 2.99780509390531e+00 , 5.22908745139920e+00 , 3.58804864345765e+00 , 2.90872115379629e+00 , 6.32898826127183e+00 , 4.51552495482869e+00 , 2.41157873756936e+00 , 3.90515470301220e+00 , 3.73248962779382e+00 , 2.03810827469954e+00 , 2.81540114626890e+00 , 4.14385783489665e+00 , 2.51158474333925e+00 , 3.90427408855215e+00 , 3.24191332378665e+00 , 7.37705952617010e-01 , 2.65549606729918e+00 , 3.04134331251243e+00 , -1.08677222532784e-01 , 3.03374418258581e+00 , 2.72186464645366e+00 , -1.53959171143427e+00 , 1.57968791847728e+00 , 2.19657951904758e+00 , 4.97326997898410e-01 , 4.13736379675307e-01 , 2.53301933374089e+00 , 5.25518331164459e-01 , 2.00637403029016e+00 , 1.01094458268083e+00 , 1.07907903832468e+00 , 1.18101528704331e+00 , 9.45136804738401e-02 , 1.69233228752184e+00 , 2.02882813167391e+00 , -1.12732424294064e+00 , 2.00575221268911e+00 , 5.53896090649999e-01 , 6.08271107573916e-01 , 2.92842091817883e+00 , -6.33075809288131e-01 , 3.50412805654254e-01 , 3.16722686530329e+00 , 1.32664395338748e+00 , 1.34466383120341e+00 , 3.82050202372060e+00 , 8.56900020281219e-01 , 1.95945966251021e+00 , 5.02994153920588e+00 , 2.03888961235672e+00 , 2.64114884413221e+00 , 5.64944655306628e+00 , -3.43476150263057e-01 , 2.91644234646218e+00 , 4.97050093225404e+00 , -1.15339178958262e+00 , 3.05499745666966e+00 , 5.90016689498669e+00 , -4.84163074687500e-01 , 3.59060214801384e+00 , 3.84752234703474e+00 , -1.50370391596201e+00 , 4.54804841951908e+00 , 3.49533660645804e+00 , -7.13302044273382e-01 , 5.40474294273752e+00 , 2.44968501069186e+00 , -2.77242998921563e+00 , 3.87392423478275e+00 , 2.91279805481020e+00 , -3.82494033075986e+00 , 4.47946128165195e+00 , 2.82242534232936e+00 , -2.60761860638666e+00 , 2.65976206398845e+00 , 2.43691711549907e+00 , -3.74754034078466e+00 , 1.84164235626245e+00 , 2.01148186853148e+00 , -3.40872433891289e+00 , 8.75986337224676e-01 , 9.08870838393818e-01 , -4.31570343382940e+00 , 1.06527902394077e+00 , 3.23811722831961e+00 , -5.51904595554738e+00 , 8.54379198401675e-01 , 3.32877288881578e+00 , -3.39789087362984e+00 , 6.75544372858960e-01 , 4.16646799533518e+00 , -3.74083287107551e+00 , 3.74649832889368e-02 , 5.45074936620928e+00 , -2.38337571287417e+00 , -3.19020711104221e-01 , 6.17196940319086e+00 , -4.47088777474719e+00 , 1.00204341019923e+00 , 6.44114945541213e+00 , -5.34102035078252e+00 , 6.06039466412292e-01 , 7.20680167942385e+00 , -6.24192748330466e+00 , 3.57947773859450e+00 , 6.71469633163971e+00 , -6.93770493403295e+00 , 4.29699569742557e+00 , 7.45145361667983e+00 , -6.75095708241872e+00 , 3.19935601312637e+00 , 5.51977222423106e+00 , -4.12776835616795e+00 , 2.27137817021339e+00 , 6.44930464900907e+00 , -4.83338156729211e+00 , 3.19114462708207e+00 , 7.22074730215993e+00 , -4.10488051315969e+00 , 4.58647369597667e+00 , 7.29453646157747e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.13381355030095e-01 , 3.42072155991049e-03 , 9.49621200786667e-01 ). +colvars: Colvar "one" has value ( -3.12760327150548e-01 , 3.49835932914566e-03 , 9.49825636231559e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 7.05473892361697e+00 , -2.03978069585531e+00 , -9.56696656116159e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 , 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 7.08982096830755e+00 , -3.51166956940753e-01 , 4.28741001920924e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 , 5.86122840089223e+00 , 2.24694565302836e+00 , 2.99780509390531e+00 , 5.22908745139920e+00 , 3.58804864345765e+00 , 2.90872115379629e+00 , 6.32898826127183e+00 , 4.51552495482869e+00 , 2.41157873756936e+00 , 3.90515470301220e+00 , 3.73248962779382e+00 , 2.03810827469954e+00 , 2.81540114626890e+00 , 4.14385783489665e+00 , 2.51158474333925e+00 , 3.90427408855215e+00 , 3.24191332378665e+00 , 7.37705952617010e-01 , 2.65549606729918e+00 , 3.04134331251243e+00 , -1.08677222532784e-01 , 3.03374418258581e+00 , 2.72186464645366e+00 , -1.53959171143427e+00 , 1.57968791847728e+00 , 2.19657951904758e+00 , 4.97326997898410e-01 , 4.13736379675307e-01 , 2.53301933374089e+00 , 5.25518331164459e-01 , 2.00637403029016e+00 , 1.01094458268083e+00 , 1.07907903832468e+00 , 1.18101528704331e+00 , 9.45136804738401e-02 , 1.69233228752184e+00 , 2.02882813167391e+00 , -1.12732424294064e+00 , 2.00575221268911e+00 , 5.53896090649999e-01 , 6.08271107573916e-01 , 2.92842091817883e+00 , -6.33075809288131e-01 , 3.50412805654254e-01 , 3.16722686530329e+00 , 1.32664395338748e+00 , 1.34466383120341e+00 , 3.82050202372060e+00 , 8.56900020281219e-01 , 1.95945966251021e+00 , 5.02994153920588e+00 , 2.03888961235672e+00 , 2.64114884413221e+00 , 5.64944655306628e+00 , -3.43476150263057e-01 , 2.91644234646218e+00 , 4.97050093225404e+00 , -1.15339178958262e+00 , 3.05499745666966e+00 , 5.90016689498669e+00 , -4.84163074687500e-01 , 3.59060214801384e+00 , 3.84752234703474e+00 , -1.50370391596201e+00 , 4.54804841951908e+00 , 3.49533660645804e+00 , -7.13302044273382e-01 , 5.40474294273752e+00 , 2.44968501069186e+00 , -2.77242998921563e+00 , 3.87392423478275e+00 , 2.91279805481020e+00 , -3.82494033075986e+00 , 4.47946128165195e+00 , 2.82242534232936e+00 , -2.60761860638666e+00 , 2.65976206398845e+00 , 2.43691711549907e+00 , -3.74754034078466e+00 , 1.84164235626245e+00 , 2.01148186853148e+00 , -3.40872433891289e+00 , 8.75986337224676e-01 , 9.08870838393818e-01 , -4.31570343382940e+00 , 1.06527902394077e+00 , 3.23811722831961e+00 , -5.51904595554738e+00 , 8.54379198401675e-01 , 3.32877288881578e+00 , -3.39789087362984e+00 , 6.75544372858960e-01 , 4.16646799533518e+00 , -3.74083287107551e+00 , 3.74649832889368e-02 , 5.45074936620928e+00 , -2.38337571287417e+00 , -3.19020711104221e-01 , 6.17196940319086e+00 , -4.47088777474719e+00 , 1.00204341019923e+00 , 6.44114945541213e+00 , -5.34102035078252e+00 , 6.06039466412292e-01 , 7.20680167942385e+00 , -6.24192748330466e+00 , 3.57947773859450e+00 , 6.71469633163971e+00 , -6.93770493403295e+00 , 4.29699569742557e+00 , 7.45145361667983e+00 , -6.75095708241872e+00 , 3.19935601312637e+00 , 5.51977222423106e+00 , -4.12776835616795e+00 , 2.27137817021339e+00 , 6.44930464900907e+00 , -4.83338156729211e+00 , 3.19114462708207e+00 , 7.22074730215993e+00 , -4.10488051315969e+00 , 4.58647369597667e+00 , 7.29453646157747e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.7856 , 1.88339 , -15.0888 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.4696 , 6.64696 , 13.2939 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.7856 , 1.88339 , -15.0888 ) to colvar "one". -colvars: Adding total bias energy: 44.8059 +colvars: Adding biasing force ( 66.4696 , 6.64696 , 13.2939 ) to colvar "one". +colvars: Adding total bias energy: 57.161 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.7856 , 1.88339 , -15.0888 ) +colvars: Force to be applied: ( 66.4696 , 6.64696 , 13.2939 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.89693 , -0.54314 , -1.49067 ) -colvars: ( -4.19912 , -0.465743 , -1.27825 ) -colvars: ( -4.19912 , -0.465743 , -1.27825 ) -colvars: ( -5.59335 , -0.620383 , -1.70266 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17602 , -0.573193 , -1.57197 ) +colvars: ( -4.43844 , -0.491513 , -1.34796 ) +colvars: ( -4.43844 , -0.491513 , -1.34796 ) +colvars: ( -5.91212 , -0.65471 , -1.79553 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.896062 , 0.19488 , 0.627909 ) -colvars: ( 0.77563 , 0.265958 , 0.652727 ) -colvars: ( 0.760162 , 0.258914 , 0.634186 ) -colvars: ( 0.662675 , 0.267095 , 0.587964 ) -colvars: ( 0.650697 , 0.200562 , 0.491542 ) -colvars: ( 0.575271 , 0.344628 , 0.64084 ) -colvars: ( 0.466927 , 0.358998 , 0.596562 ) -colvars: ( 0.389476 , 0.456497 , 0.682104 ) -colvars: ( 0.384924 , 0.314619 , 0.488809 ) -colvars: ( 0.349661 , 0.273193 , 0.412456 ) -colvars: ( 0.35591 , 0.319854 , 0.478815 ) -colvars: ( 0.284496 , 0.277115 , 0.37948 ) -colvars: ( 0.257749 , 0.306063 , 0.402676 ) -colvars: ( 0.34755 , 0.179104 , 0.284801 ) -colvars: ( 0.288408 , 0.135947 , 0.192106 ) -colvars: ( 0.471359 , 0.141714 , 0.307225 ) -colvars: ( 0.544565 , 0.0501234 , 0.22713 ) -colvars: ( 0.675349 , 0.0287385 , 0.275152 ) -colvars: ( 0.552693 , 0.0184069 , 0.189287 ) -colvars: ( 0.536818 , -0.0466096 , 0.0926157 ) -colvars: ( 0.573292 , 0.0663963 , 0.265854 ) -colvars: ( 0.571227 , 0.0503754 , 0.243116 ) -colvars: ( 0.607636 , 0.115115 , 0.351467 ) -colvars: ( 0.445781 , 0.0552093 , 0.175989 ) -colvars: ( 0.438724 , -0.000654933 , 0.0967894 ) -colvars: ( 0.343133 , 0.121088 , 0.204259 ) -colvars: ( 0.217586 , 0.130009 , 0.142564 ) -colvars: ( 0.125515 , 0.215967 , 0.20402 ) -colvars: ( 0.189491 , 0.0562604 , 0.0269888 ) -colvars: ( 0.139661 , 0.0202625 , -0.0506217 ) -colvars: ( 0.223861 , 0.0304813 , 0.0125235 ) -colvars: ( 0.210088 , -0.0420717 , -0.0930394 ) -colvars: ( 0.24622 , -0.0456473 , -0.0766386 ) -colvars: ( 0.285768 , -0.128173 , -0.164308 ) -colvars: ( 0.241472 , -0.181187 , -0.261532 ) -colvars: ( 0.401657 , -0.143431 , -0.116795 ) -colvars: ( 0.479513 , -0.219066 , -0.172724 ) -colvars: ( 0.611624 , -0.22196 , -0.0990785 ) -colvars: ( 0.431351 , -0.22331 , -0.206691 ) -colvars: ( 0.436852 , -0.291369 , -0.294906 ) -colvars: ( 0.38186 , -0.14979 , -0.136957 ) -colvars: ( 0.326718 , -0.14328 , -0.160573 ) -colvars: ( 0.3097 , -0.0564607 , -0.0539117 ) -colvars: ( 0.202547 , -0.151783 , -0.244871 ) -colvars: ( 0.17771 , -0.193668 , -0.315723 ) -colvars: ( 0.000566621 , -0.197244 , -0.42449 ) -colvars: ( -0.0910223 , -0.214828 , -0.501867 ) -colvars: ( 0.101994 , -0.247486 , -0.432468 ) -colvars: ( 0.120448 , -0.111055 , -0.238332 ) -colvars: ( 0.000320215 , -0.115163 , -0.314353 ) -colvars: ( -0.0891587 , -0.0343271 , -0.258257 ) +colvars: ( 0.946712 , 0.205975 , 0.662886 ) +colvars: ( 0.819508 , 0.281034 , 0.689114 ) +colvars: ( 0.803148 , 0.273617 , 0.669559 ) +colvars: ( 0.700214 , 0.282196 , 0.620725 ) +colvars: ( 0.68756 , 0.211908 , 0.518899 ) +colvars: ( 0.607907 , 0.36407 , 0.676568 ) +colvars: ( 0.493485 , 0.379209 , 0.629809 ) +colvars: ( 0.411689 , 0.482179 , 0.72015 ) +colvars: ( 0.40686 , 0.33232 , 0.516037 ) +colvars: ( 0.369622 , 0.28854 , 0.435399 ) +colvars: ( 0.376195 , 0.337866 , 0.505506 ) +colvars: ( 0.300753 , 0.292714 , 0.400624 ) +colvars: ( 0.272483 , 0.323311 , 0.425143 ) +colvars: ( 0.367344 , 0.189196 , 0.300633 ) +colvars: ( 0.304877 , 0.14359 , 0.202749 ) +colvars: ( 0.49811 , 0.149732 , 0.324302 ) +colvars: ( 0.575424 , 0.0529983 , 0.23971 ) +colvars: ( 0.713552 , 0.0304494 , 0.290417 ) +colvars: ( 0.584028 , 0.0194723 , 0.199725 ) +colvars: ( 0.567259 , -0.0492145 , 0.0976371 ) +colvars: ( 0.605804 , 0.0701527 , 0.280565 ) +colvars: ( 0.603642 , 0.0532042 , 0.256533 ) +colvars: ( 0.642115 , 0.121586 , 0.370937 ) +colvars: ( 0.47115 , 0.0582724 , 0.185652 ) +colvars: ( 0.463702 , -0.000752424 , 0.102007 ) +colvars: ( 0.36273 , 0.127845 , 0.215524 ) +colvars: ( 0.230128 , 0.137235 , 0.150384 ) +colvars: ( 0.13288 , 0.228023 , 0.215301 ) +colvars: ( 0.200439 , 0.0593355 , 0.0283459 ) +colvars: ( 0.147814 , 0.0212863 , -0.0536166 ) +colvars: ( 0.23672 , 0.0321345 , 0.0130851 ) +colvars: ( 0.222158 , -0.0444971 , -0.0983801 ) +colvars: ( 0.260299 , -0.0482397 , -0.0810428 ) +colvars: ( 0.302095 , -0.135441 , -0.173659 ) +colvars: ( 0.255306 , -0.191455 , -0.276327 ) +colvars: ( 0.424505 , -0.151539 , -0.123504 ) +colvars: ( 0.506743 , -0.231429 , -0.182586 ) +colvars: ( 0.646283 , -0.234456 , -0.104831 ) +colvars: ( 0.455892 , -0.235947 , -0.21847 ) +colvars: ( 0.461704 , -0.307847 , -0.311634 ) +colvars: ( 0.403636 , -0.15831 , -0.144835 ) +colvars: ( 0.345413 , -0.15147 , -0.169787 ) +colvars: ( 0.327456 , -0.0597754 , -0.0571584 ) +colvars: ( 0.21426 , -0.160481 , -0.258793 ) +colvars: ( 0.188036 , -0.204746 , -0.333624 ) +colvars: ( 0.00089215 , -0.208518 , -0.448424 ) +colvars: ( -0.0958473 , -0.227114 , -0.530125 ) +colvars: ( 0.108008 , -0.261554 , -0.45685 ) +colvars: ( 0.127535 , -0.117461 , -0.251864 ) +colvars: ( 0.000649719 , -0.121827 , -0.332128 ) +colvars: ( -0.093864 , -0.036446 , -0.272869 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.89693 , 0.54314 , 1.49067 ) -colvars: ( 4.19912 , 0.465743 , 1.27825 ) -colvars: ( 4.19912 , 0.465743 , 1.27825 ) -colvars: ( 5.59335 , 0.620383 , 1.70266 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17602 , 0.573193 , 1.57197 ) +colvars: ( 4.43844 , 0.491513 , 1.34796 ) +colvars: ( 4.43844 , 0.491513 , 1.34796 ) +colvars: ( 5.91212 , 0.65471 , 1.79553 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.618496 , -0.0806149 , -0.378058 ) -colvars: ( -0.555788 , -0.162705 , -0.348536 ) -colvars: ( -0.50734 , -0.140971 , -0.291022 ) -colvars: ( -0.515355 , -0.190103 , -0.319095 ) -colvars: ( -0.505768 , -0.13186 , -0.285729 ) -colvars: ( -0.489488 , -0.281326 , -0.330296 ) -colvars: ( -0.455431 , -0.321425 , -0.312435 ) -colvars: ( -0.432747 , -0.427762 , -0.332992 ) -colvars: ( -0.392748 , -0.286584 , -0.235282 ) -colvars: ( -0.387554 , -0.261602 , -0.219884 ) -colvars: ( -0.34446 , -0.281078 , -0.184541 ) -colvars: ( -0.284452 , -0.244711 , -0.109453 ) -colvars: ( -0.236886 , -0.259549 , -0.0677292 ) -colvars: ( -0.304679 , -0.142491 , -0.0881057 ) -colvars: ( -0.273141 , -0.113625 , -0.0446677 ) -colvars: ( -0.360008 , -0.0854921 , -0.120443 ) -colvars: ( -0.387406 , 0.0118607 , -0.108282 ) -colvars: ( -0.438886 , 0.0592028 , -0.140688 ) -colvars: ( -0.423876 , 0.0267656 , -0.138834 ) -colvars: ( -0.412513 , 0.082931 , -0.104531 ) -colvars: ( -0.466922 , -0.0266532 , -0.203837 ) -colvars: ( -0.499978 , -0.0280777 , -0.237616 ) -colvars: ( -0.549023 , -0.0927275 , -0.313221 ) -colvars: ( -0.446858 , -0.0579919 , -0.19646 ) -colvars: ( -0.453286 , -0.0143645 , -0.185134 ) -colvars: ( -0.391369 , -0.131721 , -0.170781 ) -colvars: ( -0.332947 , -0.162915 , -0.12482 ) -colvars: ( -0.282256 , -0.252332 , -0.110354 ) -colvars: ( -0.292527 , -0.0908966 , -0.0548743 ) -colvars: ( -0.278633 , -0.0725512 , -0.0334434 ) -colvars: ( -0.274153 , -0.0464481 , -0.0183049 ) -colvars: ( -0.23969 , 0.0274924 , 0.0464418 ) -colvars: ( -0.219982 , 0.0536461 , 0.0768936 ) -colvars: ( -0.283855 , 0.1135 , 0.0371394 ) -colvars: ( -0.257123 , 0.154754 , 0.0808005 ) -colvars: ( -0.353349 , 0.141547 , -0.0212231 ) -colvars: ( -0.402159 , 0.217108 , -0.039447 ) -colvars: ( -0.473778 , 0.239682 , -0.102174 ) -colvars: ( -0.412205 , 0.197427 , -0.0575574 ) -colvars: ( -0.416646 , 0.257635 , -0.0374789 ) -colvars: ( -0.415434 , 0.11168 , -0.0957474 ) -colvars: ( -0.421015 , 0.0817616 , -0.113546 ) -colvars: ( -0.441413 , -0.010599 , -0.171675 ) -colvars: ( -0.353835 , 0.070382 , -0.0507148 ) -colvars: ( -0.356437 , 0.0963937 , -0.0427266 ) -colvars: ( -0.193897 , 0.10236 , 0.122945 ) -colvars: ( -0.144124 , 0.104041 , 0.173619 ) -colvars: ( -0.221847 , 0.1741 , 0.124114 ) -colvars: ( -0.291665 , 0.0298963 , -0.00477766 ) -colvars: ( -0.224551 , 0.0162011 , 0.057044 ) -colvars: ( -0.170545 , -0.0662015 , 0.0776982 ) +colvars: ( -0.653392 , -0.0852277 , -0.398852 ) +colvars: ( -0.587189 , -0.171921 , -0.367658 ) +colvars: ( -0.53598 , -0.148981 , -0.306921 ) +colvars: ( -0.544531 , -0.200832 , -0.336597 ) +colvars: ( -0.534404 , -0.139307 , -0.301405 ) +colvars: ( -0.517253 , -0.297169 , -0.3484 ) +colvars: ( -0.481333 , -0.339496 , -0.329558 ) +colvars: ( -0.457412 , -0.451801 , -0.351227 ) +colvars: ( -0.415127 , -0.302686 , -0.248124 ) +colvars: ( -0.409664 , -0.276283 , -0.231901 ) +colvars: ( -0.364096 , -0.296882 , -0.194537 ) +colvars: ( -0.300709 , -0.258465 , -0.11528 ) +colvars: ( -0.250441 , -0.274152 , -0.0711987 ) +colvars: ( -0.322044 , -0.150503 , -0.0927811 ) +colvars: ( -0.288748 , -0.119999 , -0.0469496 ) +colvars: ( -0.380442 , -0.0903201 , -0.126924 ) +colvars: ( -0.40935 , 0.0124993 , -0.114121 ) +colvars: ( -0.463673 , 0.062476 , -0.148324 ) +colvars: ( -0.447902 , 0.0282598 , -0.14641 ) +colvars: ( -0.435901 , 0.0875914 , -0.110229 ) +colvars: ( -0.493396 , -0.028156 , -0.215027 ) +colvars: ( -0.528347 , -0.0296422 , -0.250716 ) +colvars: ( -0.580171 , -0.097926 , -0.330515 ) +colvars: ( -0.472286 , -0.0612122 , -0.207281 ) +colvars: ( -0.479087 , -0.0151197 , -0.19536 ) +colvars: ( -0.413702 , -0.139078 , -0.180145 ) +colvars: ( -0.352035 , -0.172003 , -0.131633 ) +colvars: ( -0.298515 , -0.266443 , -0.116322 ) +colvars: ( -0.309323 , -0.0959344 , -0.0578153 ) +colvars: ( -0.294673 , -0.0765394 , -0.03522 ) +colvars: ( -0.289869 , -0.0490068 , -0.0191979 ) +colvars: ( -0.253443 , 0.0290885 , 0.0491336 ) +colvars: ( -0.232578 , 0.0566887 , 0.0813056 ) +colvars: ( -0.300077 , 0.119931 , 0.0392716 ) +colvars: ( -0.27185 , 0.163517 , 0.0853366 ) +colvars: ( -0.373457 , 0.149541 , -0.0223465 ) +colvars: ( -0.424999 , 0.229351 , -0.0416234 ) +colvars: ( -0.500614 , 0.253174 , -0.107838 ) +colvars: ( -0.435659 , 0.208588 , -0.0607695 ) +colvars: ( -0.44035 , 0.272189 , -0.0396079 ) +colvars: ( -0.439113 , 0.118034 , -0.10107 ) +colvars: ( -0.445057 , 0.086458 , -0.119882 ) +colvars: ( -0.466637 , -0.0110886 , -0.181223 ) +colvars: ( -0.37413 , 0.0744591 , -0.0535623 ) +colvars: ( -0.376901 , 0.10195 , -0.0451618 ) +colvars: ( -0.205196 , 0.108248 , 0.129765 ) +colvars: ( -0.152646 , 0.11004 , 0.183247 ) +colvars: ( -0.234664 , 0.183999 , 0.130996 ) +colvars: ( -0.308466 , 0.031697 , -0.00504002 ) +colvars: ( -0.237605 , 0.0172501 , 0.060217 ) +colvars: ( -0.180579 , -0.0697833 , 0.082061 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 15. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 15. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 15, atoms_new_colvar_forces = { ( -4.61936778687056e+00 , -4.28875636713662e-01 , -1.24081622411012e+00 ), ( -3.97927752576044e+00 , -3.62490025082989e-01 , -9.74055099879345e-01 ), ( -4.05179905979518e+00 , -3.88751327715992e-01 , -1.00937787142554e+00 ), ( -5.44842004583146e+00 , -5.51681403457618e-01 , -1.49684846013888e+00 ), ( 2.52821496214122e-01 , 1.17943316152049e-01 , 3.43164616568188e-01 ), ( 4.98271733248943e+00 , 6.06442794201924e-01 , 1.80121182861804e+00 ), ( 4.21061603961148e+00 , 5.03315796242880e-01 , 1.56237371200815e+00 ), ( -4.32710129312120e-02 , 2.87355680351474e-02 , 3.49112196479845e-01 ), ( 4.19129571918370e+00 , 4.93777804565713e-01 , 1.53177353365320e+00 ), ( 5.55545587967625e+00 , 6.31974408426609e-01 , 1.89523312767131e+00 ), ( 1.14506186431756e-02 , 3.87761552168734e-02 , 2.94273707334107e-01 ), ( 4.47403535131508e-05 , 3.24038890923857e-02 , 2.70027462202968e-01 ), ( 2.08632792242771e-02 , 4.65134994254886e-02 , 3.34946572921082e-01 ), ( 4.28713634419879e-02 , 3.66136569733684e-02 , 1.96694969207058e-01 ), ( 1.52672190829746e-02 , 2.23220680487652e-02 , 1.47438481940793e-01 ), ( 1.11351342254400e-01 , 5.62214403208874e-02 , 1.86781868289036e-01 ), ( 1.57158812685396e-01 , 6.19840632516422e-02 , 1.18848149279894e-01 ), ( 2.36463080192088e-01 , 8.79413782569101e-02 , 1.34464225633902e-01 ), ( 1.28816645976026e-01 , 4.51725228088821e-02 , 5.04521585599663e-02 ), ( 1.24305385881526e-01 , 3.63213320186521e-02 , -1.19157963869323e-02 ), ( 1.06370910416383e-01 , 3.97430970902821e-02 , 6.20166558677490e-02 ), ( 7.12495144637919e-02 , 2.22977053019278e-02 , 5.50002839875133e-03 ), ( 5.86131152589200e-02 , 2.23880094676876e-02 , 3.82455591518973e-02 ), ( -1.07704656601298e-03 , -2.78261183358337e-03 , -2.04708797724387e-02 ), ( -1.45618160768809e-02 , -1.50194445426009e-02 , -8.83448048199977e-02 ), ( -4.82362131464319e-02 , -1.06332435126323e-02 , 3.34779953099402e-02 ), ( -1.15361008057320e-01 , -3.29058859531983e-02 , 1.77439890509237e-02 ), ( -1.56740321099998e-01 , -3.63654446716120e-02 , 9.36664496342354e-02 ), ( -1.03036083099045e-01 , -3.46362317737734e-02 , -2.78854511395982e-02 ), ( -1.38972489535878e-01 , -5.22887107320162e-02 , -8.40650628899017e-02 ), ( -5.02920638383860e-02 , -1.59668314607233e-02 , -5.78142132838359e-03 ), ( -2.96014978638097e-02 , -1.45792306693401e-02 , -4.65975861319859e-02 ), ( 2.62376192155431e-02 , 7.99876823009550e-03 , 2.55030979381593e-04 ), ( 1.91266694880055e-03 , -1.46732001437521e-02 , -1.27168189169222e-01 ), ( -1.56515108032224e-02 , -2.64323801435717e-02 , -1.80731878028861e-01 ), ( 4.83081575192512e-02 , -1.88468610713632e-03 , -1.38018070881387e-01 ), ( 7.73544978807220e-02 , -1.95832211906594e-03 , -2.12171150083733e-01 ), ( 1.37846408225428e-01 , 1.77223172321023e-02 , -2.01252771691206e-01 ), ( 1.91459825565006e-02 , -2.58825952833994e-02 , -2.64248404027074e-01 ), ( 2.02061702671993e-02 , -3.37336648216094e-02 , -3.32384401030002e-01 ), ( -3.35737155292727e-02 , -3.81094310150237e-02 , -2.32704434239873e-01 ), ( -9.42968709869637e-02 , -6.15183467315491e-02 , -2.74118782184220e-01 ), ( -1.31712528632276e-01 , -6.70597105056869e-02 , -2.25586794937362e-01 ), ( -1.51287838040672e-01 , -8.14010829483994e-02 , -2.95585625795411e-01 ), ( -1.78726480391682e-01 , -9.72746618564433e-02 , -3.58449667649919e-01 ), ( -1.93330816872829e-01 , -9.48840436070342e-02 , -3.01544761332582e-01 ), ( -2.35145990876308e-01 , -1.10786116175523e-01 , -3.28248003595132e-01 ), ( -1.19852575288214e-01 , -7.33859881344482e-02 , -3.08353821134834e-01 ), ( -1.71216704970340e-01 , -8.11587345035392e-02 , -2.43109562889482e-01 ), ( -2.24230906343134e-01 , -9.89619596618653e-02 , -2.57308526737973e-01 ), ( -2.59704088455363e-01 , -1.00528638482483e-01 , -1.80558815329004e-01 ) } +colvars: Step 15, atoms_new_colvar_forces = { ( -4.88269920507628e+00 , -4.52446296131558e-01 , -1.30793548225431e+00 ), ( -4.20611587681103e+00 , -3.82399893859511e-01 , -1.02650748532271e+00 ), ( -4.28275267144583e+00 , -4.10149646689628e-01 , -1.06383505425101e+00 ), ( -5.75896944246471e+00 , -5.82108338049370e-01 , -1.57803144821227e+00 ), ( 2.67167838331193e-01 , 1.24635912226521e-01 , 3.62637157105136e-01 ), ( 5.26667330554919e+00 , 6.40093984399705e-01 , 1.90013694587171e+00 ), ( 4.45058709416635e+00 , 5.31226649470670e-01 , 1.64821406679998e+00 ), ( -4.57231772146376e-02 , 3.03788119582362e-02 , 3.68923300930360e-01 ), ( 4.43016851438168e+00 , 5.21146462072069e-01 , 1.61587533915400e+00 ), ( 5.87208256040792e+00 , 6.66966037131744e-01 , 1.99902447209852e+00 ), ( 1.20992510865886e-02 , 4.09836572718097e-02 , 3.10968892154521e-01 ), ( 4.41576239948449e-05 , 3.42486843759318e-02 , 2.85344604846735e-01 ), ( 2.20418775550471e-02 , 4.91589889477537e-02 , 3.53944779970346e-01 ), ( 4.53008401131758e-02 , 3.86936503603045e-02 , 2.07851624900147e-01 ), ( 1.61296855682379e-02 , 2.35905015140426e-02 , 1.55799501443613e-01 ), ( 1.17667364997870e-01 , 5.94115147834406e-02 , 1.97377423365764e-01 ), ( 1.66074248252500e-01 , 6.54975790518631e-02 , 1.25589791146712e-01 ), ( 2.49878928883532e-01 , 9.29254155549144e-02 , 1.42092918383800e-01 ), ( 1.36125714727971e-01 , 4.77320975442177e-02 , 5.33151062366599e-02 ), ( 1.31358123360124e-01 , 3.83769537146051e-02 , -1.25918825871648e-02 ), ( 1.12408343580062e-01 , 4.19966431490401e-02 , 6.55378831375178e-02 ), ( 7.52959074036862e-02 , 2.35619297623028e-02 , 5.81652390007492e-03 ), ( 6.19445296609211e-02 , 2.36596463126856e-02 , 4.04222111122794e-02 ), ( -1.13532110248166e-03 , -2.93978045519981e-03 , -2.16291147558315e-02 ), ( -1.53847854912670e-02 , -1.58721287379464e-02 , -9.33535919889726e-02 ), ( -5.09716149404266e-02 , -1.12331166127158e-02 , 3.53790405616591e-02 ), ( -1.21906202655111e-01 , -3.47678772676525e-02 , 1.87508249365284e-02 ), ( -1.65634601266584e-01 , -3.84205550864689e-02 , 9.89794175263195e-02 ), ( -1.08883651419844e-01 , -3.65988996337234e-02 , -2.94694085072222e-02 ), ( -1.46859062817992e-01 , -5.52531677969171e-02 , -8.88365963969102e-02 ), ( -5.31484187072113e-02 , -1.68722510187382e-02 , -6.11277646832457e-03 ), ( -3.12854672664357e-02 , -1.54085590957590e-02 , -4.92465091713178e-02 ), ( 2.77203872094699e-02 , 8.44899722432180e-03 , 2.62789756932502e-04 ), ( 2.01794387650917e-03 , -1.55108290900512e-02 , -1.34387102720003e-01 ), ( -1.65435535450074e-02 , -2.79383755473416e-02 , -1.90990750694173e-01 ), ( 5.10477677815733e-02 , -1.99796019264700e-03 , -1.45850322064685e-01 ), ( 8.17435406255514e-02 , -2.07837568905500e-03 , -2.24209044576675e-01 ), ( 1.45669481857759e-01 , 1.87176896380716e-02 , -2.12669033776203e-01 ), ( 2.02335267984439e-02 , -2.73587912813237e-02 , -2.79239787620972e-01 ), ( 2.13540042872654e-02 , -3.56572232534428e-02 , -3.51241498814213e-01 ), ( -3.54765541163397e-02 , -4.02760621005897e-02 , -2.45905189320064e-01 ), ( -9.96440130627073e-02 , -6.50115381496472e-02 , -2.89668188567758e-01 ), ( -1.39181299517898e-01 , -7.08639356256818e-02 , -2.38381206857471e-01 ), ( -1.59870259209741e-01 , -8.60215496701822e-02 , -3.12355024514433e-01 ), ( -1.88865265737409e-01 , -1.02796285654035e-01 , -3.78785329546590e-01 ), ( -2.04304019274105e-01 , -1.00270408319716e-01 , -3.18658401055721e-01 ), ( -2.48492988643436e-01 , -1.17074441350643e-01 , -3.46878222183423e-01 ), ( -1.26656717155222e-01 , -7.75556009689559e-02 , -3.25853670132928e-01 ), ( -1.80931870289518e-01 , -8.57640870766624e-02 , -2.56903918050239e-01 ), ( -2.36955766172313e-01 , -1.04576569693729e-01 , -2.71910565139110e-01 ), ( -2.74443132683073e-01 , -1.06229262365360e-01 , -1.90808009788618e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 15, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5212,10 +8422,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 16, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 16, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 16, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 16, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 16, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 16, atoms_positions[size = 51] = { ( 8.30584559981966e+00 , 4.18920549749206e-02 , -7.62827408931917e-01 ), ( 6.97262709713975e+00 , -5.47679445776029e-01 , -6.05379216725242e-01 ), ( 6.16442418297579e+00 , -3.42831690267079e-01 , 7.05931054367244e-01 ), ( 4.97232239227887e+00 , -1.78455396513559e-01 , 7.11230999580600e-01 ), ( 7.05471751299227e+00 , -2.04221082906437e+00 , -9.51795507911699e-01 ), ( 6.88578088427731e+00 , -2.63182714075398e-01 , 1.87940202984847e+00 ), ( 6.18614345503480e+00 , -1.36473813325527e-01 , 3.19564118935261e+00 ), ( 7.08484621753552e+00 , -3.53106619971983e-01 , 4.29079136214221e+00 ), ( 5.29603872645111e+00 , 1.10689714471731e+00 , 3.33681046754548e+00 ), ( 4.14768145433506e+00 , 1.03511929553146e+00 , 3.66687942828962e+00 ), ( 5.85714968570103e+00 , 2.24693035412113e+00 , 2.99689244175829e+00 ), ( 5.23297324872810e+00 , 3.58605603227763e+00 , 2.91238409842110e+00 ), ( 6.32721524124312e+00 , 4.51094539045354e+00 , 2.40314480031856e+00 ), ( 3.90154546852211e+00 , 3.72839311188602e+00 , 2.03999828208399e+00 ), ( 2.80849424265705e+00 , 4.14770271386909e+00 , 2.50712703510101e+00 ), ( 3.91341734146436e+00 , 3.24221542915919e+00 , 7.35649238406860e-01 ), ( 2.65347398432954e+00 , 3.03056273185891e+00 , -1.08515797703818e-01 ), ( 3.03560344150804e+00 , 2.72018000543168e+00 , -1.53188357851366e+00 ), ( 1.58478245190695e+00 , 2.19680139496657e+00 , 4.84857448280314e-01 ), ( 4.05794748764460e-01 , 2.54310721789363e+00 , 5.22821481379191e-01 ), ( 2.01446392954469e+00 , 1.01872007024961e+00 , 1.07966365627172e+00 ), ( 1.17915363246752e+00 , 1.01958011700901e-01 , 1.69272268033936e+00 ), ( 2.03131320678593e+00 , -1.12186760591478e+00 , 2.00555250086458e+00 ), ( 5.55592531194352e-01 , 6.08183415383067e-01 , 2.92855945885333e+00 ), ( -6.26628569428618e-01 , 3.49842512123108e-01 , 3.16581279764676e+00 ), ( 1.32585687459329e+00 , 1.34529651624049e+00 , 3.81290372877736e+00 ), ( 8.54391449652899e-01 , 1.96425722534732e+00 , 5.02806857936199e+00 ), ( 2.04534224079621e+00 , 2.64985450952519e+00 , 5.65529063448693e+00 ), ( -3.41096704626099e-01 , 2.91631272770942e+00 , 4.96913317798965e+00 ), ( -1.15045517335613e+00 , 3.05689153647007e+00 , 5.89811906253420e+00 ), ( -4.90079775575702e-01 , 3.57766943315727e+00 , 3.84829906622339e+00 ), ( -1.50764355151631e+00 , 4.54710277212402e+00 , 3.48510009579148e+00 ), ( -7.09277419933967e-01 , 5.40675475620672e+00 , 2.45329350157170e+00 ), ( -2.77189891941281e+00 , 3.87423545331641e+00 , 2.91026949655478e+00 ), ( -3.82290568167701e+00 , 4.48571771041692e+00 , 2.82046138947987e+00 ), ( -2.60994695095092e+00 , 2.66578909698494e+00 , 2.43019103733966e+00 ), ( -3.75350896178922e+00 , 1.83058251763696e+00 , 2.00706483018988e+00 ), ( -3.40531891511751e+00 , 8.80191524655614e-01 , 9.01240964699100e-01 ), ( -4.32035334073315e+00 , 1.06609845153730e+00 , 3.23257900543483e+00 ), ( -5.51434680845415e+00 , 8.47387690179261e-01 , 3.32846100676540e+00 ), ( -3.39045698875149e+00 , 6.78587857596137e-01 , 4.17564412594035e+00 ), ( -3.73232648521104e+00 , 3.60304998623892e-02 , 5.44499178317187e+00 ), ( -2.38438798972812e+00 , -3.16150344974704e-01 , 6.17296653876527e+00 ), ( -4.46889966652845e+00 , 1.00211281854870e+00 , 6.44231557083538e+00 ), ( -5.34487080038993e+00 , 6.04639147144351e-01 , 7.20969187830549e+00 ), ( -6.23694677428182e+00 , 3.58394366005188e+00 , 6.71779129577674e+00 ), ( -6.94267244320899e+00 , 4.29762860792866e+00 , 7.45679689719063e+00 ), ( -6.75169210203605e+00 , 3.19653741058694e+00 , 5.51757902146330e+00 ), ( -4.12950759068337e+00 , 2.26487192367640e+00 , 6.44115742181759e+00 ), ( -4.82630490172218e+00 , 3.19133533958257e+00 , 7.22420135575370e+00 ), ( -4.10514951256287e+00 , 4.58788744247899e+00 , 7.29320145958151e+00 ) } +colvars: Step 16, atoms_positions[size = 51] = { ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 ), ( 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 ), ( 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 ), ( 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 ), ( 7.05466781602202e+00 , -2.04223860168671e+00 , -9.51736464236291e-01 ), ( 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 ), ( 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 ), ( 7.08509320289695e+00 , -3.53142554632854e-01 , 4.29109682955083e+00 ), ( 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 ), ( 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 ), ( 5.85739937943113e+00 , 2.24705372923822e+00 , 2.99693495627931e+00 ), ( 5.23296605450751e+00 , 3.58606110840864e+00 , 2.91247709599507e+00 ), ( 6.32721498626626e+00 , 4.51096054330538e+00 , 2.40323812095780e+00 ), ( 3.90156078362489e+00 , 3.72839123981515e+00 , 2.04006304240512e+00 ), ( 2.80849747987868e+00 , 4.14770815693897e+00 , 2.50716653162687e+00 ), ( 3.91345048213876e+00 , 3.24223237482255e+00 , 7.35704502186487e-01 ), ( 2.65352192938508e+00 , 3.03058219725472e+00 , -1.08478988734758e-01 ), ( 3.03566821421468e+00 , 2.72020402497637e+00 , -1.53184494858950e+00 ), ( 1.58482182237910e+00 , 2.19681594444141e+00 , 4.84874977263818e-01 ), ( 4.05830752628882e-01 , 2.54311622034941e+00 , 5.22818761318913e-01 ), ( 2.01449434615761e+00 , 1.01873319035267e+00 , 1.07968478091619e+00 ), ( 1.17917508255272e+00 , 1.01965607587946e-01 , 1.69272590185043e+00 ), ( 2.03133511102619e+00 , -1.12185634481181e+00 , 2.00557055177542e+00 ), ( 5.55595461399606e-01 , 6.08182757174921e-01 , 2.92855358667179e+00 ), ( -6.26630685382450e-01 , 3.49839117918140e-01 , 3.16579064902669e+00 ), ( 1.32586966564794e+00 , 1.34528872112012e+00 , 3.81291116809697e+00 ), ( 8.54359432097506e-01 , 1.96424557858562e+00 , 5.02807312514457e+00 ), ( 2.04529922472684e+00 , 2.64984360296788e+00 , 5.65531328010371e+00 ), ( -3.41128378670846e-01 , 2.91630064517151e+00 , 4.96912331758290e+00 ), ( -1.15049440600122e+00 , 3.05687835727132e+00 , 5.89809994139646e+00 ), ( -4.90094551484171e-01 , 3.57766459827628e+00 , 3.84829453823356e+00 ), ( -1.50765232127455e+00 , 4.54709892177202e+00 , 3.48508471341254e+00 ), ( -7.09271116590437e-01 , 5.40675620645661e+00 , 2.45329243023343e+00 ), ( -2.77189930799630e+00 , 3.87423248244704e+00 , 2.91022951952803e+00 ), ( -3.82290860556533e+00 , 4.48571014839430e+00 , 2.82041394135468e+00 ), ( -2.60993400144245e+00 , 2.66578802597967e+00 , 2.43015018541631e+00 ), ( -3.75348641347962e+00 , 1.83058299040785e+00 , 2.00699787203871e+00 ), ( -3.40528105969574e+00 , 8.80194500244144e-01 , 9.01181203965098e-01 ), ( -4.32034616015787e+00 , 1.06608828721428e+00 , 3.23249604753155e+00 ), ( -5.51434095786223e+00 , 8.47378908615441e-01 , 3.32837306747542e+00 ), ( -3.39046668325370e+00 , 6.78575600903094e-01 , 4.17557341126074e+00 ), ( -3.73235707258592e+00 , 3.60092331314798e-02 , 5.44490895554789e+00 ), ( -2.38442507637343e+00 , -3.16166941813654e-01 , 6.17290186463125e+00 ), ( -4.46894807425871e+00 , 1.00208941164697e+00 , 6.44222120545526e+00 ), ( -5.34491764662130e+00 , 6.04613365323989e-01 , 7.20959762112996e+00 ), ( -6.23700731007577e+00 , 3.58391531958642e+00 , 6.71770325102584e+00 ), ( -6.94273363851727e+00 , 4.29759822630906e+00 , 7.45670916706203e+00 ), ( -6.75173034342212e+00 , 3.19651736390297e+00 , 5.51748939476038e+00 ), ( -4.12955702796124e+00 , 2.26484894211344e+00 , 6.44108485141110e+00 ), ( -4.82637252427413e+00 , 3.19130489622522e+00 , 7.22412139903855e+00 ), ( -4.10522391931655e+00 , 4.58785764103600e+00 , 7.29314746797526e+00 ) } colvars: Step 16, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 16, atom_groups_ids[size = 0] = @@ -5233,162 +8443,301 @@ colvars: Collective variables module, step no. 16 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.11271197951965e-01 , 2.91633047576440e-03 , 9.50316650565539e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.10587038251228e-01 , 3.00315024001721e-03 , 9.50540200495995e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 7.05466781602202e+00 , -2.04223860168671e+00 , -9.51736464236291e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 , 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 7.08509320289695e+00 , -3.53142554632854e-01 , 4.29109682955083e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 , 5.85739937943113e+00 , 2.24705372923822e+00 , 2.99693495627931e+00 , 5.23296605450751e+00 , 3.58606110840864e+00 , 2.91247709599507e+00 , 6.32721498626626e+00 , 4.51096054330538e+00 , 2.40323812095780e+00 , 3.90156078362489e+00 , 3.72839123981515e+00 , 2.04006304240512e+00 , 2.80849747987868e+00 , 4.14770815693897e+00 , 2.50716653162687e+00 , 3.91345048213876e+00 , 3.24223237482255e+00 , 7.35704502186487e-01 , 2.65352192938508e+00 , 3.03058219725472e+00 , -1.08478988734758e-01 , 3.03566821421468e+00 , 2.72020402497637e+00 , -1.53184494858950e+00 , 1.58482182237910e+00 , 2.19681594444141e+00 , 4.84874977263818e-01 , 4.05830752628882e-01 , 2.54311622034941e+00 , 5.22818761318913e-01 , 2.01449434615761e+00 , 1.01873319035267e+00 , 1.07968478091619e+00 , 1.17917508255272e+00 , 1.01965607587946e-01 , 1.69272590185043e+00 , 2.03133511102619e+00 , -1.12185634481181e+00 , 2.00557055177542e+00 , 5.55595461399606e-01 , 6.08182757174921e-01 , 2.92855358667179e+00 , -6.26630685382450e-01 , 3.49839117918140e-01 , 3.16579064902669e+00 , 1.32586966564794e+00 , 1.34528872112012e+00 , 3.81291116809697e+00 , 8.54359432097506e-01 , 1.96424557858562e+00 , 5.02807312514457e+00 , 2.04529922472684e+00 , 2.64984360296788e+00 , 5.65531328010371e+00 , -3.41128378670846e-01 , 2.91630064517151e+00 , 4.96912331758290e+00 , -1.15049440600122e+00 , 3.05687835727132e+00 , 5.89809994139646e+00 , -4.90094551484171e-01 , 3.57766459827628e+00 , 3.84829453823356e+00 , -1.50765232127455e+00 , 4.54709892177202e+00 , 3.48508471341254e+00 , -7.09271116590437e-01 , 5.40675620645661e+00 , 2.45329243023343e+00 , -2.77189930799630e+00 , 3.87423248244704e+00 , 2.91022951952803e+00 , -3.82290860556533e+00 , 4.48571014839430e+00 , 2.82041394135468e+00 , -2.60993400144245e+00 , 2.66578802597967e+00 , 2.43015018541631e+00 , -3.75348641347962e+00 , 1.83058299040785e+00 , 2.00699787203871e+00 , -3.40528105969574e+00 , 8.80194500244144e-01 , 9.01181203965098e-01 , -4.32034616015787e+00 , 1.06608828721428e+00 , 3.23249604753155e+00 , -5.51434095786223e+00 , 8.47378908615441e-01 , 3.32837306747542e+00 , -3.39046668325370e+00 , 6.78575600903094e-01 , 4.17557341126074e+00 , -3.73235707258592e+00 , 3.60092331314798e-02 , 5.44490895554789e+00 , -2.38442507637343e+00 , -3.16166941813654e-01 , 6.17290186463125e+00 , -4.46894807425871e+00 , 1.00208941164697e+00 , 6.44222120545526e+00 , -5.34491764662130e+00 , 6.04613365323989e-01 , 7.20959762112996e+00 , -6.23700731007577e+00 , 3.58391531958642e+00 , 6.71770325102584e+00 , -6.94273363851727e+00 , 4.29759822630906e+00 , 7.45670916706203e+00 , -6.75173034342212e+00 , 3.19651736390297e+00 , 5.51748939476038e+00 , -4.12955702796124e+00 , 2.26484894211344e+00 , 6.44108485141110e+00 , -4.82637252427413e+00 , 3.19130489622522e+00 , 7.22412139903855e+00 , -4.10522391931655e+00 , 4.58785764103600e+00 , 7.29314746797526e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.11271197951965e-01 , 2.91633047576440e-03 , 9.50316650565539e-01 ). +colvars: Colvar "one" has value ( -3.10587038251228e-01 , 3.00315024001721e-03 , 9.50540200495995e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 7.05466781602202e+00 , -2.04223860168671e+00 , -9.51736464236291e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 , 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 7.08509320289695e+00 , -3.53142554632854e-01 , 4.29109682955083e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 , 5.85739937943113e+00 , 2.24705372923822e+00 , 2.99693495627931e+00 , 5.23296605450751e+00 , 3.58606110840864e+00 , 2.91247709599507e+00 , 6.32721498626626e+00 , 4.51096054330538e+00 , 2.40323812095780e+00 , 3.90156078362489e+00 , 3.72839123981515e+00 , 2.04006304240512e+00 , 2.80849747987868e+00 , 4.14770815693897e+00 , 2.50716653162687e+00 , 3.91345048213876e+00 , 3.24223237482255e+00 , 7.35704502186487e-01 , 2.65352192938508e+00 , 3.03058219725472e+00 , -1.08478988734758e-01 , 3.03566821421468e+00 , 2.72020402497637e+00 , -1.53184494858950e+00 , 1.58482182237910e+00 , 2.19681594444141e+00 , 4.84874977263818e-01 , 4.05830752628882e-01 , 2.54311622034941e+00 , 5.22818761318913e-01 , 2.01449434615761e+00 , 1.01873319035267e+00 , 1.07968478091619e+00 , 1.17917508255272e+00 , 1.01965607587946e-01 , 1.69272590185043e+00 , 2.03133511102619e+00 , -1.12185634481181e+00 , 2.00557055177542e+00 , 5.55595461399606e-01 , 6.08182757174921e-01 , 2.92855358667179e+00 , -6.26630685382450e-01 , 3.49839117918140e-01 , 3.16579064902669e+00 , 1.32586966564794e+00 , 1.34528872112012e+00 , 3.81291116809697e+00 , 8.54359432097506e-01 , 1.96424557858562e+00 , 5.02807312514457e+00 , 2.04529922472684e+00 , 2.64984360296788e+00 , 5.65531328010371e+00 , -3.41128378670846e-01 , 2.91630064517151e+00 , 4.96912331758290e+00 , -1.15049440600122e+00 , 3.05687835727132e+00 , 5.89809994139646e+00 , -4.90094551484171e-01 , 3.57766459827628e+00 , 3.84829453823356e+00 , -1.50765232127455e+00 , 4.54709892177202e+00 , 3.48508471341254e+00 , -7.09271116590437e-01 , 5.40675620645661e+00 , 2.45329243023343e+00 , -2.77189930799630e+00 , 3.87423248244704e+00 , 2.91022951952803e+00 , -3.82290860556533e+00 , 4.48571014839430e+00 , 2.82041394135468e+00 , -2.60993400144245e+00 , 2.66578802597967e+00 , 2.43015018541631e+00 , -3.75348641347962e+00 , 1.83058299040785e+00 , 2.00699787203871e+00 , -3.40528105969574e+00 , 8.80194500244144e-01 , 9.01181203965098e-01 , -4.32034616015787e+00 , 1.06608828721428e+00 , 3.23249604753155e+00 , -5.51434095786223e+00 , 8.47378908615441e-01 , 3.32837306747542e+00 , -3.39046668325370e+00 , 6.78575600903094e-01 , 4.17557341126074e+00 , -3.73235707258592e+00 , 3.60092331314798e-02 , 5.44490895554789e+00 , -2.38442507637343e+00 , -3.16166941813654e-01 , 6.17290186463125e+00 , -4.46894807425871e+00 , 1.00208941164697e+00 , 6.44222120545526e+00 , -5.34491764662130e+00 , 6.04613365323989e-01 , 7.20959762112996e+00 , -6.23700731007577e+00 , 3.58391531958642e+00 , 6.71770325102584e+00 , -6.94273363851727e+00 , 4.29759822630906e+00 , 7.45670916706203e+00 , -6.75173034342212e+00 , 3.19651736390297e+00 , 5.51748939476038e+00 , -4.12955702796124e+00 , 2.26484894211344e+00 , 6.44108485141110e+00 , -4.82637252427413e+00 , 3.19130489622522e+00 , 7.22412139903855e+00 , -4.10522391931655e+00 , 4.58785764103600e+00 , 7.29314746797526e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.7434 , 1.89347 , -15.1027 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.3644 , 6.63644 , 13.2729 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.7434 , 1.89347 , -15.1027 ) to colvar "one". -colvars: Adding total bias energy: 44.7201 +colvars: Adding biasing force ( 66.3644 , 6.63644 , 13.2729 ) to colvar "one". +colvars: Adding total bias energy: 57.0105 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.7434 , 1.89347 , -15.1027 ) +colvars: Force to be applied: ( 66.3644 , 6.63644 , 13.2729 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.90144 , -0.540656 , -1.48135 ) -colvars: ( -4.20298 , -0.463612 , -1.27026 ) -colvars: ( -4.20298 , -0.463612 , -1.27026 ) -colvars: ( -5.59849 , -0.617545 , -1.69202 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.1737 , -0.569699 , -1.55962 ) +colvars: ( -4.43645 , -0.488516 , -1.33737 ) +colvars: ( -4.43645 , -0.488516 , -1.33737 ) +colvars: ( -5.90947 , -0.650718 , -1.78142 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.895334 , 0.19502 , 0.625909 ) -colvars: ( 0.775113 , 0.266007 , 0.650628 ) -colvars: ( 0.759544 , 0.259012 , 0.632133 ) -colvars: ( 0.662425 , 0.267048 , 0.586015 ) -colvars: ( 0.650467 , 0.200528 , 0.489858 ) -colvars: ( 0.575234 , 0.344484 , 0.638723 ) -colvars: ( 0.467159 , 0.358752 , 0.59454 ) -colvars: ( 0.389894 , 0.456157 , 0.679825 ) -colvars: ( 0.385248 , 0.314359 , 0.487064 ) -colvars: ( 0.350098 , 0.272903 , 0.410914 ) -colvars: ( 0.356179 , 0.319621 , 0.477089 ) -colvars: ( 0.284828 , 0.276879 , 0.378011 ) -colvars: ( 0.258016 , 0.30585 , 0.401134 ) -colvars: ( 0.347739 , 0.178947 , 0.28361 ) -colvars: ( 0.288709 , 0.135763 , 0.191158 ) -colvars: ( 0.471297 , 0.141654 , 0.306004 ) -colvars: ( 0.544346 , 0.0501441 , 0.22615 ) -colvars: ( 0.674839 , 0.0288683 , 0.274073 ) -colvars: ( 0.552568 , 0.0183948 , 0.188415 ) -colvars: ( 0.536722 , -0.046613 , 0.0920087 ) -colvars: ( 0.573228 , 0.0663415 , 0.264776 ) -colvars: ( 0.571279 , 0.0502753 , 0.242103 ) -colvars: ( 0.60771 , 0.114982 , 0.350163 ) -colvars: ( 0.446102 , 0.0550132 , 0.175129 ) -colvars: ( 0.439099 , -0.000857086 , 0.0961485 ) -colvars: ( 0.343627 , 0.120816 , 0.203294 ) -colvars: ( 0.218331 , 0.129648 , 0.141738 ) -colvars: ( 0.126408 , 0.215534 , 0.202999 ) -colvars: ( 0.190214 , 0.055934 , 0.0264756 ) -colvars: ( 0.140519 , 0.0198964 , -0.0509319 ) -colvars: ( 0.224407 , 0.0302324 , 0.0120582 ) -colvars: ( 0.210581 , -0.0422751 , -0.0932161 ) -colvars: ( 0.246522 , -0.0457739 , -0.0768527 ) -colvars: ( 0.28615 , -0.128317 , -0.164266 ) -colvars: ( 0.24193 , -0.181342 , -0.261233 ) -colvars: ( 0.401858 , -0.143513 , -0.116855 ) -colvars: ( 0.479609 , -0.219094 , -0.172608 ) -colvars: ( 0.611487 , -0.221909 , -0.0991328 ) -colvars: ( 0.431649 , -0.223415 , -0.206492 ) -colvars: ( 0.437155 , -0.291459 , -0.29446 ) -colvars: ( 0.382333 , -0.149983 , -0.136964 ) -colvars: ( 0.327402 , -0.143556 , -0.160527 ) -colvars: ( 0.310499 , -0.0568076 , -0.0541659 ) -colvars: ( 0.203452 , -0.152131 , -0.244624 ) -colvars: ( 0.178717 , -0.194045 , -0.315285 ) -colvars: ( 0.00167065 , -0.197631 , -0.423798 ) -colvars: ( -0.0897546 , -0.215265 , -0.500984 ) -colvars: ( 0.102838 , -0.247765 , -0.431729 ) -colvars: ( 0.121435 , -0.111436 , -0.238125 ) -colvars: ( 0.00151303 , -0.115612 , -0.313966 ) -colvars: ( -0.0878372 , -0.0348387 , -0.25805 ) +colvars: ( 0.944607 , 0.20584 , 0.659788 ) +colvars: ( 0.81781 , 0.280695 , 0.685873 ) +colvars: ( 0.801363 , 0.273342 , 0.666398 ) +colvars: ( 0.69897 , 0.28175 , 0.617744 ) +colvars: ( 0.686355 , 0.211574 , 0.516346 ) +colvars: ( 0.607022 , 0.3634 , 0.673328 ) +colvars: ( 0.49305 , 0.378406 , 0.626738 ) +colvars: ( 0.411569 , 0.481128 , 0.716676 ) +colvars: ( 0.406645 , 0.331569 , 0.513426 ) +colvars: ( 0.369581 , 0.287816 , 0.43312 ) +colvars: ( 0.375965 , 0.337137 , 0.502933 ) +colvars: ( 0.300696 , 0.292045 , 0.398477 ) +colvars: ( 0.272397 , 0.322626 , 0.422886 ) +colvars: ( 0.36704 , 0.18876 , 0.298925 ) +colvars: ( 0.304781 , 0.143189 , 0.20144 ) +colvars: ( 0.497351 , 0.149458 , 0.322526 ) +colvars: ( 0.574389 , 0.05295 , 0.238312 ) +colvars: ( 0.712009 , 0.0305527 , 0.288838 ) +colvars: ( 0.583081 , 0.019435 , 0.198497 ) +colvars: ( 0.566366 , -0.0491453 , 0.0968372 ) +colvars: ( 0.604892 , 0.0699965 , 0.278999 ) +colvars: ( 0.602858 , 0.0530218 , 0.255068 ) +colvars: ( 0.641301 , 0.12127 , 0.368997 ) +colvars: ( 0.470842 , 0.0579777 , 0.184454 ) +colvars: ( 0.463462 , -0.000970741 , 0.101161 ) +colvars: ( 0.36276 , 0.127369 , 0.214173 ) +colvars: ( 0.230615 , 0.136648 , 0.149276 ) +colvars: ( 0.133662 , 0.227228 , 0.213895 ) +colvars: ( 0.200944 , 0.0588968 , 0.0277473 ) +colvars: ( 0.148538 , 0.0208576 , -0.0538817 ) +colvars: ( 0.236983 , 0.0318197 , 0.0125609 ) +colvars: ( 0.222384 , -0.0446536 , -0.0984358 ) +colvars: ( 0.260266 , -0.0483063 , -0.0811615 ) +colvars: ( 0.302089 , -0.135405 , -0.173376 ) +colvars: ( 0.255448 , -0.191351 , -0.275622 ) +colvars: ( 0.424132 , -0.151411 , -0.123404 ) +colvars: ( 0.506141 , -0.23113 , -0.182216 ) +colvars: ( 0.645235 , -0.234067 , -0.104755 ) +colvars: ( 0.45558 , -0.235727 , -0.217962 ) +colvars: ( 0.461388 , -0.307508 , -0.31073 ) +colvars: ( 0.403585 , -0.158296 , -0.144652 ) +colvars: ( 0.345671 , -0.151557 , -0.169513 ) +colvars: ( 0.327862 , -0.0600698 , -0.057366 ) +colvars: ( 0.214939 , -0.160634 , -0.258174 ) +colvars: ( 0.188861 , -0.204867 , -0.332696 ) +colvars: ( 0.00208578 , -0.208646 , -0.447054 ) +colvars: ( -0.0943418 , -0.227271 , -0.528434 ) +colvars: ( 0.108771 , -0.261487 , -0.455418 ) +colvars: ( 0.128424 , -0.117711 , -0.251296 ) +colvars: ( 0.00193934 , -0.122144 , -0.331251 ) +colvars: ( -0.0923028 , -0.0369526 , -0.272266 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.90144 , 0.540656 , 1.48135 ) -colvars: ( 4.20298 , 0.463612 , 1.27026 ) -colvars: ( 4.20298 , 0.463612 , 1.27026 ) -colvars: ( 5.59849 , 0.617545 , 1.69202 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.1737 , 0.569699 , 1.55962 ) +colvars: ( 4.43645 , 0.488516 , 1.33737 ) +colvars: ( 4.43645 , 0.488516 , 1.33737 ) +colvars: ( 5.90947 , 0.650718 , 1.78142 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.61783 , -0.0806685 , -0.37611 ) -colvars: ( -0.555318 , -0.162767 , -0.346399 ) -colvars: ( -0.50667 , -0.141033 , -0.288821 ) -colvars: ( -0.515173 , -0.190132 , -0.317114 ) -colvars: ( -0.505587 , -0.131847 , -0.284037 ) -colvars: ( -0.489558 , -0.281373 , -0.32812 ) -colvars: ( -0.455804 , -0.321446 , -0.310364 ) -colvars: ( -0.433344 , -0.427816 , -0.330625 ) -colvars: ( -0.393144 , -0.28656 , -0.233427 ) -colvars: ( -0.388083 , -0.261541 , -0.218278 ) -colvars: ( -0.344718 , -0.281056 , -0.182601 ) -colvars: ( -0.2847 , -0.244648 , -0.107704 ) -colvars: ( -0.236989 , -0.259502 , -0.0657893 ) -colvars: ( -0.304754 , -0.142389 , -0.0866822 ) -colvars: ( -0.27331 , -0.113481 , -0.0434853 ) -colvars: ( -0.35983 , -0.0854043 , -0.119035 ) -colvars: ( -0.387049 , 0.0119807 , -0.107167 ) -colvars: ( -0.438221 , 0.0592963 , -0.139493 ) -colvars: ( -0.423686 , 0.0269086 , -0.137937 ) -colvars: ( -0.412333 , 0.0831164 , -0.10392 ) -colvars: ( -0.466878 , -0.0265381 , -0.202801 ) -colvars: ( -0.500129 , -0.0279457 , -0.236745 ) -colvars: ( -0.549281 , -0.0926381 , -0.312118 ) -colvars: ( -0.447283 , -0.0578258 , -0.195723 ) -colvars: ( -0.45378 , -0.0141613 , -0.184672 ) -colvars: ( -0.391951 , -0.131566 , -0.169855 ) -colvars: ( -0.333773 , -0.16273 , -0.123997 ) -colvars: ( -0.283216 , -0.252173 , -0.109242 ) -colvars: ( -0.293256 , -0.0906646 , -0.0543248 ) -colvars: ( -0.279511 , -0.0722817 , -0.0331302 ) -colvars: ( -0.274622 , -0.0462174 , -0.0177337 ) -colvars: ( -0.24003 , 0.0277647 , 0.0467622 ) -colvars: ( -0.220048 , 0.0539029 , 0.0773391 ) -colvars: ( -0.284099 , 0.113803 , 0.03715 ) -colvars: ( -0.25742 , 0.155101 , 0.08055 ) -colvars: ( -0.353455 , 0.141829 , -0.0211905 ) -colvars: ( -0.402184 , 0.217416 , -0.0396867 ) -colvars: ( -0.473602 , 0.239956 , -0.102306 ) -colvars: ( -0.412505 , 0.197757 , -0.0579583 ) -colvars: ( -0.416947 , 0.258005 , -0.0381715 ) -colvars: ( -0.415976 , 0.111986 , -0.0959595 ) -colvars: ( -0.421839 , 0.0820857 , -0.113878 ) -colvars: ( -0.442428 , -0.0103161 , -0.17173 ) -colvars: ( -0.354849 , 0.0707449 , -0.0511966 ) -colvars: ( -0.357579 , 0.0967915 , -0.0434553 ) -colvars: ( -0.194937 , 0.102795 , 0.122221 ) -colvars: ( -0.145302 , 0.104512 , 0.172736 ) -colvars: ( -0.222582 , 0.174532 , 0.123341 ) -colvars: ( -0.292705 , 0.0302538 , -0.00511103 ) -colvars: ( -0.225763 , 0.0165932 , 0.0565887 ) -colvars: ( -0.171861 , -0.0658343 , 0.0775239 ) +colvars: ( -0.65176 , -0.0851704 , -0.396176 ) +colvars: ( -0.585863 , -0.171747 , -0.364826 ) +colvars: ( -0.534513 , -0.148841 , -0.30411 ) +colvars: ( -0.543576 , -0.200578 , -0.333977 ) +colvars: ( -0.533465 , -0.139096 , -0.299145 ) +colvars: ( -0.516607 , -0.296793 , -0.345555 ) +colvars: ( -0.481063 , -0.339028 , -0.326853 ) +colvars: ( -0.457418 , -0.451205 , -0.348174 ) +colvars: ( -0.414977 , -0.302224 , -0.245771 ) +colvars: ( -0.409663 , -0.275818 , -0.229836 ) +colvars: ( -0.363872 , -0.296431 , -0.192171 ) +colvars: ( -0.300565 , -0.258026 , -0.113235 ) +colvars: ( -0.250214 , -0.273709 , -0.0690157 ) +colvars: ( -0.321684 , -0.150179 , -0.0911177 ) +colvars: ( -0.288536 , -0.119674 , -0.0456116 ) +colvars: ( -0.379726 , -0.0901 , -0.125227 ) +colvars: ( -0.4084 , 0.0126043 , -0.112755 ) +colvars: ( -0.462315 , 0.0624779 , -0.146821 ) +colvars: ( -0.447076 , 0.0283682 , -0.145228 ) +colvars: ( -0.435103 , 0.08766 , -0.109407 ) +colvars: ( -0.492662 , -0.0279949 , -0.213596 ) +colvars: ( -0.527771 , -0.0294592 , -0.249409 ) +colvars: ( -0.579636 , -0.0976893 , -0.328842 ) +colvars: ( -0.472085 , -0.0609448 , -0.206182 ) +colvars: ( -0.47895 , -0.0148782 , -0.194572 ) +colvars: ( -0.413753 , -0.138709 , -0.178884 ) +colvars: ( -0.352436 , -0.171552 , -0.130554 ) +colvars: ( -0.299137 , -0.265883 , -0.114958 ) +colvars: ( -0.309681 , -0.0955438 , -0.0571377 ) +colvars: ( -0.295213 , -0.0761353 , -0.0348284 ) +colvars: ( -0.289977 , -0.0486875 , -0.018554 ) +colvars: ( -0.253466 , 0.0293387 , 0.0494086 ) +colvars: ( -0.232336 , 0.0568803 , 0.0816669 ) +colvars: ( -0.299929 , 0.120083 , 0.0392305 ) +colvars: ( -0.271799 , 0.163652 , 0.0849483 ) +colvars: ( -0.373055 , 0.149627 , -0.0222728 ) +colvars: ( -0.424437 , 0.229348 , -0.0418119 ) +colvars: ( -0.499727 , 0.253099 , -0.107813 ) +colvars: ( -0.435376 , 0.208642 , -0.0611021 ) +colvars: ( -0.440061 , 0.272194 , -0.0402834 ) +colvars: ( -0.439085 , 0.118195 , -0.101142 ) +colvars: ( -0.445324 , 0.0866856 , -0.120053 ) +colvars: ( -0.467077 , -0.010763 , -0.181008 ) +colvars: ( -0.374702 , 0.0747471 , -0.0539929 ) +colvars: ( -0.377606 , 0.102236 , -0.0458685 ) +colvars: ( -0.206038 , 0.108564 , 0.128805 ) +colvars: ( -0.153712 , 0.110393 , 0.182037 ) +colvars: ( -0.235137 , 0.1842 , 0.129981 ) +colvars: ( -0.30916 , 0.0320409 , -0.00538378 ) +colvars: ( -0.238585 , 0.0176534 , 0.0596462 ) +colvars: ( -0.181753 , -0.0692805 , 0.0817579 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 16. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 16. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 16, atoms_new_colvar_forces = { ( -4.62393221994104e+00 , -4.26304109748047e-01 , -1.23155000779684e+00 ), ( -3.98318603531314e+00 , -3.60372108360054e-01 , -9.66028370108865e-01 ), ( -4.05572906156253e+00 , -3.86695296424297e-01 , -1.00135532784653e+00 ), ( -5.45361353122923e+00 , -5.48863813909308e-01 , -1.48619709209284e+00 ), ( 2.52873349102304e-01 , 1.17979161073234e-01 , 3.43312429647552e-01 ), ( 4.98711309987895e+00 , 6.03766465373158e-01 , 1.79195207617560e+00 ), ( 4.21433667248663e+00 , 5.00917723629509e-01 , 1.55443256372642e+00 ), ( -4.34509018936229e-02 , 2.83409155196254e-02 , 3.49199878225349e-01 ), ( 4.19508480578038e+00 , 4.91411459582331e-01 , 1.52389360384485e+00 ), ( 5.56050830394954e+00 , 6.28906469020644e-01 , 1.88465503116507e+00 ), ( 1.14609845957472e-02 , 3.85658689595760e-02 , 2.94488073046964e-01 ), ( 1.27972527221687e-04 , 3.22310406436168e-02 , 2.70307449217059e-01 ), ( 2.10269967585273e-02 , 4.63479945043058e-02 , 3.35344556452762e-01 ), ( 4.29845307156735e-02 , 3.65575299112754e-02 , 1.96928091449742e-01 ), ( 1.53990706991032e-02 , 2.22815859547440e-02 , 1.47672467222464e-01 ), ( 1.11466818929663e-01 , 5.62494583844813e-02 , 1.86969220263956e-01 ), ( 1.57297015412835e-01 , 6.21248231237574e-02 , 1.18983177604912e-01 ), ( 2.36617773495052e-01 , 8.81645796904891e-02 , 1.34580054820728e-01 ), ( 1.28881605333126e-01 , 4.53034398687004e-02 , 5.04787839400021e-02 ), ( 1.24388989691166e-01 , 3.65034654339361e-02 , -1.19115824517484e-02 ), ( 1.06349848594728e-01 , 3.98034081902991e-02 , 6.19751654442269e-02 ), ( 7.11507274984183e-02 , 2.23295978975600e-02 , 5.35801563736707e-03 ), ( 5.84283560220867e-02 , 2.23437665274223e-02 , 3.80447398278145e-02 ), ( -1.18086227742220e-03 , -2.81254785985447e-03 , -2.05933119714489e-02 ), ( -1.46808640692542e-02 , -1.50183451313337e-02 , -8.85235865653149e-02 ), ( -4.83238099615155e-02 , -1.07498888367066e-02 , 3.34393788547477e-02 ), ( -1.15441803819559e-01 , -3.30814562972608e-02 , 1.77415080275554e-02 ), ( -1.56807837943647e-01 , -3.66395915031185e-02 , 9.37569562921980e-02 ), ( -1.03041454392351e-01 , -3.47305835195608e-02 , -2.78491686386393e-02 ), ( -1.38991943713039e-01 , -5.23853203067249e-02 , -8.40620945991603e-02 ), ( -5.02155919001466e-02 , -1.59849815189438e-02 , -5.67549560984493e-03 ), ( -2.94489968667291e-02 , -1.45103988130709e-02 , -4.64538439984492e-02 ), ( 2.64740740958471e-02 , 8.12899888277881e-03 , 4.86459219254942e-04 ), ( 2.05035652520458e-03 , -1.45137341331953e-02 , -1.27116438945519e-01 ), ( -1.54898780905774e-02 , -2.62406155173920e-02 , -1.80682876297122e-01 ), ( 4.84039048901975e-02 , -1.68369371236871e-03 , -1.38045731313653e-01 ), ( 7.74254302074487e-02 , -1.67866867920424e-03 , -2.12295182255925e-01 ), ( 1.37885532338481e-01 , 1.80465692151712e-02 , -2.01438523605025e-01 ), ( 1.91442638224501e-02 , -2.56580641944545e-02 , -2.64450629657562e-01 ), ( 2.02083750589916e-02 , -3.34536379663548e-02 , -3.32631882603284e-01 ), ( -3.36433698722798e-02 , -3.79965538351294e-02 , -2.32923431372171e-01 ), ( -9.44372493111604e-02 , -6.14707751958226e-02 , -2.74404826691171e-01 ), ( -1.31929428397296e-01 , -6.71237319317913e-02 , -2.25895616606678e-01 ), ( -1.51397203547389e-01 , -8.13864419500957e-02 , -2.95820424585032e-01 ), ( -1.78862185823288e-01 , -9.72530075209848e-02 , -3.58740462775067e-01 ), ( -1.93266703998240e-01 , -9.48366795602419e-02 , -3.01577382798790e-01 ), ( -2.35057038029502e-01 , -1.10753556421043e-01 , -3.28248678270264e-01 ), ( -1.19743248264548e-01 , -7.32329493047166e-02 , -3.08388176355380e-01 ), ( -1.71269786765332e-01 , -8.11824467058980e-02 , -2.43236089767739e-01 ), ( -2.24249528089155e-01 , -9.90183537439328e-02 , -2.57377396881962e-01 ), ( -2.59698323337768e-01 , -1.00672968785710e-01 , -1.80526047644573e-01 ) } +colvars: Step 16, atoms_new_colvar_forces = { ( -4.88085068907305e+00 , -4.49028551929164e-01 , -1.29600505074684e+00 ), ( -4.20449836752702e+00 , -3.79568369070789e-01 , -1.01632430649201e+00 ), ( -4.28105116741037e+00 , -4.07344508252640e-01 , -1.05360440146138e+00 ), ( -5.75658405057599e+00 , -5.78239321822000e-01 , -1.56421676933607e+00 ), ( 2.66850654120383e-01 , 1.24500399472507e-01 , 3.62288258170644e-01 ), ( 5.26411349601398e+00 , 6.36305546643621e-01 , 1.88739008042324e+00 ), ( 4.44843204232688e+00 , 5.27894380406265e-01 , 1.63725644529032e+00 ), ( -4.58487427383804e-02 , 2.99224912067624e-02 , 3.68502409691058e-01 ), ( 4.42811375763588e+00 , 5.17861510298295e-01 , 1.60502694631232e+00 ), ( 5.86939152786686e+00 , 6.62716429830793e-01 , 1.98470143797970e+00 ), ( 1.20931357692768e-02 , 4.07061075669419e-02 , 3.10761607549823e-01 ), ( 1.31340163474214e-04 , 3.40197974706165e-02 , 2.85241839288116e-01 ), ( 2.21829629885617e-02 , 4.89171257411371e-02 , 3.53870531155421e-01 ), ( 4.53565873031619e-02 , 3.85810582605524e-02 , 2.07807414821818e-01 ), ( 1.62456401933390e-02 , 2.35153115016368e-02 , 1.55828556996292e-01 ), ( 1.17624936312603e-01 , 5.93584234737399e-02 , 1.97299748725069e-01 ), ( 1.65988430475053e-01 , 6.55543247547084e-02 , 1.25557009390830e-01 ), ( 2.49693910649660e-01 , 9.30305591635169e-02 , 1.42017065999787e-01 ), ( 1.36004655248192e-01 , 4.78031666460733e-02 , 5.32689860115979e-02 ), ( 1.31263310514551e-01 , 3.85147594908248e-02 , -1.25699010391985e-02 ), ( 1.12229911337970e-01 , 4.20015694953329e-02 , 6.54032439735829e-02 ), ( 7.50874790384561e-02 , 2.35626187995924e-02 , 5.65936400585526e-03 ), ( 6.16643556147614e-02 , 2.35802880442146e-02 , 4.01551900984536e-02 ), ( -1.24275646121408e-03 , -2.96714532752347e-03 , -2.17275868271735e-02 ), ( -1.54883657321769e-02 , -1.58489738486194e-02 , -9.34115097600717e-02 ), ( -5.09927657674062e-02 , -1.13399247924184e-02 , 3.52892877895157e-02 ), ( -1.21821584896125e-01 , -3.49038099162917e-02 , 1.87221033278634e-02 ), ( -1.65475291476308e-01 , -3.86548292634590e-02 , 9.89367627981799e-02 ), ( -1.08737900127232e-01 , -3.66470484735752e-02 , -2.93903836734535e-02 ), ( -1.46675271595853e-01 , -5.52777771765367e-02 , -8.87100220773765e-02 ), ( -5.29942156615225e-02 , -1.68678241372460e-02 , -5.99308463064763e-03 ), ( -3.10817890375260e-02 , -1.53148785160445e-02 , -4.90271339168488e-02 ), ( 2.79301716201383e-02 , 8.57398547511687e-03 , 5.05415453358665e-04 ), ( 2.15981680450927e-03 , -1.53219240057637e-02 , -1.34145923449791e-01 ), ( -1.63506978351837e-02 , -2.76983110422327e-02 , -1.90673765340870e-01 ), ( 5.10774365366631e-02 , -1.78427629910211e-03 , -1.45676560806550e-01 ), ( 8.17045196869475e-02 , -1.78206317383400e-03 , -2.24027507928624e-01 ), ( 1.45508176742863e-01 , 1.90318905822752e-02 , -2.12568317990047e-01 ), ( 2.02037544016062e-02 , -2.70852204318984e-02 , -2.79063859139157e-01 ), ( 2.13268364197606e-02 , -3.53138998393175e-02 , -3.51012977347652e-01 ), ( -3.55002405032920e-02 , -4.01017152862368e-02 , -2.45793237538160e-01 ), ( -9.96527391486413e-02 , -6.48713729919172e-02 , -2.89565809604738e-01 ), ( -1.39215450944104e-01 , -7.08327482746793e-02 , -2.38374063955150e-01 ), ( -1.59762673449301e-01 , -8.58867346246306e-02 , -3.12167322151533e-01 ), ( -1.88744993147753e-01 , -1.02630820233226e-01 , -3.78564068420618e-01 ), ( -2.03952470610454e-01 , -1.00081398696425e-01 , -3.18249682314534e-01 ), ( -2.48053903344336e-01 , -1.16877610053149e-01 , -3.46396743410593e-01 ), ( -1.26365629683014e-01 , -7.72872597662565e-02 , -3.25436738108755e-01 ), ( -1.80735927282973e-01 , -8.56698452581875e-02 , -2.56679643610762e-01 ), ( -2.36645737830085e-01 , -1.04490468464590e-01 , -2.71604912806018e-01 ), ( -2.74055423926221e-01 , -1.06233113356772e-01 , -1.90508421368227e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 16, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5426,10 +8775,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 17, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 17, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 17, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 17, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 17, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 17, atoms_positions[size = 51] = { ( 8.30014175749540e+00 , 4.14209336321197e-02 , -7.61076479752835e-01 ), ( 6.96510579831744e+00 , -5.48867673275960e-01 , -5.98745578066627e-01 ), ( 6.15938433081102e+00 , -3.51865155810142e-01 , 7.10959937129136e-01 ), ( 4.96814369829621e+00 , -1.74599055654912e-01 , 7.14405530876505e-01 ), ( 7.05408190991051e+00 , -2.04462705476435e+00 , -9.47086827310487e-01 ), ( 6.88091650377089e+00 , -2.62817011227806e-01 , 1.88604566025066e+00 ), ( 6.18480477574462e+00 , -1.42066901477744e-01 , 3.19873946451125e+00 ), ( 7.08149559817778e+00 , -3.54482354608875e-01 , 4.29542762480813e+00 ), ( 5.30104254983498e+00 , 1.10445470535622e+00 , 3.34071996229546e+00 ), ( 4.15143839661535e+00 , 1.03247761763336e+00 , 3.67272010695036e+00 ), ( 5.85323568922793e+00 , 2.24790632228913e+00 , 2.99560209916197e+00 ), ( 5.23618370718149e+00 , 3.58403251276659e+00 , 2.91569931192652e+00 ), ( 6.32567170250395e+00 , 4.50737419565728e+00 , 2.39424603863690e+00 ), ( 3.89715551171003e+00 , 3.72365196675080e+00 , 2.04164791600279e+00 ), ( 2.80268853248701e+00 , 4.15138165055561e+00 , 2.50252266455473e+00 ), ( 3.92169594309874e+00 , 3.24225447989746e+00 , 7.34057635628520e-01 ), ( 2.65289180099164e+00 , 3.02148462948114e+00 , -1.07929070913402e-01 ), ( 3.03852321246946e+00 , 2.71763698861064e+00 , -1.52536700526375e+00 ), ( 1.58985441651868e+00 , 2.19523956422429e+00 , 4.73259858316049e-01 ), ( 3.97932369926968e-01 , 2.55316545017503e+00 , 5.19991029316518e-01 ), ( 2.02279620946447e+00 , 1.02897519386683e+00 , 1.07894198045913e+00 ), ( 1.17672175709072e+00 , 1.07868540491865e-01 , 1.69345045832561e+00 ), ( 2.03396198359163e+00 , -1.11666031273628e+00 , 2.00593010227910e+00 ), ( 5.57165429018075e-01 , 6.08512629021110e-01 , 2.93037236873306e+00 ), ( -6.20129990467547e-01 , 3.49518171000439e-01 , 3.16445900786119e+00 ), ( 1.32439666649378e+00 , 1.34553301855622e+00 , 3.80421179966588e+00 ), ( 8.51427613206044e-01 , 1.96865383405773e+00 , 5.02675980213683e+00 ), ( 2.05301471733063e+00 , 2.65904315802423e+00 , 5.66163036121760e+00 ), ( -3.39220706008036e-01 , 2.91610450769908e+00 , 4.96817542695472e+00 ), ( -1.14734730315266e+00 , 3.05856795143061e+00 , 5.89578123130764e+00 ), ( -4.95755321705192e-01 , 3.56540563470383e+00 , 3.84877399242367e+00 ), ( -1.51129798305328e+00 , 4.54595447511705e+00 , 3.47450439012542e+00 ), ( -7.05768396183657e-01 , 5.40875014273645e+00 , 2.45650999812695e+00 ), ( -2.77014863891599e+00 , 3.87590513998068e+00 , 2.90736321587238e+00 ), ( -3.82120833571270e+00 , 4.49192703814357e+00 , 2.81867411885874e+00 ), ( -2.61276063570700e+00 , 2.67035471524129e+00 , 2.42320099140277e+00 ), ( -3.75910904387670e+00 , 1.82091769837248e+00 , 2.00348296427044e+00 ), ( -3.40146962560496e+00 , 8.83369634242150e-01 , 8.93971629103607e-01 ), ( -4.32377740955311e+00 , 1.06721184527503e+00 , 3.22672314401887e+00 ), ( -5.50993764092784e+00 , 8.40320182188524e-01 , 3.32834082542474e+00 ), ( -3.38367687218931e+00 , 6.81582725519902e-01 , 4.18453821945106e+00 ), ( -3.72390265898211e+00 , 3.63543918288892e-02 , 5.44008888275078e+00 ), ( -2.38577336322952e+00 , -3.14731306612742e-01 , 6.17325615932580e+00 ), ( -4.46685846755194e+00 , 1.00074373587177e+00 , 6.44268001437340e+00 ), ( -5.34874107970129e+00 , 6.03083005153393e-01 , 7.21231651517560e+00 ), ( -6.23394045531279e+00 , 3.58885199384197e+00 , 6.72131981410933e+00 ), ( -6.94750461378181e+00 , 4.29803921723237e+00 , 7.46191661025079e+00 ), ( -6.75132061314708e+00 , 3.19332815548683e+00 , 5.51501496038582e+00 ), ( -4.13044393384095e+00 , 2.25884438608562e+00 , 6.43280193532708e+00 ), ( -4.82027285112013e+00 , 3.19298004975302e+00 , 7.22815140325672e+00 ), ( -4.10447055911947e+00 , 4.58725873797147e+00 , 7.29113600902870e+00 ) } +colvars: Step 17, atoms_positions[size = 51] = { ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 ), ( 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 ), ( 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 ), ( 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 ), ( 7.05401205499525e+00 , -2.04466496196176e+00 , -9.47025224643584e-01 ), ( 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 ), ( 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 ), ( 7.08180008292897e+00 , -3.54527947160232e-01 , 4.29578748165592e+00 ), ( 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 ), ( 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 ), ( 5.85353964216460e+00 , 2.24805367878793e+00 , 2.99564529754523e+00 ), ( 5.23617716524237e+00 , 3.58403856898060e+00 , 2.91580391446837e+00 ), ( 6.32567014767930e+00 , 4.50739171941522e+00 , 2.39434985203635e+00 ), ( 3.89717224079018e+00 , 3.72364808759139e+00 , 2.04172037680312e+00 ), ( 2.80269239899311e+00 , 4.15138746672595e+00 , 2.50256701998378e+00 ), ( 3.92173322094697e+00 , 3.24227328210126e+00 , 7.34119595710529e-01 ), ( 2.65294502133193e+00 , 3.02150622781071e+00 , -1.07888117039870e-01 ), ( 3.03859524831226e+00 , 2.71766366155127e+00 , -1.52532419541117e+00 ), ( 1.58989830929609e+00 , 2.19525577378701e+00 , 4.73279518474310e-01 ), ( 3.97972879861437e-01 , 2.55317558768447e+00 , 5.19988069580460e-01 ), ( 2.02283025509722e+00 , 1.02899009908521e+00 , 1.07896597392129e+00 ), ( 1.17674558381348e+00 , 1.07877021809743e-01 , 1.69345406222270e+00 ), ( 2.03398696349812e+00 , -1.11664678353804e+00 , 2.00595125140644e+00 ), ( 5.57169446916974e-01 , 6.08511901276892e-01 , 2.93036595334865e+00 ), ( -6.20132087452973e-01 , 3.49514498441553e-01 , 3.16443432152830e+00 ), ( 1.32441366100069e+00 , 1.34552384914899e+00 , 3.80422012118166e+00 ), ( 8.51392719277319e-01 , 1.96864047989828e+00 , 5.02676461538075e+00 ), ( 2.05296717375719e+00 , 2.65903093218392e+00 , 5.66165528212752e+00 ), ( -3.39255843615151e-01 , 2.91609096609937e+00 , 4.96816447095012e+00 ), ( -1.14739149507487e+00 , 3.05855318833902e+00 , 5.89576004198849e+00 ), ( -4.95771802962824e-01 , 3.56540022601166e+00 , 3.84876866783091e+00 ), ( -1.51130776109123e+00 , 4.54595027404692e+00 , 3.47448716055517e+00 ), ( -7.05761485073891e-01 , 5.40875166463922e+00 , 2.45650875447642e+00 ), ( -2.77014896565513e+00 , 3.87590188849051e+00 , 2.90731888751016e+00 ), ( -3.82121150232841e+00 , 4.49191857250776e+00 , 2.81862093367446e+00 ), ( -2.61274613472344e+00 , 2.67035355842889e+00 , 2.42315521373217e+00 ), ( -3.75908420821069e+00 , 1.82091842133627e+00 , 2.00340852740520e+00 ), ( -3.40142771648094e+00 , 8.83372833544946e-01 , 8.93904987990678e-01 ), ( -4.32376956288346e+00 , 1.06720052773644e+00 , 3.22663102893285e+00 ), ( -5.50993104352038e+00 , 8.40310379958154e-01 , 3.32824213757474e+00 ), ( -3.38368770649199e+00 , 6.81568860254830e-01 , 4.18445906796119e+00 ), ( -3.72393675184907e+00 , 3.63303732430072e-02 , 5.43999666145482e+00 ), ( -2.38581451310621e+00 , -3.14749731928899e-01 , 6.17318424960760e+00 ), ( -4.46691229519516e+00 , 1.00071778705061e+00 , 6.44257521748917e+00 ), ( -5.34879366000581e+00 , 6.03054059269892e-01 , 7.21221079627413e+00 ), ( -6.23400738802797e+00 , 3.58882051711940e+00 , 6.72122229308845e+00 ), ( -6.94757329189829e+00 , 4.29800521007193e+00 , 7.46181835839354e+00 ), ( -6.75136403999623e+00 , 3.19330560929844e+00 , 5.51491429812448e+00 ), ( -4.13049910086630e+00 , 2.25881881766199e+00 , 6.43272068120323e+00 ), ( -4.82034787571045e+00 , 3.19294621544736e+00 , 7.22806234855601e+00 ), ( -4.10455323138208e+00 , 4.58722558592033e+00 , 7.29107578696250e+00 ) } colvars: Step 17, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 17, atom_groups_ids[size = 0] = @@ -5447,162 +8796,301 @@ colvars: Collective variables module, step no. 17 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.09319308134653e-01 , 2.30226602992589e-03 , 9.50955448581177e-01 ). +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.08571789563032e-01 , 2.39854344479993e-03 , 9.51198032838174e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 7.05401205499525e+00 , -2.04466496196176e+00 , -9.47025224643584e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 , 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 7.08180008292897e+00 , -3.54527947160232e-01 , 4.29578748165592e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 , 5.85353964216460e+00 , 2.24805367878793e+00 , 2.99564529754523e+00 , 5.23617716524237e+00 , 3.58403856898060e+00 , 2.91580391446837e+00 , 6.32567014767930e+00 , 4.50739171941522e+00 , 2.39434985203635e+00 , 3.89717224079018e+00 , 3.72364808759139e+00 , 2.04172037680312e+00 , 2.80269239899311e+00 , 4.15138746672595e+00 , 2.50256701998378e+00 , 3.92173322094697e+00 , 3.24227328210126e+00 , 7.34119595710529e-01 , 2.65294502133193e+00 , 3.02150622781071e+00 , -1.07888117039870e-01 , 3.03859524831226e+00 , 2.71766366155127e+00 , -1.52532419541117e+00 , 1.58989830929609e+00 , 2.19525577378701e+00 , 4.73279518474310e-01 , 3.97972879861437e-01 , 2.55317558768447e+00 , 5.19988069580460e-01 , 2.02283025509722e+00 , 1.02899009908521e+00 , 1.07896597392129e+00 , 1.17674558381348e+00 , 1.07877021809743e-01 , 1.69345406222270e+00 , 2.03398696349812e+00 , -1.11664678353804e+00 , 2.00595125140644e+00 , 5.57169446916974e-01 , 6.08511901276892e-01 , 2.93036595334865e+00 , -6.20132087452973e-01 , 3.49514498441553e-01 , 3.16443432152830e+00 , 1.32441366100069e+00 , 1.34552384914899e+00 , 3.80422012118166e+00 , 8.51392719277319e-01 , 1.96864047989828e+00 , 5.02676461538075e+00 , 2.05296717375719e+00 , 2.65903093218392e+00 , 5.66165528212752e+00 , -3.39255843615151e-01 , 2.91609096609937e+00 , 4.96816447095012e+00 , -1.14739149507487e+00 , 3.05855318833902e+00 , 5.89576004198849e+00 , -4.95771802962824e-01 , 3.56540022601166e+00 , 3.84876866783091e+00 , -1.51130776109123e+00 , 4.54595027404692e+00 , 3.47448716055517e+00 , -7.05761485073891e-01 , 5.40875166463922e+00 , 2.45650875447642e+00 , -2.77014896565513e+00 , 3.87590188849051e+00 , 2.90731888751016e+00 , -3.82121150232841e+00 , 4.49191857250776e+00 , 2.81862093367446e+00 , -2.61274613472344e+00 , 2.67035355842889e+00 , 2.42315521373217e+00 , -3.75908420821069e+00 , 1.82091842133627e+00 , 2.00340852740520e+00 , -3.40142771648094e+00 , 8.83372833544946e-01 , 8.93904987990678e-01 , -4.32376956288346e+00 , 1.06720052773644e+00 , 3.22663102893285e+00 , -5.50993104352038e+00 , 8.40310379958154e-01 , 3.32824213757474e+00 , -3.38368770649199e+00 , 6.81568860254830e-01 , 4.18445906796119e+00 , -3.72393675184907e+00 , 3.63303732430072e-02 , 5.43999666145482e+00 , -2.38581451310621e+00 , -3.14749731928899e-01 , 6.17318424960760e+00 , -4.46691229519516e+00 , 1.00071778705061e+00 , 6.44257521748917e+00 , -5.34879366000581e+00 , 6.03054059269892e-01 , 7.21221079627413e+00 , -6.23400738802797e+00 , 3.58882051711940e+00 , 6.72122229308845e+00 , -6.94757329189829e+00 , 4.29800521007193e+00 , 7.46181835839354e+00 , -6.75136403999623e+00 , 3.19330560929844e+00 , 5.51491429812448e+00 , -4.13049910086630e+00 , 2.25881881766199e+00 , 6.43272068120323e+00 , -4.82034787571045e+00 , 3.19294621544736e+00 , 7.22806234855601e+00 , -4.10455323138208e+00 , 4.58722558592033e+00 , 7.29107578696250e+00 ). colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.09319308134653e-01 , 2.30226602992589e-03 , 9.50955448581177e-01 ). +colvars: Colvar "one" has value ( -3.08571789563032e-01 , 2.39854344479993e-03 , 9.51198032838174e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 7.05401205499525e+00 , -2.04466496196176e+00 , -9.47025224643584e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 , 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 7.08180008292897e+00 , -3.54527947160232e-01 , 4.29578748165592e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 , 5.85353964216460e+00 , 2.24805367878793e+00 , 2.99564529754523e+00 , 5.23617716524237e+00 , 3.58403856898060e+00 , 2.91580391446837e+00 , 6.32567014767930e+00 , 4.50739171941522e+00 , 2.39434985203635e+00 , 3.89717224079018e+00 , 3.72364808759139e+00 , 2.04172037680312e+00 , 2.80269239899311e+00 , 4.15138746672595e+00 , 2.50256701998378e+00 , 3.92173322094697e+00 , 3.24227328210126e+00 , 7.34119595710529e-01 , 2.65294502133193e+00 , 3.02150622781071e+00 , -1.07888117039870e-01 , 3.03859524831226e+00 , 2.71766366155127e+00 , -1.52532419541117e+00 , 1.58989830929609e+00 , 2.19525577378701e+00 , 4.73279518474310e-01 , 3.97972879861437e-01 , 2.55317558768447e+00 , 5.19988069580460e-01 , 2.02283025509722e+00 , 1.02899009908521e+00 , 1.07896597392129e+00 , 1.17674558381348e+00 , 1.07877021809743e-01 , 1.69345406222270e+00 , 2.03398696349812e+00 , -1.11664678353804e+00 , 2.00595125140644e+00 , 5.57169446916974e-01 , 6.08511901276892e-01 , 2.93036595334865e+00 , -6.20132087452973e-01 , 3.49514498441553e-01 , 3.16443432152830e+00 , 1.32441366100069e+00 , 1.34552384914899e+00 , 3.80422012118166e+00 , 8.51392719277319e-01 , 1.96864047989828e+00 , 5.02676461538075e+00 , 2.05296717375719e+00 , 2.65903093218392e+00 , 5.66165528212752e+00 , -3.39255843615151e-01 , 2.91609096609937e+00 , 4.96816447095012e+00 , -1.14739149507487e+00 , 3.05855318833902e+00 , 5.89576004198849e+00 , -4.95771802962824e-01 , 3.56540022601166e+00 , 3.84876866783091e+00 , -1.51130776109123e+00 , 4.54595027404692e+00 , 3.47448716055517e+00 , -7.05761485073891e-01 , 5.40875166463922e+00 , 2.45650875447642e+00 , -2.77014896565513e+00 , 3.87590188849051e+00 , 2.90731888751016e+00 , -3.82121150232841e+00 , 4.49191857250776e+00 , 2.81862093367446e+00 , -2.61274613472344e+00 , 2.67035355842889e+00 , 2.42315521373217e+00 , -3.75908420821069e+00 , 1.82091842133627e+00 , 2.00340852740520e+00 , -3.40142771648094e+00 , 8.83372833544946e-01 , 8.93904987990678e-01 , -4.32376956288346e+00 , 1.06720052773644e+00 , 3.22663102893285e+00 , -5.50993104352038e+00 , 8.40310379958154e-01 , 3.32824213757474e+00 , -3.38368770649199e+00 , 6.81568860254830e-01 , 4.18445906796119e+00 , -3.72393675184907e+00 , 3.63303732430072e-02 , 5.43999666145482e+00 , -2.38581451310621e+00 , -3.14749731928899e-01 , 6.17318424960760e+00 , -4.46691229519516e+00 , 1.00071778705061e+00 , 6.44257521748917e+00 , -5.34879366000581e+00 , 6.03054059269892e-01 , 7.21221079627413e+00 , -6.23400738802797e+00 , 3.58882051711940e+00 , 6.72122229308845e+00 , -6.94757329189829e+00 , 4.29800521007193e+00 , 7.46181835839354e+00 , -6.75136403999623e+00 , 3.19330560929844e+00 , 5.51491429812448e+00 , -4.13049910086630e+00 , 2.25881881766199e+00 , 6.43272068120323e+00 , -4.82034787571045e+00 , 3.19294621544736e+00 , 7.22806234855601e+00 , -4.10455323138208e+00 , 4.58722558592033e+00 , 7.29107578696250e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.7044 , 1.90575 , -15.1155 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.2679 , 6.62679 , 13.2536 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.7044 , 1.90575 , -15.1155 ) to colvar "one". -colvars: Adding total bias energy: 44.6413 +colvars: Adding biasing force ( 66.2679 , 6.62679 , 13.2536 ) to colvar "one". +colvars: Adding total bias energy: 56.8721 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.7044 , 1.90575 , -15.1155 ) +colvars: Force to be applied: ( 66.2679 , 6.62679 , 13.2536 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.90552 , -0.538416 , -1.47279 ) -colvars: ( -4.20649 , -0.461692 , -1.26292 ) -colvars: ( -4.20649 , -0.461692 , -1.26292 ) -colvars: ( -5.60316 , -0.614987 , -1.68225 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17255 , -0.566649 , -1.54858 ) +colvars: ( -4.43546 , -0.485901 , -1.32791 ) +colvars: ( -4.43546 , -0.485901 , -1.32791 ) +colvars: ( -5.90816 , -0.647234 , -1.76881 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.894611 , 0.195151 , 0.624031 ) -colvars: ( 0.774592 , 0.266058 , 0.648644 ) -colvars: ( 0.758926 , 0.259102 , 0.630183 ) -colvars: ( 0.662161 , 0.267013 , 0.584175 ) -colvars: ( 0.650223 , 0.200501 , 0.488274 ) -colvars: ( 0.575175 , 0.344362 , 0.636717 ) -colvars: ( 0.46736 , 0.35854 , 0.592624 ) -colvars: ( 0.390272 , 0.455863 , 0.677658 ) -colvars: ( 0.385538 , 0.314132 , 0.485408 ) -colvars: ( 0.350497 , 0.272647 , 0.409457 ) -colvars: ( 0.356416 , 0.319415 , 0.475443 ) -colvars: ( 0.285127 , 0.276667 , 0.376604 ) -colvars: ( 0.258254 , 0.305657 , 0.399647 ) -colvars: ( 0.347901 , 0.178802 , 0.282476 ) -colvars: ( 0.28898 , 0.135594 , 0.190255 ) -colvars: ( 0.471217 , 0.141597 , 0.304847 ) -colvars: ( 0.544116 , 0.0501577 , 0.22523 ) -colvars: ( 0.674329 , 0.0289792 , 0.273061 ) -colvars: ( 0.552429 , 0.0183811 , 0.187609 ) -colvars: ( 0.53661 , -0.0466204 , 0.0914579 ) -colvars: ( 0.573146 , 0.0662933 , 0.263778 ) -colvars: ( 0.571309 , 0.0501891 , 0.241174 ) -colvars: ( 0.607759 , 0.11487 , 0.348961 ) -colvars: ( 0.446392 , 0.0548408 , 0.174345 ) -colvars: ( 0.43944 , -0.00103527 , 0.0955791 ) -colvars: ( 0.344082 , 0.120576 , 0.2024 ) -colvars: ( 0.219029 , 0.129327 , 0.140973 ) -colvars: ( 0.127248 , 0.215148 , 0.202037 ) -colvars: ( 0.190892 , 0.0556403 , 0.0260067 ) -colvars: ( 0.141328 , 0.0195668 , -0.0512037 ) -colvars: ( 0.224915 , 0.030005 , 0.0116299 ) -colvars: ( 0.211039 , -0.0424656 , -0.0933706 ) -colvars: ( 0.246797 , -0.0458984 , -0.0770501 ) -colvars: ( 0.286501 , -0.128455 , -0.164202 ) -colvars: ( 0.242356 , -0.181491 , -0.260921 ) -colvars: ( 0.402035 , -0.143593 , -0.11688 ) -colvars: ( 0.479684 , -0.219126 , -0.172455 ) -colvars: ( 0.611338 , -0.221869 , -0.0991352 ) -colvars: ( 0.43192 , -0.223515 , -0.206253 ) -colvars: ( 0.43743 , -0.291545 , -0.29398 ) -colvars: ( 0.382771 , -0.150157 , -0.136921 ) -colvars: ( 0.328043 , -0.143803 , -0.160429 ) -colvars: ( 0.311248 , -0.0571134 , -0.0543544 ) -colvars: ( 0.204306 , -0.152444 , -0.244339 ) -colvars: ( 0.17967 , -0.194382 , -0.314812 ) -colvars: ( 0.00271907 , -0.197987 , -0.423107 ) -colvars: ( -0.088548 , -0.215667 , -0.500114 ) -colvars: ( 0.103637 , -0.248025 , -0.43099 ) -colvars: ( 0.122369 , -0.11178 , -0.237889 ) -colvars: ( 0.00264585 , -0.116017 , -0.313564 ) -colvars: ( -0.0865806 , -0.0353011 , -0.257831 ) +colvars: ( 0.942806 , 0.205761 , 0.657029 ) +colvars: ( 0.816365 , 0.280444 , 0.682975 ) +colvars: ( 0.799832 , 0.273143 , 0.663561 ) +colvars: ( 0.697932 , 0.281403 , 0.615076 ) +colvars: ( 0.685352 , 0.211315 , 0.514064 ) +colvars: ( 0.606305 , 0.362869 , 0.670421 ) +colvars: ( 0.492736 , 0.377759 , 0.623981 ) +colvars: ( 0.411536 , 0.480277 , 0.713551 ) +colvars: ( 0.406522 , 0.330957 , 0.511075 ) +colvars: ( 0.369616 , 0.287221 , 0.43107 ) +colvars: ( 0.375819 , 0.336543 , 0.500605 ) +colvars: ( 0.300699 , 0.291494 , 0.396524 ) +colvars: ( 0.272364 , 0.322063 , 0.420823 ) +colvars: ( 0.366823 , 0.188398 , 0.297374 ) +colvars: ( 0.304748 , 0.14285 , 0.200245 ) +colvars: ( 0.49673 , 0.149236 , 0.320922 ) +colvars: ( 0.573522 , 0.0529108 , 0.237054 ) +colvars: ( 0.710691 , 0.0306454 , 0.287424 ) +colvars: ( 0.582302 , 0.0194021 , 0.197402 ) +colvars: ( 0.565635 , -0.0490957 , 0.0961282 ) +colvars: ( 0.604151 , 0.0698694 , 0.277608 ) +colvars: ( 0.60224 , 0.052871 , 0.253776 ) +colvars: ( 0.640662 , 0.121015 , 0.367284 ) +colvars: ( 0.470647 , 0.0577265 , 0.183396 ) +colvars: ( 0.46333 , -0.00116355 , 0.100423 ) +colvars: ( 0.362862 , 0.126967 , 0.212967 ) +colvars: ( 0.231122 , 0.136147 , 0.14828 ) +colvars: ( 0.134429 , 0.226557 , 0.212619 ) +colvars: ( 0.201462 , 0.0585118 , 0.0272056 ) +colvars: ( 0.149254 , 0.0204749 , -0.0541222 ) +colvars: ( 0.237279 , 0.0315381 , 0.0120808 ) +colvars: ( 0.222642 , -0.0448099 , -0.0984984 ) +colvars: ( 0.260286 , -0.0483854 , -0.0812874 ) +colvars: ( 0.302144 , -0.135403 , -0.173125 ) +colvars: ( 0.255635 , -0.1913 , -0.274991 ) +colvars: ( 0.423867 , -0.151329 , -0.123305 ) +colvars: ( 0.505677 , -0.230907 , -0.181863 ) +colvars: ( 0.644377 , -0.233762 , -0.104658 ) +colvars: ( 0.455381 , -0.235574 , -0.217479 ) +colvars: ( 0.461187 , -0.307261 , -0.309887 ) +colvars: ( 0.403622 , -0.158311 , -0.144461 ) +colvars: ( 0.345991 , -0.15166 , -0.169237 ) +colvars: ( 0.328318 , -0.0603387 , -0.0575217 ) +colvars: ( 0.215631 , -0.160799 , -0.257598 ) +colvars: ( 0.189687 , -0.205011 , -0.331836 ) +colvars: ( 0.00321864 , -0.208804 , -0.445827 ) +colvars: ( -0.0929334 , -0.227459 , -0.526923 ) +colvars: ( 0.109519 , -0.261482 , -0.454131 ) +colvars: ( 0.129296 , -0.117957 , -0.250777 ) +colvars: ( 0.00316332 , -0.122453 , -0.330463 ) +colvars: ( -0.0908424 , -0.0374179 , -0.271737 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.90552 , 0.538416 , 1.47279 ) -colvars: ( 4.20649 , 0.461692 , 1.26292 ) -colvars: ( 4.20649 , 0.461692 , 1.26292 ) -colvars: ( 5.60316 , 0.614987 , 1.68225 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17255 , 0.566649 , 1.54858 ) +colvars: ( 4.43546 , 0.485901 , 1.32791 ) +colvars: ( 4.43546 , 0.485901 , 1.32791 ) +colvars: ( 5.90816 , 0.647234 , 1.76881 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.617237 , -0.0807303 , -0.374353 ) -colvars: ( -0.554897 , -0.162858 , -0.344449 ) -colvars: ( -0.506049 , -0.141113 , -0.286791 ) -colvars: ( -0.515016 , -0.1902 , -0.315303 ) -colvars: ( -0.505431 , -0.131861 , -0.282494 ) -colvars: ( -0.489635 , -0.281484 , -0.326122 ) -colvars: ( -0.456159 , -0.321546 , -0.30846 ) -colvars: ( -0.433907 , -0.427976 , -0.32844 ) -colvars: ( -0.393509 , -0.286606 , -0.231707 ) -colvars: ( -0.388571 , -0.261549 , -0.216792 ) -colvars: ( -0.34494 , -0.281098 , -0.180784 ) -colvars: ( -0.2849 , -0.24464 , -0.106048 ) -colvars: ( -0.237041 , -0.259509 , -0.0639373 ) -colvars: ( -0.304795 , -0.142318 , -0.0853353 ) -colvars: ( -0.273433 , -0.113364 , -0.0423571 ) -colvars: ( -0.359643 , -0.0853307 , -0.117715 ) -colvars: ( -0.386699 , 0.0121101 , -0.106128 ) -colvars: ( -0.437592 , 0.059415 , -0.138388 ) -colvars: ( -0.423504 , 0.0270588 , -0.137115 ) -colvars: ( -0.412158 , 0.0833205 , -0.103365 ) -colvars: ( -0.466844 , -0.0264316 , -0.201865 ) -colvars: ( -0.500287 , -0.0278286 , -0.235977 ) -colvars: ( -0.549552 , -0.092581 , -0.31115 ) -colvars: ( -0.447689 , -0.0576861 , -0.19507 ) -colvars: ( -0.454253 , -0.0139774 , -0.184281 ) -colvars: ( -0.392492 , -0.131455 , -0.16901 ) -colvars: ( -0.334533 , -0.162599 , -0.123235 ) -colvars: ( -0.284091 , -0.252089 , -0.108198 ) -colvars: ( -0.293915 , -0.0904689 , -0.0538069 ) -colvars: ( -0.28031 , -0.0720481 , -0.0328328 ) -colvars: ( -0.275032 , -0.0460069 , -0.0171853 ) -colvars: ( -0.240311 , 0.0280361 , 0.0470878 ) -colvars: ( -0.220064 , 0.0541718 , 0.0777931 ) -colvars: ( -0.284299 , 0.114125 , 0.0371728 ) -colvars: ( -0.257664 , 0.155473 , 0.0803347 ) -colvars: ( -0.353538 , 0.142137 , -0.0211656 ) -colvars: ( -0.402203 , 0.217765 , -0.0399309 ) -colvars: ( -0.473447 , 0.240278 , -0.102466 ) -colvars: ( -0.412788 , 0.198118 , -0.0583619 ) -colvars: ( -0.417232 , 0.258417 , -0.0388506 ) -colvars: ( -0.416489 , 0.112299 , -0.0961911 ) -colvars: ( -0.422621 , 0.0824026 , -0.114228 ) -colvars: ( -0.443394 , -0.0100647 , -0.17183 ) -colvars: ( -0.355796 , 0.0710954 , -0.0516714 ) -colvars: ( -0.358649 , 0.0971788 , -0.044165 ) -colvars: ( -0.195873 , 0.103228 , 0.121567 ) -colvars: ( -0.146359 , 0.104978 , 0.171945 ) -colvars: ( -0.223235 , 0.174984 , 0.122637 ) -colvars: ( -0.293662 , 0.0305917 , -0.00542789 ) -colvars: ( -0.226867 , 0.0169606 , 0.0561745 ) -colvars: ( -0.173052 , -0.0655097 , 0.0773882 ) +colvars: ( -0.650412 , -0.0851487 , -0.393828 ) +colvars: ( -0.584774 , -0.171656 , -0.362311 ) +colvars: ( -0.533266 , -0.148767 , -0.30158 ) +colvars: ( -0.542818 , -0.200428 , -0.331645 ) +colvars: ( -0.532719 , -0.138957 , -0.297141 ) +colvars: ( -0.51613 , -0.296577 , -0.343011 ) +colvars: ( -0.480925 , -0.338751 , -0.324432 ) +colvars: ( -0.457529 , -0.450862 , -0.345428 ) +colvars: ( -0.414923 , -0.30193 , -0.243641 ) +colvars: ( -0.409748 , -0.275511 , -0.227976 ) +colvars: ( -0.363723 , -0.296141 , -0.190001 ) +colvars: ( -0.300464 , -0.257726 , -0.111329 ) +colvars: ( -0.25001 , -0.273408 , -0.0669523 ) +colvars: ( -0.321388 , -0.149935 , -0.0895674 ) +colvars: ( -0.288366 , -0.119414 , -0.0443482 ) +colvars: ( -0.379121 , -0.0899235 , -0.123665 ) +colvars: ( -0.407588 , 0.0127227 , -0.111507 ) +colvars: ( -0.461142 , 0.0625256 , -0.145463 ) +colvars: ( -0.4464 , 0.0284925 , -0.144175 ) +colvars: ( -0.434447 , 0.0877751 , -0.108679 ) +colvars: ( -0.492093 , -0.0278521 , -0.212341 ) +colvars: ( -0.527368 , -0.0293015 , -0.248291 ) +colvars: ( -0.579296 , -0.0975175 , -0.327417 ) +colvars: ( -0.472011 , -0.0607248 , -0.205238 ) +colvars: ( -0.47894 , -0.0146624 , -0.193921 ) +colvars: ( -0.413889 , -0.13843 , -0.177767 ) +colvars: ( -0.352877 , -0.171212 , -0.129583 ) +colvars: ( -0.299762 , -0.265486 , -0.113703 ) +colvars: ( -0.310063 , -0.0952221 , -0.0565129 ) +colvars: ( -0.29576 , -0.0757936 , -0.0344652 ) +colvars: ( -0.290113 , -0.0484053 , -0.0179415 ) +colvars: ( -0.253504 , 0.0295965 , 0.0497036 ) +colvars: ( -0.232114 , 0.0571015 , 0.0820614 ) +colvars: ( -0.299828 , 0.120291 , 0.0392144 ) +colvars: ( -0.271777 , 0.163866 , 0.0846245 ) +colvars: ( -0.372747 , 0.149785 , -0.0222142 ) +colvars: ( -0.424001 , 0.229459 , -0.0420176 ) +colvars: ( -0.499019 , 0.253153 , -0.107852 ) +colvars: ( -0.435211 , 0.208792 , -0.0614555 ) +colvars: ( -0.439893 , 0.272327 , -0.0409552 ) +colvars: ( -0.439163 , 0.118397 , -0.101265 ) +colvars: ( -0.445683 , 0.0869319 , -0.120281 ) +colvars: ( -0.46761 , -0.0104746 , -0.180897 ) +colvars: ( -0.375318 , 0.0750445 , -0.0544314 ) +colvars: ( -0.37835 , 0.102543 , -0.0465675 ) +colvars: ( -0.206832 , 0.108912 , 0.12796 ) +colvars: ( -0.154695 , 0.110775 , 0.180984 ) +colvars: ( -0.235595 , 0.184479 , 0.129083 ) +colvars: ( -0.30986 , 0.0323734 , -0.00571091 ) +colvars: ( -0.239523 , 0.0180352 , 0.0591387 ) +colvars: ( -0.182847 , -0.0688451 , 0.0815215 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 17. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 17. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 17, atoms_new_colvar_forces = { ( -4.62815055561045e+00 , -4.23995474056573e-01 , -1.22311616501379e+00 ), ( -3.98679069559760e+00 , -3.58492590906031e-01 , -9.58726707117377e-01 ), ( -4.05934086166424e+00 , -3.84879073764890e-01 , -9.94048635242549e-01 ), ( -5.45836875016544e+00 , -5.46346704818888e-01 , -1.47646699315704e+00 ), ( 2.52877053876661e-01 , 1.17989351327774e-01 , 3.43392302604611e-01 ), ( 4.99106492956269e+00 , 6.01294492452920e-01 , 1.78338870866727e+00 ), ( 4.21768619258938e+00 , 4.98685681530818e-01 , 1.54708569213552e+00 ), ( -4.36349218542222e-02 , 2.78872965849131e-02 , 3.49217919851065e-01 ), ( 4.19851532526447e+00 , 4.89217470186831e-01 , 1.51662220660519e+00 ), ( 5.56508736105459e+00 , 6.26085860745317e-01 , 1.87491240442127e+00 ), ( 1.14761685523073e-02 , 3.83176410846751e-02 , 2.94658316670772e-01 ), ( 2.27311673549169e-04 , 3.20265038522220e-02 , 2.70556427835990e-01 ), ( 2.12130772158747e-02 , 4.61477749858128e-02 , 3.35709262009671e-01 ), ( 4.31054331259390e-02 , 3.64840174182485e-02 , 1.97140949175543e-01 ), ( 1.55466729079566e-02 , 2.22293637359794e-02 , 1.47898206938958e-01 ), ( 1.11573320369336e-01 , 5.62662571760795e-02 , 1.87132033920166e-01 ), ( 1.57416364867810e-01 , 6.22677753523262e-02 , 1.19102499061421e-01 ), ( 2.36736555308689e-01 , 8.83942194578691e-02 , 1.34672750830872e-01 ), ( 1.28924120467800e-01 , 4.54398987681336e-02 , 5.04939991814637e-02 ), ( 1.24452217835664e-01 , 3.67001262824173e-02 , -1.19068248412217e-02 ), ( 1.06301448613530e-01 , 3.98616790001095e-02 , 6.19125172956823e-02 ), ( 7.10223742608336e-02 , 2.23605128215839e-02 , 5.19743014273452e-03 ), ( 5.82071950869493e-02 , 2.22888161008216e-02 , 3.78115516688273e-02 ), ( -1.29770098089821e-03 , -2.84524603756130e-03 , -2.07246157958354e-02 ), ( -1.48129777873950e-02 , -1.50126748989254e-02 , -8.87015980687740e-02 ), ( -4.84097029276451e-02 , -1.08789016345353e-02 , 3.33898046253918e-02 ), ( -1.15503942874981e-01 , -3.32715684439314e-02 , 1.77371433366362e-02 ), ( -1.56843277971266e-01 , -3.69405728415567e-02 , 9.38393334526097e-02 ), ( -1.03022840015482e-01 , -3.48285999653236e-02 , -2.78002302319697e-02 ), ( -1.38981558459396e-01 , -5.24813106230892e-02 , -8.40364777156737e-02 ), ( -5.01174570159802e-02 , -1.60018360314190e-02 , -5.55539161786267e-03 ), ( -2.92713756063540e-02 , -1.44294281775459e-02 , -4.62827759124423e-02 ), ( 2.67333624896054e-02 , 8.27334936254839e-03 , 7.42980987567671e-04 ), ( 2.20187413035811e-03 , -1.43299766622657e-02 , -1.27029725469207e-01 ), ( -1.53083045192691e-02 , -2.60173723692135e-02 , -1.80586518115724e-01 ), ( 4.84966864707551e-02 , -1.45595191817147e-03 , -1.38045751109204e-01 ), ( 7.74816097863003e-02 , -1.36166205491367e-03 , -2.12385846533022e-01 ), ( 1.37891378301253e-01 , 1.84092284257072e-02 , -2.01601574458287e-01 ), ( 1.91319457446069e-02 , -2.53970370368797e-02 , -2.64614947504997e-01 ), ( 2.01987378424113e-02 , -3.31277439678343e-02 , -3.32830833499215e-01 ), ( -3.37184298029777e-02 , -3.78585727143166e-02 , -2.33112510165987e-01 ), ( -9.45777953167765e-02 , -6.14004526724902e-02 , -2.74657573486360e-01 ), ( -1.32145748965112e-01 , -6.71780544534610e-02 , -2.26184033479536e-01 ), ( -1.51489395053466e-01 , -8.13484963423917e-02 , -2.96010071115899e-01 ), ( -1.78978606748064e-01 , -9.72029263997774e-02 , -3.58977277777855e-01 ), ( -1.93153776379780e-01 , -9.47590584128483e-02 , -3.01540114875522e-01 ), ( -2.34906524564462e-01 , -1.10688762799213e-01 , -3.28168874229867e-01 ), ( -1.19597666023818e-01 , -7.30413168729495e-02 , -3.08352844175269e-01 ), ( -1.71292715350085e-01 , -8.11882935299329e-02 , -2.43317078256175e-01 ), ( -2.24221046364581e-01 , -9.90568445452535e-02 , -2.57389918940128e-01 ), ( -2.59632089779584e-01 , -1.00810811700924e-01 , -1.80442533512445e-01 ) } +colvars: Step 17, atoms_new_colvar_forces = { ( -4.88015736595259e+00 , -4.46036198466336e-01 , -1.28538242749713e+00 ), ( -4.20387001123164e+00 , -3.77113297704594e-01 , -1.00724497223348e+00 ), ( -4.28034760920542e+00 , -4.04925824031137e-01 , -1.04447955016954e+00 ), ( -5.75552983118959e+00 , -5.74876520659967e-01 , -1.55189131627040e+00 ), ( 2.66566163465579e-01 , 1.24376770580220e-01 , 3.61980821479692e-01 ), ( 5.26272633610233e+00 , 6.32939844268853e-01 , 1.87599298139621e+00 ), ( 4.44727222712034e+00 , 5.24909665742374e-01 , 1.62745911753024e+00 ), ( -4.59924977081408e-02 , 2.94146333875059e-02 , 3.68123311003704e-01 ), ( 4.42706088684963e+00 , 5.14927536420531e-01 , 1.59534358645283e+00 ), ( 5.86803042983167e+00 , 6.58944285120950e-01 , 1.97190872671386e+00 ), ( 1.20958419018421e-02 , 4.04019894378879e-02 , 3.10604533441209e-01 ), ( 2.35273637626099e-04 , 3.37687214393134e-02 , 2.85194908722332e-01 ), ( 2.23540544025670e-02 , 4.86545337689300e-02 , 3.53870868081869e-01 ), ( 4.54343450249216e-02 , 3.84624174007937e-02 , 2.07806245999574e-01 ), ( 1.63828773126952e-02 , 2.34352507899631e-02 , 1.55897031745500e-01 ), ( 1.17609543873743e-01 , 5.93120332139072e-02 , 1.97257460581520e-01 ), ( 1.65934326070678e-01 , 6.56334972416600e-02 , 1.25546604874536e-01 ), ( 2.49548804174806e-01 , 9.31709615394787e-02 , 1.41960982152818e-01 ), ( 1.35902355594962e-01 , 4.78946561276440e-02 , 5.32274527181748e-02 ), ( 1.31187898310386e-01 , 3.86793842526439e-02 , -1.25512940907047e-02 ), ( 1.12057892619085e-01 , 4.20173245501222e-02 , 6.52669276381761e-02 ), ( 7.48717170204336e-02 , 2.35695622374883e-02 , 5.48483858983992e-03 ), ( 6.13656977317324e-02 , 2.34971707001845e-02 , 3.98672506841835e-02 ), ( -1.36399002557974e-03 , -2.99826090073294e-03 , -2.18418427601044e-02 ), ( -1.56102032596058e-02 , -1.58259772689461e-02 , -9.34973375290691e-02 ), ( -5.10278337643778e-02 , -1.14629605756471e-02 , 3.51991594606000e-02 ), ( -1.21755229879134e-01 , -3.50654650420195e-02 , 1.86972666066966e-02 ), ( -1.65333822554622e-01 , -3.89286491415851e-02 , 9.89162576270934e-02 ), ( -1.08600922782521e-01 , -3.67102543226608e-02 , -2.93073426226554e-02 ), ( -1.46505926294895e-01 , -5.53187629098834e-02 , -8.85873850071875e-02 ), ( -5.28340182021141e-02 , -1.68672612934411e-02 , -5.86065249106413e-03 ), ( -3.08618359440838e-02 , -1.52134167946242e-02 , -4.87947597045069e-02 ), ( 2.81720536253082e-02 , 8.71614272212562e-03 , 7.73940470895157e-04 ), ( 2.31652781295405e-03 , -1.51127155601899e-02 , -1.33910083243585e-01 ), ( -1.61424316645498e-02 , -2.74343489564569e-02 , -1.90366760629126e-01 ), ( 5.11196992026257e-02 , -1.54358524293582e-03 , -1.45519225047703e-01 ), ( 8.16753453628619e-02 , -1.44781366450614e-03 , -2.23880614084183e-01 ), ( 1.45357281505606e-01 , 1.93915246217626e-02 , -2.12509706563197e-01 ), ( 2.01691592912764e-02 , -2.67823785971957e-02 , -2.78934795395103e-01 ), ( 2.12938793740244e-02 , -3.49341821079345e-02 , -3.50842529360566e-01 ), ( -3.55405244895096e-02 , -3.99138378223871e-02 , -2.45726096946784e-01 ), ( -9.96924264046057e-02 , -6.47277205650604e-02 , -2.89518191861758e-01 ), ( -1.39291942293498e-01 , -7.08133520162364e-02 , -2.38419162901851e-01 ), ( -1.59686699407018e-01 , -8.57543336741377e-02 , -3.12029126662255e-01 ), ( -1.88663105921427e-01 , -1.02467642653652e-01 , -3.78403643139270e-01 ), ( -2.03613559494271e-01 , -9.98920233820327e-02 , -3.17866923464479e-01 ), ( -2.47627914849571e-01 , -1.16683548586711e-01 , -3.45938981774479e-01 ), ( -1.26076243452396e-01 , -7.70029494703876e-02 , -3.25048223242792e-01 ), ( -1.80564661927748e-01 , -8.55835606815858e-02 , -2.56487415131268e-01 ), ( -2.36360145018347e-01 , -1.04418081972694e-01 , -2.71324767663208e-01 ), ( -2.73689864302419e-01 , -1.06262981498663e-01 , -1.90215146484118e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 17, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5640,10 +9128,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 18, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 18, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 18, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 18, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 18, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 18, atoms_positions[size = 51] = { ( 8.29492152155911e+00 , 4.10024056305554e-02 , -7.59019667114383e-01 ), ( 6.95618155035659e+00 , -5.49833619361815e-01 , -5.91623253556879e-01 ), ( 6.15659892821855e+00 , -3.60531379712544e-01 , 7.16586949149385e-01 ), ( 4.96307247456961e+00 , -1.70696146174729e-01 , 7.17351902015087e-01 ), ( 7.05280967742796e+00 , -2.04696348665916e+00 , -9.42573254324749e-01 ), ( 6.87542220778904e+00 , -2.62710186718871e-01 , 1.89300813102855e+00 ), ( 6.18260834605906e+00 , -1.48157496608870e-01 , 3.19940156458429e+00 ), ( 7.07963398728163e+00 , -3.55228365303318e-01 , 4.30095170934118e+00 ), ( 5.30685666094591e+00 , 1.10160129721062e+00 , 3.34453180267969e+00 ), ( 4.15455369109859e+00 , 1.02991906392327e+00 , 3.67895321427891e+00 ), ( 5.84944342689905e+00 , 2.24949092199651e+00 , 2.99399791380715e+00 ), ( 5.23835844225534e+00 , 3.58204670292676e+00 , 2.91840033581230e+00 ), ( 6.32437832438070e+00 , 4.50466681167845e+00 , 2.38491279094262e+00 ), ( 3.89221877193473e+00 , 3.71835966899616e+00 , 2.04295099665439e+00 ), ( 2.79801904872082e+00 , 4.15482742037216e+00 , 2.49773994541295e+00 ), ( 3.92880130252089e+00 , 3.24189250822501e+00 , 7.32819184438415e-01 ), ( 2.65405535884173e+00 , 3.01431699509412e+00 , -1.06941989163933e-01 ), ( 3.04243371748930e+00 , 2.71422805612423e+00 , -1.52032791683391e+00 ), ( 1.59411926756975e+00 , 2.19214687403451e+00 , 4.62787625886367e-01 ), ( 3.90604897647063e-01 , 2.56299942017237e+00 , 5.16970677862218e-01 ), ( 2.03119076698977e+00 , 1.04139606573325e+00 , 1.07692525488152e+00 ), ( 1.17400121263943e+00 , 1.12193966005497e-01 , 1.69452603466745e+00 ), ( 2.03679213424400e+00 , -1.11178217044486e+00 , 2.00689466057382e+00 ), ( 5.58724204903462e-01 , 6.09266033385929e-01 , 2.93359437401471e+00 ), ( -6.13747703330975e-01 , 3.49405809176778e-01 , 3.16324925195188e+00 ), ( 1.32232324727817e+00 , 1.34555114489065e+00 , 3.79478096702290e+00 ), ( 8.48308168825283e-01 , 1.97259021903522e+00 , 5.02593907633248e+00 ), ( 2.06158253431628e+00 , 2.66855924761502e+00 , 5.66831477006168e+00 ), ( -3.37929735335485e-01 , 2.91578888090203e+00 , 4.96768359448415e+00 ), ( -1.14405270425054e+00 , 3.06004939013347e+00 , 5.89322661576763e+00 ), ( -5.01234152634331e-01 , 3.55410676952643e+00 , 3.84872885656980e+00 ), ( -1.51441323034894e+00 , 4.54437249663840e+00 , 3.46392939262252e+00 ), ( -7.02913269087333e-01 , 5.41070128543474e+00 , 2.45932269473302e+00 ), ( -2.76742081648498e+00 , 3.87903079094641e+00 , 2.90396643486297e+00 ), ( -3.81978812863135e+00 , 4.49805218747342e+00 , 2.81711356351771e+00 ), ( -2.61619616729560e+00 , 2.67319283641547e+00 , 2.41603045036765e+00 ), ( -3.76421874631865e+00 , 1.81305869882987e+00 , 2.00085114262667e+00 ), ( -3.39733086851704e+00 , 8.85493386658980e-01 , 8.87088549541825e-01 ), ( -4.32548524241508e+00 , 1.06838804267476e+00 , 3.22110038486433e+00 ), ( -5.50601091655025e+00 , 8.33186724849965e-01 , 3.32846497103526e+00 ), ( -3.37774616414948e+00 , 6.84675166407712e-01 , 4.19260529643886e+00 ), ( -3.71576174878836e+00 , 3.83323758973222e-02 , 5.43648659170493e+00 ), ( -2.38733434575455e+00 , -3.14579981967497e-01 , 6.17288950008614e+00 ), ( -4.46487998291990e+00 , 9.97762808571827e-01 , 6.44233038019791e+00 ), ( -5.35244342243093e+00 , 6.01457615387527e-01 , 7.21465836873856e+00 ), ( -6.23311164917986e+00 , 3.59417372126332e+00 , 6.72526640259087e+00 ), ( -6.95204434573434e+00 , 4.29820420496905e+00 , 7.46681012789176e+00 ), ( -6.74956380232919e+00 , 3.18981640634602e+00 , 5.51239575556105e+00 ), ( -4.13057047178864e+00 , 2.25360069240219e+00 , 6.42460267132524e+00 ), ( -4.81532476982100e+00 , 3.19612160868296e+00 , 7.23253448093177e+00 ), ( -4.10260344332175e+00 , 4.58477295425590e+00 , 7.28859187637104e+00 ) } +colvars: Step 18, atoms_positions[size = 51] = { ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 ), ( 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 ), ( 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 ), ( 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 ), ( 7.05271607976549e+00 , -2.04701294245329e+00 , -9.42509469880201e-01 ), ( 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 ), ( 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 ), ( 7.08000330134620e+00 , -3.55284910533089e-01 , 4.30137053149054e+00 ), ( 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 ), ( 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 ), ( 5.84980798357323e+00 , 2.24966439635277e+00 , 2.99404129701435e+00 ), ( 5.23835337285908e+00 , 3.58205403294845e+00 , 2.91851704152070e+00 ), ( 6.32437505535570e+00 , 4.50468705973972e+00 , 2.38502757286954e+00 ), ( 3.89223690233319e+00 , 3.71835333345391e+00 , 2.04303158103372e+00 ), ( 2.79802365953788e+00 , 4.15483351289799e+00 , 2.49778941064640e+00 ), ( 3.92884294881576e+00 , 3.24191316831157e+00 , 7.32888194378791e-01 ), ( 2.65411407264995e+00 , 3.01434081602324e+00 , -1.06896703721620e-01 ), ( 3.04251330256935e+00 , 2.71425750935877e+00 , -1.52028070078280e+00 ), ( 1.59416792303023e+00 , 2.19216481262863e+00 , 4.62809499393612e-01 ), ( 3.90650117951124e-01 , 2.56301077867888e+00 , 5.16967514650667e-01 ), ( 2.03122863395248e+00 , 1.04141285375615e+00 , 1.07695231315893e+00 ), ( 1.17402749138365e+00 , 1.12203382713304e-01 , 1.69452997945191e+00 ), ( 2.03682040442338e+00 , -1.11176603037732e+00 , 2.00691923601827e+00 ), ( 5.58729567815095e-01 , 6.09265222101686e-01 , 2.93358745222653e+00 ), ( -6.13749682045257e-01 , 3.49401893418533e-01 , 3.16322193706003e+00 ), ( 1.32234499813337e+00 , 1.34554049175721e+00 , 3.79479022984922e+00 ), ( 8.48270476285389e-01 , 1.97257500422287e+00 , 5.02594407760662e+00 ), ( 2.06153029458319e+00 , 2.66854561045493e+00 , 5.66834200488296e+00 ), ( -3.37968453786755e-01 , 2.91577381023611e+00 , 4.96767152152444e+00 ), ( -1.14410211403567e+00 , 3.06003295903836e+00 , 5.89320327706122e+00 ), ( -5.01252397644797e-01 , 3.55410076723207e+00 , 3.84872265133012e+00 ), ( -1.51442408648012e+00 , 4.54436794679331e+00 , 3.46391022195393e+00 ), ( -7.02905739367337e-01 , 5.41070286617546e+00 , 2.45932126291340e+00 ), ( -2.76742104498482e+00 , 3.87902722252102e+00 , 2.90391761406626e+00 ), ( -3.81979153228129e+00 , 4.49804278244187e+00 , 2.81705435893745e+00 ), ( -2.61618004736925e+00 , 2.67319162189029e+00 , 2.41597950443951e+00 ), ( -3.76419154983186e+00 , 1.81305967817032e+00 , 2.00076893150958e+00 ), ( -3.39728475255780e+00 , 8.85496773526211e-01 , 8.87014667580360e-01 ), ( -4.32547677394703e+00 , 1.06837556076424e+00 , 3.22099878492571e+00 ), ( -5.50600355198686e+00 , 8.33175855060729e-01 , 3.32835499000222e+00 ), ( -3.37775813338197e+00 , 6.84659597766296e-01 , 4.19251734685362e+00 ), ( -3.71579947164811e+00 , 3.83055166333904e-02 , 5.43638450809476e+00 ), ( -2.38737980508660e+00 , -3.14600305794011e-01 , 6.17281002928248e+00 ), ( -4.46493940928512e+00 , 9.97734180499877e-01 , 6.44221479322284e+00 ), ( -5.35250204695175e+00 , 6.01425334398934e-01 , 7.21454062498389e+00 ), ( -6.23318516478668e+00 , 3.59413898038086e+00 , 6.72515897775978e+00 ), ( -6.95212090530336e+00 , 4.29816642791007e+00 , 7.46670089388892e+00 ), ( -6.74961276587329e+00 , 3.18979119729720e+00 , 5.51228345741242e+00 ), ( -4.13063161466044e+00 , 2.25357244122872e+00 , 6.42451233409495e+00 ), ( -4.81540752225174e+00 , 3.19608420035191e+00 , 7.23243596757610e+00 ), ( -4.10269470555908e+00 , 4.58473628518885e+00 , 7.28852513722620e+00 ) } colvars: Step 18, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 18, atom_groups_ids[size = 0] = @@ -5661,162 +9149,301 @@ colvars: Collective variables module, step no. 18 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.07543552262695e-01 , 1.57772719634005e-03 , 9.51532697409047e-01 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.06732608270377e-01 , 1.68371747048719e-03 , 9.51794238330497e-01 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 7.05271607976549e+00 , -2.04701294245329e+00 , -9.42509469880201e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 , 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 7.08000330134620e+00 , -3.55284910533089e-01 , 4.30137053149054e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 , 5.84980798357323e+00 , 2.24966439635277e+00 , 2.99404129701435e+00 , 5.23835337285908e+00 , 3.58205403294845e+00 , 2.91851704152070e+00 , 6.32437505535570e+00 , 4.50468705973972e+00 , 2.38502757286954e+00 , 3.89223690233319e+00 , 3.71835333345391e+00 , 2.04303158103372e+00 , 2.79802365953788e+00 , 4.15483351289799e+00 , 2.49778941064640e+00 , 3.92884294881576e+00 , 3.24191316831157e+00 , 7.32888194378791e-01 , 2.65411407264995e+00 , 3.01434081602324e+00 , -1.06896703721620e-01 , 3.04251330256935e+00 , 2.71425750935877e+00 , -1.52028070078280e+00 , 1.59416792303023e+00 , 2.19216481262863e+00 , 4.62809499393612e-01 , 3.90650117951124e-01 , 2.56301077867888e+00 , 5.16967514650667e-01 , 2.03122863395248e+00 , 1.04141285375615e+00 , 1.07695231315893e+00 , 1.17402749138365e+00 , 1.12203382713304e-01 , 1.69452997945191e+00 , 2.03682040442338e+00 , -1.11176603037732e+00 , 2.00691923601827e+00 , 5.58729567815095e-01 , 6.09265222101686e-01 , 2.93358745222653e+00 , -6.13749682045257e-01 , 3.49401893418533e-01 , 3.16322193706003e+00 , 1.32234499813337e+00 , 1.34554049175721e+00 , 3.79479022984922e+00 , 8.48270476285389e-01 , 1.97257500422287e+00 , 5.02594407760662e+00 , 2.06153029458319e+00 , 2.66854561045493e+00 , 5.66834200488296e+00 , -3.37968453786755e-01 , 2.91577381023611e+00 , 4.96767152152444e+00 , -1.14410211403567e+00 , 3.06003295903836e+00 , 5.89320327706122e+00 , -5.01252397644797e-01 , 3.55410076723207e+00 , 3.84872265133012e+00 , -1.51442408648012e+00 , 4.54436794679331e+00 , 3.46391022195393e+00 , -7.02905739367337e-01 , 5.41070286617546e+00 , 2.45932126291340e+00 , -2.76742104498482e+00 , 3.87902722252102e+00 , 2.90391761406626e+00 , -3.81979153228129e+00 , 4.49804278244187e+00 , 2.81705435893745e+00 , -2.61618004736925e+00 , 2.67319162189029e+00 , 2.41597950443951e+00 , -3.76419154983186e+00 , 1.81305967817032e+00 , 2.00076893150958e+00 , -3.39728475255780e+00 , 8.85496773526211e-01 , 8.87014667580360e-01 , -4.32547677394703e+00 , 1.06837556076424e+00 , 3.22099878492571e+00 , -5.50600355198686e+00 , 8.33175855060729e-01 , 3.32835499000222e+00 , -3.37775813338197e+00 , 6.84659597766296e-01 , 4.19251734685362e+00 , -3.71579947164811e+00 , 3.83055166333904e-02 , 5.43638450809476e+00 , -2.38737980508660e+00 , -3.14600305794011e-01 , 6.17281002928248e+00 , -4.46493940928512e+00 , 9.97734180499877e-01 , 6.44221479322284e+00 , -5.35250204695175e+00 , 6.01425334398934e-01 , 7.21454062498389e+00 , -6.23318516478668e+00 , 3.59413898038086e+00 , 6.72515897775978e+00 , -6.95212090530336e+00 , 4.29816642791007e+00 , 7.46670089388892e+00 , -6.74961276587329e+00 , 3.18979119729720e+00 , 5.51228345741242e+00 , -4.13063161466044e+00 , 2.25357244122872e+00 , 6.42451233409495e+00 , -4.81540752225174e+00 , 3.19608420035191e+00 , 7.23243596757610e+00 , -4.10269470555908e+00 , 4.58473628518885e+00 , 7.28852513722620e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.07543552262695e-01 , 1.57772719634005e-03 , 9.51532697409047e-01 ). +colvars: Colvar "one" has value ( -3.06732608270377e-01 , 1.68371747048719e-03 , 9.51794238330497e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 7.05271607976549e+00 , -2.04701294245329e+00 , -9.42509469880201e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 , 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 7.08000330134620e+00 , -3.55284910533089e-01 , 4.30137053149054e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 , 5.84980798357323e+00 , 2.24966439635277e+00 , 2.99404129701435e+00 , 5.23835337285908e+00 , 3.58205403294845e+00 , 2.91851704152070e+00 , 6.32437505535570e+00 , 4.50468705973972e+00 , 2.38502757286954e+00 , 3.89223690233319e+00 , 3.71835333345391e+00 , 2.04303158103372e+00 , 2.79802365953788e+00 , 4.15483351289799e+00 , 2.49778941064640e+00 , 3.92884294881576e+00 , 3.24191316831157e+00 , 7.32888194378791e-01 , 2.65411407264995e+00 , 3.01434081602324e+00 , -1.06896703721620e-01 , 3.04251330256935e+00 , 2.71425750935877e+00 , -1.52028070078280e+00 , 1.59416792303023e+00 , 2.19216481262863e+00 , 4.62809499393612e-01 , 3.90650117951124e-01 , 2.56301077867888e+00 , 5.16967514650667e-01 , 2.03122863395248e+00 , 1.04141285375615e+00 , 1.07695231315893e+00 , 1.17402749138365e+00 , 1.12203382713304e-01 , 1.69452997945191e+00 , 2.03682040442338e+00 , -1.11176603037732e+00 , 2.00691923601827e+00 , 5.58729567815095e-01 , 6.09265222101686e-01 , 2.93358745222653e+00 , -6.13749682045257e-01 , 3.49401893418533e-01 , 3.16322193706003e+00 , 1.32234499813337e+00 , 1.34554049175721e+00 , 3.79479022984922e+00 , 8.48270476285389e-01 , 1.97257500422287e+00 , 5.02594407760662e+00 , 2.06153029458319e+00 , 2.66854561045493e+00 , 5.66834200488296e+00 , -3.37968453786755e-01 , 2.91577381023611e+00 , 4.96767152152444e+00 , -1.14410211403567e+00 , 3.06003295903836e+00 , 5.89320327706122e+00 , -5.01252397644797e-01 , 3.55410076723207e+00 , 3.84872265133012e+00 , -1.51442408648012e+00 , 4.54436794679331e+00 , 3.46391022195393e+00 , -7.02905739367337e-01 , 5.41070286617546e+00 , 2.45932126291340e+00 , -2.76742104498482e+00 , 3.87902722252102e+00 , 2.90391761406626e+00 , -3.81979153228129e+00 , 4.49804278244187e+00 , 2.81705435893745e+00 , -2.61618004736925e+00 , 2.67319162189029e+00 , 2.41597950443951e+00 , -3.76419154983186e+00 , 1.81305967817032e+00 , 2.00076893150958e+00 , -3.39728475255780e+00 , 8.85496773526211e-01 , 8.87014667580360e-01 , -4.32547677394703e+00 , 1.06837556076424e+00 , 3.22099878492571e+00 , -5.50600355198686e+00 , 8.33175855060729e-01 , 3.32835499000222e+00 , -3.37775813338197e+00 , 6.84659597766296e-01 , 4.19251734685362e+00 , -3.71579947164811e+00 , 3.83055166333904e-02 , 5.43638450809476e+00 , -2.38737980508660e+00 , -3.14600305794011e-01 , 6.17281002928248e+00 , -4.46493940928512e+00 , 9.97734180499877e-01 , 6.44221479322284e+00 , -5.35250204695175e+00 , 6.01425334398934e-01 , 7.21454062498389e+00 , -6.23318516478668e+00 , 3.59413898038086e+00 , 6.72515897775978e+00 , -6.95212090530336e+00 , 4.29816642791007e+00 , 7.46670089388892e+00 , -6.74961276587329e+00 , 3.18979119729720e+00 , 5.51228345741242e+00 , -4.13063161466044e+00 , 2.25357244122872e+00 , 6.42451233409495e+00 , -4.81540752225174e+00 , 3.19608420035191e+00 , 7.23243596757610e+00 , -4.10269470555908e+00 , 4.58473628518885e+00 , 7.28852513722620e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.6689 , 1.92025 , -15.1271 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.181 , 6.6181 , 13.2362 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.6689 , 1.92025 , -15.1271 ) to colvar "one". -colvars: Adding total bias energy: 44.5703 +colvars: Adding biasing force ( 66.181 , 6.6181 , 13.2362 ) to colvar "one". +colvars: Adding total bias energy: 56.7471 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.6689 , 1.92025 , -15.1271 ) +colvars: Force to be applied: ( 66.181 , 6.6181 , 13.2362 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.90917 , -0.53644 , -1.46508 ) -colvars: ( -4.20961 , -0.459997 , -1.2563 ) -colvars: ( -4.20961 , -0.459997 , -1.2563 ) -colvars: ( -5.60733 , -0.61273 , -1.67343 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17251 , -0.564055 , -1.53892 ) +colvars: ( -4.43543 , -0.483677 , -1.31963 ) +colvars: ( -4.43543 , -0.483677 , -1.31963 ) +colvars: ( -5.90812 , -0.644271 , -1.75778 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.8939 , 0.195273 , 0.62229 ) -colvars: ( 0.774075 , 0.266109 , 0.646792 ) -colvars: ( 0.758316 , 0.259184 , 0.628354 ) -colvars: ( 0.661889 , 0.266989 , 0.582458 ) -colvars: ( 0.649971 , 0.200483 , 0.486803 ) -colvars: ( 0.575098 , 0.344265 , 0.634839 ) -colvars: ( 0.467529 , 0.358366 , 0.590832 ) -colvars: ( 0.390611 , 0.45562 , 0.675622 ) -colvars: ( 0.385794 , 0.31394 , 0.483856 ) -colvars: ( 0.350857 , 0.272431 , 0.408097 ) -colvars: ( 0.356622 , 0.319239 , 0.473889 ) -colvars: ( 0.285393 , 0.276481 , 0.375272 ) -colvars: ( 0.258461 , 0.305484 , 0.398227 ) -colvars: ( 0.348037 , 0.178673 , 0.281409 ) -colvars: ( 0.28922 , 0.13544 , 0.189407 ) -colvars: ( 0.471121 , 0.141544 , 0.303763 ) -colvars: ( 0.543878 , 0.0501641 , 0.224378 ) -colvars: ( 0.673824 , 0.0290706 , 0.272125 ) -colvars: ( 0.552277 , 0.018366 , 0.186874 ) -colvars: ( 0.536486 , -0.0466322 , 0.0909679 ) -colvars: ( 0.573048 , 0.0662525 , 0.262867 ) -colvars: ( 0.571318 , 0.0501177 , 0.240339 ) -colvars: ( 0.607786 , 0.114781 , 0.347871 ) -colvars: ( 0.446648 , 0.0546935 , 0.173643 ) -colvars: ( 0.439746 , -0.00118822 , 0.0950862 ) -colvars: ( 0.344496 , 0.12037 , 0.201585 ) -colvars: ( 0.219674 , 0.129049 , 0.140274 ) -colvars: ( 0.128029 , 0.214814 , 0.201142 ) -colvars: ( 0.19152 , 0.0553815 , 0.0255864 ) -colvars: ( 0.142081 , 0.0192761 , -0.0514344 ) -colvars: ( 0.225381 , 0.0298007 , 0.0112426 ) -colvars: ( 0.211459 , -0.0426421 , -0.093501 ) -colvars: ( 0.247042 , -0.0460203 , -0.0772285 ) -colvars: ( 0.286819 , -0.128586 , -0.164116 ) -colvars: ( 0.242746 , -0.181634 , -0.2606 ) -colvars: ( 0.402186 , -0.143671 , -0.116869 ) -colvars: ( 0.479739 , -0.219163 , -0.172265 ) -colvars: ( 0.611178 , -0.22184 , -0.0990857 ) -colvars: ( 0.43216 , -0.223608 , -0.205975 ) -colvars: ( 0.437676 , -0.291627 , -0.293469 ) -colvars: ( 0.38317 , -0.150312 , -0.13683 ) -colvars: ( 0.328636 , -0.144018 , -0.16028 ) -colvars: ( 0.311943 , -0.057376 , -0.0544758 ) -colvars: ( 0.205103 , -0.152719 , -0.244018 ) -colvars: ( 0.18056 , -0.194679 , -0.314308 ) -colvars: ( 0.00370186 , -0.198308 , -0.422421 ) -colvars: ( -0.0874139 , -0.216031 , -0.499261 ) -colvars: ( 0.104382 , -0.248265 , -0.430257 ) -colvars: ( 0.123241 , -0.112085 , -0.237626 ) -colvars: ( 0.00370811 , -0.116378 , -0.313151 ) -colvars: ( -0.0854004 , -0.0357115 , -0.257601 ) +colvars: ( 0.941307 , 0.205735 , 0.654619 ) +colvars: ( 0.815175 , 0.280281 , 0.680429 ) +colvars: ( 0.798556 , 0.27302 , 0.661057 ) +colvars: ( 0.697098 , 0.281156 , 0.612729 ) +colvars: ( 0.68455 , 0.21113 , 0.512062 ) +colvars: ( 0.605754 , 0.362475 , 0.667859 ) +colvars: ( 0.49254 , 0.377268 , 0.621548 ) +colvars: ( 0.411587 , 0.479628 , 0.710786 ) +colvars: ( 0.406486 , 0.330484 , 0.508992 ) +colvars: ( 0.369721 , 0.286756 , 0.429257 ) +colvars: ( 0.375754 , 0.336083 , 0.498533 ) +colvars: ( 0.300757 , 0.291061 , 0.394774 ) +colvars: ( 0.272383 , 0.32162 , 0.418963 ) +colvars: ( 0.366689 , 0.188109 , 0.295985 ) +colvars: ( 0.304776 , 0.142571 , 0.19917 ) +colvars: ( 0.496246 , 0.149063 , 0.319496 ) +colvars: ( 0.572824 , 0.0528804 , 0.235941 ) +colvars: ( 0.709597 , 0.0307268 , 0.286179 ) +colvars: ( 0.581689 , 0.0193738 , 0.196445 ) +colvars: ( 0.565064 , -0.0490656 , 0.0955139 ) +colvars: ( 0.603578 , 0.0697717 , 0.276395 ) +colvars: ( 0.601783 , 0.0527522 , 0.25266 ) +colvars: ( 0.640194 , 0.120821 , 0.365803 ) +colvars: ( 0.47056 , 0.0575198 , 0.182482 ) +colvars: ( 0.463303 , -0.00132976 , 0.0997985 ) +colvars: ( 0.36303 , 0.12664 , 0.21191 ) +colvars: ( 0.231643 , 0.135733 , 0.147402 ) +colvars: ( 0.135172 , 0.22601 , 0.211482 ) +colvars: ( 0.201987 , 0.0581821 , 0.0267243 ) +colvars: ( 0.149955 , 0.0201401 , -0.0543355 ) +colvars: ( 0.237603 , 0.031291 , 0.0116486 ) +colvars: ( 0.222926 , -0.0449648 , -0.0985654 ) +colvars: ( 0.260353 , -0.0484762 , -0.0814178 ) +colvars: ( 0.302256 , -0.135436 , -0.172902 ) +colvars: ( 0.25586 , -0.191302 , -0.274434 ) +colvars: ( 0.423703 , -0.151291 , -0.123206 ) +colvars: ( 0.505345 , -0.23076 , -0.181528 ) +colvars: ( 0.643704 , -0.23354 , -0.104538 ) +colvars: ( 0.455288 , -0.235486 , -0.217023 ) +colvars: ( 0.461095 , -0.307105 , -0.309108 ) +colvars: ( 0.403741 , -0.158354 , -0.144264 ) +colvars: ( 0.346363 , -0.151775 , -0.168959 ) +colvars: ( 0.328815 , -0.0605802 , -0.0576239 ) +colvars: ( 0.216326 , -0.160973 , -0.257063 ) +colvars: ( 0.190503 , -0.205174 , -0.331046 ) +colvars: ( 0.00428134 , -0.208989 , -0.444743 ) +colvars: ( -0.0916322 , -0.227677 , -0.525594 ) +colvars: ( 0.110242 , -0.261535 , -0.45299 ) +colvars: ( 0.13014 , -0.118197 , -0.250306 ) +colvars: ( 0.00431179 , -0.122752 , -0.329765 ) +colvars: ( -0.0894927 , -0.0378388 , -0.271279 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.90917 , 0.53644 , 1.46508 ) -colvars: ( 4.20961 , 0.459997 , 1.2563 ) -colvars: ( 4.20961 , 0.459997 , 1.2563 ) -colvars: ( 5.60733 , 0.61273 , 1.67343 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17251 , 0.564055 , 1.53892 ) +colvars: ( 4.43543 , 0.483677 , 1.31963 ) +colvars: ( 4.43543 , 0.483677 , 1.31963 ) +colvars: ( 5.90812 , 0.644271 , 1.75778 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.616722 , -0.0807982 , -0.372798 ) -colvars: ( -0.554528 , -0.162976 , -0.342697 ) -colvars: ( -0.505478 , -0.141207 , -0.284944 ) -colvars: ( -0.514886 , -0.190308 , -0.313672 ) -colvars: ( -0.505299 , -0.131902 , -0.28111 ) -colvars: ( -0.489717 , -0.281659 , -0.324314 ) -colvars: ( -0.456497 , -0.321727 , -0.306733 ) -colvars: ( -0.434433 , -0.428244 , -0.326449 ) -colvars: ( -0.393839 , -0.286725 , -0.230132 ) -colvars: ( -0.389018 , -0.261627 , -0.215436 ) -colvars: ( -0.345125 , -0.281206 , -0.179099 ) -colvars: ( -0.285049 , -0.244689 , -0.104492 ) -colvars: ( -0.237039 , -0.25957 , -0.0621805 ) -colvars: ( -0.304801 , -0.142279 , -0.0840717 ) -colvars: ( -0.273509 , -0.113274 , -0.0412886 ) -colvars: ( -0.359448 , -0.0852709 , -0.11649 ) -colvars: ( -0.386358 , 0.0122499 , -0.10517 ) -colvars: ( -0.437 , 0.0595613 , -0.137381 ) -colvars: ( -0.42333 , 0.0272166 , -0.136376 ) -colvars: ( -0.411988 , 0.083544 , -0.10287 ) -colvars: ( -0.46682 , -0.0263338 , -0.201037 ) -colvars: ( -0.500452 , -0.0277269 , -0.23532 ) -colvars: ( -0.549835 , -0.0925569 , -0.310325 ) -colvars: ( -0.448075 , -0.0575743 , -0.194509 ) -colvars: ( -0.454704 , -0.0138146 , -0.183967 ) -colvars: ( -0.392991 , -0.13139 , -0.168255 ) -colvars: ( -0.335224 , -0.162526 , -0.122542 ) -colvars: ( -0.284879 , -0.252083 , -0.107226 ) -colvars: ( -0.294502 , -0.0903123 , -0.0533253 ) -colvars: ( -0.281025 , -0.0718538 , -0.0325549 ) -colvars: ( -0.27538 , -0.0458184 , -0.0166637 ) -colvars: ( -0.240528 , 0.0283054 , 0.0474158 ) -colvars: ( -0.220027 , 0.0544522 , 0.0782529 ) -colvars: ( -0.284452 , 0.114463 , 0.0372056 ) -colvars: ( -0.257853 , 0.15587 , 0.0801535 ) -colvars: ( -0.353599 , 0.142469 , -0.0211515 ) -colvars: ( -0.402215 , 0.218155 , -0.0401827 ) -colvars: ( -0.473312 , 0.24065 , -0.10266 ) -colvars: ( -0.413051 , 0.198507 , -0.0587711 ) -colvars: ( -0.417499 , 0.25887 , -0.0395181 ) -colvars: ( -0.41697 , 0.112615 , -0.0964458 ) -colvars: ( -0.423357 , 0.0827095 , -0.114601 ) -colvars: ( -0.444308 , -0.00984817 , -0.17198 ) -colvars: ( -0.356671 , 0.07143 , -0.0521415 ) -colvars: ( -0.35964 , 0.0975518 , -0.0448576 ) -colvars: ( -0.196699 , 0.103655 , 0.120983 ) -colvars: ( -0.147286 , 0.105437 , 0.171247 ) -colvars: ( -0.223801 , 0.175452 , 0.122003 ) -colvars: ( -0.29453 , 0.0309065 , -0.00573036 ) -colvars: ( -0.227859 , 0.017299 , 0.0558005 ) -colvars: ( -0.174111 , -0.0652325 , 0.07729 ) +colvars: ( -0.649345 , -0.0851595 , -0.391818 ) +colvars: ( -0.583919 , -0.171647 , -0.360118 ) +colvars: ( -0.532237 , -0.148753 , -0.299339 ) +colvars: ( -0.542254 , -0.200381 , -0.329609 ) +colvars: ( -0.532162 , -0.138891 , -0.295399 ) +colvars: ( -0.515816 , -0.296521 , -0.340776 ) +colvars: ( -0.480915 , -0.338661 , -0.3223 ) +colvars: ( -0.45774 , -0.450772 , -0.342996 ) +colvars: ( -0.414959 , -0.301806 , -0.241742 ) +colvars: ( -0.409914 , -0.275364 , -0.226324 ) +colvars: ( -0.363646 , -0.296011 , -0.188032 ) +colvars: ( -0.300401 , -0.257564 , -0.109567 ) +colvars: ( -0.249827 , -0.273248 , -0.0650135 ) +colvars: ( -0.321154 , -0.14977 , -0.0881351 ) +colvars: ( -0.288234 , -0.11922 , -0.0431636 ) +colvars: ( -0.378623 , -0.0897894 , -0.122243 ) +colvars: ( -0.40691 , 0.0128555 , -0.110382 ) +colvars: ( -0.46015 , 0.0626209 , -0.144254 ) +colvars: ( -0.445869 , 0.0286332 , -0.143254 ) +colvars: ( -0.433931 , 0.0879368 , -0.10805 ) +colvars: ( -0.491684 , -0.0277273 , -0.211266 ) +colvars: ( -0.527134 , -0.0291693 , -0.247367 ) +colvars: ( -0.579145 , -0.0974105 , -0.326245 ) +colvars: ( -0.472059 , -0.060553 , -0.204454 ) +colvars: ( -0.479053 , -0.0144737 , -0.193411 ) +colvars: ( -0.414107 , -0.138243 , -0.1768 ) +colvars: ( -0.353352 , -0.170987 , -0.128725 ) +colvars: ( -0.300384 , -0.265252 , -0.112562 ) +colvars: ( -0.310461 , -0.094971 , -0.0559445 ) +colvars: ( -0.296308 , -0.0755168 , -0.0341337 ) +colvars: ( -0.290271 , -0.0481617 , -0.0173639 ) +colvars: ( -0.253553 , 0.0298604 , 0.0500156 ) +colvars: ( -0.231907 , 0.0573518 , 0.0824862 ) +colvars: ( -0.299769 , 0.120552 , 0.0392208 ) +colvars: ( -0.27178 , 0.164155 , 0.0843627 ) +colvars: ( -0.372529 , 0.150015 , -0.0221739 ) +colvars: ( -0.423688 , 0.229684 , -0.0422434 ) +colvars: ( -0.498487 , 0.253337 , -0.107958 ) +colvars: ( -0.435159 , 0.209035 , -0.0618327 ) +colvars: ( -0.439841 , 0.272585 , -0.0416259 ) +colvars: ( -0.43934 , 0.118641 , -0.101443 ) +colvars: ( -0.446128 , 0.0871937 , -0.120569 ) +colvars: ( -0.468228 , -0.0102267 , -0.180895 ) +colvars: ( -0.375971 , 0.0753477 , -0.0548807 ) +colvars: ( -0.379126 , 0.102866 , -0.0472612 ) +colvars: ( -0.207572 , 0.109286 , 0.12723 ) +colvars: ( -0.155587 , 0.111183 , 0.180086 ) +colvars: ( -0.236033 , 0.184831 , 0.128299 ) +colvars: ( -0.310561 , 0.0326909 , -0.00602394 ) +colvars: ( -0.240414 , 0.0183914 , 0.0586924 ) +colvars: ( -0.183858 , -0.0684813 , 0.0813497 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 18. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 18. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 18, atoms_new_colvar_forces = { ( -4.63199186926414e+00 , -4.21965218396545e-01 , -1.21558574633418e+00 ), ( -3.99006508628367e+00 , -3.56864437027678e-01 , -9.52209324073797e-01 ), ( -4.06260952482650e+00 , -3.83316071324867e-01 , -9.87517423191293e-01 ), ( -5.46265396933560e+00 , -5.44148820171854e-01 , -1.46774025745692e+00 ), ( 2.52838450519886e-01 , 1.17976408809654e-01 , 3.43409753316738e-01 ), ( 4.99455074893902e+00 , 5.99046314440739e-01 , 1.77560204659984e+00 ), ( 4.22064457405113e+00 , 4.96636169794268e-01 , 1.54040251442313e+00 ), ( -4.38227043909202e-02 , 2.73760811980873e-02 , 3.49172967335116e-01 ), ( 4.20156671415350e+00 , 4.87212114671244e-01 , 1.51002822680228e+00 ), ( 5.56916470083263e+00 , 6.23533520962560e-01 , 1.86609441161746e+00 ), ( 1.14972342676729e-02 , 3.80328002454685e-02 , 2.94789823873343e-01 ), ( 3.43451000375694e-04 , 3.17914452486105e-02 , 2.70779342072598e-01 ), ( 2.14227181961660e-02 , 4.59143646767022e-02 , 3.36046732369687e-01 ), ( 4.32353490996562e-02 , 3.63941370787423e-02 , 1.97336988514932e-01 ), ( 1.57106058911772e-02 , 2.21660889396837e-02 , 1.48118317334512e-01 ), ( 1.11673421408274e-01 , 5.62730903723445e-02 , 1.87273358297197e-01 ), ( 1.57520102373723e-01 , 6.24140613543656e-02 , 1.19207758041775e-01 ), ( 2.36824231820393e-01 , 8.86318286882992e-02 , 1.34743992062622e-01 ), ( 1.28946764504298e-01 , 4.55826367881988e-02 , 5.04983062515025e-02 ), ( 1.24497354942834e-01 , 3.69117589338607e-02 , -1.19021651496601e-02 ), ( 1.06227975373663e-01 , 3.99186171610424e-02 , 6.18295321419749e-02 ), ( 7.08659593229584e-02 , 2.23907783048436e-02 , 5.01819221063698e-03 ), ( 5.79510803244978e-02 , 2.22235891960562e-02 , 3.75465936627963e-02 ), ( -1.42753015197761e-03 , -2.88078605485102e-03 , -2.08651223555693e-02 ), ( -1.49585663463941e-02 , -1.50028625361222e-02 , -8.88803735389048e-02 ), ( -4.84946350473997e-02 , -1.10203210850865e-02 , 3.33300764096249e-02 ), ( -1.15549522598168e-01 , -3.34766052013843e-02 , 1.77316149988748e-02 ), ( -1.56849335140040e-01 , -3.72686111642727e-02 , 9.39158243774778e-02 ), ( -1.02982312572491e-01 , -3.49308227331173e-02 , -2.77388268008082e-02 ), ( -1.38944250648061e-01 , -5.25776131427206e-02 , -8.39893211297022e-02 ), ( -4.99987340279306e-02 , -1.60176358727117e-02 , -5.42109089872812e-03 ), ( -2.90695086701666e-02 , -1.43366633820372e-02 , -4.60852118931290e-02 ), ( 2.70157370241507e-02 , 8.43189607754159e-03 , 1.02442138214723e-03 ), ( 2.36673869014287e-03 , -1.41224930282780e-02 , -1.26910456329147e-01 ), ( -1.51077929558593e-02 , -2.57635245274974e-02 , -1.80446153831180e-01 ), ( 4.85869347753608e-02 , -1.20187823586984e-03 , -1.38020865097516e-01 ), ( 7.75238442668547e-02 , -1.00792117951987e-03 , -2.12447325162941e-01 ), ( 1.37865992739589e-01 , 1.88099748420454e-02 , -2.01746080504194e-01 ), ( 1.91086354015031e-02 , -2.51005877528302e-02 , -2.64746288558128e-01 ), ( 2.01766844828190e-02 , -3.27573501001041e-02 , -3.32987445882389e-01 ), ( -3.38001451271146e-02 , -3.76966301635223e-02 , -2.33275827648116e-01 ), ( -9.47209793171819e-02 , -6.13089407095653e-02 , -2.74881724704049e-01 ), ( -1.32364462259639e-01 , -6.72241704556363e-02 , -2.26455704643539e-01 ), ( -1.51568083687360e-01 , -8.12891381825588e-02 , -2.96159498581740e-01 ), ( -1.79080099878639e-01 , -9.71266931889652e-02 , -3.59166108508444e-01 ), ( -1.92996725924340e-01 , -9.46532932510188e-02 , -3.01437941426688e-01 ), ( -2.34700057458484e-01 , -1.10594138940201e-01 , -3.28013947671509e-01 ), ( -1.19419164758656e-01 , -7.28129396647109e-02 , -3.08253181647993e-01 ), ( -1.71289457234405e-01 , -8.11780271490729e-02 , -2.43356455227854e-01 ), ( -2.24150534071262e-01 , -9.90794672795882e-02 , -2.57350130661441e-01 ), ( -2.59510952425891e-01 , -1.00944015882171e-01 , -1.80310795186701e-01 ) } +colvars: Step 18, atoms_new_colvar_forces = { ( -4.88055193397894e+00 , -4.43478910108217e-01 , -1.27612127602987e+00 ), ( -4.20417305438709e+00 , -3.75042739796872e-01 , -9.99314366272996e-01 ), ( -4.28058523683773e+00 , -4.02901954553682e-01 , -1.03650554418330e+00 ), ( -5.75573229032827e+00 , -5.72031674256922e-01 , -1.54111669298228e+00 ), ( 2.66318501216363e-01 , 1.24266758922591e-01 , 3.61718003296263e-01 ), ( 5.26245078426296e+00 , 6.30009218048564e-01 , 1.86600457302523e+00 ), ( 4.44705461385751e+00 , 5.22282976675805e-01 , 1.61887303421573e+00 ), ( -4.61538444750539e-02 , 2.88561944776561e-02 , 3.67790243298683e-01 ), ( 4.42695650367718e+00 , 5.12354875967253e-01 , 1.58687593843419e+00 ), ( 5.86792736008040e+00 , 6.55662845665289e-01 , 1.96071222741343e+00 ), ( 1.21083892763216e-02 , 4.00722555898481e-02 , 3.10501115119141e-01 ), ( 3.56729122269750e-04 , 3.34963142396088e-02 , 2.85207034264299e-01 ), ( 2.25563370014032e-02 , 4.83723396037330e-02 , 3.53949728091593e-01 ), ( 4.55351802266005e-02 , 3.83384706650591e-02 , 2.07850323953260e-01 ), ( 1.65419654283315e-02 , 2.33508396129858e-02 , 1.56006654147788e-01 ), ( 1.17623071559089e-01 , 5.92732325055574e-02 , 1.97252398101077e-01 ), ( 1.65914171330411e-01 , 6.57358934809209e-02 , 1.25559452111701e-01 ), ( 2.49446866519542e-01 , 9.33476751587075e-02 , 1.41925441933804e-01 ), ( 1.35820530901668e-01 , 4.80070651290457e-02 , 5.31906530259548e-02 ), ( 1.31133350000300e-01 , 3.88711228798389e-02 , -1.25366315702819e-02 ), ( 1.11893800416555e-01 , 4.20443734061019e-02 , 6.51292744036224e-02 ), ( 7.46495670413767e-02 , 2.35829464428652e-02 , 5.29272412948312e-03 ), ( 6.10494845332212e-02 , 2.34105382084128e-02 , 3.95585779705800e-02 ), ( -1.49904702789122e-03 , -3.03320911966064e-03 , -2.19721513373768e-02 ), ( -1.57506866378678e-02 , -1.58034704681422e-02 , -9.36121029512557e-02 ), ( -5.10772738514363e-02 , -1.16022560104394e-02 , 3.51092021854199e-02 ), ( -1.21708473978073e-01 , -3.52530958312200e-02 , 1.86769218150234e-02 ), ( -1.65211821674086e-01 , -3.92421347287457e-02 , 9.89195626694808e-02 ), ( -1.08474076072152e-01 , -3.67888706144353e-02 , -2.92202414212849e-02 ), ( -1.46352990341894e-01 , -5.53767489712473e-02 , -8.84691794821692e-02 ), ( -5.26685027683792e-02 , -1.68706990068804e-02 , -5.71534278842813e-03 ), ( -3.06261870181251e-02 , -1.51043739933480e-02 , -4.85497857183163e-02 ), ( 2.84462460092408e-02 , 8.87557161011229e-03 , 1.06834129297995e-03 ), ( 2.48765332295214e-03 , -1.48835771769152e-02 , -1.33681054412397e-01 ), ( -1.59195681968530e-02 , -2.71470722396890e-02 , -1.90071771994133e-01 ), ( 5.11746940255364e-02 , -1.27618104709343e-03 , -1.45380096964017e-01 ), ( 8.16563048292831e-02 , -1.07608224995226e-03 , -2.23771136294045e-01 ), ( 1.45217880141445e-01 , 1.97963220172846e-02 , -2.12496073319685e-01 ), ( 2.01291864255175e-02 , -2.64510443993880e-02 , -2.78855795220795e-01 ), ( 2.12543849167845e-02 , -3.45190587966575e-02 , -3.50734163088580e-01 ), ( -3.55984867246216e-02 , -3.97132551308617e-02 , -2.45706420571687e-01 ), ( -9.97649977540289e-02 , -6.45817026217195e-02 , -2.89528277972865e-01 ), ( -1.39412977565508e-01 , -7.08068240309979e-02 , -2.38518757703770e-01 ), ( -1.59645044756055e-01 , -8.56256780612288e-02 , -3.11943417990449e-01 ), ( -1.88622827480064e-01 , -1.02308355531449e-01 , -3.78307685579187e-01 ), ( -2.03290614725154e-01 , -9.97037153885587e-02 , -3.17512971009593e-01 ), ( -2.47218961600788e-01 , -1.16493877672746e-01 , -3.45507940216820e-01 ), ( -1.25791019609101e-01 , -7.67039286620122e-02 , -3.24691307323793e-01 ), ( -1.80420898008196e-01 , -8.55064433798007e-02 , -2.56329502163869e-01 ), ( -2.36102526876132e-01 , -1.04360796236778e-01 , -2.71072364016474e-01 ), ( -2.73350213448780e-01 , -1.06320100221581e-01 , -1.89929374319025e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 18, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5854,10 +9481,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 19, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 19, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 19, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 19, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 19, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 19, atoms_positions[size = 51] = { ( 8.29016568556080e+00 , 4.06698503088023e-02 , -7.56709873943808e-01 ), ( 6.94599735216919e+00 , -5.50749837223836e-01 , -5.84155006258614e-01 ), ( 6.15580748001842e+00 , -3.68606829803745e-01 , 7.22837908152150e-01 ), ( 4.95723322053989e+00 , -1.66817333386827e-01 , 7.20083807400076e-01 ), ( 7.05086328351688e+00 , -2.04918183568107e+00 , -9.38184814770755e-01 ), ( 6.86940055722009e+00 , -2.62917482731473e-01 , 1.90028356504105e+00 ), ( 6.17947606996176e+00 , -1.54655252538254e-01 , 3.19785930273638e+00 ), ( 7.07927530556238e+00 , -3.55345958464858e-01 , 4.30722872042406e+00 ), ( 5.31311935542799e+00 , 1.09841937380163e+00 , 3.34822921101458e+00 ), ( 4.15713014090365e+00 , 1.02743973859713e+00 , 3.68556971830120e+00 ), ( 5.84591971680664e+00 , 2.25139529107553e+00 , 2.99218364269678e+00 ), ( 5.23918055313769e+00 , 3.58015005617468e+00 , 2.92033481435295e+00 ), ( 6.32331086605058e+00 , 4.50264880133564e+00 , 2.37526441506070e+00 ), ( 3.88701121106020e+00 , 3.71260739307479e+00 , 2.04386771633033e+00 ), ( 2.79448765359408e+00 , 4.15798984046697e+00 , 2.49279276475371e+00 ), ( 3.93450135362444e+00 , 3.24102272227666e+00 , 7.31874880796859e-01 ), ( 2.65719957690435e+00 , 3.00921494798025e+00 , -1.05547997265674e-01 ), ( 3.04727261327806e+00 , 2.71000869800488e+00 , -1.51691695139718e+00 ), ( 1.59692527577294e+00 , 2.18794488778601e+00 , 4.53626036616700e-01 ), ( 3.84266461533483e-01 , 2.57240994422366e+00 , 5.13706922516542e-01 ), ( 2.03949616752687e+00 , 1.05549421048506e+00 , 1.07375909314133e+00 ), ( 1.17132402764887e+00 , 1.15024769904997e-01 , 1.69589156927417e+00 ), ( 2.03984308916360e+00 , -1.10731133916195e+00 , 2.00844855140052e+00 ), ( 5.60352100194501e-01 , 6.10391271265693e-01 , 2.93787520299176e+00 ), ( -6.07650884272349e-01 , 3.49472309543588e-01 , 3.16225774381691e+00 ), ( 1.31972169446706e+00 , 1.34555701252330e+00 , 3.78503503912101e+00 ), ( 8.45312959777899e-01 , 1.97599832312103e+00 , 5.02552145167832e+00 ), ( 2.07062385644138e+00 , 2.67821594555621e+00 , 5.67519151395927e+00 ), ( -3.37294919573754e-01 , 2.91533326166685e+00 , 4.96765032089662e+00 ), ( -1.14061183342495e+00 , 3.06135069610087e+00 , 5.89053374083556e+00 ), ( -5.06564556008585e-01 , 3.54401302021891e+00 , 3.84796570257251e+00 ), ( -1.51673772132311e+00 , 4.54216454055818e+00 , 3.45374233777667e+00 ), ( -7.00831591912167e-01 , 5.41258555929861e+00 , 2.46174052642702e+00 ), ( -2.76400858138880e+00 , 3.88360415598215e+00 , 2.89991349394933e+00 ), ( -3.81857294493020e+00 , 4.50405658125091e+00 , 2.81578739240627e+00 ), ( -2.62033145837470e+00 , 2.67416887011665e+00 , 2.40875873374679e+00 ), ( -3.76876185319620e+00 , 1.80728258250921e+00 , 1.99916822343542e+00 ), ( -3.39303477301733e+00 , 8.86584790958229e-01 , 8.80525528609449e-01 ), ( -4.32513260189623e+00 , 1.06939488468089e+00 , 3.21616052977844e+00 ), ( -5.50268179432501e+00 , 8.25997951798771e-01 , 3.32880254088488e+00 ), ( -3.37283314174368e+00 , 6.87984528108069e-01 , 4.19931112945264e+00 ), ( -3.70810082719424e+00 , 4.17326140614362e-02 , 5.43447083064241e+00 ), ( -2.38890674390546e+00 , -3.15458062771559e-01 , 6.17186901939838e+00 ), ( -4.46312730645682e+00 , 9.93104584934617e-01 , 6.44131280303784e+00 ), ( -5.35584048260438e+00 , 5.99806496682841e-01 , 7.21661752816569e+00 ), ( -6.23456552528205e+00 , 3.59979020155176e+00 , 6.72948111301887e+00 ), ( -6.95624590919136e+00 , 4.29811286783759e+00 , 7.47143281594149e+00 ), ( -6.74626091907508e+00 , 3.18609816515879e+00 , 5.50997186268318e+00 ), ( -4.12995356453422e+00 , 2.24935615826763e+00 , 6.41684281705873e+00 ), ( -4.81151193535090e+00 , 3.20071974677728e+00 , 7.23716453085567e+00 ), ( -4.09944363849299e+00 , 4.58072674342841e+00 , 7.28577850117491e+00 ) } +colvars: Step 19, atoms_positions[size = 51] = { ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 ), ( 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 ), ( 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 ), ( 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 ), ( 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 ), ( 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 ), ( 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 ), ( 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 ), ( 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 ), ( 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 ), ( 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 ), ( 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 ), ( 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 ), ( 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 ), ( 2.79449313515955e+00 , 4.15799608277627e+00 , 2.49284759025593e+00 ), ( 3.93454759904606e+00 , 3.24104521362461e+00 , 7.31951298720477e-01 ), ( 2.65726401670662e+00 , 3.00924108365266e+00 , -1.05498188100982e-01 ), ( 3.04736003109482e+00 , 2.71004105763005e+00 , -1.51686507513849e+00 ), ( 1.59697894003139e+00 , 2.18796462741218e+00 , 4.53650193681246e-01 ), ( 3.84316586534183e-01 , 2.57242261776813e+00 , 5.13703608345861e-01 ), ( 2.03953806329203e+00 , 1.05551294165828e+00 , 1.07378939657437e+00 ), ( 1.17135282528705e+00 , 1.15035186348851e-01 , 1.69589580000055e+00 ), ( 2.03987486871026e+00 , -1.10729221445392e+00 , 2.00847688085443e+00 ), ( 5.60359091293224e-01 , 6.10390355972048e-01 , 2.93786782504420e+00 ), ( -6.07652617336230e-01 , 3.49468198602874e-01 , 3.16222771402236e+00 ), ( 1.31974871895307e+00 , 1.34554477618616e+00 , 3.78504529634619e+00 ), ( 8.45272575166906e-01 , 1.97598108814588e+00 , 5.02552654623703e+00 ), ( 2.07056674430801e+00 , 2.67820079829358e+00 , 5.67522110011561e+00 ), ( -3.37337329784998e-01 , 2.91531659103695e+00 , 4.96763711296850e+00 ), ( -1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 ), ( -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 ), ( -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 ), ( -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 ), ( -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 ), ( -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 ), ( -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 ), ( -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 ), ( -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 ), ( -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 ), ( -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 ), ( -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 ), ( -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 ), ( -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 ), ( -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 ), ( -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 ), ( -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 ), ( -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 ), ( -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 ), ( -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 ), ( -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 ), ( -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ) } colvars: Step 19, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 19, atom_groups_ids[size = 0] = @@ -5874,163 +9501,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 19 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.05951823016640e-01 , 7.43277606547324e-04 , 9.52046705540854e-01 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.05077482584572e-01 , 8.59223702593821e-04 , 9.52327145131592e-01 ). +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 , 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 , 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 , 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 , 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 , 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 , 2.79449313515955e+00 , 4.15799608277627e+00 , 2.49284759025593e+00 , 3.93454759904606e+00 , 3.24104521362461e+00 , 7.31951298720477e-01 , 2.65726401670662e+00 , 3.00924108365266e+00 , -1.05498188100982e-01 , 3.04736003109482e+00 , 2.71004105763005e+00 , -1.51686507513849e+00 , 1.59697894003139e+00 , 2.18796462741218e+00 , 4.53650193681246e-01 , 3.84316586534183e-01 , 2.57242261776813e+00 , 5.13703608345861e-01 , 2.03953806329203e+00 , 1.05551294165828e+00 , 1.07378939657437e+00 , 1.17135282528705e+00 , 1.15035186348851e-01 , 1.69589580000055e+00 , 2.03987486871026e+00 , -1.10729221445392e+00 , 2.00847688085443e+00 , 5.60359091293224e-01 , 6.10390355972048e-01 , 2.93786782504420e+00 , -6.07652617336230e-01 , 3.49468198602874e-01 , 3.16222771402236e+00 , 1.31974871895307e+00 , 1.34554477618616e+00 , 3.78504529634619e+00 , 8.45272575166906e-01 , 1.97598108814588e+00 , 5.02552654623703e+00 , 2.07056674430801e+00 , 2.67820079829358e+00 , 5.67522110011561e+00 , -3.37337329784998e-01 , 2.91531659103695e+00 , 4.96763711296850e+00 , -1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 , -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 , -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 , -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 , -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 , -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 , -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 , -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 , -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 , -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 , -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 , -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 , -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 , -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 , -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 , -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 , -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 , -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 , -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 , -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 , -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 , -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.05951823016640e-01 , 7.43277606547324e-04 , 9.52046705540854e-01 ). +colvars: Colvar "one" has value ( -3.05077482584572e-01 , 8.59223702593821e-04 , 9.52327145131592e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 , 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 , 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 , 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 , 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 , 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 , 2.79449313515955e+00 , 4.15799608277627e+00 , 2.49284759025593e+00 , 3.93454759904606e+00 , 3.24104521362461e+00 , 7.31951298720477e-01 , 2.65726401670662e+00 , 3.00924108365266e+00 , -1.05498188100982e-01 , 3.04736003109482e+00 , 2.71004105763005e+00 , -1.51686507513849e+00 , 1.59697894003139e+00 , 2.18796462741218e+00 , 4.53650193681246e-01 , 3.84316586534183e-01 , 2.57242261776813e+00 , 5.13703608345861e-01 , 2.03953806329203e+00 , 1.05551294165828e+00 , 1.07378939657437e+00 , 1.17135282528705e+00 , 1.15035186348851e-01 , 1.69589580000055e+00 , 2.03987486871026e+00 , -1.10729221445392e+00 , 2.00847688085443e+00 , 5.60359091293224e-01 , 6.10390355972048e-01 , 2.93786782504420e+00 , -6.07652617336230e-01 , 3.49468198602874e-01 , 3.16222771402236e+00 , 1.31974871895307e+00 , 1.34554477618616e+00 , 3.78504529634619e+00 , 8.45272575166906e-01 , 1.97598108814588e+00 , 5.02552654623703e+00 , 2.07056674430801e+00 , 2.67820079829358e+00 , 5.67522110011561e+00 , -3.37337329784998e-01 , 2.91531659103695e+00 , 4.96763711296850e+00 , -1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 , -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 , -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 , -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 , -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 , -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 , -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 , -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 , -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 , -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 , -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 , -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 , -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 , -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 , -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 , -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 , -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 , -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 , -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 , -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 , -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 , -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.637 , 1.93693 , -15.1373 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.1038 , 6.61038 , 13.2208 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.637 , 1.93693 , -15.1373 ) to colvar "one". -colvars: Adding total bias energy: 44.5074 +colvars: Adding biasing force ( 66.1038 , 6.61038 , 13.2208 ) to colvar "one". +colvars: Adding total bias energy: 56.6361 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.637 , 1.93693 , -15.1373 ) +colvars: Force to be applied: ( 66.1038 , 6.61038 , 13.2208 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.91237 , -0.534728 , -1.45823 ) -colvars: ( -4.21236 , -0.458529 , -1.25043 ) -colvars: ( -4.21236 , -0.458529 , -1.25043 ) -colvars: ( -5.61098 , -0.610774 , -1.66561 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17347 , -0.561901 , -1.53062 ) +colvars: ( -4.43625 , -0.48183 , -1.31251 ) +colvars: ( -4.43625 , -0.48183 , -1.31251 ) +colvars: ( -5.90921 , -0.641811 , -1.7483 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.893209 , 0.195386 , 0.620693 ) -colvars: ( 0.773567 , 0.266161 , 0.645082 ) -colvars: ( 0.757723 , 0.259258 , 0.626656 ) -colvars: ( 0.661613 , 0.266978 , 0.580875 ) -colvars: ( 0.649714 , 0.200474 , 0.485452 ) -colvars: ( 0.575004 , 0.344193 , 0.633099 ) -colvars: ( 0.467669 , 0.358228 , 0.589172 ) -colvars: ( 0.390909 , 0.455426 , 0.673728 ) -colvars: ( 0.386015 , 0.313783 , 0.482417 ) -colvars: ( 0.351178 , 0.272252 , 0.406842 ) -colvars: ( 0.356799 , 0.319091 , 0.47244 ) -colvars: ( 0.285626 , 0.27632 , 0.374024 ) -colvars: ( 0.258641 , 0.305333 , 0.396887 ) -colvars: ( 0.348148 , 0.178559 , 0.280415 ) -colvars: ( 0.28943 , 0.135304 , 0.188619 ) -colvars: ( 0.471015 , 0.141495 , 0.30276 ) -colvars: ( 0.543638 , 0.050164 , 0.223599 ) -colvars: ( 0.673331 , 0.0291432 , 0.27127 ) -colvars: ( 0.552116 , 0.0183499 , 0.186215 ) -colvars: ( 0.536351 , -0.0466477 , 0.0905406 ) -colvars: ( 0.572936 , 0.066219 , 0.262047 ) -colvars: ( 0.571306 , 0.0500609 , 0.239598 ) -colvars: ( 0.60779 , 0.114714 , 0.346896 ) -colvars: ( 0.44687 , 0.0545709 , 0.173025 ) -colvars: ( 0.440015 , -0.00131615 , 0.0946694 ) -colvars: ( 0.344868 , 0.120196 , 0.200851 ) -colvars: ( 0.220265 , 0.128813 , 0.139645 ) -colvars: ( 0.128747 , 0.214531 , 0.200319 ) -colvars: ( 0.192095 , 0.0551573 , 0.0252167 ) -colvars: ( 0.142773 , 0.0190241 , -0.0516236 ) -colvars: ( 0.225804 , 0.0296196 , 0.0108987 ) -colvars: ( 0.211839 , -0.0428041 , -0.093606 ) -colvars: ( 0.247259 , -0.0461388 , -0.0773854 ) -colvars: ( 0.287103 , -0.128709 , -0.164008 ) -colvars: ( 0.243098 , -0.18177 , -0.26027 ) -colvars: ( 0.402312 , -0.143747 , -0.116824 ) -colvars: ( 0.479773 , -0.219203 , -0.172041 ) -colvars: ( 0.611009 , -0.221822 , -0.0989879 ) -colvars: ( 0.432369 , -0.223694 , -0.205663 ) -colvars: ( 0.437889 , -0.291706 , -0.292934 ) -colvars: ( 0.383527 , -0.150447 , -0.136694 ) -colvars: ( 0.329175 , -0.144203 , -0.160085 ) -colvars: ( 0.312579 , -0.0575961 , -0.0545338 ) -colvars: ( 0.205835 , -0.152957 , -0.243667 ) -colvars: ( 0.181381 , -0.194935 , -0.313781 ) -colvars: ( 0.00461293 , -0.198596 , -0.421745 ) -colvars: ( -0.0863596 , -0.216357 , -0.498433 ) -colvars: ( 0.105069 , -0.248485 , -0.429535 ) -colvars: ( 0.124046 , -0.11235 , -0.237339 ) -colvars: ( 0.004693 , -0.116695 , -0.312729 ) -colvars: ( -0.0843039 , -0.0360702 , -0.257362 ) +colvars: ( 0.940097 , 0.205758 , 0.652548 ) +colvars: ( 0.814226 , 0.280198 , 0.678227 ) +colvars: ( 0.797523 , 0.272966 , 0.658881 ) +colvars: ( 0.696458 , 0.281001 , 0.610698 ) +colvars: ( 0.683936 , 0.211014 , 0.510333 ) +colvars: ( 0.605357 , 0.362211 , 0.665633 ) +colvars: ( 0.492452 , 0.376922 , 0.619433 ) +colvars: ( 0.411711 , 0.479167 , 0.708375 ) +colvars: ( 0.40653 , 0.330141 , 0.507174 ) +colvars: ( 0.369889 , 0.286411 , 0.427677 ) +colvars: ( 0.375764 , 0.33575 , 0.496712 ) +colvars: ( 0.300867 , 0.290737 , 0.393226 ) +colvars: ( 0.272449 , 0.321292 , 0.417307 ) +colvars: ( 0.366633 , 0.187889 , 0.29476 ) +colvars: ( 0.304857 , 0.14235 , 0.198216 ) +colvars: ( 0.495889 , 0.148937 , 0.318246 ) +colvars: ( 0.572284 , 0.0528582 , 0.234973 ) +colvars: ( 0.708717 , 0.0307971 , 0.285102 ) +colvars: ( 0.581231 , 0.0193501 , 0.195623 ) +colvars: ( 0.564642 , -0.0490533 , 0.0949931 ) +colvars: ( 0.603162 , 0.0697015 , 0.275358 ) +colvars: ( 0.601476 , 0.0526639 , 0.251717 ) +colvars: ( 0.639884 , 0.120685 , 0.364548 ) +colvars: ( 0.47057 , 0.0573557 , 0.181708 ) +colvars: ( 0.463367 , -0.00146975 , 0.0992828 ) +colvars: ( 0.363256 , 0.126384 , 0.211 ) +colvars: ( 0.232171 , 0.135403 , 0.146641 ) +colvars: ( 0.135887 , 0.225581 , 0.210482 ) +colvars: ( 0.202513 , 0.0579058 , 0.0263043 ) +colvars: ( 0.150633 , 0.0198521 , -0.0545199 ) +colvars: ( 0.237947 , 0.0310775 , 0.0112659 ) +colvars: ( 0.223232 , -0.0451169 , -0.0986334 ) +colvars: ( 0.260464 , -0.0485769 , -0.0815483 ) +colvars: ( 0.302418 , -0.135499 , -0.172705 ) +colvars: ( 0.256118 , -0.19135 , -0.273948 ) +colvars: ( 0.423633 , -0.151294 , -0.123106 ) +colvars: ( 0.505134 , -0.230682 , -0.181209 ) +colvars: ( 0.643205 , -0.233396 , -0.104397 ) +colvars: ( 0.455291 , -0.235458 , -0.216593 ) +colvars: ( 0.4611 , -0.307031 , -0.308392 ) +colvars: ( 0.403931 , -0.15842 , -0.14406 ) +colvars: ( 0.346777 , -0.151901 , -0.16868 ) +colvars: ( 0.329342 , -0.0607935 , -0.0576753 ) +colvars: ( 0.217013 , -0.161154 , -0.256569 ) +colvars: ( 0.191298 , -0.205353 , -0.330326 ) +colvars: ( 0.00526842 , -0.209198 , -0.443796 ) +colvars: ( -0.0904425 , -0.227918 , -0.52444 ) +colvars: ( 0.110934 , -0.261641 , -0.451991 ) +colvars: ( 0.130949 , -0.118429 , -0.249881 ) +colvars: ( 0.00537865 , -0.123038 , -0.329151 ) +colvars: ( -0.0882579 , -0.0382154 , -0.270889 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.91237 , 0.534728 , 1.45823 ) -colvars: ( 4.21236 , 0.458529 , 1.25043 ) -colvars: ( 4.21236 , 0.458529 , 1.25043 ) -colvars: ( 5.61098 , 0.610774 , 1.66561 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17347 , 0.561901 , 1.53062 ) +colvars: ( 4.43625 , 0.48183 , 1.31251 ) +colvars: ( 4.43625 , 0.48183 , 1.31251 ) +colvars: ( 5.90921 , 0.641811 , 1.7483 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.616281 , -0.0808693 , -0.371446 ) -colvars: ( -0.554208 , -0.163117 , -0.341145 ) -colvars: ( -0.504957 , -0.141314 , -0.283282 ) -colvars: ( -0.514782 , -0.190453 , -0.312224 ) -colvars: ( -0.505192 , -0.131969 , -0.279887 ) -colvars: ( -0.489805 , -0.281897 , -0.322697 ) -colvars: ( -0.456816 , -0.321986 , -0.305186 ) -colvars: ( -0.434924 , -0.428618 , -0.324653 ) -colvars: ( -0.394137 , -0.286915 , -0.228703 ) -colvars: ( -0.389424 , -0.261776 , -0.214211 ) -colvars: ( -0.345273 , -0.281379 , -0.177549 ) -colvars: ( -0.285149 , -0.244794 , -0.10304 ) -colvars: ( -0.236984 , -0.259684 , -0.0605206 ) -colvars: ( -0.304772 , -0.14227 , -0.0828934 ) -colvars: ( -0.273538 , -0.113211 , -0.0402819 ) -colvars: ( -0.359244 , -0.0852239 , -0.115362 ) -colvars: ( -0.386025 , 0.0124012 , -0.104297 ) -colvars: ( -0.436444 , 0.0597364 , -0.136473 ) -colvars: ( -0.423163 , 0.0273829 , -0.135722 ) -colvars: ( -0.411823 , 0.0837869 , -0.102439 ) -colvars: ( -0.466804 , -0.0262438 , -0.20032 ) -colvars: ( -0.500623 , -0.02764 , -0.234778 ) -colvars: ( -0.550128 , -0.092565 , -0.309646 ) -colvars: ( -0.44844 , -0.0574902 , -0.194041 ) -colvars: ( -0.455133 , -0.0136732 , -0.183732 ) -colvars: ( -0.393448 , -0.131371 , -0.16759 ) -colvars: ( -0.335847 , -0.162511 , -0.12192 ) -colvars: ( -0.285578 , -0.252156 , -0.10633 ) -colvars: ( -0.295018 , -0.0901954 , -0.0528822 ) -colvars: ( -0.281658 , -0.0716997 , -0.0322992 ) -colvars: ( -0.275665 , -0.0456524 , -0.0161714 ) -colvars: ( -0.240684 , 0.0285716 , 0.0477436 ) -colvars: ( -0.219937 , 0.0547437 , 0.0787162 ) -colvars: ( -0.284558 , 0.114817 , 0.0372456 ) -colvars: ( -0.257987 , 0.15629 , 0.0800034 ) -colvars: ( -0.353636 , 0.142825 , -0.021151 ) -colvars: ( -0.402219 , 0.218585 , -0.0404446 ) -colvars: ( -0.473196 , 0.241071 , -0.10289 ) -colvars: ( -0.413294 , 0.198924 , -0.0591888 ) -colvars: ( -0.417747 , 0.259362 , -0.040177 ) -colvars: ( -0.417417 , 0.112935 , -0.0967264 ) -colvars: ( -0.424045 , 0.0830049 , -0.115 ) -colvars: ( -0.445169 , -0.00966785 , -0.172183 ) -colvars: ( -0.357473 , 0.0717467 , -0.05261 ) -colvars: ( -0.360553 , 0.0979081 , -0.0455363 ) -colvars: ( -0.197415 , 0.104074 , 0.120466 ) -colvars: ( -0.148086 , 0.105884 , 0.17064 ) -colvars: ( -0.224281 , 0.175935 , 0.121437 ) -colvars: ( -0.295311 , 0.0311961 , -0.00602135 ) -colvars: ( -0.228738 , 0.0176059 , 0.0554637 ) -colvars: ( -0.175039 , -0.0650049 , 0.0772264 ) +colvars: ( -0.648543 , -0.0851979 , -0.390134 ) +colvars: ( -0.583282 , -0.171711 , -0.358239 ) +colvars: ( -0.531413 , -0.148795 , -0.29738 ) +colvars: ( -0.541871 , -0.20043 , -0.327861 ) +colvars: ( -0.531781 , -0.13889 , -0.293912 ) +colvars: ( -0.515655 , -0.296613 , -0.338841 ) +colvars: ( -0.481021 , -0.338751 , -0.320452 ) +colvars: ( -0.458043 , -0.450919 , -0.340869 ) +colvars: ( -0.415078 , -0.301841 , -0.240067 ) +colvars: ( -0.410152 , -0.275368 , -0.224877 ) +colvars: ( -0.363633 , -0.296032 , -0.186259 ) +colvars: ( -0.300371 , -0.257534 , -0.107946 ) +colvars: ( -0.249658 , -0.273221 , -0.0631978 ) +colvars: ( -0.320974 , -0.14968 , -0.0868193 ) +colvars: ( -0.288134 , -0.119088 , -0.042058 ) +colvars: ( -0.378223 , -0.0896943 , -0.12096 ) +colvars: ( -0.406355 , 0.0130035 , -0.109377 ) +colvars: ( -0.459327 , 0.0627639 , -0.143192 ) +colvars: ( -0.445471 , 0.0287905 , -0.142464 ) +colvars: ( -0.433542 , 0.0881434 , -0.107519 ) +colvars: ( -0.491424 , -0.0276187 , -0.210367 ) +colvars: ( -0.527054 , -0.0290611 , -0.246635 ) +colvars: ( -0.579168 , -0.097365 , -0.325319 ) +colvars: ( -0.472218 , -0.0604278 , -0.203827 ) +colvars: ( -0.479277 , -0.0143118 , -0.193039 ) +colvars: ( -0.414397 , -0.138142 , -0.17598 ) +colvars: ( -0.353853 , -0.17087 , -0.127979 ) +colvars: ( -0.300997 , -0.265176 , -0.111534 ) +colvars: ( -0.310871 , -0.0947888 , -0.0554333 ) +colvars: ( -0.296851 , -0.075304 , -0.0338356 ) +colvars: ( -0.290445 , -0.0479556 , -0.0168229 ) +colvars: ( -0.253607 , 0.0301291 , 0.0503411 ) +colvars: ( -0.231711 , 0.0576293 , 0.0829371 ) +colvars: ( -0.299745 , 0.120864 , 0.0392458 ) +colvars: ( -0.271801 , 0.164513 , 0.0841578 ) +colvars: ( -0.372391 , 0.150311 , -0.0221541 ) +colvars: ( -0.423487 , 0.230015 , -0.0424916 ) +colvars: ( -0.498115 , 0.253642 , -0.108132 ) +colvars: ( -0.435207 , 0.209366 , -0.0622356 ) +colvars: ( -0.439892 , 0.272962 , -0.0422984 ) +colvars: ( -0.439606 , 0.11892 , -0.101676 ) +colvars: ( -0.446649 , 0.0874676 , -0.120917 ) +colvars: ( -0.468922 , -0.0100199 , -0.180999 ) +colvars: ( -0.376653 , 0.0756528 , -0.055343 ) +colvars: ( -0.379925 , 0.1032 , -0.0479525 ) +colvars: ( -0.208254 , 0.109681 , 0.126607 ) +colvars: ( -0.156387 , 0.111609 , 0.179335 ) +colvars: ( -0.236446 , 0.185251 , 0.127623 ) +colvars: ( -0.311256 , 0.0329906 , -0.00632615 ) +colvars: ( -0.241254 , 0.0187193 , 0.0583023 ) +colvars: ( -0.184781 , -0.0681894 , 0.0812374 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 19. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 19. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 19, atoms_new_colvar_forces = { ( -4.63544419501644e+00 , -4.20210469307563e-01 , -1.20898324434841e+00 ), ( -3.99299929210782e+00 , -3.55484946274648e-01 , -9.46494606331090e-01 ), ( -4.06552732790182e+00 , -3.82004235259854e-01 , -9.81780927731090e-01 ), ( -5.46646077617497e+00 , -5.42268393306697e-01 , -1.46004673915677e+00 ), ( 2.52765676023864e-01 , 1.17943473821310e-01 , 3.43374038057664e-01 ), ( 4.99757064299401e+00 , 5.97023835288657e-01 , 1.76863174513226e+00 ), ( 4.22321014388509e+00 , 4.94770460584830e-01 , 1.53441767442586e+00 ), ( -4.40146132019498e-02 , 2.68083709672712e-02 , 3.49075063476128e-01 ), ( 4.20423660521184e+00 , 4.85396409558875e-01 , 1.50414549465258e+00 ), ( 5.57273604367227e+00 , 6.21250028134693e-01 , 1.85824202630381e+00 ), ( 1.15251448703177e-02 , 3.77126122577807e-02 , 2.94890992779568e-01 ), ( 4.76902213796149e-04 , 3.15269557008686e-02 , 2.70983941329410e-01 ), ( 2.16571142784051e-02 , 4.56492628647812e-02 , 3.36366548282541e-01 ), ( 4.33758665823508e-02 , 3.62889824542237e-02 , 1.97521770142452e-01 ), ( 1.58915225452573e-02 , 2.20924654085242e-02 , 1.48337017459659e-01 ), ( 1.11770702205321e-01 , 5.62714872358337e-02 , 1.87398314401606e-01 ), ( 1.57612989988102e-01 , 6.25652553499279e-02 , 1.19302032624286e-01 ), ( 2.36887918663062e-01 , 8.88795957536135e-02 , 1.34797126490583e-01 ), ( 1.28953381376549e-01 , 4.57327536623671e-02 , 5.04928714782447e-02 ), ( 1.24527961342896e-01 , 3.71391809380055e-02 , -1.18982067115387e-02 ), ( 1.06132711925979e-01 , 3.99752107865736e-02 , 6.17277360600108e-02 ), ( 7.06836776109986e-02 , 2.24209086479583e-02 , 4.82027046087513e-03 ), ( 5.76619801736108e-02 , 2.21486419863283e-02 , 3.72507779259702e-02 ), ( -1.57033537758844e-03 , -2.91926072372384e-03 , -2.10154422166415e-02 ), ( -1.51181454784769e-02 , -1.49893684729367e-02 , -8.90624391297327e-02 ), ( -4.85798776472883e-02 , -1.11743496473575e-02 , 3.32612396381922e-02 ), ( -1.15581829917278e-01 , -3.36972984351649e-02 , 1.77256734256328e-02 ), ( -1.56830362014264e-01 , -3.76244193630479e-02 , 9.39894503345342e-02 ), ( -1.02922960304374e-01 , -3.50380799375384e-02 , -2.76655221950742e-02 ), ( -1.38884275259951e-01 , -5.26755323611779e-02 , -8.39227179726776e-02 ), ( -4.98609822060870e-02 , -1.60327515367708e-02 , -5.27262388788827e-03 ), ( -2.88445005473107e-02 , -1.42324936551007e-02 , -4.58623778592838e-02 ), ( 2.73217648587229e-02 , 8.60482871675118e-03 , 1.33078963528227e-03 ), ( 2.54461228523750e-03 , -1.38917787217629e-02 , -1.26762239167059e-01 ), ( -1.48893347255525e-02 , -2.54799046904008e-02 , -1.80266877552548e-01 ), ( 4.86756905373570e-02 , -9.21690811915205e-04 , -1.37975108490852e-01 ), ( 7.75538908664742e-02 , -6.17762008428668e-04 , -2.12485848399988e-01 ), ( 1.37812964599545e-01 , 1.92489557605193e-02 , -2.01878106175641e-01 ), ( 1.90743275152562e-02 , -2.47696484195315e-02 , -2.64852259364505e-01 ), ( 2.01420904417423e-02 , -3.23436555785761e-02 , -3.33111277628311e-01 ), ( -3.38899456892007e-02 , -3.75118991156526e-02 , -2.33419984883303e-01 ), ( -9.48700463302962e-02 , -6.11980027987171e-02 , -2.75084946294434e-01 ), ( -1.32589743279693e-01 , -6.72639097669000e-02 , -2.26716841639927e-01 ), ( -1.51638265224316e-01 , -8.12106124351630e-02 , -2.96276848845635e-01 ), ( -1.79172581375629e-01 , -9.70269974915623e-02 , -3.59316840047847e-01 ), ( -1.92801949632925e-01 , -9.45219403171258e-02 , -3.01279033292902e-01 ), ( -2.34445343723124e-01 , -1.10472638436355e-01 , -3.27792731520741e-01 ), ( -1.19212032757414e-01 , -7.25498898294642e-02 , -3.08097710642036e-01 ), ( -1.71265530471300e-01 , -8.11538179058320e-02 , -2.43360800467069e-01 ), ( -2.24045130281263e-01 , -9.90888167582585e-02 , -2.57264887939209e-01 ), ( -2.59342950021729e-01 , -1.01075112512468e-01 , -1.80135404624953e-01 ) } +colvars: Step 19, atoms_new_colvar_forces = { ( -4.88191171719184e+00 , -4.41340748118462e-01 , -1.26820824536058e+00 ), ( -4.20530221680057e+00 , -3.73342976770697e-01 , -9.92520433481477e-01 ), ( -4.28165931112879e+00 , -4.01259264608975e-01 , -1.02967036003239e+00 ), ( -5.75705258921491e+00 , -5.69686746119912e-01 , -1.53187762037129e+00 ), ( 2.66110051993996e-01 , 1.24170798212882e-01 , 3.61501230465698e-01 ), ( 5.26316777428457e+00 , 6.27498310071210e-01 , 1.85741369607553e+00 ), ( 4.44767675245246e+00 , 5.20001094476915e-01 , 1.61148885882558e+00 ), ( -4.63322505446268e-02 , 2.82473186619320e-02 , 3.67505260898104e-01 ), ( 4.42769795664276e+00 , 5.10130300487824e-01 , 1.57961461004834e+00 ), ( 5.86894508044445e+00 , 6.52854373367683e-01 , 1.95109862860026e+00 ), ( 1.21315126980281e-02 , 3.97171205298853e-02 , 3.10453126119482e-01 ), ( 4.96304438557249e-04 , 3.32027922309193e-02 , 2.85279954745149e-01 ), ( 2.27906777543655e-02 , 4.80708483874093e-02 , 3.54109275355419e-01 ), ( 4.56597958389400e-02 , 3.82094250766497e-02 , 2.07940850769046e-01 ), ( 1.67233174273261e-02 , 2.32622384094650e-02 , 1.56158425509746e-01 ), ( 1.17666638015727e-01 , 5.92422707318476e-02 , 1.97285509487435e-01 ), ( 1.65929222178092e-01 , 6.58617567097613e-02 , 1.25595978990976e-01 ), ( 2.49389894292330e-01 , 9.35610160162401e-02 , 1.41910759755505e-01 ), ( 1.35760111023169e-01 , 4.81405430433821e-02 , 5.31585978127963e-02 ), ( 1.31100423685580e-01 , 3.90900854400270e-02 , -1.25262494798617e-02 ), ( 1.11738458009229e-01 , 4.20828261715862e-02 , 6.49903348382647e-02 ), ( 7.44215102507678e-02 , 2.36027894382352e-02 , 5.08274108428097e-03 ), ( 6.07162010857553e-02 , 2.33203908347595e-02 , 3.92290332781103e-02 ), ( -1.64796713521265e-03 , -3.07204273987724e-03 , -2.21187490800692e-02 ), ( -1.59100927771452e-02 , -1.57815680205100e-02 , -9.37564347734113e-02 ), ( -5.11413081282260e-02 , -1.17578540735976e-02 , 3.50196613746180e-02 ), ( -1.21682005274002e-01 , -3.54668009988348e-02 , 1.86614180094759e-02 ), ( -1.65110072478926e-01 , -3.95953568229259e-02 , 9.89476231459412e-02 ), ( -1.08358081653477e-01 , -3.68829912496071e-02 , -2.91289612228090e-02 ), ( -1.46217540157399e-01 , -5.54518984572675e-02 , -8.83555420336157e-02 ), ( -5.24980141277098e-02 , -1.68781488453493e-02 , -5.55696233807787e-03 ), ( -3.03751562906074e-02 , -1.49877474249199e-02 , -4.82922428985002e-02 ), ( 2.87528869169160e-02 , 9.05237715686172e-03 , 1.38880574068770e-03 ), ( 2.67290144676630e-03 , -1.46345448100467e-02 , -1.33459465872841e-01 ), ( -1.56826354748457e-02 , -2.68365573891298e-02 , -1.89789678322153e-01 ), ( 5.12424070455644e-02 , -9.82089695742538e-04 , -1.45260050778780e-01 ), ( 8.16474062134026e-02 , -6.66934530635710e-04 , -2.23700511610446e-01 ), ( 1.45090396667341e-01 , 2.02462557789115e-02 , -2.12528996987919e-01 ), ( 2.00833633686362e-02 , -2.60913869136274e-02 , -2.78828527022585e-01 ), ( 2.12077334206092e-02 , -3.40687437189181e-02 , -3.50689961213515e-01 ), ( -3.56748573250362e-02 , -3.95001765829997e-02 , -2.45735608642734e-01 ), ( -9.98716562022168e-02 , -6.44336257370528e-02 , -2.89597625160121e-01 ), ( -1.39579880116700e-01 , -7.08134918227497e-02 , -2.38674087078582e-01 ), ( -1.59639329639736e-01 , -8.55011180542551e-02 , -3.11911686917638e-01 ), ( -1.88626091817599e-01 , -1.02153381409446e-01 , -3.78278020535754e-01 ), ( -2.02985561273833e-01 , -9.95167954380901e-02 , -3.17189040017282e-01 ), ( -2.46829299567918e-01 , -1.16308956872553e-01 , -3.45104849554674e-01 ), ( -1.25511433933694e-01 , -7.63904543746538e-02 , -3.24367407250947e-01 ), ( -1.80306272262975e-01 , -8.54388010075336e-02 , -2.56206956184511e-01 ), ( -2.35874895896961e-01 , -1.04318953534194e-01 , -2.70848650142971e-01 ), ( -2.73038541180380e-01 , -1.06404775091823e-01 , -1.89651456564909e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 19, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -6068,10 +9834,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 20, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 20, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 20, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 20, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 20, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 20, atoms_positions[size = 51] = { ( 8.28582291037697e+00 , 4.04506123830901e-02 , -7.54196570963580e-01 ), ( 6.93477801011369e+00 , -5.51786262542508e-01 , -5.76525850220028e-01 ), ( 6.15654135511678e+00 , -3.75844216369432e-01 , 7.29702736243887e-01 ), ( 4.95083684588076e+00 , -1.63049873260700e-01 , 7.22622667146212e-01 ), ( 7.04822840425256e+00 , -2.05125822808654e+00 , -9.33838802325873e-01 ), ( 6.86298879544170e+00 , -2.63492033772352e-01 , 1.90782093039187e+00 ), ( 6.17535476862579e+00 , -1.61467873005207e-01 , 3.19447807763223e+00 ), ( 7.08038697584318e+00 , -3.54878074422017e-01 , 4.31410976849832e+00 ), ( 5.31942679106160e+00 , 1.09501065270932e+00 , 3.35178346295725e+00 ), ( 4.15930443602701e+00 , 1.02503542539263e+00 , 3.69255428523693e+00 ), ( 5.84279477371476e+00 , 2.25334627387652e+00 , 2.99025393459074e+00 ), ( 5.23840438125392e+00 , 3.57836450753976e+00 , 2.92139319672716e+00 ), ( 6.32240747113683e+00 , 4.50111704883458e+00 , 2.36542025527039e+00 ), ( 3.88181028160009e+00 , 3.70648484501399e+00 , 2.04436620458568e+00 ), ( 2.79206714766409e+00 , 4.16082999865321e+00 , 2.48770343635868e+00 ), ( 3.93862881447229e+00 , 3.23956170779748e+00 , 7.31179710249667e-01 ), ( 2.66241903927475e+00 , 3.00625645576357e+00 , -1.03744703501063e-01 ), ( 3.05292822088169e+00 , 2.70506278162700e+00 , -1.51518325748210e+00 ), ( 1.59778880440673e+00 , 2.18316923674870e+00 , 4.45871092830035e-01 ), ( 3.79300149359787e-01 , 2.58119961872434e+00 , 5.10156322737722e-01 ), ( 2.04754425768075e+00 , 1.07062955324807e+00 , 1.06969022583418e+00 ), ( 1.16903854050100e+00 , 1.16571453589181e-01 , 1.69741818249094e+00 ), ( 2.04314486967146e+00 , -1.10332707217033e+00 , 2.01056812233467e+00 ), ( 5.62094900755023e-01 , 6.11786092234871e-01 , 2.94281295395090e+00 ), ( -6.01998257745626e-01 , 3.49689451878813e-01 , 3.16156299845539e+00 ), ( 1.31668822516108e+00 , 1.34577563521962e+00 , 3.77543109832579e+00 ), ( 8.42716504335045e-01 , 1.97881846216304e+00 , 5.02541834392960e+00 ), ( 2.07967786415177e+00 , 2.68782307153212e+00 , 5.68209741884907e+00 ), ( -3.37344843382937e-01 , 2.91471449609425e+00 , 4.96800851820805e+00 ), ( -1.13708588001649e+00 , 3.06248956541986e+00 , 5.88780199616476e+00 ), ( -5.11775330469444e-01 , 3.53529724018143e+00 , 3.84632332050881e+00 ), ( -1.51803710380555e+00 , 4.53919531397891e+00 , 3.44428420949964e+00 ), ( -6.99624398507824e-01 , 5.41439381873403e+00 , 2.46379309418166e+00 ), ( -2.76022882703025e+00 , 3.88950508193880e+00 , 2.89503343674671e+00 ), ( -3.81748583539279e+00 , 4.50991617428220e+00 , 2.81470056115434e+00 ), ( -2.62519097171536e+00 , 2.67328985787292e+00 , 2.40149432612104e+00 ), ( -3.77272853459107e+00 , 1.80371700509528e+00 , 1.99837671356181e+00 ), ( -3.38871455409835e+00 , 8.86717902389388e-01 , 8.74187404183740e-01 ), ( -4.32255998423662e+00 , 1.07002307118320e+00 , 3.21229150831233e+00 ), ( -5.49998182564857e+00 , 8.18774137488647e-01 , 3.32931951742222e+00 ), ( -3.36904919026829e+00 , 6.91596678914569e-01 , 4.20423547278276e+00 ), ( -3.70107974783840e+00 , 4.62390697929325e-02 , 5.43421582390532e+00 ), ( -2.39033524019067e+00 , -3.17074981101270e-01 , 6.17020508472989e+00 ), ( -4.46175815649799e+00 , 9.86843632633000e-01 , 6.43971260203245e+00 ), ( -5.35881205025882e+00 , 5.98149506814076e-01 , 7.21810107144495e+00 ), ( -6.23824517782367e+00 , 3.60552411038818e+00 , 6.73377298524042e+00 ), ( -6.96012228941194e+00 , 4.29779275147404e+00 , 7.47577581613682e+00 ), ( -6.74134298930255e+00 , 3.18228858940767e+00 , 5.50798663651289e+00 ), ( -4.12867862719011e+00 , 2.24624582899316e+00 , 6.40977342732153e+00 ), ( -4.80883733708504e+00 , 3.20667234951756e+00 , 7.24182070504870e+00 ), ( -4.09497949178953e+00 , 4.57553386748493e+00 , 7.28289299072206e+00 ) } +colvars: Step 20, atoms_positions[size = 51] = { ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 ), ( 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 ), ( 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 ), ( 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ), ( 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 ), ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 ), ( 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 ), ( 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 ), ( 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 ), ( 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ), ( 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 ), ( 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 ), ( 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 ), ( 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 ), ( 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 ), ( 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 ), ( 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 ), ( 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 ), ( 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 ), ( 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 ), ( 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 ), ( 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 ), ( 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 ), ( 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 ), ( -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 ), ( 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 ), ( 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 ), ( 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 ), ( -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 ), ( -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 ), ( -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 ), ( -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 ), ( -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 ), ( -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 ), ( -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 ), ( -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 ), ( -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 ), ( -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 ), ( -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 ), ( -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 ), ( -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 ), ( -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 ), ( -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 ), ( -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 ), ( -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 ), ( -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 ), ( -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 ), ( -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 ), ( -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 ), ( -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 ), ( -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) } colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_ids[size = 0] = @@ -6090,153 +9856,289 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: Colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.6088 , 1.95578 , -15.1464 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.0363 , 6.60363 , 13.2073 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.6088 , 1.95578 , -15.1464 ) to colvar "one". -colvars: Adding total bias energy: 44.4525 +colvars: Adding biasing force ( 66.0363 , 6.60363 , 13.2073 ) to colvar "one". +colvars: Adding total bias energy: 56.5387 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.6088 , 1.95578 , -15.1464 ) +colvars: Force to be applied: ( 66.0363 , 6.60363 , 13.2073 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.91515 , -0.533261 , -1.45224 ) -colvars: ( -4.21474 , -0.457271 , -1.24529 ) -colvars: ( -4.21474 , -0.457271 , -1.24529 ) -colvars: ( -5.61415 , -0.609098 , -1.65877 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17524 , -0.560146 , -1.5236 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -5.91123 , -0.639807 , -1.74028 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.892544 , 0.19549 , 0.619241 ) -colvars: ( 0.773074 , 0.266213 , 0.643516 ) -colvars: ( 0.757152 , 0.259324 , 0.625094 ) -colvars: ( 0.661335 , 0.266975 , 0.579425 ) -colvars: ( 0.649454 , 0.200472 , 0.484222 ) -colvars: ( 0.574898 , 0.344142 , 0.631501 ) -colvars: ( 0.46778 , 0.358122 , 0.587647 ) -colvars: ( 0.391169 , 0.455275 , 0.67198 ) -colvars: ( 0.386205 , 0.313656 , 0.481093 ) -colvars: ( 0.351459 , 0.272107 , 0.405694 ) -colvars: ( 0.356948 , 0.318969 , 0.471099 ) -colvars: ( 0.285831 , 0.276183 , 0.372867 ) -colvars: ( 0.258798 , 0.3052 , 0.395635 ) -colvars: ( 0.348239 , 0.178457 , 0.2795 ) -colvars: ( 0.289613 , 0.135181 , 0.187896 ) -colvars: ( 0.470901 , 0.14145 , 0.301842 ) -colvars: ( 0.543399 , 0.0501585 , 0.222894 ) -colvars: ( 0.672857 , 0.0291993 , 0.270498 ) -colvars: ( 0.551951 , 0.0183336 , 0.18563 ) -colvars: ( 0.536209 , -0.0466654 , 0.0901744 ) -colvars: ( 0.572815 , 0.0661925 , 0.261317 ) -colvars: ( 0.571276 , 0.0500177 , 0.238949 ) -colvars: ( 0.607772 , 0.114667 , 0.346033 ) -colvars: ( 0.447058 , 0.0544713 , 0.172488 ) -colvars: ( 0.440246 , -0.00142063 , 0.0943242 ) -colvars: ( 0.345197 , 0.120053 , 0.200198 ) -colvars: ( 0.220799 , 0.128616 , 0.139087 ) -colvars: ( 0.129402 , 0.214294 , 0.19957 ) -colvars: ( 0.192616 , 0.0549651 , 0.0248969 ) -colvars: ( 0.143405 , 0.018808 , -0.0517726 ) -colvars: ( 0.226186 , 0.0294603 , 0.0105991 ) -colvars: ( 0.212182 , -0.0429517 , -0.0936848 ) -colvars: ( 0.247451 , -0.0462529 , -0.0775182 ) -colvars: ( 0.287355 , -0.128824 , -0.16388 ) -colvars: ( 0.243414 , -0.181898 , -0.259935 ) -colvars: ( 0.402414 , -0.143819 , -0.116748 ) -colvars: ( 0.479789 , -0.219244 , -0.17179 ) -colvars: ( 0.610834 , -0.221812 , -0.0988481 ) -colvars: ( 0.432546 , -0.223771 , -0.205325 ) -colvars: ( 0.438072 , -0.291778 , -0.292383 ) -colvars: ( 0.383843 , -0.150562 , -0.136519 ) -colvars: ( 0.329659 , -0.144357 , -0.159851 ) -colvars: ( 0.313151 , -0.0577764 , -0.0545361 ) -colvars: ( 0.206501 , -0.15316 , -0.243293 ) -colvars: ( 0.182128 , -0.195153 , -0.313237 ) -colvars: ( 0.00545045 , -0.19885 , -0.421084 ) -colvars: ( -0.0853872 , -0.216646 , -0.497632 ) -colvars: ( 0.105698 , -0.248684 , -0.428829 ) -colvars: ( 0.124781 , -0.112578 , -0.237034 ) -colvars: ( 0.00559788 , -0.116969 , -0.312302 ) -colvars: ( -0.0832935 , -0.0363805 , -0.257115 ) +colvars: ( 0.939145 , 0.205822 , 0.650791 ) +colvars: ( 0.813493 , 0.280183 , 0.676344 ) +colvars: ( 0.79671 , 0.272971 , 0.657011 ) +colvars: ( 0.695988 , 0.280925 , 0.60896 ) +colvars: ( 0.683489 , 0.210958 , 0.508858 ) +colvars: ( 0.605096 , 0.362058 , 0.663721 ) +colvars: ( 0.492454 , 0.376702 , 0.617613 ) +colvars: ( 0.411895 , 0.478868 , 0.706292 ) +colvars: ( 0.40664 , 0.329912 , 0.505603 ) +colvars: ( 0.370107 , 0.286173 , 0.426316 ) +colvars: ( 0.375838 , 0.335525 , 0.495129 ) +colvars: ( 0.30102 , 0.290509 , 0.391871 ) +colvars: ( 0.272557 , 0.321061 , 0.415847 ) +colvars: ( 0.366646 , 0.187731 , 0.293691 ) +colvars: ( 0.304985 , 0.14218 , 0.19738 ) +colvars: ( 0.495648 , 0.148851 , 0.317164 ) +colvars: ( 0.571887 , 0.0528434 , 0.234141 ) +colvars: ( 0.70803 , 0.0308578 , 0.284183 ) +colvars: ( 0.580911 , 0.0193309 , 0.194928 ) +colvars: ( 0.564352 , -0.0490553 , 0.0945605 ) +colvars: ( 0.602884 , 0.069656 , 0.274483 ) +colvars: ( 0.601296 , 0.052603 , 0.250934 ) +colvars: ( 0.639709 , 0.120601 , 0.363501 ) +colvars: ( 0.470661 , 0.05723 , 0.181065 ) +colvars: ( 0.463505 , -0.0015853 , 0.098867 ) +colvars: ( 0.363526 , 0.126191 , 0.210227 ) +colvars: ( 0.232697 , 0.135147 , 0.145989 ) +colvars: ( 0.136568 , 0.225255 , 0.209612 ) +colvars: ( 0.203032 , 0.0576775 , 0.0259439 ) +colvars: ( 0.151284 , 0.019607 , -0.0546754 ) +colvars: ( 0.238306 , 0.0308947 , 0.0109328 ) +colvars: ( 0.223552 , -0.0452647 , -0.0986978 ) +colvars: ( 0.260612 , -0.0486848 , -0.0816732 ) +colvars: ( 0.30262 , -0.135586 , -0.17253 ) +colvars: ( 0.256401 , -0.191436 , -0.273522 ) +colvars: ( 0.423642 , -0.151329 , -0.123003 ) +colvars: ( 0.505029 , -0.230661 , -0.180906 ) +colvars: ( 0.642858 , -0.233317 , -0.104237 ) +colvars: ( 0.455372 , -0.235478 , -0.216188 ) +colvars: ( 0.461185 , -0.307026 , -0.307735 ) +colvars: ( 0.404175 , -0.158505 , -0.14385 ) +colvars: ( 0.347218 , -0.152033 , -0.168403 ) +colvars: ( 0.329883 , -0.0609799 , -0.0576822 ) +colvars: ( 0.217684 , -0.161336 , -0.256114 ) +colvars: ( 0.192064 , -0.205541 , -0.32967 ) +colvars: ( 0.00617868 , -0.209423 , -0.442974 ) +colvars: ( -0.0893621 , -0.228177 , -0.523444 ) +colvars: ( 0.111592 , -0.261789 , -0.451119 ) +colvars: ( 0.131717 , -0.118651 , -0.249498 ) +colvars: ( 0.00636188 , -0.12331 , -0.328614 ) +colvars: ( -0.0871363 , -0.0385503 , -0.270558 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.91515 , 0.533261 , 1.45224 ) -colvars: ( 4.21474 , 0.457271 , 1.24529 ) -colvars: ( 4.21474 , 0.457271 , 1.24529 ) -colvars: ( 5.61415 , 0.609098 , 1.65877 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17524 , 0.560146 , 1.5236 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 5.91123 , 0.639807 , 1.74028 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.615911 , -0.0809403 , -0.370289 ) -colvars: ( -0.553936 , -0.163279 , -0.339783 ) -colvars: ( -0.504483 , -0.14143 , -0.281796 ) -colvars: ( -0.514701 , -0.190631 , -0.31095 ) -colvars: ( -0.505106 , -0.132058 , -0.278819 ) -colvars: ( -0.489899 , -0.282191 , -0.321263 ) -colvars: ( -0.457119 , -0.322318 , -0.303811 ) -colvars: ( -0.435381 , -0.42909 , -0.323043 ) -colvars: ( -0.394403 , -0.287171 , -0.227415 ) -colvars: ( -0.389791 , -0.261989 , -0.213114 ) -colvars: ( -0.345387 , -0.281611 , -0.176126 ) -colvars: ( -0.285203 , -0.244949 , -0.101686 ) -colvars: ( -0.23688 , -0.259846 , -0.058954 ) -colvars: ( -0.30471 , -0.142288 , -0.0817978 ) -colvars: ( -0.273523 , -0.113172 , -0.0393358 ) -colvars: ( -0.359032 , -0.0851872 , -0.114328 ) -colvars: ( -0.385698 , 0.0125647 , -0.103504 ) -colvars: ( -0.43592 , 0.0599408 , -0.135661 ) -colvars: ( -0.423002 , 0.0275581 , -0.13515 ) -colvars: ( -0.411661 , 0.0840489 , -0.10207 ) -colvars: ( -0.466795 , -0.0261598 , -0.199708 ) -colvars: ( -0.500798 , -0.0275661 , -0.234345 ) -colvars: ( -0.55043 , -0.0926022 , -0.309107 ) -colvars: ( -0.448784 , -0.057432 , -0.193664 ) -colvars: ( -0.455539 , -0.013552 , -0.183575 ) -colvars: ( -0.393864 , -0.131394 , -0.167013 ) -colvars: ( -0.336404 , -0.16255 , -0.121366 ) -colvars: ( -0.286194 , -0.252303 , -0.105507 ) -colvars: ( -0.295464 , -0.0901165 , -0.0524782 ) -colvars: ( -0.282212 , -0.0715846 , -0.032067 ) -colvars: ( -0.275892 , -0.045508 , -0.0157091 ) -colvars: ( -0.240779 , 0.0288343 , 0.048069 ) -colvars: ( -0.219798 , 0.0550453 , 0.0791805 ) -colvars: ( -0.284619 , 0.115186 , 0.0372899 ) -colvars: ( -0.258068 , 0.156731 , 0.0798802 ) -colvars: ( -0.35365 , 0.143204 , -0.0211658 ) -colvars: ( -0.402215 , 0.219052 , -0.0407192 ) -colvars: ( -0.473097 , 0.241538 , -0.103157 ) -colvars: ( -0.413517 , 0.199366 , -0.0596175 ) -colvars: ( -0.417976 , 0.25989 , -0.0408311 ) -colvars: ( -0.417832 , 0.113257 , -0.0970347 ) -colvars: ( -0.424688 , 0.0832879 , -0.115426 ) -colvars: ( -0.445978 , -0.00952294 , -0.17244 ) -colvars: ( -0.358207 , 0.0720446 , -0.0530801 ) -colvars: ( -0.361391 , 0.0982463 , -0.0462049 ) -colvars: ( -0.198027 , 0.104482 , 0.120009 ) -colvars: ( -0.148764 , 0.106318 , 0.170115 ) -colvars: ( -0.224679 , 0.176429 , 0.120931 ) -colvars: ( -0.296008 , 0.0314599 , -0.00630443 ) -colvars: ( -0.229511 , 0.0178807 , 0.0551591 ) -colvars: ( -0.175844 , -0.0648266 , 0.0771928 ) +colvars: ( -0.647974 , -0.0852573 , -0.388753 ) +colvars: ( -0.582839 , -0.171838 , -0.35665 ) +colvars: ( -0.530769 , -0.148883 , -0.295681 ) +colvars: ( -0.541646 , -0.200563 , -0.326377 ) +colvars: ( -0.531553 , -0.138947 , -0.29266 ) +colvars: ( -0.515626 , -0.296838 , -0.337183 ) +colvars: ( -0.481227 , -0.338999 , -0.318864 ) +colvars: ( -0.458422 , -0.451281 , -0.339024 ) +colvars: ( -0.415265 , -0.302019 , -0.238601 ) +colvars: ( -0.41045 , -0.275508 , -0.22362 ) +colvars: ( -0.363672 , -0.296189 , -0.184669 ) +colvars: ( -0.300365 , -0.257621 , -0.106457 ) +colvars: ( -0.2495 , -0.273312 , -0.0614974 ) +colvars: ( -0.320837 , -0.149656 , -0.0856129 ) +colvars: ( -0.288058 , -0.119011 , -0.0410273 ) +colvars: ( -0.377907 , -0.0896324 , -0.119807 ) +colvars: ( -0.405907 , 0.0131673 , -0.108485 ) +colvars: ( -0.458652 , 0.0629527 , -0.142267 ) +colvars: ( -0.445189 , 0.028964 , -0.141797 ) +colvars: ( -0.433263 , 0.0883914 , -0.107081 ) +colvars: ( -0.491292 , -0.0275236 , -0.209633 ) +colvars: ( -0.527109 , -0.028974 , -0.246079 ) +colvars: ( -0.579343 , -0.0973742 , -0.324623 ) +colvars: ( -0.472472 , -0.0603448 , -0.203347 ) +colvars: ( -0.479594 , -0.0141749 , -0.192798 ) +colvars: ( -0.414746 , -0.138121 , -0.175297 ) +colvars: ( -0.354373 , -0.170853 , -0.127338 ) +colvars: ( -0.301597 , -0.265244 , -0.110611 ) +colvars: ( -0.311285 , -0.09467 , -0.0549772 ) +colvars: ( -0.297384 , -0.0751509 , -0.0335708 ) +colvars: ( -0.290629 , -0.0477842 , -0.0163181 ) +colvars: ( -0.253661 , 0.0304013 , 0.050676 ) +colvars: ( -0.23152 , 0.0579314 , 0.0834089 ) +colvars: ( -0.299747 , 0.121221 , 0.039285 ) +colvars: ( -0.271833 , 0.164934 , 0.084002 ) +colvars: ( -0.37232 , 0.150668 , -0.022156 ) +colvars: ( -0.42338 , 0.230441 , -0.0427631 ) +colvars: ( -0.497883 , 0.254059 , -0.108372 ) +colvars: ( -0.435341 , 0.209775 , -0.062665 ) +colvars: ( -0.440031 , 0.273443 , -0.0429754 ) +colvars: ( -0.439945 , 0.119231 , -0.101963 ) +colvars: ( -0.447231 , 0.0877498 , -0.121324 ) +colvars: ( -0.469676 , -0.00985306 , -0.181203 ) +colvars: ( -0.377354 , 0.0759564 , -0.0558201 ) +colvars: ( -0.380737 , 0.103539 , -0.0486444 ) +colvars: ( -0.208877 , 0.110092 , 0.126079 ) +colvars: ( -0.157097 , 0.112049 , 0.178715 ) +colvars: ( -0.23683 , 0.185727 , 0.127043 ) +colvars: ( -0.311938 , 0.0332713 , -0.00662132 ) +colvars: ( -0.242039 , 0.0190178 , 0.0579609 ) +colvars: ( -0.185619 , -0.0679661 , 0.0811767 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 20. colvars: colvarmodule::write_traj_files() @@ -6247,8 +10149,11 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 20. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 20, atoms_new_colvar_forces = { ( -4.63851454459905e+00 , -4.18710833064850e-01 , -1.20328608426652e+00 ), ( -3.99559989640659e+00 , -3.54336474175720e-01 , -9.41559888235754e-01 ), ( -4.06810357739189e+00 , -3.80926713958037e-01 , -9.76817699772113e-01 ), ( -5.46980368326514e+00 , -5.40683985020084e-01 , -1.45336332622448e+00 ), ( 2.52668502795200e-01 , 1.17894094436429e-01 , 3.43297404486922e-01 ), ( 5.00014590643842e+00 , 5.95211961482009e-01 , 1.76247508244524e+00 ), ( 4.22539890920215e+00 , 4.93075099844339e-01 , 1.52912952520700e+00 ), ( -4.42117205218343e-02 , 2.61849910581687e-02 , 3.48936847549760e-01 ), ( 4.20654020656410e+00 , 4.83756625787825e-01 , 1.49897132736399e+00 ), ( 5.57582044888118e+00 , 6.19216324851961e-01 , 1.85134641932113e+00 ), ( 1.15606722969959e-02 , 3.73582371308533e-02 , 2.94972551667663e-01 ), ( 6.27937109112076e-04 , 3.12340160260255e-02 , 2.71180143655928e-01 ), ( 2.19173365638969e-02 , 4.53538862226682e-02 , 3.36681036424671e-01 ), ( 4.35287412741041e-02 , 3.61696681282234e-02 , 1.97702509024789e-01 ), ( 1.60900816481230e-02 , 2.20091820921404e-02 , 1.48559775115973e-01 ), ( 1.11869449595165e-01 , 5.62631531725342e-02 , 1.87513672922987e-01 ), ( 1.57700920362817e-01 , 6.27232419132576e-02 , 1.19389577713856e-01 ), ( 2.36936463271923e-01 , 8.91401887092676e-02 , 1.34836894262539e-01 ), ( 1.28948776005967e-01 , 4.58916180710906e-02 , 5.04794295830226e-02 ), ( 1.24548587393342e-01 , 3.73834994690693e-02 , -1.18954687815839e-02 ), ( 1.06019698806145e-01 , 4.00326507775761e-02 , 6.16092423921068e-02 ), ( 7.04782471949013e-02 , 2.24515586964271e-02 , 4.60369604053695e-03 ), ( 5.73422381960390e-02 , 2.20646170469042e-02 , 3.69252747449674e-02 ), ( -1.72611395560524e-03 , -2.96077010773500e-03 , -2.11764063442688e-02 ), ( -1.52922851265740e-02 , -1.49726615376669e-02 , -8.92510974662055e-02 ), ( -4.86671260953066e-02 , -1.13413226333090e-02 , 3.31845028045236e-02 ), ( -1.15605077666369e-01 , -3.39346522378186e-02 , 1.77200417262677e-02 ), ( -1.56792026456609e-01 , -3.80091057503520e-02 , 9.40637658323593e-02 ), ( -1.02848641736711e-01 , -3.51514140984507e-02 , -2.75812107087965e-02 ), ( -1.38806884416938e-01 , -5.27766427227216e-02 , -8.38395789565467e-02 ), ( -4.97061267723764e-02 , -1.60476509528009e-02 , -5.11007628540459e-03 ), ( -2.85976059219338e-02 , -1.41173315546320e-02 , -4.56158111816652e-02 ), ( 2.76522679529432e-02 , 8.79242656069489e-03 , 1.66225761229807e-03 ), ( 2.73532411285460e-03 , -1.36382491455301e-02 , -1.26589601375052e-01 ), ( -1.46538330736033e-02 , -2.51672766893284e-02 , -1.80055129011821e-01 ), ( 4.87645210478707e-02 , -6.15426656884632e-04 , -1.37913496336073e-01 ), ( 7.75743232463488e-02 , -1.91225606735068e-04 , -2.12509192428131e-01 ), ( 1.37737148977943e-01 , 1.97267169501107e-02 , -2.02005130353156e-01 ), ( 1.90294174661668e-02 , -2.44049904625063e-02 , -2.64942523670217e-01 ), ( 2.00953061744231e-02 , -3.18876654614701e-02 , -3.33214475874042e-01 ), ( -3.39893131361256e-02 , -3.73055310094134e-02 , -2.33553485918890e-01 ), ( -9.50287381727212e-02 , -6.10695052311506e-02 , -2.75277236233374e-01 ), ( -1.32826616258851e-01 , -6.72993193787387e-02 , -2.26975689078502e-01 ), ( -1.51705844975594e-01 , -8.11153781239003e-02 , -2.96372806931386e-01 ), ( -1.79263034470665e-01 , -9.69067785137090e-02 , -3.59442438261914e-01 ), ( -1.92577034615937e-01 , -9.43678359874191e-02 , -3.01074097881565e-01 ), ( -2.34151572355940e-01 , -1.10327571437585e-01 , -3.27516835071365e-01 ), ( -1.18981164358574e-01 , -7.22543491267554e-02 , -3.07897440415716e-01 ), ( -1.71227554375326e-01 , -8.11181099169558e-02 , -2.43338813862098e-01 ), ( -2.23913463549683e-01 , -9.90878668961794e-02 , -2.57143314677739e-01 ), ( -2.59137952902184e-01 , -1.01207120969136e-01 , -1.79922622294137e-01 ) } +colvars: Step 20, atoms_new_colvar_forces = { ( -4.88406726017846e+00 , -4.39582030019637e-01 , -1.26156546289831e+00 ), ( -4.20711207586693e+00 , -3.71980090924366e-01 , -9.86796367004215e-01 ), ( -4.28342445948863e+00 , -3.99963693514908e-01 , -1.02390709400074e+00 ), ( -5.75929727923110e+00 , -5.67796041518724e-01 , -1.52408480248038e+00 ), ( 2.65941268390902e-01 , 1.24088041235363e-01 , 3.61330101161847e-01 ), ( 5.26470856148017e+00 , 6.25365994053560e-01 , 1.85014148432867e+00 ), ( 4.44899395969789e+00 , 5.18028786716414e-01 , 1.60523898998076e+00 ), ( -4.65272910606424e-02 , 2.75874394655633e-02 , 3.67268098303653e-01 ), ( 4.42914052995064e+00 , 5.08218685700347e-01 , 1.57349215273307e+00 ), ( 5.87089063969169e+00 , 6.50472344458009e-01 , 1.94297816123059e+00 ), ( 1.21655890342579e-02 , 3.93361229409889e-02 , 3.10460529518665e-01 ), ( 6.54352727631202e-04 , 3.28877838588784e-02 , 2.85413778669853e-01 ), ( 2.30575218111934e-02 , 4.77496012635013e-02 , 3.54349709040753e-01 ), ( 4.58084561993378e-02 , 3.80749776841854e-02 , 2.08077917584342e-01 ), ( 1.69271357430614e-02 , 2.31692671284452e-02 , 1.56352523085799e-01 ), ( 1.17740497737709e-01 , 5.92187670987907e-02 , 1.97356769209817e-01 ), ( 1.65979650547149e-01 , 6.60107587124940e-02 , 1.25656124587784e-01 ), ( 2.49378084035319e-01 , 9.38105312411004e-02 , 1.41916759655613e-01 ), ( 1.35721171926268e-01 , 4.82948683031030e-02 , 5.31311614239589e-02 ), ( 1.31089117563867e-01 , 3.93361615661934e-02 , -1.25202269468064e-02 ), ( 1.11591946272047e-01 , 4.21324308431365e-02 , 6.48498773882783e-02 ), ( 7.41875459869102e-02 , 2.36289347234540e-02 , 4.85459631934207e-03 ), ( 6.03658790245055e-02 , 2.32264957257031e-02 , 3.88781977774767e-02 ), ( -1.81078736534573e-03 , -3.11478153248525e-03 , -2.22818060419844e-02 ), ( -1.60885473686671e-02 , -1.57601748864797e-02 , -9.39304968271742e-02 ), ( -5.12199048641456e-02 , -1.19297840935810e-02 , 3.49304717831433e-02 ), ( -1.21675813902335e-01 , -3.57064899870657e-02 , 1.86508224653453e-02 ), ( -1.65028468419942e-01 , -3.99882775272279e-02 , 9.90005933951236e-02 ), ( -1.08252979508245e-01 , -3.69924344963437e-02 , -2.90333247285238e-02 ), ( -1.46099690198963e-01 , -5.55439012742997e-02 , -8.82462486637547e-02 ), ( -5.23225535297807e-02 , -1.68894940154288e-02 , -5.38529268697861e-03 ), ( -3.01087883421307e-02 , -1.48633476968855e-02 , -4.80218171751865e-02 ), ( 2.90920024039188e-02 , 9.24664271438187e-03 , 1.73568422449372e-03 ), ( 2.87212446123969e-03 , -1.43653564917826e-02 , -1.33245075124415e-01 ), ( -1.54318476939863e-02 , -2.65024240836628e-02 , -1.89520159508813e-01 ), ( 5.13226740441255e-02 , -6.61117676194450e-04 , -1.45158995615856e-01 ), ( 8.16483892005009e-02 , -2.20115925109621e-04 , -2.23668733880816e-01 ), ( 1.44974583626733e-01 , 2.07414644297433e-02 , -2.12608633585807e-01 ), ( 2.00313536000674e-02 , -2.57030285264907e-02 , -2.78852997194507e-01 ), ( 2.11535019058627e-02 , -3.35827543487625e-02 , -3.50709917556565e-01 ), ( -3.57699416572513e-02 , -3.92742347993370e-02 , -2.45813691592460e-01 ), ( -1.00012769612954e-01 , -6.42830113991747e-02 , -2.89726269929375e-01 ), ( -1.39792965314805e-01 , -7.08329385419267e-02 , -2.38885255145827e-01 ), ( -1.59669948187276e-01 , -8.53800481419532e-02 , -3.11933814118016e-01 ), ( -1.88673377030574e-01 , -1.02001994075380e-01 , -3.78314516895504e-01 ), ( -2.02698784283931e-01 , -9.93305031383851e-02 , -3.16894644449761e-01 ), ( -2.46459346918119e-01 , -1.16127914776370e-01 , -3.44729104647447e-01 ), ( -1.25237872776220e-01 , -7.60618339454901e-02 , -3.24076090847715e-01 ), ( -1.80221106740230e-01 , -8.53800525072640e-02 , -2.56119533999097e-01 ), ( -2.35677590614575e-01 , -1.04291860665546e-01 , -2.70653229134327e-01 ), ( -2.72755086907763e-01 , -1.06516369333094e-01 , -1.89380901188017e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped index 39c658b7f..37633c6e6 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,22 @@ configuration { colvar { name one - x ( -0.3045417105333 , -0.00019915241487762 , 0.95249897999093 ) + x ( -0.30360404081666 , -7.3012941347679e-05 , 0.95279828981212 ) +} + +colvar { + name group1 + x ( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 ) +} + +colvar { + name group2 + x ( 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 ) +} + +colvar { + name fitting_group1 + x ( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 7.0480762025172 , -2.0513347736704 , -0.93377134820149 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 , 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 7.0809081020816 , -0.35496020632887 , 4.3146586251214 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 , 5.8432995748295 , 2.2535778944039 , 2.9902963417856 , 5.2384055225152 , 3.5783754026257 , 2.9215354050906 , 6.3223993673226 , 4.5011441587991 , 2.3655584831763 , 3.8818312912342 , 3.7064721784147 , 2.0444644100133 , 2.7920736373314 , 4.1608362314759 , 2.4877638737485 , 3.9386798899873 , 3.2395859717867 , 0.73126389979658 , 2.6624894551197 , 3.0062849992536 , -0.10369017207615 , 3.0530237576774 , 2.7050981729996 , -1.515126439405 , 1.5978477264343 , 2.1831908534433 , 0.4458975934194 , 0.37935536668417 , 2.5812137098021 , 0.51015292695301 , 2.0475904030464 , 1.0706502363152 , 1.069723927279 , 1.1690699177228 , 0.11658295312925 , 1.6974226380185 , 2.0431803877623 , -1.1033045581944 , 2.0106005316873 , 0.56210382605836 , 0.61178504571473 , 2.9428051810465 , -0.60199958586972 , 0.34968520789238 , 3.1615301713297 , 1.3167209916681 , 1.3457617287353 , 3.7754423945574 , 0.84267356054463 , 1.9787990415851 , 5.0254234233262 , 2.0796156959584 , 2.6878063101542 , 5.6821293955537 , -0.33739104868865 , 2.9146961524331 , 4.9679941584516 , -1.1371464701093 , 3.062469534534 , 5.8877740932039 , -0.51179726121506 , 3.5352900024754 , 3.8463150986082 , -1.5180503491383 , 4.5391900691402 , 3.4442608843563 , -0.69961559166787 , 5.4143954882994 , 2.4637912416459 , -2.7602287545827 , 3.8895007500064 , 2.8949751960402 , -3.8174896819283 , 4.5099047856922 , 2.8146284855071 , -2.6251714284554 , 2.6732886369457 , 2.4014323234568 , -3.7726963733907 , 1.8037184430191 , 1.9982779981764 , -3.3886595184775 , 0.88672154595831 , 0.87409788378727 , -4.3225504216986 , 1.0700082818202 , 3.2121699488068 , -5.4999729212229 , 0.81876098547252 , 3.3291853384002 , -3.3690633481624 , 0.69157744271515 , 4.2041288719456 , -3.7011250996533 , 0.046206366217123 , 5.434092539774 , -2.3903901778542 , -0.31709933730245 , 6.1701094743001 , -4.4618292827148 , 0.98680918149928 , 6.4395743693712 , -5.3588837067265 , 0.5981100423375 , 7.2179576344598 , -6.2383325096938 , 3.6054824579338 , 6.7336443061013 , -6.9602157879944 , 4.2977470185681 , 7.4756432850253 , -6.741403987979 , 3.1822575304318 , 5.5078493030856 , -4.1287524553974 , 2.2462119095443 , 6.4096637239512 , -4.8089365560512 , 3.2066271871716 , 7.2417022510827 , -4.0950888618816 , 4.5754896432564 , 7.2828123626203 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj index e14fbd39b..0269cb435 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 0 ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ) ( 2.63141320070998e+01 , 1.79666571613238e+00 , -1.49056671814885e+01 ) - 1 ( -3.39359239792396e-01 , 6.97253156444326e-03 , 9.40631006384071e-01 ) ( 2.63051862548186e+01 , 1.81234951460820e+00 , -1.49090198358873e+01 ) - 2 ( -3.38680441300733e-01 , 6.30491679893380e-03 , 9.40880336017551e-01 ) ( 2.62916102849853e+01 , 1.82570180991839e+00 , -1.49140064285569e+01 ) - 3 ( -3.37759603496395e-01 , 5.75914840711148e-03 , 9.41214790818537e-01 ) ( 2.62731935288986e+01 , 1.83661717775484e+00 , -1.49206955245766e+01 ) - 4 ( -3.36592560477046e-01 , 5.33466425476265e-03 , 9.41635274184647e-01 ) ( 2.62498526685116e+01 , 1.84510686080181e+00 , -1.49291051918988e+01 ) - 5 ( -3.35182699996778e-01 , 5.02452781962055e-03 , 9.42139751705160e-01 ) ( 2.62216554589062e+01 , 1.85130958950466e+00 , -1.49391947423091e+01 ) - 6 ( -3.33541437426750e-01 , 4.81523415673580e-03 , 9.42723142306008e-01 ) ( 2.61888302075057e+01 , 1.85549546276235e+00 , -1.49508625543260e+01 ) - 7 ( -3.31688046920632e-01 , 4.68707413595258e-03 , 9.43377480580293e-01 ) ( 2.61517623973833e+01 , 1.85805866317801e+00 , -1.49639493198117e+01 ) - 8 ( -3.29649003636170e-01 , 4.61519105247550e-03 , 9.44092280666053e-01 ) ( 2.61109815316941e+01 , 1.85949632484756e+00 , -1.49782453215269e+01 ) - 9 ( -3.27457007407554e-01 , 4.57131359996204e-03 , 9.44855021361299e-01 ) ( 2.60671416071217e+01 , 1.86037387389783e+00 , -1.49935001354318e+01 ) - 10 ( -3.25149814022648e-01 , 4.52596031009924e-03 , 9.45651687527870e-01 ) ( 2.60209977394236e+01 , 1.86128093969508e+00 , -1.50094334587633e+01 ) - 11 ( -3.22768924320888e-01 , 4.45076971931406e-03 , 9.46467332844427e-01 ) ( 2.59733799453884e+01 , 1.86278475151079e+00 , -1.50257463650944e+01 ) - 12 ( -3.20358118183599e-01 , 4.32056543368708e-03 , 9.47286656101624e-01 ) ( 2.59251638226427e+01 , 1.86538883722332e+00 , -1.50421328302383e+01 ) - 13 ( -3.17961771860725e-01 , 4.11480979755661e-03 , 9.48094604971212e-01 ) ( 2.58772368961852e+01 , 1.86950394994593e+00 , -1.50582918076301e+01 ) - 14 ( -3.15622953688594e-01 , 3.81824775894985e-03 , 9.48877005775216e-01 ) ( 2.58304605327425e+01 , 1.87543519071807e+00 , -1.50739398237102e+01 ) - 15 ( -3.13381355030095e-01 , 3.42072155991049e-03 , 9.49621200786667e-01 ) ( 2.57856285595726e+01 , 1.88338571469886e+00 , -1.50888237239392e+01 ) - 16 ( -3.11271197951965e-01 , 2.91633047576440e-03 , 9.50316650565539e-01 ) ( 2.57434254180100e+01 , 1.89347353638178e+00 , -1.51027327195166e+01 ) - 17 ( -3.09319308134653e-01 , 2.30226602992589e-03 , 9.50955448581177e-01 ) ( 2.57043876216637e+01 , 1.90575482529855e+00 , -1.51155086798294e+01 ) - 18 ( -3.07543552262695e-01 , 1.57772719634005e-03 , 9.51532697409047e-01 ) ( 2.56688725042246e+01 , 1.92024560197027e+00 , -1.51270536563868e+01 ) - 19 ( -3.05951823016640e-01 , 7.43277606547324e-04 , 9.52046705540854e-01 ) ( 2.56370379193035e+01 , 1.93693459376612e+00 , -1.51373338190230e+01 ) - 20 ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ) ( 2.56088356696367e+01 , 1.95578319419462e+00 , -1.51463793080245e+01 ) +# step one fa_one group1 group2 fitting_group1 E_harmonic1 + 0 ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ) ( 6.78285239239432e+01 , 6.78285239239432e+00 , 1.35657047847886e+01 ) ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ) ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ) ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) 5.90741150968082e+01 + 1 ( -3.39355617493064e-01 , 6.97292683121385e-03 , 9.40632310293086e-01 ) ( 6.78086594552381e+01 , 6.78086594552381e+00 , 1.35617318910476e+01 ) ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ) ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ) ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 , 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 , 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 , 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 , 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 , 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 , 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 , 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 , 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 , 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 , 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 , 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 , 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 , 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 , 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 , 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 , -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 , 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 , 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 , 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 , -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 , -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 , -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 , -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 , -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 , -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 , -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 , -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 , -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 , -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 , -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 , -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 , -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 , -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 , -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 , -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 , -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 , -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 , -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 , -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 , -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 , -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 , -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ) 5.90465591981215e+01 + 2 ( -3.38665979440331e-01 , 6.30649599530219e-03 , 9.40885531017447e-01 ) ( 6.77757577292584e+01 , 6.77757577292585e+00 , 1.35551515458517e+01 ) ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ) ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ) ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 , 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 , 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 , 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 , 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 , 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 , 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 , 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 , 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 , 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 , 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 , 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 , 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 , 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 , 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 , 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 , -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 , 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 , 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 , 2.07182033199839e+00 , 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2.42783652284936e+00 , -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 , -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 , -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 , -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 , -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 , -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 , -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 , -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 , -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 , -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 , -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 , -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 , -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 , -6.91604181506208e+00 , 4.29488461026496e+00 , 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7.44097322494073e+00 , -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 , -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 , -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 , -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ) 5.74906283550309e+01 + 14 ( -3.15064599275101e-01 , 3.88700842418579e-03 , 9.49062268478276e-01 ) ( 6.65823348264236e+01 , 6.65823348264236e+00 , 1.33164669652847e+01 ) ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ) ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 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2.46173889125928e+00 , -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 , -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 , -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 , -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 , -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 , -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 , -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 , -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 , -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 , -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 , -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 , -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 , -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 , -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 , -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 , -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 , -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 , -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ) 5.66360741304630e+01 + 20 ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ) ( 6.60362557644092e+01 , 6.60362557644092e+00 , 1.32072511528818e+01 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ) ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) 5.65386573831414e+01 diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out index ddc57f269..d647ffabf 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out @@ -5,6 +5,7 @@ colvars: as well as all other papers listed below for individual features used. colvars: This version was built with the C++11 standard or higher. colvars: Summary of compile-time features available in this build: colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Multiple replicas: enabled (replica number 1 of 1) colvars: - Lepton custom functions: available colvars: - Tcl interpreter: available colvars: Called colvarcript::init_commands() @@ -755,6 +756,7 @@ colvars: name one colvars: outputAppliedForce on colvars: width 0.5 colvars: distanceDir { +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -816,6 +818,7 @@ colvars: Looking for the keyword "distance" and its value. colvars: Keyword "distance" not found. colvars: Looking for the keyword "distanceDir" and its value. colvars: Keyword value = " +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -837,6 +840,7 @@ colvars: } colvars: ". colvars: Initializing a new "distanceDir" component, with configuration: colvars: +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -893,8 +897,10 @@ colvars: Keyword "forceNoPBC" not found. colvars: # forceNoPBC = off [default] colvars: DEPS: unnamed cvc of type "distanceDir" enabling "use_minimum-image_with_PBCs" colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword value = "off". +colvars: Looking for the keyword "scalable" and its value. colvars: Keyword "scalable" not found. -colvars: # scalable = on [default] +colvars: # scalable = off colvars: Done initializing cvc base object. colvars: Looking for the keyword "group1" and its value. colvars: Keyword value = " @@ -906,17 +912,6 @@ colvars: indexGroup heavy_atoms colvars: } colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: ". -colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" -colvars: scalable_calculation_of_centers_of_mass requires exclude explicit_gradient -colvars: scalable_calculation_of_centers_of_mass requires self scalable_calculation -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation" -colvars: scalable_calculation requires exclude explicit_gradient -colvars: DEPS: feature "scalable_calculation" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. -colvars: scalable_calculation_of_centers_of_mass requires self function_of_centers_of_mass -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "function_of_centers_of_mass" -colvars: DEPS: bumping ref_count to 1 -colvars: DEPS: feature "scalable_calculation_of_centers_of_mass" in unnamed cvc of type "distanceDir" enabled, ref_count = 1. colvars: Initializing atom group "group1". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. @@ -1137,8 +1132,6 @@ colvars: indexGroup heavy_atoms colvars: } colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: ". -colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "distanceDir" -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "scalable_calculation_of_centers_of_mass" colvars: Initializing atom group "group2". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. @@ -1209,18 +1202,1033 @@ colvars: # centerToOrigin = off [default] colvars: DEPS: disabling feature "center_to_origin" in atom group fittingGroup colvars: Looking for the keyword "centerReference" and its value. colvars: Keyword "centerReference" not found. -colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "fittingGroup". +colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: Configuration string for "fittingGroup": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: DEPS: atom group group2 enabling "fitting_group" +colvars: DEPS: feature "fitting_group" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "refPositions" and its value. +colvars: Keyword "refPositions" not found. +colvars: # refPositions = [default] +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword value = "heavy_atoms_refpos.xyz". +colvars: Looking for the keyword "refPositionsFile" and its value. +colvars: Keyword "refPositionsFile" not found. +colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" +colvars: Looking for the keyword "refPositionsCol" and its value. +colvars: Keyword "refPositionsCol" not found. +colvars: # refPositionsCol = "" [default] +colvars: Warning: atom group "group2" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: DEPS: atom group group2 enabling "fit_gradients" +colvars: fit_gradients requires self explicit_atom_gradient +colvars: DEPS: atom group group2 enabling "explicit_atom_gradient" +colvars: DEPS: feature "explicit_atom_gradient" in atom group group2 enabled, ref_count = 1. +colvars: DEPS: feature "fit_gradients" in atom group group2 enabled, ref_count = 1. +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "group2". +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" +colvars: Configuration string for "group2": " +colvars: +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: ". +colvars: Looking for the keyword "oneSiteSystemForce" and its value. +colvars: Keyword "oneSiteSystemForce" not found. +colvars: # oneSiteSystemForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Looking for the keyword "oneSiteTotalForce" and its value. +colvars: Keyword "oneSiteTotalForce" not found. +colvars: # oneSiteTotalForce = off [default] +colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" +colvars: Configuration string for "distanceDir": " +colvars: +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group1 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group1" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group1 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group1 +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group1 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group1 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group1 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group1 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group1 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group1 +colvars: DEPS: colvar group1 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group1 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group1 testing "linear" +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group1". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group2" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group2 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group2" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group2 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group2 +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: feature "linear" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group2 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group2 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group2 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group2 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group2 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group2 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group2 +colvars: DEPS: colvar group2 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group2 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group2 testing "linear" +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group2". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting_group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms colvars: Looking for the keyword "centerToReference" and its value. colvars: Keyword "centerToReference" not found. colvars: # centerToReference = off [default] -colvars: DEPS: disabling feature "center_to_reference" in atom group fittingGroup +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms colvars: Looking for the keyword "rotateReference" and its value. colvars: Keyword "rotateReference" not found. -colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms colvars: Looking for the keyword "rotateToReference" and its value. colvars: Keyword "rotateToReference" not found. colvars: # rotateToReference = off [default] -colvars: DEPS: disabling feature "rotate_to_origin" in atom group fittingGroup +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms colvars: Looking for the keyword "atomsOfGroup" and its value. colvars: Keyword "atomsOfGroup" not found. colvars: # atomsOfGroup = "" [default] @@ -1252,81 +2260,47 @@ colvars: # enableFitGradients = on [default] colvars: Looking for the keyword "printAtomIDs" and its value. colvars: Keyword "printAtomIDs" not found. colvars: # printAtomIDs = off [default] -colvars: Done initializing atom group "fittingGroup". -colvars: Atom group "fittingGroup" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. -colvars: Configuration string for "fittingGroup": " -colvars: -colvars: indexGroup heavy_atoms -colvars: ". -colvars: DEPS: atom group group2 enabling "fitting_group" -colvars: DEPS: feature "fitting_group" in atom group group2 enabled, ref_count = 1. -colvars: Looking for the keyword "refPositions" and its value. -colvars: Keyword "refPositions" not found. -colvars: # refPositions = [default] -colvars: Looking for the keyword "refPositionsFile" and its value. -colvars: Keyword value = "heavy_atoms_refpos.xyz". -colvars: Looking for the keyword "refPositionsFile" and its value. -colvars: Keyword "refPositionsFile" not found. -colvars: # refPositionsFile = "heavy_atoms_refpos.xyz" -colvars: Looking for the keyword "refPositionsCol" and its value. -colvars: Keyword "refPositionsCol" not found. -colvars: # refPositionsCol = "" [default] -colvars: Warning: atom group "group2" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use fittingGroup (or a different definition for it if already defined) to align the coordinates. -colvars: Looking for the keyword "enableFitGradients" and its value. -colvars: Keyword "enableFitGradients" not found. -colvars: # enableFitGradients = on [default] -colvars: DEPS: atom group group2 enabling "fit_gradients" -colvars: fit_gradients requires self explicit_atom_gradient -colvars: DEPS: atom group group2 enabling "explicit_atom_gradient" -colvars: DEPS: feature "explicit_atom_gradient" in atom group group2 enabled, ref_count = 1. -colvars: DEPS: feature "fit_gradients" in atom group group2 enabled, ref_count = 1. -colvars: Looking for the keyword "printAtomIDs" and its value. -colvars: Keyword "printAtomIDs" not found. -colvars: # printAtomIDs = off [default] -colvars: Done initializing atom group "group2". -colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. -colvars: DEPS: unnamed cvc of type "distanceDir" enabling "explicit_atom_groups" -colvars: Configuration string for "group2": " +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " colvars: -colvars: indexGroup group2 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: indexGroup heavy_atoms colvars: ". -colvars: Looking for the keyword "oneSiteSystemForce" and its value. -colvars: Keyword "oneSiteSystemForce" not found. -colvars: # oneSiteSystemForce = off [default] -colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" -colvars: Looking for the keyword "oneSiteTotalForce" and its value. -colvars: Keyword "oneSiteTotalForce" not found. -colvars: # oneSiteTotalForce = off [default] -colvars: DEPS: disabling feature "total_force_from_one_group" in unnamed cvc of type "distanceDir" -colvars: Configuration string for "distanceDir": " -colvars: -colvars: group1 { -colvars: indexGroup group1 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz -colvars: } -colvars: group2 { -colvars: indexGroup group2 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms colvars: } colvars: ". -colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Done initializing a "cartesian" component, named "cartesian0001". colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. colvars: Looking for the keyword "distanceDir" and its value. colvars: Keyword "distanceDir" not found. colvars: Looking for the keyword "distanceInv" and its value. @@ -1394,42 +2368,40 @@ colvars: Looking for the keyword "customFunction" and its value. colvars: Keyword "customFunction" not found. colvars: Looking for the keyword "scriptedFunction" and its value. colvars: Keyword "scriptedFunction" not found. -colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. -colvars: DEPS: disabling feature "scalar" in colvar one -colvars: DEPS: colvar one enabling "linear" -colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. -colvars: DEPS: colvar one enabling "homogeneous" -colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. -colvars: DEPS: colvar one enabling "single_component" -colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting_group1 enabled, ref_count = 1. colvars: Looking for the keyword "timeStepFactor" and its value. colvars: Keyword "timeStepFactor" not found. colvars: # timeStepFactor = 1 [default] colvars: Looking for the keyword "width" and its value. -colvars: Keyword value = "0.5". -colvars: Looking for the keyword "width" and its value. colvars: Keyword "width" not found. -colvars: # width = 0.5 +colvars: # width = 1 [default] colvars: Looking for the keyword "hardLowerBoundary" and its value. colvars: Keyword "hardLowerBoundary" not found. colvars: # hardLowerBoundary = off [default] -colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting_group1 colvars: Looking for the keyword "hardUpperBoundary" and its value. colvars: Keyword "hardUpperBoundary" not found. colvars: # hardUpperBoundary = off [default] -colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting_group1 colvars: Looking for the keyword "expandBoundaries" and its value. colvars: Keyword "expandBoundaries" not found. colvars: # expandBoundaries = off [default] colvars: Looking for the keyword "extendedLagrangian" and its value. colvars: Keyword "extendedLagrangian" not found. colvars: # extendedLagrangian = off [default] -colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting_group1 colvars: Looking for the keyword "outputValue" and its value. colvars: Keyword "outputValue" not found. colvars: # outputValue = on [default] -colvars: DEPS: colvar one enabling "output_value" -colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting_group1 enabled, ref_count = 1. colvars: Looking for the keyword "outputVelocity" and its value. colvars: Keyword "outputVelocity" not found. colvars: # outputVelocity = off [default] @@ -1438,63 +2410,43 @@ colvars: Keyword "outputSystemForce" not found. colvars: Looking for the keyword "outputTotalForce" and its value. colvars: Keyword "outputTotalForce" not found. colvars: # outputTotalForce = off [default] -colvars: DEPS: disabling feature "output_total_force" in colvar one -colvars: Looking for the keyword "outputAppliedForce" and its value. -colvars: Keyword value = "on". +colvars: DEPS: disabling feature "output_total_force" in colvar fitting_group1 colvars: Looking for the keyword "outputAppliedForce" and its value. colvars: Keyword "outputAppliedForce" not found. -colvars: # outputAppliedForce = on -colvars: DEPS: colvar one enabling "output_applied_force" -colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting_group1 colvars: Looking for the keyword "subtractAppliedForce" and its value. colvars: Keyword "subtractAppliedForce" not found. colvars: # subtractAppliedForce = off [default] -colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one -colvars: DEPS: colvar one enabling "active" +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "active" colvars: active requires alt scalar -colvars: DEPS: colvar one testing "scalar" +colvars: DEPS: colvar fitting_group1 testing "scalar" colvars: active requires alt linear -colvars: DEPS: colvar one testing "linear" -colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: colvar fitting_group1 testing "linear" +colvars: DEPS: colvar fitting_group1 enabling "linear" colvars: DEPS: bumping ref_count to 1 -colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: DEPS: feature "active" in colvar fitting_group1 enabled, ref_count = 1. colvars: Looking for the keyword "runAve" and its value. colvars: Keyword "runAve" not found. colvars: # runAve = off [default] colvars: Looking for the keyword "corrFunc" and its value. colvars: Keyword "corrFunc" not found. colvars: # corrFunc = off [default] -colvars: Done initializing collective variable "one". +colvars: Done initializing collective variable "fitting_group1". colvars: Configuration string for "colvar": " colvars: -colvars: name one -colvars: outputAppliedForce on -colvars: width 0.5 -colvars: distanceDir { -colvars: group1 { -colvars: indexGroup group1 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz -colvars: } -colvars: group2 { -colvars: indexGroup group2 -colvars: centerToReference yes -colvars: rotateToReference yes -colvars: fittingGroup { -colvars: indexGroup heavy_atoms -colvars: } -colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms colvars: } colvars: } colvars: ". colvars: Looking for the keyword "colvar" and its value. colvars: Keyword "colvar" not found. colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. +colvars: Collective variables initialized, 4 in total. colvars: Initializing the collective variables biases. colvars: Looking for the keyword "abf" and its value. colvars: Keyword "abf" not found. @@ -1507,6 +2459,7 @@ colvars: Keyword value = " colvars: colvars one colvars: centers (1.0, 0.1, 0.2) colvars: forceConstant 10.0 +colvars: outputEnergy on colvars: ". colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. @@ -1524,8 +2477,10 @@ colvars: Keyword "stepZeroData" not found. colvars: # stepZeroData = off [default] colvars: DEPS: disabling feature "step_zero_data" in bias harmonic1 colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputEnergy" and its value. colvars: Keyword "outputEnergy" not found. -colvars: # outputEnergy = off [default] +colvars: # outputEnergy = on colvars: Looking for the keyword "outputFreq" and its value. colvars: Keyword "outputFreq" not found. colvars: # outputFreq = 10 [default] @@ -1615,9 +2570,9 @@ colvars: - Jacobian_derivative colvars: - total_force_from_one_group colvars: - debug_gradient colvars: - ON use_minimum-image_with_PBCs -colvars: - ON function_of_centers_of_mass (1) -colvars: - ON scalable_calculation (1) -colvars: - ON scalable_calculation_of_centers_of_mass +colvars: - ON function_of_centers_of_mass +colvars: - scalable_calculation +colvars: - scalable_calculation_of_centers_of_mass colvars: - collect_atom_ids colvars: * child 1 colvars: Features of "atom group group1" (refcount) @@ -1690,6 +2645,7 @@ colvars: colvars: colvars one colvars: centers (1.0, 0.1, 0.2) colvars: forceConstant 10.0 +colvars: outputEnergy on colvars: ". colvars: Looking for the keyword "harmonic" and its value. colvars: Keyword "harmonic" not found. @@ -1716,6 +2672,7 @@ colvars: name one colvars: outputAppliedForce on colvars: width 0.5 colvars: distanceDir { +colvars: scalable off colvars: group1 { colvars: indexGroup group1 colvars: centerToReference yes @@ -1735,11 +2692,36 @@ colvars: } colvars: refPositionsFile heavy_atoms_refpos.xyz colvars: } colvars: } -colvars: } +colvars: } +colvars: colvar { +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } colvars: harmonic { colvars: colvars one colvars: centers (1.0, 0.1, 0.2) colvars: forceConstant 10.0 +colvars: outputEnergy on colvars: } colvars: ". colvars: ---------------------------------------------------------------------- @@ -1757,6 +2739,7 @@ colvars: - Colvars-NAMD interface: colvars: - Harmonic colvar bias implementation: colvars: - Moving frame of reference: colvars: - Optimal rotation via flexible fitting: +colvars: - cartesian colvar component: colvars: - distance colvar component: colvars: - distanceDir colvar component (derived from distance): colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 @@ -1783,7 +2766,7 @@ colvars: Keyword value = "20". colvars: Looking for the keyword "step" and its value. colvars: Keyword "step" not found. colvars: Looking for the keyword "version" and its value. -colvars: Keyword value = "2024-06-04". +colvars: Keyword value = "2024-10-11". colvars: Looking for the keyword "version" and its value. colvars: Keyword "version" not found. colvars: Looking for the keyword "units" and its value. @@ -1793,10 +2776,67 @@ colvars: Keyword value = "one". colvars: Looking for the keyword "name" and its value. colvars: Keyword "name" not found. colvars: Looking for the keyword "x" and its value. -colvars: Keyword value = "( -0.3045417105333 , -0.00019915241487762 , 0.95249897999093 )". +colvars: Keyword value = "( -0.30360404081666 , -7.3012941347679e-05 , 0.95279828981212 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "one" from value: ( -0.303604 , -7.30129e-05 , 0.952798 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "group1": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "group1" from value: ( 8.28396 , 0.0403341 , -0.754693 , 6.93309 , -0.55189 , -0.576983 , 6.1554 , -0.375947 , 0.729836 , 4.94923 , -0.163317 , 0.722359 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "group2": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "group2": this colvar is named "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "group2" from value: ( 6.8638 , -0.263219 , 1.90772 , 6.17692 , -0.161108 , 3.19479 , 5.32108 , 1.09516 , 3.35245 , 4.16123 , 1.02516 , 3.69346 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting_group1": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting_group1": this colvar is named "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting_group1": this colvar is named "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 7.0480762025172 , -2.0513347736704 , -0.93377134820149 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 , 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 7.0809081020816 , -0.35496020632887 , 4.3146586251214 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 , 5.8432995748295 , 2.2535778944039 , 2.9902963417856 , 5.2384055225152 , 3.5783754026257 , 2.9215354050906 , 6.3223993673226 , 4.5011441587991 , 2.3655584831763 , 3.8818312912342 , 3.7064721784147 , 2.0444644100133 , 2.7920736373314 , 4.1608362314759 , 2.4877638737485 , 3.9386798899873 , 3.2395859717867 , 0.73126389979658 , 2.6624894551197 , 3.0062849992536 , -0.10369017207615 , 3.0530237576774 , 2.7050981729996 , -1.515126439405 , 1.5978477264343 , 2.1831908534433 , 0.4458975934194 , 0.37935536668417 , 2.5812137098021 , 0.51015292695301 , 2.0475904030464 , 1.0706502363152 , 1.069723927279 , 1.1690699177228 , 0.11658295312925 , 1.6974226380185 , 2.0431803877623 , -1.1033045581944 , 2.0106005316873 , 0.56210382605836 , 0.61178504571473 , 2.9428051810465 , -0.60199958586972 , 0.34968520789238 , 3.1615301713297 , 1.3167209916681 , 1.3457617287353 , 3.7754423945574 , 0.84267356054463 , 1.9787990415851 , 5.0254234233262 , 2.0796156959584 , 2.6878063101542 , 5.6821293955537 , -0.33739104868865 , 2.9146961524331 , 4.9679941584516 , -1.1371464701093 , 3.062469534534 , 5.8877740932039 , -0.51179726121506 , 3.5352900024754 , 3.8463150986082 , -1.5180503491383 , 4.5391900691402 , 3.4442608843563 , -0.69961559166787 , 5.4143954882994 , 2.4637912416459 , -2.7602287545827 , 3.8895007500064 , 2.8949751960402 , -3.8174896819283 , 4.5099047856922 , 2.8146284855071 , -2.6251714284554 , 2.6732886369457 , 2.4014323234568 , -3.7726963733907 , 1.8037184430191 , 1.9982779981764 , -3.3886595184775 , 0.88672154595831 , 0.87409788378727 , -4.3225504216986 , 1.0700082818202 , 3.2121699488068 , -5.4999729212229 , 0.81876098547252 , 3.3291853384002 , -3.3690633481624 , 0.69157744271515 , 4.2041288719456 , -3.7011250996533 , 0.046206366217123 , 5.434092539774 , -2.3903901778542 , -0.31709933730245 , 6.1701094743001 , -4.4618292827148 , 0.98680918149928 , 6.4395743693712 , -5.3588837067265 , 0.5981100423375 , 7.2179576344598 , -6.2383325096938 , 3.6054824579338 , 6.7336443061013 , -6.9602157879944 , 4.2977470185681 , 7.4756432850253 , -6.741403987979 , 3.1822575304318 , 5.5078493030856 , -4.1287524553974 , 2.2462119095443 , 6.4096637239512 , -4.8089365560512 , 3.2066271871716 , 7.2417022510827 , -4.0950888618816 , 4.5754896432564 , 7.2828123626203 )". colvars: Looking for the keyword "x" and its value. colvars: Keyword "x" not found. -colvars: Restarting collective variable "one" from value: ( -0.304542 , -0.000199152 , 0.952499 ) +colvars: Restarting collective variable "fitting_group1" from value: ( 8.28396 , 0.0403341 , -0.754693 , 6.93309 , -0.55189 , -0.576983 , 7.04808 , -2.05133 , -0.933771 , 6.1554 , -0.375947 , 0.729836 , 4.94923 , -0.163317 , 0.722359 , 6.8638 , -0.263219 , 1.90772 , 6.17692 , -0.161108 , 3.19479 , 7.08091 , -0.35496 , 4.31466 , 5.32108 , 1.09516 , 3.35245 , 4.16123 , 1.02516 , 3.69346 , 5.8433 , 2.25358 , 2.9903 , 5.23841 , 3.57838 , 2.92154 , 6.3224 , 4.50114 , 2.36556 , 3.88183 , 3.70647 , 2.04446 , 2.79207 , 4.16084 , 2.48776 , 3.93868 , 3.23959 , 0.731264 , 2.66249 , 3.00628 , -0.10369 , 3.05302 , 2.7051 , -1.51513 , 1.59785 , 2.18319 , 0.445898 , 0.379355 , 2.58121 , 0.510153 , 2.04759 , 1.07065 , 1.06972 , 1.16907 , 0.116583 , 1.69742 , 2.04318 , -1.1033 , 2.0106 , 0.562104 , 0.611785 , 2.94281 , -0.602 , 0.349685 , 3.16153 , 1.31672 , 1.34576 , 3.77544 , 0.842674 , 1.9788 , 5.02542 , 2.07962 , 2.68781 , 5.68213 , -0.337391 , 2.9147 , 4.96799 , -1.13715 , 3.06247 , 5.88777 , -0.511797 , 3.53529 , 3.84632 , -1.51805 , 4.53919 , 3.44426 , -0.699616 , 5.4144 , 2.46379 , -2.76023 , 3.8895 , 2.89498 , -3.81749 , 4.5099 , 2.81463 , -2.62517 , 2.67329 , 2.40143 , -3.7727 , 1.80372 , 1.99828 , -3.38866 , 0.886722 , 0.874098 , -4.32255 , 1.07001 , 3.21217 , -5.49997 , 0.818761 , 3.32919 , -3.36906 , 0.691577 , 4.20413 , -3.70113 , 0.0462064 , 5.43409 , -2.39039 , -0.317099 , 6.17011 , -4.46183 , 0.986809 , 6.43957 , -5.35888 , 0.59811 , 7.21796 , -6.23833 , 3.60548 , 6.73364 , -6.96022 , 4.29775 , 7.47564 , -6.7414 , 3.18226 , 5.50785 , -4.12875 , 2.24621 , 6.40966 , -4.80894 , 3.20663 , 7.2417 , -4.09509 , 4.57549 , 7.28281 ) colvars: Looking for the keyword "name" and its value. colvars: Keyword value = "harmonic1". colvars: Looking for the keyword "name" and its value. @@ -1824,6 +2864,9 @@ colvars: Current simulation parameters: initial step = 20, integration timestep colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "group1":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "group2":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "fitting_group1":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: ---------------------------------------------------------------------- colvars: colvarproxy_namd, step no. 20 @@ -1833,10 +2876,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 20, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 20, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 20, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 20, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 20, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 20, atoms_positions[size = 51] = { ( 8.28582291037697e+00 , 4.04506123830901e-02 , -7.54196570963580e-01 ), ( 6.93477801011369e+00 , -5.51786262542508e-01 , -5.76525850220028e-01 ), ( 6.15654135511678e+00 , -3.75844216369432e-01 , 7.29702736243887e-01 ), ( 4.95083684588076e+00 , -1.63049873260700e-01 , 7.22622667146212e-01 ), ( 7.04822840425256e+00 , -2.05125822808654e+00 , -9.33838802325873e-01 ), ( 6.86298879544170e+00 , -2.63492033772352e-01 , 1.90782093039187e+00 ), ( 6.17535476862579e+00 , -1.61467873005207e-01 , 3.19447807763223e+00 ), ( 7.08038697584318e+00 , -3.54878074422017e-01 , 4.31410976849832e+00 ), ( 5.31942679106160e+00 , 1.09501065270932e+00 , 3.35178346295725e+00 ), ( 4.15930443602701e+00 , 1.02503542539263e+00 , 3.69255428523693e+00 ), ( 5.84279477371476e+00 , 2.25334627387652e+00 , 2.99025393459074e+00 ), ( 5.23840438125392e+00 , 3.57836450753976e+00 , 2.92139319672716e+00 ), ( 6.32240747113683e+00 , 4.50111704883458e+00 , 2.36542025527039e+00 ), ( 3.88181028160009e+00 , 3.70648484501399e+00 , 2.04436620458568e+00 ), ( 2.79206714766409e+00 , 4.16082999865321e+00 , 2.48770343635868e+00 ), ( 3.93862881447229e+00 , 3.23956170779748e+00 , 7.31179710249667e-01 ), ( 2.66241903927475e+00 , 3.00625645576357e+00 , -1.03744703501063e-01 ), ( 3.05292822088169e+00 , 2.70506278162700e+00 , -1.51518325748210e+00 ), ( 1.59778880440673e+00 , 2.18316923674870e+00 , 4.45871092830035e-01 ), ( 3.79300149359787e-01 , 2.58119961872434e+00 , 5.10156322737722e-01 ), ( 2.04754425768075e+00 , 1.07062955324807e+00 , 1.06969022583418e+00 ), ( 1.16903854050100e+00 , 1.16571453589181e-01 , 1.69741818249094e+00 ), ( 2.04314486967146e+00 , -1.10332707217033e+00 , 2.01056812233467e+00 ), ( 5.62094900755023e-01 , 6.11786092234871e-01 , 2.94281295395090e+00 ), ( -6.01998257745626e-01 , 3.49689451878813e-01 , 3.16156299845539e+00 ), ( 1.31668822516108e+00 , 1.34577563521962e+00 , 3.77543109832579e+00 ), ( 8.42716504335045e-01 , 1.97881846216304e+00 , 5.02541834392960e+00 ), ( 2.07967786415177e+00 , 2.68782307153212e+00 , 5.68209741884907e+00 ), ( -3.37344843382937e-01 , 2.91471449609425e+00 , 4.96800851820805e+00 ), ( -1.13708588001649e+00 , 3.06248956541986e+00 , 5.88780199616476e+00 ), ( -5.11775330469444e-01 , 3.53529724018143e+00 , 3.84632332050881e+00 ), ( -1.51803710380555e+00 , 4.53919531397891e+00 , 3.44428420949964e+00 ), ( -6.99624398507824e-01 , 5.41439381873403e+00 , 2.46379309418166e+00 ), ( -2.76022882703025e+00 , 3.88950508193880e+00 , 2.89503343674671e+00 ), ( -3.81748583539279e+00 , 4.50991617428220e+00 , 2.81470056115434e+00 ), ( -2.62519097171536e+00 , 2.67328985787292e+00 , 2.40149432612104e+00 ), ( -3.77272853459107e+00 , 1.80371700509528e+00 , 1.99837671356181e+00 ), ( -3.38871455409835e+00 , 8.86717902389388e-01 , 8.74187404183740e-01 ), ( -4.32255998423662e+00 , 1.07002307118320e+00 , 3.21229150831233e+00 ), ( -5.49998182564857e+00 , 8.18774137488647e-01 , 3.32931951742222e+00 ), ( -3.36904919026829e+00 , 6.91596678914569e-01 , 4.20423547278276e+00 ), ( -3.70107974783840e+00 , 4.62390697929325e-02 , 5.43421582390532e+00 ), ( -2.39033524019067e+00 , -3.17074981101270e-01 , 6.17020508472989e+00 ), ( -4.46175815649799e+00 , 9.86843632633000e-01 , 6.43971260203245e+00 ), ( -5.35881205025882e+00 , 5.98149506814076e-01 , 7.21810107144495e+00 ), ( -6.23824517782367e+00 , 3.60552411038818e+00 , 6.73377298524042e+00 ), ( -6.96012228941194e+00 , 4.29779275147404e+00 , 7.47577581613682e+00 ), ( -6.74134298930255e+00 , 3.18228858940767e+00 , 5.50798663651289e+00 ), ( -4.12867862719011e+00 , 2.24624582899316e+00 , 6.40977342732153e+00 ), ( -4.80883733708504e+00 , 3.20667234951756e+00 , 7.24182070504870e+00 ), ( -4.09497949178953e+00 , 4.57553386748493e+00 , 7.28289299072206e+00 ) } +colvars: Step 20, atoms_positions[size = 51] = { ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 ), ( 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 ), ( 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 ), ( 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ), ( 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 ), ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 ), ( 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 ), ( 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 ), ( 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 ), ( 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ), ( 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 ), ( 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 ), ( 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 ), ( 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 ), ( 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 ), ( 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 ), ( 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 ), ( 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 ), ( 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 ), ( 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 ), ( 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 ), ( 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 ), ( 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 ), ( 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 ), ( -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 ), ( 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 ), ( 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 ), ( 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 ), ( -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 ), ( -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 ), ( -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 ), ( -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 ), ( -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 ), ( -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 ), ( -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 ), ( -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 ), ( -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 ), ( -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 ), ( -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 ), ( -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 ), ( -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 ), ( -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 ), ( -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 ), ( -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 ), ( -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 ), ( -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 ), ( -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 ), ( -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 ), ( -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 ), ( -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 ), ( -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) } colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_ids[size = 0] = @@ -1855,153 +2898,289 @@ colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ). +colvars: Colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.6088 , 1.95578 , -15.1464 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 66.0363 , 6.60363 , 13.2073 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.6088 , 1.95578 , -15.1464 ) to colvar "one". -colvars: Adding total bias energy: 44.4525 +colvars: Adding biasing force ( 66.0363 , 6.60363 , 13.2073 ) to colvar "one". +colvars: Adding total bias energy: 56.5387 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.6088 , 1.95578 , -15.1464 ) +colvars: Force to be applied: ( 66.0363 , 6.60363 , 13.2073 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.91515 , -0.533261 , -1.45224 ) -colvars: ( -4.21474 , -0.457271 , -1.24529 ) -colvars: ( -4.21474 , -0.457271 , -1.24529 ) -colvars: ( -5.61415 , -0.609098 , -1.65877 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17524 , -0.560146 , -1.5236 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -5.91123 , -0.639807 , -1.74028 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.892544 , 0.19549 , 0.619241 ) -colvars: ( 0.773074 , 0.266213 , 0.643516 ) -colvars: ( 0.757152 , 0.259324 , 0.625094 ) -colvars: ( 0.661335 , 0.266975 , 0.579425 ) -colvars: ( 0.649454 , 0.200472 , 0.484222 ) -colvars: ( 0.574898 , 0.344142 , 0.631501 ) -colvars: ( 0.46778 , 0.358122 , 0.587647 ) -colvars: ( 0.391169 , 0.455275 , 0.67198 ) -colvars: ( 0.386205 , 0.313656 , 0.481093 ) -colvars: ( 0.351459 , 0.272107 , 0.405694 ) -colvars: ( 0.356948 , 0.318969 , 0.471099 ) -colvars: ( 0.285831 , 0.276183 , 0.372867 ) -colvars: ( 0.258798 , 0.3052 , 0.395635 ) -colvars: ( 0.348239 , 0.178457 , 0.2795 ) -colvars: ( 0.289613 , 0.135181 , 0.187896 ) -colvars: ( 0.470901 , 0.14145 , 0.301842 ) -colvars: ( 0.543399 , 0.0501585 , 0.222894 ) -colvars: ( 0.672857 , 0.0291993 , 0.270498 ) -colvars: ( 0.551951 , 0.0183336 , 0.18563 ) -colvars: ( 0.536209 , -0.0466654 , 0.0901744 ) -colvars: ( 0.572815 , 0.0661925 , 0.261317 ) -colvars: ( 0.571276 , 0.0500177 , 0.238949 ) -colvars: ( 0.607772 , 0.114667 , 0.346033 ) -colvars: ( 0.447058 , 0.0544713 , 0.172488 ) -colvars: ( 0.440246 , -0.00142063 , 0.0943242 ) -colvars: ( 0.345197 , 0.120053 , 0.200198 ) -colvars: ( 0.220799 , 0.128616 , 0.139087 ) -colvars: ( 0.129402 , 0.214294 , 0.19957 ) -colvars: ( 0.192616 , 0.0549651 , 0.0248969 ) -colvars: ( 0.143405 , 0.018808 , -0.0517726 ) -colvars: ( 0.226186 , 0.0294603 , 0.0105991 ) -colvars: ( 0.212182 , -0.0429517 , -0.0936848 ) -colvars: ( 0.247451 , -0.0462529 , -0.0775182 ) -colvars: ( 0.287355 , -0.128824 , -0.16388 ) -colvars: ( 0.243414 , -0.181898 , -0.259935 ) -colvars: ( 0.402414 , -0.143819 , -0.116748 ) -colvars: ( 0.479789 , -0.219244 , -0.17179 ) -colvars: ( 0.610834 , -0.221812 , -0.0988481 ) -colvars: ( 0.432546 , -0.223771 , -0.205325 ) -colvars: ( 0.438072 , -0.291778 , -0.292383 ) -colvars: ( 0.383843 , -0.150562 , -0.136519 ) -colvars: ( 0.329659 , -0.144357 , -0.159851 ) -colvars: ( 0.313151 , -0.0577764 , -0.0545361 ) -colvars: ( 0.206501 , -0.15316 , -0.243293 ) -colvars: ( 0.182128 , -0.195153 , -0.313237 ) -colvars: ( 0.00545045 , -0.19885 , -0.421084 ) -colvars: ( -0.0853872 , -0.216646 , -0.497632 ) -colvars: ( 0.105698 , -0.248684 , -0.428829 ) -colvars: ( 0.124781 , -0.112578 , -0.237034 ) -colvars: ( 0.00559788 , -0.116969 , -0.312302 ) -colvars: ( -0.0832935 , -0.0363805 , -0.257115 ) +colvars: ( 0.939145 , 0.205822 , 0.650791 ) +colvars: ( 0.813493 , 0.280183 , 0.676344 ) +colvars: ( 0.79671 , 0.272971 , 0.657011 ) +colvars: ( 0.695988 , 0.280925 , 0.60896 ) +colvars: ( 0.683489 , 0.210958 , 0.508858 ) +colvars: ( 0.605096 , 0.362058 , 0.663721 ) +colvars: ( 0.492454 , 0.376702 , 0.617613 ) +colvars: ( 0.411895 , 0.478868 , 0.706292 ) +colvars: ( 0.40664 , 0.329912 , 0.505603 ) +colvars: ( 0.370107 , 0.286173 , 0.426316 ) +colvars: ( 0.375838 , 0.335525 , 0.495129 ) +colvars: ( 0.30102 , 0.290509 , 0.391871 ) +colvars: ( 0.272557 , 0.321061 , 0.415847 ) +colvars: ( 0.366646 , 0.187731 , 0.293691 ) +colvars: ( 0.304985 , 0.14218 , 0.19738 ) +colvars: ( 0.495648 , 0.148851 , 0.317164 ) +colvars: ( 0.571887 , 0.0528434 , 0.234141 ) +colvars: ( 0.70803 , 0.0308578 , 0.284183 ) +colvars: ( 0.580911 , 0.0193309 , 0.194928 ) +colvars: ( 0.564352 , -0.0490553 , 0.0945605 ) +colvars: ( 0.602884 , 0.069656 , 0.274483 ) +colvars: ( 0.601296 , 0.052603 , 0.250934 ) +colvars: ( 0.639709 , 0.120601 , 0.363501 ) +colvars: ( 0.470661 , 0.05723 , 0.181065 ) +colvars: ( 0.463505 , -0.0015853 , 0.098867 ) +colvars: ( 0.363526 , 0.126191 , 0.210227 ) +colvars: ( 0.232697 , 0.135147 , 0.145989 ) +colvars: ( 0.136568 , 0.225255 , 0.209612 ) +colvars: ( 0.203032 , 0.0576775 , 0.0259439 ) +colvars: ( 0.151284 , 0.019607 , -0.0546754 ) +colvars: ( 0.238306 , 0.0308947 , 0.0109328 ) +colvars: ( 0.223552 , -0.0452647 , -0.0986978 ) +colvars: ( 0.260612 , -0.0486848 , -0.0816732 ) +colvars: ( 0.30262 , -0.135586 , -0.17253 ) +colvars: ( 0.256401 , -0.191436 , -0.273522 ) +colvars: ( 0.423642 , -0.151329 , -0.123003 ) +colvars: ( 0.505029 , -0.230661 , -0.180906 ) +colvars: ( 0.642858 , -0.233317 , -0.104237 ) +colvars: ( 0.455372 , -0.235478 , -0.216188 ) +colvars: ( 0.461185 , -0.307026 , -0.307735 ) +colvars: ( 0.404175 , -0.158505 , -0.14385 ) +colvars: ( 0.347218 , -0.152033 , -0.168403 ) +colvars: ( 0.329883 , -0.0609799 , -0.0576822 ) +colvars: ( 0.217684 , -0.161336 , -0.256114 ) +colvars: ( 0.192064 , -0.205541 , -0.32967 ) +colvars: ( 0.00617868 , -0.209423 , -0.442974 ) +colvars: ( -0.0893621 , -0.228177 , -0.523444 ) +colvars: ( 0.111592 , -0.261789 , -0.451119 ) +colvars: ( 0.131717 , -0.118651 , -0.249498 ) +colvars: ( 0.00636188 , -0.12331 , -0.328614 ) +colvars: ( -0.0871363 , -0.0385503 , -0.270558 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.91515 , 0.533261 , 1.45224 ) -colvars: ( 4.21474 , 0.457271 , 1.24529 ) -colvars: ( 4.21474 , 0.457271 , 1.24529 ) -colvars: ( 5.61415 , 0.609098 , 1.65877 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17524 , 0.560146 , 1.5236 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 5.91123 , 0.639807 , 1.74028 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.615911 , -0.0809403 , -0.370289 ) -colvars: ( -0.553936 , -0.163279 , -0.339783 ) -colvars: ( -0.504483 , -0.14143 , -0.281796 ) -colvars: ( -0.514701 , -0.190631 , -0.31095 ) -colvars: ( -0.505106 , -0.132058 , -0.278819 ) -colvars: ( -0.489899 , -0.282191 , -0.321263 ) -colvars: ( -0.457119 , -0.322318 , -0.303811 ) -colvars: ( -0.435381 , -0.42909 , -0.323043 ) -colvars: ( -0.394403 , -0.287171 , -0.227415 ) -colvars: ( -0.389791 , -0.261989 , -0.213114 ) -colvars: ( -0.345387 , -0.281611 , -0.176126 ) -colvars: ( -0.285203 , -0.244949 , -0.101686 ) -colvars: ( -0.23688 , -0.259846 , -0.058954 ) -colvars: ( -0.30471 , -0.142288 , -0.0817978 ) -colvars: ( -0.273523 , -0.113172 , -0.0393358 ) -colvars: ( -0.359032 , -0.0851872 , -0.114328 ) -colvars: ( -0.385698 , 0.0125647 , -0.103504 ) -colvars: ( -0.43592 , 0.0599408 , -0.135661 ) -colvars: ( -0.423002 , 0.0275581 , -0.13515 ) -colvars: ( -0.411661 , 0.0840489 , -0.10207 ) -colvars: ( -0.466795 , -0.0261598 , -0.199708 ) -colvars: ( -0.500798 , -0.0275661 , -0.234345 ) -colvars: ( -0.55043 , -0.0926022 , -0.309107 ) -colvars: ( -0.448784 , -0.057432 , -0.193664 ) -colvars: ( -0.455539 , -0.013552 , -0.183575 ) -colvars: ( -0.393864 , -0.131394 , -0.167013 ) -colvars: ( -0.336404 , -0.16255 , -0.121366 ) -colvars: ( -0.286194 , -0.252303 , -0.105507 ) -colvars: ( -0.295464 , -0.0901165 , -0.0524782 ) -colvars: ( -0.282212 , -0.0715846 , -0.032067 ) -colvars: ( -0.275892 , -0.045508 , -0.0157091 ) -colvars: ( -0.240779 , 0.0288343 , 0.048069 ) -colvars: ( -0.219798 , 0.0550453 , 0.0791805 ) -colvars: ( -0.284619 , 0.115186 , 0.0372899 ) -colvars: ( -0.258068 , 0.156731 , 0.0798802 ) -colvars: ( -0.35365 , 0.143204 , -0.0211658 ) -colvars: ( -0.402215 , 0.219052 , -0.0407192 ) -colvars: ( -0.473097 , 0.241538 , -0.103157 ) -colvars: ( -0.413517 , 0.199366 , -0.0596175 ) -colvars: ( -0.417976 , 0.25989 , -0.0408311 ) -colvars: ( -0.417832 , 0.113257 , -0.0970347 ) -colvars: ( -0.424688 , 0.0832879 , -0.115426 ) -colvars: ( -0.445978 , -0.00952294 , -0.17244 ) -colvars: ( -0.358207 , 0.0720446 , -0.0530801 ) -colvars: ( -0.361391 , 0.0982463 , -0.0462049 ) -colvars: ( -0.198027 , 0.104482 , 0.120009 ) -colvars: ( -0.148764 , 0.106318 , 0.170115 ) -colvars: ( -0.224679 , 0.176429 , 0.120931 ) -colvars: ( -0.296008 , 0.0314599 , -0.00630443 ) -colvars: ( -0.229511 , 0.0178807 , 0.0551591 ) -colvars: ( -0.175844 , -0.0648266 , 0.0771928 ) +colvars: ( -0.647974 , -0.0852573 , -0.388753 ) +colvars: ( -0.582839 , -0.171838 , -0.35665 ) +colvars: ( -0.530769 , -0.148883 , -0.295681 ) +colvars: ( -0.541646 , -0.200563 , -0.326377 ) +colvars: ( -0.531553 , -0.138947 , -0.29266 ) +colvars: ( -0.515626 , -0.296838 , -0.337183 ) +colvars: ( -0.481227 , -0.338999 , -0.318864 ) +colvars: ( -0.458422 , -0.451281 , -0.339024 ) +colvars: ( -0.415265 , -0.302019 , -0.238601 ) +colvars: ( -0.41045 , -0.275508 , -0.22362 ) +colvars: ( -0.363672 , -0.296189 , -0.184669 ) +colvars: ( -0.300365 , -0.257621 , -0.106457 ) +colvars: ( -0.2495 , -0.273312 , -0.0614974 ) +colvars: ( -0.320837 , -0.149656 , -0.0856129 ) +colvars: ( -0.288058 , -0.119011 , -0.0410273 ) +colvars: ( -0.377907 , -0.0896324 , -0.119807 ) +colvars: ( -0.405907 , 0.0131673 , -0.108485 ) +colvars: ( -0.458652 , 0.0629527 , -0.142267 ) +colvars: ( -0.445189 , 0.028964 , -0.141797 ) +colvars: ( -0.433263 , 0.0883914 , -0.107081 ) +colvars: ( -0.491292 , -0.0275236 , -0.209633 ) +colvars: ( -0.527109 , -0.028974 , -0.246079 ) +colvars: ( -0.579343 , -0.0973742 , -0.324623 ) +colvars: ( -0.472472 , -0.0603448 , -0.203347 ) +colvars: ( -0.479594 , -0.0141749 , -0.192798 ) +colvars: ( -0.414746 , -0.138121 , -0.175297 ) +colvars: ( -0.354373 , -0.170853 , -0.127338 ) +colvars: ( -0.301597 , -0.265244 , -0.110611 ) +colvars: ( -0.311285 , -0.09467 , -0.0549772 ) +colvars: ( -0.297384 , -0.0751509 , -0.0335708 ) +colvars: ( -0.290629 , -0.0477842 , -0.0163181 ) +colvars: ( -0.253661 , 0.0304013 , 0.050676 ) +colvars: ( -0.23152 , 0.0579314 , 0.0834089 ) +colvars: ( -0.299747 , 0.121221 , 0.039285 ) +colvars: ( -0.271833 , 0.164934 , 0.084002 ) +colvars: ( -0.37232 , 0.150668 , -0.022156 ) +colvars: ( -0.42338 , 0.230441 , -0.0427631 ) +colvars: ( -0.497883 , 0.254059 , -0.108372 ) +colvars: ( -0.435341 , 0.209775 , -0.062665 ) +colvars: ( -0.440031 , 0.273443 , -0.0429754 ) +colvars: ( -0.439945 , 0.119231 , -0.101963 ) +colvars: ( -0.447231 , 0.0877498 , -0.121324 ) +colvars: ( -0.469676 , -0.00985306 , -0.181203 ) +colvars: ( -0.377354 , 0.0759564 , -0.0558201 ) +colvars: ( -0.380737 , 0.103539 , -0.0486444 ) +colvars: ( -0.208877 , 0.110092 , 0.126079 ) +colvars: ( -0.157097 , 0.112049 , 0.178715 ) +colvars: ( -0.23683 , 0.185727 , 0.127043 ) +colvars: ( -0.311938 , 0.0332713 , -0.00662132 ) +colvars: ( -0.242039 , 0.0190178 , 0.0579609 ) +colvars: ( -0.185619 , -0.0679661 , 0.0811767 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 20. colvars: colvarmodule::write_traj_files() @@ -2009,8 +3188,11 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: colvarmodule::end_of_step(), step = 20. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 20, atoms_new_colvar_forces = { ( -4.63851454459905e+00 , -4.18710833064850e-01 , -1.20328608426652e+00 ), ( -3.99559989640659e+00 , -3.54336474175720e-01 , -9.41559888235754e-01 ), ( -4.06810357739189e+00 , -3.80926713958037e-01 , -9.76817699772113e-01 ), ( -5.46980368326514e+00 , -5.40683985020084e-01 , -1.45336332622448e+00 ), ( 2.52668502795200e-01 , 1.17894094436429e-01 , 3.43297404486922e-01 ), ( 5.00014590643842e+00 , 5.95211961482009e-01 , 1.76247508244524e+00 ), ( 4.22539890920215e+00 , 4.93075099844339e-01 , 1.52912952520700e+00 ), ( -4.42117205218343e-02 , 2.61849910581687e-02 , 3.48936847549760e-01 ), ( 4.20654020656410e+00 , 4.83756625787825e-01 , 1.49897132736399e+00 ), ( 5.57582044888118e+00 , 6.19216324851961e-01 , 1.85134641932113e+00 ), ( 1.15606722969959e-02 , 3.73582371308533e-02 , 2.94972551667663e-01 ), ( 6.27937109112076e-04 , 3.12340160260255e-02 , 2.71180143655928e-01 ), ( 2.19173365638969e-02 , 4.53538862226682e-02 , 3.36681036424671e-01 ), ( 4.35287412741041e-02 , 3.61696681282234e-02 , 1.97702509024789e-01 ), ( 1.60900816481230e-02 , 2.20091820921404e-02 , 1.48559775115973e-01 ), ( 1.11869449595165e-01 , 5.62631531725342e-02 , 1.87513672922987e-01 ), ( 1.57700920362817e-01 , 6.27232419132576e-02 , 1.19389577713856e-01 ), ( 2.36936463271923e-01 , 8.91401887092676e-02 , 1.34836894262539e-01 ), ( 1.28948776005967e-01 , 4.58916180710906e-02 , 5.04794295830226e-02 ), ( 1.24548587393342e-01 , 3.73834994690693e-02 , -1.18954687815839e-02 ), ( 1.06019698806145e-01 , 4.00326507775761e-02 , 6.16092423921068e-02 ), ( 7.04782471949013e-02 , 2.24515586964271e-02 , 4.60369604053695e-03 ), ( 5.73422381960390e-02 , 2.20646170469042e-02 , 3.69252747449674e-02 ), ( -1.72611395560524e-03 , -2.96077010773500e-03 , -2.11764063442688e-02 ), ( -1.52922851265740e-02 , -1.49726615376669e-02 , -8.92510974662055e-02 ), ( -4.86671260953066e-02 , -1.13413226333090e-02 , 3.31845028045236e-02 ), ( -1.15605077666369e-01 , -3.39346522378186e-02 , 1.77200417262677e-02 ), ( -1.56792026456609e-01 , -3.80091057503520e-02 , 9.40637658323593e-02 ), ( -1.02848641736711e-01 , -3.51514140984507e-02 , -2.75812107087965e-02 ), ( -1.38806884416938e-01 , -5.27766427227216e-02 , -8.38395789565467e-02 ), ( -4.97061267723764e-02 , -1.60476509528009e-02 , -5.11007628540459e-03 ), ( -2.85976059219338e-02 , -1.41173315546320e-02 , -4.56158111816652e-02 ), ( 2.76522679529432e-02 , 8.79242656069489e-03 , 1.66225761229807e-03 ), ( 2.73532411285460e-03 , -1.36382491455301e-02 , -1.26589601375052e-01 ), ( -1.46538330736033e-02 , -2.51672766893284e-02 , -1.80055129011821e-01 ), ( 4.87645210478707e-02 , -6.15426656884632e-04 , -1.37913496336073e-01 ), ( 7.75743232463488e-02 , -1.91225606735068e-04 , -2.12509192428131e-01 ), ( 1.37737148977943e-01 , 1.97267169501107e-02 , -2.02005130353156e-01 ), ( 1.90294174661668e-02 , -2.44049904625063e-02 , -2.64942523670217e-01 ), ( 2.00953061744231e-02 , -3.18876654614701e-02 , -3.33214475874042e-01 ), ( -3.39893131361256e-02 , -3.73055310094134e-02 , -2.33553485918890e-01 ), ( -9.50287381727212e-02 , -6.10695052311506e-02 , -2.75277236233374e-01 ), ( -1.32826616258851e-01 , -6.72993193787387e-02 , -2.26975689078502e-01 ), ( -1.51705844975594e-01 , -8.11153781239003e-02 , -2.96372806931386e-01 ), ( -1.79263034470665e-01 , -9.69067785137090e-02 , -3.59442438261914e-01 ), ( -1.92577034615937e-01 , -9.43678359874191e-02 , -3.01074097881565e-01 ), ( -2.34151572355940e-01 , -1.10327571437585e-01 , -3.27516835071365e-01 ), ( -1.18981164358574e-01 , -7.22543491267554e-02 , -3.07897440415716e-01 ), ( -1.71227554375326e-01 , -8.11181099169558e-02 , -2.43338813862098e-01 ), ( -2.23913463549683e-01 , -9.90878668961794e-02 , -2.57143314677739e-01 ), ( -2.59137952902184e-01 , -1.01207120969136e-01 , -1.79922622294137e-01 ) } +colvars: Step 20, atoms_new_colvar_forces = { ( -4.88406726017846e+00 , -4.39582030019637e-01 , -1.26156546289831e+00 ), ( -4.20711207586693e+00 , -3.71980090924366e-01 , -9.86796367004215e-01 ), ( -4.28342445948863e+00 , -3.99963693514908e-01 , -1.02390709400074e+00 ), ( -5.75929727923110e+00 , -5.67796041518724e-01 , -1.52408480248038e+00 ), ( 2.65941268390902e-01 , 1.24088041235363e-01 , 3.61330101161847e-01 ), ( 5.26470856148017e+00 , 6.25365994053560e-01 , 1.85014148432867e+00 ), ( 4.44899395969789e+00 , 5.18028786716414e-01 , 1.60523898998076e+00 ), ( -4.65272910606424e-02 , 2.75874394655633e-02 , 3.67268098303653e-01 ), ( 4.42914052995064e+00 , 5.08218685700347e-01 , 1.57349215273307e+00 ), ( 5.87089063969169e+00 , 6.50472344458009e-01 , 1.94297816123059e+00 ), ( 1.21655890342579e-02 , 3.93361229409889e-02 , 3.10460529518665e-01 ), ( 6.54352727631202e-04 , 3.28877838588784e-02 , 2.85413778669853e-01 ), ( 2.30575218111934e-02 , 4.77496012635013e-02 , 3.54349709040753e-01 ), ( 4.58084561993378e-02 , 3.80749776841854e-02 , 2.08077917584342e-01 ), ( 1.69271357430614e-02 , 2.31692671284452e-02 , 1.56352523085799e-01 ), ( 1.17740497737709e-01 , 5.92187670987907e-02 , 1.97356769209817e-01 ), ( 1.65979650547149e-01 , 6.60107587124940e-02 , 1.25656124587784e-01 ), ( 2.49378084035319e-01 , 9.38105312411004e-02 , 1.41916759655613e-01 ), ( 1.35721171926268e-01 , 4.82948683031030e-02 , 5.31311614239589e-02 ), ( 1.31089117563867e-01 , 3.93361615661934e-02 , -1.25202269468064e-02 ), ( 1.11591946272047e-01 , 4.21324308431365e-02 , 6.48498773882783e-02 ), ( 7.41875459869102e-02 , 2.36289347234540e-02 , 4.85459631934207e-03 ), ( 6.03658790245055e-02 , 2.32264957257031e-02 , 3.88781977774767e-02 ), ( -1.81078736534573e-03 , -3.11478153248525e-03 , -2.22818060419844e-02 ), ( -1.60885473686671e-02 , -1.57601748864797e-02 , -9.39304968271742e-02 ), ( -5.12199048641456e-02 , -1.19297840935810e-02 , 3.49304717831433e-02 ), ( -1.21675813902335e-01 , -3.57064899870657e-02 , 1.86508224653453e-02 ), ( -1.65028468419942e-01 , -3.99882775272279e-02 , 9.90005933951236e-02 ), ( -1.08252979508245e-01 , -3.69924344963437e-02 , -2.90333247285238e-02 ), ( -1.46099690198963e-01 , -5.55439012742997e-02 , -8.82462486637547e-02 ), ( -5.23225535297807e-02 , -1.68894940154288e-02 , -5.38529268697861e-03 ), ( -3.01087883421307e-02 , -1.48633476968855e-02 , -4.80218171751865e-02 ), ( 2.90920024039188e-02 , 9.24664271438187e-03 , 1.73568422449372e-03 ), ( 2.87212446123969e-03 , -1.43653564917826e-02 , -1.33245075124415e-01 ), ( -1.54318476939863e-02 , -2.65024240836628e-02 , -1.89520159508813e-01 ), ( 5.13226740441255e-02 , -6.61117676194450e-04 , -1.45158995615856e-01 ), ( 8.16483892005009e-02 , -2.20115925109621e-04 , -2.23668733880816e-01 ), ( 1.44974583626733e-01 , 2.07414644297433e-02 , -2.12608633585807e-01 ), ( 2.00313536000674e-02 , -2.57030285264907e-02 , -2.78852997194507e-01 ), ( 2.11535019058627e-02 , -3.35827543487625e-02 , -3.50709917556565e-01 ), ( -3.57699416572513e-02 , -3.92742347993370e-02 , -2.45813691592460e-01 ), ( -1.00012769612954e-01 , -6.42830113991747e-02 , -2.89726269929375e-01 ), ( -1.39792965314805e-01 , -7.08329385419267e-02 , -2.38885255145827e-01 ), ( -1.59669948187276e-01 , -8.53800481419532e-02 , -3.11933814118016e-01 ), ( -1.88673377030574e-01 , -1.02001994075380e-01 , -3.78314516895504e-01 ), ( -2.02698784283931e-01 , -9.93305031383851e-02 , -3.16894644449761e-01 ), ( -2.46459346918119e-01 , -1.16127914776370e-01 , -3.44729104647447e-01 ), ( -1.25237872776220e-01 , -7.60618339454901e-02 , -3.24076090847715e-01 ), ( -1.80221106740230e-01 , -8.53800525072640e-02 , -2.56119533999097e-01 ), ( -2.35677590614575e-01 , -1.04291860665546e-01 , -2.70653229134327e-01 ), ( -2.72755086907763e-01 , -1.06516369333094e-01 , -1.89380901188017e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 20, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2048,10 +3230,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 21, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 21, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 21, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 21, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 21, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 21, atoms_positions[size = 51] = { ( 8.28180982144064e+00 , 4.03632117943420e-02 , -7.51522305517076e-01 ), ( 6.92282117186149e+00 , -5.53103008339236e-01 , -5.68946668768409e-01 ), ( 6.15817431676409e+00 , -3.81985768262077e-01 , 7.37133684205432e-01 ), ( 4.94415676071348e+00 , -1.59493575190565e-01 , 7.24998098558174e-01 ), ( 7.04491903435971e+00 , -2.05318729196479e+00 , -9.29444265677132e-01 ), ( 6.85635102170978e+00 , -2.64482457244509e-01 , 1.91552478321154e+00 ), ( 6.17022515682612e+00 , -1.68498720978849e-01 , 3.18973647048402e+00 ), ( 7.08289173522581e+00 , -3.53907252918931e-01 , 4.32144017771733e+00 ), ( 5.32536611283806e+00 , 1.09148571415860e+00 , 3.35515329207102e+00 ), ( 4.16123089994812e+00 , 1.02270267230411e+00 , 3.69988826087271e+00 ), ( 5.84018046278717e+00 , 2.25510641156531e+00 , 2.98828769631725e+00 ), ( 5.23587224285778e+00 , 3.57667790378110e+00 , 2.92151344030494e+00 ), ( 6.32158086117518e+00 , 4.49985476177825e+00 , 2.35550053278041e+00 ), ( 3.87686982786362e+00 , 3.70008117015323e+00 , 2.04442214020625e+00 ), ( 2.79070884592407e+00 , 4.16331882660186e+00 , 2.48250033805889e+00 ), ( 3.94109497487038e+00 , 3.23745357393277e+00 , 7.30710158843963e-01 ), ( 2.66965416281210e+00 , 3.00544044719939e+00 , -1.01536762164985e-01 ), ( 3.05924471963822e+00 , 2.69949617675075e+00 , -1.51507639779084e+00 ), ( 1.59644807437693e+00 , 2.17841754594632e+00 , 4.39530279055366e-01 ), ( 3.75987150484748e-01 , 2.58918817813005e+00 , 5.06290010091292e-01 ), ( 2.05513241559826e+00 , 1.08606036188264e+00 , 1.06504176262207e+00 ), ( 1.16749512571148e+00 , 1.17140689118167e-01 , 1.69891782543129e+00 ), ( 2.04670833917162e+00 , -1.09990016597589e+00 , 2.01320056995010e+00 ), ( 5.63957095834067e-01 , 6.13312886215627e-01 , 2.94798433857395e+00 ), ( -5.96929929647838e-01 , 3.50034068222415e-01 , 3.16124199273713e+00 ), ( 1.31332645357206e+00 , 1.34643286624227e+00 , 3.76642698902620e+00 ), ( 8.40773797302887e-01 , 1.98100698226988e+00 , 5.02554690429120e+00 ), ( 2.08826803285072e+00 , 2.69720522357921e+00 , 5.68886943540120e+00 ), ( -3.38064874142760e-01 , 2.91392015283261e+00 , 4.96863248251904e+00 ), ( -1.13355401890519e+00 , 3.06348555057185e+00 , 5.88514771970272e+00 ), ( -5.16867469126270e-01 , 3.52805375720305e+00 , 3.84368677302349e+00 ), ( -1.51811690408844e+00 , 4.53539704647674e+00 , 3.43584551271010e+00 ), ( -6.99370800306209e-01 , 5.41613700843609e+00 , 2.46552934668629e+00 ), ( -2.75639412467584e+00 , 3.89650316598925e+00 , 2.88916479315839e+00 ), ( -3.81645391301319e+00 , 4.51562346198390e+00 , 2.81385309793028e+00 ), ( -2.63074454584207e+00 , 2.67070215903842e+00 , 2.39436849186767e+00 ), ( -3.77616839293599e+00 , 1.80233294721421e+00 , 1.99836789333910e+00 ), ( -3.38449240191245e+00 , 8.86020902736430e-01 , 8.67964646598369e-01 ), ( -4.31780739760532e+00 , 1.07009890178842e+00 , 3.20979010835984e+00 ), ( -5.49785604495399e+00 , 8.11545411383148e-01 , 3.32998166249016e+00 ), ( -3.36643319479492e+00 , 6.95550042589655e-01 , 4.20710184038517e+00 ), ( -3.69481482827732e+00 , 5.14816562374844e-02 , 5.43576555656035e+00 ), ( -2.39148179599744e+00 , -3.19110327206271e-01 , 6.16791671623623e+00 ), ( -4.46091515849428e+00 , 9.79194091149395e-01 , 6.43764801078358e+00 ), ( -5.36126211530540e+00 , 5.96481497769695e-01 , 7.21902898040563e+00 ), ( -6.24393584634194e+00 , 3.61115232827763e+00 , 6.73793062424253e+00 ), ( -6.96374054841084e+00 , 4.29730433911356e+00 , 7.47986193898876e+00 ), ( -6.73483228541235e+00 , 3.17851373057506e+00 , 5.50665660752860e+00 ), ( -4.12684263466858e+00 , 2.24431932714025e+00 , 6.40360191191022e+00 ), ( -4.80725733449393e+00 , 3.21381335861946e+00 , 7.24626740560762e+00 ), ( -4.08929591791521e+00 , 4.56969008482376e+00 , 7.28010753422389e+00 ) } +colvars: Step 21, atoms_positions[size = 51] = { ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 ), ( 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 ), ( 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 ), ( 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ), ( 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 ), ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 ), ( 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 ), ( 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 ), ( 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 ), ( 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ), ( 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 ), ( 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 ), ( 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 ), ( 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 ), ( 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 ), ( 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 ), ( 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 ), ( 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 ), ( 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 ), ( 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 ), ( 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 ), ( 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 ), ( 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 ), ( 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 ), ( -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 ), ( 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 ), ( 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 ), ( 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 ), ( -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 ), ( -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 ), ( -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 ), ( -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 ), ( -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 ), ( -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 ), ( -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 ), ( -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 ), ( -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 ), ( -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 ), ( -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 ), ( -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 ), ( -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 ), ( -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 ), ( -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 ), ( -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 ), ( -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 ), ( -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 ), ( -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 ), ( -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 ), ( -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 ), ( -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 ), ( -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ) } colvars: Step 21, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 21, atom_groups_ids[size = 0] = @@ -2069,162 +3251,301 @@ colvars: Collective variables module, step no. 21 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.03300920671651e-01 , -1.24565183823531e-03 , 9.52894012926530e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.02299978352974e-01 , -1.10908187249818e-03 , 9.53212197270467e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ). +colvars: Calculating colvar components. colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group2". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 , 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 , 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 , 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 , 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 , 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 , 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 , 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 , 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 , 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 , 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 , 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 , 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 , 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 , 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 , 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 , -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 , 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 , 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 , 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 , -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 , -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 , -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 , -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 , -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 , -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 , -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 , -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 , -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 , -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 , -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 , -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 , -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 , -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 , -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 , -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 , -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 , -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 , -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 , -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 , -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 , -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 , -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.03300920671651e-01 , -1.24565183823531e-03 , 9.52894012926530e-01 ). +colvars: Colvar "one" has value ( -3.02299978352974e-01 , -1.10908187249818e-03 , 9.53212197270467e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 , 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 , 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 , 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 , 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 , 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 , 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 , 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 , 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 , 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 , 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 , 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 , 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 , 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 , 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 , 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 , -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 , 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 , 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 , 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 , -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 , -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 , -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 , -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 , -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 , -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 , -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 , -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 , -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 , -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 , -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 , -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 , -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 , -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 , -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 , -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 , -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 , -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 , -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 , -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 , -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 , -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 , -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.584 , 1.97671 , -15.1543 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.9776 , 6.59776 , 13.1955 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.584 , 1.97671 , -15.1543 ) to colvar "one". -colvars: Adding total bias energy: 44.4051 +colvars: Adding biasing force ( 65.9776 , 6.59776 , 13.1955 ) to colvar "one". +colvars: Adding total bias energy: 56.454 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.584 , 1.97671 , -15.1543 ) +colvars: Force to be applied: ( 65.9776 , 6.59776 , 13.1955 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.91753 , -0.532009 , -1.44704 ) -colvars: ( -4.21678 , -0.456197 , -1.24084 ) -colvars: ( -4.21678 , -0.456197 , -1.24084 ) -colvars: ( -5.61688 , -0.607668 , -1.65283 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17763 , -0.55873 , -1.51773 ) +colvars: ( -4.43981 , -0.479111 , -1.30145 ) +colvars: ( -4.43981 , -0.479111 , -1.30145 ) +colvars: ( -5.91396 , -0.638189 , -1.73357 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.891906 , 0.195586 , 0.617925 ) -colvars: ( 0.772598 , 0.266263 , 0.642089 ) -colvars: ( 0.756608 , 0.259381 , 0.623664 ) -colvars: ( 0.66106 , 0.266979 , 0.578105 ) -colvars: ( 0.649197 , 0.200475 , 0.483109 ) -colvars: ( 0.574782 , 0.344106 , 0.63004 ) -colvars: ( 0.467865 , 0.358038 , 0.586254 ) -colvars: ( 0.391392 , 0.455155 , 0.670375 ) -colvars: ( 0.386367 , 0.313552 , 0.479882 ) -colvars: ( 0.351705 , 0.271987 , 0.404649 ) -colvars: ( 0.357075 , 0.318864 , 0.469867 ) -colvars: ( 0.286012 , 0.276062 , 0.371802 ) -colvars: ( 0.258937 , 0.305079 , 0.394476 ) -colvars: ( 0.348314 , 0.178367 , 0.278665 ) -colvars: ( 0.289775 , 0.135071 , 0.187238 ) -colvars: ( 0.470785 , 0.141408 , 0.301007 ) -colvars: ( 0.543166 , 0.0501492 , 0.222262 ) -colvars: ( 0.672405 , 0.0292428 , 0.269806 ) -colvars: ( 0.551783 , 0.018318 , 0.185115 ) -colvars: ( 0.536065 , -0.0466832 , 0.089865 ) -colvars: ( 0.572685 , 0.0661722 , 0.260671 ) -colvars: ( 0.571228 , 0.0499863 , 0.238383 ) -colvars: ( 0.607733 , 0.114636 , 0.345269 ) -colvars: ( 0.447214 , 0.054391 , 0.172023 ) -colvars: ( 0.440442 , -0.00150451 , 0.0940415 ) -colvars: ( 0.345486 , 0.119934 , 0.19962 ) -colvars: ( 0.22128 , 0.12845 , 0.138593 ) -colvars: ( 0.129997 , 0.214092 , 0.198894 ) -colvars: ( 0.193087 , 0.0548001 , 0.0246244 ) -colvars: ( 0.143977 , 0.0186226 , -0.051885 ) -colvars: ( 0.226529 , 0.0293201 , 0.0103425 ) -colvars: ( 0.212492 , -0.0430854 , -0.0937372 ) -colvars: ( 0.247623 , -0.0463613 , -0.0776246 ) -colvars: ( 0.287579 , -0.128929 , -0.163733 ) -colvars: ( 0.243698 , -0.182016 , -0.259597 ) -colvars: ( 0.402497 , -0.143885 , -0.116644 ) -colvars: ( 0.47979 , -0.219282 , -0.171518 ) -colvars: ( 0.610655 , -0.221803 , -0.0986752 ) -colvars: ( 0.432694 , -0.223837 , -0.204969 ) -colvars: ( 0.438223 , -0.29184 , -0.291827 ) -colvars: ( 0.384118 , -0.150658 , -0.136315 ) -colvars: ( 0.330088 , -0.144484 , -0.15959 ) -colvars: ( 0.31366 , -0.0579219 , -0.0544944 ) -colvars: ( 0.2071 , -0.15333 , -0.242905 ) -colvars: ( 0.182803 , -0.195335 , -0.31269 ) -colvars: ( 0.00621687 , -0.199073 , -0.42044 ) -colvars: ( -0.0844942 , -0.2169 , -0.496861 ) -colvars: ( 0.106271 , -0.248861 , -0.428141 ) -colvars: ( 0.125447 , -0.112773 , -0.236717 ) -colvars: ( 0.0064244 , -0.117204 , -0.311877 ) -colvars: ( -0.082367 , -0.0366491 , -0.256863 ) +colvars: ( 0.938409 , 0.205917 , 0.649308 ) +colvars: ( 0.812939 , 0.280222 , 0.674741 ) +colvars: ( 0.796084 , 0.273021 , 0.655411 ) +colvars: ( 0.695659 , 0.280911 , 0.607479 ) +colvars: ( 0.683179 , 0.210948 , 0.507605 ) +colvars: ( 0.604944 , 0.361991 , 0.662085 ) +colvars: ( 0.492527 , 0.376581 , 0.616054 ) +colvars: ( 0.412122 , 0.478697 , 0.704501 ) +colvars: ( 0.4068 , 0.329772 , 0.504253 ) +colvars: ( 0.37036 , 0.286018 , 0.425148 ) +colvars: ( 0.375962 , 0.335386 , 0.49376 ) +colvars: ( 0.301207 , 0.290356 , 0.390692 ) +colvars: ( 0.272701 , 0.320908 , 0.414568 ) +colvars: ( 0.366714 , 0.18762 , 0.292764 ) +colvars: ( 0.305151 , 0.142051 , 0.196652 ) +colvars: ( 0.495502 , 0.148798 , 0.316233 ) +colvars: ( 0.57161 , 0.0528351 , 0.233434 ) +colvars: ( 0.707507 , 0.0309113 , 0.283406 ) +colvars: ( 0.580703 , 0.0193165 , 0.194346 ) +colvars: ( 0.56417 , -0.049067 , 0.0942064 ) +colvars: ( 0.602717 , 0.0696309 , 0.273751 ) +colvars: ( 0.601217 , 0.052565 , 0.250287 ) +colvars: ( 0.639638 , 0.120557 , 0.362631 ) +colvars: ( 0.47081 , 0.0571361 , 0.180534 ) +colvars: ( 0.463698 , -0.0016794 , 0.0985368 ) +colvars: ( 0.363826 , 0.126049 , 0.209575 ) +colvars: ( 0.233212 , 0.134951 , 0.145435 ) +colvars: ( 0.137212 , 0.225013 , 0.20886 ) +colvars: ( 0.203537 , 0.0574894 , 0.0256383 ) +colvars: ( 0.151903 , 0.0193983 , -0.054803 ) +colvars: ( 0.238672 , 0.0307383 , 0.0106473 ) +colvars: ( 0.223882 , -0.0454067 , -0.098754 ) +colvars: ( 0.260791 , -0.0487962 , -0.0817865 ) +colvars: ( 0.302852 , -0.135689 , -0.17237 ) +colvars: ( 0.256701 , -0.191549 , -0.273147 ) +colvars: ( 0.423714 , -0.151388 , -0.122896 ) +colvars: ( 0.505007 , -0.230683 , -0.180616 ) +colvars: ( 0.642633 , -0.233287 , -0.104063 ) +colvars: ( 0.455513 , -0.235533 , -0.215807 ) +colvars: ( 0.461329 , -0.307071 , -0.307132 ) +colvars: ( 0.404456 , -0.158601 , -0.143639 ) +colvars: ( 0.34767 , -0.152165 , -0.168129 ) +colvars: ( 0.330422 , -0.0611416 , -0.0576542 ) +colvars: ( 0.218327 , -0.161517 , -0.255695 ) +colvars: ( 0.19279 , -0.205733 , -0.329075 ) +colvars: ( 0.00701507 , -0.209656 , -0.442258 ) +colvars: ( -0.0883831 , -0.228444 , -0.522584 ) +colvars: ( 0.112213 , -0.261965 , -0.450357 ) +colvars: ( 0.132438 , -0.118861 , -0.249152 ) +colvars: ( 0.00726368 , -0.123565 , -0.328143 ) +colvars: ( -0.0861204 , -0.0388487 , -0.270274 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.91753 , 0.532009 , 1.44704 ) -colvars: ( 4.21678 , 0.456197 , 1.24084 ) -colvars: ( 4.21678 , 0.456197 , 1.24084 ) -colvars: ( 5.61688 , 0.607668 , 1.65283 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17763 , 0.55873 , 1.51773 ) +colvars: ( 4.43981 , 0.479111 , 1.30145 ) +colvars: ( 4.43981 , 0.479111 , 1.30145 ) +colvars: ( 5.91396 , 0.638189 , 1.73357 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.615602 , -0.0810076 , -0.369309 ) -colvars: ( -0.553704 , -0.163454 , -0.338593 ) -colvars: ( -0.50405 , -0.141549 , -0.28047 ) -colvars: ( -0.514641 , -0.190835 , -0.309834 ) -colvars: ( -0.505038 , -0.132164 , -0.277892 ) -colvars: ( -0.489997 , -0.282534 , -0.319994 ) -colvars: ( -0.457405 , -0.322712 , -0.302592 ) -colvars: ( -0.435808 , -0.429648 , -0.321602 ) -colvars: ( -0.394641 , -0.287483 , -0.226254 ) -colvars: ( -0.390123 , -0.262259 , -0.212131 ) -colvars: ( -0.34547 , -0.281893 , -0.174821 ) -colvars: ( -0.285215 , -0.245148 , -0.100423 ) -colvars: ( -0.236733 , -0.260049 , -0.0574722 ) -colvars: ( -0.304618 , -0.142329 , -0.0807779 ) -colvars: ( -0.273469 , -0.113154 , -0.0384457 ) -colvars: ( -0.358811 , -0.0851582 , -0.11338 ) -colvars: ( -0.385376 , 0.0127408 , -0.102787 ) -colvars: ( -0.435425 , 0.0601736 , -0.134937 ) -colvars: ( -0.422845 , 0.0277427 , -0.134655 ) -colvars: ( -0.411501 , 0.0843291 , -0.101759 ) -colvars: ( -0.466792 , -0.02608 , -0.199194 ) -colvars: ( -0.500975 , -0.0275029 , -0.234014 ) -colvars: ( -0.550739 , -0.0926642 , -0.308698 ) -colvars: ( -0.449109 , -0.0573964 , -0.193372 ) -colvars: ( -0.455923 , -0.0134487 , -0.183492 ) -colvars: ( -0.394244 , -0.131456 , -0.166519 ) -colvars: ( -0.336904 , -0.162639 , -0.120878 ) -colvars: ( -0.286737 , -0.252516 , -0.104752 ) -colvars: ( -0.29585 , -0.090072 , -0.0521115 ) -colvars: ( -0.282695 , -0.0715052 , -0.0318585 ) -colvars: ( -0.276066 , -0.0453829 , -0.0152762 ) -colvars: ( -0.240822 , 0.0290937 , 0.0483898 ) -colvars: ( -0.219615 , 0.0553562 , 0.0796435 ) -colvars: ( -0.28464 , 0.115567 , 0.0373355 ) -colvars: ( -0.258101 , 0.15719 , 0.0797783 ) -colvars: ( -0.353642 , 0.143602 , -0.0211973 ) -colvars: ( -0.402202 , 0.219553 , -0.041008 ) -colvars: ( -0.47301 , 0.242047 , -0.10346 ) -colvars: ( -0.41372 , 0.19983 , -0.0600593 ) -colvars: ( -0.418186 , 0.26045 , -0.0414842 ) -colvars: ( -0.418217 , 0.113579 , -0.0973709 ) -colvars: ( -0.425289 , 0.0835588 , -0.11588 ) -colvars: ( -0.44674 , -0.00941062 , -0.172747 ) -colvars: ( -0.358877 , 0.0723239 , -0.0535549 ) -colvars: ( -0.362162 , 0.0985662 , -0.0468683 ) -colvars: ( -0.198547 , 0.104879 , 0.119604 ) -colvars: ( -0.149335 , 0.106738 , 0.169661 ) -colvars: ( -0.225003 , 0.176932 , 0.120476 ) -colvars: ( -0.29663 , 0.0316992 , -0.00658352 ) -colvars: ( -0.230189 , 0.0181247 , 0.0548804 ) -colvars: ( -0.17654 , -0.0646942 , 0.0771833 ) +colvars: ( -0.647597 , -0.08533 , -0.387635 ) +colvars: ( -0.582553 , -0.172014 , -0.355315 ) +colvars: ( -0.530273 , -0.149005 , -0.294208 ) +colvars: ( -0.54155 , -0.200763 , -0.325126 ) +colvars: ( -0.531451 , -0.139049 , -0.291615 ) +colvars: ( -0.515703 , -0.297172 , -0.335767 ) +colvars: ( -0.481511 , -0.33938 , -0.317504 ) +colvars: ( -0.45886 , -0.451822 , -0.337425 ) +colvars: ( -0.415505 , -0.302316 , -0.237317 ) +colvars: ( -0.410791 , -0.275762 , -0.222529 ) +colvars: ( -0.363752 , -0.296458 , -0.183238 ) +colvars: ( -0.300376 , -0.257805 , -0.105085 ) +colvars: ( -0.249345 , -0.2735 , -0.0598991 ) +colvars: ( -0.320733 , -0.149685 , -0.0845037 ) +colvars: ( -0.287998 , -0.11898 , -0.0400642 ) +colvars: ( -0.377658 , -0.0895964 , -0.118768 ) +colvars: ( -0.405546 , 0.0133467 , -0.107695 ) +colvars: ( -0.458097 , 0.0631835 , -0.141463 ) +colvars: ( -0.445 , 0.0291528 , -0.141238 ) +colvars: ( -0.433071 , 0.0886758 , -0.106725 ) +colvars: ( -0.491263 , -0.0274384 , -0.209044 ) +colvars: ( -0.52727 , -0.0289039 , -0.245679 ) +colvars: ( -0.579639 , -0.0974287 , -0.324126 ) +colvars: ( -0.472798 , -0.0602975 , -0.202995 ) +colvars: ( -0.479984 , -0.0140596 , -0.192671 ) +colvars: ( -0.415139 , -0.138167 , -0.174734 ) +colvars: ( -0.354901 , -0.170922 , -0.12679 ) +colvars: ( -0.302178 , -0.265433 , -0.109782 ) +colvars: ( -0.311696 , -0.0946061 , -0.0545715 ) +colvars: ( -0.297902 , -0.0750502 , -0.0333377 ) +colvars: ( -0.290814 , -0.0476428 , -0.0158476 ) +colvars: ( -0.253709 , 0.0306758 , 0.0510159 ) +colvars: ( -0.231328 , 0.0582544 , 0.0838957 ) +colvars: ( -0.299767 , 0.121614 , 0.0393331 ) +colvars: ( -0.271869 , 0.165405 , 0.0838853 ) +colvars: ( -0.372299 , 0.151075 , -0.0221797 ) +colvars: ( -0.423348 , 0.230947 , -0.0430581 ) +colvars: ( -0.497764 , 0.254569 , -0.108671 ) +colvars: ( -0.43554 , 0.210247 , -0.0631204 ) +colvars: ( -0.440237 , 0.274011 , -0.0436597 ) +colvars: ( -0.44034 , 0.119566 , -0.1023 ) +colvars: ( -0.447858 , 0.0880366 , -0.121783 ) +colvars: ( -0.470473 , -0.0097224 , -0.181497 ) +colvars: ( -0.378063 , 0.0762557 , -0.0563131 ) +colvars: ( -0.381553 , 0.10388 , -0.0493399 ) +colvars: ( -0.209444 , 0.110513 , 0.12563 ) +colvars: ( -0.157725 , 0.112495 , 0.178205 ) +colvars: ( -0.237182 , 0.186248 , 0.126541 ) +colvars: ( -0.312603 , 0.0335326 , -0.0069135 ) +colvars: ( -0.242773 , 0.0192876 , 0.0576581 ) +colvars: ( -0.186378 , -0.0678045 , 0.0811573 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 21. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 21. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 21, atoms_new_colvar_forces = { ( -4.64122776904015e+00 , -4.17430462035631e-01 , -1.19842694137483e+00 ), ( -3.99788899167886e+00 , -3.53388097492481e-01 , -9.37343738530352e-01 ), ( -4.07036342226094e+00 , -3.80053411283391e-01 , -9.72567817047775e-01 ), ( -5.47271843477268e+00 , -5.39356608605815e-01 , -1.44761651153678e+00 ), ( 2.52557618430625e-01 , 1.17832033814582e-01 , 3.43194187277646e-01 ), ( 5.00231710964028e+00 , 5.93580565697120e-01 , 1.75708806280753e+00 ), ( 4.22724308789953e+00 , 4.91523742388943e-01 , 1.52450102653856e+00 ), ( -4.44156059175932e-02 , 2.55069516317784e-02 , 3.48772662262247e-01 ), ( 4.20850881223129e+00 , 4.82266099920002e-01 , 1.49446742226968e+00 ), ( 5.57845842449923e+00 , 6.17396054603903e-01 , 1.84535056502956e+00 ), ( 1.16042863660146e-02 , 3.69709529684829e-02 , 2.95046652017487e-01 ), ( 7.96432107015188e-04 , 3.09136859029808e-02 , 2.71379106274306e-01 ), ( 2.22040284266436e-02 , 4.50297362282180e-02 , 3.37004061353848e-01 ), ( 4.36956298307483e-02 , 3.60373642448502e-02 , 1.97887370271810e-01 ), ( 1.63067370046763e-02 , 2.19169468887107e-02 , 1.48792708452083e-01 ), ( 1.11974233351976e-01 , 5.62498704593333e-02 , 1.87627235244391e-01 ), ( 1.57790381080519e-01 , 6.28899649707613e-02 , 1.19475425943700e-01 ), ( 2.36979706130974e-01 , 8.94163656617664e-02 , 1.34869027391466e-01 ), ( 1.28938337913741e-01 , 4.60606453470170e-02 , 5.04601588302178e-02 ), ( 1.24564403423756e-01 , 3.76458353164540e-02 , -1.18943459271851e-02 ), ( 1.05893496825123e-01 , 4.00922005344408e-02 , 6.14766757574045e-02 ), ( 7.02528486399241e-02 , 2.24834468030063e-02 , 4.36872407426400e-03 ), ( 5.69946237581154e-02 , 2.19722584686867e-02 , 3.65716659864114e-02 ), ( -1.89475792886762e-03 , -3.00538690278939e-03 , -2.13488795274948e-02 ), ( -1.54814285062692e-02 , -1.49532101107763e-02 , -8.94500255718244e-02 ), ( -4.87583053309668e-02 , -1.15215500406721e-02 , 3.31011992449969e-02 ), ( -1.15624059454000e-01 , -3.41896795614565e-02 , 1.77153613311154e-02 ), ( -1.56740904653225e-01 , -3.84237775734388e-02 , 9.41425203159714e-02 ), ( -1.02763736823437e-01 , -3.52719162074792e-02 , -2.74871114356013e-02 ), ( -1.38717967225407e-01 , -5.28825983432749e-02 , -8.37434673842979e-02 ), ( -4.95364227181623e-02 , -1.60628499684035e-02 , -4.93370527315155e-03 ), ( -2.83303107873536e-02 , -1.39916722755991e-02 , -4.53474253713426e-02 ), ( 2.80080137569232e-02 , 8.99489712055920e-03 , 2.01889728907423e-03 ), ( 2.93875292420265e-03 , -1.33624173413813e-02 , -1.26397763016215e-01 ), ( -1.44021922603752e-02 , -2.48265383234662e-02 , -1.79818345390667e-01 ), ( 4.88553431363245e-02 , -2.83192569295265e-04 , -1.37841673828266e-01 ), ( 7.75883326310623e-02 , 2.71567253110505e-04 , -2.12526047690265e-01 ), ( 1.37644360337415e-01 , 2.02437628589764e-02 , -2.02135359298212e-01 ), ( 1.89747254421979e-02 , -2.40074827799895e-02 , -2.65027972415543e-01 ), ( 2.00371917930195e-02 , -3.13905103999074e-02 , -3.33310741492471e-01 ), ( -3.40995722470154e-02 , -3.70787587257643e-02 , -2.33685967415618e-01 ), ( -9.52008606975520e-02 , -6.09254108785846e-02 , -2.75469993003236e-01 ), ( -1.33080367679862e-01 , -6.73325112630011e-02 , -2.27241681799490e-01 ), ( -1.51777101665849e-01 , -8.10060318373823e-02 , -2.96459688598563e-01 ), ( -1.79358866936844e-01 , -9.67691394141569e-02 , -3.59557835653087e-01 ), ( -1.92330306847282e-01 , -9.41940326348025e-02 , -3.00835691903202e-01 ), ( -2.33828886709127e-01 , -1.10162499250053e-01 , -3.27199939583203e-01 ), ( -1.18731823077427e-01 , -7.19287057155311e-02 , -3.07665152024204e-01 ), ( -1.71182740158695e-01 , -8.10734910111616e-02 , -2.43300648476592e-01 ), ( -2.23765053760146e-01 , -9.90797730868727e-02 , -2.56996178086910e-01 ), ( -2.58907028443240e-01 , -1.01343233451123e-01 , -1.79680067307387e-01 ) } +colvars: Step 21, atoms_new_colvar_forces = { ( -4.88681301186317e+00 , -4.38142611451578e-01 , -1.25605632275411e+00 ), ( -4.20942626585542e+00 , -3.70902641485592e-01 , -9.82025645932571e-01 ), ( -4.28570386568547e+00 , -3.98963378348128e-01 , -1.01909902049081e+00 ), ( -5.76223057131802e+00 , -5.66289864819247e-01 , -1.51758168776074e+00 ), ( 2.65810606302739e-01 , 1.24016480312968e-01 , 3.61202368754497e-01 ), ( 5.26686559508448e+00 , 6.23549055462795e-01 , 1.84404742943105e+00 ), ( 4.45082867480974e+00 , 5.16312088873669e-01 , 1.60000276006648e+00 ), ( -4.67385379774749e-02 , 2.68758955307641e-02 , 3.67076186758324e-01 ), ( 4.43110671587295e+00 , 5.06566237586873e-01 , 1.56838816363311e+00 ), ( 5.87352774759951e+00 , 6.48445584579502e-01 , 1.93619144039310e+00 ), ( 1.22105484682847e-02 , 3.89284962080426e-02 , 3.10521313852066e-01 ), ( 8.30806279725038e-04 , 3.25506410605702e-02 , 2.85606721608083e-01 ), ( 2.33566070435660e-02 , 4.74077026791327e-02 , 3.54668873907143e-01 ), ( 4.59808096591225e-02 , 3.79344612434137e-02 , 2.08260281796434e-01 ), ( 1.71532152156076e-02 , 2.30715085108427e-02 , 1.56588051806439e-01 ), ( 1.17843888649354e-01 , 5.92017591302691e-02 , 1.97465023267645e-01 ), ( 1.66064399253842e-01 , 6.61818901802171e-02 , 1.25739234136756e-01 ), ( 2.49409891604407e-01 , 9.40948051046991e-02 , 1.41942715167110e-01 ), ( 1.35702889108031e-01 , 4.84693232741650e-02 , 5.31080880870635e-02 ), ( 1.31098615693591e-01 , 3.96088076835292e-02 , -1.25183758706906e-02 ), ( 1.11453651775268e-01 , 4.21925387711198e-02 , 6.47074859023176e-02 ), ( 7.39473382241158e-02 , 2.36610277247961e-02 , 4.60818526619372e-03 ), ( 5.99983354497177e-02 , 2.31284701305178e-02 , 3.85056635527237e-02 ), ( -1.98740889840437e-03 , -3.16138005557178e-03 , -2.24612720389368e-02 ), ( -1.62858593716134e-02 , -1.57390193591765e-02 , -9.41337890726690e-02 ), ( -5.13126973059539e-02 , -1.21179100784611e-02 , 3.48413140346601e-02 ), ( -1.21689139585961e-01 , -3.59716748440565e-02 , 1.86449118538971e-02 ), ( -1.64966012524163e-01 , -4.04203988914852e-02 , 9.90777284254870e-02 ), ( -1.08158151523756e-01 , -3.71166524479201e-02 , -2.89331725816984e-02 ), ( -1.45998597057365e-01 , -5.56519067784839e-02 , -8.81407756172215e-02 ), ( -5.21418898735860e-02 , -1.69044790281512e-02 , -5.20024110085091e-03 ), ( -2.98270445056342e-02 , -1.47309100218884e-02 , -4.77380634500729e-02 ), ( 2.94632244389206e-02 , 9.45826634269505e-03 , 2.10918770612323e-03 ), ( 3.08518437828148e-03 , -1.40757002641254e-02 , -1.33036887430632e-01 ), ( -1.51672610063517e-02 , -2.61441463003034e-02 , -1.89261836390765e-01 ), ( 5.14151178066671e-02 , -3.13146900668526e-04 , -1.45075886124961e-01 ), ( 8.16587237509778e-02 , 2.64533872962491e-04 , -2.23674261611173e-01 ), ( 1.44869579244897e-01 , 2.12817967175752e-02 , -2.12733528087116e-01 ), ( 1.99730376436439e-02 , -2.52854174630152e-02 , -2.78927384985975e-01 ), ( 2.10915592826001e-02 , -3.30603781613270e-02 , -3.50791739134924e-01 ), ( -3.58834833768484e-02 , -3.90347146482197e-02 , -2.45939138853539e-01 ), ( -1.00187657538689e-01 , -6.41287669796099e-02 , -2.89912474780319e-01 ), ( -1.40051259963949e-01 , -7.08640215953256e-02 , -2.39150934755377e-01 ), ( -1.59735908643585e-01 , -8.52610549438823e-02 , -3.12007902837183e-01 ), ( -1.88763505911318e-01 , -1.01852501930192e-01 , -3.78414875914119e-01 ), ( -2.02429196905031e-01 , -9.91431990223937e-02 , -3.16627707005783e-01 ), ( -2.46107790543223e-01 , -1.15948849811382e-01 , -3.44378434217234e-01 ), ( -1.24969727827573e-01 , -7.57167501644633e-02 , -3.23815174894414e-01 ), ( -1.80164339933053e-01 , -8.53288138440845e-02 , -2.56065656112749e-01 ), ( -2.35509264809481e-01 , -1.04277848727155e-01 , -2.70484408150589e-01 ), ( -2.72498312834940e-01 , -1.06653232615234e-01 , -1.89116531449463e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 21, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2262,10 +3583,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 22, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 22, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 22, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 22, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 22, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 22, atoms_positions[size = 51] = { ( 8.27801368548645e+00 , 4.04154521083087e-02 , -7.48719982598039e-01 ), ( 6.91048178254831e+00 , -5.54844282628265e-01 , -5.61634053620293e-01 ), ( 6.15998899334806e+00 , -3.86782407248557e-01 , 7.45045201710521e-01 ), ( 4.93749817908694e+00 , -1.56253382351994e-01 , 7.27247784002906e-01 ), ( 7.04098154871646e+00 , -2.05498381202224e+00 , -9.24907126413291e-01 ), ( 6.84966641870068e+00 , -2.65929151842961e-01 , 1.92326030422572e+00 ), ( 6.16411047750865e+00 , -1.75644521264806e-01 , 3.18419807209405e+00 ), ( 7.08666977735157e+00 , -3.52549395488943e-01 , 4.32906605591399e+00 ), ( 5.33054928299867e+00 , 1.08795425891365e+00 , 3.35828589703570e+00 ), ( 4.16306444568256e+00 , 1.02043984362175e+00 , 3.70755243742096e+00 ), ( 5.83816978757841e+00 , 2.25648918402764e+00 , 2.98634353700412e+00 ), ( 5.23152682468208e+00 , 3.57504348819360e+00 , 2.92067986950805e+00 ), ( 6.32073118016360e+00 , 4.49864518648533e+00 , 2.34563264114075e+00 ), ( 3.87239920163604e+00 , 3.69348580097200e+00 , 2.04401894200599e+00 ), ( 2.79034998960965e+00 , 4.16543533240563e+00 , 2.47721565504201e+00 ), ( 3.94189801034716e+00 , 3.23467094726968e+00 , 7.30468754417991e-01 ), ( 2.67869166196476e+00 , 3.00668951225046e+00 , -9.89393079298166e-02 ), ( 3.06603237459020e+00 , 2.69343802200018e+00 , -1.51644963865935e+00 ), ( 1.59289453841614e+00 , 2.17429256358265e+00 , 4.34530642985326e-01 ), ( 3.74485678271048e-01 , 2.59622737458133e+00 , 5.02096956065577e-01 ), ( 2.06201476025277e+00 , 1.10100531237450e+00 , 1.06018100447220e+00 ), ( 1.16703150703526e+00 , 1.17105031827408e-01 , 1.70016527342674e+00 ), ( 2.05051994686606e+00 , -1.09708230155034e+00 , 2.01626231749083e+00 ), ( 5.65903621217232e-01 , 6.14817009609931e-01 , 2.95297475259653e+00 ), ( -5.92561426515437e-01 , 3.50487432559455e-01 , 3.16136472744381e+00 ), ( 1.30974532827807e+00 , 1.34773684194957e+00 , 3.75844830461877e+00 ), ( 8.39707064595765e-01 , 1.98254371176299e+00 , 5.02583861033260e+00 ), ( 2.09592827731066e+00 , 2.70621573826577e+00 , 5.69535413725560e+00 ), ( -3.39399534006099e-01 , 2.91294858047198e+00 , 4.96934567299248e+00 ), ( -1.13010863238801e+00 , 3.06435911406876e+00 , 5.88269806602876e+00 ), ( -5.21808874577016e-01 , 3.52229240623140e+00 , 3.83999327035536e+00 ), ( -1.51684318188244e+00 , 4.53077501028791e+00 , 3.42864730545594e+00 ), ( -7.00125566595635e-01 , 5.41784807086397e+00 , 2.46701516327173e+00 ), ( -2.75278692152346e+00 , 3.90427029165478e+00 , 2.88217147780035e+00 ), ( -3.81541548100356e+00 , 4.52118941609546e+00 , 2.81323829061783e+00 ), ( -2.63691140783605e+00 , 2.66667837316107e+00 , 2.38752564076698e+00 ), ( -3.77917708262115e+00 , 1.80294678257828e+00 , 1.99899140484426e+00 ), ( -3.38046820857936e+00 , 8.84672501592023e-01 , 8.61750110511929e-01 ), ( -4.31111065580452e+00 , 1.06949443621696e+00 , 3.20884013303441e+00 ), ( -5.49616869540039e+00 , 8.04350552343177e-01 , 3.33075762198025e+00 ), ( -3.36494439475654e+00 , 6.99826790509561e-01 , 4.20779518487570e+00 ), ( -3.68937388538685e+00 , 5.70683934546486e-02 , 5.43902454796261e+00 ), ( -2.39223176981692e+00 , -3.21238995641683e-01 , 6.16503443092707e+00 ), ( -4.46071627154088e+00 , 9.70497508552942e-01 , 6.43526153201309e+00 ), ( -5.36312442796754e+00 , 5.94773058318206e-01 , 7.21933927948785e+00 ), ( -6.25128250148289e+00 , 3.61642458062405e+00 , 6.74174670270379e+00 ), ( -6.96721167211321e+00 , 4.29673229531940e+00 , 7.48373785142574e+00 ), ( -6.72683623372741e+00 , 3.17490139551974e+00 , 5.50615470481645e+00 ), ( -4.12455101670872e+00 , 2.24354090977720e+00 , 6.39848415514813e+00 ), ( -4.80668381925186e+00 , 3.22191549136373e+00 , 7.25027330885431e+00 ), ( -4.08255995005786e+00 , 4.56373205282011e+00 , 7.27756286077104e+00 ) } +colvars: Step 22, atoms_positions[size = 51] = { ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 ), ( 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 ), ( 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 ), ( 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ), ( 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 ), ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 ), ( 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 ), ( 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 ), ( 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 ), ( 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ), ( 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 ), ( 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 ), ( 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 ), ( 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 ), ( 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 ), ( 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 ), ( 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 ), ( 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 ), ( 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 ), ( 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 ), ( 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 ), ( 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 ), ( 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 ), ( 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 ), ( -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 ), ( 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 ), ( 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 ), ( 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 ), ( -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 ), ( -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 ), ( -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 ), ( -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 ), ( -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 ), ( -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 ), ( -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 ), ( -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 ), ( -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 ), ( -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 ), ( -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 ), ( -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 ), ( -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 ), ( -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 ), ( -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 ), ( -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 ), ( -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 ), ( -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 ), ( -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 ), ( -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 ), ( -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 ), ( -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 ), ( -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ) } colvars: Step 22, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 22, atom_groups_ids[size = 0] = @@ -2282,163 +3603,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 22 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.02208395802458e-01 , -2.38936177499928e-03 , 9.53238887402740e-01 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.01144188109486e-01 , -2.24212177402314e-03 , 9.53575980642250e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 , 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 , 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 , 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 , 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 , 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 , 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 , 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 , 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 , 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 , 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 , 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 , 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 , 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 , 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 , 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 , -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 , 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 , 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 , 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 , -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 , -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 , -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 , -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 , -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 , -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 , -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 , -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 , -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 , -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 , -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 , -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 , -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 , -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 , -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 , -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 , -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 , -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 , -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 , -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 , -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 , -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 , -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.02208395802458e-01 , -2.38936177499928e-03 , 9.53238887402740e-01 ). +colvars: Colvar "one" has value ( -3.01144188109486e-01 , -2.24212177402314e-03 , 9.53575980642250e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 , 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 , 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 , 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 , 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 , 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 , 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 , 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 , 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 , 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 , 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 , 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 , 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 , 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 , 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 , 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 , -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 , 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 , 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 , 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 , -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 , -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 , -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 , -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 , -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 , -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 , -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 , -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 , -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 , -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 , -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 , -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 , -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 , -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 , -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 , -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 , -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 , -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 , -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 , -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 , -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 , -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 , -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.5622 , 1.99959 , -15.1612 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.9267 , 6.59267 , 13.1853 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.5622 , 1.99959 , -15.1612 ) to colvar "one". -colvars: Adding total bias energy: 44.3642 +colvars: Adding biasing force ( 65.9267 , 6.59267 , 13.1853 ) to colvar "one". +colvars: Adding total bias energy: 56.3804 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.5622 , 1.99959 , -15.1612 ) +colvars: Force to be applied: ( 65.9267 , 6.59267 , 13.1853 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.91958 , -0.530926 , -1.44255 ) -colvars: ( -4.21854 , -0.455269 , -1.23699 ) -colvars: ( -4.21854 , -0.455269 , -1.23699 ) -colvars: ( -5.61922 , -0.606431 , -1.6477 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.18039 , -0.557572 , -1.51281 ) +colvars: ( -4.44219 , -0.478118 , -1.29723 ) +colvars: ( -4.44219 , -0.478118 , -1.29723 ) +colvars: ( -5.91712 , -0.636867 , -1.72795 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.891298 , 0.195673 , 0.616732 ) -colvars: ( 0.772142 , 0.266308 , 0.640787 ) -colvars: ( 0.756094 , 0.259429 , 0.622359 ) -colvars: ( 0.66079 , 0.266983 , 0.576903 ) -colvars: ( 0.648943 , 0.200479 , 0.482099 ) -colvars: ( 0.574658 , 0.344074 , 0.628704 ) -colvars: ( 0.467927 , 0.357967 , 0.58498 ) -colvars: ( 0.391581 , 0.455051 , 0.668902 ) -colvars: ( 0.386503 , 0.31346 , 0.478778 ) -colvars: ( 0.351918 , 0.271883 , 0.403698 ) -colvars: ( 0.357184 , 0.318769 , 0.46874 ) -colvars: ( 0.286175 , 0.27595 , 0.370829 ) -colvars: ( 0.259067 , 0.304963 , 0.393412 ) -colvars: ( 0.348379 , 0.178282 , 0.277908 ) -colvars: ( 0.289922 , 0.134969 , 0.186646 ) -colvars: ( 0.470672 , 0.141367 , 0.300252 ) -colvars: ( 0.542945 , 0.0501378 , 0.2217 ) -colvars: ( 0.671979 , 0.0292779 , 0.269189 ) -colvars: ( 0.551617 , 0.0183043 , 0.184664 ) -colvars: ( 0.535921 , -0.0466986 , 0.0896053 ) -colvars: ( 0.572551 , 0.0661567 , 0.260098 ) -colvars: ( 0.571165 , 0.0499642 , 0.237887 ) -colvars: ( 0.607674 , 0.114617 , 0.344591 ) -colvars: ( 0.447341 , 0.0543257 , 0.171619 ) -colvars: ( 0.440603 , -0.00157168 , 0.093809 ) -colvars: ( 0.345737 , 0.119833 , 0.199108 ) -colvars: ( 0.221711 , 0.128306 , 0.138157 ) -colvars: ( 0.130535 , 0.213916 , 0.198285 ) -colvars: ( 0.193512 , 0.0546557 , 0.0243941 ) -colvars: ( 0.144496 , 0.0184613 , -0.0519658 ) -colvars: ( 0.22684 , 0.0291951 , 0.0101261 ) -colvars: ( 0.212775 , -0.0432064 , -0.0937638 ) -colvars: ( 0.247784 , -0.0464628 , -0.0777029 ) -colvars: ( 0.28778 , -0.129023 , -0.163572 ) -colvars: ( 0.243957 , -0.182121 , -0.259256 ) -colvars: ( 0.402565 , -0.143942 , -0.11652 ) -colvars: ( 0.479778 , -0.219312 , -0.171233 ) -colvars: ( 0.610473 , -0.221791 , -0.09848 ) -colvars: ( 0.432816 , -0.22389 , -0.204604 ) -colvars: ( 0.438348 , -0.291888 , -0.291274 ) -colvars: ( 0.384354 , -0.150735 , -0.136093 ) -colvars: ( 0.330464 , -0.144587 , -0.159315 ) -colvars: ( 0.314107 , -0.0580393 , -0.0544232 ) -colvars: ( 0.207637 , -0.153472 , -0.242513 ) -colvars: ( 0.183407 , -0.195486 , -0.312148 ) -colvars: ( 0.00691859 , -0.199267 , -0.419816 ) -colvars: ( -0.0836733 , -0.217123 , -0.49612 ) -colvars: ( 0.106795 , -0.249015 , -0.427476 ) -colvars: ( 0.126051 , -0.112939 , -0.236394 ) -colvars: ( 0.00717829 , -0.117409 , -0.311455 ) -colvars: ( -0.0815173 , -0.0368843 , -0.256607 ) +colvars: ( 0.937837 , 0.206033 , 0.648045 ) +colvars: ( 0.812522 , 0.280295 , 0.673367 ) +colvars: ( 0.795602 , 0.2731 , 0.654034 ) +colvars: ( 0.695433 , 0.280937 , 0.606208 ) +colvars: ( 0.68297 , 0.21097 , 0.506535 ) +colvars: ( 0.60487 , 0.361982 , 0.660675 ) +colvars: ( 0.492646 , 0.376527 , 0.614708 ) +colvars: ( 0.412372 , 0.478612 , 0.702948 ) +colvars: ( 0.406991 , 0.329692 , 0.503084 ) +colvars: ( 0.370632 , 0.285921 , 0.42414 ) +colvars: ( 0.376121 , 0.335305 , 0.49257 ) +colvars: ( 0.301419 , 0.290253 , 0.389663 ) +colvars: ( 0.272874 , 0.320806 , 0.413447 ) +colvars: ( 0.366824 , 0.187542 , 0.29196 ) +colvars: ( 0.305344 , 0.141951 , 0.196021 ) +colvars: ( 0.495429 , 0.148768 , 0.315432 ) +colvars: ( 0.571426 , 0.0528323 , 0.232832 ) +colvars: ( 0.707113 , 0.0309606 , 0.282747 ) +colvars: ( 0.58058 , 0.0193069 , 0.193858 ) +colvars: ( 0.564069 , -0.049083 , 0.093918 ) +colvars: ( 0.60263 , 0.0696209 , 0.273135 ) +colvars: ( 0.601208 , 0.0525443 , 0.249749 ) +colvars: ( 0.639636 , 0.120543 , 0.361902 ) +colvars: ( 0.470996 , 0.0570661 , 0.180093 ) +colvars: ( 0.463921 , -0.00175612 , 0.0982735 ) +colvars: ( 0.364139 , 0.125944 , 0.209023 ) +colvars: ( 0.233708 , 0.134797 , 0.144962 ) +colvars: ( 0.137817 , 0.224829 , 0.208208 ) +colvars: ( 0.204024 , 0.0573313 , 0.0253808 ) +colvars: ( 0.152487 , 0.0192176 , -0.0549051 ) +colvars: ( 0.239038 , 0.0306024 , 0.0104057 ) +colvars: ( 0.224216 , -0.0455418 , -0.0987971 ) +colvars: ( 0.260994 , -0.0489072 , -0.0818819 ) +colvars: ( 0.303103 , -0.1358 , -0.172218 ) +colvars: ( 0.25701 , -0.191677 , -0.272809 ) +colvars: ( 0.42383 , -0.151459 , -0.122784 ) +colvars: ( 0.505043 , -0.230729 , -0.180339 ) +colvars: ( 0.642498 , -0.233286 , -0.10388 ) +colvars: ( 0.45569 , -0.235607 , -0.215448 ) +colvars: ( 0.46151 , -0.307145 , -0.306577 ) +colvars: ( 0.404754 , -0.158699 , -0.14343 ) +colvars: ( 0.348115 , -0.152294 , -0.167864 ) +colvars: ( 0.330943 , -0.0612825 , -0.0576031 ) +colvars: ( 0.218936 , -0.16169 , -0.255308 ) +colvars: ( 0.19347 , -0.205921 , -0.328533 ) +colvars: ( 0.00778441 , -0.209889 , -0.441625 ) +colvars: ( -0.0874925 , -0.22871 , -0.521829 ) +colvars: ( 0.112797 , -0.262155 , -0.44968 ) +colvars: ( 0.133112 , -0.119059 , -0.248836 ) +colvars: ( 0.00809018 , -0.123806 , -0.327722 ) +colvars: ( -0.0851976 , -0.0391176 , -0.270024 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.91958 , 0.530926 , 1.44255 ) -colvars: ( 4.21854 , 0.455269 , 1.23699 ) -colvars: ( 4.21854 , 0.455269 , 1.23699 ) -colvars: ( 5.61922 , 0.606431 , 1.6477 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.18039 , 0.557572 , 1.51281 ) +colvars: ( 4.44219 , 0.478118 , 1.29723 ) +colvars: ( 4.44219 , 0.478118 , 1.29723 ) +colvars: ( 5.91712 , 0.636867 , 1.72795 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.615342 , -0.081068 , -0.368479 ) -colvars: ( -0.553505 , -0.163637 , -0.33755 ) -colvars: ( -0.50365 , -0.141668 , -0.279279 ) -colvars: ( -0.514596 , -0.191058 , -0.308853 ) -colvars: ( -0.504985 , -0.132281 , -0.277084 ) -colvars: ( -0.490097 , -0.282912 , -0.318866 ) -colvars: ( -0.457678 , -0.323156 , -0.301505 ) -colvars: ( -0.436209 , -0.430275 , -0.320304 ) -colvars: ( -0.394855 , -0.28784 , -0.225202 ) -colvars: ( -0.390426 , -0.262575 , -0.211248 ) -colvars: ( -0.345528 , -0.282217 , -0.173614 ) -colvars: ( -0.285194 , -0.245382 , -0.0992369 ) -colvars: ( -0.23655 , -0.260285 , -0.0560627 ) -colvars: ( -0.304502 , -0.142388 , -0.0798233 ) -colvars: ( -0.273381 , -0.113153 , -0.0376045 ) -colvars: ( -0.358583 , -0.0851334 , -0.112505 ) -colvars: ( -0.385057 , 0.0129294 , -0.102135 ) -colvars: ( -0.434952 , 0.0604325 , -0.134289 ) -colvars: ( -0.42269 , 0.0279367 , -0.134226 ) -colvars: ( -0.41134 , 0.0846256 , -0.1015 ) -colvars: ( -0.466792 , -0.0260017 , -0.198765 ) -colvars: ( -0.501154 , -0.027447 , -0.233771 ) -colvars: ( -0.551051 , -0.0927449 , -0.308398 ) -colvars: ( -0.449417 , -0.0573788 , -0.193153 ) -colvars: ( -0.456289 , -0.0133598 , -0.183472 ) -colvars: ( -0.394593 , -0.131548 , -0.166095 ) -colvars: ( -0.337355 , -0.162769 , -0.120445 ) -colvars: ( -0.287219 , -0.252785 , -0.104056 ) -colvars: ( -0.296185 , -0.0900562 , -0.0517789 ) -colvars: ( -0.283119 , -0.0714562 , -0.0316726 ) -colvars: ( -0.276195 , -0.0452739 , -0.0148702 ) -colvars: ( -0.24082 , 0.0293502 , 0.0487042 ) -colvars: ( -0.219394 , 0.055675 , 0.0801032 ) -colvars: ( -0.284625 , 0.115958 , 0.0373792 ) -colvars: ( -0.258092 , 0.157662 , 0.0796913 ) -colvars: ( -0.353614 , 0.144017 , -0.0212458 ) -colvars: ( -0.402179 , 0.220082 , -0.0413122 ) -colvars: ( -0.472932 , 0.242591 , -0.103797 ) -colvars: ( -0.413904 , 0.200311 , -0.0605158 ) -colvars: ( -0.418379 , 0.261034 , -0.0421404 ) -colvars: ( -0.418576 , 0.113902 , -0.097734 ) -colvars: ( -0.425854 , 0.0838187 , -0.11636 ) -colvars: ( -0.447463 , -0.00932624 , -0.173101 ) -colvars: ( -0.359495 , 0.0725864 , -0.0540374 ) -colvars: ( -0.362874 , 0.098869 , -0.0475311 ) -colvars: ( -0.198989 , 0.105264 , 0.119238 ) -colvars: ( -0.149815 , 0.107142 , 0.169263 ) -colvars: ( -0.225264 , 0.177439 , 0.120061 ) -colvars: ( -0.297189 , 0.0319164 , -0.00686269 ) -colvars: ( -0.230788 , 0.018341 , 0.05462 ) -colvars: ( -0.177144 , -0.0646021 , 0.077191 ) +colvars: ( -0.647364 , -0.0854076 , -0.38673 ) +colvars: ( -0.582385 , -0.172223 , -0.354183 ) +colvars: ( -0.529887 , -0.149147 , -0.29292 ) +colvars: ( -0.541548 , -0.201012 , -0.324061 ) +colvars: ( -0.531439 , -0.139183 , -0.290737 ) +colvars: ( -0.515857 , -0.297587 , -0.334546 ) +colvars: ( -0.48185 , -0.339862 , -0.316327 ) +colvars: ( -0.459337 , -0.452499 , -0.336023 ) +colvars: ( -0.415779 , -0.302705 , -0.236181 ) +colvars: ( -0.41116 , -0.276103 , -0.221573 ) +colvars: ( -0.363856 , -0.296811 , -0.181939 ) +colvars: ( -0.300394 , -0.258063 , -0.103809 ) +colvars: ( -0.249187 , -0.273762 , -0.0583855 ) +colvars: ( -0.320649 , -0.149755 , -0.0834752 ) +colvars: ( -0.287944 , -0.118983 , -0.0391583 ) +colvars: ( -0.377454 , -0.0895778 , -0.117824 ) +colvars: ( -0.405245 , 0.013541 , -0.106988 ) +colvars: ( -0.457631 , 0.0634506 , -0.140759 ) +colvars: ( -0.444876 , 0.0293556 , -0.140769 ) +colvars: ( -0.432942 , 0.0889898 , -0.106438 ) +colvars: ( -0.491307 , -0.0273588 , -0.208572 ) +colvars: ( -0.527507 , -0.0288458 , -0.245405 ) +colvars: ( -0.580022 , -0.097517 , -0.323791 ) +colvars: ( -0.473173 , -0.0602778 , -0.20275 ) +colvars: ( -0.480422 , -0.0139616 , -0.192638 ) +colvars: ( -0.415558 , -0.138265 , -0.174271 ) +colvars: ( -0.355429 , -0.171058 , -0.126319 ) +colvars: ( -0.302738 , -0.265719 , -0.10903 ) +colvars: ( -0.312097 , -0.0945859 , -0.0542093 ) +colvars: ( -0.2984 , -0.0749921 , -0.0331333 ) +colvars: ( -0.290994 , -0.0475251 , -0.0154077 ) +colvars: ( -0.253747 , 0.0309515 , 0.0513563 ) +colvars: ( -0.231129 , 0.0585939 , 0.0843908 ) +colvars: ( -0.299791 , 0.122034 , 0.0393848 ) +colvars: ( -0.271899 , 0.165915 , 0.083796 ) +colvars: ( -0.372311 , 0.15152 , -0.0222244 ) +colvars: ( -0.423366 , 0.231516 , -0.0433753 ) +colvars: ( -0.497724 , 0.255152 , -0.109021 ) +colvars: ( -0.435782 , 0.210769 , -0.0636002 ) +colvars: ( -0.440487 , 0.274644 , -0.0443533 ) +colvars: ( -0.440769 , 0.119918 , -0.102679 ) +colvars: ( -0.448509 , 0.0883243 , -0.122288 ) +colvars: ( -0.471295 , -0.00962246 , -0.181865 ) +colvars: ( -0.37877 , 0.076548 , -0.056822 ) +colvars: ( -0.382363 , 0.104218 , -0.0500419 ) +colvars: ( -0.209959 , 0.110937 , 0.125241 ) +colvars: ( -0.158279 , 0.112941 , 0.177779 ) +colvars: ( -0.237503 , 0.186802 , 0.126099 ) +colvars: ( -0.313245 , 0.0337755 , -0.00720674 ) +colvars: ( -0.243457 , 0.0195311 , 0.0573828 ) +colvars: ( -0.187067 , -0.067695 , 0.0811675 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 22. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 22. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 22, atoms_new_colvar_forces = { ( -4.64362435756377e+00 , -4.16321194704651e-01 , -1.19429889473242e+00 ), ( -3.99990228228794e+00 , -3.52598135092567e-01 , -9.33750729130365e-01 ), ( -4.07234574656897e+00 , -3.79343361453849e-01 , -9.68937574346586e-01 ), ( -5.47525911635614e+00 , -5.38233018229667e-01 , -1.44268823995777e+00 ), ( 2.52443878974175e-01 , 1.17761098390893e-01 , 3.43079799840084e-01 ), ( 5.00414122367090e+00 , 5.92087663798134e-01 , 1.75238933474071e+00 ), ( 4.22878886327925e+00 , 4.90080094159747e-01 , 1.52046305842616e+00 ), ( -4.46280359178790e-02 , 2.47762004595115e-02 , 3.48597602711519e-01 ), ( 4.21018749106888e+00 , 4.80888127688503e-01 , 1.49056312857843e+00 ), ( 5.58070893782491e+00 , 6.15739269805591e-01 , 1.84015406971542e+00 ), ( 1.16560390185008e-02 , 3.65525467641691e-02 , 2.95125823351423e-01 ), ( 9.81659743208296e-04 , 3.05674320767270e-02 , 2.71592117412813e-01 ), ( 2.25169962255657e-02 , 4.46787080637800e-02 , 3.37349563480097e-01 ), ( 4.38777508747790e-02 , 3.58933885204249e-02 , 1.98084615347076e-01 ), ( 1.65414412495288e-02 , 2.18165616472960e-02 , 1.49041838759211e-01 ), ( 1.12089410180446e-01 , 5.62334033509360e-02 , 1.87747091678590e-01 ), ( 1.57887832402783e-01 , 6.30671026451442e-02 , 1.19564898123775e-01 ), ( 2.37027646426410e-01 , 8.97104619239126e-02 , 1.34899768599632e-01 ), ( 1.28927625299104e-01 , 4.62409997861884e-02 , 5.04375352603180e-02 ), ( 1.24580777446472e-01 , 3.79269316016676e-02 , -1.18950734070895e-02 ), ( 1.05758966362700e-01 , 4.01550369258798e-02 , 6.13331183007590e-02 ), ( 7.00111307789357e-02 , 2.25172608486911e-02 , 4.11608199695629e-03 ), ( 5.66225054757612e-02 , 2.18724627965876e-02 , 3.61922221764853e-02 ), ( -2.07586912512614e-03 , -3.05310394112909e-03 , -2.15334968345647e-02 ), ( -1.56856338671580e-02 , -1.49314828907843e-02 , -8.96627593190330e-02 ), ( -4.88553187575593e-02 , -1.17150805661757e-02 , 3.30127740516600e-02 ), ( -1.15643753911786e-01 , -3.44630269244757e-02 , 1.77121421923910e-02 ), ( -1.56684032691026e-01 , -3.88689624831749e-02 , 9.42292664262888e-02 ), ( -1.02672896972464e-01 , -3.54005052022133e-02 , -2.73847821124761e-02 ), ( -1.38623680370081e-01 , -5.29948936680882e-02 , -8.36384310820289e-02 ), ( -4.93544699417768e-02 , -1.60788539367000e-02 , -4.74412059617574e-03 ), ( -2.80445145685205e-02 , -1.38562043370483e-02 , -4.50596633993366e-02 ), ( 2.83892512819499e-02 , 9.21212993929264e-03 , 2.40027252997335e-03 ), ( 3.15461838966752e-03 , -1.30651888932173e-02 , -1.26192440651879e-01 ), ( -1.41355141392519e-02 , -2.44590685877909e-02 , -1.79564641180884e-01 ), ( 4.89501835535262e-02 , 7.44406614283932e-05 , -1.37765548961327e-01 ), ( 7.75994828162370e-02 , 7.69860807433909e-04 , -2.12545309095866e-01 ), ( 1.37541041867537e-01 , 2.07998907278499e-02 , -2.02276924639687e-01 ), ( 1.89115205871051e-02 , -2.35785218526706e-02 , -2.65119764355857e-01 ), ( 1.99691487776887e-02 , -3.08539813306087e-02 , -3.33414135038022e-01 ), ( -3.42216386398688e-02 , -3.68330974030720e-02 , -2.33827287304473e-01 ), ( -9.53897625555590e-02 , -6.07678345582899e-02 , -2.75674898888469e-01 ), ( -1.33355821119989e-01 , -6.73654953556458e-02 , -2.27524402127826e-01 ), ( -1.51858084555335e-01 , -8.08852759274181e-02 , -2.96550372965769e-01 ), ( -1.79467185481772e-01 , -9.66173181891047e-02 , -3.59678625643018e-01 ), ( -1.92070427972810e-01 , -9.40038035575220e-02 , -3.00577504538688e-01 ), ( -2.33487922282650e-01 , -1.09981192810187e-01 , -3.26857082818203e-01 ), ( -1.18469480902050e-01 , -7.15757868124807e-02 , -3.07414654052692e-01 ), ( -1.71138351879817e-01 , -8.10225781627923e-02 , -2.43257156571619e-01 ), ( -2.23609708137560e-01 , -9.90676724726366e-02 , -2.56835211377563e-01 ), ( -2.58661817009153e-01 , -1.01486434045830e-01 , -1.79416398570087e-01 ) } +colvars: Step 22, atoms_new_colvar_forces = { ( -4.88991995188348e+00 , -4.36946445275235e-01 , -1.25149461155740e+00 ), ( -4.21204835856932e+00 , -3.70045365021465e-01 , -9.78049932265430e-01 ), ( -4.28830017318750e+00 , -3.98192282580132e-01 , -1.01508752696021e+00 ), ( -5.76558894916333e+00 , -5.65079608774376e-01 , -1.51215513117753e+00 ), ( 2.65714588002630e-01 , 1.23953162992971e-01 , 3.61114033541836e-01 ), ( 5.26940568272368e+00 , 6.21967404854857e-01 , 1.83893911324893e+00 ), ( 4.45298177352149e+00 , 5.14782959611222e-01 , 1.59561479154313e+00 ), ( -4.69653548536075e-02 , 2.61128669902641e-02 , 3.66924827739270e-01 ), ( 4.43339738650594e+00 , 5.05105060382023e-01 , 1.56413748727237e+00 ), ( 5.87659165785773e+00 , 6.46684102044952e-01 , 1.93052040100729e+00 ), ( 1.22657857418941e-02 , 3.84937365477269e-02 , 3.10631368933218e-01 ), ( 1.02494327094066e-03 , 3.21909155756814e-02 , 2.85854826252792e-01 ), ( 2.36865799529954e-02 , 4.70443236203994e-02 , 3.55061815992946e-01 ), ( 4.61756614547097e-02 , 3.77870723926189e-02 , 2.08485111756280e-01 ), ( 1.74006656661443e-02 , 2.29684679904045e-02 , 1.56862733462639e-01 ), ( 1.17974872682656e-01 , 5.91897907116165e-02 , 1.97607824197787e-01 ), ( 1.66181044062799e-01 , 6.63733125927542e-02 , 1.25843935345487e-01 ), ( 2.49481938764797e-01 , 9.44111917516189e-02 , 1.41987290852278e-01 ), ( 1.35703529942543e-01 , 4.86625189401672e-02 , 5.30890090442296e-02 ), ( 1.31127257116666e-01 , 3.99067370549339e-02 , -1.25202432380951e-02 ), ( 1.11322397989908e-01 , 4.22620650541622e-02 , 6.45627197135051e-02 ), ( 7.37004755222272e-02 , 2.36984886005551e-02 , 4.34388828501744e-03 ), ( 5.96135757901188e-02 , 2.30259159161144e-02 , 3.81114773666195e-02 ), ( -2.17739370652986e-03 , -3.21167852637620e-03 , -2.26566557148560e-02 ), ( -1.65012835652354e-02 , -1.57177052995119e-02 , -9.43648859583682e-02 ), ( -5.14188739398183e-02 , -1.23217047604133e-02 , 3.47517177224063e-02 ), ( -1.21720438664443e-01 , -3.62611662717751e-02 , 1.86431783259751e-02 ), ( -1.64920872577396e-01 , -4.08902450237653e-02 , 9.91772771063290e-02 ), ( -1.08072408022284e-01 , -3.72546053487651e-02 , -2.88284781753466e-02 ), ( -1.45912540068657e-01 , -5.57744380285779e-02 , -8.80384104123101e-02 ), ( -5.19557555905013e-02 , -1.69227001208000e-02 , -5.00206290059414e-03 ), ( -2.95301122443954e-02 , -1.45902680960036e-02 , -4.74407408728579e-02 ), ( 2.98653644956911e-02 , 9.68671388074512e-03 , 2.50893473059546e-03 ), ( 3.31172592715373e-03 , -1.37655931017732e-02 , -1.32833386301177e-01 ), ( -1.48890495525763e-02 , -2.57615300512833e-02 , -1.89012552501226e-01 ), ( 5.15190514455810e-02 , 6.14202551529885e-05 , -1.45008800370079e-01 ), ( 8.16776106883810e-02 , 7.86456634676358e-04 , -2.23713976281361e-01 ), ( 1.44774027279720e-01 , 2.18661324134917e-02 , -2.12900431025935e-01 ), ( 1.99086080623049e-02 , -2.48383951721095e-02 , -2.79047907498041e-01 ), ( 2.10221735453149e-02 , -3.25013833690241e-02 , -3.50930690512529e-01 ), ( -3.60145013731311e-02 , -3.87809076824542e-02 , -2.46108666501084e-01 ), ( -1.00394342916154e-01 , -6.39694589856976e-02 , -2.90152454127178e-01 ), ( -1.40352158627249e-01 , -7.09049175416535e-02 , -2.39468004797145e-01 ), ( -1.59834696369235e-01 , -8.51421622671409e-02 , -3.12130135994516e-01 ), ( -1.88893469108966e-01 , -1.01702550693814e-01 , -3.78574445271921e-01 ), ( -2.02174476583266e-01 , -9.89526975671664e-02 , -3.16384827623661e-01 ), ( -2.45771905014202e-01 , -1.15769166566491e-01 , -3.44049265510704e-01 ), ( -1.24705642671454e-01 , -7.53537734390434e-02 , -3.23580986419401e-01 ), ( -1.80133532150737e-01 , -8.52830504276501e-02 , -2.56042427496679e-01 ), ( -2.35367008744962e-01 , -1.04274392403073e-01 , -2.70339355104522e-01 ), ( -2.72265128865591e-01 , -1.06812624413538e-01 , -1.88856770870786e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 22, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2476,10 +3936,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 23, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 23, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 23, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 23, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 23, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 23, atoms_positions[size = 51] = { ( 8.27429746962521e+00 , 4.06036157509702e-02 , -7.45811221333781e-01 ), ( 6.89814895970433e+00 , -5.57132158139863e-01 , -5.54788356134842e-01 ), ( 6.16125272567578e+00 , -3.90016952341577e-01 , 7.53315803491462e-01 ), ( 4.93116392242098e+00 , -1.53429427840197e-01 , 7.29416490736373e-01 ), ( 7.03649688185551e+00 , -2.05668176170026e+00 , -9.20135873083620e-01 ), ( 6.84311409611181e+00 , -2.67859649183596e-01 , 1.93086202222441e+00 ), ( 6.15708313102884e+00 , -1.82794871701656e-01 , 3.17847681418513e+00 ), ( 7.09156141113962e+00 , -3.50944028932900e-01 , 4.33683961026652e+00 ), ( 5.33464473956692e+00 , 1.08451682096381e+00 , 3.36111981091096e+00 ), ( 4.16494434116522e+00 , 1.01824808487741e+00 , 3.71552930081859e+00 ), ( 5.83683575193611e+00 , 2.25736920570107e+00 , 2.98445776181100e+00 ), ( 5.22541833598088e+00 , 3.57338366341035e+00 , 2.91891741946717e+00 ), ( 6.31975668496333e+00 , 4.49728306687404e+00 , 2.33595952085990e+00 ), ( 3.86854834426804e+00 , 3.68678879862976e+00 , 2.04314849685128e+00 ), ( 2.79092021797047e+00 , 4.16716484800730e+00 , 2.47188339052941e+00 ), ( 3.94112456132453e+00 , 3.23121327161743e+00 , 7.30485435503054e-01 ), ( 2.68917923481445e+00 , 3.00985703632277e+00 , -9.59822598095681e-02 ), ( 3.07308339945478e+00 , 2.68704707092774e+00 , -1.51906596728011e+00 ), ( 1.58737847579211e+00 , 2.17134676522185e+00 , 4.30734536433780e-01 ), ( 3.74821443213923e-01 , 2.60221365390555e+00 , 4.97585218223441e-01 ), ( 2.06790892817259e+00 , 1.11471083676162e+00 , 1.05548307716818e+00 ), ( 1.16795595293091e+00 , 1.16868356395829e-01 , 1.70092692741333e+00 ), ( 2.05454167484371e+00 , -1.09489668855112e+00 , 2.01963989919140e+00 ), ( 5.67866725486009e-01 , 6.16146933472038e-01 , 2.95740603646982e+00 ), ( -5.88980055708600e-01 , 3.51033993940136e-01 , 3.16198944729408e+00 ), ( 1.30605835604312e+00 , 1.34986049662244e+00 , 3.75185787266952e+00 ), ( 8.39694040643978e-01 , 1.98343834749641e+00 , 5.02624629998882e+00 ), ( 2.10223057455384e+00 , 2.71474388011875e+00 , 5.70141476330299e+00 ), ( -3.41257639357982e-01 , 2.91180788190043e+00 , 4.96993475672268e+00 ), ( -1.12684878864093e+00 , 3.06513076193413e+00 , 5.88058299115213e+00 ), ( -5.26532904763311e-01 , 3.51793805397593e+00 , 3.83523410140131e+00 ), ( -1.51415914887447e+00 , 4.52540752968940e+00 , 3.42282884797735e+00 ), ( -7.01916490147006e-01 , 5.41957919293459e+00 , 2.46832911241757e+00 ), ( -2.74963874236576e+00 , 3.91240327457789e+00 , 2.87395787177507e+00 ), ( -3.81432478709398e+00 , 4.52664284036742e+00 , 2.81284146638220e+00 ), ( -2.64356861389524e+00 , 2.66159465661507e+00 , 2.38111124489002e+00 ), ( -3.78187860183613e+00 , 1.80523304800468e+00 , 2.00006801750482e+00 ), ( -3.37671144410218e+00 , 8.82891697112618e-01 , 8.55454353608698e-01 ), ( -4.30287987719178e+00 , 1.06813451849581e+00 , 3.20949923764685e+00 ), ( -5.49471689898236e+00 , 7.97234279198013e-01 , 3.33162209619445e+00 ), ( -3.36446502722670e+00 , 7.04350371015529e-01 , 4.20636710688359e+00 ), ( -3.68477391160051e+00 , 6.26164951003031e-02 , 5.44375977334306e+00 ), ( -2.39249633019791e+00 , -3.23155733881825e-01 , 6.16160494964322e+00 ), ( -4.46124577897500e+00 , 9.61199961240979e-01 , 6.43270939921157e+00 ), ( -5.36436620737384e+00 , 5.92973254830113e-01 , 7.21899210478604e+00 ), ( -6.25981886385414e+00 , 3.62108568985818e+00 , 6.74504377670797e+00 ), ( -6.97067612820316e+00 , 4.29617417823745e+00 , 7.48746343048008e+00 ), ( -6.71753772535898e+00 , 3.17157222271881e+00 , 5.50659759266702e+00 ), ( -4.12191899872338e+00 , 2.24379465112528e+00 , 6.39452046099481e+00 ), ( -4.80698644005936e+00 , 3.23069779342996e+00 , 7.25362618631062e+00 ), ( -4.07499670009177e+00 , 4.55819783133641e+00 , 7.27536757501923e+00 ) } +colvars: Step 23, atoms_positions[size = 51] = { ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 ), ( 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 ), ( 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 ), ( 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ), ( 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 ), ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 ), ( 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 ), ( 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 ), ( 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 ), ( 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ), ( 5.83759674592644e+00 , 2.25770089769487e+00 , 2.98449539776859e+00 ), ( 5.22544047027611e+00 , 3.57340227971898e+00 , 2.91910068664912e+00 ), ( 6.31973750751939e+00 , 4.49732575828523e+00 , 2.33613701154318e+00 ), ( 3.86857472003622e+00 , 3.68676300605869e+00 , 2.04327709509885e+00 ), ( 2.79093067267769e+00 , 4.16716972365170e+00 , 2.47196221045982e+00 ), ( 3.94119151819773e+00 , 3.23124212258785e+00 , 7.30595183661825e-01 ), ( 2.68926925665233e+00 , 3.00989334754145e+00 , -9.59122997804579e-02 ), ( 3.07320511801156e+00 , 2.68709232043194e+00 , -1.51899240103286e+00 ), ( 1.58745463578995e+00 , 2.17137449129282e+00 , 4.30768375140066e-01 ), ( 3.74893053327457e-01 , 2.60223269819607e+00 , 4.97582150370188e-01 ), ( 2.06796916608957e+00 , 1.11473680732208e+00 , 1.05552745142886e+00 ), ( 1.16799543789882e+00 , 1.16883822816026e-01 , 1.70093177320460e+00 ), ( 2.05458997515211e+00 , -1.09486128414112e+00 , 2.01968650669132e+00 ), ( 5.67883464785948e-01 , 6.16145271973744e-01 , 2.95739749655181e+00 ), ( -5.88978848799477e-01 , 3.51029880586444e-01 , 3.16194777116286e+00 ), ( 1.30611054901562e+00 , 1.34984121792820e+00 , 3.75187246907796e+00 ), ( 8.39644418143578e-01 , 1.98341133130423e+00 , 5.02625058152132e+00 ), ( 2.10215209936077e+00 , 2.71472163130683e+00 , 5.70145420435647e+00 ), ( -3.41315746205403e-01 , 2.91178403953984e+00 , 4.96991681387973e+00 ), ( -1.12692790956357e+00 , 3.06510460555331e+00 , 5.88054746281053e+00 ), ( -5.26560721980815e-01 , 3.51792887631429e+00 , 3.83522223943442e+00 ), ( -1.51417661879093e+00 , 4.52540121678735e+00 , 3.42279866771453e+00 ), ( -7.01905641915050e-01 , 5.41958098611354e+00 , 2.46832654436502e+00 ), ( -2.74963800407086e+00 , 3.91239748034020e+00 , 2.87388428339751e+00 ), ( -3.81432915765696e+00 , 4.52662820628417e+00 , 2.81274804277420e+00 ), ( -2.64354354981511e+00 , 2.66159372775565e+00 , 2.38103086872300e+00 ), ( -3.78183833193364e+00 , 1.80523478755800e+00 , 1.99994175515576e+00 ), ( -3.37664147509234e+00 , 8.82895505941315e-01 , 8.55338259758225e-01 ), ( -4.30286895448029e+00 , 1.06811651610639e+00 , 3.20934511498940e+00 ), ( -5.49470587750599e+00 , 7.97217291484228e-01 , 3.33144764474570e+00 ), ( -3.36448212751923e+00 , 7.04325113298133e-01 , 4.20622989499706e+00 ), ( -3.68483166538681e+00 , 6.25748844992158e-02 , 5.44360082864042e+00 ), ( -2.39256797298429e+00 , -3.23186883095115e-01 , 6.16148240638997e+00 ), ( -4.46133565763009e+00 , 9.61155447571340e-01 , 6.43253440601395e+00 ), ( -5.36445983873112e+00 , 5.92921715202873e-01 , 7.21880615656639e+00 ), ( -6.25992913038621e+00 , 3.62103269698498e+00 , 6.74487895486376e+00 ), ( -6.97079787066806e+00 , 4.29611545936923e+00 , 7.48729266024479e+00 ), ( -6.71761880599661e+00 , 3.17153101534265e+00 , 5.50641855142913e+00 ), ( -4.12201369887225e+00 , 2.24375136131545e+00 , 6.39437863736119e+00 ), ( -4.80711291753279e+00 , 3.23063933516567e+00 , 7.25347545818975e+00 ), ( -4.07513539547727e+00 , 4.55814099458782e+00 , 7.27526406844747e+00 ) } colvars: Step 23, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 23, atom_groups_ids[size = 0] = @@ -2497,162 +3957,301 @@ colvars: Collective variables module, step no. 23 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.01235983053210e-01 , -3.61953298784803e-03 , 9.53542752840645e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.00108439186526e-01 , -3.46138019158803e-03 , 9.53898812021588e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 , 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 , 5.83759674592644e+00 , 2.25770089769487e+00 , 2.98449539776859e+00 , 5.22544047027611e+00 , 3.57340227971898e+00 , 2.91910068664912e+00 , 6.31973750751939e+00 , 4.49732575828523e+00 , 2.33613701154318e+00 , 3.86857472003622e+00 , 3.68676300605869e+00 , 2.04327709509885e+00 , 2.79093067267769e+00 , 4.16716972365170e+00 , 2.47196221045982e+00 , 3.94119151819773e+00 , 3.23124212258785e+00 , 7.30595183661825e-01 , 2.68926925665233e+00 , 3.00989334754145e+00 , -9.59122997804579e-02 , 3.07320511801156e+00 , 2.68709232043194e+00 , -1.51899240103286e+00 , 1.58745463578995e+00 , 2.17137449129282e+00 , 4.30768375140066e-01 , 3.74893053327457e-01 , 2.60223269819607e+00 , 4.97582150370188e-01 , 2.06796916608957e+00 , 1.11473680732208e+00 , 1.05552745142886e+00 , 1.16799543789882e+00 , 1.16883822816026e-01 , 1.70093177320460e+00 , 2.05458997515211e+00 , -1.09486128414112e+00 , 2.01968650669132e+00 , 5.67883464785948e-01 , 6.16145271973744e-01 , 2.95739749655181e+00 , -5.88978848799477e-01 , 3.51029880586444e-01 , 3.16194777116286e+00 , 1.30611054901562e+00 , 1.34984121792820e+00 , 3.75187246907796e+00 , 8.39644418143578e-01 , 1.98341133130423e+00 , 5.02625058152132e+00 , 2.10215209936077e+00 , 2.71472163130683e+00 , 5.70145420435647e+00 , -3.41315746205403e-01 , 2.91178403953984e+00 , 4.96991681387973e+00 , -1.12692790956357e+00 , 3.06510460555331e+00 , 5.88054746281053e+00 , -5.26560721980815e-01 , 3.51792887631429e+00 , 3.83522223943442e+00 , -1.51417661879093e+00 , 4.52540121678735e+00 , 3.42279866771453e+00 , -7.01905641915050e-01 , 5.41958098611354e+00 , 2.46832654436502e+00 , -2.74963800407086e+00 , 3.91239748034020e+00 , 2.87388428339751e+00 , -3.81432915765696e+00 , 4.52662820628417e+00 , 2.81274804277420e+00 , -2.64354354981511e+00 , 2.66159372775565e+00 , 2.38103086872300e+00 , -3.78183833193364e+00 , 1.80523478755800e+00 , 1.99994175515576e+00 , -3.37664147509234e+00 , 8.82895505941315e-01 , 8.55338259758225e-01 , -4.30286895448029e+00 , 1.06811651610639e+00 , 3.20934511498940e+00 , -5.49470587750599e+00 , 7.97217291484228e-01 , 3.33144764474570e+00 , -3.36448212751923e+00 , 7.04325113298133e-01 , 4.20622989499706e+00 , -3.68483166538681e+00 , 6.25748844992158e-02 , 5.44360082864042e+00 , -2.39256797298429e+00 , -3.23186883095115e-01 , 6.16148240638997e+00 , -4.46133565763009e+00 , 9.61155447571340e-01 , 6.43253440601395e+00 , -5.36445983873112e+00 , 5.92921715202873e-01 , 7.21880615656639e+00 , -6.25992913038621e+00 , 3.62103269698498e+00 , 6.74487895486376e+00 , -6.97079787066806e+00 , 4.29611545936923e+00 , 7.48729266024479e+00 , -6.71761880599661e+00 , 3.17153101534265e+00 , 5.50641855142913e+00 , -4.12201369887225e+00 , 2.24375136131545e+00 , 6.39437863736119e+00 , -4.80711291753279e+00 , 3.23063933516567e+00 , 7.25347545818975e+00 , -4.07513539547727e+00 , 4.55814099458782e+00 , 7.27526406844747e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.01235983053210e-01 , -3.61953298784803e-03 , 9.53542752840645e-01 ). +colvars: Colvar "one" has value ( -3.00108439186526e-01 , -3.46138019158803e-03 , 9.53898812021588e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 , 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 , 5.83759674592644e+00 , 2.25770089769487e+00 , 2.98449539776859e+00 , 5.22544047027611e+00 , 3.57340227971898e+00 , 2.91910068664912e+00 , 6.31973750751939e+00 , 4.49732575828523e+00 , 2.33613701154318e+00 , 3.86857472003622e+00 , 3.68676300605869e+00 , 2.04327709509885e+00 , 2.79093067267769e+00 , 4.16716972365170e+00 , 2.47196221045982e+00 , 3.94119151819773e+00 , 3.23124212258785e+00 , 7.30595183661825e-01 , 2.68926925665233e+00 , 3.00989334754145e+00 , -9.59122997804579e-02 , 3.07320511801156e+00 , 2.68709232043194e+00 , -1.51899240103286e+00 , 1.58745463578995e+00 , 2.17137449129282e+00 , 4.30768375140066e-01 , 3.74893053327457e-01 , 2.60223269819607e+00 , 4.97582150370188e-01 , 2.06796916608957e+00 , 1.11473680732208e+00 , 1.05552745142886e+00 , 1.16799543789882e+00 , 1.16883822816026e-01 , 1.70093177320460e+00 , 2.05458997515211e+00 , -1.09486128414112e+00 , 2.01968650669132e+00 , 5.67883464785948e-01 , 6.16145271973744e-01 , 2.95739749655181e+00 , -5.88978848799477e-01 , 3.51029880586444e-01 , 3.16194777116286e+00 , 1.30611054901562e+00 , 1.34984121792820e+00 , 3.75187246907796e+00 , 8.39644418143578e-01 , 1.98341133130423e+00 , 5.02625058152132e+00 , 2.10215209936077e+00 , 2.71472163130683e+00 , 5.70145420435647e+00 , -3.41315746205403e-01 , 2.91178403953984e+00 , 4.96991681387973e+00 , -1.12692790956357e+00 , 3.06510460555331e+00 , 5.88054746281053e+00 , -5.26560721980815e-01 , 3.51792887631429e+00 , 3.83522223943442e+00 , -1.51417661879093e+00 , 4.52540121678735e+00 , 3.42279866771453e+00 , -7.01905641915050e-01 , 5.41958098611354e+00 , 2.46832654436502e+00 , -2.74963800407086e+00 , 3.91239748034020e+00 , 2.87388428339751e+00 , -3.81432915765696e+00 , 4.52662820628417e+00 , 2.81274804277420e+00 , -2.64354354981511e+00 , 2.66159372775565e+00 , 2.38103086872300e+00 , -3.78183833193364e+00 , 1.80523478755800e+00 , 1.99994175515576e+00 , -3.37664147509234e+00 , 8.82895505941315e-01 , 8.55338259758225e-01 , -4.30286895448029e+00 , 1.06811651610639e+00 , 3.20934511498940e+00 , -5.49470587750599e+00 , 7.97217291484228e-01 , 3.33144764474570e+00 , -3.36448212751923e+00 , 7.04325113298133e-01 , 4.20622989499706e+00 , -3.68483166538681e+00 , 6.25748844992158e-02 , 5.44360082864042e+00 , -2.39256797298429e+00 , -3.23186883095115e-01 , 6.16148240638997e+00 , -4.46133565763009e+00 , 9.61155447571340e-01 , 6.43253440601395e+00 , -5.36445983873112e+00 , 5.92921715202873e-01 , 7.21880615656639e+00 , -6.25992913038621e+00 , 3.62103269698498e+00 , 6.74487895486376e+00 , -6.97079787066806e+00 , 4.29611545936923e+00 , 7.48729266024479e+00 , -6.71761880599661e+00 , 3.17153101534265e+00 , 5.50641855142913e+00 , -4.12201369887225e+00 , 2.24375136131545e+00 , 6.39437863736119e+00 , -4.80711291753279e+00 , 3.23063933516567e+00 , 7.25347545818975e+00 , -4.07513539547727e+00 , 4.55814099458782e+00 , 7.27526406844747e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.5427 , 2.02419 , -15.1673 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.8822 , 6.58822 , 13.1764 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.5427 , 2.02419 , -15.1673 ) to colvar "one". -colvars: Adding total bias energy: 44.3287 +colvars: Adding biasing force ( 65.8822 , 6.58822 , 13.1764 ) to colvar "one". +colvars: Adding total bias energy: 56.3159 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.5427 , 2.02419 , -15.1673 ) +colvars: Force to be applied: ( 65.8822 , 6.58822 , 13.1764 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.92136 , -0.529959 , -1.43864 ) -colvars: ( -4.22006 , -0.45444 , -1.23363 ) -colvars: ( -4.22006 , -0.45444 , -1.23363 ) -colvars: ( -5.62125 , -0.605327 , -1.64323 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.1833 , -0.556583 , -1.50862 ) +colvars: ( -4.44468 , -0.477269 , -1.29364 ) +colvars: ( -4.44468 , -0.477269 , -1.29364 ) +colvars: ( -5.92044 , -0.635737 , -1.72317 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.890716 , 0.195751 , 0.615641 ) -colvars: ( 0.771705 , 0.266344 , 0.639594 ) -colvars: ( 0.75561 , 0.259466 , 0.621163 ) -colvars: ( 0.660525 , 0.266983 , 0.575802 ) -colvars: ( 0.648693 , 0.200481 , 0.481178 ) -colvars: ( 0.574528 , 0.344039 , 0.627476 ) -colvars: ( 0.46797 , 0.357895 , 0.583809 ) -colvars: ( 0.391741 , 0.454946 , 0.667544 ) -colvars: ( 0.386619 , 0.313369 , 0.477765 ) -colvars: ( 0.352104 , 0.271783 , 0.40283 ) -colvars: ( 0.357281 , 0.318673 , 0.467708 ) -colvars: ( 0.286328 , 0.275838 , 0.369941 ) -colvars: ( 0.259195 , 0.304846 , 0.39244 ) -colvars: ( 0.348441 , 0.178198 , 0.277222 ) -colvars: ( 0.290061 , 0.134871 , 0.186115 ) -colvars: ( 0.470567 , 0.141325 , 0.29957 ) -colvars: ( 0.542738 , 0.0501261 , 0.221198 ) -colvars: ( 0.671582 , 0.0293096 , 0.268637 ) -colvars: ( 0.551456 , 0.0182934 , 0.184265 ) -colvars: ( 0.535781 , -0.0467091 , 0.0893861 ) -colvars: ( 0.572413 , 0.0661445 , 0.259585 ) -colvars: ( 0.571088 , 0.0499483 , 0.237445 ) -colvars: ( 0.607595 , 0.114604 , 0.343977 ) -colvars: ( 0.447441 , 0.0542698 , 0.171263 ) -colvars: ( 0.440734 , -0.00162684 , 0.0936123 ) -colvars: ( 0.345957 , 0.119742 , 0.198649 ) -colvars: ( 0.222099 , 0.128175 , 0.13777 ) -colvars: ( 0.131027 , 0.213751 , 0.197734 ) -colvars: ( 0.193899 , 0.0545245 , 0.0241991 ) -colvars: ( 0.144969 , 0.0183161 , -0.0520214 ) -colvars: ( 0.227127 , 0.0290807 , 0.00994534 ) -colvars: ( 0.21304 , -0.0433161 , -0.0937664 ) -colvars: ( 0.24794 , -0.0465565 , -0.0777525 ) -colvars: ( 0.287966 , -0.129104 , -0.163398 ) -colvars: ( 0.244197 , -0.182211 , -0.258915 ) -colvars: ( 0.402621 , -0.143988 , -0.11638 ) -colvars: ( 0.479757 , -0.21933 , -0.170943 ) -colvars: ( 0.610292 , -0.221769 , -0.0982739 ) -colvars: ( 0.432914 , -0.223926 , -0.204241 ) -colvars: ( 0.438448 , -0.291918 , -0.290735 ) -colvars: ( 0.384556 , -0.150796 , -0.135865 ) -colvars: ( 0.330792 , -0.144668 , -0.159037 ) -colvars: ( 0.314496 , -0.0581364 , -0.0543378 ) -colvars: ( 0.208117 , -0.15359 , -0.242127 ) -colvars: ( 0.183948 , -0.195611 , -0.311622 ) -colvars: ( 0.00756533 , -0.199437 , -0.419212 ) -colvars: ( -0.0829134 , -0.217319 , -0.495407 ) -colvars: ( 0.107278 , -0.249147 , -0.426832 ) -colvars: ( 0.126598 , -0.113083 , -0.236073 ) -colvars: ( 0.00786893 , -0.117588 , -0.311042 ) -colvars: ( -0.080734 , -0.0370963 , -0.256349 ) +colvars: ( 0.937369 , 0.206157 , 0.646941 ) +colvars: ( 0.812191 , 0.280383 , 0.672161 ) +colvars: ( 0.795216 , 0.27319 , 0.652825 ) +colvars: ( 0.69527 , 0.280983 , 0.605092 ) +colvars: ( 0.682821 , 0.211007 , 0.505598 ) +colvars: ( 0.604839 , 0.361999 , 0.659432 ) +colvars: ( 0.492784 , 0.376503 , 0.61352 ) +colvars: ( 0.412625 , 0.478565 , 0.701573 ) +colvars: ( 0.407195 , 0.32964 , 0.502054 ) +colvars: ( 0.370905 , 0.285851 , 0.423253 ) +colvars: ( 0.376299 , 0.33525 , 0.49152 ) +colvars: ( 0.301644 , 0.290176 , 0.388756 ) +colvars: ( 0.273067 , 0.320728 , 0.412456 ) +colvars: ( 0.36696 , 0.187481 , 0.291256 ) +colvars: ( 0.305554 , 0.141867 , 0.19547 ) +colvars: ( 0.495405 , 0.148749 , 0.314732 ) +colvars: ( 0.571303 , 0.0528337 , 0.232312 ) +colvars: ( 0.706806 , 0.031009 , 0.282179 ) +colvars: ( 0.580509 , 0.0193019 , 0.193441 ) +colvars: ( 0.564018 , -0.0490979 , 0.0936797 ) +colvars: ( 0.602589 , 0.0696201 , 0.272604 ) +colvars: ( 0.601233 , 0.0525344 , 0.249288 ) +colvars: ( 0.639666 , 0.120544 , 0.361271 ) +colvars: ( 0.471192 , 0.0570108 , 0.179716 ) +colvars: ( 0.464149 , -0.00182034 , 0.0980557 ) +colvars: ( 0.364447 , 0.125858 , 0.208543 ) +colvars: ( 0.234179 , 0.134668 , 0.144552 ) +colvars: ( 0.138384 , 0.224675 , 0.207634 ) +colvars: ( 0.204488 , 0.0571917 , 0.0251625 ) +colvars: ( 0.153036 , 0.0190555 , -0.0549852 ) +colvars: ( 0.239397 , 0.0304802 , 0.0102023 ) +colvars: ( 0.224549 , -0.0456687 , -0.0988228 ) +colvars: ( 0.261214 , -0.049014 , -0.0819538 ) +colvars: ( 0.303362 , -0.135908 , -0.172068 ) +colvars: ( 0.257321 , -0.191804 , -0.272491 ) +colvars: ( 0.42397 , -0.15153 , -0.122667 ) +colvars: ( 0.505112 , -0.230782 , -0.180071 ) +colvars: ( 0.642414 , -0.233293 , -0.103694 ) +colvars: ( 0.455881 , -0.235683 , -0.215108 ) +colvars: ( 0.461703 , -0.307226 , -0.306062 ) +colvars: ( 0.405049 , -0.158793 , -0.143225 ) +colvars: ( 0.348538 , -0.152413 , -0.167611 ) +colvars: ( 0.331431 , -0.0614071 , -0.0575418 ) +colvars: ( 0.219503 , -0.161853 , -0.254948 ) +colvars: ( 0.194098 , -0.206098 , -0.328034 ) +colvars: ( 0.00849678 , -0.210114 , -0.44105 ) +colvars: ( -0.0866731 , -0.228968 , -0.521146 ) +colvars: ( 0.113348 , -0.262344 , -0.449064 ) +colvars: ( 0.133738 , -0.119242 , -0.248541 ) +colvars: ( 0.00885107 , -0.12403 , -0.327337 ) +colvars: ( -0.0843512 , -0.0393653 , -0.269794 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.92136 , 0.529959 , 1.43864 ) -colvars: ( 4.22006 , 0.45444 , 1.23363 ) -colvars: ( 4.22006 , 0.45444 , 1.23363 ) -colvars: ( 5.62125 , 0.605327 , 1.64323 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.1833 , 0.556583 , 1.50862 ) +colvars: ( 4.44468 , 0.477269 , 1.29364 ) +colvars: ( 4.44468 , 0.477269 , 1.29364 ) +colvars: ( 5.92044 , 0.635737 , 1.72317 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.615116 , -0.0811182 , -0.367766 ) -colvars: ( -0.553328 , -0.163822 , -0.336621 ) -colvars: ( -0.503272 , -0.141781 , -0.278193 ) -colvars: ( -0.514562 , -0.191291 , -0.307976 ) -colvars: ( -0.50494 , -0.132404 , -0.27637 ) -colvars: ( -0.490199 , -0.283315 , -0.317847 ) -colvars: ( -0.45794 , -0.323634 , -0.300521 ) -colvars: ( -0.436592 , -0.43095 , -0.319117 ) -colvars: ( -0.39505 , -0.288229 , -0.224236 ) -colvars: ( -0.390705 , -0.262923 , -0.210442 ) -colvars: ( -0.345565 , -0.282568 , -0.172486 ) -colvars: ( -0.285146 , -0.245641 , -0.0981115 ) -colvars: ( -0.23634 , -0.260542 , -0.05471 ) -colvars: ( -0.304365 , -0.142459 , -0.0789207 ) -colvars: ( -0.273267 , -0.113162 , -0.036803 ) -colvars: ( -0.358348 , -0.0851094 , -0.111689 ) -colvars: ( -0.384739 , 0.0131297 , -0.101534 ) -colvars: ( -0.434493 , 0.0607143 , -0.133702 ) -colvars: ( -0.422534 , 0.0281399 , -0.133851 ) -colvars: ( -0.411178 , 0.0849359 , -0.101284 ) -colvars: ( -0.466792 , -0.0259224 , -0.198403 ) -colvars: ( -0.50133 , -0.0273947 , -0.233597 ) -colvars: ( -0.551365 , -0.0928377 , -0.308187 ) -colvars: ( -0.449709 , -0.0573736 , -0.192993 ) -colvars: ( -0.456638 , -0.0132811 , -0.183504 ) -colvars: ( -0.394917 , -0.131663 , -0.165728 ) -colvars: ( -0.337768 , -0.162929 , -0.120059 ) -colvars: ( -0.287655 , -0.253095 , -0.103407 ) -colvars: ( -0.29648 , -0.0900622 , -0.0514752 ) -colvars: ( -0.283499 , -0.0714308 , -0.0315074 ) -colvars: ( -0.27629 , -0.0451769 , -0.0144878 ) -colvars: ( -0.240783 , 0.0296042 , 0.0490107 ) -colvars: ( -0.219144 , 0.056 , 0.0805576 ) -colvars: ( -0.284583 , 0.116356 , 0.0374181 ) -colvars: ( -0.258052 , 0.158144 , 0.0796121 ) -colvars: ( -0.35357 , 0.144444 , -0.0213105 ) -colvars: ( -0.402146 , 0.220631 , -0.0416319 ) -colvars: ( -0.472858 , 0.243162 , -0.104163 ) -colvars: ( -0.414073 , 0.200805 , -0.0609873 ) -colvars: ( -0.418555 , 0.261637 , -0.0428032 ) -colvars: ( -0.418912 , 0.114225 , -0.0981215 ) -colvars: ( -0.42639 , 0.0840693 , -0.116866 ) -colvars: ( -0.448153 , -0.00926365 , -0.173495 ) -colvars: ( -0.360071 , 0.0728344 , -0.0545299 ) -colvars: ( -0.363542 , 0.0991567 , -0.0481978 ) -colvars: ( -0.199371 , 0.105637 , 0.118898 ) -colvars: ( -0.150226 , 0.107532 , 0.168903 ) -colvars: ( -0.225477 , 0.177948 , 0.119672 ) -colvars: ( -0.297699 , 0.0321153 , -0.00714581 ) -colvars: ( -0.231326 , 0.0185339 , 0.0543697 ) -colvars: ( -0.17768 , -0.0645428 , 0.0772082 ) +colvars: ( -0.64722 , -0.0854819 , -0.385978 ) +colvars: ( -0.582287 , -0.172448 , -0.3532 ) +colvars: ( -0.529568 , -0.149296 , -0.291765 ) +colvars: ( -0.5416 , -0.201288 , -0.323134 ) +colvars: ( -0.531479 , -0.139334 , -0.289981 ) +colvars: ( -0.516053 , -0.298051 , -0.333467 ) +colvars: ( -0.482216 , -0.340407 , -0.315285 ) +colvars: ( -0.459832 , -0.453265 , -0.334766 ) +colvars: ( -0.416068 , -0.303151 , -0.235153 ) +colvars: ( -0.411539 , -0.276501 , -0.220717 ) +colvars: ( -0.363969 , -0.297218 , -0.180735 ) +colvars: ( -0.300408 , -0.258367 , -0.102605 ) +colvars: ( -0.249022 , -0.274069 , -0.056936 ) +colvars: ( -0.32057 , -0.149849 , -0.0825079 ) +colvars: ( -0.287886 , -0.119007 , -0.0382971 ) +colvars: ( -0.377274 , -0.0895675 , -0.11695 ) +colvars: ( -0.404977 , 0.0137486 , -0.106344 ) +colvars: ( -0.457217 , 0.0637466 , -0.140131 ) +colvars: ( -0.444789 , 0.0295703 , -0.140368 ) +colvars: ( -0.432845 , 0.0893255 , -0.106205 ) +colvars: ( -0.491392 , -0.0272806 , -0.208189 ) +colvars: ( -0.527786 , -0.0287939 , -0.245226 ) +colvars: ( -0.580454 , -0.0976259 , -0.323574 ) +colvars: ( -0.473572 , -0.0602761 , -0.202583 ) +colvars: ( -0.480882 , -0.0138754 , -0.192677 ) +colvars: ( -0.415985 , -0.138398 , -0.173882 ) +colvars: ( -0.355946 , -0.171241 , -0.125907 ) +colvars: ( -0.303275 , -0.266069 , -0.108338 ) +colvars: ( -0.312482 , -0.0945964 , -0.053882 ) +colvars: ( -0.298875 , -0.0749649 , -0.0329531 ) +colvars: ( -0.291161 , -0.0474238 , -0.0149939 ) +colvars: ( -0.253768 , 0.0312272 , 0.0516926 ) +colvars: ( -0.230918 , 0.0589448 , 0.0848873 ) +colvars: ( -0.299812 , 0.122472 , 0.0394347 ) +colvars: ( -0.271919 , 0.166448 , 0.0837218 ) +colvars: ( -0.372336 , 0.151992 , -0.0222881 ) +colvars: ( -0.423408 , 0.232125 , -0.0437123 ) +colvars: ( -0.497728 , 0.255785 , -0.10941 ) +colvars: ( -0.436042 , 0.211321 , -0.064101 ) +colvars: ( -0.440757 , 0.275319 , -0.0450575 ) +colvars: ( -0.441211 , 0.120281 , -0.103093 ) +colvars: ( -0.449167 , 0.0886095 , -0.122829 ) +colvars: ( -0.472122 , -0.00954615 , -0.182289 ) +colvars: ( -0.379465 , 0.0768315 , -0.0573463 ) +colvars: ( -0.383157 , 0.104549 , -0.0507523 ) +colvars: ( -0.210428 , 0.111357 , 0.124889 ) +colvars: ( -0.158775 , 0.113382 , 0.177408 ) +colvars: ( -0.237792 , 0.187372 , 0.125695 ) +colvars: ( -0.313863 , 0.034002 , -0.00750483 ) +colvars: ( -0.244098 , 0.0197518 , 0.0571226 ) +colvars: ( -0.1877 , -0.0676254 , 0.0811942 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 23. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 23. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 23, atoms_new_colvar_forces = { ( -4.64575743161289e+00 , -4.15326505613297e-01 , -1.19076296803634e+00 ), ( -4.00168649092185e+00 , -3.51917355348099e-01 , -9.30658258525421e-01 ), ( -4.07410036359722e+00 , -3.78747790308645e-01 , -9.65806221149623e-01 ), ( -5.47749434496204e+00 , -5.37249924020170e-01 , -1.43842446864572e+00 ), ( 2.52337569752722e-01 , 1.17684984808824e-01 , 3.42969682070111e-01 ), ( 5.00568797229590e+00 , 5.90683442199245e-01 , 1.74826643842408e+00 ), ( 4.23009348282879e+00 , 4.88701588795172e-01 , 1.51691973520631e+00 ), ( -4.48506074491610e-02 , 2.39964121041804e-02 , 3.48426543992292e-01 ), ( 4.21163211404291e+00 , 4.79579587722694e-01 , 1.48716072007476e+00 ), ( 5.58264553620788e+00 , 6.14187100999375e-01 , 1.83562067933871e+00 ), ( 1.17154659552674e-02 , 3.61057291843637e-02 , 2.95221900517982e-01 ), ( 1.18209149819765e-03 , 3.01974765346887e-02 , 2.71829459849482e-01 ), ( 2.28548090668328e-02 , 4.43034216412574e-02 , 3.37730058256575e-01 ), ( 4.40755488767677e-02 , 3.57393096815321e-02 , 1.98301723434123e-01 ), ( 1.67933492779154e-02 , 2.17090047723988e-02 , 1.49312323153462e-01 ), ( 1.12218626939172e-01 , 5.62154114348050e-02 , 1.87880852793175e-01 ), ( 1.57999076492278e-01 , 6.32557423895876e-02 , 1.19663089947760e-01 ), ( 2.37089595724080e-01 , 9.00238756066837e-02 , 1.34935360934111e-01 ), ( 1.28921942478751e-01 , 4.64332948188317e-02 , 5.04141739618137e-02 ), ( 1.24602841198467e-01 , 3.82267546652744e-02 , -1.18977005562169e-02 ), ( 1.05621047589969e-01 , 4.02220936174156e-02 , 6.11820468842756e-02 ), ( 6.97572206409900e-02 , 2.25535655601284e-02 , 3.84721902750745e-03 ), ( 5.62300373090633e-02 , 2.17663372155614e-02 , 3.57901822997330e-02 ), ( -2.26856832183570e-03 , -3.10378001723801e-03 , -2.17303933299124e-02 ), ( -1.59043130583791e-02 , -1.49079527395067e-02 , -8.98921637339600e-02 ), ( -4.89597869999016e-02 , -1.19214583726327e-02 , 3.29207740570250e-02 ), ( -1.15668917471507e-01 , -3.47545911866313e-02 , 1.77107199605389e-02 ), ( -1.56628441055632e-01 , -3.93440147550789e-02 , 9.43269694789447e-02 ), ( -1.02580792170127e-01 , -3.55377061897655e-02 , -2.72761258967842e-02 ), ( -1.38530076890726e-01 , -5.31146259469866e-02 , -8.35288200314778e-02 ), ( -4.91632319023408e-02 , -1.60961005962525e-02 , -4.54246659236648e-03 ), ( -2.77427244171411e-02 , -1.37119281359061e-02 , -4.47556526852855e-02 ), ( 2.87952298701709e-02 , 9.44344188904662e-03 , 2.80501871740882e-03 ), ( 3.38225490613692e-03 , -1.27481720264506e-02 , -1.25979646178916e-01 ), ( -1.38553165859354e-02 , -2.40670947864300e-02 , -1.79302478598568e-01 ), ( 4.90509220560931e-02 , 4.56027763740180e-04 , -1.37690919185591e-01 ), ( 7.76114436868072e-02 , 1.30168634415467e-03 , -2.12575353587131e-01 ), ( 1.37433913707760e-01 , 2.13935019699319e-02 , -2.02437070743730e-01 ), ( 1.88415277808113e-02 , -2.31204846158066e-02 , -2.65228343518005e-01 ), ( 1.98931297036014e-02 , -3.02810928129784e-02 , -3.33537853596992e-01 ), ( -3.43557749957396e-02 , -3.65705614186257e-02 , -2.33986587762447e-01 ), ( -9.55978177063489e-02 , -6.05991137373955e-02 , -2.75902768015860e-01 ), ( -1.33656605971950e-01 , -6.74000200873311e-02 , -2.27832501128480e-01 ), ( -1.51954015420723e-01 , -8.07559029622601e-02 , -2.96657197009173e-01 ), ( -1.79594076018584e-01 , -9.64546783264336e-02 , -3.59819710675989e-01 ), ( -1.91806007504498e-01 , -9.38006688845488e-02 , -3.00313608283580e-01 ), ( -2.33139361551305e-01 , -1.09787613794228e-01 , -3.26503908255684e-01 ), ( -1.18199679569238e-01 , -7.11991167996441e-02 , -3.07160010584178e-01 ), ( -1.71101171967787e-01 , -8.09679159362541e-02 , -2.43219104040647e-01 ), ( -2.23456922888711e-01 , -9.90544977745803e-02 , -2.56672402983881e-01 ), ( -2.58413908875762e-01 , -1.01639124525717e-01 , -1.79140969048224e-01 ) } +colvars: Step 23, atoms_new_colvar_forces = { ( -4.89314969389035e+00 , -4.35907137065574e-01 , -1.24765646733718e+00 ), ( -4.21477401221486e+00 , -3.69333721068355e-01 , -9.74679364978744e-01 ), ( -4.29100768593370e+00 , -3.97574682406545e-01 , -1.01168245402456e+00 ), ( -5.76909754228417e+00 , -5.64064012876958e-01 , -1.50754931217094e+00 ), ( 2.65647982056842e-01 , 1.23894479901734e-01 , 3.61059540383409e-01 ), ( 5.27208481710348e+00 , 6.20530406439631e-01 , 1.83458495674507e+00 ), ( 4.45524528716730e+00 , 5.13364888628985e-01 , 1.59187595082763e+00 ), ( -4.72066769307715e-02 , 2.53003561132784e-02 , 3.66807496622965e-01 ), ( 4.43580435738879e+00 , 5.03758669118885e-01 , 1.56054100287330e+00 ), ( 5.87980588495882e+00 , 6.45086157379882e-01 , 1.92570262804706e+00 ), ( 1.23300936446108e-02 , 3.80322097438575e-02 , 3.10784463856866e-01 ), ( 1.23516685310776e-03 , 3.18088674650605e-02 , 2.86151774428636e-01 ), ( 2.40446317099675e-02 , 4.66592456226977e-02 , 3.55520449396829e-01 ), ( 4.63907693763088e-02 , 3.76321269229097e-02 , 2.08747794627587e-01 ), ( 1.76676424568742e-02 , 2.28597506509051e-02 , 1.57172642590895e-01 ), ( 1.18130225018854e-01 , 5.91810339714630e-02 , 1.97781322269948e-01 ), ( 1.66325716747012e-01 , 6.65822400602615e-02 , 1.25968044082477e-01 ), ( 2.49589011677952e-01 , 9.47555887836199e-02 , 1.42048514184550e-01 ), ( 1.35720495711020e-01 , 4.88722394536000e-02 , 5.30734688426321e-02 ), ( 1.31172548010176e-01 , 4.02276207050443e-02 , -1.25251264924779e-02 ), ( 1.11196622837668e-01 , 4.23394699460265e-02 , 6.44152907848379e-02 ), ( 7.34467643592223e-02 , 2.37404968034808e-02 , 4.06286851783905e-03 ), ( 5.92122318410697e-02 , 2.29185708403596e-02 , 3.76966007488264e-02 ), ( -2.37975725320438e-03 , -3.26535363717052e-03 , -2.28668074312608e-02 ), ( -1.67332878195299e-02 , -1.56957741515205e-02 , -9.46212012221707e-02 ), ( -5.15370806614827e-02 , -1.25400226966476e-02 , 3.46611814337565e-02 ), ( -1.21767390465137e-01 , -3.65727788305644e-02 , 1.86448501550935e-02 ), ( -1.64890487711056e-01 , -4.13948489082473e-02 , 9.92964181665753e-02 ), ( -1.07994115777278e-01 , -3.74046514749819e-02 , -2.87194668954239e-02 ), ( -1.45839060119007e-01 , -5.59093326149074e-02 , -8.79383847404050e-02 ), ( -5.17640665749411e-02 , -1.69436044010904e-02 , -4.79158573032616e-03 ), ( -2.92187372042236e-02 , -1.44415415137458e-02 , -4.71301677964168e-02 ), ( 3.02959845424302e-02 , 9.93076877737005e-03 , 2.93348973091517e-03 ), ( 3.55093488455888e-03 , -1.34357795361606e-02 , -1.32632812986454e-01 ), ( -1.45978076103804e-02 , -2.53552203687047e-02 , -1.88769723481286e-01 ), ( 5.16333866955254e-02 , 4.61201424862168e-04 , -1.44955071525014e-01 ), ( 8.17039952653785e-02 , 1.34373147957856e-03 , -2.23783221111909e-01 ), ( 1.44686235761542e-01 , 2.24916926317148e-02 , -2.13104193749752e-01 ), ( 1.98386555000443e-02 , -2.43627951147422e-02 , -2.79208778152793e-01 ), ( 2.09461059634538e-02 , -3.19067697320235e-02 , -3.51119555670142e-01 ), ( -3.61611505030088e-02 , -3.85124983394166e-02 , -2.46317122521031e-01 ), ( -1.00629349898272e-01 , -6.38036286111886e-02 , -2.90440187066860e-01 ), ( -1.40691133450162e-01 , -7.09532054445123e-02 , -2.39831253054555e-01 ), ( -1.59962208142437e-01 , -8.50211287502061e-02 , -3.12294725781383e-01 ), ( -1.89058332749189e-01 , -1.01549489241001e-01 , -3.78786145436480e-01 ), ( -2.01931398764172e-01 , -9.87566631838512e-02 , -3.16161649965062e-01 ), ( -2.45447988208696e-01 , -1.15585984090497e-01 , -3.43737194989054e-01 ), ( -1.24443831071177e-01 , -7.49719303565766e-02 , -3.23368729472479e-01 ), ( -1.80124949712414e-01 , -8.52402792912854e-02 , -2.56045733255299e-01 ), ( -2.35246572579257e-01 , -1.04278288000303e-01 , -2.70214333657193e-01 ), ( -2.72051230003134e-01 , -1.06990691158431e-01 , -1.88599978621055e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 23, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2690,10 +4289,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 24, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 24, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 24, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 24, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 24, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 24, atoms_positions[size = 51] = { ( 8.27050693486260e+00 , 4.09127624982683e-02 , -7.42806090655381e-01 ), ( 6.88621568670105e+00 , -5.60059310726248e-01 , -5.48572870137821e-01 ), ( 6.16129515518780e+00 , -3.91528458308412e-01 , 7.61792087129228e-01 ), ( 4.92542029440314e+00 , -1.51106013324024e-01 , 7.31554147396332e-01 ), ( 7.03158015113448e+00 , -2.05833099972738e+00 , -9.15047607445865e-01 ), ( 6.83685602186459e+00 , -2.70283755271464e-01 , 1.93814536333249e+00 ), ( 6.14926766592578e+00 , -1.89834653758469e-01 , 3.17319789943851e+00 ), ( 7.09737077078941e+00 , -3.49242475123280e-01 , 4.34462371079293e+00 ), ( 5.33740413028451e+00 , 1.08125850749346e+00 , 3.36358957320595e+00 ), ( 4.16698029952191e+00 , 1.01613213148207e+00 , 3.72380456879332e+00 ), ( 5.83622822234833e+00 , 2.25768751732082e+00 , 2.98264484758702e+00 ), ( 5.21770525001130e+00 , 3.57159769982799e+00 , 2.91628322785553e+00 ), ( 6.31856084523342e+00 , 4.49558404118750e+00 , 2.32664546080003e+00 ), ( 3.86540003615781e+00 , 3.68008032912721e+00 , 2.04181222945337e+00 ), ( 2.79234653437798e+00 , 4.16849762794638e+00 , 2.46653775960343e+00 ), ( 3.93894407351176e+00 , 3.22710308982714e+00 , 7.30815791996592e-01 ), ( 2.70065275513418e+00 , 3.01473889718690e+00 , -9.27152726836277e-02 ), ( 3.08019268103090e+00 , 2.68051811103968e+00 , -1.52260975474361e+00 ), ( 1.58038830167703e+00 , 2.17003449741302e+00 , 4.27962272263170e-01 ), ( 3.76890274720497e-01 , 2.60709693889937e+00 , 4.92780740745977e-01 ), ( 2.07252038371650e+00 , 1.12651473936430e+00 , 1.05129402273852e+00 ), ( 1.17052731382972e+00 , 1.16829247964910e-01 , 1.70099197039943e+00 ), ( 2.05871543839403e+00 , -1.09333228271432e+00 , 2.02319394446356e+00 ), ( 5.69756880392859e-01 , 6.17173953491876e-01 , 2.96096018787920e+00 ), ( -5.86243433177253e-01 , 3.51659672810033e-01 , 3.16315867736680e+00 ), ( 1.30238298539933e+00 , 1.35292658013224e+00 , 3.74693045288870e+00 ), ( 8.40858366637640e-01 , 1.98373489008161e+00 , 5.02674892399775e+00 ), ( 2.10681210803961e+00 , 2.72271512704815e+00 , 5.70693551908920e+00 ), ( -3.43519716856437e-01 , 2.91051405358141e+00 , 4.97016881234955e+00 ), ( -1.12387250168073e+00 , 3.06582026354575e+00 , 5.87892589210738e+00 ), ( -5.30941070523270e-01 , 3.51483565419997e+00 , 3.82945260072042e+00 ), ( -1.51009601578230e+00 , 4.51944029487591e+00 , 3.41844225089706e+00 ), ( -7.04741000935523e-01 , 5.42139590392118e+00 , 2.46955612833754e+00 ), ( -2.74711625974549e+00 , 3.92045483929236e+00 , 2.86448152596536e+00 ), ( -3.81315408423867e+00 , 4.53202703049446e+00 , 2.81263944285830e+00 ), ( -2.65056261819155e+00 , 2.65589992586603e+00 , 2.37525860555684e+00 ), ( -3.78440623690736e+00 , 1.80874861947133e+00 , 2.00140403543296e+00 ), ( -3.37325789577578e+00 , 8.80921883554445e-01 , 8.49016180122185e-01 ), ( -4.29366231321076e+00 , 1.06600016042967e+00 , 3.21169541573497e+00 ), ( -5.49325096069121e+00 , 7.90243302203479e-01 , 3.33255878205230e+00 ), ( -3.36481210388283e+00 , 7.08989670222816e-01 , 4.20302865597447e+00 ), ( -3.68098259644715e+00 , 6.77797847171094e-02 , 5.44961457973166e+00 ), ( -2.39221081333703e+00 , -3.24595516895883e-01 , 6.15769699700810e+00 ), ( -4.46254628074192e+00 , 9.51820412579295e-01 , 6.43014976591291e+00 ), ( -5.36498975547215e+00 , 5.91014109823318e-01 , 7.21797246583130e+00 ), ( -6.26900483511788e+00 , 3.62489895007615e+00 , 6.74769857767828e+00 ), ( -6.97428682336797e+00 , 4.29572777976654e+00 , 7.49109946089408e+00 ), ( -6.70718335849590e+00 , 3.16863207438861e+00 , 5.50803787349925e+00 ), ( -4.11907560491057e+00 , 2.24489507816142e+00 , 6.39175562171674e+00 ), ( -4.80799524228886e+00 , 3.23983746770053e+00 , 7.25614184578735e+00 ), ( -4.06686554058490e+00 , 4.55359210114628e+00 , 7.27360166871903e+00 ) } +colvars: Step 24, atoms_positions[size = 51] = { ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 ), ( 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 ), ( 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 ), ( 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 ), ( 7.03126813606480e+00 , -2.05847485579762e+00 , -9.14970306289443e-01 ), ( 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 ), ( 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 ), ( 7.09828140808973e+00 , -3.49387967535437e-01 , 4.34546489528286e+00 ), ( 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 ), ( 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 ), ( 5.83708577362795e+00 , 2.25805562238920e+00 , 2.98267974249273e+00 ), ( 5.21773856017340e+00 , 3.57161922298348e+00 , 2.91648092208761e+00 ), ( 6.31853699913758e+00 , 4.49563391089305e+00 , 2.32683719497759e+00 ), ( 3.86542883065045e+00 , 3.68004921258471e+00 , 2.04195217412088e+00 ), ( 2.79235867300471e+00 , 4.16850146661707e+00 , 2.46662324468102e+00 ), ( 3.93901678661429e+00 , 3.22713308244348e+00 , 7.30934829859977e-01 ), ( 2.70074991752688e+00 , 3.01477796821894e+00 , -9.26397229315416e-02 ), ( 3.08032379131617e+00 , 2.68056690895662e+00 , -1.52252992080645e+00 ), ( 1.58047066505810e+00 , 2.17006440922225e+00 , 4.27998664327955e-01 ), ( 3.76967736525154e-01 , 2.60711789557844e+00 , 4.92778015884306e-01 ), ( 2.07258571616031e+00 , 1.12654210139324e+00 , 1.05134192945661e+00 ), ( 1.17056965170568e+00 , 1.16846335574401e-01 , 1.70099692768423e+00 ), ( 2.05876861292423e+00 , -1.09329159651842e+00 , 2.02324596919490e+00 ), ( 5.69776935670213e-01 , 6.17172001264618e-01 , 2.96095152671806e+00 ), ( -5.86240810892193e-01 , 3.51655835381281e-01 , 3.16311391312009e+00 ), ( 1.30244214709959e+00 , 1.35290545677039e+00 , 3.74694619494776e+00 ), ( 8.40806889312496e-01 , 1.98370498943023e+00 , 5.02675267008423e+00 ), ( 2.10672782636876e+00 , 2.72269083586604e+00 , 5.70697757475891e+00 ), ( -3.43581917981181e-01 , 2.91048819849154e+00 , 4.97014961072114e+00 ), ( -1.12395824489167e+00 , 3.06579184791982e+00 , 5.87888757790117e+00 ), ( -5.30970941621663e-01 , 3.51482581213725e+00 , 3.82943937819702e+00 ), ( -1.51011506620662e+00 , 4.51943360596667e+00 , 3.41840963676036e+00 ), ( -7.04729435523050e-01 , 5.42139775431779e+00 , 2.46955331052980e+00 ), ( -2.74711525410010e+00 , 3.92044849944355e+00 , 2.86440245108706e+00 ), ( -3.81315857722728e+00 , 4.53201123870925e+00 , 2.81253836569199e+00 ), ( -2.65053563595890e+00 , 2.65589915977239e+00 , 2.37517162843526e+00 ), ( -3.78436308048801e+00 , 1.80875030731400e+00 , 2.00126773291067e+00 ), ( -3.37318244314476e+00 , 8.80925739265677e-01 , 8.48890367251137e-01 ), ( -4.29365096406740e+00 , 1.06598119459501e+00 , 3.21152967601072e+00 ), ( -5.49323932631666e+00 , 7.90224912843538e-01 , 3.33236985776319e+00 ), ( -3.36483009077098e+00 , 7.08962306720196e-01 , 4.20288051489971e+00 ), ( -3.68104475168581e+00 , 6.77352039955146e-02 , 5.44944272745980e+00 ), ( -2.39228872483380e+00 , -3.24629174087243e-01 , 6.15756470761386e+00 ), ( -4.46264273224480e+00 , 9.51772161204549e-01 , 6.42996170595173e+00 ), ( -5.36509137781691e+00 , 5.90958189414682e-01 , 7.21777131508051e+00 ), ( -6.26912352257721e+00 , 3.62484190850191e+00 , 6.74752042761964e+00 ), ( -6.97441870236570e+00 , 4.29566443046527e+00 , 7.49091504085849e+00 ), ( -6.70727158666970e+00 , 3.16858712993869e+00 , 5.50784391680945e+00 ), ( -4.11917776391675e+00 , 2.24484839689618e+00 , 6.39160224714446e+00 ), ( -4.80813146866083e+00 , 3.23977411463558e+00 , 7.25597976490504e+00 ), ( -4.06701458125265e+00 , 4.55353074713024e+00 , 7.27349002869644e+00 ) } colvars: Step 24, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 24, atom_groups_ids[size = 0] = @@ -2710,163 +4309,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 24 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -3.00350438745275e-01 , -4.92097847437880e-03 , 9.53816228587234e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.99159391330660e-01 , -4.75166803868142e-03 , 9.54191322654696e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 7.03126813606480e+00 , -2.05847485579762e+00 , -9.14970306289443e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 , 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 7.09828140808973e+00 , -3.49387967535437e-01 , 4.34546489528286e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 , 5.83708577362795e+00 , 2.25805562238920e+00 , 2.98267974249273e+00 , 5.21773856017340e+00 , 3.57161922298348e+00 , 2.91648092208761e+00 , 6.31853699913758e+00 , 4.49563391089305e+00 , 2.32683719497759e+00 , 3.86542883065045e+00 , 3.68004921258471e+00 , 2.04195217412088e+00 , 2.79235867300471e+00 , 4.16850146661707e+00 , 2.46662324468102e+00 , 3.93901678661429e+00 , 3.22713308244348e+00 , 7.30934829859977e-01 , 2.70074991752688e+00 , 3.01477796821894e+00 , -9.26397229315416e-02 , 3.08032379131617e+00 , 2.68056690895662e+00 , -1.52252992080645e+00 , 1.58047066505810e+00 , 2.17006440922225e+00 , 4.27998664327955e-01 , 3.76967736525154e-01 , 2.60711789557844e+00 , 4.92778015884306e-01 , 2.07258571616031e+00 , 1.12654210139324e+00 , 1.05134192945661e+00 , 1.17056965170568e+00 , 1.16846335574401e-01 , 1.70099692768423e+00 , 2.05876861292423e+00 , -1.09329159651842e+00 , 2.02324596919490e+00 , 5.69776935670213e-01 , 6.17172001264618e-01 , 2.96095152671806e+00 , -5.86240810892193e-01 , 3.51655835381281e-01 , 3.16311391312009e+00 , 1.30244214709959e+00 , 1.35290545677039e+00 , 3.74694619494776e+00 , 8.40806889312496e-01 , 1.98370498943023e+00 , 5.02675267008423e+00 , 2.10672782636876e+00 , 2.72269083586604e+00 , 5.70697757475891e+00 , -3.43581917981181e-01 , 2.91048819849154e+00 , 4.97014961072114e+00 , -1.12395824489167e+00 , 3.06579184791982e+00 , 5.87888757790117e+00 , -5.30970941621663e-01 , 3.51482581213725e+00 , 3.82943937819702e+00 , -1.51011506620662e+00 , 4.51943360596667e+00 , 3.41840963676036e+00 , -7.04729435523050e-01 , 5.42139775431779e+00 , 2.46955331052980e+00 , -2.74711525410010e+00 , 3.92044849944355e+00 , 2.86440245108706e+00 , -3.81315857722728e+00 , 4.53201123870925e+00 , 2.81253836569199e+00 , -2.65053563595890e+00 , 2.65589915977239e+00 , 2.37517162843526e+00 , -3.78436308048801e+00 , 1.80875030731400e+00 , 2.00126773291067e+00 , -3.37318244314476e+00 , 8.80925739265677e-01 , 8.48890367251137e-01 , -4.29365096406740e+00 , 1.06598119459501e+00 , 3.21152967601072e+00 , -5.49323932631666e+00 , 7.90224912843538e-01 , 3.33236985776319e+00 , -3.36483009077098e+00 , 7.08962306720196e-01 , 4.20288051489971e+00 , -3.68104475168581e+00 , 6.77352039955146e-02 , 5.44944272745980e+00 , -2.39228872483380e+00 , -3.24629174087243e-01 , 6.15756470761386e+00 , -4.46264273224480e+00 , 9.51772161204549e-01 , 6.42996170595173e+00 , -5.36509137781691e+00 , 5.90958189414682e-01 , 7.21777131508051e+00 , -6.26912352257721e+00 , 3.62484190850191e+00 , 6.74752042761964e+00 , -6.97441870236570e+00 , 4.29566443046527e+00 , 7.49091504085849e+00 , -6.70727158666970e+00 , 3.16858712993869e+00 , 5.50784391680945e+00 , -4.11917776391675e+00 , 2.24484839689618e+00 , 6.39160224714446e+00 , -4.80813146866083e+00 , 3.23977411463558e+00 , 7.25597976490504e+00 , -4.06701458125265e+00 , 4.55353074713024e+00 , 7.27349002869644e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -3.00350438745275e-01 , -4.92097847437880e-03 , 9.53816228587234e-01 ). +colvars: Colvar "one" has value ( -2.99159391330660e-01 , -4.75166803868142e-03 , 9.54191322654696e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 7.03126813606480e+00 , -2.05847485579762e+00 , -9.14970306289443e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 , 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 7.09828140808973e+00 , -3.49387967535437e-01 , 4.34546489528286e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 , 5.83708577362795e+00 , 2.25805562238920e+00 , 2.98267974249273e+00 , 5.21773856017340e+00 , 3.57161922298348e+00 , 2.91648092208761e+00 , 6.31853699913758e+00 , 4.49563391089305e+00 , 2.32683719497759e+00 , 3.86542883065045e+00 , 3.68004921258471e+00 , 2.04195217412088e+00 , 2.79235867300471e+00 , 4.16850146661707e+00 , 2.46662324468102e+00 , 3.93901678661429e+00 , 3.22713308244348e+00 , 7.30934829859977e-01 , 2.70074991752688e+00 , 3.01477796821894e+00 , -9.26397229315416e-02 , 3.08032379131617e+00 , 2.68056690895662e+00 , -1.52252992080645e+00 , 1.58047066505810e+00 , 2.17006440922225e+00 , 4.27998664327955e-01 , 3.76967736525154e-01 , 2.60711789557844e+00 , 4.92778015884306e-01 , 2.07258571616031e+00 , 1.12654210139324e+00 , 1.05134192945661e+00 , 1.17056965170568e+00 , 1.16846335574401e-01 , 1.70099692768423e+00 , 2.05876861292423e+00 , -1.09329159651842e+00 , 2.02324596919490e+00 , 5.69776935670213e-01 , 6.17172001264618e-01 , 2.96095152671806e+00 , -5.86240810892193e-01 , 3.51655835381281e-01 , 3.16311391312009e+00 , 1.30244214709959e+00 , 1.35290545677039e+00 , 3.74694619494776e+00 , 8.40806889312496e-01 , 1.98370498943023e+00 , 5.02675267008423e+00 , 2.10672782636876e+00 , 2.72269083586604e+00 , 5.70697757475891e+00 , -3.43581917981181e-01 , 2.91048819849154e+00 , 4.97014961072114e+00 , -1.12395824489167e+00 , 3.06579184791982e+00 , 5.87888757790117e+00 , -5.30970941621663e-01 , 3.51482581213725e+00 , 3.82943937819702e+00 , -1.51011506620662e+00 , 4.51943360596667e+00 , 3.41840963676036e+00 , -7.04729435523050e-01 , 5.42139775431779e+00 , 2.46955331052980e+00 , -2.74711525410010e+00 , 3.92044849944355e+00 , 2.86440245108706e+00 , -3.81315857722728e+00 , 4.53201123870925e+00 , 2.81253836569199e+00 , -2.65053563595890e+00 , 2.65589915977239e+00 , 2.37517162843526e+00 , -3.78436308048801e+00 , 1.80875030731400e+00 , 2.00126773291067e+00 , -3.37318244314476e+00 , 8.80925739265677e-01 , 8.48890367251137e-01 , -4.29365096406740e+00 , 1.06598119459501e+00 , 3.21152967601072e+00 , -5.49323932631666e+00 , 7.90224912843538e-01 , 3.33236985776319e+00 , -3.36483009077098e+00 , 7.08962306720196e-01 , 4.20288051489971e+00 , -3.68104475168581e+00 , 6.77352039955146e-02 , 5.44944272745980e+00 , -2.39228872483380e+00 , -3.24629174087243e-01 , 6.15756470761386e+00 , -4.46264273224480e+00 , 9.51772161204549e-01 , 6.42996170595173e+00 , -5.36509137781691e+00 , 5.90958189414682e-01 , 7.21777131508051e+00 , -6.26912352257721e+00 , 3.62484190850191e+00 , 6.74752042761964e+00 , -6.97441870236570e+00 , 4.29566443046527e+00 , 7.49091504085849e+00 , -6.70727158666970e+00 , 3.16858712993869e+00 , 5.50784391680945e+00 , -4.11917776391675e+00 , 2.24484839689618e+00 , 6.39160224714446e+00 , -4.80813146866083e+00 , 3.23977411463558e+00 , 7.25597976490504e+00 , -4.06701458125265e+00 , 4.55353074713024e+00 , 7.27349002869644e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.525 , 2.05022 , -15.1727 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.8422 , 6.58422 , 13.1684 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.525 , 2.05022 , -15.1727 ) to colvar "one". -colvars: Adding total bias energy: 44.2971 +colvars: Adding biasing force ( 65.8422 , 6.58422 , 13.1684 ) to colvar "one". +colvars: Adding total bias energy: 56.2581 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.525 , 2.05022 , -15.1727 ) +colvars: Force to be applied: ( 65.8422 , 6.58422 , 13.1684 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.92294 , -0.529051 , -1.43515 ) -colvars: ( -4.22142 , -0.453661 , -1.23064 ) -colvars: ( -4.22142 , -0.453661 , -1.23064 ) -colvars: ( -5.62305 , -0.60429 , -1.63925 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.18611 , -0.555666 , -1.50491 ) +colvars: ( -4.44708 , -0.476484 , -1.29046 ) +colvars: ( -4.44708 , -0.476484 , -1.29046 ) +colvars: ( -5.92364 , -0.63469 , -1.71893 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.890158 , 0.195821 , 0.614626 ) -colvars: ( 0.771286 , 0.26637 , 0.638486 ) -colvars: ( 0.755155 , 0.259493 , 0.620056 ) -colvars: ( 0.660266 , 0.266973 , 0.574779 ) -colvars: ( 0.648449 , 0.200476 , 0.480325 ) -colvars: ( 0.574395 , 0.343992 , 0.626335 ) -colvars: ( 0.467996 , 0.357811 , 0.58272 ) -colvars: ( 0.391877 , 0.454825 , 0.666279 ) -colvars: ( 0.38672 , 0.313268 , 0.476828 ) -colvars: ( 0.352268 , 0.271676 , 0.402028 ) -colvars: ( 0.357371 , 0.318567 , 0.466756 ) -colvars: ( 0.286477 , 0.275719 , 0.369128 ) -colvars: ( 0.259328 , 0.304718 , 0.391552 ) -colvars: ( 0.348504 , 0.178111 , 0.2766 ) -colvars: ( 0.290197 , 0.134772 , 0.185638 ) -colvars: ( 0.470472 , 0.14128 , 0.29895 ) -colvars: ( 0.542547 , 0.0501158 , 0.220746 ) -colvars: ( 0.671214 , 0.0293426 , 0.268139 ) -colvars: ( 0.551302 , 0.018286 , 0.183907 ) -colvars: ( 0.535647 , -0.0467126 , 0.0891965 ) -colvars: ( 0.572275 , 0.0661336 , 0.259116 ) -colvars: ( 0.570999 , 0.0499352 , 0.237038 ) -colvars: ( 0.607498 , 0.11459 , 0.343406 ) -colvars: ( 0.447519 , 0.0542176 , 0.170937 ) -colvars: ( 0.440839 , -0.00167516 , 0.0934357 ) -colvars: ( 0.346151 , 0.119651 , 0.19823 ) -colvars: ( 0.222452 , 0.128045 , 0.137418 ) -colvars: ( 0.13148 , 0.213583 , 0.197232 ) -colvars: ( 0.194257 , 0.0543986 , 0.0240312 ) -colvars: ( 0.145406 , 0.0181787 , -0.0520592 ) -colvars: ( 0.227396 , 0.0289722 , 0.00979407 ) -colvars: ( 0.213295 , -0.0434165 , -0.0937475 ) -colvars: ( 0.248099 , -0.0466416 , -0.0777743 ) -colvars: ( 0.288142 , -0.129171 , -0.163215 ) -colvars: ( 0.244426 , -0.182285 , -0.258574 ) -colvars: ( 0.402672 , -0.144021 , -0.116233 ) -colvars: ( 0.479732 , -0.21933 , -0.170657 ) -colvars: ( 0.610112 , -0.22173 , -0.0980683 ) -colvars: ( 0.432995 , -0.223944 , -0.203889 ) -colvars: ( 0.438529 , -0.291926 , -0.290218 ) -colvars: ( 0.384729 , -0.150841 , -0.135642 ) -colvars: ( 0.331077 , -0.144735 , -0.15877 ) -colvars: ( 0.314835 , -0.0582218 , -0.0542539 ) -colvars: ( 0.208549 , -0.153692 , -0.241757 ) -colvars: ( 0.184434 , -0.195717 , -0.311122 ) -colvars: ( 0.00816947 , -0.199587 , -0.418628 ) -colvars: ( -0.0822007 , -0.217494 , -0.494719 ) -colvars: ( 0.10773 , -0.249258 , -0.426209 ) -colvars: ( 0.127099 , -0.113212 , -0.23576 ) -colvars: ( 0.00850869 , -0.117752 , -0.31064 ) -colvars: ( -0.080003 , -0.0372957 , -0.25609 ) +colvars: ( 0.936944 , 0.206277 , 0.645931 ) +colvars: ( 0.811894 , 0.280466 , 0.671058 ) +colvars: ( 0.794877 , 0.273275 , 0.651723 ) +colvars: ( 0.695127 , 0.281024 , 0.604071 ) +colvars: ( 0.682692 , 0.211041 , 0.504743 ) +colvars: ( 0.604817 , 0.36201 , 0.658293 ) +colvars: ( 0.492915 , 0.376474 , 0.612431 ) +colvars: ( 0.412861 , 0.47851 , 0.70031 ) +colvars: ( 0.407391 , 0.329585 , 0.501112 ) +colvars: ( 0.371164 , 0.28578 , 0.422442 ) +colvars: ( 0.376477 , 0.335192 , 0.490564 ) +colvars: ( 0.30187 , 0.290096 , 0.387936 ) +colvars: ( 0.273271 , 0.320647 , 0.411562 ) +colvars: ( 0.367106 , 0.187421 , 0.290623 ) +colvars: ( 0.305768 , 0.141784 , 0.194979 ) +colvars: ( 0.495401 , 0.14873 , 0.314103 ) +colvars: ( 0.571209 , 0.0528377 , 0.23185 ) +colvars: ( 0.706543 , 0.0310594 , 0.281673 ) +colvars: ( 0.580458 , 0.0193011 , 0.193071 ) +colvars: ( 0.563984 , -0.0491063 , 0.0934744 ) +colvars: ( 0.602559 , 0.0696222 , 0.272124 ) +colvars: ( 0.601258 , 0.0525286 , 0.24887 ) +colvars: ( 0.639691 , 0.120548 , 0.360691 ) +colvars: ( 0.471375 , 0.0569605 , 0.179376 ) +colvars: ( 0.46436 , -0.0018774 , 0.0978609 ) +colvars: ( 0.364737 , 0.125777 , 0.208109 ) +colvars: ( 0.234617 , 0.134543 , 0.144183 ) +colvars: ( 0.138914 , 0.224523 , 0.207115 ) +colvars: ( 0.204925 , 0.0570589 , 0.0249731 ) +colvars: ( 0.153549 , 0.018902 , -0.0550477 ) +colvars: ( 0.239743 , 0.0303647 , 0.01003 ) +colvars: ( 0.224876 , -0.0457868 , -0.0988281 ) +colvars: ( 0.261443 , -0.0491127 , -0.0819981 ) +colvars: ( 0.303619 , -0.136006 , -0.171911 ) +colvars: ( 0.257626 , -0.191917 , -0.272181 ) +colvars: ( 0.424112 , -0.151591 , -0.122543 ) +colvars: ( 0.505186 , -0.230821 , -0.17981 ) +colvars: ( 0.642346 , -0.233288 , -0.103511 ) +colvars: ( 0.456062 , -0.235746 , -0.214784 ) +colvars: ( 0.461885 , -0.307289 , -0.305576 ) +colvars: ( 0.405323 , -0.158874 , -0.143027 ) +colvars: ( 0.348924 , -0.152519 , -0.167372 ) +colvars: ( 0.331873 , -0.0615207 , -0.0574831 ) +colvars: ( 0.220024 , -0.162001 , -0.25461 ) +colvars: ( 0.194674 , -0.206259 , -0.327568 ) +colvars: ( 0.0091648 , -0.210322 , -0.440505 ) +colvars: ( -0.0859047 , -0.229207 , -0.520499 ) +colvars: ( 0.11387 , -0.262515 , -0.448479 ) +colvars: ( 0.134318 , -0.119413 , -0.248259 ) +colvars: ( 0.009559 , -0.12424 , -0.32697 ) +colvars: ( -0.0835612 , -0.0396007 , -0.269569 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.92294 , 0.529051 , 1.43515 ) -colvars: ( 4.22142 , 0.453661 , 1.23064 ) -colvars: ( 4.22142 , 0.453661 , 1.23064 ) -colvars: ( 5.62305 , 0.60429 , 1.63925 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.18611 , 0.555666 , 1.50491 ) +colvars: ( 4.44708 , 0.476484 , 1.29046 ) +colvars: ( 4.44708 , 0.476484 , 1.29046 ) +colvars: ( 5.92364 , 0.63469 , 1.71893 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.614908 , -0.0811558 , -0.367132 ) -colvars: ( -0.553162 , -0.164001 , -0.335769 ) -colvars: ( -0.502907 , -0.141886 , -0.277178 ) -colvars: ( -0.514532 , -0.191526 , -0.307171 ) -colvars: ( -0.504899 , -0.132525 , -0.27572 ) -colvars: ( -0.490299 , -0.283728 , -0.316903 ) -colvars: ( -0.458193 , -0.324129 , -0.299607 ) -colvars: ( -0.436961 , -0.431652 , -0.318006 ) -colvars: ( -0.395233 , -0.288635 , -0.223328 ) -colvars: ( -0.390969 , -0.263289 , -0.209691 ) -colvars: ( -0.34559 , -0.282933 , -0.171411 ) -colvars: ( -0.285081 , -0.245912 , -0.0970286 ) -colvars: ( -0.236114 , -0.260811 , -0.0533969 ) -colvars: ( -0.304216 , -0.142534 , -0.0780551 ) -colvars: ( -0.273137 , -0.113177 , -0.0360307 ) -colvars: ( -0.358108 , -0.0850827 , -0.110915 ) -colvars: ( -0.384419 , 0.0133403 , -0.100971 ) -colvars: ( -0.434041 , 0.0610141 , -0.133157 ) -colvars: ( -0.422376 , 0.0283513 , -0.133514 ) -colvars: ( -0.411012 , 0.0852568 , -0.101099 ) -colvars: ( -0.46679 , -0.0258397 , -0.198088 ) -colvars: ( -0.501503 , -0.0273424 , -0.233474 ) -colvars: ( -0.551676 , -0.0929349 , -0.308036 ) -colvars: ( -0.44999 , -0.0573747 , -0.192876 ) -colvars: ( -0.456975 , -0.0132079 , -0.183576 ) -colvars: ( -0.395224 , -0.13179 , -0.165403 ) -colvars: ( -0.338156 , -0.163108 , -0.119707 ) -colvars: ( -0.288061 , -0.25343 , -0.102794 ) -colvars: ( -0.296749 , -0.0900821 , -0.0511945 ) -colvars: ( -0.283848 , -0.071421 , -0.0313599 ) -colvars: ( -0.276362 , -0.0450871 , -0.0141246 ) -colvars: ( -0.240723 , 0.0298563 , 0.0493082 ) -colvars: ( -0.218875 , 0.056329 , 0.0810049 ) -colvars: ( -0.284522 , 0.116757 , 0.0374498 ) -colvars: ( -0.25799 , 0.158631 , 0.0795338 ) -colvars: ( -0.353513 , 0.14488 , -0.0213902 ) -colvars: ( -0.402104 , 0.221194 , -0.041966 ) -colvars: ( -0.472782 , 0.243751 , -0.104553 ) -colvars: ( -0.414228 , 0.201307 , -0.0614735 ) -colvars: ( -0.418718 , 0.26225 , -0.0434751 ) -colvars: ( -0.419231 , 0.114547 , -0.0985298 ) -colvars: ( -0.426903 , 0.0843128 , -0.117393 ) -colvars: ( -0.44882 , -0.00921564 , -0.173919 ) -colvars: ( -0.360618 , 0.0730712 , -0.0550341 ) -colvars: ( -0.364178 , 0.099432 , -0.0488725 ) -colvars: ( -0.199715 , 0.105999 , 0.118571 ) -colvars: ( -0.150593 , 0.107908 , 0.168564 ) -colvars: ( -0.225658 , 0.178455 , 0.119295 ) -colvars: ( -0.298176 , 0.0323002 , -0.00743635 ) -colvars: ( -0.231824 , 0.0187091 , 0.054121 ) -colvars: ( -0.178171 , -0.0645071 , 0.077227 ) +colvars: ( -0.647108 , -0.0855449 , -0.385318 ) +colvars: ( -0.582214 , -0.172671 , -0.352304 ) +colvars: ( -0.529273 , -0.149439 , -0.290691 ) +colvars: ( -0.541668 , -0.20157 , -0.322287 ) +colvars: ( -0.531534 , -0.139487 , -0.289298 ) +colvars: ( -0.516259 , -0.298533 , -0.332472 ) +colvars: ( -0.482583 , -0.340979 , -0.314323 ) +colvars: ( -0.460322 , -0.454068 , -0.333594 ) +colvars: ( -0.416351 , -0.303621 , -0.234192 ) +colvars: ( -0.411909 , -0.276924 , -0.219922 ) +colvars: ( -0.364075 , -0.297646 , -0.179591 ) +colvars: ( -0.300412 , -0.25869 , -0.101447 ) +colvars: ( -0.248844 , -0.274394 , -0.0555288 ) +colvars: ( -0.320483 , -0.149951 , -0.081581 ) +colvars: ( -0.287816 , -0.119039 , -0.037467 ) +colvars: ( -0.377096 , -0.0895564 , -0.116123 ) +colvars: ( -0.404716 , 0.0139673 , -0.105741 ) +colvars: ( -0.456819 , 0.064063 , -0.139549 ) +colvars: ( -0.444707 , 0.0297942 , -0.14001 ) +colvars: ( -0.432753 , 0.0896742 , -0.106007 ) +colvars: ( -0.491484 , -0.0271994 , -0.207859 ) +colvars: ( -0.528072 , -0.0287426 , -0.245103 ) +colvars: ( -0.580895 , -0.0977416 , -0.323428 ) +colvars: ( -0.473968 , -0.0602824 , -0.202466 ) +colvars: ( -0.481339 , -0.0137954 , -0.19276 ) +colvars: ( -0.416402 , -0.138548 , -0.17354 ) +colvars: ( -0.356444 , -0.171446 , -0.125534 ) +colvars: ( -0.303786 , -0.266452 , -0.107684 ) +colvars: ( -0.312847 , -0.0946234 , -0.0535798 ) +colvars: ( -0.299325 , -0.0749557 , -0.0327923 ) +colvars: ( -0.291311 , -0.0473312 , -0.0146004 ) +colvars: ( -0.25377 , 0.0315015 , 0.0520206 ) +colvars: ( -0.230692 , 0.059301 , 0.0853781 ) +colvars: ( -0.299818 , 0.122917 , 0.0394778 ) +colvars: ( -0.27192 , 0.16699 , 0.0836499 ) +colvars: ( -0.372355 , 0.152474 , -0.022368 ) +colvars: ( -0.42345 , 0.232753 , -0.0440656 ) +colvars: ( -0.497741 , 0.256442 , -0.109827 ) +colvars: ( -0.436297 , 0.211885 , -0.0646188 ) +colvars: ( -0.441021 , 0.27601 , -0.0457727 ) +colvars: ( -0.441644 , 0.120644 , -0.10353 ) +colvars: ( -0.449812 , 0.0888893 , -0.123395 ) +colvars: ( -0.472935 , -0.00948528 , -0.18275 ) +colvars: ( -0.380137 , 0.0771049 , -0.0578842 ) +colvars: ( -0.383926 , 0.104869 , -0.0514724 ) +colvars: ( -0.210861 , 0.111769 , 0.124551 ) +colvars: ( -0.159227 , 0.11381 , 0.177062 ) +colvars: ( -0.238052 , 0.187943 , 0.125306 ) +colvars: ( -0.314452 , 0.0342147 , -0.00781104 ) +colvars: ( -0.244702 , 0.0199544 , 0.0568652 ) +colvars: ( -0.18829 , -0.0675819 , 0.0812242 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 24. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 24. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 24, atoms_new_colvar_forces = { ( -4.64768925340399e+00 , -4.14385897830330e-01 , -1.18765726324132e+00 ), ( -4.00329633385016e+00 , -3.51292610341177e-01 , -9.27924699615057e-01 ), ( -4.07568479174637e+00 , -3.78213636415218e-01 , -9.63034016470924e-01 ), ( -5.47950289858256e+00 , -5.36338777500186e-01 , -1.43464549015554e+00 ), ( 2.52247728100370e-01 , 1.17607144837762e-01 , 3.42878285760502e-01 ), ( 5.00703567367485e+00 , 5.89314673083556e-01 , 1.74458359343299e+00 ), ( 4.23122189922366e+00 , 4.87343341846568e-01 , 1.51375504692721e+00 ), ( -4.50844355471096e-02 , 2.31735662897316e-02 , 3.48273210603471e-01 ), ( 4.21290595488496e+00 , 4.78294858967199e-01 , 1.48414202929429e+00 ), ( 5.58435188446993e+00 , 6.12676862849093e-01 , 1.83158756566952e+00 ), ( 1.17815309183518e-02 , 3.56344350859484e-02 , 2.95345052165564e-01 ), ( 1.39527720639177e-03 , 2.98070494706035e-02 , 2.72099411002732e-01 ), ( 2.32145233122851e-02 , 4.39074599414199e-02 , 3.38155328130077e-01 ), ( 4.42884388578303e-02 , 3.55770183824760e-02 , 1.98544622085880e-01 ), ( 1.70606064798460e-02 , 2.15954895259924e-02 , 1.49607801367326e-01 ), ( 1.12364402327663e-01 , 5.61973759167895e-02 , 1.88034958832262e-01 ), ( 1.58128706307591e-01 , 6.34561297058981e-02 , 1.19774406274265e-01 ), ( 2.37173419024315e-01 , 9.03566710502176e-02 , 1.34981565454175e-01 ), ( 1.28925952277339e-01 , 4.66373627711320e-02 , 5.03926675630357e-02 ), ( 1.24635092654600e-01 , 3.85441920074173e-02 , -1.19020764141277e-02 ), ( 1.05484534568384e-01 , 4.02939372512230e-02 , 6.10272351547240e-02 ), ( 6.94956820275506e-02 , 2.25927287032315e-02 , 3.56447470925120e-03 ), ( 5.58222546537899e-02 , 2.16552368518423e-02 , 3.53699234236275e-02 ), ( -2.47135925810860e-03 , -3.15710012834207e-03 , -2.19389956134244e-02 ), ( -1.61360408849052e-02 , -1.48830978119519e-02 , -9.01399907045330e-02 ), ( -4.90728248685874e-02 , -1.21395414838307e-02 , 3.28268230544758e-02 ), ( -1.15703711744919e-01 , -3.50632298865104e-02 , 1.77112250988428e-02 ), ( -1.56580705937949e-01 , -3.98466686837114e-02 , 9.44376794295900e-02 ), ( -1.02491861011419e-01 , -3.56834795290565e-02 , -2.71633668503098e-02 ), ( -1.38442750990986e-01 , -5.32423094681212e-02 , -8.34190841660912e-02 ), ( -4.89660148765012e-02 , -1.61149140274058e-02 , -4.33054415288853e-03 ), ( -2.74281777646190e-02 , -1.35602397762497e-02 , -4.44392822423457e-02 ), ( 2.92238361493918e-02 , 9.68738890265097e-03 , 3.23053726750785e-03 ), ( 3.62043830759501e-03 , -1.24139036315880e-02 , -1.25765456593385e-01 ), ( -1.35636932780754e-02 , -2.36539584331770e-02 , -1.79040307025521e-01 ), ( 4.91590633679874e-02 , 8.58945727306770e-04 , -1.37623114702033e-01 ), ( 7.76277306438035e-02 , 1.86343451800031e-03 , -2.12623385200723e-01 ), ( 1.37329610487336e-01 , 2.20210884399716e-02 , -2.02621448432406e-01 ), ( 1.87668989808830e-02 , -2.26370595571488e-02 , -2.65362555955722e-01 ), ( 1.98116057162201e-02 , -2.96764945622195e-02 , -3.33693128572212e-01 ), ( -3.45014111337715e-02 , -3.62938188514576e-02 , -2.34171460541389e-01 ), ( -9.58260107055832e-02 , -6.04218507684637e-02 , -2.76162522816596e-01 ), ( -1.33984559994027e-01 , -6.74374435503455e-02 , -2.28172756594489e-01 ), ( -1.52068778590725e-01 , -8.06207699928350e-02 , -2.96790945140726e-01 ), ( -1.79743992424764e-01 , -9.62846849475359e-02 , -3.59994069271663e-01 ), ( -1.91545215140248e-01 , -9.35883964956654e-02 , -3.00057696700772e-01 ), ( -2.32793478473568e-01 , -1.09585879117182e-01 , -3.26155879383167e-01 ), ( -1.17927872493770e-01 , -7.08030939809125e-02 , -3.06914765472131e-01 ), ( -1.71077019077921e-01 , -8.09118864898879e-02 , -2.43196423576792e-01 ), ( -2.23315319914395e-01 , -9.90428208980078e-02 , -2.56519288543278e-01 ), ( -2.58174232927881e-01 , -1.01802827967514e-01 , -1.78863428551754e-01 ) } +colvars: Step 24, atoms_new_colvar_forces = { ( -4.89626902453616e+00 , -4.34934047979890e-01 , -1.24429415551852e+00 ), ( -4.21740348009850e+00 , -3.68688958737982e-01 , -9.71704355524009e-01 ), ( -4.29362495193560e+00 , -3.97030214100938e-01 , -1.00867393366114e+00 ), ( -5.77248701097877e+00 , -5.63136126905229e-01 , -1.50348167626380e+00 ), ( 2.65604080467865e-01 , 1.23836488345376e-01 , 3.61032061404946e-01 ), ( 5.27466345113280e+00 , 6.19143717272684e-01 , 1.83072879871677e+00 ), ( 4.45741547617010e+00 , 5.11978879374643e-01 , 1.58856588034739e+00 ), ( -4.74608480652595e-02 , 2.44429386696295e-02 , 3.66716235475066e-01 ), ( 4.43812333803963e+00 , 5.02447893550157e-01 , 1.55737802379602e+00 ), ( 5.88289941732060e+00 , 6.43545901115343e-01 , 1.92144777727568e+00 ), ( 1.24016433386963e-02 , 3.75456368131752e-02 , 3.10972373256576e-01 ), ( 1.45886759925512e-03 , 3.14058728257868e-02 , 2.86488883408213e-01 ), ( 2.44262732103448e-02 , 4.62533087339251e-02 , 3.56033477622558e-01 ), ( 4.66227332062297e-02 , 3.74692841203345e-02 , 2.09041889539189e-01 ), ( 1.79511722286483e-02 , 2.27452144363720e-02 , 1.57512086791239e-01 ), ( 1.18305422862440e-01 , 5.91734330988370e-02 , 1.97980266559822e-01 ), ( 1.66493135046941e-01 , 6.68049109244647e-02 , 1.26108538004343e-01 ), ( 2.49724184384160e-01 , 9.51223530091758e-02 , 1.42123796070175e-01 ), ( 1.35750417810693e-01 , 4.90953697137610e-02 , 5.30609553254026e-02 ), ( 1.31231229580206e-01 , 4.05679005501801e-02 , -1.25321033842958e-02 ), ( 1.11074561932630e-01 , 4.24227818820005e-02 , 6.42652101238391e-02 ), ( 7.31864739674444e-02 , 2.37859994089552e-02 , 3.76728123495579e-03 ), ( 5.87959065637369e-02 , 2.28064395855190e-02 , 3.72632532332031e-02 ), ( -2.59282218585777e-03 , -3.32188576626139e-03 , -2.30897730450607e-02 ), ( -1.69794002718247e-02 , -1.56727660768182e-02 , -9.48988603002960e-02 ), ( -5.16653715240636e-02 , -1.27709429823289e-02 , 3.45692803765967e-02 ), ( -1.21826956291034e-01 , -3.69031440306104e-02 , 1.86489272804351e-02 ), ( -1.64871713353343e-01 , -4.19294068108170e-02 , 9.94312761794511e-02 ), ( -1.07921341588612e-01 , -3.75644978733913e-02 , -2.86067046427358e-02 ), ( -1.45775132593793e-01 , -5.60537477220428e-02 , -8.78399963980796e-02 ), ( -5.15671043676920e-02 , -1.69665033073845e-02 , -4.57036833381938e-03 ), ( -2.88944787560477e-02 , -1.42852866288890e-02 , -4.68074965365949e-02 ), ( 3.07511026606865e-02 , 1.01883566235371e-02 , 3.38002850592339e-03 ), ( 3.80135633296647e-03 , -1.30880392102020e-02 , -1.32433429512259e-01 ), ( -1.42947871960597e-02 , -2.49270998374891e-02 , -1.88530674616993e-01 ), ( 5.17565811238943e-02 , 8.83493066172997e-04 , -1.44911454793012e-01 ), ( 8.17365981274858e-02 , 1.93259663316131e-03 , -2.23875940318661e-01 ), ( 1.44604341951858e-01 , 2.31535458410976e-02 , -2.13337805515812e-01 ), ( 1.97642194162512e-02 , -2.38609104471018e-02 , -2.79402307490500e-01 ), ( 2.08646629753179e-02 , -3.12793561260939e-02 , -3.51348774530305e-01 ), ( -3.63206558482552e-02 , -3.82298862228425e-02 , -2.46557514114021e-01 ), ( -1.00887625598192e-01 , -6.36300842019940e-02 , -2.90767406376349e-01 ), ( -1.41061607304820e-01 , -7.10059932715915e-02 , -2.40233258645865e-01 ), ( -1.60112800777942e-01 , -8.48957452663499e-02 , -3.12494005513725e-01 ), ( -1.89251286005236e-01 , -1.01390732569457e-01 , -3.79040572547699e-01 ), ( -2.01696192185051e-01 , -9.85529912690795e-02 , -3.15953251461666e-01 ), ( -2.45131811811532e-01 , -1.15396540618694e-01 , -3.43437461913683e-01 ), ( -1.24182386218190e-01 , -7.45711920909637e-02 , -3.23172886379091e-01 ), ( -1.80133726500473e-01 , -8.51977949817432e-02 , -2.56070407852133e-01 ), ( -2.35142654285279e-01 , -1.04285877684321e-01 , -2.70104973972601e-01 ), ( -2.71851477173310e-01 , -1.07182542873783e-01 , -1.88344751365079e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 24, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -2904,10 +4642,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 25, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 25, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 25, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 25, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 25, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 25, atoms_positions[size = 51] = { ( 8.26647924113907e+00 , 4.13179421244837e-02 , -7.39704319030450e-01 ), ( 6.87504378717396e+00 , -5.63680794226234e-01 , -5.43097344800070e-01 ), ( 6.15957936861644e+00 , -3.91234137028024e-01 , 7.70294817300408e-01 ), ( 4.92046658609037e+00 , -1.49341302318207e-01 , 7.33713088607941e-01 ), ( 7.02637738568081e+00 , -2.05999234530478e+00 , -9.09574040424618e-01 ), ( 6.83102022020697e+00 , -2.73189407059131e-01 , 1.94492006868935e+00 ), ( 6.14083899143568e+00 , -1.96649410894756e-01 , 3.16895711496001e+00 ), ( 7.10387128111467e+00 , -3.47595762084743e-01 , 4.35229617187487e+00 ), ( 5.33868170818087e+00 , 1.07824508398872e+00 , 3.36563180334843e+00 ), ( 4.16924218668598e+00 , 1.01410089115945e+00 , 3.73236796230498e+00 ), ( 5.83636834616802e+00 , 2.25745208996869e+00 , 2.98089997359473e+00 ), ( 5.20864757810393e+00 , 3.56957245844521e+00 , 2.91285775636473e+00 ), ( 6.31705620144432e+00 , 4.49339279089957e+00 , 2.31787522863057e+00 ), ( 3.86296977967216e+00 , 3.67344909542297e+00 , 2.04002226175517e+00 ), ( 2.79455645455796e+00 , 4.16942805909256e+00 , 2.46121204790199e+00 ), ( 3.93559624390625e+00 , 3.22238101929181e+00 , 7.31536372169389e-01 ), ( 2.71257288372061e+00 , 3.02108978381586e+00 , -8.92124402548022e-02 ), ( 3.08718036466247e+00 , 2.67408286573452e+00 , -1.52670658557882e+00 ), ( 1.57260597604337e+00 , 2.17067653702486e+00 , 4.26019628236451e-01 ), ( 3.80472307064121e-01 , 2.61088420554297e+00 , 4.87723705084447e-01 ), ( 2.07558023753614e+00 , 1.13589788556777e+00 , 1.04789679267253e+00 ), ( 1.17493250223783e+00 , 1.17344948434977e-01 , 1.70020104547663e+00 ), ( 2.06297012787758e+00 , -1.09234301309062e+00 , 2.02676626443017e+00 ), ( 5.71476168770821e-01 , 6.17809229056732e-01 , 2.96339779042952e+00 ), ( -5.84379828605167e-01 , 3.52350045985900e-01 , 3.16489618716293e+00 ), ( 1.29883879500052e+00 , 1.35699639850161e+00 , 3.74383470095006e+00 ), ( 8.43262697449691e-01 , 1.98351330129065e+00 , 5.02735344011084e+00 ), ( 2.10939969981363e+00 , 2.73008646872006e+00 , 5.71182363896326e+00 ), ( -3.46047044646963e-01 , 2.90908857240431e+00 , 4.96982194901969e+00 ), ( -1.12126849545417e+00 , 3.06644595133659e+00 , 5.87783361124985e+00 ), ( -5.34909653132848e-01 , 3.51276060146897e+00 , 3.82273837551560e+00 ), ( -1.50477688260082e+00 , 4.51307521955318e+00 , 3.41545366482764e+00 ), ( -7.08562451968667e-01 , 5.42337020236753e+00 , 2.47077946899051e+00 ), ( -2.74531503184144e+00 , 3.92797028087999e+00 , 2.85376251607557e+00 ), ( -3.81189297077074e+00 , 4.53739408044238e+00 , 2.81260060017561e+00 ), ( -2.65772243228862e+00 , 2.65007890944884e+00 , 2.37007604687258e+00 ), ( -3.78688535884526e+00 , 1.81296755538521e+00 , 2.00280574981871e+00 ), ( -3.37011105180502e+00 , 8.79011922787073e-01 , 8.42406291768775e-01 ), ( -4.28409289745128e+00 , 1.06312784605231e+00 , 3.21523361808659e+00 ), ( -5.49149943216895e+00 , 7.83421661368256e-01 , 3.33356267635616e+00 ), ( -3.36575603084633e+00 , 7.13569148392799e-01 , 4.19813108139739e+00 ), ( -3.67792446450366e+00 , 7.22702883285445e-02 , 5.45613409071240e+00 ), ( -2.39132996350769e+00 , -3.25346984705185e-01 , 6.15340691029519e+00 ), ( -4.46461207121171e+00 , 9.42912929193460e-01 , 6.42773040028982e+00 ), ( -5.36503185174231e+00 , 5.88816414161381e-01 , 7.21629148964332e+00 ), ( -6.27826863574096e+00 , 3.62766812535031e+00 , 6.74966196335481e+00 ), ( -6.97819138625597e+00 , 4.29547838009075e+00 , 7.49469506730733e+00 ), ( -6.69607027180097e+00 , 3.16616660359056e+00 , 5.51046162579048e+00 ), ( -4.11616753887897e+00 , 2.24660348701733e+00 , 6.39018318393223e+00 ), ( -4.80950490461211e+00 , 3.24898521176349e+00 , 7.25766730504329e+00 ), ( -4.05844207046985e+00 , 4.55035542879320e+00 , 7.27232106602667e+00 ) } +colvars: Step 25, atoms_positions[size = 51] = { ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 ), ( 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 ), ( 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 ), ( 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 ), ( 7.02601780850771e+00 , -2.06015488067759e+00 , -9.09492224700635e-01 ), ( 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 ), ( 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 ), ( 7.10489589023969e+00 , -3.47758956392679e-01 , 4.35321300563372e+00 ), ( 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 ), ( 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 ), ( 5.83732729632828e+00 , 2.25785810405961e+00 , 2.98093128297857e+00 ), ( 5.20869462502566e+00 , 3.56959681912101e+00 , 2.91307028328090e+00 ), ( 6.31702728307081e+00 , 4.49345110958214e+00 , 2.31808179186695e+00 ), ( 3.86300150802905e+00 , 3.67341219998733e+00 , 2.04017422536762e+00 ), ( 2.79457049211183e+00 , 4.16943048780216e+00 , 2.46130448350710e+00 ), ( 3.93567494128755e+00 , 3.22241188154132e+00 , 7.31665097008206e-01 ), ( 2.71267750097800e+00 , 3.02113169189251e+00 , -8.91310614028259e-02 ), ( 3.08732123000904e+00 , 2.67413534581401e+00 , -1.52662014513167e+00 ), ( 1.57269474677811e+00 , 2.17070869266575e+00 , 4.26058642461620e-01 ), ( 3.80555829918894e-01 , 2.61090721785921e+00 , 4.87721454392032e-01 ), ( 2.07565081504512e+00 , 1.13592640012642e+00 , 1.04794811588010e+00 ), ( 1.17497779195547e+00 , 1.17363818366492e-01 , 1.70020616076127e+00 ), ( 2.06302853920080e+00 , -1.09229653109778e+00 , 2.02682408795984e+00 ), ( 5.71499907914238e-01 , 6.17806942729092e-01 , 2.96338906413119e+00 ), ( -5.84375440137461e-01 , 3.52346628945102e-01 , 3.16484827373788e+00 ), ( 1.29890503570500e+00 , 1.35697344446113e+00 , 3.74385161333402e+00 ), ( 8.43209552958302e-01 , 1.98348034433225e+00 , 5.02735651599704e+00 ), ( 2.10930944408490e+00 , 2.73006003201001e+00 , 5.71186839017599e+00 ), ( -3.46113376698924e-01 , 2.90906060189559e+00 , 4.96980143944285e+00 ), ( -1.12136107320199e+00 , 3.06641515542823e+00 , 5.87779237318429e+00 ), ( -5.34941623924234e-01 , 3.51275008627904e+00 , 3.82272372999129e+00 ), ( -1.50479759285668e+00 , 4.51306813747961e+00 , 3.41541854829753e+00 ), ( -7.08550151619272e-01 , 5.42337212444133e+00 , 2.47077640178917e+00 ), ( -2.74531373746629e+00 , 3.92796338514317e+00 , 2.85367775142689e+00 ), ( -3.81189755702219e+00 , 4.53737709243637e+00 , 2.81249160218273e+00 ), ( -2.65769350477280e+00 , 2.65007832275566e+00 , 2.36998223012328e+00 ), ( -3.78683922216990e+00 , 1.81296910506803e+00 , 2.00265894129983e+00 ), ( -3.37002983699502e+00 , 8.79015851476826e-01 , 8.42270333198377e-01 ), ( -4.28408110971430e+00 , 1.06310797908519e+00 , 3.21505584648410e+00 ), ( -5.49148724796687e+00 , 7.83401806260949e-01 , 3.33335876241182e+00 ), ( -3.36577486954441e+00 , 7.13539644075190e-01 , 4.19797163127101e+00 ), ( -3.67799115688145e+00 , 7.22227416989530e-02 , 5.45594885427104e+00 ), ( -2.39141448198009e+00 , -3.25383286486184e-01 , 6.15326448174159e+00 ), ( -4.46471526135512e+00 , 9.42860744303390e-01 , 6.42752883167951e+00 ), ( -5.36514180386212e+00 , 5.88755929827167e-01 , 7.21607462723538e+00 ), ( -6.27839620697427e+00 , 3.62760689447500e+00 , 6.74946980865791e+00 ), ( -6.97833374705994e+00 , 4.29541023538326e+00 , 7.49449652406574e+00 ), ( -6.69616584445880e+00 , 3.16611776307592e+00 , 5.51025229428525e+00 ), ( -4.11627741428843e+00 , 2.24655326574761e+00 , 6.39001782480647e+00 ), ( -4.80965119349014e+00 , 3.24891673341217e+00 , 7.25749358057592e+00 ), ( -4.05860175930149e+00 , 4.55028941202804e+00 , 7.27220105324414e+00 ) } colvars: Step 25, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 25, atom_groups_ids[size = 0] = @@ -2925,162 +4663,301 @@ colvars: Collective variables module, step no. 25 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.99515551202827e-01 , -6.27415312265916e-03 , 9.54070788563543e-01 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.98260726975113e-01 , -6.09344114517502e-03 , 9.54464985591031e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 7.02601780850771e+00 , -2.06015488067759e+00 , -9.09492224700635e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 , 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 7.10489589023969e+00 , -3.47758956392679e-01 , 4.35321300563372e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 , 5.83732729632828e+00 , 2.25785810405961e+00 , 2.98093128297857e+00 , 5.20869462502566e+00 , 3.56959681912101e+00 , 2.91307028328090e+00 , 6.31702728307081e+00 , 4.49345110958214e+00 , 2.31808179186695e+00 , 3.86300150802905e+00 , 3.67341219998733e+00 , 2.04017422536762e+00 , 2.79457049211183e+00 , 4.16943048780216e+00 , 2.46130448350710e+00 , 3.93567494128755e+00 , 3.22241188154132e+00 , 7.31665097008206e-01 , 2.71267750097800e+00 , 3.02113169189251e+00 , -8.91310614028259e-02 , 3.08732123000904e+00 , 2.67413534581401e+00 , -1.52662014513167e+00 , 1.57269474677811e+00 , 2.17070869266575e+00 , 4.26058642461620e-01 , 3.80555829918894e-01 , 2.61090721785921e+00 , 4.87721454392032e-01 , 2.07565081504512e+00 , 1.13592640012642e+00 , 1.04794811588010e+00 , 1.17497779195547e+00 , 1.17363818366492e-01 , 1.70020616076127e+00 , 2.06302853920080e+00 , -1.09229653109778e+00 , 2.02682408795984e+00 , 5.71499907914238e-01 , 6.17806942729092e-01 , 2.96338906413119e+00 , -5.84375440137461e-01 , 3.52346628945102e-01 , 3.16484827373788e+00 , 1.29890503570500e+00 , 1.35697344446113e+00 , 3.74385161333402e+00 , 8.43209552958302e-01 , 1.98348034433225e+00 , 5.02735651599704e+00 , 2.10930944408490e+00 , 2.73006003201001e+00 , 5.71186839017599e+00 , -3.46113376698924e-01 , 2.90906060189559e+00 , 4.96980143944285e+00 , -1.12136107320199e+00 , 3.06641515542823e+00 , 5.87779237318429e+00 , -5.34941623924234e-01 , 3.51275008627904e+00 , 3.82272372999129e+00 , -1.50479759285668e+00 , 4.51306813747961e+00 , 3.41541854829753e+00 , -7.08550151619272e-01 , 5.42337212444133e+00 , 2.47077640178917e+00 , -2.74531373746629e+00 , 3.92796338514317e+00 , 2.85367775142689e+00 , -3.81189755702219e+00 , 4.53737709243637e+00 , 2.81249160218273e+00 , -2.65769350477280e+00 , 2.65007832275566e+00 , 2.36998223012328e+00 , -3.78683922216990e+00 , 1.81296910506803e+00 , 2.00265894129983e+00 , -3.37002983699502e+00 , 8.79015851476826e-01 , 8.42270333198377e-01 , -4.28408110971430e+00 , 1.06310797908519e+00 , 3.21505584648410e+00 , -5.49148724796687e+00 , 7.83401806260949e-01 , 3.33335876241182e+00 , -3.36577486954441e+00 , 7.13539644075190e-01 , 4.19797163127101e+00 , -3.67799115688145e+00 , 7.22227416989530e-02 , 5.45594885427104e+00 , -2.39141448198009e+00 , -3.25383286486184e-01 , 6.15326448174159e+00 , -4.46471526135512e+00 , 9.42860744303390e-01 , 6.42752883167951e+00 , -5.36514180386212e+00 , 5.88755929827167e-01 , 7.21607462723538e+00 , -6.27839620697427e+00 , 3.62760689447500e+00 , 6.74946980865791e+00 , -6.97833374705994e+00 , 4.29541023538326e+00 , 7.49449652406574e+00 , -6.69616584445880e+00 , 3.16611776307592e+00 , 5.51025229428525e+00 , -4.11627741428843e+00 , 2.24655326574761e+00 , 6.39001782480647e+00 , -4.80965119349014e+00 , 3.24891673341217e+00 , 7.25749358057592e+00 , -4.05860175930149e+00 , 4.55028941202804e+00 , 7.27220105324414e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.99515551202827e-01 , -6.27415312265916e-03 , 9.54070788563543e-01 ). +colvars: Colvar "one" has value ( -2.98260726975113e-01 , -6.09344114517502e-03 , 9.54464985591031e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 7.02601780850771e+00 , -2.06015488067759e+00 , -9.09492224700635e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 , 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 7.10489589023969e+00 , -3.47758956392679e-01 , 4.35321300563372e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 , 5.83732729632828e+00 , 2.25785810405961e+00 , 2.98093128297857e+00 , 5.20869462502566e+00 , 3.56959681912101e+00 , 2.91307028328090e+00 , 6.31702728307081e+00 , 4.49345110958214e+00 , 2.31808179186695e+00 , 3.86300150802905e+00 , 3.67341219998733e+00 , 2.04017422536762e+00 , 2.79457049211183e+00 , 4.16943048780216e+00 , 2.46130448350710e+00 , 3.93567494128755e+00 , 3.22241188154132e+00 , 7.31665097008206e-01 , 2.71267750097800e+00 , 3.02113169189251e+00 , -8.91310614028259e-02 , 3.08732123000904e+00 , 2.67413534581401e+00 , -1.52662014513167e+00 , 1.57269474677811e+00 , 2.17070869266575e+00 , 4.26058642461620e-01 , 3.80555829918894e-01 , 2.61090721785921e+00 , 4.87721454392032e-01 , 2.07565081504512e+00 , 1.13592640012642e+00 , 1.04794811588010e+00 , 1.17497779195547e+00 , 1.17363818366492e-01 , 1.70020616076127e+00 , 2.06302853920080e+00 , -1.09229653109778e+00 , 2.02682408795984e+00 , 5.71499907914238e-01 , 6.17806942729092e-01 , 2.96338906413119e+00 , -5.84375440137461e-01 , 3.52346628945102e-01 , 3.16484827373788e+00 , 1.29890503570500e+00 , 1.35697344446113e+00 , 3.74385161333402e+00 , 8.43209552958302e-01 , 1.98348034433225e+00 , 5.02735651599704e+00 , 2.10930944408490e+00 , 2.73006003201001e+00 , 5.71186839017599e+00 , -3.46113376698924e-01 , 2.90906060189559e+00 , 4.96980143944285e+00 , -1.12136107320199e+00 , 3.06641515542823e+00 , 5.87779237318429e+00 , -5.34941623924234e-01 , 3.51275008627904e+00 , 3.82272372999129e+00 , -1.50479759285668e+00 , 4.51306813747961e+00 , 3.41541854829753e+00 , -7.08550151619272e-01 , 5.42337212444133e+00 , 2.47077640178917e+00 , -2.74531373746629e+00 , 3.92796338514317e+00 , 2.85367775142689e+00 , -3.81189755702219e+00 , 4.53737709243637e+00 , 2.81249160218273e+00 , -2.65769350477280e+00 , 2.65007832275566e+00 , 2.36998223012328e+00 , -3.78683922216990e+00 , 1.81296910506803e+00 , 2.00265894129983e+00 , -3.37002983699502e+00 , 8.79015851476826e-01 , 8.42270333198377e-01 , -4.28408110971430e+00 , 1.06310797908519e+00 , 3.21505584648410e+00 , -5.49148724796687e+00 , 7.83401806260949e-01 , 3.33335876241182e+00 , -3.36577486954441e+00 , 7.13539644075190e-01 , 4.19797163127101e+00 , -3.67799115688145e+00 , 7.22227416989530e-02 , 5.45594885427104e+00 , -2.39141448198009e+00 , -3.25383286486184e-01 , 6.15326448174159e+00 , -4.46471526135512e+00 , 9.42860744303390e-01 , 6.42752883167951e+00 , -5.36514180386212e+00 , 5.88755929827167e-01 , 7.21607462723538e+00 , -6.27839620697427e+00 , 3.62760689447500e+00 , 6.74946980865791e+00 , -6.97833374705994e+00 , 4.29541023538326e+00 , 7.49449652406574e+00 , -6.69616584445880e+00 , 3.16611776307592e+00 , 5.51025229428525e+00 , -4.11627741428843e+00 , 2.24655326574761e+00 , 6.39001782480647e+00 , -4.80965119349014e+00 , 3.24891673341217e+00 , 7.25749358057592e+00 , -4.05860175930149e+00 , 4.55028941202804e+00 , 7.27220105324414e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.5083 , 2.07728 , -15.1778 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.805 , 6.5805 , 13.161 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.5083 , 2.07728 , -15.1778 ) to colvar "one". -colvars: Adding total bias energy: 44.2678 +colvars: Adding biasing force ( 65.805 , 6.5805 , 13.161 ) to colvar "one". +colvars: Adding total bias energy: 56.2041 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.5083 , 2.07728 , -15.1778 ) +colvars: Force to be applied: ( 65.805 , 6.5805 , 13.161 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.9244 , -0.528143 , -1.43193 ) -colvars: ( -4.22267 , -0.452883 , -1.22788 ) -colvars: ( -4.22267 , -0.452883 , -1.22788 ) -colvars: ( -5.62472 , -0.603253 , -1.63557 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.18859 , -0.55473 , -1.50141 ) +colvars: ( -4.44922 , -0.475681 , -1.28746 ) +colvars: ( -4.44922 , -0.475681 , -1.28746 ) +colvars: ( -5.92649 , -0.633621 , -1.71494 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.889617 , 0.195883 , 0.613661 ) -colvars: ( 0.77088 , 0.266382 , 0.637437 ) -colvars: ( 0.754725 , 0.259507 , 0.619017 ) -colvars: ( 0.660013 , 0.266948 , 0.573812 ) -colvars: ( 0.648211 , 0.200461 , 0.479519 ) -colvars: ( 0.574259 , 0.343922 , 0.625255 ) -colvars: ( 0.46801 , 0.357704 , 0.58169 ) -colvars: ( 0.391993 , 0.454672 , 0.665082 ) -colvars: ( 0.386811 , 0.313148 , 0.475947 ) -colvars: ( 0.352417 , 0.271551 , 0.401272 ) -colvars: ( 0.35746 , 0.318442 , 0.465868 ) -colvars: ( 0.286628 , 0.275584 , 0.368377 ) -colvars: ( 0.259472 , 0.304574 , 0.390738 ) -colvars: ( 0.348575 , 0.178016 , 0.276028 ) -colvars: ( 0.290339 , 0.134668 , 0.185206 ) -colvars: ( 0.47039 , 0.141231 , 0.298377 ) -colvars: ( 0.542375 , 0.0501084 , 0.220332 ) -colvars: ( 0.670873 , 0.029381 , 0.26768 ) -colvars: ( 0.551157 , 0.0182826 , 0.183575 ) -colvars: ( 0.535521 , -0.0467075 , 0.0890249 ) -colvars: ( 0.572137 , 0.0661222 , 0.258673 ) -colvars: ( 0.570901 , 0.0499213 , 0.236649 ) -colvars: ( 0.607386 , 0.11457 , 0.342855 ) -colvars: ( 0.447581 , 0.0541633 , 0.170626 ) -colvars: ( 0.440923 , -0.00172194 , 0.0932634 ) -colvars: ( 0.346326 , 0.119553 , 0.197834 ) -colvars: ( 0.22278 , 0.127907 , 0.137089 ) -colvars: ( 0.131907 , 0.213401 , 0.196764 ) -colvars: ( 0.194595 , 0.0542703 , 0.0238812 ) -colvars: ( 0.145818 , 0.0180409 , -0.052087 ) -colvars: ( 0.227657 , 0.0288647 , 0.00966498 ) -colvars: ( 0.213547 , -0.0435099 , -0.093711 ) -colvars: ( 0.248268 , -0.0467178 , -0.0777705 ) -colvars: ( 0.288318 , -0.129226 , -0.163028 ) -colvars: ( 0.244652 , -0.182341 , -0.258236 ) -colvars: ( 0.402723 , -0.144039 , -0.116084 ) -colvars: ( 0.479706 , -0.219311 , -0.170382 ) -colvars: ( 0.609935 , -0.221671 , -0.0978739 ) -colvars: ( 0.433063 , -0.223944 , -0.203556 ) -colvars: ( 0.438597 , -0.291911 , -0.28973 ) -colvars: ( 0.384881 , -0.150874 , -0.135433 ) -colvars: ( 0.33133 , -0.144791 , -0.158525 ) -colvars: ( 0.315133 , -0.0583043 , -0.054186 ) -colvars: ( 0.208944 , -0.153783 , -0.24141 ) -colvars: ( 0.184878 , -0.195809 , -0.310654 ) -colvars: ( 0.00874516 , -0.199722 , -0.418064 ) -colvars: ( -0.0815191 , -0.217652 , -0.494053 ) -colvars: ( 0.108164 , -0.249349 , -0.425607 ) -colvars: ( 0.127567 , -0.113333 , -0.23546 ) -colvars: ( 0.00911224 , -0.117907 , -0.310252 ) -colvars: ( -0.0793083 , -0.0374929 , -0.255833 ) +colvars: ( 0.936502 , 0.206381 , 0.644948 ) +colvars: ( 0.811582 , 0.280524 , 0.66999 ) +colvars: ( 0.794534 , 0.273337 , 0.650666 ) +colvars: ( 0.694964 , 0.281038 , 0.603083 ) +colvars: ( 0.682542 , 0.211058 , 0.503917 ) +colvars: ( 0.60477 , 0.361985 , 0.657193 ) +colvars: ( 0.493015 , 0.376405 , 0.611379 ) +colvars: ( 0.413062 , 0.478405 , 0.69909 ) +colvars: ( 0.407561 , 0.329496 , 0.50021 ) +colvars: ( 0.371393 , 0.285679 , 0.421665 ) +colvars: ( 0.376639 , 0.335101 , 0.489655 ) +colvars: ( 0.302088 , 0.289988 , 0.387165 ) +colvars: ( 0.273476 , 0.320536 , 0.410729 ) +colvars: ( 0.367245 , 0.187345 , 0.290032 ) +colvars: ( 0.305975 , 0.141691 , 0.194528 ) +colvars: ( 0.495393 , 0.148701 , 0.313512 ) +colvars: ( 0.571113 , 0.0528428 , 0.231418 ) +colvars: ( 0.706282 , 0.0311145 , 0.281197 ) +colvars: ( 0.580393 , 0.0193038 , 0.19272 ) +colvars: ( 0.563938 , -0.0491038 , 0.0932843 ) +colvars: ( 0.602507 , 0.0696211 , 0.271662 ) +colvars: ( 0.601251 , 0.0525201 , 0.24846 ) +colvars: ( 0.639675 , 0.12054 , 0.360119 ) +colvars: ( 0.471523 , 0.0569059 , 0.179043 ) +colvars: ( 0.464531 , -0.00193279 , 0.0976668 ) +colvars: ( 0.364992 , 0.125683 , 0.207692 ) +colvars: ( 0.235021 , 0.134404 , 0.143831 ) +colvars: ( 0.139412 , 0.224347 , 0.206625 ) +colvars: ( 0.205335 , 0.0569213 , 0.0248015 ) +colvars: ( 0.154031 , 0.0187472 , -0.0550976 ) +colvars: ( 0.240072 , 0.0302491 , 0.00988053 ) +colvars: ( 0.225192 , -0.0458957 , -0.098811 ) +colvars: ( 0.261672 , -0.0492001 , -0.0820124 ) +colvars: ( 0.303862 , -0.136084 , -0.171743 ) +colvars: ( 0.257918 , -0.192006 , -0.271861 ) +colvars: ( 0.424238 , -0.15163 , -0.122414 ) +colvars: ( 0.50524 , -0.23083 , -0.179554 ) +colvars: ( 0.642255 , -0.233253 , -0.103335 ) +colvars: ( 0.456212 , -0.235779 , -0.214471 ) +colvars: ( 0.462036 , -0.307316 , -0.305109 ) +colvars: ( 0.405559 , -0.158937 , -0.142841 ) +colvars: ( 0.349263 , -0.152609 , -0.16715 ) +colvars: ( 0.33226 , -0.061629 , -0.0574391 ) +colvars: ( 0.220499 , -0.162132 , -0.254286 ) +colvars: ( 0.195199 , -0.2064 , -0.327124 ) +colvars: ( 0.00980286 , -0.210506 , -0.439962 ) +colvars: ( -0.0851655 , -0.22942 , -0.519855 ) +colvars: ( 0.114368 , -0.262655 , -0.447897 ) +colvars: ( 0.134859 , -0.11957 , -0.247983 ) +colvars: ( 0.0102288 , -0.124437 , -0.326605 ) +colvars: ( -0.0828059 , -0.0398325 , -0.269335 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.9244 , 0.528143 , 1.43193 ) -colvars: ( 4.22267 , 0.452883 , 1.22788 ) -colvars: ( 4.22267 , 0.452883 , 1.22788 ) -colvars: ( 5.62472 , 0.603253 , 1.63557 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.18859 , 0.55473 , 1.50141 ) +colvars: ( 4.44922 , 0.475681 , 1.28746 ) +colvars: ( 4.44922 , 0.475681 , 1.28746 ) +colvars: ( 5.92649 , 0.633621 , 1.71494 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.614702 , -0.0811791 , -0.366537 ) -colvars: ( -0.552998 , -0.164169 , -0.334955 ) -colvars: ( -0.502544 , -0.141977 , -0.276198 ) -colvars: ( -0.514499 , -0.191753 , -0.306402 ) -colvars: ( -0.504855 , -0.132639 , -0.275104 ) -colvars: ( -0.490395 , -0.284137 , -0.315995 ) -colvars: ( -0.458441 , -0.324625 , -0.29873 ) -colvars: ( -0.437323 , -0.432356 , -0.316933 ) -colvars: ( -0.395409 , -0.289041 , -0.222451 ) -colvars: ( -0.391225 , -0.263657 , -0.208968 ) -colvars: ( -0.345608 , -0.283298 , -0.170365 ) -colvars: ( -0.28501 , -0.246183 , -0.0959695 ) -colvars: ( -0.235881 , -0.261079 , -0.052106 ) -colvars: ( -0.30406 , -0.142608 , -0.077211 ) -colvars: ( -0.272999 , -0.113191 , -0.0352764 ) -colvars: ( -0.357863 , -0.0850504 , -0.110163 ) -colvars: ( -0.384095 , 0.0135592 , -0.10043 ) -colvars: ( -0.433588 , 0.0613264 , -0.132636 ) -colvars: ( -0.422214 , 0.0285695 , -0.1332 ) -colvars: ( -0.41084 , 0.0855844 , -0.100933 ) -colvars: ( -0.466783 , -0.0257515 , -0.1978 ) -colvars: ( -0.50167 , -0.0272864 , -0.233378 ) -colvars: ( -0.551981 , -0.0930292 , -0.307918 ) -colvars: ( -0.450263 , -0.0573759 , -0.192784 ) -colvars: ( -0.457302 , -0.0131355 , -0.18367 ) -colvars: ( -0.395521 , -0.13192 , -0.165102 ) -colvars: ( -0.338532 , -0.163294 , -0.119376 ) -colvars: ( -0.288454 , -0.253773 , -0.102202 ) -colvars: ( -0.297005 , -0.0901074 , -0.0509301 ) -colvars: ( -0.284184 , -0.0714187 , -0.0312266 ) -colvars: ( -0.276424 , -0.0450001 , -0.0137758 ) -colvars: ( -0.240652 , 0.0301069 , 0.0495958 ) -colvars: ( -0.218597 , 0.0566595 , 0.0814434 ) -colvars: ( -0.28445 , 0.11716 , 0.0374722 ) -colvars: ( -0.257916 , 0.159117 , 0.0794494 ) -colvars: ( -0.353447 , 0.145318 , -0.0214825 ) -colvars: ( -0.402054 , 0.221761 , -0.0423129 ) -colvars: ( -0.4727 , 0.244348 , -0.10496 ) -colvars: ( -0.414372 , 0.20181 , -0.0619728 ) -colvars: ( -0.418869 , 0.262864 , -0.044158 ) -colvars: ( -0.419538 , 0.114868 , -0.0989539 ) -colvars: ( -0.427404 , 0.0845517 , -0.117936 ) -colvars: ( -0.449473 , -0.00917436 , -0.174363 ) -colvars: ( -0.361149 , 0.0733003 , -0.0555504 ) -colvars: ( -0.364797 , 0.0996983 , -0.0495581 ) -colvars: ( -0.200041 , 0.106351 , 0.118241 ) -colvars: ( -0.150941 , 0.108272 , 0.168226 ) -colvars: ( -0.225823 , 0.178956 , 0.118916 ) -colvars: ( -0.298637 , 0.0324764 , -0.00773716 ) -colvars: ( -0.232304 , 0.0188726 , 0.053866 ) -colvars: ( -0.178644 , -0.0644851 , 0.0772396 ) +colvars: ( -0.646973 , -0.0855897 , -0.384683 ) +colvars: ( -0.582119 , -0.172876 , -0.351435 ) +colvars: ( -0.528959 , -0.149562 , -0.289642 ) +colvars: ( -0.541713 , -0.201837 , -0.321465 ) +colvars: ( -0.531566 , -0.139627 , -0.288639 ) +colvars: ( -0.516441 , -0.298999 , -0.331503 ) +colvars: ( -0.482927 , -0.341537 , -0.313386 ) +colvars: ( -0.460788 , -0.454857 , -0.332448 ) +colvars: ( -0.416612 , -0.304081 , -0.233254 ) +colvars: ( -0.412256 , -0.277339 , -0.219149 ) +colvars: ( -0.364161 , -0.298063 , -0.17847 ) +colvars: ( -0.300396 , -0.259004 , -0.10031 ) +colvars: ( -0.24865 , -0.274707 , -0.0541421 ) +colvars: ( -0.320378 , -0.150046 , -0.0806729 ) +colvars: ( -0.287728 , -0.119066 , -0.0366541 ) +colvars: ( -0.376899 , -0.089536 , -0.115314 ) +colvars: ( -0.404436 , 0.0141939 , -0.105157 ) +colvars: ( -0.456403 , 0.0643899 , -0.138987 ) +colvars: ( -0.444604 , 0.0300241 , -0.139669 ) +colvars: ( -0.432639 , 0.0900265 , -0.105824 ) +colvars: ( -0.491553 , -0.0271114 , -0.207549 ) +colvars: ( -0.528331 , -0.0286863 , -0.245 ) +colvars: ( -0.581308 , -0.0978506 , -0.323304 ) +colvars: ( -0.474337 , -0.0602864 , -0.202366 ) +colvars: ( -0.481767 , -0.0137155 , -0.19286 ) +colvars: ( -0.416793 , -0.138695 , -0.173216 ) +colvars: ( -0.356917 , -0.171651 , -0.125177 ) +colvars: ( -0.304273 , -0.266834 , -0.107048 ) +colvars: ( -0.313187 , -0.0946526 , -0.0532926 ) +colvars: ( -0.299749 , -0.0749514 , -0.0326451 ) +colvars: ( -0.291438 , -0.0472397 , -0.0142213 ) +colvars: ( -0.253752 , 0.0317731 , 0.0523361 ) +colvars: ( -0.230447 , 0.0596566 , 0.0858566 ) +colvars: ( -0.299801 , 0.123358 , 0.0395094 ) +colvars: ( -0.2719 , 0.167526 , 0.0835685 ) +colvars: ( -0.372351 , 0.152954 , -0.0224603 ) +colvars: ( -0.423466 , 0.233377 , -0.0444307 ) +colvars: ( -0.497729 , 0.257097 , -0.110258 ) +colvars: ( -0.436525 , 0.212443 , -0.065148 ) +colvars: ( -0.441257 , 0.276692 , -0.0464979 ) +colvars: ( -0.442048 , 0.121002 , -0.10398 ) +colvars: ( -0.450425 , 0.0891608 , -0.123974 ) +colvars: ( -0.473715 , -0.00943105 , -0.183225 ) +colvars: ( -0.380779 , 0.0773675 , -0.0584331 ) +colvars: ( -0.384663 , 0.105175 , -0.0522024 ) +colvars: ( -0.211268 , 0.112166 , 0.124207 ) +colvars: ( -0.159654 , 0.114222 , 0.17671 ) +colvars: ( -0.238287 , 0.188502 , 0.12491 ) +colvars: ( -0.315013 , 0.034417 , -0.00812794 ) +colvars: ( -0.245278 , 0.0201441 , 0.0565986 ) +colvars: ( -0.188854 , -0.06755 , 0.0812445 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 25. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 25. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 25, atoms_new_colvar_forces = { ( -4.64948756095428e+00 , -4.13439291828986e-01 , -1.18480670773194e+00 ), ( -4.00479132833903e+00 , -3.50670548975840e-01 , -9.25397990014676e-01 ), ( -4.07716089475674e+00 , -3.77687205838323e-01 , -9.60470723093749e-01 ), ( -5.48136916192064e+00 , -5.35430659330811e-01 , -1.43115688287139e+00 ), ( 2.52181597677831e-01 , 1.17530671406522e-01 , 3.42818191943839e-01 ), ( 5.00826689944451e+00 , 5.87929015984952e-01 , 1.74119012383961e+00 ), ( 4.23224320958635e+00 , 4.85961914117738e-01 , 1.51084005862460e+00 ), ( -4.53299383844284e-02 , 2.23161598796638e-02 , 3.48149373987012e-01 ), ( 4.21407614077276e+00 , 4.76989575965902e-01 , 1.48137569047540e+00 ), ( 5.58591707834861e+00 , 6.11147024926502e-01 , 1.82787533870091e+00 ), ( 1.18526327959609e-02 , 3.51439238842934e-02 , 2.95503028926826e-01 ), ( 1.61784480253113e-03 , 2.94004757606297e-02 , 2.72407516963776e-01 ), ( 2.35916107228643e-02 , 4.34954443323341e-02 , 3.38631494050623e-01 ), ( 4.45146884578941e-02 , 3.54087394106518e-02 , 1.98817135463419e-01 ), ( 1.73402789090328e-02 , 2.14774790721180e-02 , 1.49929958572946e-01 ), ( 1.12527853010140e-01 , 5.61805438401422e-02 , 1.88214155803622e-01 ), ( 1.58279710995860e-01 , 6.36675388980660e-02 , 1.19902201345429e-01 ), ( 2.37284957302291e-01 , 9.07073783884466e-02 , 1.35043258219505e-01 ), ( 1.28943366503910e-01 , 4.68521409286993e-02 , 5.03754339000972e-02 ), ( 1.24681081122516e-01 , 3.88769146776185e-02 , -1.19078528749632e-02 ), ( 1.05353852889349e-01 , 4.03706967490713e-02 , 6.08726120436782e-02 ), ( 6.92313967924517e-02 , 2.26348775035257e-02 , 3.27111647088477e-03 ), ( 5.54050234091135e-02 , 2.15407634451548e-02 , 3.49369558101449e-02 ), ( -2.68208617801030e-03 , -3.21256072460118e-03 , -2.21579198649446e-02 ), ( -1.63784846723828e-02 , -1.48573971962397e-02 , -9.04065980312773e-02 ), ( -4.91948928862027e-02 , -1.23674258014483e-02 , 3.27325763051586e-02 ), ( -1.15751409118683e-01 , -3.53866302937504e-02 , 1.77135703708122e-02 ), ( -1.56546557813829e-01 , -4.03728427141371e-02 , 9.45623168355812e-02 ), ( -1.02410080676360e-01 , -3.58371346035933e-02 , -2.70489822126664e-02 ), ( -1.38366528627789e-01 , -5.33777745801066e-02 , -8.33135581479110e-02 ), ( -4.87663871659194e-02 , -1.61354760258328e-02 , -4.11083565946385e-03 ), ( -2.71048443349625e-02 , -1.34029532189842e-02 , -4.41151594302592e-02 ), ( 2.96714380911476e-02 , 9.94169242311833e-03 , 3.67288250589587e-03 ), ( 3.86730902926330e-03 , -1.20659286276481e-02 , -1.25555757218082e-01 ), ( -1.32633676730242e-02 , -2.32242038655585e-02 , -1.78786182691266e-01 ), ( 4.92755720308022e-02 , 1.27927584963763e-03 , -1.37566691360937e-01 ), ( 7.76514750872815e-02 , 2.44968703026865e-03 , -2.12694926057886e-01 ), ( 1.37234330427815e-01 , 2.26770186745583e-02 , -2.02833615040340e-01 ), ( 1.86901376560987e-02 , -2.21333657959578e-02 , -2.65528976674672e-01 ), ( 1.97274783911037e-02 , -2.90466185365198e-02 , -3.33888381374860e-01 ), ( -3.46570693524684e-02 , -3.60062352467616e-02 , -2.34387324194230e-01 ), ( -9.60737018977827e-02 , -6.02389013742452e-02 , -2.76460435338491e-01 ), ( -1.34339372973070e-01 , -6.74786525812855e-02 , -2.28549402827962e-01 ), ( -1.52204573620836e-01 , -8.04827487455011e-02 , -2.96960054084250e-01 ), ( -1.79919344719066e-01 , -9.61108481712673e-02 , -3.60211790051426e-01 ), ( -1.91295411010890e-01 , -9.33709515315276e-02 , -2.99822360065218e-01 ), ( -2.32459688418046e-01 , -1.09380186994132e-01 , -3.25827501792330e-01 ), ( -1.17659239403470e-01 , -7.03930204690202e-02 , -3.06691218416824e-01 ), ( -1.71070372517956e-01 , -8.08566327727080e-02 , -2.43197581056251e-01 ), ( -2.23192168145597e-01 , -9.90347394586472e-02 , -2.56386300745341e-01 ), ( -2.57952498696039e-01 , -1.01978017846182e-01 , -1.78593282236159e-01 ) } +colvars: Step 25, atoms_new_colvar_forces = { ( -4.89906344512746e+00 , -4.33938364367410e-01 , -1.24115033796379e+00 ), ( -4.21975323856767e+00 , -3.68033246133372e-01 , -9.68907737532198e-01 ), ( -4.29596648242177e+00 , -3.96479038081813e-01 , -1.00584456901772e+00 ), ( -5.77550926213070e+00 , -5.62190338593654e-01 , -1.49965933822439e+00 ), ( 2.65575053488895e-01 , 1.23775230972432e-01 , 3.61023834344683e-01 ), ( 5.27692066837987e+00 , 6.17715929648311e-01 , 1.82710484760370e+00 ), ( 4.45930492273777e+00 , 5.10549164289448e-01 , 1.58545585835120e+00 ), ( -4.77255546796858e-02 , 2.35481056867184e-02 , 3.66642095775605e-01 ), ( 4.44016596401227e+00 , 5.01096548538967e-01 , 1.55441908869634e+00 ), ( 5.88562268790459e+00 , 6.41960795400982e-01 , 1.91745446249927e+00 ), ( 1.24780301557004e-02 , 3.70373505205272e-02 , 3.11185168550698e-01 ), ( 1.69241797134606e-03 , 3.09846409440507e-02 , 2.86855333206734e-01 ), ( 2.48253284184641e-02 , 4.58286694429199e-02 , 3.56586645172988e-01 ), ( 4.68670239076926e-02 , 3.72986979803460e-02 , 2.09359268835667e-01 ), ( 1.82471308431904e-02 , 2.26250706506449e-02 , 1.57873686277293e-01 ), ( 1.18494763765411e-01 , 5.91648545536552e-02 , 1.98198140672188e-01 ), ( 1.66676763625072e-01 , 6.70366787723358e-02 , 1.26261615730529e-01 ), ( 2.49879079930532e-01 , 9.55044108262005e-02 , 1.42210003532049e-01 ), ( 1.35789306078350e-01 , 4.93279399934362e-02 , 5.30509265501526e-02 ), ( 1.31299404400352e-01 , 4.09227746112109e-02 , -1.25400780020407e-02 ), ( 1.10954407540443e-01 , 4.25096693434524e-02 , 6.41128700817514e-02 ), ( 7.29204770810634e-02 , 2.38337472084800e-02 , 3.46033763471382e-03 ), ( 5.83673410714052e-02 , 2.26898767897394e-02 , 3.68150536138672e-02 ), ( -2.81417491461955e-03 , -3.38055311866311e-03 , -2.33227595269628e-02 ), ( -1.72361850855943e-02 , -1.56482716024989e-02 , -9.51927272087079e-02 ), ( -5.18012291731317e-02 , -1.30117255619673e-02 , 3.44757424901483e-02 ), ( -1.21895494406184e-01 , -3.72476900194439e-02 , 1.86542324467333e-02 ), ( -1.64860988387478e-01 , -4.24871995380767e-02 , 9.95770385555629e-02 ), ( -1.07851990658685e-01 , -3.77312358709509e-02 , -2.84911315327581e-02 ), ( -1.45717354015014e-01 , -5.62042458653846e-02 , -8.77426949607180e-02 ), ( -5.13656188036761e-02 , -1.69906013000250e-02 , -4.34075107217456e-03 ), ( -2.85598245708901e-02 , -1.41225759925339e-02 , -4.64748435203859e-02 ), ( 3.12251203305847e-02 , 1.04564940755888e-02 , 3.84421526758397e-03 ), ( 4.06081923678608e-03 , -1.27253296414948e-02 , -1.32233719356317e-01 ), ( -1.39820142505577e-02 , -2.44804858510322e-02 , -1.88292909504336e-01 ), ( 5.18866424281385e-02 , 1.32413341724485e-03 , -1.44874312914186e-01 ), ( 8.17739607959403e-02 , 2.54725668195610e-03 , -2.23984923597530e-01 ), ( 1.44526454345390e-01 , 2.38444392452565e-02 , -2.13592605133995e-01 ), ( 1.96867827703129e-02 , -2.33367225853583e-02 , -2.79619166290604e-01 ), ( 2.07796823395160e-02 , -3.06240695121803e-02 , -3.51606776559521e-01 ), ( -3.64893536398806e-02 , -3.79343777355108e-02 , -2.46821207445439e-01 ), ( -1.01162634768527e-01 , -6.34481201221322e-02 , -2.91123807410638e-01 ), ( -1.41455057710474e-01 , -7.10600811515679e-02 , -2.40664514657477e-01 ), ( -1.60279478554847e-01 , -8.47640865434852e-02 , -3.12718681263706e-01 ), ( -1.89463860663062e-01 , -1.01224065656580e-01 , -3.79326301540552e-01 ), ( -2.01464862171674e-01 , -9.83401100189178e-02 , -3.15754496397993e-01 ), ( -2.44819014924519e-01 , -1.15198529484133e-01 , -3.43145344898522e-01 ), ( -1.23919527404400e-01 , -7.41527837840532e-02 , -3.22987595567234e-01 ), ( -1.80154097344774e-01 , -8.51528906015948e-02 , -2.56110465485514e-01 ), ( -2.35049221177624e-01 , -1.04293297232310e-01 , -2.70006540020722e-01 ), ( -2.71660268006196e-01 , -1.07382443627761e-01 , -1.88090129283337e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 25, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3118,10 +4995,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 26, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 26, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 26, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 26, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 26, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 26, atoms_positions[size = 51] = { ( 8.26205239752480e+00 , 4.17861095508959e-02 , -7.36497976160026e-01 ), ( 6.86492861219213e+00 , -5.68006057331467e-01 , -5.38408245729133e-01 ), ( 6.15575880373052e+00 , -3.89145198560351e-01 , 7.78626756454447e-01 ), ( 4.91641141657925e+00 , -1.48159488662435e-01 , 7.35944748484878e-01 ), ( 7.02105945376621e+00 , -2.06173192940476e+00 , -9.03666871821229e-01 ), ( 6.82568670419811e+00 , -2.76540136320467e-01 , 1.95100449392704e+00 ), ( 6.13201574755223e+00 , -2.03132769618362e-01 , 3.16628161151743e+00 ), ( 7.11081336669961e+00 , -3.46144117825693e-01 , 4.35975397553465e+00 ), ( 5.33844452189291e+00 , 1.07552146128050e+00 , 3.36719199102191e+00 ), ( 4.17175427628001e+00 , 1.01216774981376e+00 , 3.74121326351912e+00 ), ( 5.83724125006816e+00 , 2.25673342517408e+00 , 2.97920302646140e+00 ), ( 5.19859217756977e+00 , 3.56719475753549e+00 , 2.90873731308147e+00 ), ( 6.31516624242152e+00 , 4.49059059497252e+00 , 2.30984432201073e+00 ), ( 3.86121298874540e+00 , 3.66697976162258e+00 , 2.03780240984338e+00 ), ( 2.79747927766635e+00 , 4.16995460021236e+00 , 2.45593795652224e+00 ), ( 3.93137273749838e+00 , 3.21710006063874e+00 , 7.32737347216327e-01 ), ( 2.72436717702653e+00 , 3.02864357442996e+00 , -8.55753859222168e-02 ), ( 3.09391136477563e+00 , 2.66800126019767e+00 , -1.53095148108278e+00 ), ( 1.56484332658655e+00 , 2.17344006797225e+00 , 4.24726928436034e-01 ), ( 3.85256113664264e-01 , 2.61363713558315e+00 , 4.82462912434993e-01 ), ( 2.07688786596953e+00 , 1.14251941696581e+00 , 1.04548290902294e+00 ), ( 1.18126391324449e+00 , 1.18698867350510e-01 , 1.69846823698885e+00 ), ( 2.06722914051942e+00 , -1.09185219296440e+00 , 2.03018947728645e+00 ), ( 5.72932284036482e-01 , 6.18016252148053e-01 , 2.96457033899761e+00 ), ( -5.83389856128054e-01 , 3.53088781229802e-01 , 3.16720495991994e+00 ), ( 1.29554352042694e+00 , 1.36206327507269e+00 , 3.74262366623888e+00 ), ( 8.46905018374119e-01 , 1.98288773896191e+00 , 5.02809351234227e+00 ), ( 2.10982943699306e+00 , 2.73683957529722e+00 , 5.71601040168050e+00 ), ( -3.48691564249082e-01 , 2.90755570990568e+00 , 4.96869716000486e+00 ), ( -1.11910830076749e+00 , 3.06702408721855e+00 , 5.87738662576611e+00 ), ( -5.38299507738895e-01 , 3.51143389068214e+00 , 3.81521826160860e+00 ), ( -1.49841316651143e+00 , 4.50655457331812e+00 , 3.41374998518704e+00 ), ( -7.13307173668709e-01 , 5.42557465211419e+00 , 2.47207181043199e+00 ), ( -2.74426074560518e+00 , 3.93452643364649e+00 , 2.84188904337389e+00 ), ( -3.81054527032278e+00 , 4.54279757655199e+00 , 2.81268540552791e+00 ), ( -2.66487287946726e+00 , 2.64461164051670e+00 , 2.36563604672446e+00 ), ( -3.78942071808140e+00 , 1.81732420609061e+00 , 2.00409239548599e+00 ), ( -3.36724691286651e+00 , 8.77397578921159e-01 , 8.35624170805012e-01 ), ( -4.27483687507342e+00 , 1.05960458804490e+00 , 3.21981228547757e+00 ), ( -5.48919671412730e+00 , 7.76806002655777e-01 , 3.33464133071916e+00 ), ( -3.36704285696833e+00 , 7.17883542668495e-01 , 4.19213543387207e+00 ), ( -3.67549156336728e+00 , 7.58723829031180e-02 , 5.46280014150180e+00 ), ( -2.38982180673833e+00 , -3.25257752944606e-01 , 6.14886247459941e+00 ), ( -4.46738429536682e+00 , 9.35025765420735e-01 , 6.42557686319628e+00 ), ( -5.36456091151722e+00 , 5.86296350961117e-01 , 7.21398596315178e+00 ), ( -6.28704969800571e+00 , 3.62925592625597e+00 , 6.75097197160871e+00 ), ( -6.98251566748287e+00 , 4.29548720179496e+00 , 7.49827636498684e+00 ), ( -6.68453148675172e+00 , 3.16423838127918e+00 , 5.51379138521932e+00 ), ( -4.11335977853752e+00 , 2.24864953726479e+00 , 6.38975320399807e+00 ), ( -4.81128217109908e+00 , 3.25778323522353e+00 , 7.25807991639679e+00 ), ( -4.05000539885017e+00 , 4.54883688938649e+00 , 7.27155992532855e+00 ) } +colvars: Step 26, atoms_positions[size = 51] = { ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 ), ( 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 ), ( 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 ), ( 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 ), ( 7.02064988657512e+00 , -2.06191346538722e+00 , -9.03579109957654e-01 ), ( 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 ), ( 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 ), ( 7.11195793669239e+00 , -3.46325495992327e-01 , 4.36074587971818e+00 ), ( 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 ), ( 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 ), ( 5.83830582474785e+00 , 2.25717890153626e+00 , 2.97922967102051e+00 ), ( 5.19865579018808e+00 , 3.56722170500424e+00 , 2.90896510948759e+00 ), ( 6.31513193976290e+00 , 4.49065881803907e+00 , 2.31006628798853e+00 ), ( 3.86124831398321e+00 , 3.66693664580130e+00 , 2.03796709771885e+00 ), ( 2.79749545867389e+00 , 4.16995519090235e+00 , 2.45603764179593e+00 ), ( 3.93145764425614e+00 , 3.21713147140614e+00 , 7.32876164373928e-01 ), ( 2.72447956284919e+00 , 3.02868839011924e+00 , -8.54879261581896e-02 ), ( 3.09406236284613e+00 , 2.66805755434709e+00 , -1.53085811413060e+00 ), ( 1.56493869037030e+00 , 2.17347451033929e+00 , 4.24768650699866e-01 ), ( 3.85345919387903e-01 , 2.61366235247257e+00 , 4.82461270335294e-01 ), ( 2.07696380666347e+00 , 1.14254884016557e+00 , 1.04553746637080e+00 ), ( 1.18131227060580e+00 , 1.18719671546719e-01 , 1.69847359328974e+00 ), ( 2.06729318897268e+00 , -1.09179940169616e+00 , 2.03025352172266e+00 ), ( 5.72960077339100e-01 , 6.18013592442385e-01 , 2.96456159475629e+00 ), ( -5.83383313581664e-01 , 3.53085945103520e-01 , 3.16715384200455e+00 ), ( 1.29561687036373e+00 , 1.36203853191918e+00 , 3.74264177973402e+00 ), ( 8.46850384517969e-01 , 1.98285156306198e+00 , 5.02809578988427e+00 ), ( 2.10973305988450e+00 , 2.73681089296750e+00 , 5.71605794165702e+00 ), ( -3.48762046412809e-01 , 2.90752551225505e+00 , 4.96867528030200e+00 ), ( -1.11920791756658e+00 , 3.06699078158662e+00 , 5.87734231670672e+00 ), ( -5.38333623730181e-01 , 3.51142269226990e+00 , 3.81520213881713e+00 ), ( -1.49843560791049e+00 , 4.50654707598769e+00 , 3.41371229948753e+00 ), ( -7.13294121656643e-01 , 5.42557666301716e+00 , 2.47206849802352e+00 ), ( -2.74425913887002e+00 , 3.93451898443147e+00 , 2.84179837821152e+00 ), ( -3.81054992169605e+00 , 4.54277935493174e+00 , 2.81256821995773e+00 ), ( -2.66484198682084e+00 , 2.64461123625328e+00 , 2.36553515139455e+00 ), ( -3.78937150597451e+00 , 1.81732553101476e+00 , 2.00393460363141e+00 ), ( -3.36715965222817e+00 , 8.77401627073931e-01 , 8.35477650714998e-01 ), ( -4.27482462124773e+00 , 1.05958388107734e+00 , 3.21962204538203e+00 ), ( -5.48918404843012e+00 , 7.76784618642079e-01 , 3.33442191610955e+00 ), ( -3.36706253375617e+00 , 7.17851868366844e-01 , 4.19196428516940e+00 ), ( -3.67556292758813e+00 , 7.58218748188693e-02 , 5.46260107999588e+00 ), ( -2.38991324934671e+00 , -3.25296840409072e-01 , 6.14870951617098e+00 ), ( -4.46749439379339e+00 , 9.34969453495375e-01 , 6.42536132477543e+00 ), ( -5.36467953327721e+00 , 5.86231116048637e-01 , 7.21375288174230e+00 ), ( -6.28718665126741e+00 , 3.62919036014076e+00 , 6.75076513126300e+00 ), ( -6.98266884576581e+00 , 4.29541408722657e+00 , 7.49806320906888e+00 ), ( -6.68463458476356e+00 , 3.16418550162232e+00 , 5.51356624786938e+00 ), ( -4.11347763262476e+00 , 2.24859562081623e+00 , 6.38957541942517e+00 ), ( -4.81143882202094e+00 , 3.25770940668724e+00 , 7.25789425619000e+00 ), ( -4.05017605728786e+00 , 4.54876606599830e+00 , 7.27143130377330e+00 ) } colvars: Step 26, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 26, atom_groups_ids[size = 0] = @@ -3139,162 +5016,301 @@ colvars: Collective variables module, step no. 26 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.98694198360127e-01 , -7.65591975074812e-03 , 9.54318166419759e-01 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 ). +colvars: Done calculating colvar "group2". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.97375216352616e-01 , -7.46356788846571e-03 , 9.54731520299612e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 7.02064988657512e+00 , -2.06191346538722e+00 , -9.03579109957654e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 , 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 7.11195793669239e+00 , -3.46325495992327e-01 , 4.36074587971818e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 , 5.83830582474785e+00 , 2.25717890153626e+00 , 2.97922967102051e+00 , 5.19865579018808e+00 , 3.56722170500424e+00 , 2.90896510948759e+00 , 6.31513193976290e+00 , 4.49065881803907e+00 , 2.31006628798853e+00 , 3.86124831398321e+00 , 3.66693664580130e+00 , 2.03796709771885e+00 , 2.79749545867389e+00 , 4.16995519090235e+00 , 2.45603764179593e+00 , 3.93145764425614e+00 , 3.21713147140614e+00 , 7.32876164373928e-01 , 2.72447956284919e+00 , 3.02868839011924e+00 , -8.54879261581896e-02 , 3.09406236284613e+00 , 2.66805755434709e+00 , -1.53085811413060e+00 , 1.56493869037030e+00 , 2.17347451033929e+00 , 4.24768650699866e-01 , 3.85345919387903e-01 , 2.61366235247257e+00 , 4.82461270335294e-01 , 2.07696380666347e+00 , 1.14254884016557e+00 , 1.04553746637080e+00 , 1.18131227060580e+00 , 1.18719671546719e-01 , 1.69847359328974e+00 , 2.06729318897268e+00 , -1.09179940169616e+00 , 2.03025352172266e+00 , 5.72960077339100e-01 , 6.18013592442385e-01 , 2.96456159475629e+00 , -5.83383313581664e-01 , 3.53085945103520e-01 , 3.16715384200455e+00 , 1.29561687036373e+00 , 1.36203853191918e+00 , 3.74264177973402e+00 , 8.46850384517969e-01 , 1.98285156306198e+00 , 5.02809578988427e+00 , 2.10973305988450e+00 , 2.73681089296750e+00 , 5.71605794165702e+00 , -3.48762046412809e-01 , 2.90752551225505e+00 , 4.96867528030200e+00 , -1.11920791756658e+00 , 3.06699078158662e+00 , 5.87734231670672e+00 , -5.38333623730181e-01 , 3.51142269226990e+00 , 3.81520213881713e+00 , -1.49843560791049e+00 , 4.50654707598769e+00 , 3.41371229948753e+00 , -7.13294121656643e-01 , 5.42557666301716e+00 , 2.47206849802352e+00 , -2.74425913887002e+00 , 3.93451898443147e+00 , 2.84179837821152e+00 , -3.81054992169605e+00 , 4.54277935493174e+00 , 2.81256821995773e+00 , -2.66484198682084e+00 , 2.64461123625328e+00 , 2.36553515139455e+00 , -3.78937150597451e+00 , 1.81732553101476e+00 , 2.00393460363141e+00 , -3.36715965222817e+00 , 8.77401627073931e-01 , 8.35477650714998e-01 , -4.27482462124773e+00 , 1.05958388107734e+00 , 3.21962204538203e+00 , -5.48918404843012e+00 , 7.76784618642079e-01 , 3.33442191610955e+00 , -3.36706253375617e+00 , 7.17851868366844e-01 , 4.19196428516940e+00 , -3.67556292758813e+00 , 7.58218748188693e-02 , 5.46260107999588e+00 , -2.38991324934671e+00 , -3.25296840409072e-01 , 6.14870951617098e+00 , -4.46749439379339e+00 , 9.34969453495375e-01 , 6.42536132477543e+00 , -5.36467953327721e+00 , 5.86231116048637e-01 , 7.21375288174230e+00 , -6.28718665126741e+00 , 3.62919036014076e+00 , 6.75076513126300e+00 , -6.98266884576581e+00 , 4.29541408722657e+00 , 7.49806320906888e+00 , -6.68463458476356e+00 , 3.16418550162232e+00 , 5.51356624786938e+00 , -4.11347763262476e+00 , 2.24859562081623e+00 , 6.38957541942517e+00 , -4.81143882202094e+00 , 3.25770940668724e+00 , 7.25789425619000e+00 , -4.05017605728786e+00 , 4.54876606599830e+00 , 7.27143130377330e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.98694198360127e-01 , -7.65591975074812e-03 , 9.54318166419759e-01 ). +colvars: Colvar "one" has value ( -2.97375216352616e-01 , -7.46356788846571e-03 , 9.54731520299612e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 7.02064988657512e+00 , -2.06191346538722e+00 , -9.03579109957654e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 , 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 7.11195793669239e+00 , -3.46325495992327e-01 , 4.36074587971818e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 , 5.83830582474785e+00 , 2.25717890153626e+00 , 2.97922967102051e+00 , 5.19865579018808e+00 , 3.56722170500424e+00 , 2.90896510948759e+00 , 6.31513193976290e+00 , 4.49065881803907e+00 , 2.31006628798853e+00 , 3.86124831398321e+00 , 3.66693664580130e+00 , 2.03796709771885e+00 , 2.79749545867389e+00 , 4.16995519090235e+00 , 2.45603764179593e+00 , 3.93145764425614e+00 , 3.21713147140614e+00 , 7.32876164373928e-01 , 2.72447956284919e+00 , 3.02868839011924e+00 , -8.54879261581896e-02 , 3.09406236284613e+00 , 2.66805755434709e+00 , -1.53085811413060e+00 , 1.56493869037030e+00 , 2.17347451033929e+00 , 4.24768650699866e-01 , 3.85345919387903e-01 , 2.61366235247257e+00 , 4.82461270335294e-01 , 2.07696380666347e+00 , 1.14254884016557e+00 , 1.04553746637080e+00 , 1.18131227060580e+00 , 1.18719671546719e-01 , 1.69847359328974e+00 , 2.06729318897268e+00 , -1.09179940169616e+00 , 2.03025352172266e+00 , 5.72960077339100e-01 , 6.18013592442385e-01 , 2.96456159475629e+00 , -5.83383313581664e-01 , 3.53085945103520e-01 , 3.16715384200455e+00 , 1.29561687036373e+00 , 1.36203853191918e+00 , 3.74264177973402e+00 , 8.46850384517969e-01 , 1.98285156306198e+00 , 5.02809578988427e+00 , 2.10973305988450e+00 , 2.73681089296750e+00 , 5.71605794165702e+00 , -3.48762046412809e-01 , 2.90752551225505e+00 , 4.96867528030200e+00 , -1.11920791756658e+00 , 3.06699078158662e+00 , 5.87734231670672e+00 , -5.38333623730181e-01 , 3.51142269226990e+00 , 3.81520213881713e+00 , -1.49843560791049e+00 , 4.50654707598769e+00 , 3.41371229948753e+00 , -7.13294121656643e-01 , 5.42557666301716e+00 , 2.47206849802352e+00 , -2.74425913887002e+00 , 3.93451898443147e+00 , 2.84179837821152e+00 , -3.81054992169605e+00 , 4.54277935493174e+00 , 2.81256821995773e+00 , -2.66484198682084e+00 , 2.64461123625328e+00 , 2.36553515139455e+00 , -3.78937150597451e+00 , 1.81732553101476e+00 , 2.00393460363141e+00 , -3.36715965222817e+00 , 8.77401627073931e-01 , 8.35477650714998e-01 , -4.27482462124773e+00 , 1.05958388107734e+00 , 3.21962204538203e+00 , -5.48918404843012e+00 , 7.76784618642079e-01 , 3.33442191610955e+00 , -3.36706253375617e+00 , 7.17851868366844e-01 , 4.19196428516940e+00 , -3.67556292758813e+00 , 7.58218748188693e-02 , 5.46260107999588e+00 , -2.38991324934671e+00 , -3.25296840409072e-01 , 6.14870951617098e+00 , -4.46749439379339e+00 , 9.34969453495375e-01 , 6.42536132477543e+00 , -5.36467953327721e+00 , 5.86231116048637e-01 , 7.21375288174230e+00 , -6.28718665126741e+00 , 3.62919036014076e+00 , 6.75076513126300e+00 , -6.98266884576581e+00 , 4.29541408722657e+00 , 7.49806320906888e+00 , -6.68463458476356e+00 , 3.16418550162232e+00 , 5.51356624786938e+00 , -4.11347763262476e+00 , 2.24859562081623e+00 , 6.38957541942517e+00 , -4.81143882202094e+00 , 3.25770940668724e+00 , 7.25789425619000e+00 , -4.05017605728786e+00 , 4.54876606599830e+00 , 7.27143130377330e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.4919 , 2.10492 , -15.1828 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.7687 , 6.57687 , 13.1537 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.4919 , 2.10492 , -15.1828 ) to colvar "one". -colvars: Adding total bias energy: 44.2392 +colvars: Adding biasing force ( 65.7687 , 6.57687 , 13.1537 ) to colvar "one". +colvars: Adding total bias energy: 56.1514 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.4919 , 2.10492 , -15.1828 ) +colvars: Force to be applied: ( 65.7687 , 6.57687 , 13.1537 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.92583 , -0.527182 , -1.42881 ) -colvars: ( -4.2239 , -0.452058 , -1.2252 ) -colvars: ( -4.2239 , -0.452058 , -1.2252 ) -colvars: ( -5.62635 , -0.602155 , -1.63201 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.19057 , -0.553687 , -1.49789 ) +colvars: ( -4.45091 , -0.474786 , -1.28444 ) +colvars: ( -4.45091 , -0.474786 , -1.28444 ) +colvars: ( -5.92875 , -0.632429 , -1.71091 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.889087 , 0.195938 , 0.612717 ) -colvars: ( 0.770486 , 0.266378 , 0.63642 ) -colvars: ( 0.754315 , 0.259511 , 0.618018 ) -colvars: ( 0.659764 , 0.266905 , 0.572873 ) -colvars: ( 0.647976 , 0.200434 , 0.478735 ) -colvars: ( 0.574123 , 0.343825 , 0.624209 ) -colvars: ( 0.468016 , 0.357563 , 0.580691 ) -colvars: ( 0.392098 , 0.454475 , 0.663925 ) -colvars: ( 0.386898 , 0.312998 , 0.475099 ) -colvars: ( 0.352559 , 0.271399 , 0.400542 ) -colvars: ( 0.357553 , 0.318289 , 0.465023 ) -colvars: ( 0.286786 , 0.275426 , 0.367672 ) -colvars: ( 0.259632 , 0.304408 , 0.389981 ) -colvars: ( 0.348656 , 0.17791 , 0.275493 ) -colvars: ( 0.29049 , 0.134555 , 0.184808 ) -colvars: ( 0.470323 , 0.141176 , 0.297838 ) -colvars: ( 0.54222 , 0.0501049 , 0.219942 ) -colvars: ( 0.670554 , 0.0294286 , 0.267244 ) -colvars: ( 0.551021 , 0.0182833 , 0.183256 ) -colvars: ( 0.535405 , -0.0466926 , 0.0888594 ) -colvars: ( 0.572001 , 0.0661081 , 0.258239 ) -colvars: ( 0.570798 , 0.0499032 , 0.236258 ) -colvars: ( 0.607261 , 0.114538 , 0.342301 ) -colvars: ( 0.447632 , 0.0541017 , 0.170314 ) -colvars: ( 0.440994 , -0.0017723 , 0.0930806 ) -colvars: ( 0.346489 , 0.119441 , 0.197447 ) -colvars: ( 0.223094 , 0.127751 , 0.13677 ) -colvars: ( 0.13232 , 0.213192 , 0.196318 ) -colvars: ( 0.194925 , 0.0541326 , 0.0237394 ) -colvars: ( 0.146217 , 0.017895 , -0.0521127 ) -colvars: ( 0.227918 , 0.0287535 , 0.0095499 ) -colvars: ( 0.213806 , -0.0435984 , -0.0936612 ) -colvars: ( 0.248453 , -0.046785 , -0.0777447 ) -colvars: ( 0.288498 , -0.129267 , -0.16284 ) -colvars: ( 0.244884 , -0.182381 , -0.2579 ) -colvars: ( 0.402778 , -0.144041 , -0.115941 ) -colvars: ( 0.479682 , -0.21927 , -0.170124 ) -colvars: ( 0.609761 , -0.221588 , -0.0977 ) -colvars: ( 0.433124 , -0.223924 , -0.203249 ) -colvars: ( 0.438657 , -0.291871 , -0.289276 ) -colvars: ( 0.38502 , -0.150898 , -0.135249 ) -colvars: ( 0.33156 , -0.144842 , -0.158311 ) -colvars: ( 0.315403 , -0.0583922 , -0.0541465 ) -colvars: ( 0.209316 , -0.15387 , -0.241091 ) -colvars: ( 0.185294 , -0.195896 , -0.310223 ) -colvars: ( 0.00930755 , -0.199847 , -0.417515 ) -colvars: ( -0.0808517 , -0.2178 , -0.493403 ) -colvars: ( 0.108592 , -0.249422 , -0.425022 ) -colvars: ( 0.128015 , -0.113453 , -0.235179 ) -colvars: ( 0.00969566 , -0.118063 , -0.309879 ) -colvars: ( -0.0786325 , -0.0376979 , -0.255578 ) +colvars: ( 0.935987 , 0.206459 , 0.643928 ) +colvars: ( 0.811207 , 0.28054 , 0.668894 ) +colvars: ( 0.794139 , 0.273363 , 0.649593 ) +colvars: ( 0.694742 , 0.281008 , 0.602072 ) +colvars: ( 0.682336 , 0.211041 , 0.503069 ) +colvars: ( 0.604666 , 0.361898 , 0.656068 ) +colvars: ( 0.493062 , 0.376268 , 0.610304 ) +colvars: ( 0.413213 , 0.478209 , 0.697849 ) +colvars: ( 0.407691 , 0.329348 , 0.499297 ) +colvars: ( 0.37158 , 0.285524 , 0.420877 ) +colvars: ( 0.376771 , 0.334951 , 0.488747 ) +colvars: ( 0.302287 , 0.289832 , 0.386407 ) +colvars: ( 0.273672 , 0.320373 , 0.409919 ) +colvars: ( 0.367362 , 0.187239 , 0.289454 ) +colvars: ( 0.306165 , 0.141576 , 0.194094 ) +colvars: ( 0.495355 , 0.148652 , 0.312927 ) +colvars: ( 0.570983 , 0.0528474 , 0.230991 ) +colvars: ( 0.70598 , 0.0311767 , 0.28072 ) +colvars: ( 0.580286 , 0.0193091 , 0.192365 ) +colvars: ( 0.563851 , -0.0490865 , 0.0930919 ) +colvars: ( 0.602403 , 0.0696111 , 0.271184 ) +colvars: ( 0.601183 , 0.0525025 , 0.248025 ) +colvars: ( 0.639588 , 0.12051 , 0.35951 ) +colvars: ( 0.471617 , 0.0568383 , 0.178693 ) +colvars: ( 0.464647 , -0.0019918 , 0.0974527 ) +colvars: ( 0.365203 , 0.125562 , 0.207264 ) +colvars: ( 0.235389 , 0.134234 , 0.143477 ) +colvars: ( 0.139882 , 0.224123 , 0.206139 ) +colvars: ( 0.205716 , 0.0567687 , 0.0246361 ) +colvars: ( 0.154486 , 0.0185821 , -0.0551404 ) +colvars: ( 0.240379 , 0.030127 , 0.00974479 ) +colvars: ( 0.225494 , -0.0459954 , -0.0987711 ) +colvars: ( 0.261894 , -0.0492736 , -0.0819963 ) +colvars: ( 0.304083 , -0.136136 , -0.171558 ) +colvars: ( 0.258192 , -0.192059 , -0.271521 ) +colvars: ( 0.424329 , -0.15164 , -0.122279 ) +colvars: ( 0.505251 , -0.230795 , -0.1793 ) +colvars: ( 0.642111 , -0.233171 , -0.103172 ) +colvars: ( 0.456315 , -0.235772 , -0.214166 ) +colvars: ( 0.462138 , -0.30729 , -0.304649 ) +colvars: ( 0.405744 , -0.158975 , -0.142666 ) +colvars: ( 0.349546 , -0.15268 , -0.166945 ) +colvars: ( 0.332587 , -0.0617376 , -0.0574198 ) +colvars: ( 0.22093 , -0.162244 , -0.253969 ) +colvars: ( 0.195677 , -0.206515 , -0.326689 ) +colvars: ( 0.0104263 , -0.210661 , -0.439396 ) +colvars: ( -0.084433 , -0.229603 , -0.519181 ) +colvars: ( 0.114849 , -0.262753 , -0.447293 ) +colvars: ( 0.135367 , -0.119716 , -0.247702 ) +colvars: ( 0.0108769 , -0.124624 , -0.326226 ) +colvars: ( -0.0820626 , -0.0400688 , -0.269078 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.92583 , 0.527182 , 1.42881 ) -colvars: ( 4.2239 , 0.452058 , 1.2252 ) -colvars: ( 4.2239 , 0.452058 , 1.2252 ) -colvars: ( 5.62635 , 0.602155 , 1.63201 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.19057 , 0.553687 , 1.49789 ) +colvars: ( 4.45091 , 0.474786 , 1.28444 ) +colvars: ( 4.45091 , 0.474786 , 1.28444 ) +colvars: ( 5.92875 , 0.632429 , 1.71091 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.614481 , -0.0811872 , -0.365942 ) -colvars: ( -0.552822 , -0.164321 , -0.334141 ) -colvars: ( -0.502171 , -0.142052 , -0.275219 ) -colvars: ( -0.514459 , -0.191964 , -0.305634 ) -colvars: ( -0.504803 , -0.13274 , -0.27449 ) -colvars: ( -0.490486 , -0.284528 , -0.315089 ) -colvars: ( -0.458685 , -0.325103 , -0.297854 ) -colvars: ( -0.437685 , -0.43304 , -0.315861 ) -colvars: ( -0.395584 , -0.289433 , -0.221578 ) -colvars: ( -0.391479 , -0.264013 , -0.20825 ) -colvars: ( -0.345626 , -0.283649 , -0.169322 ) -colvars: ( -0.284941 , -0.246443 , -0.0949155 ) -colvars: ( -0.235652 , -0.261335 , -0.0508202 ) -colvars: ( -0.303904 , -0.142673 , -0.0763727 ) -colvars: ( -0.272862 , -0.113199 , -0.0345293 ) -colvars: ( -0.357615 , -0.0850101 , -0.109417 ) -colvars: ( -0.383766 , 0.0137834 , -0.0998939 ) -colvars: ( -0.433126 , 0.0616444 , -0.13212 ) -colvars: ( -0.422044 , 0.0287924 , -0.132891 ) -colvars: ( -0.410661 , 0.0859141 , -0.100774 ) -colvars: ( -0.466768 , -0.0256561 , -0.197517 ) -colvars: ( -0.501828 , -0.0272233 , -0.233287 ) -colvars: ( -0.552277 , -0.0931133 , -0.307804 ) -colvars: ( -0.45053 , -0.0573711 , -0.192699 ) -colvars: ( -0.457622 , -0.013059 , -0.183771 ) -colvars: ( -0.395815 , -0.132043 , -0.164807 ) -colvars: ( -0.338909 , -0.163472 , -0.119052 ) -colvars: ( -0.288851 , -0.254109 , -0.101618 ) -colvars: ( -0.297263 , -0.09013 , -0.050675 ) -colvars: ( -0.284522 , -0.0714151 , -0.0311036 ) -colvars: ( -0.276486 , -0.0449113 , -0.0134363 ) -colvars: ( -0.240583 , 0.0303561 , 0.0498728 ) -colvars: ( -0.21832 , 0.0569883 , 0.0818716 ) -colvars: ( -0.284377 , 0.117558 , 0.0374836 ) -colvars: ( -0.257841 , 0.159597 , 0.0793528 ) -colvars: ( -0.353377 , 0.145753 , -0.0215846 ) -colvars: ( -0.401997 , 0.222323 , -0.0426698 ) -colvars: ( -0.472607 , 0.244942 , -0.105375 ) -colvars: ( -0.41451 , 0.202309 , -0.0624825 ) -colvars: ( -0.419013 , 0.263471 , -0.0448523 ) -colvars: ( -0.41984 , 0.115186 , -0.0993879 ) -colvars: ( -0.427899 , 0.0847884 , -0.118489 ) -colvars: ( -0.450121 , -0.00913185 , -0.174817 ) -colvars: ( -0.361678 , 0.0735255 , -0.0560788 ) -colvars: ( -0.365414 , 0.0999592 , -0.0502564 ) -colvars: ( -0.20037 , 0.106694 , 0.117897 ) -colvars: ( -0.151294 , 0.108625 , 0.167871 ) -colvars: ( -0.22599 , 0.179447 , 0.118522 ) -colvars: ( -0.299099 , 0.0326491 , -0.0080503 ) -colvars: ( -0.232789 , 0.0190311 , 0.0535972 ) -colvars: ( -0.179124 , -0.0644662 , 0.0772385 ) +colvars: ( -0.646765 , -0.0856109 , -0.384012 ) +colvars: ( -0.58196 , -0.173048 , -0.350532 ) +colvars: ( -0.528587 , -0.149656 , -0.288566 ) +colvars: ( -0.541701 , -0.202069 , -0.320614 ) +colvars: ( -0.531541 , -0.139741 , -0.287955 ) +colvars: ( -0.516571 , -0.29942 , -0.330504 ) +colvars: ( -0.483223 , -0.342046 , -0.312422 ) +colvars: ( -0.461211 , -0.455583 , -0.331273 ) +colvars: ( -0.416834 , -0.304498 , -0.232297 ) +colvars: ( -0.412564 , -0.277715 , -0.218359 ) +colvars: ( -0.364215 , -0.298439 , -0.177336 ) +colvars: ( -0.300355 , -0.259282 , -0.0991682 ) +colvars: ( -0.248438 , -0.274984 , -0.0527552 ) +colvars: ( -0.320244 , -0.150118 , -0.0797632 ) +colvars: ( -0.287614 , -0.119076 , -0.0358451 ) +colvars: ( -0.376664 , -0.0894993 , -0.1145 ) +colvars: ( -0.404113 , 0.0144248 , -0.104568 ) +colvars: ( -0.455936 , 0.0647169 , -0.138416 ) +colvars: ( -0.444453 , 0.0302562 , -0.139322 ) +colvars: ( -0.432479 , 0.0903729 , -0.10564 ) +colvars: ( -0.491569 , -0.0270136 , -0.207225 ) +colvars: ( -0.528533 , -0.0286201 , -0.244879 ) +colvars: ( -0.581658 , -0.0979401 , -0.323153 ) +colvars: ( -0.474658 , -0.0602788 , -0.202255 ) +colvars: ( -0.482146 , -0.0136302 , -0.192949 ) +colvars: ( -0.417145 , -0.138821 , -0.172883 ) +colvars: ( -0.357358 , -0.171835 , -0.124817 ) +colvars: ( -0.304737 , -0.267183 , -0.106411 ) +colvars: ( -0.3135 , -0.0946702 , -0.0530102 ) +colvars: ( -0.300148 , -0.074939 , -0.0325057 ) +colvars: ( -0.29154 , -0.047142 , -0.0138506 ) +colvars: ( -0.253712 , 0.0320404 , 0.0526359 ) +colvars: ( -0.230183 , 0.060005 , 0.0863166 ) +colvars: ( -0.299757 , 0.123784 , 0.0395259 ) +colvars: ( -0.271854 , 0.168039 , 0.0834665 ) +colvars: ( -0.372308 , 0.153418 , -0.022561 ) +colvars: ( -0.423436 , 0.233975 , -0.0448024 ) +colvars: ( -0.49766 , 0.257726 , -0.110687 ) +colvars: ( -0.436707 , 0.212976 , -0.0656826 ) +colvars: ( -0.441445 , 0.277342 , -0.0472312 ) +colvars: ( -0.442407 , 0.121347 , -0.104432 ) +colvars: ( -0.450993 , 0.0894222 , -0.124552 ) +colvars: ( -0.474448 , -0.00937457 , -0.183694 ) +colvars: ( -0.381384 , 0.0776191 , -0.0589894 ) +colvars: ( -0.385363 , 0.105467 , -0.0529413 ) +colvars: ( -0.21166 , 0.112544 , 0.123836 ) +colvars: ( -0.160072 , 0.114613 , 0.176324 ) +colvars: ( -0.238503 , 0.189034 , 0.124486 ) +colvars: ( -0.315547 , 0.0346126 , -0.00845726 ) +colvars: ( -0.245837 , 0.0203268 , 0.0563122 ) +colvars: ( -0.189409 , -0.0675153 , 0.0812428 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 26. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 26. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 26, atoms_new_colvar_forces = { ( -4.65122199350796e+00 , -4.12430965680350e-01 , -1.18203244769683e+00 ), ( -4.00623265903138e+00 , -3.50001036904643e-01 , -9.22923807473896e-01 ), ( -4.07859163157510e+00 , -3.77117596485990e-01 , -9.57963690131977e-01 ), ( -5.48317872546510e+00 , -5.34460776572132e-01 , -1.42775999062148e+00 ), ( 2.52144283009204e-01 , 1.17458214311684e-01 , 3.42799443021439e-01 ), ( 5.00946428913979e+00 , 5.86478754543285e-01 , 1.73792866801520e+00 ), ( 4.23322716506996e+00 , 4.84518484815516e-01 , 1.50803994180249e+00 ), ( -4.55867378539800e-02 , 2.14350083430519e-02 , 3.48064264481249e-01 ), ( 4.21521022765265e+00 , 4.75623826234595e-01 , 1.47872426506244e+00 ), ( 5.58743109026427e+00 , 6.09541528637903e-01 , 1.82429777907329e+00 ), ( 1.19266878857350e-02 , 3.46406576125291e-02 , 2.95700715890141e-01 ), ( 1.84563761051221e-03 , 2.89830771059171e-02 , 2.72756226117522e-01 ), ( 2.39801225301171e-02 , 4.30729307354178e-02 , 3.39160576960902e-01 ), ( 4.47514645752732e-02 , 3.52369807367713e-02 , 1.99120714153984e-01 ), ( 1.76284474102675e-02 , 2.13566551455872e-02 , 1.50278358166791e-01 ), ( 1.12708605603493e-01 , 5.61658959697750e-02 , 1.88421193981063e-01 ), ( 1.58453289204960e-01 , 6.38882845716083e-02 , 1.20048559639609e-01 ), ( 2.37427701748859e-01 , 9.10730182385947e-02 , 1.35124140860172e-01 ), ( 1.28976749968850e-01 , 4.70756905526893e-02 , 5.03645831077629e-02 ), ( 1.24743209605684e-01 , 3.92214262823626e-02 , -1.19145108360773e-02 ), ( 1.05232862567391e-01 , 4.04520538596028e-02 , 6.07220837311741e-02 ), ( 6.89693730247213e-02 , 2.26798892246959e-02 , 2.97123231983654e-03 ), ( 5.49848351625235e-02 , 2.14247203736171e-02 , 3.44977316927867e-02 ), ( -2.89799710172167e-03 , -3.26948391773036e-03 , -2.23849922959762e-02 ), ( -1.66284727461301e-02 , -1.48313220428684e-02 , -9.06908655913465e-02 ), ( -4.93257420058050e-02 , -1.26024886413324e-02 , 3.26396593706691e-02 ), ( -1.15814208905717e-01 , -3.57213584700012e-02 , 1.77174633909183e-02 ), ( -1.56530584531230e-01 , -4.09167267399266e-02 , 9.47006059954786e-02 ), ( -1.02338779740558e-01 , -3.59973401670387e-02 , -2.69355915416408e-02 ), ( -1.38305237479625e-01 , -5.35201643464268e-02 , -8.32162477592325e-02 ), ( -4.85680405386822e-02 , -1.61578171552481e-02 , -3.88642298419647e-03 ), ( -2.67772984944918e-02 , -1.32422528386300e-02 , -4.37884424156643e-02 ), ( 3.01329675171860e-02 , 1.02032965942717e-02 , 4.12686185508110e-03 ), ( 4.12040337949232e-03 , -1.17087146451299e-02 , -1.25355981658625e-01 ), ( -1.29576321734095e-02 , -2.27834682403991e-02 , -1.78547403469024e-01 ), ( 4.94007865482561e-02 , 1.71189403955313e-03 , -1.37525207437093e-01 ), ( 7.76852434754888e-02 , 3.05333934288804e-03 , -2.12793513649491e-01 ), ( 1.37153522977005e-01 , 2.33536613497733e-02 , -2.03074806101602e-01 ), ( 1.86139721968092e-02 , -2.16158358743594e-02 , -2.65731524349282e-01 ), ( 1.96439304720072e-02 , -2.83995313437912e-02 , -3.34128733916946e-01 ), ( -3.48204166235399e-02 , -3.57117957159627e-02 , -2.34637084053992e-01 ), ( -9.63386157300486e-02 , -6.00533069326539e-02 , -2.76799718063321e-01 ), ( -1.34718529429084e-01 , -6.75240404033961e-02 , -2.28963807315661e-01 ), ( -1.52361782945018e-01 , -8.03446535693402e-02 , -2.97170116172539e-01 ), ( -1.80120349475619e-01 , -9.59366354408885e-02 , -3.60479474228422e-01 ), ( -1.91062836148284e-01 , -9.31523923260678e-02 , -2.99618463388877e-01 ), ( -2.32146152594691e-01 , -1.09174704521400e-01 , -3.25531619386484e-01 ), ( -1.17398495923477e-01 , -6.99749701730693e-02 , -3.06499820913342e-01 ), ( -1.71084152004181e-01 , -8.08040007777962e-02 , -2.43229116074439e-01 ), ( -2.23093045962109e-01 , -9.90318162507992e-02 , -2.56282234357960e-01 ), ( -2.57756750613568e-01 , -1.02164092444319e-01 , -1.78339434804573e-01 ) } +colvars: Step 26, atoms_new_colvar_forces = { ( -4.90134830340811e+00 , -4.32838534106888e-01 , -1.23797148234851e+00 ), ( -4.22166551672096e+00 , -3.67294361066177e-01 , -9.66076111553409e-01 ), ( -4.29787238386828e+00 , -3.95846618103073e-01 , -1.00298079083088e+00 ), ( -5.77795036103874e+00 , -5.61128776172026e-01 , -1.49579437993151e+00 ), ( 2.65552369057024e-01 , 1.23707017344092e-01 , 3.61026525861699e-01 ), ( 5.27866578934323e+00 , 6.16164346414365e-01 , 1.82345157951742e+00 ), ( 4.46075239357411e+00 , 5.09008069397666e-01 , 1.58232076279526e+00 ), ( -4.79978613650726e-02 , 2.26261342476859e-02 , 3.66575602512266e-01 ), ( 4.44176967124551e+00 , 4.99636295182185e-01 , 1.55143793146276e+00 ), ( 5.88776065054872e+00 , 6.40238071629797e-01 , 1.91342600203500e+00 ), ( 1.25563953201117e-02 , 3.65122831702803e-02 , 3.11411663891079e-01 ), ( 1.93131901570776e-03 , 3.05492085375823e-02 , 2.87238624822341e-01 ), ( 2.52341760514982e-02 , 4.53888331213753e-02 , 3.57163324219363e-01 ), ( 4.71181684901467e-02 , 3.71210769891694e-02 , 2.09690449230305e-01 ), ( 1.85503935244117e-02 , 2.24999200605314e-02 , 1.58248660998203e-01 ), ( 1.18691620709629e-01 , 5.91532301902236e-02 , 1.98427428892123e-01 ), ( 1.66869107853703e-01 , 6.72722223839669e-02 , 1.26422837881091e-01 ), ( 2.50044263602652e-01 , 9.58935654325778e-02 , 1.42303574511977e-01 ), ( 1.35832742955127e-01 , 4.95652907963995e-02 , 5.30428277677530e-02 ), ( 1.31372715595156e-01 , 4.12863670414696e-02 , -1.25478450973073e-02 ), ( 1.10834429394443e-01 , 4.25975568390924e-02 , 6.39590476471605e-02 ), ( 7.26502653425661e-02 , 2.38823552624212e-02 , 3.14620475251415e-03 ), ( 5.79303744930678e-02 , 2.25696084109297e-02 , 3.63569311625431e-02 ), ( -3.04073876000827e-03 , -3.44045630873283e-03 , -2.35622234125922e-02 ), ( -1.74993631339265e-02 , -1.56219694704138e-02 , -9.54965949274292e-02 ), ( -5.19416587071601e-02 , -1.32588934206399e-02 , 3.43804865668219e-02 ), ( -1.21968925985347e-01 , -3.76008008019011e-02 , 1.86594793017237e-02 ), ( -1.64854509848420e-01 , -4.30598051972382e-02 , 9.97281777556352e-02 ), ( -1.07783928431990e-01 , -3.79014628017018e-02 , -2.83740304163566e-02 ), ( -1.45662130286669e-01 , -5.63569575602671e-02 , -8.76461169834020e-02 ), ( -5.11608353418905e-02 , -1.70150367783029e-02 , -4.10578440009852e-03 ), ( -2.82181429484682e-02 , -1.39549920990087e-02 , -4.61352529549631e-02 ), ( 3.17109978720648e-02 , 1.07313777416710e-02 , 4.32031562018576e-03 ), ( 4.32647986589957e-03 , -1.23517381398462e-02 , -1.32032505804376e-01 ), ( -1.36622675730687e-02 , -2.40200925147125e-02 , -1.88054283567087e-01 ), ( 5.20211908117395e-02 , 1.77759685189685e-03 , -1.44839809187743e-01 ), ( 8.18144971946119e-02 , 3.18001275358909e-03 , -2.24102147796891e-01 ), ( 1.44450751982475e-01 , 2.45549924434867e-02 , -2.13858668981877e-01 ), ( 1.96081985059248e-02 , -2.27958532330345e-02 , -2.79848803768936e-01 ), ( 2.06934393004506e-02 , -2.99478881630010e-02 , -3.51880501458444e-01 ), ( -3.66628517639210e-02 , -3.76282206819420e-02 , -2.47098296326837e-01 ), ( -1.01446643061048e-01 , -6.32576371288947e-02 , -2.91497474093415e-01 ), ( -1.41861370342853e-01 , -7.11121497690519e-02 , -2.41113794952804e-01 ), ( -1.60454224762985e-01 , -8.46246900122311e-02 , -3.12958230653173e-01 ), ( -1.89686330106093e-01 , -1.01047855434558e-01 , -3.79630375014570e-01 ), ( -2.01233460291664e-01 , -9.81171667056875e-02 , -3.15560315382003e-01 ), ( -2.44505411686068e-01 , -1.14990326731746e-01 , -3.42856436960405e-01 ), ( -1.23653766302172e-01 , -7.37192713634164e-02 , -3.22806971054668e-01 ), ( -1.80179697047576e-01 , -8.51030518346081e-02 , -2.56159372505237e-01 ), ( -2.34959848327602e-01 , -1.04296723642412e-01 , -2.69914164759479e-01 ), ( -2.71471870539900e-01 , -1.07584103000942e-01 , -1.87835674080815e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 26, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3332,10 +5348,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 27, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 27, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 27, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 27, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 27, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 27, atoms_positions[size = 51] = { ( 8.25707472183859e+00 , 4.22785545844635e-02 , -7.33175419821030e-01 ), ( 6.85606891564990e+00 , -5.72993184382743e-01 , -5.34486564205437e-01 ), ( 6.14971346582996e+00 , -3.85373599008369e-01 , 7.86581713390112e-01 ), ( 4.91325846372904e+00 , -1.47546829791428e-01 , 7.38296205810287e-01 ), ( 7.01581372425447e+00 , -2.06361573840916e+00 , -8.97301976640849e-01 ), ( 6.82087835887150e+00 , -2.80274776070182e-01 , 1.95623975081528e+00 ), ( 6.12304983126280e+00 , -2.09194224725478e-01 , 3.16559515508167e+00 ), ( 7.11793439373644e+00 , -3.45009299620143e-01 , 4.36691734274913e+00 ), ( 5.33677230759923e+00 , 1.07311241893511e+00 , 3.36823126876214e+00 ), ( 4.17449455394443e+00 , 1.01035056432143e+00 , 3.75033775452345e+00 ), ( 5.83878873373422e+00 , 2.25565506890960e+00 , 2.97752353818648e+00 ), ( 5.18795047354684e+00 , 3.56436390710717e+00 , 2.90402910828106e+00 ), ( 6.31282670043946e+00 , 4.48710215388794e+00 , 2.30274091881490e+00 ), ( 3.86003843099403e+00 , 3.66074961395375e+00 , 2.03518881628772e+00 ), ( 2.80104566768147e+00 , 4.17008041424924e+00 , 2.45074539172103e+00 ), ( 3.92659499658068e+00 , 3.21131980145144e+00 , 7.34512932575729e-01 ), ( 2.73547363376623e+00 , 3.03713617549576e+00 , -8.19334207195935e-02 ), ( 3.10030640312578e+00 , 2.66254209841518e+00 , -1.53494248536318e+00 ), ( 1.55796569836131e+00 , 2.17833489691590e+00 , 4.23945681356006e-01 ), ( 3.90870358978620e-01 , 2.61546398796180e+00 , 4.77049062459298e-01 ), ( 2.07634801048823e+00 , 1.14623546721613e+00 , 1.04413182538187e+00 ), ( 1.18950058561543e+00 , 1.21074670819899e-01 , 1.69579367795851e+00 ), ( 2.07141663863220e+00 , -1.09176100201853e+00 , 2.03329812501245e+00 ), ( 5.74051227837035e-01 , 6.17817431639855e-01 , 2.96442611850330e+00 ), ( -5.83248988561473e-01 , 3.53856649208231e-01 , 3.17006622801460e+00 ), ( 1.29260676386410e+00 , 1.36805146008650e+00 , 3.74323432458433e+00 ), ( 8.51718493279761e-01 , 1.98200105562231e+00 , 5.02902499753843e+00 ), ( 2.10805989657198e+00 , 2.74297448255918e+00 , 5.71945263723591e+00 ), ( -3.51305830993778e-01 , 2.90593982582615e+00 , 4.96664900296609e+00 ), ( -1.11743950864434e+00 , 3.06756828414869e+00 , 5.87763028936677e+00 ), ( -5.40967944065125e-01 , 3.51054118367759e+00 , 3.80704470696793e+00 ), ( -1.49129375088998e+00 , 4.50014160905025e+00 , 3.41314980510574e+00 ), ( -7.18863436720035e-01 , 5.42807854382700e+00 , 2.47348661014230e+00 ), ( -2.74391701810042e+00 , 3.93976915318521e+00 , 2.82901925908208e+00 ), ( -3.80912399494000e+00 , 4.54828466459966e+00 , 2.81284716313668e+00 ), ( -2.67184672670405e+00 , 2.63993264062169e+00 , 2.36196741368408e+00 ), ( -3.79208950657429e+00 , 1.82126070497219e+00 , 2.00510634091807e+00 ), ( -3.36462056606770e+00 , 8.76286310715767e-01 , 8.28690483062027e-01 ), ( -4.26652954382035e+00 , 1.05555900505266e+00 , 3.22504867431751e+00 ), ( -5.48611075001312e+00 , 7.70421404314483e-01 , 3.33581476316994e+00 ), ( -3.36841678980655e+00 , 7.21715307195188e-01 , 4.18557284378883e+00 ), ( -3.67355759015422e+00 , 7.84487286731862e-02 , 5.46907258756486e+00 ), ( -2.38766192379755e+00 , -3.24232250810556e-01 , 6.14422340041738e+00 ), ( -4.47074852197242e+00 , 9.28660456885802e-01 , 6.42378233765041e+00 ), ( -5.36367199328626e+00 , 5.83372383130967e-01 , 7.21111603369968e+00 ), ( -6.29483858506010e+00 , 3.62959734156973e+00 , 6.75175798337722e+00 ), ( -6.98735006179341e+00 , 4.29578222764064e+00 , 7.50183775606877e+00 ), ( -6.67291941140437e+00 , 3.16288637103370e+00 , 5.51789416999225e+00 ), ( -4.11083041741113e+00 , 2.25075669738573e+00 , 6.39038185059985e+00 ), ( -4.81307774675290e+00 , 3.26588499697105e+00 , 7.25728511232413e+00 ), ( -4.04182732129257e+00 , 4.54927180676174e+00 , 7.27132923334030e+00 ) } +colvars: Step 27, atoms_positions[size = 51] = { ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 ), ( 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 ), ( 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 ), ( 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 ), ( 7.01535203749725e+00 , -2.06381635889530e+00 , -8.97206548208713e-01 ), ( 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 ), ( 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 ), ( 7.11920452994009e+00 , -3.45209208680255e-01 , 4.36798290506035e+00 ), ( 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 ), ( 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 ), ( 5.83996242946139e+00 , 2.25614165217745e+00 , 2.97754417816735e+00 ), ( 5.18803371200831e+00 , 3.56439300374262e+00 , 2.90427264395260e+00 ), ( 6.31278682030528e+00 , 4.48718193168801e+00 , 2.30297883289902e+00 ), ( 3.86007818050917e+00 , 3.66069984853279e+00 , 2.03536695968349e+00 ), ( 2.80106427502878e+00 , 4.17007867900681e+00 , 2.45085264233098e+00 ), ( 3.92668633537448e+00 , 3.21135139059605e+00 , 7.34662256057969e-01 ), ( 2.73559409674514e+00 , 3.03718396101823e+00 , -8.18396133359087e-02 ), ( 3.10046791929361e+00 , 2.66260233391187e+00 , -1.53484189859099e+00 ), ( 1.55806782248441e+00 , 2.17837165364119e+00 , 4.23990219910245e-01 ), ( 3.90966682471660e-01 , 2.61549156173092e+00 , 4.77048162595421e-01 ), ( 2.07642940287190e+00 , 1.14626556479653e+00 , 1.04418936403971e+00 ), ( 1.18955214262897e+00 , 1.21097540077628e-01 , 1.69579939021184e+00 ), ( 2.07148676383460e+00 , -1.09170139783296e+00 , 2.03336886456757e+00 ), ( 5.74083444381060e-01 , 6.17814367178178e-01 , 2.96441739552478e+00 ), ( -5.83239870189212e-01 , 3.53854569089529e-01 , 3.17001185669136e+00 ), ( 1.29268717567358e+00 , 1.36802499737871e+00 , 3.74325367718469e+00 ), ( 8.51662531290306e-01 , 1.98196151284385e+00 , 5.02902636009038e+00 ), ( 2.10795727843958e+00 , 2.74294345881718e+00 , 5.71950307343801e+00 ), ( -3.51380465494013e-01 , 2.90590727965994e+00 , 4.96662567680565e+00 ), ( -1.11754635934422e+00 , 3.06753233047963e+00 , 5.87758275384854e+00 ), ( -5.41004249476953e-01 , 3.51052928934131e+00 , 3.80702706112940e+00 ), ( -1.49131798447236e+00 , 4.50013366924590e+00 , 3.41310948361751e+00 ), ( -7.18849617362706e-01 , 5.42808066275172e+00 , 2.47348306051379e+00 ), ( -2.74391507090231e+00 , 3.93976116451634e+00 , 2.82892247842410e+00 ), ( -3.80912868669978e+00 , 4.54826517460901e+00 , 2.81272152384039e+00 ), ( -2.67181385610276e+00 , 2.63993240683156e+00 , 2.36185920063368e+00 ), ( -3.79203712233535e+00 , 1.82126172263691e+00 , 2.00493708536667e+00 ), ( -3.36452697779479e+00 , 8.76290545235428e-01 , 8.28533001648633e-01 ), ( -4.26651678313547e+00 , 1.05553751337188e+00 , 3.22484550789925e+00 ), ( -5.48609767217338e+00 , 7.70398431245772e-01 , 3.33557934330755e+00 ), ( -3.36843730934644e+00 , 7.21681435894418e-01 , 4.18538959592939e+00 ), ( -3.67363375907043e+00 , 7.83952627655409e-02 , 5.46885930333576e+00 ), ( -2.38776057883782e+00 , -3.24274265963382e-01 , 6.14405952976137e+00 ), ( -4.47086570247857e+00 , 9.28599829856636e-01 , 6.42355235353585e+00 ), ( -5.36379962330255e+00 , 5.83302207573987e-01 , 7.21086622603019e+00 ), ( -6.29498544377212e+00 , 3.62952728769432e+00 , 6.75153578478002e+00 ), ( -6.98751438372502e+00 , 4.29570395973377e+00 , 7.50160948168672e+00 ), ( -6.67303020010390e+00 , 3.16282932646508e+00 , 5.51765282119227e+00 ), ( -4.11095650389687e+00 , 2.25069892237787e+00 , 6.39019118562185e+00 ), ( -4.81324504379703e+00 , 3.26580560272371e+00 , 7.25708721992280e+00 ), ( -4.04200929478364e+00 , 4.54919603154869e+00 , 7.27119176699306e+00 ) } colvars: Step 27, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 27, atom_groups_ids[size = 0] = @@ -3352,163 +5368,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 27 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.97850201345680e-01 , -9.04087721924012e-03 , 9.54569808917841e-01 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.96466575557498e-01 , -8.83665802952108e-03 , 9.55002347144801e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 7.01535203749725e+00 , -2.06381635889530e+00 , -8.97206548208713e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 , 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 7.11920452994009e+00 , -3.45209208680255e-01 , 4.36798290506035e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 , 5.83996242946139e+00 , 2.25614165217745e+00 , 2.97754417816735e+00 , 5.18803371200831e+00 , 3.56439300374262e+00 , 2.90427264395260e+00 , 6.31278682030528e+00 , 4.48718193168801e+00 , 2.30297883289902e+00 , 3.86007818050917e+00 , 3.66069984853279e+00 , 2.03536695968349e+00 , 2.80106427502878e+00 , 4.17007867900681e+00 , 2.45085264233098e+00 , 3.92668633537448e+00 , 3.21135139059605e+00 , 7.34662256057969e-01 , 2.73559409674514e+00 , 3.03718396101823e+00 , -8.18396133359087e-02 , 3.10046791929361e+00 , 2.66260233391187e+00 , -1.53484189859099e+00 , 1.55806782248441e+00 , 2.17837165364119e+00 , 4.23990219910245e-01 , 3.90966682471660e-01 , 2.61549156173092e+00 , 4.77048162595421e-01 , 2.07642940287190e+00 , 1.14626556479653e+00 , 1.04418936403971e+00 , 1.18955214262897e+00 , 1.21097540077628e-01 , 1.69579939021184e+00 , 2.07148676383460e+00 , -1.09170139783296e+00 , 2.03336886456757e+00 , 5.74083444381060e-01 , 6.17814367178178e-01 , 2.96441739552478e+00 , -5.83239870189212e-01 , 3.53854569089529e-01 , 3.17001185669136e+00 , 1.29268717567358e+00 , 1.36802499737871e+00 , 3.74325367718469e+00 , 8.51662531290306e-01 , 1.98196151284385e+00 , 5.02902636009038e+00 , 2.10795727843958e+00 , 2.74294345881718e+00 , 5.71950307343801e+00 , -3.51380465494013e-01 , 2.90590727965994e+00 , 4.96662567680565e+00 , -1.11754635934422e+00 , 3.06753233047963e+00 , 5.87758275384854e+00 , -5.41004249476953e-01 , 3.51052928934131e+00 , 3.80702706112940e+00 , -1.49131798447236e+00 , 4.50013366924590e+00 , 3.41310948361751e+00 , -7.18849617362706e-01 , 5.42808066275172e+00 , 2.47348306051379e+00 , -2.74391507090231e+00 , 3.93976116451634e+00 , 2.82892247842410e+00 , -3.80912868669978e+00 , 4.54826517460901e+00 , 2.81272152384039e+00 , -2.67181385610276e+00 , 2.63993240683156e+00 , 2.36185920063368e+00 , -3.79203712233535e+00 , 1.82126172263691e+00 , 2.00493708536667e+00 , -3.36452697779479e+00 , 8.76290545235428e-01 , 8.28533001648633e-01 , -4.26651678313547e+00 , 1.05553751337188e+00 , 3.22484550789925e+00 , -5.48609767217338e+00 , 7.70398431245772e-01 , 3.33557934330755e+00 , -3.36843730934644e+00 , 7.21681435894418e-01 , 4.18538959592939e+00 , -3.67363375907043e+00 , 7.83952627655409e-02 , 5.46885930333576e+00 , -2.38776057883782e+00 , -3.24274265963382e-01 , 6.14405952976137e+00 , -4.47086570247857e+00 , 9.28599829856636e-01 , 6.42355235353585e+00 , -5.36379962330255e+00 , 5.83302207573987e-01 , 7.21086622603019e+00 , -6.29498544377212e+00 , 3.62952728769432e+00 , 6.75153578478002e+00 , -6.98751438372502e+00 , 4.29570395973377e+00 , 7.50160948168672e+00 , -6.67303020010390e+00 , 3.16282932646508e+00 , 5.51765282119227e+00 , -4.11095650389687e+00 , 2.25069892237787e+00 , 6.39019118562185e+00 , -4.81324504379703e+00 , 3.26580560272371e+00 , 7.25708721992280e+00 , -4.04200929478364e+00 , 4.54919603154869e+00 , 7.27119176699306e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.97850201345680e-01 , -9.04087721924012e-03 , 9.54569808917841e-01 ). +colvars: Colvar "one" has value ( -2.96466575557498e-01 , -8.83665802952108e-03 , 9.55002347144801e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 7.01535203749725e+00 , -2.06381635889530e+00 , -8.97206548208713e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 , 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 7.11920452994009e+00 , -3.45209208680255e-01 , 4.36798290506035e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 , 5.83996242946139e+00 , 2.25614165217745e+00 , 2.97754417816735e+00 , 5.18803371200831e+00 , 3.56439300374262e+00 , 2.90427264395260e+00 , 6.31278682030528e+00 , 4.48718193168801e+00 , 2.30297883289902e+00 , 3.86007818050917e+00 , 3.66069984853279e+00 , 2.03536695968349e+00 , 2.80106427502878e+00 , 4.17007867900681e+00 , 2.45085264233098e+00 , 3.92668633537448e+00 , 3.21135139059605e+00 , 7.34662256057969e-01 , 2.73559409674514e+00 , 3.03718396101823e+00 , -8.18396133359087e-02 , 3.10046791929361e+00 , 2.66260233391187e+00 , -1.53484189859099e+00 , 1.55806782248441e+00 , 2.17837165364119e+00 , 4.23990219910245e-01 , 3.90966682471660e-01 , 2.61549156173092e+00 , 4.77048162595421e-01 , 2.07642940287190e+00 , 1.14626556479653e+00 , 1.04418936403971e+00 , 1.18955214262897e+00 , 1.21097540077628e-01 , 1.69579939021184e+00 , 2.07148676383460e+00 , -1.09170139783296e+00 , 2.03336886456757e+00 , 5.74083444381060e-01 , 6.17814367178178e-01 , 2.96441739552478e+00 , -5.83239870189212e-01 , 3.53854569089529e-01 , 3.17001185669136e+00 , 1.29268717567358e+00 , 1.36802499737871e+00 , 3.74325367718469e+00 , 8.51662531290306e-01 , 1.98196151284385e+00 , 5.02902636009038e+00 , 2.10795727843958e+00 , 2.74294345881718e+00 , 5.71950307343801e+00 , -3.51380465494013e-01 , 2.90590727965994e+00 , 4.96662567680565e+00 , -1.11754635934422e+00 , 3.06753233047963e+00 , 5.87758275384854e+00 , -5.41004249476953e-01 , 3.51052928934131e+00 , 3.80702706112940e+00 , -1.49131798447236e+00 , 4.50013366924590e+00 , 3.41310948361751e+00 , -7.18849617362706e-01 , 5.42808066275172e+00 , 2.47348306051379e+00 , -2.74391507090231e+00 , 3.93976116451634e+00 , 2.82892247842410e+00 , -3.80912868669978e+00 , 4.54826517460901e+00 , 2.81272152384039e+00 , -2.67181385610276e+00 , 2.63993240683156e+00 , 2.36185920063368e+00 , -3.79203712233535e+00 , 1.82126172263691e+00 , 2.00493708536667e+00 , -3.36452697779479e+00 , 8.76290545235428e-01 , 8.28533001648633e-01 , -4.26651678313547e+00 , 1.05553751337188e+00 , 3.22484550789925e+00 , -5.48609767217338e+00 , 7.70398431245772e-01 , 3.33557934330755e+00 , -3.36843730934644e+00 , 7.21681435894418e-01 , 4.18538959592939e+00 , -3.67363375907043e+00 , 7.83952627655409e-02 , 5.46885930333576e+00 , -2.38776057883782e+00 , -3.24274265963382e-01 , 6.14405952976137e+00 , -4.47086570247857e+00 , 9.28599829856636e-01 , 6.42355235353585e+00 , -5.36379962330255e+00 , 5.83302207573987e-01 , 7.21086622603019e+00 , -6.29498544377212e+00 , 3.62952728769432e+00 , 6.75153578478002e+00 , -6.98751438372502e+00 , 4.29570395973377e+00 , 7.50160948168672e+00 , -6.67303020010390e+00 , 3.16282932646508e+00 , 5.51765282119227e+00 , -4.11095650389687e+00 , 2.25069892237787e+00 , 6.39019118562185e+00 , -4.81324504379703e+00 , 3.26580560272371e+00 , 7.25708721992280e+00 , -4.04200929478364e+00 , 4.54919603154869e+00 , 7.27119176699306e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.475 , 2.13262 , -15.1878 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.7313 , 6.57313 , 13.1463 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.475 , 2.13262 , -15.1878 ) to colvar "one". -colvars: Adding total bias energy: 44.2097 +colvars: Adding biasing force ( 65.7313 , 6.57313 , 13.1463 ) to colvar "one". +colvars: Adding total bias energy: 56.0971 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.475 , 2.13262 , -15.1878 ) +colvars: Force to be applied: ( 65.7313 , 6.57313 , 13.1463 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.92729 , -0.526119 , -1.42562 ) -colvars: ( -4.22515 , -0.451147 , -1.22247 ) -colvars: ( -4.22515 , -0.451147 , -1.22247 ) -colvars: ( -5.62802 , -0.60094 , -1.62836 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.19189 , -0.552461 , -1.49409 ) +colvars: ( -4.45204 , -0.473736 , -1.28118 ) +colvars: ( -4.45204 , -0.473736 , -1.28118 ) +colvars: ( -5.93025 , -0.63103 , -1.70657 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.888561 , 0.195986 , 0.611767 ) -colvars: ( 0.770096 , 0.266359 , 0.635406 ) -colvars: ( 0.753917 , 0.259503 , 0.617035 ) -colvars: ( 0.659517 , 0.26684 , 0.571938 ) -colvars: ( 0.647745 , 0.200392 , 0.47795 ) -colvars: ( 0.573986 , 0.343694 , 0.62317 ) -colvars: ( 0.468019 , 0.357382 , 0.579698 ) -colvars: ( 0.392197 , 0.454225 , 0.662779 ) -colvars: ( 0.386986 , 0.312814 , 0.474263 ) -colvars: ( 0.352698 , 0.271214 , 0.399819 ) -colvars: ( 0.357652 , 0.318105 , 0.4642 ) -colvars: ( 0.286957 , 0.275242 , 0.366994 ) -colvars: ( 0.25981 , 0.304216 , 0.389264 ) -colvars: ( 0.34875 , 0.177789 , 0.27498 ) -colvars: ( 0.290655 , 0.134431 , 0.18443 ) -colvars: ( 0.47027 , 0.141114 , 0.297315 ) -colvars: ( 0.54208 , 0.0501064 , 0.219562 ) -colvars: ( 0.670252 , 0.0294884 , 0.266815 ) -colvars: ( 0.550894 , 0.0182879 , 0.182934 ) -colvars: ( 0.535298 , -0.0466676 , 0.0886882 ) -colvars: ( 0.571868 , 0.06609 , 0.257797 ) -colvars: ( 0.57069 , 0.0498781 , 0.235848 ) -colvars: ( 0.607128 , 0.11449 , 0.341724 ) -colvars: ( 0.447678 , 0.054028 , 0.169984 ) -colvars: ( 0.441058 , -0.00183084 , 0.0928738 ) -colvars: ( 0.34665 , 0.119308 , 0.197051 ) -colvars: ( 0.223405 , 0.12757 , 0.136446 ) -colvars: ( 0.132731 , 0.212948 , 0.195879 ) -colvars: ( 0.195255 , 0.0539795 , 0.0235963 ) -colvars: ( 0.146615 , 0.0177343 , -0.0521439 ) -colvars: ( 0.228187 , 0.0286348 , 0.00944027 ) -colvars: ( 0.214077 , -0.0436845 , -0.0936034 ) -colvars: ( 0.248658 , -0.0468437 , -0.0777018 ) -colvars: ( 0.288689 , -0.129297 , -0.162654 ) -colvars: ( 0.245127 , -0.182404 , -0.257569 ) -colvars: ( 0.402841 , -0.144029 , -0.115808 ) -colvars: ( 0.479665 , -0.219206 , -0.169887 ) -colvars: ( 0.609592 , -0.22148 , -0.0975542 ) -colvars: ( 0.433185 , -0.223888 , -0.202972 ) -colvars: ( 0.438717 , -0.291807 , -0.288858 ) -colvars: ( 0.385153 , -0.150917 , -0.135096 ) -colvars: ( 0.33178 , -0.144893 , -0.158134 ) -colvars: ( 0.315656 , -0.0584931 , -0.0541457 ) -colvars: ( 0.209679 , -0.15396 , -0.240806 ) -colvars: ( 0.185698 , -0.195983 , -0.309832 ) -colvars: ( 0.00987202 , -0.199967 , -0.41698 ) -colvars: ( -0.0801811 , -0.217945 , -0.492763 ) -colvars: ( 0.109025 , -0.24948 , -0.424452 ) -colvars: ( 0.128458 , -0.113579 , -0.234918 ) -colvars: ( 0.0102756 , -0.118226 , -0.309522 ) -colvars: ( -0.077958 , -0.0379191 , -0.255327 ) +colvars: ( 0.93535 , 0.206502 , 0.642814 ) +colvars: ( 0.810728 , 0.280502 , 0.667712 ) +colvars: ( 0.793651 , 0.273341 , 0.648447 ) +colvars: ( 0.694429 , 0.280918 , 0.600981 ) +colvars: ( 0.68204 , 0.210981 , 0.502152 ) +colvars: ( 0.604481 , 0.361727 , 0.654861 ) +colvars: ( 0.493039 , 0.376038 , 0.609153 ) +colvars: ( 0.413302 , 0.477894 , 0.696524 ) +colvars: ( 0.407766 , 0.329118 , 0.498328 ) +colvars: ( 0.371715 , 0.285295 , 0.420037 ) +colvars: ( 0.37686 , 0.334723 , 0.487796 ) +colvars: ( 0.302457 , 0.289608 , 0.385625 ) +colvars: ( 0.273851 , 0.32014 , 0.409095 ) +colvars: ( 0.367443 , 0.187094 , 0.288858 ) +colvars: ( 0.306328 , 0.14143 , 0.193655 ) +colvars: ( 0.495265 , 0.148577 , 0.312317 ) +colvars: ( 0.570791 , 0.0528502 , 0.230542 ) +colvars: ( 0.705601 , 0.0312475 , 0.280212 ) +colvars: ( 0.58011 , 0.0193161 , 0.191981 ) +colvars: ( 0.563698 , -0.0490518 , 0.0928808 ) +colvars: ( 0.602221 , 0.0695874 , 0.27066 ) +colvars: ( 0.60103 , 0.0524704 , 0.247537 ) +colvars: ( 0.639405 , 0.120446 , 0.358828 ) +colvars: ( 0.471642 , 0.0567505 , 0.178299 ) +colvars: ( 0.464693 , -0.00205918 , 0.0972 ) +colvars: ( 0.365361 , 0.125404 , 0.206799 ) +colvars: ( 0.235721 , 0.13402 , 0.143098 ) +colvars: ( 0.140331 , 0.223832 , 0.205631 ) +colvars: ( 0.206071 , 0.0565921 , 0.0244659 ) +colvars: ( 0.15492 , 0.0183989 , -0.0551817 ) +colvars: ( 0.240662 , 0.0299928 , 0.00961332 ) +colvars: ( 0.225779 , -0.0460863 , -0.0987095 ) +colvars: ( 0.262101 , -0.0493315 , -0.0819511 ) +colvars: ( 0.304275 , -0.136157 , -0.171353 ) +colvars: ( 0.258443 , -0.19207 , -0.271148 ) +colvars: ( 0.424373 , -0.151614 , -0.122139 ) +colvars: ( 0.5052 , -0.230706 , -0.179044 ) +colvars: ( 0.641884 , -0.233031 , -0.103024 ) +colvars: ( 0.456356 , -0.235714 , -0.213864 ) +colvars: ( 0.462177 , -0.307198 , -0.304186 ) +colvars: ( 0.405869 , -0.158986 , -0.142505 ) +colvars: ( 0.349771 , -0.152731 , -0.166757 ) +colvars: ( 0.332852 , -0.0618516 , -0.0574335 ) +colvars: ( 0.221321 , -0.162337 , -0.253652 ) +colvars: ( 0.196116 , -0.206604 , -0.326251 ) +colvars: ( 0.0110507 , -0.210784 , -0.438785 ) +colvars: ( -0.0836857 , -0.229751 , -0.518447 ) +colvars: ( 0.115321 , -0.2628 , -0.446644 ) +colvars: ( 0.135851 , -0.119851 , -0.24741 ) +colvars: ( 0.0115201 , -0.124801 , -0.32582 ) +colvars: ( -0.0813092 , -0.0403172 , -0.26879 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.92729 , 0.526119 , 1.42562 ) -colvars: ( 4.22515 , 0.451147 , 1.22247 ) -colvars: ( 4.22515 , 0.451147 , 1.22247 ) -colvars: ( 5.62802 , 0.60094 , 1.62836 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.19189 , 0.552461 , 1.49409 ) +colvars: ( 4.45204 , 0.473736 , 1.28118 ) +colvars: ( 4.45204 , 0.473736 , 1.28118 ) +colvars: ( 5.93025 , 0.63103 , 1.70657 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.614232 , -0.0811803 , -0.365307 ) -colvars: ( -0.552626 , -0.164452 , -0.33329 ) -colvars: ( -0.501779 , -0.142111 , -0.274206 ) -colvars: ( -0.514405 , -0.192153 , -0.304834 ) -colvars: ( -0.504737 , -0.132823 , -0.273847 ) -colvars: ( -0.490569 , -0.284889 , -0.314148 ) -colvars: ( -0.458928 , -0.325547 , -0.296947 ) -colvars: ( -0.43805 , -0.433682 , -0.314755 ) -colvars: ( -0.395763 , -0.289796 , -0.220681 ) -colvars: ( -0.39174 , -0.264341 , -0.207512 ) -colvars: ( -0.345651 , -0.283973 , -0.16826 ) -colvars: ( -0.284883 , -0.246681 , -0.0938493 ) -colvars: ( -0.235437 , -0.26157 , -0.0495239 ) -colvars: ( -0.303755 , -0.142724 , -0.0755256 ) -colvars: ( -0.272735 , -0.113196 , -0.033779 ) -colvars: ( -0.357365 , -0.0849601 , -0.108658 ) -colvars: ( -0.383431 , 0.0140095 , -0.0993481 ) -colvars: ( -0.432649 , 0.061961 , -0.131589 ) -colvars: ( -0.421867 , 0.0290174 , -0.132572 ) -colvars: ( -0.410475 , 0.0862409 , -0.10061 ) -colvars: ( -0.466744 , -0.0255527 , -0.197217 ) -colvars: ( -0.501976 , -0.0271507 , -0.233178 ) -colvars: ( -0.552559 , -0.0931808 , -0.307665 ) -colvars: ( -0.450794 , -0.057355 , -0.192601 ) -colvars: ( -0.45794 , -0.0129745 , -0.183864 ) -colvars: ( -0.396114 , -0.13215 , -0.164502 ) -colvars: ( -0.339298 , -0.163633 , -0.118724 ) -colvars: ( -0.289267 , -0.25442 , -0.101028 ) -colvars: ( -0.297536 , -0.0901417 , -0.0504221 ) -colvars: ( -0.284876 , -0.0714023 , -0.0309867 ) -colvars: ( -0.276561 , -0.0448166 , -0.0131011 ) -colvars: ( -0.240528 , 0.0306039 , 0.0501388 ) -colvars: ( -0.218056 , 0.0573122 , 0.0822881 ) -colvars: ( -0.284312 , 0.117949 , 0.037483 ) -colvars: ( -0.257777 , 0.160066 , 0.0792386 ) -colvars: ( -0.353307 , 0.14618 , -0.0216932 ) -colvars: ( -0.401934 , 0.222872 , -0.0430332 ) -colvars: ( -0.4725 , 0.245521 , -0.10579 ) -colvars: ( -0.414644 , 0.202796 , -0.0629994 ) -colvars: ( -0.419153 , 0.264063 , -0.0455574 ) -colvars: ( -0.420141 , 0.115502 , -0.0998255 ) -colvars: ( -0.428397 , 0.0850252 , -0.119046 ) -colvars: ( -0.450773 , -0.00908048 , -0.175269 ) -colvars: ( -0.362218 , 0.0737505 , -0.0566178 ) -colvars: ( -0.366043 , 0.100218 , -0.0509683 ) -colvars: ( -0.200724 , 0.107031 , 0.117525 ) -colvars: ( -0.151678 , 0.108971 , 0.167484 ) -colvars: ( -0.226175 , 0.179925 , 0.118103 ) -colvars: ( -0.299578 , 0.0328233 , -0.008377 ) -colvars: ( -0.233297 , 0.0191909 , 0.0533083 ) -colvars: ( -0.179635 , -0.0644404 , 0.0772172 ) +colvars: ( -0.646438 , -0.0856051 , -0.383247 ) +colvars: ( -0.5817 , -0.173176 , -0.349543 ) +colvars: ( -0.528123 , -0.149712 , -0.287416 ) +colvars: ( -0.541601 , -0.20225 , -0.319685 ) +colvars: ( -0.531429 , -0.139818 , -0.287202 ) +colvars: ( -0.516623 , -0.299769 , -0.329424 ) +colvars: ( -0.483452 , -0.342474 , -0.311382 ) +colvars: ( -0.461577 , -0.456204 , -0.330017 ) +colvars: ( -0.417004 , -0.304843 , -0.231285 ) +colvars: ( -0.412823 , -0.278025 , -0.21752 ) +colvars: ( -0.364227 , -0.298746 , -0.176156 ) +colvars: ( -0.300286 , -0.259503 , -0.0980001 ) +colvars: ( -0.248207 , -0.275201 , -0.0513497 ) +colvars: ( -0.320073 , -0.150156 , -0.0788332 ) +colvars: ( -0.287473 , -0.119059 , -0.0350276 ) +colvars: ( -0.376376 , -0.0894403 , -0.113657 ) +colvars: ( -0.403729 , 0.0146557 , -0.103955 ) +colvars: ( -0.455391 , 0.0650334 , -0.137812 ) +colvars: ( -0.444234 , 0.0304862 , -0.138945 ) +colvars: ( -0.432251 , 0.0907039 , -0.105435 ) +colvars: ( -0.491508 , -0.0269036 , -0.206855 ) +colvars: ( -0.528652 , -0.02854 , -0.244707 ) +colvars: ( -0.581915 , -0.0979989 , -0.322933 ) +colvars: ( -0.474911 , -0.060251 , -0.202103 ) +colvars: ( -0.482457 , -0.0135345 , -0.193003 ) +colvars: ( -0.417445 , -0.138912 , -0.172515 ) +colvars: ( -0.357764 , -0.171976 , -0.124435 ) +colvars: ( -0.30518 , -0.26747 , -0.105752 ) +colvars: ( -0.313786 , -0.0946636 , -0.0527228 ) +colvars: ( -0.300526 , -0.0749067 , -0.0323683 ) +colvars: ( -0.291616 , -0.0470318 , -0.0134824 ) +colvars: ( -0.253652 , 0.0323018 , 0.052917 ) +colvars: ( -0.229901 , 0.0603401 , 0.0867526 ) +colvars: ( -0.29968 , 0.124185 , 0.0395245 ) +colvars: ( -0.271782 , 0.168518 , 0.0833345 ) +colvars: ( -0.372215 , 0.153851 , -0.0226655 ) +colvars: ( -0.423343 , 0.234527 , -0.0451751 ) +colvars: ( -0.497508 , 0.258305 , -0.111101 ) +colvars: ( -0.436825 , 0.213469 , -0.0662159 ) +colvars: ( -0.441568 , 0.277938 , -0.0479697 ) +colvars: ( -0.442705 , 0.121672 , -0.104873 ) +colvars: ( -0.451502 , 0.0896716 , -0.125118 ) +colvars: ( -0.475121 , -0.00930739 , -0.184135 ) +colvars: ( -0.381949 , 0.0778601 , -0.0595491 ) +colvars: ( -0.386024 , 0.105742 , -0.0536875 ) +colvars: ( -0.212049 , 0.112899 , 0.123419 ) +colvars: ( -0.160502 , 0.11498 , 0.17588 ) +colvars: ( -0.238705 , 0.189526 , 0.124018 ) +colvars: ( -0.316055 , 0.0348052 , -0.00879985 ) +colvars: ( -0.246388 , 0.0205083 , 0.0559968 ) +colvars: ( -0.189972 , -0.0674639 , 0.0812087 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 27. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 27. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 27, atoms_new_colvar_forces = { ( -4.65296081977426e+00 , -4.11312705557336e-01 , -1.17916008772739e+00 ), ( -4.00768029090664e+00 , -3.49239975194913e-01 , -9.20352639313350e-01 ), ( -4.08003811411862e+00 , -3.76459577667287e-01 , -9.55364839374468e-01 ), ( -5.48501441621184e+00 , -5.33372168442400e-01 , -1.42426104389976e+00 ), ( 2.52138641933223e-01 , 1.17391937735812e-01 , 3.42829134871724e-01 ), ( 5.01070682101693e+00 , 5.84923668710267e-01 , 1.73464248142854e+00 ), ( 4.23424100363589e+00 , 4.82981191763409e-01 , 1.50522024816815e+00 ), ( -4.58536623926896e-02 , 2.05427050707424e-02 , 3.48024251207226e-01 ), ( 4.21637313973278e+00 , 4.74164541274561e-01 , 1.47605064479100e+00 ), ( 5.58898066213222e+00 , 6.07813101360608e-01 , 1.82067046887196e+00 ), ( 1.20012843991646e-02 , 3.41319982543776e-02 , 2.95940013966073e-01 ), ( 2.07397374634494e-03 , 2.85609252921863e-02 , 2.73144892550298e-01 ), ( 2.43730655906460e-02 , 4.26461642087121e-02 , 3.39740554537315e-01 ), ( 4.49950340960591e-02 , 3.50644361442745e-02 , 1.99454449928156e-01 ), ( 1.79204477193564e-02 , 2.12348526140277e-02 , 1.50650538172148e-01 ), ( 1.12904897239592e-01 , 5.61541437196705e-02 , 1.88656757453513e-01 ), ( 1.58648879535336e-01 , 6.41158613298745e-02 , 1.20214221008044e-01 ), ( 2.37602741866410e-01 , 9.14493290622493e-02 , 1.35226574661627e-01 ), ( 1.29027453197392e-01 , 4.73053343221808e-02 , 5.03618105822811e-02 ), ( 1.24822666774852e-01 , 3.95732743818971e-02 , -1.19214115296327e-02 ), ( 1.05124709295540e-01 , 4.05372902357212e-02 , 6.05793376808745e-02 ), ( 6.87145083550892e-02 , 2.27274122019718e-02 , 2.66950114117548e-03 ), ( 5.45684863152882e-02 , 2.13090318935963e-02 , 3.40593050796351e-02 ), ( -3.11589770804638e-03 , -3.32705763392897e-03 , -2.26173778145858e-02 ), ( -1.68821862929575e-02 , -1.48053264855598e-02 , -9.09902991383552e-02 ), ( -4.94644486604823e-02 , -1.28415349537229e-02 , 3.25496031065721e-02 ), ( -1.15893175122578e-01 , -3.60630646757415e-02 , 1.77224473323606e-02 ), ( -1.56536050944452e-01 , -4.14711124683289e-02 , 9.48511588781837e-02 ), ( -1.02280512861679e-01 , -3.61622204374825e-02 , -2.68258140137797e-02 ), ( -1.38261579627269e-01 , -5.36680204526655e-02 , -8.31306352208558e-02 ), ( -4.83746147798912e-02 , -1.61818255316141e-02 , -3.66081561889643e-03 ), ( -2.64504892957892e-02 , -1.30805877873015e-02 , -4.34645786850419e-02 ), ( 3.06022118555119e-02 , 1.04685390390452e-02 , 4.58631529407322e-03 ), ( 4.37677488117461e-03 , -1.13474290652661e-02 , -1.25170880444443e-01 ), ( -1.26501967680394e-02 , -2.23382067824819e-02 , -1.78330200676609e-01 ), ( 4.95344100922709e-02 , 2.15073650728362e-03 , -1.37501106295696e-01 ), ( 7.77309124365870e-02 , 3.66596779577744e-03 , -2.12920626180573e-01 ), ( 1.37091638773848e-01 , 2.40417941483328e-02 , -2.03343988863783e-01 ), ( 1.85411855798203e-02 , -2.10919042222366e-02 , -2.65971384318865e-01 ), ( 1.95642232487680e-02 , -2.77445444453748e-02 , -3.34415900716037e-01 ), ( -3.49884372076176e-02 , -3.54149312666511e-02 , -2.34921087245561e-01 ), ( -9.66170468589573e-02 , -5.98681899508674e-02 , -2.77180474857296e-01 ), ( -1.35117541849459e-01 , -6.75735453120726e-02 , -2.29414492495197e-01 ), ( -1.52539064568009e-01 , -8.02091633733153e-02 , -2.97423703707888e-01 ), ( -1.80345153304820e-01 , -9.57653730012568e-02 , -3.60800033095277e-01 ), ( -1.90852406581196e-01 , -9.29367337701306e-02 , -2.99454680761945e-01 ), ( -2.31859491857151e-01 , -1.08973437221603e-01 , -3.25278848708273e-01 ), ( -1.17149733614289e-01 , -6.95555299430406e-02 , -3.06348746628624e-01 ), ( -1.71119675535397e-01 , -8.07555096423477e-02 , -2.43295385378938e-01 ), ( -2.23021682685284e-01 , -9.90350769743407e-02 , -2.56213866725295e-01 ), ( -2.57593083922671e-01 , -1.02359484807312e-01 , -1.78109761274513e-01 ) } +colvars: Step 27, atoms_new_colvar_forces = { ( -4.90297655930186e+00 , -4.31564598362340e-01 , -1.23451929484002e+00 ), ( -4.22301490947878e+00 , -3.66409523998744e-01 , -9.63009441633488e-01 ), ( -4.29921507948663e+00 , -3.95067683893615e-01 , -9.99882446130243e-01 ), ( -5.77963954597886e+00 , -5.59866521172678e-01 , -1.49161677631946e+00 ), ( 2.65527260322840e-01 , 1.23628653485763e-01 , 3.61031590181063e-01 ), ( 5.27974646954245e+00 , 6.14419419153178e-01 , 1.81952345279918e+00 ), ( 4.46162967145464e+00 , 5.07299643765269e-01 , 1.57894916998740e+00 ), ( -4.82743241495473e-02 , 2.16895511471460e-02 , 3.66507217577568e-01 ), ( 4.44280460194297e+00 , 4.98010304535323e-01 , 1.54822165188190e+00 ), ( 5.88914188343682e+00 , 6.38299694509511e-01 , 1.90908373748824e+00 ), ( 1.26336184694665e-02 , 3.59767195402972e-02 , 3.11639976954039e-01 ), ( 2.17048365549943e-03 , 3.01047401153576e-02 , 2.87625220041250e-01 ), ( 2.56442106990420e-02 , 4.49384889127548e-02 , 3.57745367438639e-01 ), ( 4.73700704272918e-02 , 3.69376612171887e-02 , 2.10025072640884e-01 ), ( 1.88551353404702e-02 , 2.23707320686415e-02 , 1.58627286028723e-01 ), ( 1.18888812289482e-01 , 5.91366857630878e-02 , 1.98659980139205e-01 ), ( 1.67062115254590e-01 , 6.75058472539935e-02 , 1.26587327234455e-01 ), ( 2.50209738909345e-01 , 9.62809572487406e-02 , 1.42400655013567e-01 ), ( 1.35876110676286e-01 , 4.98023324542390e-02 , 5.30360938215380e-02 ), ( 1.31446564035049e-01 , 4.16520495316130e-02 , -1.25541724310451e-02 ), ( 1.10713057823198e-01 , 4.26837708917003e-02 , 6.38048341305867e-02 ), ( 7.23778528572883e-02 , 2.39303788995603e-02 , 2.82976345134767e-03 ), ( 5.74897230395530e-02 , 2.24466943149810e-02 , 3.58948369294677e-02 ), ( -3.26894775493036e-03 , -3.50056963281915e-03 , -2.38040628525799e-02 ), ( -1.77640583668389e-02 , -1.55936516353163e-02 , -9.58035098578173e-02 ), ( -5.20833412153556e-02 , -1.35084208200437e-02 , 3.42836272455017e-02 ), ( -1.22042937854008e-01 , -3.79561229325308e-02 , 1.86633568178097e-02 ), ( -1.64848403067069e-01 , -4.36375536383752e-02 , 9.98787618112569e-02 ), ( -1.07715082816831e-01 , -3.80714707276125e-02 , -2.82569356268102e-02 ), ( -1.45605860021386e-01 , -5.65078001143671e-02 , -8.75500698611540e-02 ), ( -5.09543775943533e-02 , -1.70389294955693e-02 , -3.86905163471307e-03 ), ( -2.78734948133564e-02 , -1.37845437989526e-02 , -4.57925150521701e-02 ), ( 3.22006418712004e-02 , 1.10085934876183e-02 , 4.80151016462491e-03 ), ( 4.59496470661985e-03 , -1.19722673451992e-02 , -1.31828992832570e-01 ), ( -1.33389425313040e-02 , -2.35517859756418e-02 , -1.87813085650682e-01 ), ( 5.21575656499301e-02 , 2.23728617328495e-03 , -1.44804100200169e-01 ), ( 8.18565414688788e-02 , 3.82166798429712e-03 , -2.24219191277604e-01 ), ( 1.44375534846891e-01 , 2.52741958145053e-02 , -2.14125341398563e-01 ), ( 1.95305507393448e-02 , -2.22452771279715e-02 , -2.80079983418342e-01 ), ( 2.06084758356913e-02 , -2.92594854232303e-02 , -3.52156060929541e-01 ), ( -3.68362960553995e-02 , -3.73144996840226e-02 , -2.47378100856292e-01 ), ( -1.01731162781690e-01 , -6.30591699462869e-02 , -2.91875472071768e-01 ), ( -1.42269404346626e-01 , -7.11589608638280e-02 , -2.41568713100870e-01 ), ( -1.60628454636257e-01 , -8.44766596906788e-02 , -3.13201406497748e-01 ), ( -1.89908259778623e-01 , -1.00861169075825e-01 , -3.79938925588426e-01 ), ( -2.00998302938112e-01 , -9.78840980049558e-02 , -3.15365899917112e-01 ), ( -2.44187218124645e-01 , -1.14771105738640e-01 , -3.42566792240620e-01 ), ( -1.23384003562032e-01 , -7.32744448733386e-02 , -3.22625351507596e-01 ), ( -1.80203911027726e-01 , -8.50461141373376e-02 , -2.56210337503168e-01 ), ( -2.34868063876506e-01 , -1.04292605055861e-01 , -2.69823037582932e-01 ), ( -2.71280713736117e-01 , -1.07781035102270e-01 , -1.87581420964736e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 27, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3546,10 +5701,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 28, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 28, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 28, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 28, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 28, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 28, atoms_positions[size = 51] = { ( 8.25141340854426e+00 , 4.27536282804912e-02 , -7.29725994031609e-01 ), ( 6.84854699653572e+00 , -5.78547352399702e-01 , -5.31252244068400e-01 ), ( 6.14156144486969e+00 , -3.80128091238656e-01 , 7.93954175858301e-01 ), ( 4.91090319376561e+00 , -1.47452241413164e-01 , 7.40807027092780e-01 ), ( 7.01083426050679e+00 , -2.06570502831762e+00 , -8.90481937115680e-01 ), ( 6.81655824705060e+00 , -2.84309611543218e-01 , 1.96050257029610e+00 ), ( 6.11421396110600e+00 , -2.14765450508097e-01 , 3.16719043487638e+00 ), ( 7.12497025687971e+00 , -3.44290203456815e-01 , 4.37373323952401e+00 ), ( 5.33384700079385e+00 , 1.07102518527734e+00 , 3.36873249068690e+00 ), ( 4.17739900898167e+00 , 1.00867135062195e+00 , 3.75974114323684e+00 ), ( 5.84090449077922e+00 , 2.25437915242626e+00 , 2.97582603771991e+00 ), ( 5.17716996576211e+00 , 3.56100320466418e+00 , 2.89884898440734e+00 ), ( 6.30998720471564e+00 , 4.48290067080877e+00 , 2.29672269161662e+00 ), ( 3.85932624226183e+00 , 3.65482484265207e+00 , 2.03223007067337e+00 ), ( 2.80518594525855e+00 , 4.16981451965320e+00 , 2.44566261000768e+00 ), ( 3.92159037766972e+00 , 3.20510104452146e+00 , 7.36950134680403e-01 ), ( 2.74538211176792e+00 , 3.04632820041106e+00 , -7.84400041895933e-02 ), ( 3.10634109201099e+00 , 2.65795581205966e+00 , -1.53831388862997e+00 ), ( 1.55281004852930e+00 , 2.18522467602309e+00 , 4.23598740903130e-01 ), ( 3.96919996569759e-01 , 2.61650672876596e+00 , 4.71528067747315e-01 ), ( 2.07399362523043e+00 , 1.14710419105956e+00 , 1.04379963922736e+00 ), ( 1.19949703016448e+00 , 1.24539394452611e-01 , 1.69226605133456e+00 ), ( 2.07546170430011e+00 , -1.09195909223405e+00 , 2.03594002120556e+00 ), ( 5.74786986110250e-01 , 6.17294307072151e-01 , 2.96300966829902e+00 ), ( -5.83910403574269e-01 , 3.54631339281729e-01 , 3.17343959820756e+00 ), ( 1.29012230674650e+00 , 1.37482080659538e+00 , 3.74549593994039e+00 ), ( 8.57574906695895e-01 , 1.98101570800191e+00 , 5.03021857247255e+00 ), ( 2.10417777431513e+00 , 2.74850558933916e+00 , 5.72213587654337e+00 ), ( -3.53752140166753e-01 , 2.90426287217386e+00 , 4.96360272743720e+00 ), ( -1.11628089028881e+00 , 3.06808899351948e+00 , 5.87856796744518e+00 ), ( -5.42781412788149e-01 , 3.50975443616853e+00 , 3.79838250670944e+00 ), ( -1.48376766275157e+00 , 4.49409930721731e+00 , 3.41341740585530e+00 ), ( -7.25083029546796e-01 , 5.43094619757340e+00 , 2.47505103414817e+00 ), ( -2.74419821951965e+00 , 3.94344555631195e+00 , 2.81537941094484e+00 ), ( -3.80764518051608e+00 , 4.55388854735453e+00 , 2.81303279853192e+00 ), ( -2.67849491347269e+00 , 2.63639349089204e+00 , 2.35905104810708e+00 ), ( -3.79493973802081e+00 , 1.82427408223173e+00 , 2.00571974234432e+00 ), ( -3.36217318157316e+00 , 8.75847101644811e-01 , 8.21638446381836e-01 ), ( -4.25971851468650e+00 , 1.05114915890384e+00 , 3.23051094510326e+00 ), ( -5.48206829895481e+00 , 7.64278204292921e-01 , 3.33711393630714e+00 ), ( -3.36963992716763e+00 , 7.24852928217748e-01 , 4.17899837112041e+00 ), ( -3.67199351459272e+00 , 7.99383341296954e-02 , 5.47443312913220e+00 ), ( -2.38482928791074e+00 , -3.22224431186230e-01 , 6.13967727718150e+00 ), ( -4.47453583041730e+00 , 9.24233948201306e-01 , 6.42240033392267e+00 ), ( -5.36247984538019e+00 , 5.79971900486630e-01 , 7.20776101314810e+00 ), ( -6.30121080914747e+00 , 3.62870685334762e+00 , 6.75223485354252e+00 ), ( -6.99273978261157e+00 , 4.29635231725488e+00 , 7.50533706521696e+00 ), ( -6.66158733267067e+00 , 3.16212698083009e+00 , 5.52259367060144e+00 ), ( -4.10875929173951e+00 , 2.25266922278055e+00 , 6.39196066096449e+00 ), ( -4.81464283416042e+00 , 3.27297540982399e+00 , 7.25521556339087e+00 ), ( -4.03416089454241e+00 , 4.55176819897888e+00 , 7.27161276872507e+00 ) } +colvars: Step 28, atoms_positions[size = 51] = { ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 ), ( 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 ), ( 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 ), ( 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 ), ( 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 ), ( 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 ), ( 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 ), ( 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 ), ( 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 ), ( 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ), ( 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 ), ( 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 ), ( 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 ), ( 3.85937142086407e+00 , 3.65476800818372e+00 , 2.03242241887767e+00 ), ( 2.80520731119718e+00 , 4.16980990587374e+00 , 2.44577776086260e+00 ), ( 3.92168837067129e+00 , 3.20513239434971e+00 , 7.37110387602193e-01 ), ( 2.74551095179179e+00 , 3.04637900756662e+00 , -7.83395650577801e-02 ), ( 3.10651351184068e+00 , 2.65802010971575e+00 , -1.53820581896094e+00 ), ( 1.55291908343130e+00 , 2.18526376293626e+00 , 4.23646231165986e-01 ), ( 3.97023085359059e-01 , 2.61653681210940e+00 , 4.71528039126549e-01 ), ( 2.07408053148835e+00 , 1.14713474881058e+00 , 1.04385983224942e+00 ), ( 1.19955193319812e+00 , 1.24564427667697e-01 , 1.69227225709674e+00 ), ( 2.07553838430586e+00 , -1.09189218971752e+00 , 2.03601799284642e+00 ), ( 5.74823989510068e-01 , 6.17290818940561e-01 , 2.96300100013889e+00 ), ( -5.83898258154936e-01 , 3.54630202666306e-01 , 3.17338193171358e+00 ), ( 1.29020966581429e+00 , 1.37479271877028e+00 , 3.74551657544280e+00 ), ( 8.57517755667383e-01 , 1.98097267107643e+00 , 5.03021891991004e+00 ), ( 2.10406883090063e+00 , 2.74847213498538e+00 , 5.72218933392951e+00 ), ( -3.53830914026017e-01 , 2.90422784614850e+00 , 4.96357786386462e+00 ), ( -1.11639515743135e+00 , 3.06805024433165e+00 , 5.87851704282217e+00 ), ( -5.42819948952781e-01 , 3.50974182912348e+00 , 3.79836330023223e+00 ), ( -1.48379373747290e+00 , 4.49409089265994e+00 , 3.41337438050243e+00 ), ( -7.25068428095970e-01 , 5.43094844567604e+00 , 2.47504725896066e+00 ), ( -2.74419589737474e+00 , 3.94343705131208e+00 , 2.81527629901103e+00 ), ( -3.80764989378887e+00 , 4.55386775866711e+00 , 2.81289844042620e+00 ), ( -2.67846005853101e+00 , 2.63639340040332e+00 , 2.35893527799379e+00 ), ( -3.79488408376771e+00 , 1.82427471834219e+00 , 2.00553854828854e+00 ), ( -3.36207299177903e+00 , 8.75851608815310e-01 , 8.21469624610845e-01 ), ( -4.25970519633382e+00 , 1.05112692742183e+00 , 3.23029437542200e+00 ), ( -5.48205487497069e+00 , 7.64253587136305e-01 , 3.33686201327005e+00 ), ( -3.36966131575411e+00 , 7.24816832000888e-01 , 4.17880261487107e+00 ), ( -3.67207461868132e+00 , 7.98819122703938e-02 , 5.47420527196600e+00 ), ( -2.38493540889624e+00 , -3.22269513423801e-01 , 6.13950212616605e+00 ), ( -4.47466027138304e+00 , 9.24168826467613e-01 , 6.42215542008482e+00 ), ( -5.36261681826659e+00 , 5.79896591202222e-01 , 7.20749397034283e+00 ), ( -6.30136810957071e+00 , 3.62863215113119e+00 , 6.75199664585806e+00 ), ( -6.99291556511097e+00 , 4.29626870478854e+00 , 7.50509315120895e+00 ), ( -6.66170596291076e+00 , 3.16206566291018e+00 , 5.52233572516693e+00 ), ( -4.10889386711924e+00 , 2.25260742398120e+00 , 6.39175665473791e+00 ), ( -4.81482104509748e+00 , 3.27289024772811e+00 , 7.25500513526501e+00 ), ( -4.03435454731309e+00 , 4.55168732224255e+00 , 7.27146621538718e+00 ) } colvars: Step 28, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 28, atom_groups_ids[size = 0] = @@ -3567,162 +5722,301 @@ colvars: Collective variables module, step no. 28 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.96949879926448e-01 , -1.04029858363134e-02 , 9.54836397870000e-01 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 , 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 , 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 , 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 , 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 , 3.85937142086407e+00 , 3.65476800818372e+00 , 2.03242241887767e+00 , 2.80520731119718e+00 , 4.16980990587374e+00 , 2.44577776086260e+00 , 3.92168837067129e+00 , 3.20513239434971e+00 , 7.37110387602193e-01 , 2.74551095179179e+00 , 3.04637900756662e+00 , -7.83395650577801e-02 , 3.10651351184068e+00 , 2.65802010971575e+00 , -1.53820581896094e+00 , 1.55291908343130e+00 , 2.18526376293626e+00 , 4.23646231165986e-01 , 3.97023085359059e-01 , 2.61653681210940e+00 , 4.71528039126549e-01 , 2.07408053148835e+00 , 1.14713474881058e+00 , 1.04385983224942e+00 , 1.19955193319812e+00 , 1.24564427667697e-01 , 1.69227225709674e+00 , 2.07553838430586e+00 , -1.09189218971752e+00 , 2.03601799284642e+00 , 5.74823989510068e-01 , 6.17290818940561e-01 , 2.96300100013889e+00 , -5.83898258154936e-01 , 3.54630202666306e-01 , 3.17338193171358e+00 , 1.29020966581429e+00 , 1.37479271877028e+00 , 3.74551657544280e+00 , 8.57517755667383e-01 , 1.98097267107643e+00 , 5.03021891991004e+00 , 2.10406883090063e+00 , 2.74847213498538e+00 , 5.72218933392951e+00 , -3.53830914026017e-01 , 2.90422784614850e+00 , 4.96357786386462e+00 , -1.11639515743135e+00 , 3.06805024433165e+00 , 5.87851704282217e+00 , -5.42819948952781e-01 , 3.50974182912348e+00 , 3.79836330023223e+00 , -1.48379373747290e+00 , 4.49409089265994e+00 , 3.41337438050243e+00 , -7.25068428095970e-01 , 5.43094844567604e+00 , 2.47504725896066e+00 , -2.74419589737474e+00 , 3.94343705131208e+00 , 2.81527629901103e+00 , -3.80764989378887e+00 , 4.55386775866711e+00 , 2.81289844042620e+00 , -2.67846005853101e+00 , 2.63639340040332e+00 , 2.35893527799379e+00 , -3.79488408376771e+00 , 1.82427471834219e+00 , 2.00553854828854e+00 , -3.36207299177903e+00 , 8.75851608815310e-01 , 8.21469624610845e-01 , -4.25970519633382e+00 , 1.05112692742183e+00 , 3.23029437542200e+00 , -5.48205487497069e+00 , 7.64253587136305e-01 , 3.33686201327005e+00 , -3.36966131575411e+00 , 7.24816832000888e-01 , 4.17880261487107e+00 , -3.67207461868132e+00 , 7.98819122703938e-02 , 5.47420527196600e+00 , -2.38493540889624e+00 , -3.22269513423801e-01 , 6.13950212616605e+00 , -4.47466027138304e+00 , 9.24168826467613e-01 , 6.42215542008482e+00 , -5.36261681826659e+00 , 5.79896591202222e-01 , 7.20749397034283e+00 , -6.30136810957071e+00 , 3.62863215113119e+00 , 6.75199664585806e+00 , -6.99291556511097e+00 , 4.29626870478854e+00 , 7.50509315120895e+00 , -6.66170596291076e+00 , 3.16206566291018e+00 , 5.52233572516693e+00 , -4.10889386711924e+00 , 2.25260742398120e+00 , 6.39175665473791e+00 , -4.81482104509748e+00 , 3.27289024772811e+00 , 7.25500513526501e+00 , -4.03435454731309e+00 , 4.55168732224255e+00 , 7.27146621538718e+00 ). +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.95501027381301e-01 , -1.01866880614680e-02 , 9.55288110573420e-01 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.96949879926448e-01 , -1.04029858363134e-02 , 9.54836397870000e-01 ). +colvars: Colvar "one" has value ( -2.95501027381301e-01 , -1.01866880614680e-02 , 9.55288110573420e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 , 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 , 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 , 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 , 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 , 3.85937142086407e+00 , 3.65476800818372e+00 , 2.03242241887767e+00 , 2.80520731119718e+00 , 4.16980990587374e+00 , 2.44577776086260e+00 , 3.92168837067129e+00 , 3.20513239434971e+00 , 7.37110387602193e-01 , 2.74551095179179e+00 , 3.04637900756662e+00 , -7.83395650577801e-02 , 3.10651351184068e+00 , 2.65802010971575e+00 , -1.53820581896094e+00 , 1.55291908343130e+00 , 2.18526376293626e+00 , 4.23646231165986e-01 , 3.97023085359059e-01 , 2.61653681210940e+00 , 4.71528039126549e-01 , 2.07408053148835e+00 , 1.14713474881058e+00 , 1.04385983224942e+00 , 1.19955193319812e+00 , 1.24564427667697e-01 , 1.69227225709674e+00 , 2.07553838430586e+00 , -1.09189218971752e+00 , 2.03601799284642e+00 , 5.74823989510068e-01 , 6.17290818940561e-01 , 2.96300100013889e+00 , -5.83898258154936e-01 , 3.54630202666306e-01 , 3.17338193171358e+00 , 1.29020966581429e+00 , 1.37479271877028e+00 , 3.74551657544280e+00 , 8.57517755667383e-01 , 1.98097267107643e+00 , 5.03021891991004e+00 , 2.10406883090063e+00 , 2.74847213498538e+00 , 5.72218933392951e+00 , -3.53830914026017e-01 , 2.90422784614850e+00 , 4.96357786386462e+00 , -1.11639515743135e+00 , 3.06805024433165e+00 , 5.87851704282217e+00 , -5.42819948952781e-01 , 3.50974182912348e+00 , 3.79836330023223e+00 , -1.48379373747290e+00 , 4.49409089265994e+00 , 3.41337438050243e+00 , -7.25068428095970e-01 , 5.43094844567604e+00 , 2.47504725896066e+00 , -2.74419589737474e+00 , 3.94343705131208e+00 , 2.81527629901103e+00 , -3.80764989378887e+00 , 4.55386775866711e+00 , 2.81289844042620e+00 , -2.67846005853101e+00 , 2.63639340040332e+00 , 2.35893527799379e+00 , -3.79488408376771e+00 , 1.82427471834219e+00 , 2.00553854828854e+00 , -3.36207299177903e+00 , 8.75851608815310e-01 , 8.21469624610845e-01 , -4.25970519633382e+00 , 1.05112692742183e+00 , 3.23029437542200e+00 , -5.48205487497069e+00 , 7.64253587136305e-01 , 3.33686201327005e+00 , -3.36966131575411e+00 , 7.24816832000888e-01 , 4.17880261487107e+00 , -3.67207461868132e+00 , 7.98819122703938e-02 , 5.47420527196600e+00 , -2.38493540889624e+00 , -3.22269513423801e-01 , 6.13950212616605e+00 , -4.47466027138304e+00 , 9.24168826467613e-01 , 6.42215542008482e+00 , -5.36261681826659e+00 , 5.79896591202222e-01 , 7.20749397034283e+00 , -6.30136810957071e+00 , 3.62863215113119e+00 , 6.75199664585806e+00 , -6.99291556511097e+00 , 4.29626870478854e+00 , 7.50509315120895e+00 , -6.66170596291076e+00 , 3.16206566291018e+00 , 5.52233572516693e+00 , -4.10889386711924e+00 , 2.25260742398120e+00 , 6.39175665473791e+00 , -4.81482104509748e+00 , 3.27289024772811e+00 , 7.25500513526501e+00 , -4.03435454731309e+00 , 4.55168732224255e+00 , 7.27146621538718e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.457 , 2.15986 , -15.1931 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.6912 , 6.56912 , 13.1382 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.457 , 2.15986 , -15.1931 ) to colvar "one". -colvars: Adding total bias energy: 44.1777 +colvars: Adding biasing force ( 65.6912 , 6.56912 , 13.1382 ) to colvar "one". +colvars: Adding total bias energy: 56.0388 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.457 , 2.15986 , -15.1931 ) +colvars: Force to be applied: ( 65.6912 , 6.56912 , 13.1382 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.92886 , -0.524915 , -1.42221 ) -colvars: ( -4.2265 , -0.450114 , -1.21955 ) -colvars: ( -4.2265 , -0.450114 , -1.21955 ) -colvars: ( -5.62981 , -0.599565 , -1.62447 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.19244 , -0.550995 , -1.4898 ) +colvars: ( -4.45251 , -0.472478 , -1.2775 ) +colvars: ( -4.45251 , -0.472478 , -1.2775 ) +colvars: ( -5.93088 , -0.629354 , -1.70167 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.888032 , 0.196029 , 0.610784 ) -colvars: ( 0.769705 , 0.266323 , 0.634369 ) -colvars: ( 0.753524 , 0.259486 , 0.61604 ) -colvars: ( 0.65927 , 0.266753 , 0.57098 ) -colvars: ( 0.647515 , 0.200333 , 0.477142 ) -colvars: ( 0.573849 , 0.343527 , 0.622111 ) -colvars: ( 0.468022 , 0.357157 , 0.578685 ) -colvars: ( 0.392296 , 0.453916 , 0.661616 ) -colvars: ( 0.387079 , 0.31259 , 0.473415 ) -colvars: ( 0.352842 , 0.27099 , 0.39908 ) -colvars: ( 0.357762 , 0.317885 , 0.463377 ) -colvars: ( 0.287142 , 0.275029 , 0.366325 ) -colvars: ( 0.260008 , 0.303996 , 0.388569 ) -colvars: ( 0.34886 , 0.177651 , 0.274472 ) -colvars: ( 0.290837 , 0.134293 , 0.184058 ) -colvars: ( 0.470229 , 0.141045 , 0.296791 ) -colvars: ( 0.541952 , 0.0501137 , 0.219177 ) -colvars: ( 0.669961 , 0.0295627 , 0.266379 ) -colvars: ( 0.550776 , 0.0182965 , 0.182597 ) -colvars: ( 0.5352 , -0.0466322 , 0.0885004 ) -colvars: ( 0.571739 , 0.0660664 , 0.25733 ) -colvars: ( 0.570582 , 0.0498437 , 0.235403 ) -colvars: ( 0.606988 , 0.114422 , 0.341103 ) -colvars: ( 0.447725 , 0.0539386 , 0.169623 ) -colvars: ( 0.441123 , -0.00190145 , 0.0926315 ) -colvars: ( 0.346815 , 0.119151 , 0.196634 ) -colvars: ( 0.223722 , 0.127358 , 0.136106 ) -colvars: ( 0.133151 , 0.212663 , 0.195432 ) -colvars: ( 0.195597 , 0.053806 , 0.0234426 ) -colvars: ( 0.147024 , 0.0175533 , -0.0521877 ) -colvars: ( 0.22847 , 0.0285052 , 0.00932752 ) -colvars: ( 0.214367 , -0.0437703 , -0.0935429 ) -colvars: ( 0.248884 , -0.0468944 , -0.0776473 ) -colvars: ( 0.288896 , -0.129316 , -0.162474 ) -colvars: ( 0.245388 , -0.182412 , -0.257242 ) -colvars: ( 0.402916 , -0.144003 , -0.115691 ) -colvars: ( 0.479656 , -0.219119 , -0.169676 ) -colvars: ( 0.609427 , -0.221345 , -0.0974421 ) -colvars: ( 0.433252 , -0.223835 , -0.202728 ) -colvars: ( 0.438783 , -0.291721 , -0.288477 ) -colvars: ( 0.38529 , -0.150933 , -0.134978 ) -colvars: ( 0.332 , -0.144951 , -0.158 ) -colvars: ( 0.315906 , -0.0586135 , -0.054191 ) -colvars: ( 0.210046 , -0.154058 , -0.240555 ) -colvars: ( 0.186105 , -0.196079 , -0.30948 ) -colvars: ( 0.0104534 , -0.200089 , -0.416454 ) -colvars: ( -0.0794907 , -0.218091 , -0.492128 ) -colvars: ( 0.109476 , -0.249528 , -0.423891 ) -colvars: ( 0.12891 , -0.113716 , -0.234681 ) -colvars: ( 0.0108686 , -0.118403 , -0.30918 ) -colvars: ( -0.0772672 , -0.0381642 , -0.255081 ) +colvars: ( 0.934549 , 0.206504 , 0.641555 ) +colvars: ( 0.81011 , 0.280399 , 0.66639 ) +colvars: ( 0.793032 , 0.273262 , 0.647179 ) +colvars: ( 0.693998 , 0.280756 , 0.599764 ) +colvars: ( 0.68163 , 0.210868 , 0.501124 ) +colvars: ( 0.604194 , 0.361456 , 0.653521 ) +colvars: ( 0.492933 , 0.375698 , 0.607876 ) +colvars: ( 0.413321 , 0.477434 , 0.695063 ) +colvars: ( 0.407777 , 0.328791 , 0.497262 ) +colvars: ( 0.371791 , 0.284978 , 0.41911 ) +colvars: ( 0.376895 , 0.3344 , 0.486761 ) +colvars: ( 0.302591 , 0.289303 , 0.384787 ) +colvars: ( 0.274005 , 0.319823 , 0.408224 ) +colvars: ( 0.367478 , 0.1869 , 0.288219 ) +colvars: ( 0.306457 , 0.141245 , 0.19319 ) +colvars: ( 0.495104 , 0.148469 , 0.311653 ) +colvars: ( 0.570515 , 0.0528501 , 0.230048 ) +colvars: ( 0.705113 , 0.0313286 , 0.279648 ) +colvars: ( 0.579844 , 0.019324 , 0.191548 ) +colvars: ( 0.563458 , -0.0489979 , 0.0926362 ) +colvars: ( 0.60194 , 0.0695462 , 0.270064 ) +colvars: ( 0.600775 , 0.0524196 , 0.24697 ) +colvars: ( 0.639108 , 0.120341 , 0.358039 ) +colvars: ( 0.471589 , 0.0566364 , 0.177843 ) +colvars: ( 0.46466 , -0.00213892 , 0.0968931 ) +colvars: ( 0.365462 , 0.125197 , 0.206276 ) +colvars: ( 0.236021 , 0.13375 , 0.142678 ) +colvars: ( 0.140767 , 0.223459 , 0.205081 ) +colvars: ( 0.206402 , 0.0563844 , 0.0242802 ) +colvars: ( 0.155338 , 0.0181912 , -0.0552269 ) +colvars: ( 0.240919 , 0.0298421 , 0.00947681 ) +colvars: ( 0.226045 , -0.0461692 , -0.0986283 ) +colvars: ( 0.262287 , -0.0493725 , -0.08188 ) +colvars: ( 0.304431 , -0.136145 , -0.171126 ) +colvars: ( 0.258669 , -0.192032 , -0.270733 ) +colvars: ( 0.424356 , -0.151547 , -0.121994 ) +colvars: ( 0.505072 , -0.230553 , -0.178785 ) +colvars: ( 0.641553 , -0.232824 , -0.102895 ) +colvars: ( 0.456325 , -0.2356 , -0.21356 ) +colvars: ( 0.462143 , -0.307029 , -0.30371 ) +colvars: ( 0.405929 , -0.158968 , -0.142357 ) +colvars: ( 0.349938 , -0.152762 , -0.166586 ) +colvars: ( 0.333058 , -0.0619757 , -0.0574861 ) +colvars: ( 0.221679 , -0.162411 , -0.253329 ) +colvars: ( 0.196525 , -0.206665 , -0.3258 ) +colvars: ( 0.011691 , -0.210872 , -0.438109 ) +colvars: ( -0.0829034 , -0.229862 , -0.517629 ) +colvars: ( 0.115791 , -0.262792 , -0.445928 ) +colvars: ( 0.136322 , -0.119979 , -0.247101 ) +colvars: ( 0.0121751 , -0.124972 , -0.325374 ) +colvars: ( -0.0805249 , -0.0405837 , -0.268461 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.92886 , 0.524915 , 1.42221 ) -colvars: ( 4.2265 , 0.450114 , 1.21955 ) -colvars: ( 4.2265 , 0.450114 , 1.21955 ) -colvars: ( 5.62981 , 0.599565 , 1.62447 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.19244 , 0.550995 , 1.4898 ) +colvars: ( 4.45251 , 0.472478 , 1.2775 ) +colvars: ( 4.45251 , 0.472478 , 1.2775 ) +colvars: ( 5.93088 , 0.629354 , 1.70167 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.61394 , -0.08116 , -0.364598 ) -colvars: ( -0.5524 , -0.16456 , -0.332368 ) -colvars: ( -0.501359 , -0.142153 , -0.273129 ) -colvars: ( -0.514332 , -0.192314 , -0.303969 ) -colvars: ( -0.504653 , -0.132886 , -0.273149 ) -colvars: ( -0.490642 , -0.285209 , -0.313141 ) -colvars: ( -0.459171 , -0.325945 , -0.29598 ) -colvars: ( -0.438424 , -0.434263 , -0.313583 ) -colvars: ( -0.39595 , -0.290117 , -0.219738 ) -colvars: ( -0.392011 , -0.26463 , -0.206734 ) -colvars: ( -0.345688 , -0.284259 , -0.167157 ) -colvars: ( -0.284844 , -0.246888 , -0.0927553 ) -colvars: ( -0.235245 , -0.261775 , -0.0482031 ) -colvars: ( -0.303619 , -0.142757 , -0.0746565 ) -colvars: ( -0.272626 , -0.113179 , -0.0330162 ) -colvars: ( -0.357116 , -0.0848995 , -0.107872 ) -colvars: ( -0.383087 , 0.0142335 , -0.0987784 ) -colvars: ( -0.432152 , 0.0622684 , -0.131027 ) -colvars: ( -0.42168 , 0.0292414 , -0.132228 ) -colvars: ( -0.410281 , 0.0865596 , -0.100428 ) -colvars: ( -0.466708 , -0.025441 , -0.196882 ) -colvars: ( -0.502111 , -0.0270668 , -0.233032 ) -colvars: ( -0.552826 , -0.0932266 , -0.307474 ) -colvars: ( -0.451058 , -0.057323 , -0.192474 ) -colvars: ( -0.458258 , -0.0128784 , -0.183933 ) -colvars: ( -0.396424 , -0.132232 , -0.16417 ) -colvars: ( -0.33971 , -0.163765 , -0.118378 ) -colvars: ( -0.289716 , -0.254691 , -0.100421 ) -colvars: ( -0.297834 , -0.0901355 , -0.0501647 ) -colvars: ( -0.285261 , -0.0713728 , -0.0308719 ) -colvars: ( -0.27666 , -0.0447125 , -0.0127652 ) -colvars: ( -0.240496 , 0.0308498 , 0.0503938 ) -colvars: ( -0.217812 , 0.0576278 , 0.0826918 ) -colvars: ( -0.284263 , 0.118328 , 0.0374699 ) -colvars: ( -0.257733 , 0.160517 , 0.0791024 ) -colvars: ( -0.35324 , 0.146593 , -0.0218048 ) -colvars: ( -0.401866 , 0.223398 , -0.0433994 ) -colvars: ( -0.472375 , 0.246076 , -0.106196 ) -colvars: ( -0.414778 , 0.203266 , -0.0635194 ) -colvars: ( -0.419291 , 0.26463 , -0.0462717 ) -colvars: ( -0.420448 , 0.115812 , -0.10026 ) -colvars: ( -0.428904 , 0.0852642 , -0.1196 ) -colvars: ( -0.451436 , -0.00901328 , -0.175706 ) -colvars: ( -0.36278 , 0.0739788 , -0.0571654 ) -colvars: ( -0.366695 , 0.100478 , -0.0516932 ) -colvars: ( -0.201121 , 0.107362 , 0.117117 ) -colvars: ( -0.152114 , 0.109311 , 0.167051 ) -colvars: ( -0.226392 , 0.180386 , 0.117647 ) -colvars: ( -0.300087 , 0.0330038 , -0.00871765 ) -colvars: ( -0.233849 , 0.0193583 , 0.0529941 ) -colvars: ( -0.180198 , -0.0643977 , 0.07717 ) +colvars: ( -0.645957 , -0.0855706 , -0.382339 ) +colvars: ( -0.58131 , -0.173249 , -0.348419 ) +colvars: ( -0.527541 , -0.149725 , -0.286148 ) +colvars: ( -0.541388 , -0.202367 , -0.318635 ) +colvars: ( -0.531208 , -0.139849 , -0.286341 ) +colvars: ( -0.516576 , -0.300023 , -0.328217 ) +colvars: ( -0.4836 , -0.342794 , -0.310225 ) +colvars: ( -0.461873 , -0.456682 , -0.328635 ) +colvars: ( -0.417112 , -0.305093 , -0.230183 ) +colvars: ( -0.413023 , -0.278246 , -0.2166 ) +colvars: ( -0.364189 , -0.298962 , -0.174903 ) +colvars: ( -0.300187 , -0.259646 , -0.0967859 ) +colvars: ( -0.247958 , -0.27534 , -0.0499097 ) +colvars: ( -0.319862 , -0.15015 , -0.0778664 ) +colvars: ( -0.287301 , -0.119007 , -0.0341909 ) +colvars: ( -0.376025 , -0.089355 , -0.112766 ) +colvars: ( -0.403268 , 0.0148817 , -0.103298 ) +colvars: ( -0.454747 , 0.065329 , -0.137151 ) +colvars: ( -0.443929 , 0.0307098 , -0.138518 ) +colvars: ( -0.431942 , 0.0910107 , -0.105194 ) +colvars: ( -0.491351 , -0.0267805 , -0.206413 ) +colvars: ( -0.528669 , -0.0284432 , -0.244453 ) +colvars: ( -0.582057 , -0.0980181 , -0.322603 ) +colvars: ( -0.475084 , -0.0601962 , -0.201887 ) +colvars: ( -0.482685 , -0.0134243 , -0.192999 ) +colvars: ( -0.417685 , -0.138953 , -0.17209 ) +colvars: ( -0.358134 , -0.172057 , -0.124013 ) +colvars: ( -0.305606 , -0.267669 , -0.105058 ) +colvars: ( -0.314046 , -0.0946219 , -0.0524217 ) +colvars: ( -0.300883 , -0.0748439 , -0.0322276 ) +colvars: ( -0.291667 , -0.0469035 , -0.0131112 ) +colvars: ( -0.253575 , 0.0325556 , 0.0531774 ) +colvars: ( -0.229602 , 0.0606559 , 0.0871603 ) +colvars: ( -0.299569 , 0.124552 , 0.0395031 ) +colvars: ( -0.271685 , 0.168949 , 0.0831651 ) +colvars: ( -0.372063 , 0.154243 , -0.0227692 ) +colvars: ( -0.423174 , 0.235015 , -0.0455429 ) +colvars: ( -0.497253 , 0.258814 , -0.111487 ) +colvars: ( -0.436869 , 0.213908 , -0.0667411 ) +colvars: ( -0.441615 , 0.278461 , -0.0487097 ) +colvars: ( -0.442934 , 0.121971 , -0.105293 ) +colvars: ( -0.451945 , 0.0899081 , -0.125659 ) +colvars: ( -0.475725 , -0.00922189 , -0.18453 ) +colvars: ( -0.382473 , 0.0780912 , -0.0601077 ) +colvars: ( -0.386644 , 0.106001 , -0.0544383 ) +colvars: ( -0.212447 , 0.11323 , 0.122942 ) +colvars: ( -0.160958 , 0.115321 , 0.175356 ) +colvars: ( -0.238901 , 0.189969 , 0.123491 ) +colvars: ( -0.316543 , 0.0349987 , -0.00915565 ) +colvars: ( -0.246943 , 0.0206943 , 0.0556451 ) +colvars: ( -0.190557 , -0.0673832 , 0.0811333 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 28. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 28. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 28, atoms_new_colvar_forces = { ( -4.65476812955759e+00 , -4.10045996947463e-01 , -1.17602627053731e+00 ), ( -4.00919047605904e+00 , -3.48351339099113e-01 , -9.17545331736287e-01 ), ( -4.08155711778757e+00 , -3.75675728317876e-01 , -9.52536146563627e-01 ), ( -5.48695296182584e+00 , -5.32118393030834e-01 , -1.42047838166992e+00 ), ( 2.52165400875046e-01 , 1.17333527735657e-01 , 3.42911262032302e-01 ), ( 5.01206675503852e+00 , 5.83232939253654e-01 , 1.73118138788782e+00 ), ( 4.23534680006229e+00 , 4.81326584524782e-01 , 1.50225204283461e+00 ), ( -4.61288191429134e-02 , 1.96528860056323e-02 , 3.48032787079061e-01 ), ( 4.21762464441680e+00 , 4.72587014941585e-01 , 1.47322332645969e+00 ), ( 5.59064587845707e+00 , 6.05925444067054e-01 , 1.81681779345799e+00 ), ( 1.20738874940310e-02 , 3.36258089171626e-02 , 2.96220005207911e-01 ), ( 2.29798203928566e-03 , 2.81405175212899e-02 , 2.73570080702721e-01 ), ( 2.47629158927604e-02 , 4.22217640943423e-02 , 3.40365812986325e-01 ), ( 4.52410721441125e-02 , 3.48938705627658e-02 , 1.99815318408579e-01 ), ( 1.82112042517809e-02 , 2.11139811399131e-02 , 1.51042308591674e-01 ), ( 1.13113824739186e-01 , 5.61457566187413e-02 , 1.88919585237016e-01 ), ( 1.58864369542766e-01 , 6.43471729409368e-02 , 1.20398624464579e-01 ), ( 2.37808950079305e-01 , 9.18311328291469e-02 , 1.35351524138479e-01 ), ( 1.29095661454724e-01 , 4.75378728697175e-02 , 5.03683180846414e-02 ), ( 1.24919473592923e-01 , 3.99273648323862e-02 , -1.19278687483283e-02 ), ( 1.05031737468460e-01 , 4.06253752835865e-02 , 6.04476526193786e-02 ), ( 6.84713480458817e-02 , 2.27769076335840e-02 , 2.37089042450869e-03 ), ( 5.41627061514108e-02 , 2.11956434725954e-02 , 3.36289132160833e-02 ), ( -3.33235988143127e-03 , -3.38439301768139e-03 , -2.28517792585316e-02 ), ( -1.71354304230992e-02 , -1.47798435189928e-02 , -9.13012720837809e-02 ), ( -4.96095178023854e-02 , -1.30810065829210e-02 , 3.24637873151127e-02 ), ( -1.15988281381791e-01 , -3.64067874593997e-02 , 1.77279658818581e-02 ), ( -1.56564834085649e-01 , -4.20278731472885e-02 , 9.50116798854930e-02 ), ( -1.02237003830339e-01 , -3.63295082040771e-02 , -2.67221132056988e-02 ), ( -1.38237108558767e-01 , -5.38194321132817e-02 , -8.30595184101709e-02 ), ( -4.81895154744584e-02 , -1.62072680224376e-02 , -3.43772607775143e-03 ), ( -2.61294590358489e-02 , -1.29205333531506e-02 , -4.31490010360505e-02 ), ( 3.10722386606848e-02 , 1.07333928007365e-02 , 5.04450116982869e-03 ), ( 4.63316821339083e-03 , -1.09876373558418e-02 , -1.25004344944768e-01 ), ( -1.23449908203879e-02 , -2.18953257600948e-02 , -1.78139518761754e-01 ), ( 4.96755595934390e-02 , 2.58916802575213e-03 , -1.37495704434840e-01 ), ( 7.77895977856998e-02 , 4.27833880291345e-03 , -2.13075808840435e-01 ), ( 1.37051955652804e-01 , 2.47311820808655e-02 , -2.03638146602475e-01 ), ( 1.84744211386928e-02 , -2.05695887295308e-02 , -2.66247194822574e-01 ), ( 1.94914637038850e-02 , -2.70916913745008e-02 , -3.34748408375694e-01 ), ( -3.51576903850040e-02 , -3.51202989156158e-02 , -2.35237322598323e-01 ), ( -9.69042283388186e-02 , -5.96866435063923e-02 , -2.77599946885010e-01 ), ( -1.35530400030107e-01 , -6.76267423189185e-02 , -2.29897428265782e-01 ), ( -1.52733628638114e-01 , -8.00787590584912e-02 , -2.97720470395002e-01 ), ( -1.80590177992081e-01 , -9.56001638513193e-02 , -3.61172824965231e-01 ), ( -1.90667631628592e-01 , -9.27278108950850e-02 , -2.99337209654511e-01 ), ( -2.31604641098833e-01 , -1.08780110183448e-01 , -3.25077189622499e-01 ), ( -1.16916318483069e-01 , -6.91414811356912e-02 , -3.06243655941052e-01 ), ( -1.71176778451799e-01 , -8.07123558763408e-02 , -2.43398496883655e-01 ), ( -2.22979978003921e-01 , -9.90450628986568e-02 , -2.56185743873434e-01 ), ( -2.57465537777492e-01 , -1.02561872280358e-01 , -1.77910742891168e-01 ) } +colvars: Step 28, atoms_new_colvar_forces = { ( -4.90384292994753e+00 , -4.30061181581498e-01 , -1.23057952812698e+00 ), ( -4.22371186491589e+00 , -3.65328134592081e-01 , -9.59528374484244e-01 ), ( -4.29990290450085e+00 , -3.94089117624900e-01 , -9.96370093803767e-01 ), ( -5.78045406497317e+00 , -5.58335320147910e-01 , -1.48688424495571e+00 ), ( 2.65491211108552e-01 , 1.23537620122648e-01 , 3.61030596854383e-01 ), ( 5.28005307439269e+00 , 6.12427671368205e-01 , 1.81509982664923e+00 ), ( 4.46184518444030e+00 , 5.05381939262143e-01 , 1.57515106003945e+00 ), ( -4.85511434600487e-02 , 2.07523457083486e-02 , 3.66427779977786e-01 ), ( 4.44317734724211e+00 , 4.96175596962890e-01 , 1.54457853589311e+00 ), ( 5.88964346729490e+00 , 6.36085627200129e-01 , 1.90417721308489e+00 ), ( 1.27065569628440e-02 , 3.54379029990088e-02 , 3.11858139856113e-01 ), ( 2.40460741769399e-03 , 2.96572082798891e-02 , 2.88001274027708e-01 ), ( 2.60464416327941e-02 , 4.44832211558429e-02 , 3.58314100587555e-01 ), ( 4.76164130373470e-02 , 3.67501453875118e-02 , 2.10352464448447e-01 ), ( 1.91552247804718e-02 , 2.22387880855930e-02 , 1.58999439605174e-01 ), ( 1.19079038755758e-01 , 5.91136525176453e-02 , 1.98887416976434e-01 ), ( 1.67247634293701e-01 , 6.77318328512975e-02 , 1.26749993997087e-01 ), ( 2.50365492999829e-01 , 9.66576024456339e-02 , 1.42497236290738e-01 ), ( 1.35914831022483e-01 , 5.00338541708416e-02 , 5.30301367535333e-02 ), ( 1.31516340541352e-01 , 4.20128478226181e-02 , -1.25578957164632e-02 ), ( 1.10588937804259e-01 , 4.27656964481660e-02 , 6.36515136061283e-02 ), ( 7.21056067747657e-02 , 2.39763933217968e-02 , 2.51627788784559e-03 ), ( 5.70506452097048e-02 , 2.23224487984691e-02 , 3.54353290813819e-02 ), ( -3.49498224547207e-03 , -3.55980944662710e-03 , -2.40438716129163e-02 ), ( -1.80251213873387e-02 , -1.55632398454448e-02 , -9.61061720210136e-02 ), ( -5.22228202101327e-02 , -1.37559842833952e-02 , 3.41854584073593e-02 ), ( -1.22113199988620e-01 , -3.83069555546568e-02 , 1.86646247074351e-02 ), ( -1.64838877506732e-01 , -4.42101195798790e-02 , 1.00022815522024e-01 ), ( -1.07643528114771e-01 , -3.82374689828629e-02 , -2.81415013149803e-02 ), ( -1.45545107039339e-01 , -5.66527208265858e-02 , -8.74544759496076e-02 ), ( -5.07481347952446e-02 , -1.70614277419447e-02 , -3.63442572658323e-03 ), ( -2.75303586094378e-02 , -1.36135315070125e-02 , -4.54508915928700e-02 ), ( 3.26854205876072e-02 , 1.12833999575029e-02 , 5.28033027176517e-03 ), ( 4.86257228490999e-03 , -1.15925166900537e-02 , -1.31622750055179e-01 ), ( -1.30158458610466e-02 , -2.30822092133307e-02 , -1.87568050888589e-01 ), ( 5.22929541320235e-02 , 2.69594482492658e-03 , -1.44763519972368e-01 ), ( 8.18983854683275e-02 , 4.46209863263042e-03 , -2.24327679868213e-01 ), ( 1.44299232500828e-01 , 2.59900880514667e-02 , -2.14381841188795e-01 ), ( 1.94559709679941e-02 , -2.16928875058797e-02 , -2.80301373302201e-01 ), ( 2.05273767674185e-02 , -2.85686888289193e-02 , -3.52419464644292e-01 ), ( -3.70047024666399e-02 , -3.69969429078039e-02 , -2.47649729164660e-01 ), ( -1.02007495861232e-01 , -6.28538507615143e-02 , -2.92244523767052e-01 ), ( -1.42667681901288e-01 , -7.11975564555364e-02 , -2.42016381025123e-01 ), ( -1.60793536960711e-01 , -8.43197125593010e-02 , -3.13436781697989e-01 ), ( -1.90119143852607e-01 , -1.00663821186063e-01 , -3.80237852238786e-01 ), ( -2.00756150443214e-01 , -9.76416131339598e-02 , -3.15166820975150e-01 ), ( -2.43861219043207e-01 , -1.14540863153326e-01 , -3.42272967562807e-01 ), ( -1.23109579423653e-01 , -7.28230655412529e-02 , -3.22437483096700e-01 ), ( -1.80220249912241e-01 , -8.49803842830974e-02 , -2.56256592503782e-01 ), ( -2.34767687699287e-01 , -1.04277862695358e-01 , -2.69728540895261e-01 ), ( -2.71081637300971e-01 , -1.07966939745010e-01 , -1.87327736373501e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 28, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3760,10 +6054,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 29, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 29, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 29, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 29, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 29, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 29, atoms_positions[size = 51] = { ( 8.24496138808168e+00 , 4.31696617009711e-02 , -7.26144896093100e-01 ), ( 6.84232247426870e+00 , -5.84524722450423e-01 , -5.28573266826814e-01 ), ( 6.13164468639699e+00 , -3.73699905659251e-01 , 8.00548954494365e-01 ), ( 4.90914110199627e+00 , -1.47792375751190e-01 , 7.43506777214514e-01 ), ( 7.00631140322438e+00 , -2.06805294892657e+00 , -8.83236646834291e-01 ), ( 6.81263376358257e+00 , -2.88542671960002e-01 , 1.96371574058638e+00 ), ( 6.10578932678212e+00 , -2.19803667256985e-01 , 3.17121049962957e+00 ), ( 7.13166755204546e+00 , -3.44061232085154e-01 , 4.38017766658372e+00 ), ( 5.32993294139157e+00 , 1.06925331121861e+00 , 3.36870511542620e+00 ), ( 4.18037027744364e+00 , 1.00715570332890e+00 , 3.76942404051173e+00 ), ( 5.84343425506103e+00 , 2.25308779944875e+00 , 2.97407534749559e+00 ), ( 5.16670178200228e+00 , 3.55706968834576e+00 , 2.89332095680574e+00 ), ( 6.30661364560706e+00 , 4.47800974454676e+00 , 2.29189326246384e+00 ), ( 3.85894836095718e+00 , 3.64925687156038e+00 , 2.02898673489838e+00 ), ( 2.80982764874967e+00 , 4.16917318049284e+00 , 2.44071659063784e+00 ), ( 3.91666894951431e+00 , 3.19850135757316e+00 , 7.40116628974484e-01 ), ( 2.75367085851993e+00 , 3.05602432092180e+00 , -7.52655643942308e-02 ), ( 3.11203335116034e+00 , 2.65444460648948e+00 , -1.54076284315453e+00 ), ( 1.55010470025782e+00 , 2.19385032442025e+00 , 4.23680650168264e-01 ), ( 4.03023766497359e-01 , 2.61692523559002e+00 , 4.65935578917440e-01 ), ( 2.06998946133020e+00 , 1.14537990473560e+00 , 1.04431888027783e+00 ), ( 1.21098258133945e+00 , 1.29037058993668e-01 , 1.68805594186284e+00 ), ( 2.07930062216384e+00 , -1.09233521711463e+00 , 2.03798648300783e+00 ), ( 5.75126953005429e-01 , 6.16581675883185e-01 , 2.96045522085957e+00 ), ( -5.85307758248492e-01 , 3.55388145161849e-01 , 3.17726424655820e+00 ), ( 1.28816079063222e+00 , 1.38217698582714e+00 , 3.74914636804183e+00 ), ( 8.64291464259602e-01 , 1.98010175305726e+00 , 5.03175022927395e+00 ), ( 2.09839475624342e+00 , 2.75346067402022e+00 , 5.72407913019983e+00 ), ( -3.55909994471641e-01 , 2.90254232076419e+00 , 4.95956773823758e+00 ), ( -1.11561987567268e+00 , 3.06859309354974e+00 , 5.88015681122639e+00 ), ( -5.43627798137215e-01 , 3.50875435559019e+00 , 3.78939503753594e+00 ), ( -1.47622161559560e+00 , 4.48866909636002e+00 , 3.41427878800857e+00 ), ( -7.31785633997068e-01 , 5.43423662577483e+00 , 2.47676181149411e+00 ), ( -2.74498543237162e+00 , 3.94542770599967e+00 , 2.80125835034849e+00 ), ( -3.80612156567671e+00 , 4.55962236672602e+00 , 2.81318360675681e+00 ), ( -2.68469459647624e+00 , 2.63423255024100e+00 , 2.35681928446616e+00 ), ( -3.79799201892991e+00 , 1.82595810604839e+00 , 2.00583757586995e+00 ), ( -3.35983872216255e+00 , 8.76205411708678e-01 , 8.14507318830490e-01 ), ( -4.25481381552370e+00 , 1.04654833296319e+00 , 3.23575420221390e+00 ), ( -5.47697540325327e+00 , 7.58370076846867e-01 , 3.33857794941254e+00 ), ( -3.37050768005777e+00 , 7.27108621774589e-01 , 4.17294251406612e+00 ), ( -3.67068236925121e+00 , 8.03484199349822e-02 , 5.47842770098067e+00 ), ( -2.38130405574370e+00 , -3.19228682540857e-01 , 6.13543053245953e+00 ), ( -4.47852896853978e+00 , 9.22046457306445e-01 , 6.42144130767386e+00 ), ( -5.36111030389346e+00 , 5.76037218940877e-01 , 7.20401337907534e+00 ), ( -6.30585224909303e+00 , 3.62667918534697e+00 , 6.75268695987722e+00 ), ( -6.99867967050315e+00 , 4.29714524440254e+00 , 7.50869529813025e+00 ), ( -6.65086956854691e+00 , 3.16195575138039e+00 , 5.52768532598170e+00 ), ( -4.10731209823951e+00 , 2.25417776325648e+00 , 6.39436352277790e+00 ), ( -4.81574900061354e+00 , 3.27878997363146e+00 , 7.25183376897882e+00 ), ( -4.02722822094389e+00 , 4.55630501417280e+00 , 7.27236308788831e+00 ) } +colvars: Step 29, atoms_positions[size = 51] = { ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 ), ( 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 ), ( 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 ), ( 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 ), ( 7.00574000274244e+00 , -2.06829116643861e+00 , -8.83119811461982e-01 ), ( 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 ), ( 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 ), ( 7.13320400449730e+00 , -3.44298734592438e-01 , 4.38138305680023e+00 ), ( 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 ), ( 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 ), ( 5.84483325162435e+00 , 2.25366187654745e+00 , 2.97407896818342e+00 ), ( 5.16683406263612e+00 , 3.55710110763794e+00 , 2.89359751215032e+00 ), ( 6.30656262174781e+00 , 4.47811840330492e+00 , 2.29216448789625e+00 ), ( 3.85900015836979e+00 , 3.64919255486691e+00 , 2.02919404735743e+00 ), ( 2.80985216815857e+00 , 4.16916506605627e+00 , 2.44083999838906e+00 ), ( 3.91677382204270e+00 , 3.19853200587872e+00 , 7.40288243836124e-01 ), ( 2.75380836420530e+00 , 3.05607818870335e+00 , -7.51581894515900e-02 ), ( 3.11221705383647e+00 , 2.65451308061572e+00 , -1.54064705756131e+00 ), ( 1.55022078277182e+00 , 2.19389175197648e+00 , 4.23731258073612e-01 ), ( 4.03133879451812e-01 , 2.61695797841092e+00 , 4.65936542913617e-01 ), ( 2.07008191781880e+00 , 1.14541073584410e+00 , 1.04438132515448e+00 ), ( 1.21104098873384e+00 , 1.29064314915337e-01 , 1.68806278825048e+00 ), ( 2.07938437129022e+00 , -1.09226055507971e+00 , 2.03807229463835e+00 ), ( 5.75169096535490e-01 , 6.16577762840044e-01 , 2.96044663850816e+00 ), ( -5.85292110472713e-01 , 3.55388149199515e-01 , 3.17720325125777e+00 ), ( 1.28825494086657e+00 , 1.38214738369001e+00 , 3.74916833208051e+00 ), ( 8.64233237372221e-01 , 1.98005512142267e+00 , 5.03174948282925e+00 ), ( 2.09827944546896e+00 , 2.75342470994007e+00 , 5.72413575586123e+00 ), ( -3.55992882575887e-01 , 2.90250467361778e+00 , 4.95954123194611e+00 ), ( -1.11574172694153e+00 , 3.06855139255186e+00 , 5.88010232961502e+00 ), ( -5.43668601286061e-01 , 3.50874101319027e+00 , 3.78937424004920e+00 ), ( -1.47624956703860e+00 , 4.48866017004579e+00 , 3.41423298783339e+00 ), ( -7.31770235550961e-01 , 5.43423902569644e+00 , 2.47675782651417e+00 ), ( -2.74498269317940e+00 , 3.94541871314426e+00 , 2.80114869378689e+00 ), ( -3.80612628970205e+00 , 4.55960025539404e+00 , 2.81304026673475e+00 ), ( -2.68465775625360e+00 , 2.63423256162810e+00 , 2.35669571741840e+00 ), ( -3.79793299657600e+00 , 1.82595829823249e+00 , 2.00564398238562e+00 ), ( -3.35973166964488e+00 , 8.76210294949400e-01 , 8.14326802538322e-01 ), ( -4.25479988283804e+00 , 1.04652539212958e+00 , 3.23552373700253e+00 ), ( -5.47696169161307e+00 , 7.58343767602588e-01 , 3.33830903166301e+00 ), ( -3.37052998783529e+00 , 7.27070269086146e-01 , 4.17273383545135e+00 ), ( -3.67076853636612e+00 , 8.02890411004126e-02 , 5.47818496853563e+00 ), ( -2.38141785804304e+00 , -3.19276966689693e-01 , 6.13524375348765e+00 ), ( -4.47866085407106e+00 , 9.21976672545687e-01 , 6.42118098012691e+00 ), ( -5.36125694717558e+00 , 5.75956580523933e-01 , 7.20372858904930e+00 ), ( -6.30602052652239e+00 , 3.62659966444639e+00 , 6.75243212712343e+00 ), ( -6.99886722165190e+00 , 4.29705609045011e+00 , 7.50843520996675e+00 ), ( -6.65099617909420e+00 , 3.16189006812619e+00 , 5.52741041258270e+00 ), ( -4.10745542008092e+00 , 2.25411177669687e+00 , 6.39414571125951e+00 ), ( -4.81593837698548e+00 , 3.27869885909781e+00 , 7.25161049228686e+00 ), ( -4.02743393174070e+00 , 4.55621888094300e+00 , 7.27220719639921e+00 ) } colvars: Step 29, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 29, atom_groups_ids[size = 0] = @@ -3781,162 +6075,301 @@ colvars: Collective variables module, step no. 29 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.94448500277034e-01 , -1.14886070422289e-02 , 9.55598290388192e-01 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating gradients of colvar "group2". colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.95963250214387e-01 , -1.17171742424022e-02 , 9.55127458693503e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 7.00574000274244e+00 , -2.06829116643861e+00 , -8.83119811461982e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 , 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 7.13320400449730e+00 , -3.44298734592438e-01 , 4.38138305680023e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 , 5.84483325162435e+00 , 2.25366187654745e+00 , 2.97407896818342e+00 , 5.16683406263612e+00 , 3.55710110763794e+00 , 2.89359751215032e+00 , 6.30656262174781e+00 , 4.47811840330492e+00 , 2.29216448789625e+00 , 3.85900015836979e+00 , 3.64919255486691e+00 , 2.02919404735743e+00 , 2.80985216815857e+00 , 4.16916506605627e+00 , 2.44083999838906e+00 , 3.91677382204270e+00 , 3.19853200587872e+00 , 7.40288243836124e-01 , 2.75380836420530e+00 , 3.05607818870335e+00 , -7.51581894515900e-02 , 3.11221705383647e+00 , 2.65451308061572e+00 , -1.54064705756131e+00 , 1.55022078277182e+00 , 2.19389175197648e+00 , 4.23731258073612e-01 , 4.03133879451812e-01 , 2.61695797841092e+00 , 4.65936542913617e-01 , 2.07008191781880e+00 , 1.14541073584410e+00 , 1.04438132515448e+00 , 1.21104098873384e+00 , 1.29064314915337e-01 , 1.68806278825048e+00 , 2.07938437129022e+00 , -1.09226055507971e+00 , 2.03807229463835e+00 , 5.75169096535490e-01 , 6.16577762840044e-01 , 2.96044663850816e+00 , -5.85292110472713e-01 , 3.55388149199515e-01 , 3.17720325125777e+00 , 1.28825494086657e+00 , 1.38214738369001e+00 , 3.74916833208051e+00 , 8.64233237372221e-01 , 1.98005512142267e+00 , 5.03174948282925e+00 , 2.09827944546896e+00 , 2.75342470994007e+00 , 5.72413575586123e+00 , -3.55992882575887e-01 , 2.90250467361778e+00 , 4.95954123194611e+00 , -1.11574172694153e+00 , 3.06855139255186e+00 , 5.88010232961502e+00 , -5.43668601286061e-01 , 3.50874101319027e+00 , 3.78937424004920e+00 , -1.47624956703860e+00 , 4.48866017004579e+00 , 3.41423298783339e+00 , -7.31770235550961e-01 , 5.43423902569644e+00 , 2.47675782651417e+00 , -2.74498269317940e+00 , 3.94541871314426e+00 , 2.80114869378689e+00 , -3.80612628970205e+00 , 4.55960025539404e+00 , 2.81304026673475e+00 , -2.68465775625360e+00 , 2.63423256162810e+00 , 2.35669571741840e+00 , -3.79793299657600e+00 , 1.82595829823249e+00 , 2.00564398238562e+00 , -3.35973166964488e+00 , 8.76210294949400e-01 , 8.14326802538322e-01 , -4.25479988283804e+00 , 1.04652539212958e+00 , 3.23552373700253e+00 , -5.47696169161307e+00 , 7.58343767602588e-01 , 3.33830903166301e+00 , -3.37052998783529e+00 , 7.27070269086146e-01 , 4.17273383545135e+00 , -3.67076853636612e+00 , 8.02890411004126e-02 , 5.47818496853563e+00 , -2.38141785804304e+00 , -3.19276966689693e-01 , 6.13524375348765e+00 , -4.47866085407106e+00 , 9.21976672545687e-01 , 6.42118098012691e+00 , -5.36125694717558e+00 , 5.75956580523933e-01 , 7.20372858904930e+00 , -6.30602052652239e+00 , 3.62659966444639e+00 , 6.75243212712343e+00 , -6.99886722165190e+00 , 4.29705609045011e+00 , 7.50843520996675e+00 , -6.65099617909420e+00 , 3.16189006812619e+00 , 5.52741041258270e+00 , -4.10745542008092e+00 , 2.25411177669687e+00 , 6.39414571125951e+00 , -4.81593837698548e+00 , 3.27869885909781e+00 , 7.25161049228686e+00 , -4.02743393174070e+00 , 4.55621888094300e+00 , 7.27220719639921e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.95963250214387e-01 , -1.17171742424022e-02 , 9.55127458693503e-01 ). +colvars: Colvar "one" has value ( -2.94448500277034e-01 , -1.14886070422289e-02 , 9.55598290388192e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 7.00574000274244e+00 , -2.06829116643861e+00 , -8.83119811461982e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 , 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 7.13320400449730e+00 , -3.44298734592438e-01 , 4.38138305680023e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 , 5.84483325162435e+00 , 2.25366187654745e+00 , 2.97407896818342e+00 , 5.16683406263612e+00 , 3.55710110763794e+00 , 2.89359751215032e+00 , 6.30656262174781e+00 , 4.47811840330492e+00 , 2.29216448789625e+00 , 3.85900015836979e+00 , 3.64919255486691e+00 , 2.02919404735743e+00 , 2.80985216815857e+00 , 4.16916506605627e+00 , 2.44083999838906e+00 , 3.91677382204270e+00 , 3.19853200587872e+00 , 7.40288243836124e-01 , 2.75380836420530e+00 , 3.05607818870335e+00 , -7.51581894515900e-02 , 3.11221705383647e+00 , 2.65451308061572e+00 , -1.54064705756131e+00 , 1.55022078277182e+00 , 2.19389175197648e+00 , 4.23731258073612e-01 , 4.03133879451812e-01 , 2.61695797841092e+00 , 4.65936542913617e-01 , 2.07008191781880e+00 , 1.14541073584410e+00 , 1.04438132515448e+00 , 1.21104098873384e+00 , 1.29064314915337e-01 , 1.68806278825048e+00 , 2.07938437129022e+00 , -1.09226055507971e+00 , 2.03807229463835e+00 , 5.75169096535490e-01 , 6.16577762840044e-01 , 2.96044663850816e+00 , -5.85292110472713e-01 , 3.55388149199515e-01 , 3.17720325125777e+00 , 1.28825494086657e+00 , 1.38214738369001e+00 , 3.74916833208051e+00 , 8.64233237372221e-01 , 1.98005512142267e+00 , 5.03174948282925e+00 , 2.09827944546896e+00 , 2.75342470994007e+00 , 5.72413575586123e+00 , -3.55992882575887e-01 , 2.90250467361778e+00 , 4.95954123194611e+00 , -1.11574172694153e+00 , 3.06855139255186e+00 , 5.88010232961502e+00 , -5.43668601286061e-01 , 3.50874101319027e+00 , 3.78937424004920e+00 , -1.47624956703860e+00 , 4.48866017004579e+00 , 3.41423298783339e+00 , -7.31770235550961e-01 , 5.43423902569644e+00 , 2.47675782651417e+00 , -2.74498269317940e+00 , 3.94541871314426e+00 , 2.80114869378689e+00 , -3.80612628970205e+00 , 4.55960025539404e+00 , 2.81304026673475e+00 , -2.68465775625360e+00 , 2.63423256162810e+00 , 2.35669571741840e+00 , -3.79793299657600e+00 , 1.82595829823249e+00 , 2.00564398238562e+00 , -3.35973166964488e+00 , 8.76210294949400e-01 , 8.14326802538322e-01 , -4.25479988283804e+00 , 1.04652539212958e+00 , 3.23552373700253e+00 , -5.47696169161307e+00 , 7.58343767602588e-01 , 3.33830903166301e+00 , -3.37052998783529e+00 , 7.27070269086146e-01 , 4.17273383545135e+00 , -3.67076853636612e+00 , 8.02890411004126e-02 , 5.47818496853563e+00 , -2.38141785804304e+00 , -3.19276966689693e-01 , 6.13524375348765e+00 , -4.47866085407106e+00 , 9.21976672545687e-01 , 6.42118098012691e+00 , -5.36125694717558e+00 , 5.75956580523933e-01 , 7.20372858904930e+00 , -6.30602052652239e+00 , 3.62659966444639e+00 , 6.75243212712343e+00 , -6.99886722165190e+00 , 4.29705609045011e+00 , 7.50843520996675e+00 , -6.65099617909420e+00 , 3.16189006812619e+00 , 5.52741041258270e+00 , -4.10745542008092e+00 , 2.25411177669687e+00 , 6.39414571125951e+00 , -4.81593837698548e+00 , 3.27869885909781e+00 , 7.25161049228686e+00 , -4.02743393174070e+00 , 4.55621888094300e+00 , 7.27220719639921e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.4373 , 2.18614 , -15.1989 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.6468 , 6.56468 , 13.1294 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.4373 , 2.18614 , -15.1989 ) to colvar "one". -colvars: Adding total bias energy: 44.1421 +colvars: Adding biasing force ( 65.6468 , 6.56468 , 13.1294 ) to colvar "one". +colvars: Adding total bias energy: 55.9741 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.4373 , 2.18614 , -15.1989 ) +colvars: Force to be applied: ( 65.6468 , 6.56468 , 13.1294 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.9306 , -0.523543 , -1.41844 ) -colvars: ( -4.22799 , -0.448938 , -1.21631 ) -colvars: ( -4.22799 , -0.448938 , -1.21631 ) -colvars: ( -5.6318 , -0.597998 , -1.62016 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.19215 , -0.549244 , -1.48483 ) +colvars: ( -4.45226 , -0.470977 , -1.27324 ) +colvars: ( -4.45226 , -0.470977 , -1.27324 ) +colvars: ( -5.93055 , -0.627354 , -1.696 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.887491 , 0.196068 , 0.609742 ) -colvars: ( 0.769309 , 0.266273 , 0.633282 ) -colvars: ( 0.753128 , 0.259462 , 0.615007 ) -colvars: ( 0.659022 , 0.266643 , 0.569974 ) -colvars: ( 0.647285 , 0.200259 , 0.476289 ) -colvars: ( 0.573713 , 0.343324 , 0.621005 ) -colvars: ( 0.468029 , 0.356885 , 0.577627 ) -colvars: ( 0.392401 , 0.453544 , 0.660409 ) -colvars: ( 0.387181 , 0.312325 , 0.472534 ) -colvars: ( 0.352997 , 0.270725 , 0.398308 ) -colvars: ( 0.357885 , 0.317629 , 0.462531 ) -colvars: ( 0.287345 , 0.274784 , 0.365646 ) -colvars: ( 0.260226 , 0.303748 , 0.387874 ) -colvars: ( 0.348985 , 0.177497 , 0.273952 ) -colvars: ( 0.291038 , 0.13414 , 0.183681 ) -colvars: ( 0.4702 , 0.140969 , 0.29625 ) -colvars: ( 0.541833 , 0.0501276 , 0.218772 ) -colvars: ( 0.669674 , 0.0296538 , 0.265918 ) -colvars: ( 0.550664 , 0.0183091 , 0.18223 ) -colvars: ( 0.535111 , -0.0465865 , 0.088286 ) -colvars: ( 0.571614 , 0.0660369 , 0.256824 ) -colvars: ( 0.570477 , 0.0497983 , 0.23491 ) -colvars: ( 0.606848 , 0.114333 , 0.340423 ) -colvars: ( 0.44778 , 0.0538309 , 0.169219 ) -colvars: ( 0.441195 , -0.00198709 , 0.0923439 ) -colvars: ( 0.346991 , 0.118965 , 0.196181 ) -colvars: ( 0.224057 , 0.127112 , 0.135738 ) -colvars: ( 0.133593 , 0.212332 , 0.194964 ) -colvars: ( 0.195959 , 0.0536085 , 0.0232699 ) -colvars: ( 0.147456 , 0.0173478 , -0.0522501 ) -colvars: ( 0.228774 , 0.0283622 , 0.00920348 ) -colvars: ( 0.214679 , -0.0438579 , -0.0934848 ) -colvars: ( 0.249134 , -0.0469379 , -0.0775872 ) -colvars: ( 0.289123 , -0.129327 , -0.162304 ) -colvars: ( 0.245672 , -0.182408 , -0.25692 ) -colvars: ( 0.403005 , -0.143965 , -0.115594 ) -colvars: ( 0.479657 , -0.219012 , -0.169493 ) -colvars: ( 0.609267 , -0.221184 , -0.0973677 ) -colvars: ( 0.43333 , -0.22377 , -0.202517 ) -colvars: ( 0.438859 , -0.291615 , -0.288129 ) -colvars: ( 0.385438 , -0.15095 , -0.134898 ) -colvars: ( 0.332232 , -0.145019 , -0.157909 ) -colvars: ( 0.316167 , -0.0587586 , -0.0542876 ) -colvars: ( 0.210431 , -0.154169 , -0.240339 ) -colvars: ( 0.186531 , -0.196187 , -0.309164 ) -colvars: ( 0.0110653 , -0.200218 , -0.415933 ) -colvars: ( -0.0787655 , -0.218245 , -0.49149 ) -colvars: ( 0.109954 , -0.249569 , -0.423334 ) -colvars: ( 0.129385 , -0.11387 , -0.234467 ) -colvars: ( 0.0114899 , -0.118601 , -0.308851 ) -colvars: ( -0.076544 , -0.0384391 , -0.25484 ) +colvars: ( 0.933555 , 0.206463 , 0.64011 ) +colvars: ( 0.809328 , 0.280226 , 0.664886 ) +colvars: ( 0.792255 , 0.273123 , 0.645744 ) +colvars: ( 0.69343 , 0.280516 , 0.598381 ) +colvars: ( 0.681086 , 0.210698 , 0.499951 ) +colvars: ( 0.603789 , 0.361076 , 0.652005 ) +colvars: ( 0.492735 , 0.375235 , 0.606434 ) +colvars: ( 0.413267 , 0.476816 , 0.693419 ) +colvars: ( 0.407719 , 0.328356 , 0.496064 ) +colvars: ( 0.371807 , 0.284561 , 0.418066 ) +colvars: ( 0.37687 , 0.333974 , 0.485609 ) +colvars: ( 0.302685 , 0.288909 , 0.383863 ) +colvars: ( 0.274125 , 0.319413 , 0.407274 ) +colvars: ( 0.367457 , 0.186651 , 0.287512 ) +colvars: ( 0.306545 , 0.141018 , 0.192681 ) +colvars: ( 0.494858 , 0.148324 , 0.31091 ) +colvars: ( 0.570137 , 0.0528469 , 0.229489 ) +colvars: ( 0.704491 , 0.0314211 , 0.279004 ) +colvars: ( 0.579471 , 0.0193324 , 0.191047 ) +colvars: ( 0.563117 , -0.0489236 , 0.0923454 ) +colvars: ( 0.601545 , 0.0694852 , 0.269374 ) +colvars: ( 0.600405 , 0.052347 , 0.246303 ) +colvars: ( 0.638685 , 0.120189 , 0.357117 ) +colvars: ( 0.471451 , 0.0564921 , 0.177306 ) +colvars: ( 0.464545 , -0.00223408 , 0.0965196 ) +colvars: ( 0.365504 , 0.124937 , 0.205675 ) +colvars: ( 0.236292 , 0.133418 , 0.1422 ) +colvars: ( 0.141197 , 0.222994 , 0.204467 ) +colvars: ( 0.206715 , 0.0561406 , 0.0240697 ) +colvars: ( 0.15575 , 0.0179541 , -0.0552811 ) +colvars: ( 0.24115 , 0.0296715 , 0.00932647 ) +colvars: ( 0.22629 , -0.0462448 , -0.0985307 ) +colvars: ( 0.262446 , -0.0493964 , -0.0817871 ) +colvars: ( 0.304549 , -0.136097 , -0.170874 ) +colvars: ( 0.258869 , -0.191943 , -0.270271 ) +colvars: ( 0.424271 , -0.151438 , -0.121847 ) +colvars: ( 0.504857 , -0.230333 , -0.17852 ) +colvars: ( 0.641101 , -0.232543 , -0.102785 ) +colvars: ( 0.456217 , -0.235427 , -0.21325 ) +colvars: ( 0.46203 , -0.30678 , -0.30321 ) +colvars: ( 0.405921 , -0.15892 , -0.142222 ) +colvars: ( 0.350049 , -0.152774 , -0.166428 ) +colvars: ( 0.33321 , -0.0621138 , -0.0575816 ) +colvars: ( 0.222013 , -0.162468 , -0.252993 ) +colvars: ( 0.196915 , -0.2067 , -0.325323 ) +colvars: ( 0.012361 , -0.210925 , -0.437352 ) +colvars: ( -0.0820684 , -0.229936 , -0.516708 ) +colvars: ( 0.116268 , -0.262725 , -0.445131 ) +colvars: ( 0.13679 , -0.120101 , -0.246768 ) +colvars: ( 0.0128574 , -0.12514 , -0.324878 ) +colvars: ( -0.079691 , -0.0408737 , -0.268085 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.9306 , 0.523543 , 1.41844 ) -colvars: ( 4.22799 , 0.448938 , 1.21631 ) -colvars: ( 4.22799 , 0.448938 , 1.21631 ) -colvars: ( 5.6318 , 0.597998 , 1.62016 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.19215 , 0.549244 , 1.48483 ) +colvars: ( 4.45226 , 0.470977 , 1.27324 ) +colvars: ( 4.45226 , 0.470977 , 1.27324 ) +colvars: ( 5.93055 , 0.627354 , 1.696 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.613596 , -0.0811287 , -0.363784 ) -colvars: ( -0.552137 , -0.164644 , -0.331345 ) -colvars: ( -0.500905 , -0.142178 , -0.271961 ) -colvars: ( -0.514235 , -0.192443 , -0.303014 ) -colvars: ( -0.504547 , -0.132926 , -0.272372 ) -colvars: ( -0.490703 , -0.28548 , -0.312041 ) -colvars: ( -0.459416 , -0.326283 , -0.294925 ) -colvars: ( -0.43881 , -0.434764 , -0.312318 ) -colvars: ( -0.39615 , -0.290387 , -0.218727 ) -colvars: ( -0.3923 , -0.264869 , -0.205894 ) -colvars: ( -0.345742 , -0.284499 , -0.165994 ) -colvars: ( -0.284832 , -0.247055 , -0.09162 ) -colvars: ( -0.235083 , -0.261941 , -0.0468463 ) -colvars: ( -0.3035 , -0.142769 , -0.0737538 ) -colvars: ( -0.272543 , -0.113144 , -0.0322326 ) -colvars: ( -0.356868 , -0.0848283 , -0.107043 ) -colvars: ( -0.382736 , 0.0144512 , -0.0981723 ) -colvars: ( -0.43163 , 0.062559 , -0.130419 ) -colvars: ( -0.421483 , 0.0294607 , -0.131845 ) -colvars: ( -0.410078 , 0.0868648 , -0.100219 ) -colvars: ( -0.466658 , -0.0253218 , -0.196494 ) -colvars: ( -0.502233 , -0.0269706 , -0.232829 ) -colvars: ( -0.553074 , -0.0932467 , -0.307209 ) -colvars: ( -0.451324 , -0.0572715 , -0.192303 ) -colvars: ( -0.458579 , -0.0127682 , -0.183963 ) -colvars: ( -0.39675 , -0.132282 , -0.163797 ) -colvars: ( -0.340155 , -0.163859 , -0.118004 ) -colvars: ( -0.29021 , -0.25491 , -0.0997851 ) -colvars: ( -0.298168 , -0.0901052 , -0.0498965 ) -colvars: ( -0.285688 , -0.07132 , -0.0307548 ) -colvars: ( -0.27679 , -0.044596 , -0.0124243 ) -colvars: ( -0.240498 , 0.0310932 , 0.050638 ) -colvars: ( -0.217599 , 0.0579317 , 0.0830817 ) -colvars: ( -0.284237 , 0.118692 , 0.0374444 ) -colvars: ( -0.257718 , 0.160946 , 0.0789408 ) -colvars: ( -0.353182 , 0.146985 , -0.0219155 ) -colvars: ( -0.401796 , 0.223893 , -0.0437641 ) -colvars: ( -0.472231 , 0.246595 , -0.106585 ) -colvars: ( -0.414915 , 0.203713 , -0.0640381 ) -colvars: ( -0.419431 , 0.265164 , -0.0469928 ) -colvars: ( -0.420763 , 0.116117 , -0.100684 ) -colvars: ( -0.429427 , 0.0855069 , -0.120144 ) -colvars: ( -0.452117 , -0.00892433 , -0.176119 ) -colvars: ( -0.363373 , 0.0742132 , -0.0577187 ) -colvars: ( -0.367382 , 0.100743 , -0.0524296 ) -colvars: ( -0.201576 , 0.107689 , 0.116663 ) -colvars: ( -0.152619 , 0.109647 , 0.166558 ) -colvars: ( -0.226654 , 0.180829 , 0.117147 ) -colvars: ( -0.300639 , 0.033195 , -0.00907176 ) -colvars: ( -0.234458 , 0.0195389 , 0.0526508 ) -colvars: ( -0.180832 , -0.0643294 , 0.0770926 ) +colvars: ( -0.645293 , -0.0855079 , -0.381244 ) +colvars: ( -0.580767 , -0.173263 , -0.34712 ) +colvars: ( -0.526819 , -0.149691 , -0.284729 ) +colvars: ( -0.541046 , -0.202411 , -0.317426 ) +colvars: ( -0.53086 , -0.139829 , -0.285341 ) +colvars: ( -0.516416 , -0.300167 , -0.326848 ) +colvars: ( -0.483655 , -0.342984 , -0.308916 ) +colvars: ( -0.462091 , -0.456987 , -0.32709 ) +colvars: ( -0.417152 , -0.305228 , -0.228965 ) +colvars: ( -0.413161 , -0.27836 , -0.215573 ) +colvars: ( -0.364098 , -0.29907 , -0.173554 ) +colvars: ( -0.300056 , -0.259696 , -0.0955096 ) +colvars: ( -0.247693 , -0.275384 , -0.0484223 ) +colvars: ( -0.319606 , -0.150091 , -0.0768493 ) +colvars: ( -0.2871 , -0.118912 , -0.033326 ) +colvars: ( -0.375602 , -0.0892412 , -0.111808 ) +colvars: ( -0.402719 , 0.0150979 , -0.102584 ) +colvars: ( -0.453989 , 0.0655939 , -0.136414 ) +colvars: ( -0.443527 , 0.0309225 , -0.138022 ) +colvars: ( -0.43154 , 0.0912854 , -0.104903 ) +colvars: ( -0.491084 , -0.0266443 , -0.205874 ) +colvars: ( -0.528569 , -0.028328 , -0.244092 ) +colvars: ( -0.582066 , -0.0979911 , -0.322132 ) +colvars: ( -0.475166 , -0.0601092 , -0.201583 ) +colvars: ( -0.482822 , -0.0132967 , -0.192917 ) +colvars: ( -0.417861 , -0.138934 , -0.171589 ) +colvars: ( -0.358468 , -0.172064 , -0.123537 ) +colvars: ( -0.306019 , -0.267761 , -0.104313 ) +colvars: ( -0.314282 , -0.0945364 , -0.0520991 ) +colvars: ( -0.301227 , -0.074742 , -0.0320782 ) +colvars: ( -0.291694 , -0.0467533 , -0.0127323 ) +colvars: ( -0.253484 , 0.0328004 , 0.0534159 ) +colvars: ( -0.22929 , 0.0609474 , 0.0875362 ) +colvars: ( -0.299424 , 0.124878 , 0.0394608 ) +colvars: ( -0.271566 , 0.169325 , 0.0829526 ) +colvars: ( -0.371847 , 0.154584 , -0.0228674 ) +colvars: ( -0.422919 , 0.235424 , -0.0459 ) +colvars: ( -0.496881 , 0.259234 , -0.111833 ) +colvars: ( -0.43683 , 0.21428 , -0.0672517 ) +colvars: ( -0.441577 , 0.278895 , -0.0494469 ) +colvars: ( -0.443085 , 0.122241 , -0.105681 ) +colvars: ( -0.452316 , 0.0901308 , -0.126164 ) +colvars: ( -0.476255 , -0.00911166 , -0.184862 ) +colvars: ( -0.382954 , 0.0783136 , -0.0606604 ) +colvars: ( -0.387224 , 0.106244 , -0.0551903 ) +colvars: ( -0.212865 , 0.113534 , 0.122393 ) +colvars: ( -0.161457 , 0.115635 , 0.174736 ) +colvars: ( -0.239098 , 0.190354 , 0.122893 ) +colvars: ( -0.317013 , 0.0351964 , -0.00952375 ) +colvars: ( -0.247511 , 0.0208901 , 0.055252 ) +colvars: ( -0.191179 , -0.0672623 , 0.0810102 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 29. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 29. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 29, atoms_new_colvar_forces = { ( -4.65670159896063e+00 , -4.08603245295588e-01 , -1.17248338832359e+00 ), ( -4.01081376059348e+00 , -3.47308389336129e-01 , -9.14376974525829e-01 ), ( -4.08319913905012e+00 , -3.74737763463260e-01 , -9.49353477771137e-01 ), ( -5.48906241479621e+00 , -5.30665138777830e-01 , -1.41624757619421e+00 ), ( 2.52223437262611e-01 , 1.17284250024612e-01 , 3.43046777243059e-01 ), ( 5.01360736918691e+00 , 5.81386139237082e-01 , 1.72740619230722e+00 ), ( 4.23659945449720e+00 , 4.79540278728374e-01 , 1.49901573079741e+00 ), ( -4.64097000039294e-02 , 1.87794700133804e-02 , 3.48090574780212e-01 ), ( 4.21901745949712e+00 , 4.70875623332618e-01 , 1.47012036760910e+00 ), ( 5.59249756172167e+00 , 6.03854352079664e-01 , 1.81257809150848e+00 ), ( 1.21420596463037e-02 , 3.31300536477400e-02 , 2.96537315922656e-01 ), ( 2.51295238291405e-03 , 2.77284524975311e-02 , 2.74026059475105e-01 ), ( 2.51421681268256e-02 , 4.18064178338594e-02 , 3.41027837901573e-01 ), ( 4.54850116818478e-02 , 3.47280177999697e-02 , 2.00198561189227e-01 ), ( 1.84955889131971e-02 , 2.09959552992393e-02 , 1.51448159221894e-01 ), ( 1.13331676742972e-01 , 5.61410166432581e-02 , 1.89206719646637e-01 ), ( 1.59096415911424e-01 , 6.45788001457709e-02 , 1.20600031918681e-01 ), ( 2.38043327640614e-01 , 9.22127564609505e-02 , 1.35498585969918e-01 ), ( 1.29180529304181e-01 , 4.77698309462621e-02 , 5.03847641696983e-02 ), ( 1.25032612853243e-01 , 4.02783067915264e-02 , -1.19332314880314e-02 ), ( 1.04955467542364e-01 , 4.07150739558410e-02 , 6.03297392363021e-02 ), ( 6.82438775493076e-02 , 2.28277004719674e-02 , 2.08034221619557e-03 ), ( 5.37738046835708e-02 , 2.10864232617241e-02 , 3.32135610827194e-02 ), ( -3.54394089022969e-03 , -3.44058762846728e-03 , -2.30846602652034e-02 ), ( -1.73839271660975e-02 , -1.47552893298079e-02 , -9.16193368580235e-02 ), ( -4.97590224128163e-02 , -1.33172069675699e-02 , 3.23834025334986e-02 ), ( -1.16098532855008e-01 , -3.67472864829769e-02 , 1.77334420465540e-02 ), ( -1.56617457444929e-01 , -4.25784809673612e-02 , 9.51792402380099e-02 ), ( -1.02209152476269e-01 , -3.64967191819821e-02 , -2.66266524781619e-02 ), ( -1.38232294586396e-01 , -5.39722136465613e-02 , -8.30048967703130e-02 ), ( -4.80157555533287e-02 , -1.62338174601158e-02 , -3.22083761748142e-03 ), ( -2.58190670978757e-02 , -1.27646491473488e-02 , -4.28468377510776e-02 ), ( 3.15358576418900e-02 , 1.09937270877574e-02 , 5.49450268599003e-03 ), ( 4.88620365064174e-03 , -1.06349913601279e-02 , -1.24859303680468e-01 ), ( -1.20459642122228e-02 , -2.14618069143226e-02 , -1.77978899604409e-01 ), ( 4.98228494490220e-02 , 3.02036764157301e-03 , -1.37509267139386e-01 ), ( 7.78616316904814e-02 , 4.88094120234234e-03 , -2.13256942338586e-01 ), ( 1.37036486962564e-01 , 2.54111895390794e-02 , -2.03952705998990e-01 ), ( 1.84159931481138e-02 , -2.00570645719621e-02 , -2.66555412586245e-01 ), ( 1.94283757548011e-02 , -2.64511957672210e-02 , -3.35122039918450e-01 ), ( -3.53246008274327e-02 , -3.48325692850346e-02 , -2.35581780810036e-01 ), ( -9.71947768698217e-02 , -5.95116441472318e-02 , -2.78052948298791e-01 ), ( -1.35950125977703e-01 , -6.76829710476064e-02 , -2.30406485867260e-01 ), ( -1.52941623455422e-01 , -7.99556941520047e-02 , -2.98057449210995e-01 ), ( -1.80850595746373e-01 , -9.54438451521055e-02 , -3.61594031021475e-01 ), ( -1.90510651540727e-01 , -9.25291744751124e-02 , -2.99269665468407e-01 ), ( -2.31384846837763e-01 , -1.08598088089967e-01 , -3.24931828297016e-01 ), ( -1.16700860208935e-01 , -6.87394953148224e-02 , -3.06187647134030e-01 ), ( -1.71254047595557e-01 , -8.06754525103905e-02 , -2.43538397776284e-01 ), ( -2.22968165961279e-01 , -9.90619272759284e-02 , -2.56200122489818e-01 ), ( -2.57376150321236e-01 , -1.02768436893290e-01 , -1.77747202016434e-01 ) } +colvars: Step 29, atoms_new_colvar_forces = { ( -4.90388470444026e+00 , -4.28289104919460e-01 , -1.22596789453914e+00 ), ( -4.22370330889374e+00 , -3.64013340286007e-01 , -9.55479082116101e-01 ), ( -4.29988082918930e+00 , -3.92871668764587e-01 , -9.92289815064867e-01 ), ( -5.78032017698676e+00 , -5.56485710829078e-01 , -1.48138875975285e+00 ), ( 2.65436412419126e-01 , 1.23432205013646e-01 , 3.61015504658820e-01 ), ( 5.27951965394827e+00 , 6.10153151808775e-01 , 1.80999086904950e+00 ), ( 4.46134472541105e+00 , 5.03228023946892e-01 , 1.57076293939137e+00 ), ( -4.88243202180547e-02 , 1.98291196022474e-02 , 3.66328893876211e-01 ), ( 4.44283179133334e+00 , 4.94104124514341e-01 , 1.54034330697099e+00 ), ( 5.88919200362309e+00 , 6.33555443350639e-01 , 1.89849095076082e+00 ), ( 1.27722939774814e-02 , 3.49036002064003e-02 , 3.12054682102050e-01 ), ( 2.62855837803455e-03 , 2.92130414109863e-02 , 2.88353353101378e-01 ), ( 2.64321191832927e-02 , 4.40291847042301e-02 , 3.58851302354692e-01 ), ( 4.78510755342696e-02 , 3.65605819176930e-02 , 2.10662183138591e-01 ), ( 1.94446358242152e-02 , 2.21056133467002e-02 , 1.59355152750432e-01 ), ( 1.19255318064586e-01 , 5.90829601993783e-02 , 1.99101529679476e-01 ), ( 1.67417865358364e-01 , 6.79447725851201e-02 , 1.26905750536153e-01 ), ( 2.50502022208297e-01 , 9.70149229774446e-02 , 1.42589273410329e-01 ), ( 1.35944591084775e-01 , 5.02548302993018e-02 , 5.30243228988204e-02 ), ( 1.31577645234685e-01 , 4.23618557494827e-02 , -1.25580151752921e-02 ), ( 1.10460962785987e-01 , 4.28409226539961e-02 , 6.35004209083846e-02 ), ( 7.18360525468564e-02 , 2.40190650859722e-02 , 2.21104358600527e-03 ), ( 5.66185743156440e-02 , 2.21983420701025e-02 , 3.49851238161996e-02 ), ( -3.71501795080909e-03 , -3.61710716139713e-03 , -2.42772046554661e-02 ), ( -1.82774681201741e-02 , -1.55307982010578e-02 , -9.63973408755327e-02 ), ( -5.23566890301552e-02 , -1.39972246478159e-02 , 3.40864271931882e-02 ), ( -1.22175571268548e-01 , -3.86466486191643e-02 , 1.86622092763202e-02 ), ( -1.64822359079624e-01 , -4.47671337353124e-02 , 1.00154681170970e-01 ), ( -1.07567551526852e-01 , -3.83958029009566e-02 , -2.80293564394553e-02 ), ( -1.45476752410774e-01 , -5.67879292724929e-02 , -8.73592958614700e-02 ), ( -5.05441106137904e-02 , -1.70817490308973e-02 , -3.40580986306796e-03 ), ( -2.71933321735205e-02 , -1.34443945792793e-02 , -4.51148137209192e-02 ), ( 3.31567041165365e-02 , 1.15510292059906e-02 , 5.74912202390174e-03 ), ( 5.12548771500154e-03 , -1.12183356352275e-02 , -1.31413667649949e-01 ), ( -1.26969732526753e-02 , -2.26183691537531e-02 , -1.87318333347491e-01 ), ( 5.24245184693471e-02 , 3.14609573447067e-03 , -1.44714743694516e-01 ), ( 8.19383039125556e-02 , 5.09086058050195e-03 , -2.24419711810447e-01 ), ( 1.44220385621418e-01 , 2.66904650807004e-02 , -2.14617859029491e-01 ), ( 1.93864419091029e-02 , -2.11470238825605e-02 , -2.80502113489434e-01 ), ( 2.04525315757620e-02 , -2.78858915037756e-02 , -3.52657316455056e-01 ), ( -3.71632993521555e-02 , -3.66797004597271e-02 , -2.47902622416249e-01 ), ( -1.02267285942677e-01 , -6.26433434786494e-02 , -2.92591665316858e-01 ), ( -1.43045087993155e-01 , -7.12254412658033e-02 , -2.42444060097500e-01 ), ( -1.60941311107296e-01 , -8.41541902437907e-02 , -3.13653263595172e-01 ), ( -1.90309037605197e-01 , -1.00456379160913e-01 , -3.80513460538421e-01 ), ( -2.00504352349957e-01 , -9.73911287359829e-02 , -3.14959089005219e-01 ), ( -2.43524891112127e-01 , -1.14300390862316e-01 , -3.41971994990497e-01 ), ( -1.22830298603008e-01 , -7.23705604781537e-02 , -3.22238645318066e-01 ), ( -1.80222707121762e-01 , -8.49047305933428e-02 , -2.56291639019387e-01 ), ( -2.34653139435091e-01 , -1.04250056839972e-01 , -2.69626339802510e-01 ), ( -2.70870098773619e-01 , -1.08136056803538e-01 , -1.87075129014182e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 29, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -3974,10 +6407,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 30, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 30, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 30, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 30, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 30, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 30, atoms_positions[size = 51] = { ( 8.23764193151924e+00 , 4.34878621784569e-02 , -7.22437387351404e-01 ), ( 6.83724067727916e+00 , -5.90741777013381e-01 , -5.26277494276041e-01 ), ( 6.12049077818646e+00 , -3.66440296478970e-01 , 8.06190454945147e-01 ), ( 4.90768664730820e+00 , -1.48460272081974e-01 , 7.46413529312125e-01 ), ( 7.00242145471206e+00 , -2.07070238324471e+00 , -8.75621911133484e-01 ), ( 6.80896701816145e+00 , -2.92859449865948e-01 , 1.96585507175947e+00 ), ( 6.09805478625004e+00 , -2.24291356172958e-01 , 3.17764083144861e+00 ), ( 7.13779513547567e+00 , -3.44372284591930e-01 , 4.38625597261496e+00 ), ( 5.32534991678670e+00 , 1.06778123422510e+00 , 3.36818872219414e+00 ), ( 4.18328955469913e+00 , 1.00583200263353e+00 , 3.77938602514822e+00 ), ( 5.84618264800347e+00 , 2.25196209074770e+00 , 2.97224130362163e+00 ), ( 5.15696718996734e+00 , 3.55256190620906e+00 , 2.88757690727946e+00 ), ( 6.30269107155688e+00 , 4.47250092280947e+00 , 2.28828329070379e+00 ), ( 3.85878899047357e+00 , 3.64407916479059e+00 , 2.02553026289166e+00 ), ( 2.81489301642761e+00 , 4.16818120475770e+00 , 2.43593349206520e+00 ), ( 3.91210307526539e+00 , 3.19157198544600e+00 , 7.44048834694064e-01 ), ( 2.76003615434961e+00 , 3.06608629331018e+00 , -7.25874883058444e-02 ), ( 3.11742337169011e+00 , 2.65213617856577e+00 , -1.54206552610553e+00 ), ( 1.55039770860550e+00 , 2.20386198781653e+00 , 4.24256136232630e-01 ), ( 4.08849667016392e-01 , 2.61688082708039e+00 , 4.60293697403412e-01 ), ( 2.06461603838958e+00 , 1.14149691206851e+00 , 1.04541097965762e+00 ), ( 1.22357232347860e+00 , 1.34393220866268e-01 , 1.68340199992315e+00 ), ( 2.08287824275055e+00 , -1.09278633478080e+00 , 2.03934021088462e+00 ), ( 5.75092496965859e-01 , 6.15856553332651e-01 , 2.95697480938450e+00 ), ( -5.87357636235547e-01 , 3.56101442773918e-01 , 3.18146113194469e+00 ), ( 1.28676477647157e+00 , 1.38988639904308e+00 , 3.75385474851258e+00 ), ( 8.71640430576094e-01 , 1.97942310063133e+00 , 5.03369067882944e+00 ), ( 2.09103448113220e+00 , 2.75788254961826e+00 , 5.72533971686084e+00 ), ( -3.57681243375300e-01 , 2.90078969757531e+00 , 4.95464372313808e+00 ), ( -1.11541264578088e+00 , 3.06908366402439e+00 , 5.88230677576328e+00 ), ( -5.43427370177526e-01 , 3.50725177810262e+00 , 3.78023131228879e+00 ), ( -1.46905417259948e+00 , 4.48405143604890e+00 , 3.41543895300378e+00 ), ( -7.38765937891440e-01 , 5.43800335188954e+00 , 2.47858519576284e+00 ), ( -2.74614344700853e+00 , 3.94572527756033e+00 , 2.78699832532386e+00 ), ( -3.80455714654773e+00 , 4.56547520913436e+00 , 2.81323605280181e+00 ), ( -2.69035509257330e+00 , 2.63355514221594e+00 , 2.35515850510570e+00 ), ( -3.80124210147649e+00 , 1.82603550884334e+00 , 2.00539763392691e+00 ), ( -3.35755012040177e+00 , 8.77442195063242e-01 , 8.07339675899194e-01 ), ( -4.25205059122558e+00 , 1.04193013701143e+00 , 3.24035718745224e+00 ), ( -5.47083100450072e+00 , 7.52673426353046e-01 , 3.34025030578420e+00 ), ( -3.37085931211436e+00 , 7.28334365476863e-01 , 4.16786494900867e+00 ), ( -3.66953107693088e+00 , 7.97427501274149e-02 , 5.48070385346425e+00 ), ( -2.37706726794794e+00 , -3.15272299660837e-01 , 6.13169480962639e+00 ), ( -4.48247484924873e+00 , 9.22257244466278e-01 , 6.42087370465327e+00 ), ( -5.35969050463327e+00 , 5.71530653848507e-01 , 7.19997128922252e+00 ), ( -6.30857477849050e+00 , 3.62368382711476e+00 , 6.75344333301841e+00 ), ( -7.00511359239387e+00 , 4.29806989977957e+00 , 7.51180125044996e+00 ), ( -6.64106161108270e+00 , 3.16234887923283e+00 , 5.53295301740457e+00 ), ( -4.10662351090596e+00 , 2.25514070803843e+00 , 6.39745035366231e+00 ), ( -4.81620877959101e+00 , 3.28313127591232e+00 , 7.24713868314063e+00 ), ( -4.02120918464972e+00 , 4.56274305514335e+00 , 7.27350034759277e+00 ) } +colvars: Step 30, atoms_positions[size = 51] = { ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 ), ( 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 ), ( 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 ), ( 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 ), ( 7.00179272944133e+00 , -2.07095885497099e+00 , -8.75491056010624e-01 ), ( 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 ), ( 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 ), ( 7.13947148087372e+00 , -3.44628618609811e-01 , 4.38752600282718e+00 ), ( 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 ), ( 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 ), ( 5.84769593592378e+00 , 2.25258259280822e+00 , 2.97223352646978e+00 ), ( 5.15712897643352e+00 , 3.55259326287517e+00 , 2.88787080381333e+00 ), ( 6.30263481720254e+00 , 4.47262732959847e+00 , 2.28857170764563e+00 ), ( 3.85884878145450e+00 , 3.64400695573177e+00 , 2.02575330229727e+00 ), ( 2.81492116217015e+00 , 4.16816889347436e+00 , 2.43606553713223e+00 ), ( 3.91221506128496e+00 , 3.19160143027793e+00 , 7.44232253440439e-01 ), ( 2.76018260154900e+00 , 3.06614324543301e+00 , -7.24728508156735e-02 ), ( 3.11761872578935e+00 , 2.65220893877964e+00 , -1.54194181951570e+00 ), ( 1.55052096634640e+00 , 2.20390576899866e+00 , 4.24310057950213e-01 ), ( 4.08967072570339e-01 , 2.61691637371786e+00 , 4.60295766316534e-01 ), ( 2.06471405218342e+00 , 1.14152786367528e+00 , 1.04547520577357e+00 ), ( 1.22363440295663e+00 , 1.34422713256255e-01 , 1.68340962837078e+00 ), ( 2.08296960540123e+00 , -1.09270347969594e+00 , 2.03943454632966e+00 ), ( 5.75140118533064e-01 , 6.15852237276473e-01 , 2.95696634425776e+00 ), ( -5.87337993010753e-01 , 3.56102791107019e-01 , 3.18139678367157e+00 ), ( 1.28686553960385e+00 , 1.38985539851835e+00 , 3.75387808173765e+00 ), ( 8.71581213781113e-01 , 1.97937280596719e+00 , 5.03368878532427e+00 ), ( 2.09091280725987e+00 , 2.75784401097805e+00 , 5.72539968524939e+00 ), ( -3.57768212748633e-01 , 2.90074927861900e+00 , 4.95461545553292e+00 ), ( -1.11554222952123e+00 , 3.06903884572973e+00 , 5.88224856520018e+00 ), ( -5.43470468797353e-01 , 3.50723766989847e+00 , 3.78020889899794e+00 ), ( -1.46908402225090e+00 , 4.48404195684652e+00 , 3.41539030314352e+00 ), ( -7.38749726302167e-01 , 5.43800592755974e+00 , 2.47858102155479e+00 ), ( -2.74614024084795e+00 , 3.94571582605938e+00 , 2.78688191587597e+00 ), ( -3.80456188043702e+00 , 4.56545175952191e+00 , 2.81308347109975e+00 ), ( -2.69031627012295e+00 , 2.63355520190254e+00 , 2.35502689986891e+00 ), ( -3.80117961442763e+00 , 1.82603520976220e+00 , 2.00519120200254e+00 ), ( -3.35743595995106e+00 , 8.77447571394055e-01 , 8.07147138799860e-01 ), ( -4.25203598650743e+00 , 1.04190649943011e+00 , 3.24011232459274e+00 ), ( -5.47081705260917e+00 , 7.52645385579587e-01 , 3.33996390727483e+00 ), ( -3.37088261372906e+00 , 7.28293718826388e-01 , 4.16764293445449e+00 ), ( -3.66962243217793e+00 , 7.96804089726750e-02 , 5.48044598803836e+00 ), ( -2.37718892734588e+00 , -3.15323915248872e-01 , 6.13149608054584e+00 ), ( -4.48261437121052e+00 , 9.22182642162836e-01 , 6.42059748851612e+00 ), ( -5.35984713546564e+00 , 5.71444489587300e-01 , 7.19966823538954e+00 ), ( -6.30875455261292e+00 , 3.62359930558049e+00 , 6.75317130616448e+00 ), ( -7.00531321202099e+00 , 4.29797500437580e+00 , 7.51152444314271e+00 ), ( -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 ), ( -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 ), ( -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 ), ( -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ) } colvars: Step 30, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 30, atom_groups_ids[size = 0] = @@ -3995,154 +6428,290 @@ colvars: Collective variables module, step no. 30 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.94864820949374e-01 , -1.29606427096605e-02 , 9.55451076249876e-01 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.93283423674133e-01 , -1.27196382432982e-02 , 9.55940920873742e-01 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group1". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 7.00179272944133e+00 , -2.07095885497099e+00 , -8.75491056010624e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 , 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 7.13947148087372e+00 , -3.44628618609811e-01 , 4.38752600282718e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 , 5.84769593592378e+00 , 2.25258259280822e+00 , 2.97223352646978e+00 , 5.15712897643352e+00 , 3.55259326287517e+00 , 2.88787080381333e+00 , 6.30263481720254e+00 , 4.47262732959847e+00 , 2.28857170764563e+00 , 3.85884878145450e+00 , 3.64400695573177e+00 , 2.02575330229727e+00 , 2.81492116217015e+00 , 4.16816889347436e+00 , 2.43606553713223e+00 , 3.91221506128496e+00 , 3.19160143027793e+00 , 7.44232253440439e-01 , 2.76018260154900e+00 , 3.06614324543301e+00 , -7.24728508156735e-02 , 3.11761872578935e+00 , 2.65220893877964e+00 , -1.54194181951570e+00 , 1.55052096634640e+00 , 2.20390576899866e+00 , 4.24310057950213e-01 , 4.08967072570339e-01 , 2.61691637371786e+00 , 4.60295766316534e-01 , 2.06471405218342e+00 , 1.14152786367528e+00 , 1.04547520577357e+00 , 1.22363440295663e+00 , 1.34422713256255e-01 , 1.68340962837078e+00 , 2.08296960540123e+00 , -1.09270347969594e+00 , 2.03943454632966e+00 , 5.75140118533064e-01 , 6.15852237276473e-01 , 2.95696634425776e+00 , -5.87337993010753e-01 , 3.56102791107019e-01 , 3.18139678367157e+00 , 1.28686553960385e+00 , 1.38985539851835e+00 , 3.75387808173765e+00 , 8.71581213781113e-01 , 1.97937280596719e+00 , 5.03368878532427e+00 , 2.09091280725987e+00 , 2.75784401097805e+00 , 5.72539968524939e+00 , -3.57768212748633e-01 , 2.90074927861900e+00 , 4.95461545553292e+00 , -1.11554222952123e+00 , 3.06903884572973e+00 , 5.88224856520018e+00 , -5.43470468797353e-01 , 3.50723766989847e+00 , 3.78020889899794e+00 , -1.46908402225090e+00 , 4.48404195684652e+00 , 3.41539030314352e+00 , -7.38749726302167e-01 , 5.43800592755974e+00 , 2.47858102155479e+00 , -2.74614024084795e+00 , 3.94571582605938e+00 , 2.78688191587597e+00 , -3.80456188043702e+00 , 4.56545175952191e+00 , 2.81308347109975e+00 , -2.69031627012295e+00 , 2.63355520190254e+00 , 2.35502689986891e+00 , -3.80117961442763e+00 , 1.82603520976220e+00 , 2.00519120200254e+00 , -3.35743595995106e+00 , 8.77447571394055e-01 , 8.07147138799860e-01 , -4.25203598650743e+00 , 1.04190649943011e+00 , 3.24011232459274e+00 , -5.47081705260917e+00 , 7.52645385579587e-01 , 3.33996390727483e+00 , -3.37088261372906e+00 , 7.28293718826388e-01 , 4.16764293445449e+00 , -3.66962243217793e+00 , 7.96804089726750e-02 , 5.48044598803836e+00 , -2.37718892734588e+00 , -3.15323915248872e-01 , 6.13149608054584e+00 , -4.48261437121052e+00 , 9.22182642162836e-01 , 6.42059748851612e+00 , -5.35984713546564e+00 , 5.71444489587300e-01 , 7.19966823538954e+00 , -6.30875455261292e+00 , 3.62359930558049e+00 , 6.75317130616448e+00 , -7.00531321202099e+00 , 4.29797500437580e+00 , 7.51152444314271e+00 , -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 , -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 , -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 , -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.94864820949374e-01 , -1.29606427096605e-02 , 9.55451076249876e-01 ). +colvars: Colvar "one" has value ( -2.93283423674133e-01 , -1.27196382432982e-02 , 9.55940920873742e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 7.00179272944133e+00 , -2.07095885497099e+00 , -8.75491056010624e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 , 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 7.13947148087372e+00 , -3.44628618609811e-01 , 4.38752600282718e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 , 5.84769593592378e+00 , 2.25258259280822e+00 , 2.97223352646978e+00 , 5.15712897643352e+00 , 3.55259326287517e+00 , 2.88787080381333e+00 , 6.30263481720254e+00 , 4.47262732959847e+00 , 2.28857170764563e+00 , 3.85884878145450e+00 , 3.64400695573177e+00 , 2.02575330229727e+00 , 2.81492116217015e+00 , 4.16816889347436e+00 , 2.43606553713223e+00 , 3.91221506128496e+00 , 3.19160143027793e+00 , 7.44232253440439e-01 , 2.76018260154900e+00 , 3.06614324543301e+00 , -7.24728508156735e-02 , 3.11761872578935e+00 , 2.65220893877964e+00 , -1.54194181951570e+00 , 1.55052096634640e+00 , 2.20390576899866e+00 , 4.24310057950213e-01 , 4.08967072570339e-01 , 2.61691637371786e+00 , 4.60295766316534e-01 , 2.06471405218342e+00 , 1.14152786367528e+00 , 1.04547520577357e+00 , 1.22363440295663e+00 , 1.34422713256255e-01 , 1.68340962837078e+00 , 2.08296960540123e+00 , -1.09270347969594e+00 , 2.03943454632966e+00 , 5.75140118533064e-01 , 6.15852237276473e-01 , 2.95696634425776e+00 , -5.87337993010753e-01 , 3.56102791107019e-01 , 3.18139678367157e+00 , 1.28686553960385e+00 , 1.38985539851835e+00 , 3.75387808173765e+00 , 8.71581213781113e-01 , 1.97937280596719e+00 , 5.03368878532427e+00 , 2.09091280725987e+00 , 2.75784401097805e+00 , 5.72539968524939e+00 , -3.57768212748633e-01 , 2.90074927861900e+00 , 4.95461545553292e+00 , -1.11554222952123e+00 , 3.06903884572973e+00 , 5.88224856520018e+00 , -5.43470468797353e-01 , 3.50723766989847e+00 , 3.78020889899794e+00 , -1.46908402225090e+00 , 4.48404195684652e+00 , 3.41539030314352e+00 , -7.38749726302167e-01 , 5.43800592755974e+00 , 2.47858102155479e+00 , -2.74614024084795e+00 , 3.94571582605938e+00 , 2.78688191587597e+00 , -3.80456188043702e+00 , 4.56545175952191e+00 , 2.81308347109975e+00 , -2.69031627012295e+00 , 2.63355520190254e+00 , 2.35502689986891e+00 , -3.80117961442763e+00 , 1.82603520976220e+00 , 2.00519120200254e+00 , -3.35743595995106e+00 , 8.77447571394055e-01 , 8.07147138799860e-01 , -4.25203598650743e+00 , 1.04190649943011e+00 , 3.24011232459274e+00 , -5.47081705260917e+00 , 7.52645385579587e-01 , 3.33996390727483e+00 , -3.37088261372906e+00 , 7.28293718826388e-01 , 4.16764293445449e+00 , -3.66962243217793e+00 , 7.96804089726750e-02 , 5.48044598803836e+00 , -2.37718892734588e+00 , -3.15323915248872e-01 , 6.13149608054584e+00 , -4.48261437121052e+00 , 9.22182642162836e-01 , 6.42059748851612e+00 , -5.35984713546564e+00 , 5.71444489587300e-01 , 7.19966823538954e+00 , -6.30875455261292e+00 , 3.62359930558049e+00 , 6.75317130616448e+00 , -7.00531321202099e+00 , 4.29797500437580e+00 , 7.51152444314271e+00 , -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 , -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 , -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 , -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.4153 , 2.21101 , -15.2054 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.5967 , 6.55967 , 13.1193 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.4153 , 2.21101 , -15.2054 ) to colvar "one". -colvars: Adding total bias energy: 44.1015 +colvars: Adding biasing force ( 65.5967 , 6.55967 , 13.1193 ) to colvar "one". +colvars: Adding total bias energy: 55.9013 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.4153 , 2.21101 , -15.2054 ) +colvars: Force to be applied: ( 65.5967 , 6.55967 , 13.1193 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.93255 , -0.521985 , -1.41418 ) -colvars: ( -4.22966 , -0.447602 , -1.21266 ) -colvars: ( -4.22966 , -0.447602 , -1.21266 ) -colvars: ( -5.63404 , -0.596219 , -1.6153 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.191 , -0.547183 , -1.47905 ) +colvars: ( -4.45128 , -0.46921 , -1.26828 ) +colvars: ( -4.45128 , -0.46921 , -1.26828 ) +colvars: ( -5.92923 , -0.625001 , -1.68939 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.886932 , 0.196107 , 0.608619 ) -colvars: ( 0.768901 , 0.26621 , 0.63212 ) -colvars: ( 0.752721 , 0.259434 , 0.613913 ) -colvars: ( 0.65877 , 0.266512 , 0.5689 ) -colvars: ( 0.647051 , 0.20017 , 0.475371 ) -colvars: ( 0.573578 , 0.343084 , 0.619829 ) -colvars: ( 0.468045 , 0.356567 , 0.576502 ) -colvars: ( 0.392518 , 0.45311 , 0.659131 ) -colvars: ( 0.387297 , 0.312018 , 0.471599 ) -colvars: ( 0.353168 , 0.270417 , 0.397482 ) -colvars: ( 0.358021 , 0.317335 , 0.461643 ) -colvars: ( 0.287566 , 0.274508 , 0.364938 ) -colvars: ( 0.260463 , 0.303472 , 0.38716 ) -colvars: ( 0.349126 , 0.177326 , 0.273406 ) -colvars: ( 0.291259 , 0.133972 , 0.183283 ) -colvars: ( 0.470178 , 0.140887 , 0.295676 ) -colvars: ( 0.541718 , 0.0501492 , 0.218335 ) -colvars: ( 0.669382 , 0.0297634 , 0.265418 ) -colvars: ( 0.550556 , 0.018326 , 0.181823 ) -colvars: ( 0.535027 , -0.0465307 , 0.088036 ) -colvars: ( 0.571492 , 0.0660015 , 0.256265 ) -colvars: ( 0.570375 , 0.0497414 , 0.234355 ) -colvars: ( 0.606709 , 0.114222 , 0.339668 ) -colvars: ( 0.447847 , 0.0537034 , 0.168761 ) -colvars: ( 0.44128 , -0.00208979 , 0.0920032 ) -colvars: ( 0.347186 , 0.11875 , 0.195681 ) -colvars: ( 0.224417 , 0.126828 , 0.13533 ) -colvars: ( 0.134065 , 0.211952 , 0.194462 ) -colvars: ( 0.196348 , 0.0533846 , 0.0230707 ) -colvars: ( 0.147919 , 0.0171144 , -0.0523364 ) -colvars: ( 0.229103 , 0.028204 , 0.00906062 ) -colvars: ( 0.215019 , -0.043949 , -0.0934342 ) -colvars: ( 0.249408 , -0.0469752 , -0.0775274 ) -colvars: ( 0.289373 , -0.129331 , -0.162144 ) -colvars: ( 0.245982 , -0.182393 , -0.256602 ) -colvars: ( 0.40311 , -0.143915 , -0.115519 ) -colvars: ( 0.479671 , -0.218884 , -0.169338 ) -colvars: ( 0.609111 , -0.220998 , -0.0973333 ) -colvars: ( 0.433424 , -0.223693 , -0.20234 ) -colvars: ( 0.438952 , -0.291493 , -0.287813 ) -colvars: ( 0.385605 , -0.150971 , -0.134859 ) -colvars: ( 0.332487 , -0.1451 , -0.157863 ) -colvars: ( 0.316452 , -0.0589326 , -0.0544384 ) -colvars: ( 0.210846 , -0.154298 , -0.240155 ) -colvars: ( 0.186989 , -0.196314 , -0.308882 ) -colvars: ( 0.0117196 , -0.200357 , -0.415411 ) -colvars: ( -0.0779919 , -0.218412 , -0.490842 ) -colvars: ( 0.110468 , -0.249607 , -0.422778 ) -colvars: ( 0.129894 , -0.114046 , -0.234275 ) -colvars: ( 0.0121534 , -0.118823 , -0.308533 ) -colvars: ( -0.0757742 , -0.0387487 , -0.254604 ) +colvars: ( 0.932346 , 0.206377 , 0.638445 ) +colvars: ( 0.808364 , 0.279981 , 0.663164 ) +colvars: ( 0.791301 , 0.272923 , 0.64411 ) +colvars: ( 0.692712 , 0.280195 , 0.5968 ) +colvars: ( 0.680396 , 0.210468 , 0.498605 ) +colvars: ( 0.603259 , 0.360583 , 0.650278 ) +colvars: ( 0.492442 , 0.374646 , 0.604794 ) +colvars: ( 0.413138 , 0.476033 , 0.691557 ) +colvars: ( 0.407588 , 0.327808 , 0.494705 ) +colvars: ( 0.371761 , 0.28404 , 0.416878 ) +colvars: ( 0.376781 , 0.333439 , 0.484309 ) +colvars: ( 0.302734 , 0.288423 , 0.382828 ) +colvars: ( 0.274208 , 0.318908 , 0.406218 ) +colvars: ( 0.367376 , 0.186346 , 0.286716 ) +colvars: ( 0.30659 , 0.140745 , 0.192111 ) +colvars: ( 0.494516 , 0.148142 , 0.310066 ) +colvars: ( 0.569644 , 0.0528405 , 0.228848 ) +colvars: ( 0.703717 , 0.0315265 , 0.27826 ) +colvars: ( 0.578982 , 0.0193411 , 0.190463 ) +colvars: ( 0.562665 , -0.0488283 , 0.0919979 ) +colvars: ( 0.601028 , 0.0694035 , 0.268572 ) +colvars: ( 0.599913 , 0.0522514 , 0.245521 ) +colvars: ( 0.63813 , 0.11999 , 0.356042 ) +colvars: ( 0.471228 , 0.0563151 , 0.176676 ) +colvars: ( 0.464346 , -0.00234667 , 0.0960701 ) +colvars: ( 0.365488 , 0.124619 , 0.204982 ) +colvars: ( 0.236541 , 0.133018 , 0.141651 ) +colvars: ( 0.141629 , 0.222432 , 0.203776 ) +colvars: ( 0.207013 , 0.0558573 , 0.0238263 ) +colvars: ( 0.156162 , 0.0176842 , -0.0553488 ) +colvars: ( 0.241358 , 0.0294788 , 0.00915434 ) +colvars: ( 0.226516 , -0.0463143 , -0.0984203 ) +colvars: ( 0.262575 , -0.0494032 , -0.0816775 ) +colvars: ( 0.304627 , -0.136013 , -0.170599 ) +colvars: ( 0.259041 , -0.191803 , -0.269757 ) +colvars: ( 0.424114 , -0.151285 , -0.121699 ) +colvars: ( 0.504548 , -0.230045 , -0.178247 ) +colvars: ( 0.640519 , -0.232189 , -0.102696 ) +colvars: ( 0.456029 , -0.235192 , -0.212931 ) +colvars: ( 0.461837 , -0.30645 , -0.30268 ) +colvars: ( 0.405848 , -0.158843 , -0.142099 ) +colvars: ( 0.35011 , -0.152769 , -0.166282 ) +colvars: ( 0.333317 , -0.0622691 , -0.0577221 ) +colvars: ( 0.222332 , -0.162509 , -0.252638 ) +colvars: ( 0.197298 , -0.206712 , -0.324813 ) +colvars: ( 0.0130725 , -0.210946 , -0.436504 ) +colvars: ( -0.0811659 , -0.229975 , -0.515669 ) +colvars: ( 0.116757 , -0.262599 , -0.444241 ) +colvars: ( 0.137266 , -0.12022 , -0.246407 ) +colvars: ( 0.0135809 , -0.125308 , -0.324327 ) +colvars: ( -0.0787918 , -0.0411915 , -0.267659 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.93255 , 0.521985 , 1.41418 ) -colvars: ( 4.22966 , 0.447602 , 1.21266 ) -colvars: ( 4.22966 , 0.447602 , 1.21266 ) -colvars: ( 5.63404 , 0.596219 , 1.6153 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.191 , 0.547183 , 1.47905 ) +colvars: ( 4.45128 , 0.46921 , 1.26828 ) +colvars: ( 4.45128 , 0.46921 , 1.26828 ) +colvars: ( 5.92923 , 0.625001 , 1.68939 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.613189 , -0.0810902 , -0.362837 ) -colvars: ( -0.55183 , -0.164703 , -0.330196 ) -colvars: ( -0.500411 , -0.142189 , -0.270679 ) -colvars: ( -0.514113 , -0.192538 , -0.301946 ) -colvars: ( -0.504416 , -0.132943 , -0.271493 ) -colvars: ( -0.490751 , -0.285696 , -0.310822 ) -colvars: ( -0.459664 , -0.326552 , -0.293761 ) -colvars: ( -0.439211 , -0.435174 , -0.310935 ) -colvars: ( -0.396365 , -0.290596 , -0.21763 ) -colvars: ( -0.392608 , -0.265048 , -0.204978 ) -colvars: ( -0.345817 , -0.284683 , -0.164757 ) -colvars: ( -0.284851 , -0.247177 , -0.0904324 ) -colvars: ( -0.234959 , -0.262065 , -0.0454442 ) -colvars: ( -0.303403 , -0.142757 , -0.072808 ) -colvars: ( -0.27249 , -0.11309 , -0.0314217 ) -colvars: ( -0.356624 , -0.0847472 , -0.106162 ) -colvars: ( -0.382377 , 0.014658 , -0.0975193 ) -colvars: ( -0.431081 , 0.062825 , -0.129752 ) -colvars: ( -0.421276 , 0.0296717 , -0.131412 ) -colvars: ( -0.409867 , 0.0871514 , -0.099973 ) -colvars: ( -0.466595 , -0.0251964 , -0.196037 ) -colvars: ( -0.50234 , -0.0268624 , -0.232553 ) -colvars: ( -0.553302 , -0.0932388 , -0.306848 ) -colvars: ( -0.451595 , -0.0571982 , -0.192073 ) -colvars: ( -0.458904 , -0.0126423 , -0.183943 ) -colvars: ( -0.397096 , -0.132296 , -0.163371 ) -colvars: ( -0.340639 , -0.163907 , -0.117592 ) -colvars: ( -0.290758 , -0.255066 , -0.0991117 ) -colvars: ( -0.298545 , -0.0900459 , -0.0496119 ) -colvars: ( -0.286166 , -0.0712385 , -0.0306315 ) -colvars: ( -0.276959 , -0.0444651 , -0.0120742 ) -colvars: ( -0.240542 , 0.0313336 , 0.0508715 ) -colvars: ( -0.217422 , 0.0582208 , 0.0834569 ) -colvars: ( -0.284241 , 0.119036 , 0.0374067 ) -colvars: ( -0.257738 , 0.161349 , 0.0787514 ) -colvars: ( -0.353136 , 0.147353 , -0.0220217 ) -colvars: ( -0.401725 , 0.224349 , -0.0441229 ) -colvars: ( -0.472065 , 0.247069 , -0.106949 ) -colvars: ( -0.415057 , 0.204131 , -0.0645506 ) -colvars: ( -0.419575 , 0.26566 , -0.0477175 ) -colvars: ( -0.421091 , 0.116415 , -0.10109 ) -colvars: ( -0.42997 , 0.0857542 , -0.120669 ) -colvars: ( -0.452821 , -0.0088089 , -0.176496 ) -colvars: ( -0.364005 , 0.0744563 , -0.0582742 ) -colvars: ( -0.36811 , 0.101015 , -0.053175 ) -colvars: ( -0.202102 , 0.108013 , 0.116158 ) -colvars: ( -0.15321 , 0.109981 , 0.165997 ) -colvars: ( -0.226973 , 0.181251 , 0.116596 ) -colvars: ( -0.301243 , 0.0334005 , -0.00943806 ) -colvars: ( -0.235138 , 0.0197377 , 0.0522761 ) -colvars: ( -0.181551 , -0.0642274 , 0.0769818 ) +colvars: ( -0.644429 , -0.0854198 , -0.37993 ) +colvars: ( -0.580056 , -0.173214 , -0.345616 ) +colvars: ( -0.525945 , -0.149611 , -0.283131 ) +colvars: ( -0.540562 , -0.202376 , -0.316032 ) +colvars: ( -0.530375 , -0.139755 , -0.284174 ) +colvars: ( -0.516134 , -0.300189 , -0.325286 ) +colvars: ( -0.483611 , -0.343029 , -0.307427 ) +colvars: ( -0.462228 , -0.457099 , -0.325353 ) +colvars: ( -0.41712 , -0.305235 , -0.227609 ) +colvars: ( -0.413232 , -0.278353 , -0.214421 ) +colvars: ( -0.363952 , -0.299057 , -0.17209 ) +colvars: ( -0.299897 , -0.259644 , -0.0941589 ) +colvars: ( -0.247415 , -0.275325 , -0.046878 ) +colvars: ( -0.319307 , -0.149975 , -0.0757713 ) +colvars: ( -0.286872 , -0.118772 , -0.0324257 ) +colvars: ( -0.375105 , -0.0890983 , -0.110772 ) +colvars: ( -0.402078 , 0.0152993 , -0.101798 ) +colvars: ( -0.453106 , 0.0658187 , -0.135587 ) +colvars: ( -0.44302 , 0.0311195 , -0.137445 ) +colvars: ( -0.431038 , 0.0915208 , -0.104552 ) +colvars: ( -0.4907 , -0.0264961 , -0.20522 ) +colvars: ( -0.528341 , -0.0281942 , -0.243602 ) +colvars: ( -0.581931 , -0.0979139 , -0.321491 ) +colvars: ( -0.475153 , -0.0599866 , -0.201176 ) +colvars: ( -0.482863 , -0.0131499 , -0.19274 ) +colvars: ( -0.41797 , -0.138847 , -0.170995 ) +colvars: ( -0.358767 , -0.171987 , -0.122995 ) +colvars: ( -0.306425 , -0.26773 , -0.103507 ) +colvars: ( -0.314499 , -0.0944004 , -0.0517483 ) +colvars: ( -0.30156 , -0.0745943 , -0.0319157 ) +colvars: ( -0.291702 , -0.0465781 , -0.0123412 ) +colvars: ( -0.253383 , 0.0330348 , 0.0536317 ) +colvars: ( -0.228969 , 0.0612102 , 0.0878779 ) +colvars: ( -0.299247 , 0.125157 , 0.0393974 ) +colvars: ( -0.271427 , 0.169636 , 0.0826935 ) +colvars: ( -0.371565 , 0.154866 , -0.022956 ) +colvars: ( -0.422574 , 0.235743 , -0.046241 ) +colvars: ( -0.496382 , 0.259552 , -0.112128 ) +colvars: ( -0.436706 , 0.214576 , -0.0677412 ) +colvars: ( -0.441452 , 0.279228 , -0.0501769 ) +colvars: ( -0.443156 , 0.122476 , -0.106028 ) +colvars: ( -0.452613 , 0.0903393 , -0.126623 ) +colvars: ( -0.476708 , -0.00897167 , -0.185118 ) +colvars: ( -0.383397 , 0.0785284 , -0.0612022 ) +colvars: ( -0.387767 , 0.106472 , -0.0559396 ) +colvars: ( -0.213313 , 0.113811 , 0.121765 ) +colvars: ( -0.162011 , 0.115924 , 0.174008 ) +colvars: ( -0.239304 , 0.190677 , 0.122216 ) +colvars: ( -0.317472 , 0.0354017 , -0.00990243 ) +colvars: ( -0.248101 , 0.0211007 , 0.0548143 ) +colvars: ( -0.191851 , -0.0670919 , 0.0808348 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 30. colvars: colvarmodule::write_traj_files() @@ -4153,8 +6722,11 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 30. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 30, atoms_new_colvar_forces = { ( -4.65881091939876e+00 , -4.06968120314540e-01 , -1.16840238818501e+00 ), ( -4.01259358032102e+00 , -3.46094103673623e-01 , -9.10739126726648e-01 ), ( -4.08500707211808e+00 , -3.73627074879122e-01 , -9.45708790057030e-01 ), ( -5.49140042669050e+00 , -5.28990826826190e-01 , -1.41142445350943e+00 ), ( 2.52310153882297e-01 , 1.17245050973893e-01 , 3.43233812656448e-01 ), ( 5.01538155268732e+00 , 5.79373455956572e-01 , 1.72319150686184e+00 ), ( 4.23804539388424e+00 , 4.77616972499955e-01 , 1.49540352721395e+00 ), ( -4.66932933661841e-02 , 1.79360249762789e-02 , 3.48195888080529e-01 ), ( 4.22059604661739e+00 , 4.69023894582741e-01 , 1.46663195302982e+00 ), ( 5.59459557872950e+00 , 6.01587933622038e-01 , 1.80780689775655e+00 ), ( 1.22036576053411e-02 , 3.26524769744383e-02 , 2.96886579167257e-01 ), ( 2.71463857431481e-03 , 2.73311738642717e-02 , 2.74505365585359e-01 ), ( 2.55038209539085e-02 , 4.14066479723788e-02 , 3.41715979929007e-01 ), ( 4.57223673038846e-02 , 3.45695136287414e-02 , 2.00598114581399e-01 ), ( 1.87687384216944e-02 , 2.08826494366835e-02 , 1.51861686024796e-01 ), ( 1.13554277538003e-01 , 5.61400918390356e-02 , 1.89513813429391e-01 ), ( 1.59340801145138e-01 , 6.48072574791715e-02 , 1.20815692473921e-01 ), ( 2.38301424210039e-01 , 9.25884298643695e-02 , 1.35666078056799e-01 ), ( 1.29280362701120e-01 , 4.79976864448071e-02 , 5.04112447680767e-02 ), ( 1.25160204334001e-01 , 4.06207218780376e-02 , -1.19369634997108e-02 ), ( 1.04896631401357e-01 , 4.08050540322550e-02 , 6.02276324059099e-02 ), ( 6.80353805583742e-02 , 2.28790287623235e-02 , 1.80250378573932e-03 ), ( 5.34073998551376e-02 , 2.09830827474990e-02 , 3.28196814256284e-02 ), ( -3.74737265029546e-03 , -3.49478322671525e-03 , -2.33124478720126e-02 ), ( -1.76235755051978e-02 , -1.47320771849530e-02 , -9.19395380793947e-02 ), ( -4.99107481254734e-02 , -1.35464979593908e-02 , 3.23094349505738e-02 ), ( -1.16222130293656e-01 , -3.70793398559244e-02 , 1.77383571994701e-02 ), ( -1.56693200381850e-01 , -4.31144610918196e-02 , 9.53505650187003e-02 ), ( -1.02197093582566e-01 , -3.66613140666613e-02 , -2.65411825785693e-02 ), ( -1.38246652814804e-01 , -5.41240772698316e-02 , -8.29679131441682e-02 ), ( -4.78558447552094e-02 , -1.62610800080856e-02 , -3.01360594317225e-03 ), ( -2.55237677150758e-02 , -1.26153609324877e-02 , -4.25626857807359e-02 ), ( 3.19860317098683e-02 , 1.12455380919655e-02 , 5.92957814641218e-03 ), ( 5.13253613542508e-03 , -1.02949683798535e-02 , -1.24737697548967e-01 ), ( -1.17569251341706e-02 , -2.10443969816043e-02 , -1.77850474287525e-01 ), ( 4.99744876498038e-02 , 3.43765614314540e-03 , -1.37541144724287e-01 ), ( 7.79465816443118e-02 , 5.46443654812256e-03 , -2.13460583700742e-01 ), ( 1.37045972366390e-01 , 2.60713052287931e-02 , -2.04282010464686e-01 ), ( 1.83677323443324e-02 , -1.95623160281763e-02 , -2.66890762743745e-01 ), ( 1.93771121279581e-02 , -2.58330372192186e-02 , -3.35530387264055e-01 ), ( -3.54857268323370e-02 , -3.45562660806737e-02 , -2.35948882720711e-01 ), ( -9.74831256497132e-02 , -5.93460093254548e-02 , -2.78532379609905e-01 ), ( -1.36369320069997e-01 , -6.77414792650407e-02 , -2.30933941610206e-01 ), ( -1.53158546674371e-01 , -7.98420084693437e-02 , -2.98429456801982e-01 ), ( -1.81120831575947e-01 , -9.52989983892606e-02 , -3.62057158421327e-01 ), ( -1.90382370507147e-01 , -9.23440416893015e-02 , -2.99253140362582e-01 ), ( -2.31201787327718e-01 , -1.08430352512025e-01 , -3.24845129873043e-01 ), ( -1.16505248632433e-01 , -6.83559056895193e-02 , -3.06181368845499e-01 ), ( -1.71349111804265e-01 , -8.06454986331246e-02 , -2.43713070981057e-01 ), ( -2.22985072315737e-01 , -9.90855597099133e-02 , -2.56257046623407e-01 ), ( -2.57325140138640e-01 , -1.02976127885664e-01 , -1.77622160587966e-01 ) } +colvars: Step 30, atoms_new_colvar_forces = { ( -4.90307975326005e+00 , -4.26225733543381e-01 , -1.22053308603671e+00 ), ( -4.22297087183505e+00 , -3.62442494199016e-01 , -9.50735661238479e-01 ), ( -4.29912876445352e+00 , -3.91390533005689e-01 , -9.87515580247239e-01 ), ( -5.77921092303390e+00 , -5.54287649069281e-01 , -1.47495977987086e+00 ), ( 2.65356136002934e-01 , 1.23311593976203e-01 , 3.60978862767604e-01 ), ( 5.27812205617514e+00 , 6.07577602247141e-01 , 1.80404050943655e+00 ), ( 4.46010973872665e+00 , 5.00825927650522e-01 , 1.56565042090778e+00 ), ( -4.90897880799366e-02 , 1.89343442395363e-02 , 3.66203231954696e-01 ), ( 4.44174750876430e+00 , 4.91782779902844e-01 , 1.53537982250556e+00 ), ( 5.88776138997431e+00 , 6.30688490985852e-01 , 1.89184786482823e+00 ), ( 1.28283537456188e-02 , 3.43817190501085e-02 , 3.12219109929325e-01 ), ( 2.83771733227506e-03 , 2.87788165107353e-02 , 2.88669034847300e-01 ), ( 2.67932791979905e-02 , 4.35828210810016e-02 , 3.59340026944051e-01 ), ( 4.80684918524901e-02 , 3.63712934235141e-02 , 2.10944480492789e-01 ), ( 1.97178060164150e-02 , 2.19729176863718e-02 , 1.59685074926066e-01 ), ( 1.19411355480934e-01 , 5.90439089539159e-02 , 1.99294600559298e-01 ), ( 1.67565738963702e-01 , 6.81398575978061e-02 , 1.27049685373802e-01 ), ( 2.50610767595632e-01 , 9.73451889769484e-02 , 1.42672772601171e-01 ), ( 1.35961527713089e-01 , 5.04606763981971e-02 , 5.30179462490662e-02 ), ( 1.31626466862644e-01 , 4.26925863778725e-02 , -1.25537800418007e-02 ), ( 1.10328293789497e-01 , 4.29073593685366e-02 , 6.33528096761839e-02 ), ( 7.15716970003757e-02 , 2.40572059566817e-02 , 1.91907793334617e-03 ), ( 5.61987920052449e-02 , 2.20759052549978e-02 , 3.45506974196925e-02 ), ( -3.92544322628813e-03 , -3.67147461751479e-03 , -2.44998085731401e-02 ), ( -1.85163739274176e-02 , -1.54965444868468e-02 , -9.66701812716143e-02 ), ( -5.24817497216751e-02 , -1.42279729139575e-02 , 3.39871081690175e-02 ), ( -1.22226267813040e-01 , -3.89689410312519e-02 , 1.86552866093206e-02 ), ( -1.64795590399548e-01 , -4.52987029464466e-02 , 1.00269326059522e-01 ), ( -1.07485701129673e-01 , -3.85431349333781e-02 , -2.79219738188176e-02 ), ( -1.45398113546843e-01 , -5.69100868662167e-02 , -8.72644510579588e-02 ), ( -5.03442862864434e-02 , -1.70992094567624e-02 , -3.18690917892174e-03 ), ( -2.68668696109236e-02 , -1.32795723850870e-02 , -4.47886120406747e-02 ), ( 3.36063332857089e-02 , 1.18069508173135e-02 , 6.20045228222160e-03 ), ( 5.37996985271089e-03 , -1.08555182075379e-02 , -1.31201903447125e-01 ), ( -1.23863135856905e-02 , -2.21672711799062e-02 , -1.87063462802220e-01 ), ( 5.25495022970470e-02 , 3.58042204385178e-03 , -1.44654917000879e-01 ), ( 8.19745689427886e-02 , 5.69771351052933e-03 , -2.24488208253491e-01 ), ( 1.44137616563263e-01 , 2.73634872833788e-02 , -2.14824060751566e-01 ), ( 1.93236245879557e-02 , -2.06160606388858e-02 , -2.80672285281673e-01 ), ( 2.03859247467640e-02 , -2.72215389072033e-02 , -3.52857389215979e-01 ), ( -3.73078227940338e-02 , -3.63671480543213e-02 , -2.48127007216322e-01 ), ( -1.02502990872602e-01 , -6.24297787506450e-02 , -2.92904792063159e-01 ), ( -1.43391468186843e-01 , -7.12407323732318e-02 , -2.42839706278146e-01 ), ( -1.61064523353043e-01 , -8.39810555831483e-02 , -3.13840511755964e-01 ), ( -1.90469091696610e-01 , -1.00240151837942e-01 , -3.80752983783105e-01 ), ( -2.00240955151833e-01 , -9.71346913169516e-02 , -3.14739172740795e-01 ), ( -2.43176487154285e-01 , -1.14051226274309e-01 , -3.41661320813026e-01 ), ( -1.22546440124743e-01 , -7.19227416119533e-02 , -3.22024727428344e-01 ), ( -1.80206054113815e-01 , -8.48186453910810e-02 , -2.56309436200485e-01 ), ( -2.34519685297022e-01 , -1.04207509689336e-01 , -2.69512431299437e-01 ), ( -2.70642328820642e-01 , -1.08283450022580e-01 , -1.86824062764667e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 30, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4192,10 +6764,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 31, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 31, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 31, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 31, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 31, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 31, atoms_positions[size = 51] = { ( 8.22941084026228e+00 , 4.36749769543978e-02 , -7.18621583689367e-01 ), ( 6.83305420288219e+00 , -5.96988975407460e-01 , -5.24166185980071e-01 ), ( 6.10875524310126e+00 , -3.58733500923816e-01 , 8.10731339652800e-01 ), ( 4.90620094583905e+00 , -1.49336137565181e-01 , 7.49533505038693e-01 ), ( 6.99931696608724e+00 , -2.07368476449803e+00 , -8.67716105921819e-01 ), ( 6.80539003638100e+00 , -2.97139186636095e-01 , 1.96695212025050e+00 ), ( 6.09127797716714e+00 , -2.28232556248832e-01 , 3.18631289136950e+00 ), ( 7.14315406746370e+00 , -3.45249092142572e-01 , 4.39200054025935e+00 ), ( 5.32044209121276e+00 , 1.06658887182539e+00 , 3.36725510049905e+00 ), ( 4.18603037560149e+00 , 1.00473045623169e+00 , 3.78962333808555e+00 ), ( 5.84892705851717e+00 , 2.25116097769853e+00 , 2.97030239169369e+00 ), ( 5.14832632924866e+00 , 3.54752561087709e+00 , 2.88175441289174e+00 ), ( 6.29822649453593e+00 , 4.46648668649917e+00 , 2.28584013479202e+00 ), ( 3.85876266979869e+00 , 3.63930487835275e+00 , 2.02194135992216e+00 ), ( 2.82029704916939e+00 , 4.16687282796321e+00 , 2.43133907059033e+00 ), ( 3.90811144966727e+00 , 3.18435644065381e+00 , 7.48741431967163e-01 ), ( 2.76431355179194e+00 , 3.07643748956219e+00 , -7.05785399871600e-02 ), ( 3.12255235446029e+00 , 2.65106606563690e+00 , -1.54208321619305e+00 ), ( 1.55400022995286e+00 , 2.21485573332563e+00 , 4.25446502440629e-01 ), ( 4.14145201665343e-01 , 2.61652135448712e+00 , 4.54610465312730e-01 ), ( 2.05823839185384e+00 , 1.13604124284228e+00 , 1.04671185348618e+00 ), ( 1.23678874253541e+00 , 1.40330017506145e-01 , 1.67859216312030e+00 ), ( 2.08614956330000e+00 , -1.09322444702513e+00 , 2.03993981786123e+00 ), ( 5.74734786829843e-01 , 6.15323230609918e-01 , 2.95284198190612e+00 ), ( -5.89961581429437e-01 , 3.56746753170733e-01 , 3.18593612454118e+00 ), ( 1.28594774705375e+00 , 1.39769439973023e+00 , 3.75924844058372e+00 ), ( 8.79360863105517e-01 , 1.97912354248784e+00 , 5.03609488066649e+00 ), ( 2.08250915154670e+00 , 2.76183205204844e+00 , 5.72601543567959e+00 ), ( -3.58992529289012e-01 , 2.89900987599641e+00 , 4.94901836297140e+00 ), ( -1.11558684442524e+00 , 3.06956005806150e+00 , 5.88488327078344e+00 ), ( -5.42141757288871e-01 , 3.50500614815991e+00 , 3.77101523755500e+00 ), ( -1.46264856467718e+00 , 4.48038996091603e+00 , 3.41659970972265e+00 ), ( -7.45803378814604e-01 , 5.44229325687175e+00 , 2.48046156663435e+00 ), ( -2.74753671508654e+00 , 3.94448582899662e+00 , 2.77298201048496e+00 ), ( -3.80294354604345e+00 , 4.57141070604620e+00 , 2.81312284409483e+00 ), ( -2.69542189659159e+00 , 2.63432658681899e+00 , 2.35391468138239e+00 ), ( -3.80466204071939e+00 , 1.82437737008172e+00 , 2.00436847669041e+00 ), ( -3.35524475150449e+00 , 8.79595506689076e-01 , 8.00182337387689e-01 ), ( -4.25146804812157e+00 , 1.03745427117025e+00 , 3.24395614338712e+00 ), ( -5.46373221310415e+00 , 7.47148061980620e-01 , 3.34217475200824e+00 ), ( -3.37058427268309e+00 , 7.28435592423857e-01 , 4.16411508250186e+00 ), ( -3.66847776419296e+00 , 7.82294633074592e-02 , 5.48104017014891e+00 ), ( -2.37210241559387e+00 , -3.10411740259109e-01 , 6.12867005167131e+00 ), ( -4.48610335711135e+00 , 9.24869842126096e-01 , 6.42062931423176e+00 ), ( -5.35833854877040e+00 , 5.66438513069246e-01 , 7.19573018552646e+00 ), ( -6.30932159115756e+00 , 3.61995396072790e+00 , 6.75484613630149e+00 ), ( -7.01193811435146e+00 , 4.29900249317163e+00 , 7.51452057012353e+00 ), ( -6.63240230872822e+00 , 3.16326438018767e+00 , 5.53818626220439e+00 ), ( -4.10678338443630e+00 , 2.25549878696156e+00 , 6.40106808876789e+00 ), ( -4.81589387776778e+00 , 3.28588167151493e+00 , 7.24117541390520e+00 ), ( -4.01623305667354e+00 , 4.57084667656110e+00 , 7.27491591648259e+00 ) } +colvars: Step 31, atoms_positions[size = 51] = { ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 ), ( 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 ), ( 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 ), ( 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ), ( 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 ), ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 ), ( 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 ), ( 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 ), ( 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 ), ( 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ), ( 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 ), ( 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 ), ( 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 ), ( 3.85883200520895e+00 , 3.63922436728402e+00 , 2.02218088752858e+00 ), ( 2.82032938923108e+00 , 4.16685554537813e+00 , 2.43148015867431e+00 ), ( 3.90823079911895e+00 , 3.18438414673290e+00 , 7.48937105961854e-01 ), ( 2.76446920336375e+00 , 3.07649753215611e+00 , -7.04562871516674e-02 ), ( 3.12275971679476e+00 , 2.65114321973004e+00 , -1.54195140972224e+00 ), ( 1.55413078649145e+00 , 2.21490189090784e+00 , 4.25503959006978e-01 ), ( 4.14270175753656e-01 , 2.61655984189511e+00 , 4.54613742887889e-01 ), ( 2.05834193471718e+00 , 1.13607220316182e+00 , 1.04677734263664e+00 ), ( 1.23685466879391e+00 , 1.40361714181966e-01 , 1.67860069408059e+00 ), ( 2.08624910163651e+00 , -1.09313299449642e+00 , 2.04004343834517e+00 ), ( 5.74788204227826e-01 , 6.15318561758292e-01 , 2.95283366787829e+00 ), ( -5.89937439010981e-01 , 3.56749652514227e-01 , 3.18586841039378e+00 ), ( 1.28605494288232e+00 , 1.39766210774256e+00 , 3.75927316980631e+00 ), ( 8.79300716591884e-01 , 1.97906955320727e+00 , 5.03609181574402e+00 ), ( 2.08238116459080e+00 , 2.76179089252899e+00 , 5.72607895327535e+00 ), ( -3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 ), ( -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 ), ( -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 ), ( -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 ), ( -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 ), ( -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 ), ( -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 ), ( -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 ), ( -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 ), ( -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 ), ( -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 ), ( -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 ), ( -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 ), ( -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 ), ( -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 ), ( -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 ), ( -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 ), ( -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 ), ( -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 ), ( -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 ), ( -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 ), ( -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 ), ( -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ) } colvars: Step 31, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 31, atom_groups_ids[size = 0] = @@ -4212,163 +6784,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 31 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.93633996751009e-01 , -1.41137029745784e-02 , 9.55813726277445e-01 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.91985130036785e-01 , -1.38601172701375e-02 , 9.56322425224181e-01 ). +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 , 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 , 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 , 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 , 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 , 3.85883200520895e+00 , 3.63922436728402e+00 , 2.02218088752858e+00 , 2.82032938923108e+00 , 4.16685554537813e+00 , 2.43148015867431e+00 , 3.90823079911895e+00 , 3.18438414673290e+00 , 7.48937105961854e-01 , 2.76446920336375e+00 , 3.07649753215611e+00 , -7.04562871516674e-02 , 3.12275971679476e+00 , 2.65114321973004e+00 , -1.54195140972224e+00 , 1.55413078649145e+00 , 2.21490189090784e+00 , 4.25503959006978e-01 , 4.14270175753656e-01 , 2.61655984189511e+00 , 4.54613742887889e-01 , 2.05834193471718e+00 , 1.13607220316182e+00 , 1.04677734263664e+00 , 1.23685466879391e+00 , 1.40361714181966e-01 , 1.67860069408059e+00 , 2.08624910163651e+00 , -1.09313299449642e+00 , 2.04004343834517e+00 , 5.74788204227826e-01 , 6.15318561758292e-01 , 2.95283366787829e+00 , -5.89937439010981e-01 , 3.56749652514227e-01 , 3.18586841039378e+00 , 1.28605494288232e+00 , 1.39766210774256e+00 , 3.75927316980631e+00 , 8.79300716591884e-01 , 1.97906955320727e+00 , 5.03609181574402e+00 , 2.08238116459080e+00 , 2.76179089252899e+00 , 5.72607895327535e+00 , -3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 , -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 , -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 , -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 , -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 , -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 , -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 , -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 , -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 , -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 , -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 , -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 , -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 , -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 , -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 , -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 , -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 , -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 , -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 , -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 , -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 , -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 , -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.93633996751009e-01 , -1.41137029745784e-02 , 9.55813726277445e-01 ). +colvars: Colvar "one" has value ( -2.91985130036785e-01 , -1.38601172701375e-02 , 9.56322425224181e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 , 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 , 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 , 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 , 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 , 3.85883200520895e+00 , 3.63922436728402e+00 , 2.02218088752858e+00 , 2.82032938923108e+00 , 4.16685554537813e+00 , 2.43148015867431e+00 , 3.90823079911895e+00 , 3.18438414673290e+00 , 7.48937105961854e-01 , 2.76446920336375e+00 , 3.07649753215611e+00 , -7.04562871516674e-02 , 3.12275971679476e+00 , 2.65114321973004e+00 , -1.54195140972224e+00 , 1.55413078649145e+00 , 2.21490189090784e+00 , 4.25503959006978e-01 , 4.14270175753656e-01 , 2.61655984189511e+00 , 4.54613742887889e-01 , 2.05834193471718e+00 , 1.13607220316182e+00 , 1.04677734263664e+00 , 1.23685466879391e+00 , 1.40361714181966e-01 , 1.67860069408059e+00 , 2.08624910163651e+00 , -1.09313299449642e+00 , 2.04004343834517e+00 , 5.74788204227826e-01 , 6.15318561758292e-01 , 2.95283366787829e+00 , -5.89937439010981e-01 , 3.56749652514227e-01 , 3.18586841039378e+00 , 1.28605494288232e+00 , 1.39766210774256e+00 , 3.75927316980631e+00 , 8.79300716591884e-01 , 1.97906955320727e+00 , 5.03609181574402e+00 , 2.08238116459080e+00 , 2.76179089252899e+00 , 5.72607895327535e+00 , -3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 , -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 , -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 , -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 , -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 , -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 , -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 , -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 , -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 , -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 , -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 , -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 , -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 , -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 , -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 , -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 , -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 , -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 , -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 , -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 , -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 , -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 , -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.3907 , 2.23407 , -15.2127 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.54 , 6.554 , 13.108 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.3907 , 2.23407 , -15.2127 ) to colvar "one". -colvars: Adding total bias energy: 44.0552 +colvars: Adding biasing force ( 65.54 , 6.554 , 13.108 ) to colvar "one". +colvars: Adding total bias energy: 55.8186 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.3907 , 2.23407 , -15.2127 ) +colvars: Force to be applied: ( 65.54 , 6.554 , 13.108 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.93477 , -0.520235 , -1.40933 ) -colvars: ( -4.23157 , -0.446101 , -1.2085 ) -colvars: ( -4.23157 , -0.446101 , -1.2085 ) -colvars: ( -5.63657 , -0.59422 , -1.60976 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.189 , -0.544804 , -1.47232 ) +colvars: ( -4.44957 , -0.467169 , -1.26252 ) +colvars: ( -4.44957 , -0.467169 , -1.26252 ) +colvars: ( -5.92695 , -0.622283 , -1.68171 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.886349 , 0.196149 , 0.607395 ) -colvars: ( 0.768477 , 0.266139 , 0.630863 ) -colvars: ( 0.752296 , 0.259407 , 0.612734 ) -colvars: ( 0.658511 , 0.266364 , 0.567736 ) -colvars: ( 0.646813 , 0.200069 , 0.474371 ) -colvars: ( 0.573444 , 0.342812 , 0.61856 ) -colvars: ( 0.468071 , 0.356205 , 0.575288 ) -colvars: ( 0.392652 , 0.452617 , 0.65776 ) -colvars: ( 0.387428 , 0.311671 , 0.470592 ) -colvars: ( 0.35336 , 0.270069 , 0.396589 ) -colvars: ( 0.358173 , 0.317008 , 0.460693 ) -colvars: ( 0.287807 , 0.274203 , 0.364183 ) -colvars: ( 0.260719 , 0.30317 , 0.386408 ) -colvars: ( 0.349281 , 0.17714 , 0.272819 ) -colvars: ( 0.291499 , 0.13379 , 0.182854 ) -colvars: ( 0.470162 , 0.140801 , 0.295053 ) -colvars: ( 0.541603 , 0.0501797 , 0.217853 ) -colvars: ( 0.66908 , 0.0298935 , 0.264867 ) -colvars: ( 0.550452 , 0.0183477 , 0.181365 ) -colvars: ( 0.534949 , -0.0464645 , 0.087743 ) -colvars: ( 0.571373 , 0.0659609 , 0.255641 ) -colvars: ( 0.570281 , 0.0496732 , 0.23373 ) -colvars: ( 0.606576 , 0.114089 , 0.338826 ) -colvars: ( 0.447932 , 0.0535557 , 0.168241 ) -colvars: ( 0.441385 , -0.00221057 , 0.0916032 ) -colvars: ( 0.347404 , 0.118504 , 0.195123 ) -colvars: ( 0.224811 , 0.126505 , 0.134875 ) -colvars: ( 0.134576 , 0.211522 , 0.193915 ) -colvars: ( 0.196773 , 0.0531328 , 0.0228387 ) -colvars: ( 0.148422 , 0.0168513 , -0.0524507 ) -colvars: ( 0.229462 , 0.0280296 , 0.00889228 ) -colvars: ( 0.215387 , -0.044045 , -0.0933953 ) -colvars: ( 0.249705 , -0.0470071 , -0.0774734 ) -colvars: ( 0.289648 , -0.12933 , -0.161998 ) -colvars: ( 0.24632 , -0.182371 , -0.256288 ) -colvars: ( 0.403232 , -0.143856 , -0.11547 ) -colvars: ( 0.479698 , -0.21874 , -0.169211 ) -colvars: ( 0.608958 , -0.220789 , -0.0973402 ) -colvars: ( 0.433538 , -0.223609 , -0.202194 ) -colvars: ( 0.439065 , -0.291356 , -0.287524 ) -colvars: ( 0.385796 , -0.150999 , -0.134859 ) -colvars: ( 0.332773 , -0.145199 , -0.15786 ) -colvars: ( 0.316771 , -0.059138 , -0.0546447 ) -colvars: ( 0.211303 , -0.154449 , -0.240002 ) -colvars: ( 0.187493 , -0.196463 , -0.308628 ) -colvars: ( 0.0124262 , -0.200513 , -0.414884 ) -colvars: ( -0.077159 , -0.218597 , -0.490178 ) -colvars: ( 0.111025 , -0.249646 , -0.422215 ) -colvars: ( 0.130449 , -0.114246 , -0.234104 ) -colvars: ( 0.0128707 , -0.119075 , -0.308223 ) -colvars: ( -0.0749454 , -0.0390967 , -0.254372 ) +colvars: ( 0.930911 , 0.20625 , 0.636538 ) +colvars: ( 0.80721 , 0.279668 , 0.661201 ) +colvars: ( 0.790157 , 0.272663 , 0.642249 ) +colvars: ( 0.691838 , 0.279795 , 0.594997 ) +colvars: ( 0.679555 , 0.210179 , 0.497067 ) +colvars: ( 0.602599 , 0.359978 , 0.648316 ) +colvars: ( 0.492055 , 0.373929 , 0.602931 ) +colvars: ( 0.412938 , 0.475086 , 0.689449 ) +colvars: ( 0.407387 , 0.327149 , 0.493166 ) +colvars: ( 0.371657 , 0.283416 , 0.41553 ) +colvars: ( 0.376626 , 0.332796 , 0.482841 ) +colvars: ( 0.302739 , 0.287844 , 0.381662 ) +colvars: ( 0.274252 , 0.318307 , 0.405035 ) +colvars: ( 0.367231 , 0.185985 , 0.285815 ) +colvars: ( 0.306589 , 0.140427 , 0.191466 ) +colvars: ( 0.494073 , 0.147924 , 0.309106 ) +colvars: ( 0.569027 , 0.0528321 , 0.22811 ) +colvars: ( 0.70278 , 0.0316464 , 0.277403 ) +colvars: ( 0.578371 , 0.0193509 , 0.189785 ) +colvars: ( 0.562095 , -0.0487117 , 0.0915853 ) +colvars: ( 0.600385 , 0.0693014 , 0.267646 ) +colvars: ( 0.599299 , 0.0521327 , 0.244612 ) +colvars: ( 0.637443 , 0.119742 , 0.3548 ) +colvars: ( 0.47092 , 0.0561049 , 0.175943 ) +colvars: ( 0.464067 , -0.00247766 , 0.0955378 ) +colvars: ( 0.365418 , 0.124243 , 0.204185 ) +colvars: ( 0.236774 , 0.13255 , 0.141022 ) +colvars: ( 0.142071 , 0.22177 , 0.202993 ) +colvars: ( 0.207302 , 0.0555329 , 0.0235434 ) +colvars: ( 0.156581 , 0.0173793 , -0.0554341 ) +colvars: ( 0.241544 , 0.0292629 , 0.0089535 ) +colvars: ( 0.226724 , -0.046379 , -0.0983013 ) +colvars: ( 0.262671 , -0.0493937 , -0.0815566 ) +colvars: ( 0.304665 , -0.135895 , -0.170302 ) +colvars: ( 0.259187 , -0.191614 , -0.269189 ) +colvars: ( 0.423883 , -0.15109 , -0.121551 ) +colvars: ( 0.504145 , -0.229688 , -0.177966 ) +colvars: ( 0.639803 , -0.231759 , -0.102628 ) +colvars: ( 0.455764 , -0.234899 , -0.212599 ) +colvars: ( 0.461566 , -0.306038 , -0.302114 ) +colvars: ( 0.405713 , -0.158739 , -0.141987 ) +colvars: ( 0.350128 , -0.152749 , -0.166146 ) +colvars: ( 0.333387 , -0.0624439 , -0.0579083 ) +colvars: ( 0.222646 , -0.162539 , -0.252261 ) +colvars: ( 0.197685 , -0.206702 , -0.324263 ) +colvars: ( 0.0138353 , -0.210938 , -0.435556 ) +colvars: ( -0.0801846 , -0.229983 , -0.514502 ) +colvars: ( 0.117266 , -0.262419 , -0.443249 ) +colvars: ( 0.137759 , -0.120339 , -0.246015 ) +colvars: ( 0.0143571 , -0.12548 , -0.323714 ) +colvars: ( -0.0778146 , -0.0415406 , -0.26718 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.93477 , 0.520235 , 1.40933 ) -colvars: ( 4.23157 , 0.446101 , 1.2085 ) -colvars: ( 4.23157 , 0.446101 , 1.2085 ) -colvars: ( 5.63657 , 0.59422 , 1.60976 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.189 , 0.544804 , 1.47232 ) +colvars: ( 4.44957 , 0.467169 , 1.26252 ) +colvars: ( 4.44957 , 0.467169 , 1.26252 ) +colvars: ( 5.92695 , 0.622283 , 1.68171 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.612714 , -0.0810492 , -0.361736 ) -colvars: ( -0.551476 , -0.164739 , -0.328901 ) -colvars: ( -0.499874 , -0.14219 , -0.269266 ) -colvars: ( -0.513961 , -0.192597 , -0.300744 ) -colvars: ( -0.504259 , -0.132936 , -0.270497 ) -colvars: ( -0.490784 , -0.285851 , -0.309466 ) -colvars: ( -0.459915 , -0.326746 , -0.29247 ) -colvars: ( -0.439628 , -0.435481 , -0.309415 ) -colvars: ( -0.396598 , -0.290738 , -0.216433 ) -colvars: ( -0.39294 , -0.265163 , -0.203971 ) -colvars: ( -0.345916 , -0.284807 , -0.163432 ) -colvars: ( -0.284907 , -0.247248 , -0.0891838 ) -colvars: ( -0.234877 , -0.262141 , -0.0439898 ) -colvars: ( -0.303332 , -0.142719 , -0.0718115 ) -colvars: ( -0.272473 , -0.113014 , -0.0305779 ) -colvars: ( -0.356384 , -0.0846576 , -0.105218 ) -colvars: ( -0.38201 , 0.0148495 , -0.0968107 ) -colvars: ( -0.430502 , 0.0630591 , -0.129016 ) -colvars: ( -0.421059 , 0.0298703 , -0.130918 ) -colvars: ( -0.409649 , 0.087414 , -0.0996817 ) -colvars: ( -0.466518 , -0.0250669 , -0.195499 ) -colvars: ( -0.502432 , -0.0267431 , -0.232189 ) -colvars: ( -0.553507 , -0.0932021 , -0.306374 ) -colvars: ( -0.451871 , -0.0571019 , -0.191773 ) -colvars: ( -0.459236 , -0.0125001 , -0.18386 ) -colvars: ( -0.397466 , -0.132269 , -0.162881 ) -colvars: ( -0.341167 , -0.163903 , -0.117133 ) -colvars: ( -0.291366 , -0.25515 , -0.0983926 ) -colvars: ( -0.298973 , -0.0899536 , -0.0493056 ) -colvars: ( -0.286701 , -0.0711241 , -0.0304981 ) -colvars: ( -0.277174 , -0.0443182 , -0.0117114 ) -colvars: ( -0.240635 , 0.0315701 , 0.0510948 ) -colvars: ( -0.217289 , 0.0584922 , 0.0838168 ) -colvars: ( -0.284279 , 0.119358 , 0.0373577 ) -colvars: ( -0.257801 , 0.161721 , 0.0785326 ) -colvars: ( -0.353104 , 0.147691 , -0.0221197 ) -colvars: ( -0.401655 , 0.224759 , -0.0444717 ) -colvars: ( -0.471878 , 0.24749 , -0.10728 ) -colvars: ( -0.415207 , 0.204516 , -0.0650523 ) -colvars: ( -0.419726 , 0.26611 , -0.0484419 ) -colvars: ( -0.421434 , 0.116703 , -0.101473 ) -colvars: ( -0.430537 , 0.0860067 , -0.121169 ) -colvars: ( -0.453551 , -0.00866356 , -0.176826 ) -colvars: ( -0.364682 , 0.0747098 , -0.0588278 ) -colvars: ( -0.368888 , 0.101295 , -0.0539257 ) -colvars: ( -0.202709 , 0.108337 , 0.115597 ) -colvars: ( -0.153897 , 0.110317 , 0.165361 ) -colvars: ( -0.227356 , 0.181649 , 0.115992 ) -colvars: ( -0.301908 , 0.0336233 , -0.00981448 ) -colvars: ( -0.235899 , 0.0199591 , 0.0518689 ) -colvars: ( -0.182366 , -0.0640851 , 0.0768356 ) +colvars: ( -0.643354 , -0.0853105 , -0.378373 ) +colvars: ( -0.579171 , -0.173105 , -0.343885 ) +colvars: ( -0.524912 , -0.149487 , -0.281335 ) +colvars: ( -0.539931 , -0.20226 , -0.31443 ) +colvars: ( -0.529746 , -0.139626 , -0.282823 ) +colvars: ( -0.515725 , -0.300083 , -0.323511 ) +colvars: ( -0.483467 , -0.342921 , -0.305739 ) +colvars: ( -0.462281 , -0.457004 , -0.323404 ) +colvars: ( -0.417016 , -0.305106 , -0.2261 ) +colvars: ( -0.413239 , -0.278216 , -0.213128 ) +colvars: ( -0.363753 , -0.298916 , -0.170499 ) +colvars: ( -0.29971 , -0.259483 , -0.0927249 ) +colvars: ( -0.247128 , -0.275156 , -0.0452702 ) +colvars: ( -0.318967 , -0.1498 , -0.0746245 ) +colvars: ( -0.286619 , -0.118584 , -0.0314847 ) +colvars: ( -0.374531 , -0.0889273 , -0.109646 ) +colvars: ( -0.401342 , 0.0154809 , -0.100933 ) +colvars: ( -0.452096 , 0.0659954 , -0.134659 ) +colvars: ( -0.442409 , 0.0312965 , -0.136775 ) +colvars: ( -0.430436 , 0.0917109 , -0.10413 ) +colvars: ( -0.490195 , -0.0263381 , -0.204436 ) +colvars: ( -0.527984 , -0.0280429 , -0.242967 ) +colvars: ( -0.581647 , -0.0977853 , -0.320662 ) +colvars: ( -0.475043 , -0.059827 , -0.200651 ) +colvars: ( -0.482805 , -0.0129832 , -0.192456 ) +colvars: ( -0.418013 , -0.138687 , -0.170296 ) +colvars: ( -0.359036 , -0.171818 , -0.122378 ) +colvars: ( -0.306827 , -0.267566 , -0.102631 ) +colvars: ( -0.314699 , -0.0942094 , -0.0513639 ) +colvars: ( -0.301888 , -0.0743957 , -0.0317357 ) +colvars: ( -0.291694 , -0.0463761 , -0.0119346 ) +colvars: ( -0.253279 , 0.0332576 , 0.053825 ) +colvars: ( -0.228644 , 0.0614407 , 0.088184 ) +colvars: ( -0.299042 , 0.125385 , 0.0393137 ) +colvars: ( -0.271275 , 0.169878 , 0.0823858 ) +colvars: ( -0.371218 , 0.155082 , -0.0230309 ) +colvars: ( -0.422139 , 0.235961 , -0.046561 ) +colvars: ( -0.495753 , 0.259757 , -0.112364 ) +colvars: ( -0.436495 , 0.214791 , -0.068204 ) +colvars: ( -0.441237 , 0.279452 , -0.050895 ) +colvars: ( -0.443148 , 0.122675 , -0.106327 ) +colvars: ( -0.452837 , 0.0905332 , -0.127027 ) +colvars: ( -0.477085 , -0.00879841 , -0.185284 ) +colvars: ( -0.383803 , 0.0787369 , -0.0617281 ) +colvars: ( -0.388277 , 0.106685 , -0.0566816 ) +colvars: ( -0.2138 , 0.114063 , 0.121052 ) +colvars: ( -0.162631 , 0.116188 , 0.173164 ) +colvars: ( -0.239525 , 0.190933 , 0.121456 ) +colvars: ( -0.317925 , 0.0356172 , -0.0102892 ) +colvars: ( -0.248721 , 0.0213301 , 0.054331 ) +colvars: ( -0.192581 , -0.0668646 , 0.0806049 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 31. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 31. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 31, atoms_new_colvar_forces = { ( -4.66113688161655e+00 , -4.05135184602716e-01 , -1.16367389088499e+00 ), ( -4.01456544465088e+00 , -3.44700949904404e-01 , -9.06540597900646e-01 ), ( -4.08701549031908e+00 , -3.72334593613221e-01 , -9.41510912939705e-01 ), ( -5.49401334502561e+00 , -5.27086362162900e-01 , -1.40588628005506e+00 ), ( 2.52421883872536e-01 , 1.17216689223596e-01 , 3.43468021005117e-01 ), ( 5.01743120489049e+00 , 5.77195319297558e-01 , 1.71842718291959e+00 ), ( 4.23972195655386e+00 , 4.75559997317382e-01 , 1.49132072934045e+00 ), ( -4.69761885536258e-02 , 1.71353376620547e-02 , 3.48344991781273e-01 ), ( 4.22239605110036e+00 , 4.67034094164927e-01 , 1.46266171952488e+00 ), ( 5.59698801797817e+00 , 5.99126131386157e-01 , 1.80237850317957e+00 ), ( 1.22569785677200e-02 , 3.22004023080397e-02 , 2.97260925795616e-01 ), ( 2.89947393451162e-03 , 2.69548120952914e-02 , 2.74999354104193e-01 ), ( 2.58417341654628e-02 , 4.10286803199074e-02 , 3.42418185431564e-01 ), ( 4.59489894821550e-02 , 3.44208720431577e-02 , 2.01007023311371e-01 ), ( 1.90262889382226e-02 , 2.07758823646663e-02 , 1.52275976849330e-01 ), ( 1.13777293155053e-01 , 5.61431198344201e-02 , 1.89835449907698e-01 ), ( 1.59592774129915e-01 , 6.50292072234674e-02 , 1.21042022707783e-01 ), ( 2.38577766740824e-01 , 9.29526113299943e-02 , 1.35851173213925e-01 ), ( 1.29392819497884e-01 , 4.82180540366782e-02 , 5.04473049042816e-02 ), ( 1.25299698040462e-01 , 4.09494793887644e-02 , -1.19387084039878e-02 ), ( 1.04855255729952e-01 , 4.08939797955200e-02 , 6.01426459633320e-02 ), ( 6.78483766348649e-02 , 2.29300856713723e-02 , 1.54153626017012e-03 ), ( 5.30682546953771e-02 , 2.08871268240285e-02 , 3.24529105020316e-02 ), ( -3.93969744826089e-03 , -3.54621076703741e-03 , -2.35316890863778e-02 ), ( -1.78506448584630e-02 , -1.47106388087243e-02 , -9.22566850467691e-02 ), ( -5.00623230433725e-02 , -1.37654444146957e-02 , 3.22426742561518e-02 ), ( -1.16356650433801e-01 , -3.73979693387564e-02 , 1.77423188685170e-02 ), ( -1.56790262395194e-01 , -4.36277265470911e-02 , 9.55222918925579e-02 ), ( -1.02200295341637e-01 , -3.68208284205977e-02 , -2.64669747004680e-02 ), ( -1.38278910459662e-01 , -5.42727798771095e-02 , -8.29488556952516e-02 ), ( -4.77117382083829e-02 , -1.62886195485267e-02 , -2.81911927980735e-03 ), ( -2.52474673249706e-02 , -1.24748809918986e-02 , -4.23004726359222e-02 ), ( 3.24161849539219e-02 , 1.14851209317580e-02 , 6.34341234101454e-03 ), ( 5.36897028621786e-03 , -9.97269336708345e-03 , -1.24640530757740e-01 ), ( -1.14814323175646e-02 , -2.06494007483504e-02 , -1.77755054636872e-01 ), ( 5.01283712737642e-02 , 3.83472494588458e-03 , -1.37589945559419e-01 ), ( 7.80433069604085e-02 , 6.01997205558669e-03 , -2.13682326641160e-01 ), ( 1.37079947324538e-01 , 2.67015156433917e-02 , -2.04619770554298e-01 ), ( 1.83308867736479e-02 , -1.90929088493055e-02 , -2.67246705008063e-01 ), ( 1.93391319359338e-02 , -2.52466680488760e-02 , -3.35965427889963e-01 ), ( -3.56379696936009e-02 , -3.42956768451885e-02 , -2.36331912240935e-01 ), ( -9.77638844851895e-02 , -5.91924040976156e-02 , -2.79029743364876e-01 ), ( -1.36780622728546e-01 , -6.78015637844769e-02 , -2.31470958944401e-01 ), ( -1.53379621117242e-01 , -7.97395827371071e-02 , -2.98829541778815e-01 ), ( -1.81395019090666e-01 , -9.51680105579518e-02 , -3.62553593115967e-01 ), ( -1.90282656778418e-01 , -9.21753079908156e-02 , -2.99286406032441e-01 ), ( -2.31055786305619e-01 , -1.08279539418096e-01 , -3.24816807636920e-01 ), ( -1.16330744662527e-01 , -6.79965825131494e-02 , -3.06223265951223e-01 ), ( -1.71458942561447e-01 , -8.06230705850004e-02 , -2.43918805502511e-01 ), ( -2.23028420531419e-01 , -9.91157231288625e-02 , -2.56354539021633e-01 ), ( -2.57311177664526e-01 , -1.03181894194047e-01 , -1.77536832794198e-01 ) } +colvars: Step 31, atoms_new_colvar_forces = { ( -4.90144222016788e+00 , -4.23864257099841e-01 , -1.21415720448235e+00 ), ( -4.22152714599171e+00 , -3.60606652926227e-01 , -9.45200369488746e-01 ), ( -4.29765787123894e+00 , -3.89634933189831e-01 , -9.81949458363150e-01 ), ( -5.77714122557610e+00 , -5.51729841418288e-01 , -1.46746457308585e+00 ), ( 2.65244985751738e-01 , 1.23175919990679e-01 , 3.60913931938642e-01 ), ( 5.27587366386101e+00 , 6.04699578189318e-01 , 1.79712677627654e+00 ), ( 4.45815359902672e+00 , 4.98177747468405e-01 , 1.55970854735073e+00 ), ( -4.93435107962240e-02 , 1.80818210618536e-02 , 3.66044731198671e-01 ), ( 4.43993612550304e+00 , 4.89212550815491e-01 , 1.52958148500933e+00 ), ( 5.88536791075441e+00 , 6.27482878378142e-01 , 1.88410969097645e+00 ), ( 1.28728543357713e-02 , 3.38800306994377e-02 , 3.12342235519133e-01 ), ( 3.02822265175950e-03 , 2.83610379603259e-02 , 2.88937327860488e-01 ), ( 2.71231346340420e-02 , 4.31506543398560e-02 , 3.59765182140659e-01 ), ( 4.82639070398871e-02 , 3.61848084920411e-02 , 2.11190624263480e-01 ), ( 1.99698947164141e-02 , 2.18425541911243e-02 , 1.59980804519905e-01 ), ( 1.19541803339789e-01 , 5.89963159669183e-02 , 1.99459627645205e-01 ), ( 1.67685179467105e-01 , 6.83130744210906e-02 , 1.27177181741412e-01 ), ( 2.50684414945042e-01 , 9.76418262240051e-02 , 1.42743844983514e-01 ), ( 1.35962352709605e-01 , 5.06474272574466e-02 , 5.30102049910314e-02 ), ( 1.31659305261756e-01 , 4.29992197584826e-02 , -1.25447496959555e-02 ), ( 1.10190365494213e-01 , 4.29633137144669e-02 , 6.32097506790836e-02 ), ( 7.13148945687689e-02 , 2.40898048632275e-02 , 1.64489252262806e-03 ), ( 5.57961860012975e-02 , 2.19566534196813e-02 , 3.41379911528583e-02 ), ( -4.12301707828355e-03 , -3.72205361655326e-03 , -2.47077891875423e-02 ), ( -1.87376859605212e-02 , -1.54608598283945e-02 , -9.69185106205518e-02 ), ( -5.25951259489728e-02 , -1.44444125662340e-02 , 3.38881817813012e-02 ), ( -1.22261978100019e-01 , -3.92681995555317e-02 , 1.86433422852362e-02 ), ( -1.64755694359793e-01 , -4.57957779646179e-02 , 1.00362561077624e-01 ), ( -1.07396813606457e-01 , -3.86765688817021e-02 , -2.78205718323948e-02 ), ( -1.45307020710455e-01 , -5.70164349484808e-02 , -8.71697605177388e-02 ), ( -5.01505174429595e-02 , -1.71132398292599e-02 , -2.98106270317924e-03 ), ( -2.65550870531150e-02 , -1.31213981811457e-02 , -4.44763148658900e-02 ), ( 3.40269595685157e-02 , 1.20470666639079e-02 , 6.62740678459722e-03 ), ( 5.62248896412298e-03 , -1.05095785421364e-02 , -1.30987834272355e-01 ), ( -1.20877032066805e-02 , -2.17356493494404e-02 , -1.86803299055070e-01 ), ( 5.26653065073497e-02 , 3.99204202264597e-03 , -1.44581740234569e-01 ), ( 8.20054579045542e-02 , 6.27299736081671e-03 , -2.24527154211662e-01 ), ( 1.44049600904254e-01 , 2.79981112550022e-02 , -2.14992441317378e-01 ), ( 1.92687340086861e-02 , -2.01081097732543e-02 , -2.80803235316266e-01 ), ( 2.03289853616425e-02 , -2.65857576566909e-02 , -3.53009021152050e-01 ), ( -3.74347269455836e-02 , -3.60637435431861e-02 , -2.48314209794155e-01 ), ( -1.02708217603532e-01 , -6.22157029994321e-02 , -2.93173037870197e-01 ), ( -1.43698052848084e-01 , -7.12422629468525e-02 , -2.43192352918266e-01 ), ( -1.61157131361194e-01 , -8.38018816078552e-02 , -3.13989221872837e-01 ), ( -1.90591925485021e-01 , -1.00017171316205e-01 , -3.80944937908953e-01 ), ( -1.99964764452263e-01 , -9.68749058109831e-02 , -3.14503989721018e-01 ), ( -2.42815078108033e-01 , -1.13795597600375e-01 , -3.41338735400356e-01 ), ( -1.22258752994438e-01 , -7.14855908353005e-02 , -3.21792260756661e-01 ), ( -1.80166041310635e-01 , -8.47222792156294e-02 , -2.56304520193778e-01 ), ( -2.34363599989835e-01 , -1.04149378931977e-01 , -2.69383160504516e-01 ), ( -2.70395424944746e-01 , -1.08405194378942e-01 , -1.86574805355087e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 31, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4406,10 +7117,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 32, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 32, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 32, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 32, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 32, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 32, atoms_positions[size = 51] = { ( 8.22025644610011e+00 , 4.37055216046504e-02 , -7.14729272559206e-01 ), ( 6.82945426398495e+00 , -6.03046869416644e-01 , -5.22029034574170e-01 ), ( 6.09715063681014e+00 , -3.50969027036988e-01 , 8.14060420824796e-01 ), ( 4.90432535135465e+00 , -1.50298573950058e-01 , 7.52861782547554e-01 ), ( 6.99711789817992e+00 , -2.07701949038308e+00 , -8.59615092260211e-01 ), ( 6.80172294492906e+00 , -3.01261013154195e-01 , 1.96709235130160e+00 ), ( 6.08570759058685e+00 , -2.31646840319499e-01 , 3.19691902165685e+00 ), ( 7.14758531481322e+00 , -3.46692917288126e-01 , 4.39746558807305e+00 ), ( 5.31554628571039e+00 , 1.06565571809091e+00 , 3.36600902078069e+00 ), ( 4.18847267881250e+00 , 1.00388202075946e+00 , 3.80012630742550e+00 ), ( 5.85143706628531e+00 , 2.25080272687727e+00 , 2.96824791658596e+00 ), ( 5.14105246611948e+00 , 3.54205701785969e+00 , 2.87599097505194e+00 ), ( 6.29325062239867e+00 , 4.46010982708403e+00 , 2.28442810266564e+00 ), ( 3.85882774184686e+00 , 3.63492568223562e+00 , 2.01830788491864e+00 ), ( 2.82594672314431e+00 , 4.16529189701689e+00 , 2.42695896512935e+00 ), ( 3.90484865349249e+00 , 3.17689088390449e+00 , 7.54139586863759e-01 ), ( 2.76648942503954e+00 , 3.08705804793703e+00 , -6.93950152739506e-02 ), ( 3.12744558504317e+00 , 2.65117133289642e+00 , -1.54076214646921e+00 ), ( 1.56095038348625e+00 , 2.22641149158040e+00 , 4.27405594623885e-01 ), ( 4.18759538363859e-01 , 2.61596969517098e+00 , 4.48882249112137e-01 ), ( 2.05126769093368e+00 , 1.12970817680754e+00 , 1.04780851641551e+00 ), ( 1.25009173358664e+00 , 1.46490578823352e-01 , 1.67394197125757e+00 ), ( 2.08908230800507e+00 , -1.09358117505684e+00 , 2.03976049277909e+00 ), ( 5.74126662252645e-01 , 6.15195831391415e-01 , 2.94837225818096e+00 ), ( -5.93007809274588e-01 , 3.57303106276294e-01 , 3.19058391237586e+00 ), ( 1.28569765285871e+00 , 1.40534509336286e+00 , 3.76494171092987e+00 ), ( 8.87171580784718e-01 , 1.97931419064781e+00 , 5.03899291928245e+00 ), ( 2.07328712171941e+00 , 2.76539047549728e+00 , 5.72624147199300e+00 ), ( -3.59795059105076e-01 , 2.89720122350267e+00 , 4.94295627919127e+00 ), ( -1.11604658839503e+00 , 3.07001831801347e+00 , 5.88771348640713e+00 ), ( -5.39780564301514e-01 , 3.50183967049821e+00 , 3.76183834391896e+00 ), ( -1.45734630089973e+00 , 4.47776051640672e+00 , 3.41747718600615e+00 ), ( -7.52674298789564e-01 , 5.44714386066550e+00 , 2.48231410243051e+00 ), ( -2.74904247712941e+00 , 3.94198243376910e+00 , 2.75961592016998e+00 ), ( -3.80125888774024e+00 , 4.57736842353900e+00 , 2.81277453690773e+00 ), ( -2.69987873691698e+00 , 2.63637905734000e+00 , 2.35290162243892e+00 ), ( -3.80819914573231e+00 , 1.82100792831724e+00 , 2.00274632498308e+00 ), ( -3.35286891891693e+00 , 8.82663495728610e-01 , 7.93089446633534e-01 ), ( -4.25290670435825e+00 , 1.03325407596833e+00 , 3.24627259364973e+00 ), ( -5.45587046822941e+00 , 7.41739074756565e-01 , 3.34439122005340e+00 ), ( -3.36962569338273e+00 , 7.27381920070494e-01 , 4.16190335803550e+00 ), ( -3.66749372898384e+00 , 7.59509805069767e-02 , 5.47936541279648e+00 ), ( -2.36639900794246e+00 , -3.04732995730435e-01 , 6.12652629112228e+00 ), ( -4.48915051854569e+00 , 9.29727693847123e-01 , 6.42061214899054e+00 ), ( -5.35715343423749e+00 , 5.60773925730106e-01 , 7.19137430986862e+00 ), ( -6.30816257618388e+00 , 3.61577064167445e+00 , 6.75721558358170e+00 ), ( -7.01900994077516e+00 , 4.29979617627293e+00 , 7.51670827752640e+00 ), ( -6.62506000808668e+00 , 3.16464319275810e+00 , 5.54319705967107e+00 ), ( -4.10782923883749e+00 , 2.25528114373913e+00 , 6.40505076511689e+00 ), ( -4.81474827357504e+00 , 3.28701158886541e+00 , 7.23404586108623e+00 ), ( -4.01237364420152e+00 , 4.58031152041965e+00 , 7.27648138133984e+00 ) } +colvars: Step 32, atoms_positions[size = 51] = { ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 ), ( 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 ), ( 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 ), ( 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 ), ( 6.99636965808843e+00 , -2.07731145361172e+00 , -8.59449502083637e-01 ), ( 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 ), ( 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 ), ( 7.14955265421951e+00 , -3.46986465905089e-01 , 4.39885094483582e+00 ), ( 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 ), ( 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 ), ( 5.85317742297030e+00 , 2.25152071574275e+00 , 2.96821115597796e+00 ), ( 5.14128268036406e+00 , 3.54208563801708e+00 , 2.87632129489601e+00 ), ( 6.29318546387223e+00 , 4.46027939653308e+00 , 2.28475137700503e+00 ), ( 3.85890832969753e+00 , 3.63483645880957e+00 , 2.01856465892203e+00 ), ( 2.82598393890567e+00 , 4.16526878663514e+00 , 2.42710952820913e+00 ), ( 3.90497564120259e+00 , 3.17691629066992e+00 , 7.54347976532677e-01 ), ( 2.76665453227033e+00 , 3.08712116761594e+00 , -6.92647638868437e-02 ), ( 3.12766530233767e+00 , 2.65125298941404e+00 , -1.54062208706149e+00 ), ( 1.56108836342069e+00 , 2.22646006317573e+00 , 4.27466820905454e-01 ), ( 4.18892362207154e-01 , 2.61601125231008e+00 , 4.48886833088300e-01 ), ( 2.05137669540285e+00 , 1.12973908190385e+00 , 1.04787473634801e+00 ), ( 1.25016168604201e+00 , 1.46524404541997e-01 , 1.67395149106674e+00 ), ( 2.08919058564287e+00 , -1.09348074895053e+00 , 2.03987423391713e+00 ), ( 5.74186168979523e-01 , 6.15190892667854e-01 , 2.94836413187145e+00 ), ( -5.92978661025754e-01 , 3.57307762930446e-01 , 3.19051283305154e+00 ), ( 1.28581112343911e+00 , 1.40531159189369e+00 , 3.76496783945832e+00 ), ( 8.87110543080602e-01 , 1.97925651490093e+00 , 5.03898868931191e+00 ), ( 2.07315291122048e+00 , 2.76534667037865e+00 , 5.72630877966077e+00 ), ( -3.59890086708776e-01 , 2.89715477683727e+00 , 4.94292409024734e+00 ), ( -1.11619198406425e+00 , 3.06996673284450e+00 , 5.88764729411060e+00 ), ( -5.39828293654177e-01 , 3.50182389775589e+00 , 3.76181263491333e+00 ), ( -1.45737995469276e+00 , 4.47774979548157e+00 , 3.41742259521307e+00 ), ( -7.52656402540314e-01 , 5.44714686176258e+00 , 2.48230963624217e+00 ), ( -2.74903816285443e+00 , 3.94197213054861e+00 , 2.75948540916468e+00 ), ( -3.80126368217889e+00 , 4.57734229189021e+00 , 2.81260271492884e+00 ), ( -2.69983596459315e+00 , 2.63637902047927e+00 , 2.35275320372801e+00 ), ( -3.80812945779466e+00 , 1.82100657589145e+00 , 2.00251302485744e+00 ), ( -3.35273987959584e+00 , 8.82670239652218e-01 , 7.92872005460967e-01 ), ( -4.25289060329676e+00 , 1.03322899973819e+00 , 3.24599742591875e+00 ), ( -5.45585612158692e+00 , 7.41707491159396e-01 , 3.34406841611962e+00 ), ( -3.36965129496242e+00 , 7.27336540574501e-01 , 4.16165346261809e+00 ), ( -3.66759582428271e+00 , 7.58826722683877e-02 , 5.47907665313511e+00 ), ( -2.36653676520567e+00 , -3.04791642260045e-01 , 6.12630281893083e+00 ), ( -4.48930593261884e+00 , 9.29643058404834e-01 , 6.42030281138112e+00 ), ( -5.35733093367902e+00 , 5.60676121557277e-01 , 7.19103315777678e+00 ), ( -6.30836676717657e+00 , 3.61567551810552e+00 , 6.75690769854272e+00 ), ( -7.01923456785992e+00 , 4.29968920159194e+00 , 7.51639637407081e+00 ), ( -6.62521134252802e+00 , 3.16456400975179e+00 , 5.54286904467815e+00 ), ( -4.10800032264489e+00 , 2.25520167794132e+00 , 6.40478878792620e+00 ), ( -4.81497251925987e+00 , 3.28690173612652e+00 , 7.23378205285441e+00 ), ( -4.01261784991035e+00 , 4.58020866242027e+00 , 7.27629588974665e+00 ) } colvars: Step 32, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 32, atom_groups_ids[size = 0] = @@ -4427,162 +7138,301 @@ colvars: Collective variables module, step no. 32 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.92255140925596e-01 , -1.51601432225139e-02 , 9.56220216613324e-01 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.90537915957777e-01 , -1.48938555217606e-02 , 9.56747559421297e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.99636965808843e+00 , -2.07731145361172e+00 , -8.59449502083637e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 , 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 7.14955265421951e+00 , -3.46986465905089e-01 , 4.39885094483582e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 , 5.85317742297030e+00 , 2.25152071574275e+00 , 2.96821115597796e+00 , 5.14128268036406e+00 , 3.54208563801708e+00 , 2.87632129489601e+00 , 6.29318546387223e+00 , 4.46027939653308e+00 , 2.28475137700503e+00 , 3.85890832969753e+00 , 3.63483645880957e+00 , 2.01856465892203e+00 , 2.82598393890567e+00 , 4.16526878663514e+00 , 2.42710952820913e+00 , 3.90497564120259e+00 , 3.17691629066992e+00 , 7.54347976532677e-01 , 2.76665453227033e+00 , 3.08712116761594e+00 , -6.92647638868437e-02 , 3.12766530233767e+00 , 2.65125298941404e+00 , -1.54062208706149e+00 , 1.56108836342069e+00 , 2.22646006317573e+00 , 4.27466820905454e-01 , 4.18892362207154e-01 , 2.61601125231008e+00 , 4.48886833088300e-01 , 2.05137669540285e+00 , 1.12973908190385e+00 , 1.04787473634801e+00 , 1.25016168604201e+00 , 1.46524404541997e-01 , 1.67395149106674e+00 , 2.08919058564287e+00 , -1.09348074895053e+00 , 2.03987423391713e+00 , 5.74186168979523e-01 , 6.15190892667854e-01 , 2.94836413187145e+00 , -5.92978661025754e-01 , 3.57307762930446e-01 , 3.19051283305154e+00 , 1.28581112343911e+00 , 1.40531159189369e+00 , 3.76496783945832e+00 , 8.87110543080602e-01 , 1.97925651490093e+00 , 5.03898868931191e+00 , 2.07315291122048e+00 , 2.76534667037865e+00 , 5.72630877966077e+00 , -3.59890086708776e-01 , 2.89715477683727e+00 , 4.94292409024734e+00 , -1.11619198406425e+00 , 3.06996673284450e+00 , 5.88764729411060e+00 , -5.39828293654177e-01 , 3.50182389775589e+00 , 3.76181263491333e+00 , -1.45737995469276e+00 , 4.47774979548157e+00 , 3.41742259521307e+00 , -7.52656402540314e-01 , 5.44714686176258e+00 , 2.48230963624217e+00 , -2.74903816285443e+00 , 3.94197213054861e+00 , 2.75948540916468e+00 , -3.80126368217889e+00 , 4.57734229189021e+00 , 2.81260271492884e+00 , -2.69983596459315e+00 , 2.63637902047927e+00 , 2.35275320372801e+00 , -3.80812945779466e+00 , 1.82100657589145e+00 , 2.00251302485744e+00 , -3.35273987959584e+00 , 8.82670239652218e-01 , 7.92872005460967e-01 , -4.25289060329676e+00 , 1.03322899973819e+00 , 3.24599742591875e+00 , -5.45585612158692e+00 , 7.41707491159396e-01 , 3.34406841611962e+00 , -3.36965129496242e+00 , 7.27336540574501e-01 , 4.16165346261809e+00 , -3.66759582428271e+00 , 7.58826722683877e-02 , 5.47907665313511e+00 , -2.36653676520567e+00 , -3.04791642260045e-01 , 6.12630281893083e+00 , -4.48930593261884e+00 , 9.29643058404834e-01 , 6.42030281138112e+00 , -5.35733093367902e+00 , 5.60676121557277e-01 , 7.19103315777678e+00 , -6.30836676717657e+00 , 3.61567551810552e+00 , 6.75690769854272e+00 , -7.01923456785992e+00 , 4.29968920159194e+00 , 7.51639637407081e+00 , -6.62521134252802e+00 , 3.16456400975179e+00 , 5.54286904467815e+00 , -4.10800032264489e+00 , 2.25520167794132e+00 , 6.40478878792620e+00 , -4.81497251925987e+00 , 3.28690173612652e+00 , 7.23378205285441e+00 , -4.01261784991035e+00 , 4.58020866242027e+00 , 7.27629588974665e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.92255140925596e-01 , -1.51601432225139e-02 , 9.56220216613324e-01 ). +colvars: Colvar "one" has value ( -2.90537915957777e-01 , -1.48938555217606e-02 , 9.56747559421297e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.99636965808843e+00 , -2.07731145361172e+00 , -8.59449502083637e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 , 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 7.14955265421951e+00 , -3.46986465905089e-01 , 4.39885094483582e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 , 5.85317742297030e+00 , 2.25152071574275e+00 , 2.96821115597796e+00 , 5.14128268036406e+00 , 3.54208563801708e+00 , 2.87632129489601e+00 , 6.29318546387223e+00 , 4.46027939653308e+00 , 2.28475137700503e+00 , 3.85890832969753e+00 , 3.63483645880957e+00 , 2.01856465892203e+00 , 2.82598393890567e+00 , 4.16526878663514e+00 , 2.42710952820913e+00 , 3.90497564120259e+00 , 3.17691629066992e+00 , 7.54347976532677e-01 , 2.76665453227033e+00 , 3.08712116761594e+00 , -6.92647638868437e-02 , 3.12766530233767e+00 , 2.65125298941404e+00 , -1.54062208706149e+00 , 1.56108836342069e+00 , 2.22646006317573e+00 , 4.27466820905454e-01 , 4.18892362207154e-01 , 2.61601125231008e+00 , 4.48886833088300e-01 , 2.05137669540285e+00 , 1.12973908190385e+00 , 1.04787473634801e+00 , 1.25016168604201e+00 , 1.46524404541997e-01 , 1.67395149106674e+00 , 2.08919058564287e+00 , -1.09348074895053e+00 , 2.03987423391713e+00 , 5.74186168979523e-01 , 6.15190892667854e-01 , 2.94836413187145e+00 , -5.92978661025754e-01 , 3.57307762930446e-01 , 3.19051283305154e+00 , 1.28581112343911e+00 , 1.40531159189369e+00 , 3.76496783945832e+00 , 8.87110543080602e-01 , 1.97925651490093e+00 , 5.03898868931191e+00 , 2.07315291122048e+00 , 2.76534667037865e+00 , 5.72630877966077e+00 , -3.59890086708776e-01 , 2.89715477683727e+00 , 4.94292409024734e+00 , -1.11619198406425e+00 , 3.06996673284450e+00 , 5.88764729411060e+00 , -5.39828293654177e-01 , 3.50182389775589e+00 , 3.76181263491333e+00 , -1.45737995469276e+00 , 4.47774979548157e+00 , 3.41742259521307e+00 , -7.52656402540314e-01 , 5.44714686176258e+00 , 2.48230963624217e+00 , -2.74903816285443e+00 , 3.94197213054861e+00 , 2.75948540916468e+00 , -3.80126368217889e+00 , 4.57734229189021e+00 , 2.81260271492884e+00 , -2.69983596459315e+00 , 2.63637902047927e+00 , 2.35275320372801e+00 , -3.80812945779466e+00 , 1.82100657589145e+00 , 2.00251302485744e+00 , -3.35273987959584e+00 , 8.82670239652218e-01 , 7.92872005460967e-01 , -4.25289060329676e+00 , 1.03322899973819e+00 , 3.24599742591875e+00 , -5.45585612158692e+00 , 7.41707491159396e-01 , 3.34406841611962e+00 , -3.36965129496242e+00 , 7.27336540574501e-01 , 4.16165346261809e+00 , -3.66759582428271e+00 , 7.58826722683877e-02 , 5.47907665313511e+00 , -2.36653676520567e+00 , -3.04791642260045e-01 , 6.12630281893083e+00 , -4.48930593261884e+00 , 9.29643058404834e-01 , 6.42030281138112e+00 , -5.35733093367902e+00 , 5.60676121557277e-01 , 7.19103315777678e+00 , -6.30836676717657e+00 , 3.61567551810552e+00 , 6.75690769854272e+00 , -7.01923456785992e+00 , 4.29968920159194e+00 , 7.51639637407081e+00 , -6.62521134252802e+00 , 3.16456400975179e+00 , 5.54286904467815e+00 , -4.10800032264489e+00 , 2.25520167794132e+00 , 6.40478878792620e+00 , -4.81497251925987e+00 , 3.28690173612652e+00 , 7.23378205285441e+00 , -4.01261784991035e+00 , 4.58020866242027e+00 , 7.27629588974665e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.3631 , 2.255 , -15.2208 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.4759 , 6.54759 , 13.0952 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.3631 , 2.255 , -15.2208 ) to colvar "one". -colvars: Adding total bias energy: 44.0022 +colvars: Adding biasing force ( 65.4759 , 6.54759 , 13.0952 ) to colvar "one". +colvars: Adding total bias energy: 55.725 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.3631 , 2.255 , -15.2208 ) +colvars: Force to be applied: ( 65.4759 , 6.54759 , 13.0952 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.93728 , -0.518296 , -1.4038 ) -colvars: ( -4.23372 , -0.444438 , -1.20375 ) -colvars: ( -4.23372 , -0.444438 , -1.20375 ) -colvars: ( -5.63943 , -0.592005 , -1.60344 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.1862 , -0.542113 , -1.46457 ) +colvars: ( -4.44716 , -0.464862 , -1.25587 ) +colvars: ( -4.44716 , -0.464862 , -1.25587 ) +colvars: ( -5.92375 , -0.61921 , -1.67285 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.885736 , 0.196198 , 0.606052 ) -colvars: ( 0.768032 , 0.266064 , 0.62949 ) -colvars: ( 0.751846 , 0.259383 , 0.611451 ) -colvars: ( 0.658245 , 0.266201 , 0.566465 ) -colvars: ( 0.646569 , 0.199959 , 0.473274 ) -colvars: ( 0.573312 , 0.342511 , 0.61718 ) -colvars: ( 0.468111 , 0.355803 , 0.573967 ) -colvars: ( 0.392808 , 0.452068 , 0.656276 ) -colvars: ( 0.387578 , 0.311287 , 0.469496 ) -colvars: ( 0.353575 , 0.269683 , 0.395612 ) -colvars: ( 0.358341 , 0.316649 , 0.459664 ) -colvars: ( 0.288067 , 0.273871 , 0.363366 ) -colvars: ( 0.260991 , 0.302845 , 0.3856 ) -colvars: ( 0.349451 , 0.17694 , 0.272176 ) -colvars: ( 0.291759 , 0.133594 , 0.182381 ) -colvars: ( 0.470148 , 0.140712 , 0.29437 ) -colvars: ( 0.541484 , 0.0502205 , 0.217315 ) -colvars: ( 0.668761 , 0.0300459 , 0.264253 ) -colvars: ( 0.550347 , 0.0183755 , 0.180848 ) -colvars: ( 0.534872 , -0.0463878 , 0.0874003 ) -colvars: ( 0.571257 , 0.0659168 , 0.254944 ) -colvars: ( 0.570194 , 0.0495949 , 0.233026 ) -colvars: ( 0.60645 , 0.113937 , 0.337888 ) -colvars: ( 0.448036 , 0.0533883 , 0.167652 ) -colvars: ( 0.441513 , -0.00234953 , 0.0911393 ) -colvars: ( 0.34765 , 0.118229 , 0.1945 ) -colvars: ( 0.225245 , 0.126145 , 0.134365 ) -colvars: ( 0.135133 , 0.211045 , 0.193312 ) -colvars: ( 0.197237 , 0.0528526 , 0.0225684 ) -colvars: ( 0.148971 , 0.0165572 , -0.0525963 ) -colvars: ( 0.229852 , 0.0278384 , 0.00869276 ) -colvars: ( 0.215786 , -0.0441471 , -0.093372 ) -colvars: ( 0.250024 , -0.0470344 , -0.0774303 ) -colvars: ( 0.289948 , -0.129327 , -0.161866 ) -colvars: ( 0.246688 , -0.182343 , -0.255976 ) -colvars: ( 0.403372 , -0.143789 , -0.115447 ) -colvars: ( 0.479737 , -0.218579 , -0.169111 ) -colvars: ( 0.608807 , -0.220557 , -0.0973883 ) -colvars: ( 0.433673 , -0.223519 , -0.202078 ) -colvars: ( 0.439201 , -0.291209 , -0.287256 ) -colvars: ( 0.386017 , -0.151035 , -0.134897 ) -colvars: ( 0.333099 , -0.145317 , -0.157898 ) -colvars: ( 0.317133 , -0.0593765 , -0.0549063 ) -colvars: ( 0.211809 , -0.154625 , -0.239875 ) -colvars: ( 0.18805 , -0.196639 , -0.308396 ) -colvars: ( 0.0131927 , -0.200687 , -0.414345 ) -colvars: ( -0.0762583 , -0.218804 , -0.489491 ) -colvars: ( 0.111631 , -0.24969 , -0.42164 ) -colvars: ( 0.131056 , -0.114474 , -0.233952 ) -colvars: ( 0.013651 , -0.119359 , -0.307918 ) -colvars: ( -0.0740482 , -0.0394861 , -0.254144 ) +colvars: ( 0.929247 , 0.206087 , 0.634371 ) +colvars: ( 0.805863 , 0.27929 , 0.658977 ) +colvars: ( 0.788819 , 0.272351 , 0.640143 ) +colvars: ( 0.69081 , 0.279321 , 0.592956 ) +colvars: ( 0.678563 , 0.209837 , 0.495321 ) +colvars: ( 0.601814 , 0.359267 , 0.6461 ) +colvars: ( 0.491577 , 0.373091 , 0.60083 ) +colvars: ( 0.412672 , 0.473979 , 0.687076 ) +colvars: ( 0.407119 , 0.326381 , 0.491429 ) +colvars: ( 0.371498 , 0.282692 , 0.414008 ) +colvars: ( 0.376408 , 0.332051 , 0.481188 ) +colvars: ( 0.302699 , 0.287176 , 0.380351 ) +colvars: ( 0.274254 , 0.317615 , 0.403709 ) +colvars: ( 0.367022 , 0.18557 , 0.284797 ) +colvars: ( 0.306543 , 0.140065 , 0.190735 ) +colvars: ( 0.493528 , 0.147671 , 0.308016 ) +colvars: ( 0.568286 , 0.0528233 , 0.227266 ) +colvars: ( 0.701676 , 0.0317829 , 0.276421 ) +colvars: ( 0.577637 , 0.0193628 , 0.189005 ) +colvars: ( 0.561409 , -0.0485738 , 0.0911015 ) +colvars: ( 0.599617 , 0.0691808 , 0.266585 ) +colvars: ( 0.598566 , 0.0519924 , 0.243569 ) +colvars: ( 0.636629 , 0.119448 , 0.353382 ) +colvars: ( 0.470534 , 0.0558623 , 0.175101 ) +colvars: ( 0.463714 , -0.00262705 , 0.0949186 ) +colvars: ( 0.365299 , 0.12381 , 0.203276 ) +colvars: ( 0.236997 , 0.132014 , 0.140305 ) +colvars: ( 0.142531 , 0.221011 , 0.20211 ) +colvars: ( 0.207588 , 0.0551672 , 0.0232156 ) +colvars: ( 0.157015 , 0.0170386 , -0.0555402 ) +colvars: ( 0.241711 , 0.0290234 , 0.00871818 ) +colvars: ( 0.226914 , -0.04644 , -0.0981778 ) +colvars: ( 0.262733 , -0.0493688 , -0.08143 ) +colvars: ( 0.304664 , -0.135745 , -0.169983 ) +colvars: ( 0.259308 , -0.191378 , -0.268567 ) +colvars: ( 0.42358 , -0.150854 , -0.121405 ) +colvars: ( 0.503647 , -0.229266 , -0.177676 ) +colvars: ( 0.638952 , -0.231257 , -0.102582 ) +colvars: ( 0.455424 , -0.234549 , -0.212253 ) +colvars: ( 0.461221 , -0.305551 , -0.301507 ) +colvars: ( 0.405522 , -0.15861 , -0.141886 ) +colvars: ( 0.350113 , -0.152716 , -0.166017 ) +colvars: ( 0.333432 , -0.0626397 , -0.0581401 ) +colvars: ( 0.222963 , -0.162559 , -0.251858 ) +colvars: ( 0.198086 , -0.206676 , -0.323668 ) +colvars: ( 0.0146568 , -0.210905 , -0.434504 ) +colvars: ( -0.0791164 , -0.229966 , -0.513202 ) +colvars: ( 0.1178 , -0.262188 , -0.442151 ) +colvars: ( 0.138277 , -0.120462 , -0.245591 ) +colvars: ( 0.0151954 , -0.125658 , -0.323038 ) +colvars: ( -0.0767504 , -0.0419235 , -0.266647 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.93728 , 0.518296 , 1.4038 ) -colvars: ( 4.23372 , 0.444438 , 1.20375 ) -colvars: ( 4.23372 , 0.444438 , 1.20375 ) -colvars: ( 5.63943 , 0.592005 , 1.60344 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.1862 , 0.542113 , 1.46457 ) +colvars: ( 4.44716 , 0.464862 , 1.25587 ) +colvars: ( 4.44716 , 0.464862 , 1.25587 ) +colvars: ( 5.92375 , 0.61921 , 1.67285 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.612168 , -0.081011 , -0.360463 ) -colvars: ( -0.551073 , -0.164756 , -0.327442 ) -colvars: ( -0.499291 , -0.142183 , -0.267708 ) -colvars: ( -0.51378 , -0.192622 , -0.299395 ) -colvars: ( -0.504073 , -0.132909 , -0.269369 ) -colvars: ( -0.490803 , -0.285945 , -0.307958 ) -colvars: ( -0.46017 , -0.326861 , -0.291036 ) -colvars: ( -0.440063 , -0.435679 , -0.307743 ) -colvars: ( -0.39685 , -0.290809 , -0.215124 ) -colvars: ( -0.393296 , -0.265208 , -0.202862 ) -colvars: ( -0.34604 , -0.284868 , -0.162011 ) -colvars: ( -0.285003 , -0.247266 , -0.0878676 ) -colvars: ( -0.23484 , -0.262166 , -0.0424783 ) -colvars: ( -0.30329 , -0.142656 , -0.0707586 ) -colvars: ( -0.272495 , -0.112917 , -0.0296973 ) -colvars: ( -0.356151 , -0.0845614 , -0.104204 ) -colvars: ( -0.381637 , 0.0150211 , -0.0960399 ) -colvars: ( -0.429894 , 0.0632544 , -0.128202 ) -colvars: ( -0.420832 , 0.0300523 , -0.130356 ) -colvars: ( -0.409424 , 0.0876477 , -0.0993387 ) -colvars: ( -0.466427 , -0.0249362 , -0.194869 ) -colvars: ( -0.502509 , -0.0266149 , -0.231725 ) -colvars: ( -0.55369 , -0.0931371 , -0.30577 ) -colvars: ( -0.452155 , -0.0569825 , -0.191391 ) -colvars: ( -0.459575 , -0.0123419 , -0.183705 ) -colvars: ( -0.397862 , -0.1322 , -0.162317 ) -colvars: ( -0.341744 , -0.163844 , -0.11662 ) -colvars: ( -0.292039 , -0.255156 , -0.0976213 ) -colvars: ( -0.299454 , -0.0898256 , -0.0489732 ) -colvars: ( -0.287298 , -0.0709734 , -0.0303509 ) -colvars: ( -0.277437 , -0.0441544 , -0.0113328 ) -colvars: ( -0.240779 , 0.0318019 , 0.0513086 ) -colvars: ( -0.217203 , 0.0587436 , 0.0841605 ) -colvars: ( -0.284356 , 0.119654 , 0.0372984 ) -colvars: ( -0.257911 , 0.16206 , 0.0782838 ) -colvars: ( -0.35309 , 0.147995 , -0.0222064 ) -colvars: ( -0.401587 , 0.225118 , -0.0448062 ) -colvars: ( -0.47167 , 0.24785 , -0.107571 ) -colvars: ( -0.415367 , 0.204863 , -0.065538 ) -colvars: ( -0.419885 , 0.266508 , -0.0491619 ) -colvars: ( -0.421796 , 0.116981 , -0.101826 ) -colvars: ( -0.431131 , 0.0862639 , -0.121637 ) -colvars: ( -0.45431 , -0.00848623 , -0.177102 ) -colvars: ( -0.365409 , 0.0749749 , -0.0593749 ) -colvars: ( -0.369718 , 0.101586 , -0.0546776 ) -colvars: ( -0.203403 , 0.108662 , 0.114978 ) -colvars: ( -0.154688 , 0.110656 , 0.164646 ) -colvars: ( -0.227809 , 0.182023 , 0.11533 ) -colvars: ( -0.302637 , 0.0338655 , -0.0101983 ) -colvars: ( -0.236746 , 0.0202066 , 0.0514294 ) -colvars: ( -0.183284 , -0.0638968 , 0.0766535 ) +colvars: ( -0.642068 , -0.0851862 , -0.376556 ) +colvars: ( -0.578111 , -0.172937 , -0.341911 ) +colvars: ( -0.52372 , -0.149325 , -0.279328 ) +colvars: ( -0.539153 , -0.202066 , -0.312608 ) +colvars: ( -0.528976 , -0.139445 , -0.281275 ) +colvars: ( -0.51519 , -0.299847 , -0.321509 ) +colvars: ( -0.483222 , -0.342655 , -0.303838 ) +colvars: ( -0.462253 , -0.456695 , -0.321228 ) +colvars: ( -0.416844 , -0.304836 , -0.224427 ) +colvars: ( -0.413183 , -0.277948 , -0.211685 ) +colvars: ( -0.363504 , -0.298645 , -0.168772 ) +colvars: ( -0.299502 , -0.25921 , -0.0912023 ) +colvars: ( -0.246837 , -0.274876 , -0.0435951 ) +colvars: ( -0.318588 , -0.149567 , -0.0734041 ) +colvars: ( -0.286346 , -0.118348 , -0.0304997 ) +colvars: ( -0.373885 , -0.0887306 , -0.108426 ) +colvars: ( -0.400515 , 0.015638 , -0.099982 ) +colvars: ( -0.450959 , 0.0661167 , -0.133622 ) +colvars: ( -0.441693 , 0.0314491 , -0.136005 ) +colvars: ( -0.429736 , 0.0918506 , -0.103632 ) +colvars: ( -0.48957 , -0.0261733 , -0.203513 ) +colvars: ( -0.527498 , -0.0278763 , -0.242176 ) +colvars: ( -0.581214 , -0.0976062 , -0.31963 ) +colvars: ( -0.474839 , -0.0596305 , -0.199999 ) +colvars: ( -0.482652 , -0.0127972 , -0.192056 ) +colvars: ( -0.417993 , -0.138453 , -0.169485 ) +colvars: ( -0.359277 , -0.171554 , -0.121679 ) +colvars: ( -0.307231 , -0.267261 , -0.101679 ) +colvars: ( -0.314888 , -0.0939609 , -0.0509416 ) +colvars: ( -0.302217 , -0.0741435 , -0.0315347 ) +colvars: ( -0.291675 , -0.0461468 , -0.0115093 ) +colvars: ( -0.253175 , 0.033468 , 0.0539963 ) +colvars: ( -0.22832 , 0.0616366 , 0.0884538 ) +colvars: ( -0.298815 , 0.125559 , 0.0392107 ) +colvars: ( -0.271113 , 0.170048 , 0.0820294 ) +colvars: ( -0.37081 , 0.155229 , -0.0230887 ) +colvars: ( -0.421617 , 0.236074 , -0.0468554 ) +colvars: ( -0.494997 , 0.259841 , -0.112534 ) +colvars: ( -0.436202 , 0.214918 , -0.0686346 ) +colvars: ( -0.440938 , 0.279563 , -0.0515964 ) +colvars: ( -0.443064 , 0.122836 , -0.106571 ) +colvars: ( -0.452991 , 0.0907125 , -0.12737 ) +colvars: ( -0.47739 , -0.00858991 , -0.185352 ) +colvars: ( -0.384178 , 0.0789403 , -0.0622331 ) +colvars: ( -0.388758 , 0.106886 , -0.0574115 ) +colvars: ( -0.214332 , 0.11429 , 0.120253 ) +colvars: ( -0.163324 , 0.11643 , 0.1722 ) +colvars: ( -0.239769 , 0.191123 , 0.120612 ) +colvars: ( -0.318376 , 0.0358451 , -0.010681 ) +colvars: ( -0.249378 , 0.0215821 , 0.0538028 ) +colvars: ( -0.193377 , -0.0665749 , 0.0803201 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 32. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 32. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 32, atoms_new_colvar_forces = { ( -4.66371102591230e+00 , -4.03108964363214e-01 , -1.15820798596336e+00 ), ( -4.01675663350797e+00 , -3.43130137810241e-01 , -9.01707106066292e-01 ), ( -4.08925044966919e+00 , -3.70860108725764e-01 , -9.36685231752763e-01 ), ( -5.49693601592321e+00 , -5.24954207557312e-01 , -1.39953153167732e+00 ), ( 2.52554295812457e-01 , 1.17199880609433e-01 , 3.43743015528026e-01 ), ( 5.01978731179025e+00 , 5.74861572024135e-01 , 1.71301867903129e+00 ), ( 4.24165735603726e+00 , 4.73380521419315e-01 , 1.48668606921446e+00 ), ( -4.72546736643991e-02 , 1.63891815790046e-02 , 3.48532627110861e-01 ), ( 4.22444428474445e+00 , 4.64916443920783e-01 , 1.45812711877909e+00 ), ( 5.59971110612098e+00 , 5.96479709432429e-01 , 1.79618621805133e+00 ), ( 1.23008468655991e-02 , 3.17806401081756e-02 , 2.97652475730474e-01 ), ( 3.06469063464188e-03 , 2.66051153802273e-02 , 2.75498708322126e-01 ), ( 2.61508432088345e-02 , 4.06783998890108e-02 , 3.43121657631734e-01 ), ( 4.61612378118703e-02 , 3.42844957475941e-02 , 2.01417820198638e-01 ), ( 1.92645195514352e-02 , 2.06774247491469e-02 , 1.52683940566499e-01 ), ( 1.13996482945326e-01 , 5.61502908543405e-02 , 1.90165461674944e-01 ), ( 1.59847355211528e-01 , 6.52416205323519e-02 , 1.21274797105210e-01 ), ( 2.38866271080539e-01 , 9.33002275995184e-02 , 1.36050074004627e-01 ), ( 1.29515114960020e-01 , 4.84278175314965e-02 , 5.04919822170475e-02 ), ( 1.25448073601597e-01 , 4.12598532743568e-02 , -1.19383341771881e-02 ), ( 1.04830783767252e-01 , 4.09805880377966e-02 , 6.00753899202985e-02 ), ( 6.76846351085205e-02 , 2.29800541197846e-02 , 1.30100616918369e-03 ), ( 5.27602235630881e-02 , 2.07998341590421e-02 , 3.21179821468798e-02 ), ( -4.11834679177236e-03 , -3.59422003470590e-03 , -2.37391576435703e-02 ), ( -1.80618954532191e-02 , -1.46914480780025e-02 , -9.25655735811133e-02 ), ( -5.02113274078761e-02 , -1.39709047056644e-02 , 3.21837401792543e-02 ), ( -1.16499231796863e-01 , -3.76985895625691e-02 , 1.77451109272561e-02 ), ( -1.56905970204270e-01 , -4.41107915627325e-02 , 9.56911853435947e-02 ), ( -1.02217688175030e-01 , -3.69729669167259e-02 , -2.64048015758559e-02 ), ( -1.38327199632664e-01 , -5.44162375232505e-02 , -8.29472186361900e-02 ), ( -4.75848419275651e-02 , -1.63159791008098e-02 , -2.64002023231284e-03 ), ( -2.49934619343552e-02 , -1.23451677871875e-02 , -4.20634066880590e-02 ), ( 3.28203992193124e-02 , 1.17091776468809e-02 , 6.73026623476447e-03 ), ( 5.59253081824335e-03 , -9.67284311954994e-03 , -1.24567987384370e-01 ), ( -1.12227400726866e-02 , -2.02825749746560e-02 , -1.77692310560003e-01 ), ( 5.02821784521819e-02 , 4.20576744836687e-03 , -1.37653731562304e-01 ), ( 7.81500500880993e-02 , 6.53935916657833e-03 , -2.13917157994911e-01 ), ( 1.37136884228048e-01 , 2.72925288160855e-02 , -2.04959465287842e-01 ), ( 1.83060832079743e-02 , -1.86558758877152e-02 , -2.67615889250135e-01 ), ( 1.93151507462338e-02 , -2.47008717780605e-02 , -3.36418092191162e-01 ), ( -3.57787137323783e-02 , -3.40548260393282e-02 , -2.36723431730402e-01 ), ( -9.80321088681891e-02 , -5.90533841039637e-02 , -2.79535637804341e-01 ), ( -1.37177069516403e-01 , -6.78626948157561e-02 , -2.32008029886811e-01 ), ( -1.53600112564750e-01 , -7.96502197231649e-02 , -2.99249454025762e-01 ), ( -1.81667382585330e-01 , -9.50531689033827e-02 , -3.63073174329622e-01 ), ( -1.90210588269541e-01 , -9.20256077497498e-02 , -2.99366242248604e-01 ), ( -2.30946095334873e-01 , -1.08148023110278e-01 , -3.24844250519836e-01 ), ( -1.16178110918724e-01 , -6.76669024793121e-02 , -3.06309936976110e-01 ), ( -1.71580143375189e-01 , -8.06087224475810e-02 , -2.44150524929662e-01 ), ( -2.23095161228034e-01 , -9.91521899124832e-02 , -2.56488893382598e-01 ), ( -2.57331721108966e-01 , -1.03382875272694e-01 , -1.77490748029093e-01 ) } +colvars: Step 32, atoms_new_colvar_forces = { ( -4.89901623608828e+00 , -4.21212105439454e-01 , -1.20675405543204e+00 ), ( -4.21941026749058e+00 , -3.58509287615206e-01 , -9.38802091181616e-01 ), ( -4.29550516629087e+00 , -3.87606873394999e-01 , -9.75520065438497e-01 ), ( -5.77416070326823e+00 , -5.48818010972503e-01 , -1.45880616208910e+00 ), ( 2.65099014903990e-01 , 1.23026262617554e-01 , 3.60814731993440e-01 ), ( 5.27281908690535e+00 , 6.01532720199336e-01 , 1.78915998936798e+00 ), ( 4.45551616813221e+00 , 4.95298085272648e-01 , 1.55286025808800e+00 ), ( -4.95815471725800e-02 , 1.72843496173996e-02 , 3.65848675189791e-01 ), ( 4.43743592731942e+00 , 4.86406990199900e-01 , 1.52286976483447e+00 ), ( 5.88206302540194e+00 , 6.23953510095548e-01 , 1.87517495993694e+00 ), ( 1.29045883632012e-02 , 3.34059942768686e-02 , 3.12416348184590e-01 ), ( 3.19710743210999e-03 , 2.79659989125077e-02 , 2.89148900271214e-01 ), ( 2.74162961204530e-02 , 4.27391604120190e-02 , 3.60113848518582e-01 ), ( 4.84335198759082e-02 , 3.60038159593996e-02 , 2.11393076425405e-01 ), ( 2.01969306989698e-02 , 2.17164911558664e-02 , 1.60235075960962e-01 ), ( 1.19642400128311e-01 , 5.89405306509370e-02 , 1.99590445877788e-01 ), ( 1.67771244691595e-01 , 6.84613089428121e-02 , 1.27283983130076e-01 ), ( 2.50717048694493e-01 , 9.78995789947894e-02 , 1.42798733669189e-01 ), ( 1.35944414670681e-01 , 5.08118322422355e-02 , 5.30001864232874e-02 ), ( 1.31673233890351e-01 , 4.32767424108246e-02 , -1.25308255102823e-02 ), ( 1.10046878858193e-01 , 4.30075248940974e-02 , 6.30720670584440e-02 ), ( 7.10677615500781e-02 , 2.41160393221906e-02 , 1.39235609554561e-03 ), ( 5.54150999536903e-02 , 2.18420305923133e-02 , 3.37522292529012e-02 ), ( -4.30496233894195e-03 , -3.76814654740749e-03 , -2.48977117651731e-02 ), ( -1.89379453745768e-02 , -1.54242926734249e-02 , -9.71369411860667e-02 ), ( -5.26943270100179e-02 , -1.46431749814066e-02 , 3.37904161404535e-02 ), ( -1.22279922078893e-01 , -3.95395538730484e-02 , 1.86262020671471e-02 ), ( -1.64700201434934e-01 , -4.62503640619868e-02 , 1.00431159156065e-01 ), ( -1.07300021070443e-01 , -3.87937148986723e-02 , -2.77260550974223e-02 ), ( -1.45201848022389e-01 , -5.71048577355892e-02 , -8.70748982326622e-02 ), ( -4.99644683248194e-02 , -1.71233897329648e-02 , -2.79114193213090e-03 ), ( -2.62616432622688e-02 , -1.29720294014966e-02 , -4.41815213489942e-02 ), ( 3.44122448293593e-02 , 1.22678289936801e-02 , 7.02377292264314e-03 ), ( 5.84981230496784e-03 , -1.01856109948020e-02 , -1.30772013183318e-01 ), ( -1.18047324085575e-02 , -2.13297960364434e-02 , -1.86537986109577e-01 ), ( 5.27695344595943e-02 , 4.37467489199533e-03 , -1.44493504104997e-01 ), ( 8.20292579336356e-02 , 6.80785814848911e-03 , -2.24531721265885e-01 ), ( 1.43955044997743e-01 , 2.85843428374076e-02 , -2.15116515543712e-01 ), ( 1.92224718115093e-02 , -1.96308372910681e-02 , -2.80887745664687e-01 ), ( 2.02825062721775e-02 , -2.59881258034823e-02 , -3.53103323051673e-01 ), ( -3.75412989644534e-02 , -3.57739328582618e-02 , -2.48456825072293e-01 ), ( -1.02877904682546e-01 , -6.20040345771192e-02 , -2.93386981776436e-01 ), ( -1.43957691018780e-01 , -7.12296304161886e-02 , -2.43492325778459e-01 ), ( -1.61214463063843e-01 , -8.36188257382807e-02 , -3.14091273937705e-01 ), ( -1.90671822527993e-01 , -9.97901592326389e-02 , -3.81079307509172e-01 ), ( -1.99675356076596e-01 , -9.66148671802132e-02 , -3.14250876260084e-01 ), ( -2.42440547743016e-01 , -1.13536360807562e-01 , -3.41002304847089e-01 ), ( -1.21968433860914e-01 , -7.10651110429882e-02 , -3.21538410973349e-01 ), ( -1.80099495368551e-01 , -8.46164409888168e-02 , -2.56272057953793e-01 ), ( -2.34182235834206e-01 , -1.04075676068759e-01 , -2.69235211898796e-01 ), ( -2.70127379422657e-01 , -1.08498461276038e-01 , -1.86327326419902e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 32, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4620,10 +7470,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 33, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 33, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 33, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 33, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 33, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 33, atoms_positions[size = 51] = { ( 8.21019791909521e+00 , 4.35633802325072e-02 , -7.10804529210888e-01 ), ( 6.82610715402917e+00 , -6.08702601628082e-01 , -5.19660907800472e-01 ), ( 6.08636982847500e+00 , -3.43516541447193e-01 , 8.16109789822522e-01 ), ( 4.90171740614450e+00 , -1.51234661265515e-01 , 7.56383814582825e-01 ), ( 6.99590387864465e+00 , -2.08071358662901e+00 , -8.51425606012143e-01 ), ( 6.79779319273434e+00 , -3.05109564227999e-01 , 1.96640893949061e+00 ), ( 6.08156543438362e+00 , -2.34562584634943e-01 , 3.20903737278150e+00 ), ( 7.15097502010524e+00 , -3.48679337406306e-01 , 4.40271942538223e+00 ), ( 5.31096306737649e+00 , 1.06496399948851e+00 , 3.36458768786987e+00 ), ( 4.19051563911193e+00 , 1.00331723044316e+00 , 3.81087672380921e+00 ), ( 5.85349645287331e+00 , 2.25095102916827e+00 , 2.96607854054684e+00 ), ( 5.13531478217963e+00 , 3.53630270778699e+00 , 2.87041395678720e+00 ), ( 6.28781736907147e+00 , 4.45353109012302e+00 , 2.28383910326184e+00 ), ( 3.85899355872802e+00 , 3.63091209857713e+00 , 2.01472246475161e+00 ), ( 2.83174176427113e+00 , 4.16349116383337e+00 , 2.42281879466273e+00 ), ( 3.90240065601318e+00 , 3.16920614770501e+00 , 7.60134964710312e-01 ), ( 2.76670172157189e+00 , 3.09797126086086e+00 , -6.91656707907341e-02 ), ( 3.13210313366296e+00 , 2.65229591985997e+00 , -1.53813174351084e+00 ), ( 1.57100155371032e+00 , 2.23812901945626e+00 , 4.30288626030736e-01 ), ( 4.22655310526989e-01 , 2.61531683195227e+00 , 4.43098682874497e-01 ), ( 2.04412513050292e+00 , 1.12324601649572e+00 , 1.04828171708230e+00 ), ( 1.26291367643280e+00 , 1.52471038482506e-01 , 1.66977158914457e+00 ), ( 2.09166067237580e+00 , -1.09381048195222e+00 , 2.03881102148452e+00 ), ( 5.73351864534817e-01 , 6.15679762509812e-01 , 2.94390160366273e+00 ), ( -5.96372825253587e-01 , 3.57755428110507e-01 , 3.19529252919828e+00 ), ( 1.28598432385745e+00 , 1.41260095346227e+00 , 3.77056370833815e+00 ), ( 8.94784505225517e-01 , 1.98006379732528e+00 , 5.04238327326131e+00 ), ( 2.06385512913826e+00 , 2.76865949475112e+00 , 5.72618092003640e+00 ), ( -3.60062097218326e-01 , 2.89535661157304e+00 , 4.93677968134798e+00 ), ( -1.11667932050255e+00 , 3.07045197048428e+00 , 5.89059613594728e+00 ), ( -5.36405371385116e-01 , 3.49764622877992e+00 , 3.75275692967691e+00 ), ( -1.45342361975039e+00 , 4.47616593488856e+00 , 3.41781805826289e+00 ), ( -7.59165807068616e-01 , 5.45257919281522e+00 , 2.48405980664348e+00 ), ( -2.75055981152918e+00 , 3.93858955483025e+00 , 2.74731074556576e+00 ), ( -3.79946948160685e+00 , 4.58326796810441e+00 , 2.81212187429832e+00 ), ( -2.70374724078334e+00 , 2.63943159515823e+00 , 2.35191174282680e+00 ), ( -3.81177363832016e+00 , 1.81609485447502e+00 , 2.00055152302758e+00 ), ( -3.35038102202661e+00 , 8.86608142278450e-01 , 7.86125718186561e-01 ), ( -4.25602419354840e+00 , 1.02942668200217e+00 , 3.24713244968131e+00 ), ( -5.44751868472733e+00 , 7.36379853289974e-01 , 3.34693232400797e+00 ), ( -3.36798237884827e+00 , 7.25213959190701e-01 , 4.16128616031333e+00 ), ( -3.66657995644053e+00 , 7.30773804175590e-02 , 5.47576568491923e+00 ), ( -2.35995830595435e+00 , -2.98354522442641e-01 , 6.12538658020151e+00 ), ( -4.49138257388260e+00 , 9.36520548828004e-01 , 6.42070963892303e+00 ), ( -5.35620617875941e+00 , 5.54578423938489e-01 , 7.18696910577752e+00 ), ( -6.30528090797248e+00 , 3.61144313631416e+00 , 6.76081477239903e+00 ), ( -7.02615654732738e+00 , 4.30029315541803e+00 , 7.51822328567389e+00 ), ( -6.61912434425324e+00 , 3.16641104306728e+00 , 5.54783557432400e+00 ), ( -4.10974603712149e+00 , 2.25460191083565e+00 , 6.40922090787994e+00 ), ( -4.81279459463440e+00 , 3.28658348388144e+00 , 7.22591772667137e+00 ), ( -4.00964714373989e+00 , 4.59079164212638e+00 , 7.27806214886563e+00 ) } +colvars: Step 33, atoms_positions[size = 51] = { ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 ), ( 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 ), ( 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 ), ( 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 ), ( 6.99509325210347e+00 , -2.08102315018244e+00 , -8.51239526379223e-01 ), ( 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 ), ( 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 ), ( 7.15309251672616e+00 , -3.48991057622104e-01 , 4.40415429079846e+00 ), ( 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 ), ( 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 ), ( 5.85534783979395e+00 , 2.25171936216251e+00 , 2.96602427149247e+00 ), ( 5.13558337522206e+00 , 3.53632879253126e+00 , 2.87076331408032e+00 ), ( 6.28774885930353e+00 , 4.45372648078627e+00 , 2.28417976249521e+00 ), ( 3.85908723581206e+00 , 3.63081375049325e+00 , 2.01499724284678e+00 ), ( 2.83178466907853e+00 , 4.16346128405932e+00 , 2.42297929173377e+00 ), ( 3.90253559195207e+00 , 3.16922867849155e+00 , 7.60356539199559e-01 ), ( 2.76687652775309e+00 , 3.09803742331921e+00 , -6.90270019545529e-02 ), ( 3.13233554654883e+00 , 2.65238218952684e+00 , -1.53798330454818e+00 ), ( 1.57114708712370e+00 , 2.23818005953628e+00 , 4.30353855151207e-01 ), ( 4.22796268348754e-01 , 2.61536158033979e+00 , 4.43104669199612e-01 ), ( 2.04423949219399e+00 , 1.12327685472541e+00 , 1.04834816265126e+00 ), ( 1.26298783718215e+00 , 1.52506881281894e-01 , 1.66978214121657e+00 ), ( 2.09177823302583e+00 , -1.09370073248940e+00 , 2.03893578485241e+00 ), ( 5.73417726860450e-01 , 6.15674672417228e-01 , 2.94389370237568e+00 ), ( -5.96338169794170e-01 , 3.57762044608908e-01 , 3.19521810188232e+00 ), ( 1.28610395291346e+00 , 1.41256628505262e+00 , 3.77059120683749e+00 ), ( 8.94722599964565e-01 , 1.98000248398792e+00 , 5.04237791544858e+00 ), ( 2.06371481301180e+00 , 2.76861304176402e+00 , 5.72625229173133e+00 ), ( -3.60161112465007e-01 , 2.89530689759080e+00 , 4.93674531845192e+00 ), ( -1.11683273650727e+00 , 3.07039671856267e+00 , 5.89052569085821e+00 ), ( -5.36455406120775e-01 , 3.49762953162092e+00 , 3.75272953810346e+00 ), ( -1.45345915236555e+00 , 4.47615452090498e+00 , 3.41776036947466e+00 ), ( -7.59147033137468e-01 , 5.45258244167206e+00 , 2.48405525316260e+00 ), ( -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 ), ( -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 ), ( -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 ), ( -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 ), ( -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 ), ( -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 ), ( -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 ), ( -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 ), ( -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 ), ( -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 ), ( -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 ), ( -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 ), ( -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 ), ( -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 ), ( -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 ), ( -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 ), ( -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 ), ( -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ) } colvars: Step 33, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 33, atom_groups_ids[size = 0] = @@ -4641,162 +7491,301 @@ colvars: Collective variables module, step no. 33 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.90717372797486e-01 , -1.60872298396465e-02 , 9.56673721908266e-01 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.99509325210347e+00 , -2.08102315018244e+00 , -8.51239526379223e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 , 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 7.15309251672616e+00 , -3.48991057622104e-01 , 4.40415429079846e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 , 5.85534783979395e+00 , 2.25171936216251e+00 , 2.96602427149247e+00 , 5.13558337522206e+00 , 3.53632879253126e+00 , 2.87076331408032e+00 , 6.28774885930353e+00 , 4.45372648078627e+00 , 2.28417976249521e+00 , 3.85908723581206e+00 , 3.63081375049325e+00 , 2.01499724284678e+00 , 2.83178466907853e+00 , 4.16346128405932e+00 , 2.42297929173377e+00 , 3.90253559195207e+00 , 3.16922867849155e+00 , 7.60356539199559e-01 , 2.76687652775309e+00 , 3.09803742331921e+00 , -6.90270019545529e-02 , 3.13233554654883e+00 , 2.65238218952684e+00 , -1.53798330454818e+00 , 1.57114708712370e+00 , 2.23818005953628e+00 , 4.30353855151207e-01 , 4.22796268348754e-01 , 2.61536158033979e+00 , 4.43104669199612e-01 , 2.04423949219399e+00 , 1.12327685472541e+00 , 1.04834816265126e+00 , 1.26298783718215e+00 , 1.52506881281894e-01 , 1.66978214121657e+00 , 2.09177823302583e+00 , -1.09370073248940e+00 , 2.03893578485241e+00 , 5.73417726860450e-01 , 6.15674672417228e-01 , 2.94389370237568e+00 , -5.96338169794170e-01 , 3.57762044608908e-01 , 3.19521810188232e+00 , 1.28610395291346e+00 , 1.41256628505262e+00 , 3.77059120683749e+00 , 8.94722599964565e-01 , 1.98000248398792e+00 , 5.04237791544858e+00 , 2.06371481301180e+00 , 2.76861304176402e+00 , 5.72625229173133e+00 , -3.60161112465007e-01 , 2.89530689759080e+00 , 4.93674531845192e+00 , -1.11683273650727e+00 , 3.07039671856267e+00 , 5.89052569085821e+00 , -5.36455406120775e-01 , 3.49762953162092e+00 , 3.75272953810346e+00 , -1.45345915236555e+00 , 4.47615452090498e+00 , 3.41776036947466e+00 , -7.59147033137468e-01 , 5.45258244167206e+00 , 2.48405525316260e+00 , -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 , -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 , -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 , -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 , -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 , -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 , -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 , -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 , -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 , -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 , -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 , -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 , -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 , -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 , -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 , -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 , -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 , -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "fitting_group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.88930838111525e-01 , -1.58081418249705e-02 , 9.57219448945859e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.90717372797486e-01 , -1.60872298396465e-02 , 9.56673721908266e-01 ). +colvars: Colvar "one" has value ( -2.88930838111525e-01 , -1.58081418249705e-02 , 9.57219448945859e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.99509325210347e+00 , -2.08102315018244e+00 , -8.51239526379223e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 , 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 7.15309251672616e+00 , -3.48991057622104e-01 , 4.40415429079846e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 , 5.85534783979395e+00 , 2.25171936216251e+00 , 2.96602427149247e+00 , 5.13558337522206e+00 , 3.53632879253126e+00 , 2.87076331408032e+00 , 6.28774885930353e+00 , 4.45372648078627e+00 , 2.28417976249521e+00 , 3.85908723581206e+00 , 3.63081375049325e+00 , 2.01499724284678e+00 , 2.83178466907853e+00 , 4.16346128405932e+00 , 2.42297929173377e+00 , 3.90253559195207e+00 , 3.16922867849155e+00 , 7.60356539199559e-01 , 2.76687652775309e+00 , 3.09803742331921e+00 , -6.90270019545529e-02 , 3.13233554654883e+00 , 2.65238218952684e+00 , -1.53798330454818e+00 , 1.57114708712370e+00 , 2.23818005953628e+00 , 4.30353855151207e-01 , 4.22796268348754e-01 , 2.61536158033979e+00 , 4.43104669199612e-01 , 2.04423949219399e+00 , 1.12327685472541e+00 , 1.04834816265126e+00 , 1.26298783718215e+00 , 1.52506881281894e-01 , 1.66978214121657e+00 , 2.09177823302583e+00 , -1.09370073248940e+00 , 2.03893578485241e+00 , 5.73417726860450e-01 , 6.15674672417228e-01 , 2.94389370237568e+00 , -5.96338169794170e-01 , 3.57762044608908e-01 , 3.19521810188232e+00 , 1.28610395291346e+00 , 1.41256628505262e+00 , 3.77059120683749e+00 , 8.94722599964565e-01 , 1.98000248398792e+00 , 5.04237791544858e+00 , 2.06371481301180e+00 , 2.76861304176402e+00 , 5.72625229173133e+00 , -3.60161112465007e-01 , 2.89530689759080e+00 , 4.93674531845192e+00 , -1.11683273650727e+00 , 3.07039671856267e+00 , 5.89052569085821e+00 , -5.36455406120775e-01 , 3.49762953162092e+00 , 3.75272953810346e+00 , -1.45345915236555e+00 , 4.47615452090498e+00 , 3.41776036947466e+00 , -7.59147033137468e-01 , 5.45258244167206e+00 , 2.48405525316260e+00 , -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 , -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 , -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 , -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 , -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 , -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 , -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 , -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 , -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 , -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 , -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 , -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 , -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 , -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 , -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 , -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 , -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 , -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.3323 , 2.27354 , -15.2299 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.4039 , 6.54039 , 13.0808 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.3323 , 2.27354 , -15.2299 ) to colvar "one". -colvars: Adding total bias energy: 43.9423 +colvars: Adding biasing force ( 65.4039 , 6.54039 , 13.0808 ) to colvar "one". +colvars: Adding total bias energy: 55.6197 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.3323 , 2.27354 , -15.2299 ) +colvars: Force to be applied: ( 65.4039 , 6.54039 , 13.0808 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.9401 , -0.51618 , -1.3975 ) -colvars: ( -4.23613 , -0.442624 , -1.19836 ) -colvars: ( -4.23613 , -0.442624 , -1.19836 ) -colvars: ( -5.64265 , -0.589588 , -1.59624 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.18265 , -0.53913 , -1.45573 ) +colvars: ( -4.44412 , -0.462304 , -1.24829 ) +colvars: ( -4.44412 , -0.462304 , -1.24829 ) +colvars: ( -5.9197 , -0.615802 , -1.66276 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.885089 , 0.196259 , 0.604573 ) -colvars: ( 0.767564 , 0.26599 , 0.627986 ) -colvars: ( 0.751366 , 0.25937 , 0.610046 ) -colvars: ( 0.65797 , 0.266029 , 0.56507 ) -colvars: ( 0.646317 , 0.199844 , 0.472066 ) -colvars: ( 0.573181 , 0.342187 , 0.615672 ) -colvars: ( 0.468168 , 0.355366 , 0.572524 ) -colvars: ( 0.392989 , 0.451471 , 0.65466 ) -colvars: ( 0.38775 , 0.310871 , 0.468298 ) -colvars: ( 0.353818 , 0.269261 , 0.39454 ) -colvars: ( 0.358527 , 0.316263 , 0.45854 ) -colvars: ( 0.288348 , 0.273516 , 0.362473 ) -colvars: ( 0.261279 , 0.302501 , 0.38472 ) -colvars: ( 0.349634 , 0.17673 , 0.271468 ) -colvars: ( 0.292039 , 0.133387 , 0.181856 ) -colvars: ( 0.470134 , 0.140623 , 0.293614 ) -colvars: ( 0.541358 , 0.0502734 , 0.216711 ) -colvars: ( 0.668418 , 0.0302226 , 0.263564 ) -colvars: ( 0.550242 , 0.0184106 , 0.180264 ) -colvars: ( 0.534796 , -0.0463002 , 0.0870028 ) -colvars: ( 0.571143 , 0.0658711 , 0.254165 ) -colvars: ( 0.570116 , 0.0495085 , 0.232237 ) -colvars: ( 0.606336 , 0.113768 , 0.336845 ) -colvars: ( 0.448164 , 0.0532028 , 0.166989 ) -colvars: ( 0.441668 , -0.00250595 , 0.0906084 ) -colvars: ( 0.347928 , 0.117927 , 0.193805 ) -colvars: ( 0.225723 , 0.125748 , 0.133794 ) -colvars: ( 0.135742 , 0.210521 , 0.192647 ) -colvars: ( 0.197744 , 0.0525445 , 0.0222558 ) -colvars: ( 0.149572 , 0.0162317 , -0.0527755 ) -colvars: ( 0.230276 , 0.0276308 , 0.00845728 ) -colvars: ( 0.216215 , -0.0442562 , -0.0933674 ) -colvars: ( 0.250362 , -0.047058 , -0.0774025 ) -colvars: ( 0.290275 , -0.129322 , -0.161749 ) -colvars: ( 0.247086 , -0.182312 , -0.255666 ) -colvars: ( 0.403528 , -0.143715 , -0.115452 ) -colvars: ( 0.479789 , -0.218404 , -0.169037 ) -colvars: ( 0.608656 , -0.220305 , -0.0974772 ) -colvars: ( 0.433833 , -0.223425 , -0.201987 ) -colvars: ( 0.439361 , -0.291054 , -0.287006 ) -colvars: ( 0.386271 , -0.151082 , -0.134973 ) -colvars: ( 0.333469 , -0.145456 , -0.157974 ) -colvars: ( 0.317546 , -0.0596485 , -0.055222 ) -colvars: ( 0.212371 , -0.154828 , -0.239769 ) -colvars: ( 0.18867 , -0.196844 , -0.308179 ) -colvars: ( 0.0140244 , -0.200885 , -0.413789 ) -colvars: ( -0.0752839 , -0.219039 , -0.488773 ) -colvars: ( 0.112288 , -0.249744 , -0.421048 ) -colvars: ( 0.131724 , -0.114732 , -0.233816 ) -colvars: ( 0.0145014 , -0.119678 , -0.307614 ) -colvars: ( -0.0730751 , -0.0399188 , -0.253918 ) +colvars: ( 0.92736 , 0.205895 , 0.631936 ) +colvars: ( 0.804327 , 0.278857 , 0.656483 ) +colvars: ( 0.787291 , 0.271993 , 0.637781 ) +colvars: ( 0.689631 , 0.27878 , 0.590667 ) +colvars: ( 0.677425 , 0.209447 , 0.49336 ) +colvars: ( 0.600907 , 0.358459 , 0.643621 ) +colvars: ( 0.491016 , 0.372142 , 0.598481 ) +colvars: ( 0.412348 , 0.472727 , 0.684429 ) +colvars: ( 0.406788 , 0.325514 , 0.489486 ) +colvars: ( 0.371292 , 0.281874 , 0.412303 ) +colvars: ( 0.376131 , 0.33121 , 0.47934 ) +colvars: ( 0.302618 , 0.286425 , 0.378884 ) +colvars: ( 0.274215 , 0.316838 , 0.402227 ) +colvars: ( 0.366751 , 0.185107 , 0.283653 ) +colvars: ( 0.306454 , 0.139663 , 0.189911 ) +colvars: ( 0.492882 , 0.147389 , 0.306789 ) +colvars: ( 0.567421 , 0.0528162 , 0.226308 ) +colvars: ( 0.700405 , 0.0319381 , 0.275306 ) +colvars: ( 0.576784 , 0.0193783 , 0.188117 ) +colvars: ( 0.560608 , -0.0484147 , 0.0905421 ) +colvars: ( 0.598729 , 0.0690446 , 0.265385 ) +colvars: ( 0.59772 , 0.051833 , 0.242387 ) +colvars: ( 0.635697 , 0.119113 , 0.351784 ) +colvars: ( 0.470076 , 0.0555896 , 0.174146 ) +colvars: ( 0.463294 , -0.00279396 , 0.0942105 ) +colvars: ( 0.365138 , 0.123323 , 0.20225 ) +colvars: ( 0.237218 , 0.131414 , 0.139497 ) +colvars: ( 0.143015 , 0.220159 , 0.201121 ) +colvars: ( 0.207877 , 0.0547615 , 0.022839 ) +colvars: ( 0.157469 , 0.0166622 , -0.05567 ) +colvars: ( 0.241863 , 0.0287611 , 0.00844368 ) +colvars: ( 0.227089 , -0.0464987 , -0.098054 ) +colvars: ( 0.262761 , -0.0493299 , -0.0813031 ) +colvars: ( 0.304628 , -0.135566 , -0.169645 ) +colvars: ( 0.259407 , -0.1911 , -0.267893 ) +colvars: ( 0.423208 , -0.150581 , -0.121263 ) +colvars: ( 0.503059 , -0.228783 , -0.177378 ) +colvars: ( 0.637971 , -0.230687 , -0.102558 ) +colvars: ( 0.455016 , -0.234148 , -0.211891 ) +colvars: ( 0.460806 , -0.304993 , -0.300857 ) +colvars: ( 0.405283 , -0.158459 , -0.141795 ) +colvars: ( 0.350072 , -0.152675 , -0.165894 ) +colvars: ( 0.333461 , -0.0628575 , -0.0584163 ) +colvars: ( 0.223293 , -0.162574 , -0.251427 ) +colvars: ( 0.198511 , -0.206638 , -0.323023 ) +colvars: ( 0.015542 , -0.210853 , -0.433347 ) +colvars: ( -0.0779568 , -0.229931 , -0.511768 ) +colvars: ( 0.118363 , -0.261913 , -0.440945 ) +colvars: ( 0.138828 , -0.12059 , -0.245134 ) +colvars: ( 0.0161022 , -0.125847 , -0.322298 ) +colvars: ( -0.0755929 , -0.0423426 , -0.266063 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.9401 , 0.51618 , 1.3975 ) -colvars: ( 4.23613 , 0.442624 , 1.19836 ) -colvars: ( 4.23613 , 0.442624 , 1.19836 ) -colvars: ( 5.64265 , 0.589588 , 1.59624 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.18265 , 0.53913 , 1.45573 ) +colvars: ( 4.44412 , 0.462304 , 1.24829 ) +colvars: ( 4.44412 , 0.462304 , 1.24829 ) +colvars: ( 5.9197 , 0.615802 , 1.66276 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.611548 , -0.0809819 , -0.359006 ) -colvars: ( -0.550619 , -0.164757 , -0.32581 ) -colvars: ( -0.498663 , -0.142175 , -0.265995 ) -colvars: ( -0.513568 , -0.192616 , -0.297887 ) -colvars: ( -0.503859 , -0.132863 , -0.268099 ) -colvars: ( -0.490807 , -0.285977 , -0.306285 ) -colvars: ( -0.460428 , -0.326894 , -0.289449 ) -colvars: ( -0.440514 , -0.435763 , -0.305907 ) -colvars: ( -0.397122 , -0.290808 , -0.213694 ) -colvars: ( -0.393679 , -0.265181 , -0.201644 ) -colvars: ( -0.346192 , -0.284864 , -0.160487 ) -colvars: ( -0.28514 , -0.247228 , -0.0864795 ) -colvars: ( -0.234852 , -0.26214 , -0.0409069 ) -colvars: ( -0.303278 , -0.142567 , -0.0696452 ) -colvars: ( -0.272558 , -0.112798 , -0.028777 ) -colvars: ( -0.355926 , -0.084461 , -0.103116 ) -colvars: ( -0.381258 , 0.0151685 , -0.0952021 ) -colvars: ( -0.429258 , 0.0634042 , -0.127306 ) -colvars: ( -0.420598 , 0.0302137 , -0.12972 ) -colvars: ( -0.409194 , 0.0878478 , -0.0989387 ) -colvars: ( -0.466321 , -0.0248074 , -0.194139 ) -colvars: ( -0.502571 , -0.0264804 , -0.231153 ) -colvars: ( -0.55385 , -0.0930458 , -0.305027 ) -colvars: ( -0.452446 , -0.0568411 , -0.190921 ) -colvars: ( -0.459923 , -0.0121691 , -0.18347 ) -colvars: ( -0.398284 , -0.132087 , -0.161672 ) -colvars: ( -0.34237 , -0.163725 , -0.116047 ) -colvars: ( -0.292779 , -0.255078 , -0.0967922 ) -colvars: ( -0.299992 , -0.0896601 , -0.0486108 ) -colvars: ( -0.287961 , -0.0707844 , -0.0301863 ) -colvars: ( -0.277752 , -0.0439735 , -0.0109358 ) -colvars: ( -0.240979 , 0.0320283 , 0.0515134 ) -colvars: ( -0.217169 , 0.0589729 , 0.0844876 ) -colvars: ( -0.284474 , 0.119922 , 0.0372298 ) -colvars: ( -0.25807 , 0.162363 , 0.078005 ) -colvars: ( -0.353094 , 0.148261 , -0.0222785 ) -colvars: ( -0.401524 , 0.225419 , -0.0451226 ) -colvars: ( -0.471441 , 0.248141 , -0.107817 ) -colvars: ( -0.415539 , 0.205167 , -0.0660031 ) -colvars: ( -0.420056 , 0.266851 , -0.0498733 ) -colvars: ( -0.422177 , 0.117244 , -0.102143 ) -colvars: ( -0.431752 , 0.086525 , -0.122066 ) -colvars: ( -0.455098 , -0.00827615 , -0.177313 ) -colvars: ( -0.366186 , 0.075252 , -0.0599107 ) -colvars: ( -0.370603 , 0.101888 , -0.0554258 ) -colvars: ( -0.204189 , 0.108988 , 0.114301 ) -colvars: ( -0.155587 , 0.111001 , 0.16385 ) -colvars: ( -0.228336 , 0.182372 , 0.114611 ) -colvars: ( -0.303433 , 0.0341286 , -0.0105864 ) -colvars: ( -0.237683 , 0.0204831 , 0.0509591 ) -colvars: ( -0.184308 , -0.0636578 , 0.0764359 ) +colvars: ( -0.640575 , -0.0850538 , -0.374471 ) +colvars: ( -0.576881 , -0.172718 , -0.339688 ) +colvars: ( -0.522375 , -0.149129 , -0.277105 ) +colvars: ( -0.538234 , -0.201796 , -0.310558 ) +colvars: ( -0.528068 , -0.139217 , -0.279523 ) +colvars: ( -0.514534 , -0.299485 , -0.319272 ) +colvars: ( -0.482882 , -0.342234 , -0.301717 ) +colvars: ( -0.462149 , -0.456173 , -0.318818 ) +colvars: ( -0.416607 , -0.304428 , -0.222584 ) +colvars: ( -0.413069 , -0.277547 , -0.210084 ) +colvars: ( -0.363208 , -0.298243 , -0.166905 ) +colvars: ( -0.299276 , -0.258826 , -0.0895881 ) +colvars: ( -0.246546 , -0.274484 , -0.0418512 ) +colvars: ( -0.318177 , -0.149275 , -0.0721074 ) +colvars: ( -0.286058 , -0.118066 , -0.0294687 ) +colvars: ( -0.373172 , -0.0885114 , -0.107107 ) +colvars: ( -0.399601 , 0.0157662 , -0.0989418 ) +colvars: ( -0.449701 , 0.0661765 , -0.132472 ) +colvars: ( -0.440879 , 0.0315731 , -0.13513 ) +colvars: ( -0.428942 , 0.0919357 , -0.103054 ) +colvars: ( -0.488831 , -0.0260055 , -0.202445 ) +colvars: ( -0.526888 , -0.0276977 , -0.241222 ) +colvars: ( -0.580638 , -0.0973796 , -0.318386 ) +colvars: ( -0.474545 , -0.0593988 , -0.199213 ) +colvars: ( -0.482409 , -0.0125936 , -0.191531 ) +colvars: ( -0.417915 , -0.138145 , -0.168556 ) +colvars: ( -0.359496 , -0.171193 , -0.120893 ) +colvars: ( -0.307642 , -0.266814 , -0.100648 ) +colvars: ( -0.315072 , -0.0936542 , -0.050478 ) +colvars: ( -0.302551 , -0.0738361 , -0.0313093 ) +colvars: ( -0.291651 , -0.0458904 , -0.0110632 ) +colvars: ( -0.253078 , 0.0336653 , 0.0541467 ) +colvars: ( -0.228004 , 0.0617962 , 0.0886872 ) +colvars: ( -0.298569 , 0.125678 , 0.0390902 ) +colvars: ( -0.270948 , 0.170145 , 0.0816251 ) +colvars: ( -0.370348 , 0.155303 , -0.0231264 ) +colvars: ( -0.421014 , 0.236078 , -0.0471206 ) +colvars: ( -0.494119 , 0.2598 , -0.112633 ) +colvars: ( -0.435831 , 0.214956 , -0.0690286 ) +colvars: ( -0.440559 , 0.279556 , -0.0522767 ) +colvars: ( -0.442908 , 0.122957 , -0.106754 ) +colvars: ( -0.45308 , 0.0908766 , -0.127645 ) +colvars: ( -0.477626 , -0.00834566 , -0.185315 ) +colvars: ( -0.384526 , 0.0791395 , -0.0627124 ) +colvars: ( -0.389216 , 0.107076 , -0.0581242 ) +colvars: ( -0.214915 , 0.114495 , 0.11937 ) +colvars: ( -0.164097 , 0.116654 , 0.171117 ) +colvars: ( -0.24004 , 0.191246 , 0.119684 ) +colvars: ( -0.318832 , 0.0360871 , -0.0110743 ) +colvars: ( -0.250076 , 0.0218595 , 0.053232 ) +colvars: ( -0.194244 , -0.0662189 , 0.079982 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 33. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 33. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 33, atoms_new_colvar_forces = { ( -4.66655574300186e+00 , -4.00902551228220e-01 , -1.15193312667992e+00 ), ( -4.01918630331649e+00 , -3.41390444913296e-01 , -8.96180175342897e-01 ), ( -4.09172970574186e+00 , -3.69211140349797e-01 , -9.31172632754234e-01 ), ( -5.50019213997382e+00 , -5.22606887274410e-01 , -1.39227871176518e+00 ), ( 2.52702783917087e-01 , 1.17195426405282e-01 , 3.44050889792059e-01 ), ( 5.02247053472502e+00 , 5.72390204245951e-01 , 1.70688672720813e+00 ), ( 4.24387108384171e+00 , 4.71096411775340e-01 , 1.48143145527619e+00 ), ( -4.75248358392963e-02 , 1.57082050546262e-02 , 3.48752533987886e-01 ), ( 4.22675912127380e+00 , 4.62687987289125e-01 , 1.45295913779938e+00 ), ( 5.60278969040657e+00 , 5.93668745614696e-01 , 1.78914176923980e+00 ), ( 1.23346479196570e-02 , 3.13994536011904e-02 , 2.98052823653341e-01 ), ( 3.20835919647033e-03 , 2.62874237462203e-02 , 2.75993914291455e-01 ), ( 2.64272565295787e-02 , 4.03613431814258e-02 , 3.43813461473831e-01 ), ( 4.63560867491589e-02 , 3.41626951824440e-02 , 2.01822879649986e-01 ), ( 1.94804224645847e-02 , 2.05890100582586e-02 , 1.53078593040516e-01 ), ( 1.14207902246984e-01 , 5.61619147734442e-02 , 1.90497251216933e-01 ), ( 1.60099607314098e-01 , 6.54418893589465e-02 , 1.21509353208883e-01 ), ( 2.39160631010491e-01 , 9.36268397490796e-02 , 1.36258229385052e-01 ), ( 1.29644226518945e-01 , 4.86242203272269e-02 , 5.05438805427701e-02 ), ( 1.25602041419272e-01 , 4.15476220209901e-02 , -1.19359545640073e-02 ), ( 1.04822221961650e-01 , 4.10637469228252e-02 , 6.00258382021666e-02 ), ( 6.75452449747612e-02 , 2.30281370618511e-02 , 1.08384131479711e-03 ), ( 5.24862788586783e-02 , 2.07222593548226e-02 , 3.18187102291569e-02 ), ( -4.28117649710569e-03 , -3.63829511389917e-03 , -2.39319243863618e-02 ), ( -1.82546405832218e-02 , -1.46750380924692e-02 , -9.28611702470923e-02 ), ( -5.03553875248300e-02 , -1.41600832214690e-02 , 3.21331187282011e-02 ), ( -1.16646762040843e-01 , -3.79771022679259e-02 , 1.77467233426216e-02 ), ( -1.57037015614155e-01 , -4.45569027199628e-02 , 9.58543067398101e-02 ), ( -1.02247813282843e-01 , -3.71156695591439e-02 , -2.63549592165182e-02 ), ( -1.38389263824373e-01 , -5.45526099222540e-02 , -8.29618124420032e-02 ), ( -4.74760601312511e-02 , -1.63427007569159e-02 , -2.47847536744859e-03 ), ( -2.47644333951621e-02 , -1.22279128492849e-02 , -4.18539922142991e-02 ), ( 3.31935253179527e-02 , 1.19148753588699e-02 , 7.08505482883817e-03 ), ( 5.80050214181399e-03 , -9.39960248250518e-03 , -1.24519592442528e-01 ), ( -1.09837786282649e-02 , -1.99490843643051e-02 , -1.77661006407395e-01 ), ( 5.04334597901761e-02 , 4.54554852983705e-03 , -1.37730223819585e-01 ), ( 7.82645576028812e-02 , 7.01516940411967e-03 , -2.14159801717374e-01 ), ( 1.37214389368312e-01 , 2.78359038733265e-02 , -2.05294694805041e-01 ), ( 1.82933405891691e-02 , -1.82576651770395e-02 , -2.67990596393569e-01 ), ( 1.93051533878304e-02 , -2.42036996894018e-02 , -3.36878815523230e-01 ), ( -3.59059070395407e-02 , -3.38374749886532e-02 , -2.37115681710708e-01 ), ( -9.82834906838154e-02 , -5.89314424008209e-02 , -2.80040234577893e-01 ), ( -1.37552356276809e-01 , -6.79246083473129e-02 , -2.32535390494389e-01 ), ( -1.53815592270519e-01 , -7.95757209751634e-02 , -2.99680132312586e-01 ), ( -1.81932549662521e-01 , -9.49567513149216e-02 , -3.63604788171385e-01 ), ( -1.90164720332336e-01 , -9.18973887196884e-02 , -2.99487861935775e-01 ), ( -2.30871214150350e-01 , -1.08038010646822e-01 , -3.24922972744714e-01 ), ( -1.16047761909081e-01 , -6.73717649025961e-02 , -3.06436572939371e-01 ), ( -1.71709220190476e-01 , -8.06030743773704e-02 , -2.44402163509378e-01 ), ( -2.23181807344551e-01 , -9.91948579420006e-02 , -2.56655048131742e-01 ), ( -2.57383390271271e-01 , -1.03576548292250e-01 , -1.77481980535176e-01 ) } +colvars: Step 33, atoms_new_colvar_forces = { ( -4.89586815295081e+00 , -4.18288661428291e-01 , -1.19826590804559e+00 ), ( -4.21667724742114e+00 , -3.56164364871705e-01 , -9.31493539162552e-01 ), ( -4.29272685181666e+00 , -3.85319228898944e-01 , -9.68179759181285e-01 ), ( -5.77034476910618e+00 , -5.45572293537170e-01 , -1.44891957464345e+00 ), ( 2.64915722897845e-01 , 1.22864580939093e-01 , 3.60676035934643e-01 ), ( 5.26902630036997e+00 , 5.98103291404388e-01 , 1.78007941301694e+00 ), ( 4.45225704520376e+00 , 4.92211901595681e-01 , 1.54505351836818e+00 ), ( -4.98000970229364e-02 , 1.65535296997307e-02 , 3.65611674083054e-01 ), ( 4.43430513812878e+00 , 4.83390092105504e-01 , 1.51519136124869e+00 ), ( 5.87792441423127e+00 , 6.20129313106024e-01 , 1.86497520701249e+00 ), ( 1.29230396392084e-02 , 3.29666365657545e-02 , 3.12435254808471e-01 ), ( 3.34234509871706e-03 , 2.75996833065102e-02 , 2.89296152444240e-01 ), ( 2.76688487399397e-02 , 4.23546637103761e-02 , 3.60375390154767e-01 ), ( 4.85745297195058e-02 , 3.58311160222937e-02 , 2.11545556675541e-01 ), ( 2.03958682345369e-02 , 2.15967805778263e-02 , 1.60441833025958e-01 ), ( 1.19710006871534e-01 , 5.88774090515197e-02 , 1.99681770123455e-01 ), ( 1.67820160542212e-01 , 6.85823669256171e-02 , 1.27366223768150e-01 ), ( 2.50704181138953e-01 , 9.81145488528216e-02 , 1.42833830221747e-01 ), ( 1.35905706267073e-01 , 5.09513821603064e-02 , 5.29868643664593e-02 ), ( 1.31665912015475e-01 , 4.35210034266095e-02 , -1.25122522047927e-02 ), ( 1.09897779079899e-01 , 4.30391622522975e-02 , 6.29403019603845e-02 ), ( 7.08321266490427e-02 , 2.41352720145787e-02 , 1.16463071399242e-03 ), ( 5.50592541635683e-02 , 2.17333711719896e-02 , 3.33978252823109e-02 ), ( -4.46900686890672e-03 , -3.80922940105193e-03 , -2.50666492114297e-02 ), ( -1.91144356427754e-02 , -1.53875496586136e-02 , -9.73209400723725e-02 ), ( -5.27772725973002e-02 , -1.48213849078601e-02 , 3.36946470716469e-02 ), ( -1.22277863399888e-01 , -3.97789521628804e-02 , 1.86040326368210e-02 ), ( -1.64627046451288e-01 , -4.66556174907358e-02 , 1.00472884175944e-01 ), ( -1.07194738160474e-01 , -3.88927066699034e-02 , -2.76389901901821e-02 ), ( -1.45081503082860e-01 , -5.71738881989172e-02 , -8.69793720398932e-02 ), ( -4.97875743463240e-02 , -1.71293229075876e-02 , -2.61950305523130e-03 ), ( -2.59896779157611e-02 , -1.28334042956098e-02 , -4.39073317195441e-02 ), ( 3.47569491170505e-02 , 1.24662963114502e-02 , 7.38413631730400e-03 ), ( 6.05905111978139e-03 , -9.88820691397341e-03 , -1.30555126271493e-01 ), ( -1.15406889596824e-02 , -2.09554556714439e-02 , -1.86267900379892e-01 ), ( 5.28600147704486e-02 , 4.72273260669220e-03 , -1.44389080105876e-01 ), ( 8.20442708466673e-02 , 7.29437414268397e-03 , -2.24498287373445e-01 ), ( 1.43852669424415e-01 , 2.91133684798466e-02 , -2.15191368310404e-01 ), ( 1.91850096005293e-02 , -1.91913456295390e-02 , -2.80920075470312e-01 ), ( 2.02466254432048e-02 , -2.54375250906080e-02 , -3.53133227572521e-01 ), ( -3.76256921832037e-02 , -3.55020742444178e-02 , -2.48548768519691e-01 ), ( -1.03008375312877e-01 , -6.17980014296811e-02 , -2.93538718662919e-01 ), ( -1.44164924912362e-01 , -7.12031808104580e-02 , -2.43731329943684e-01 ), ( -1.61233249667508e-01 , -8.34345673503705e-02 , -3.14139775300582e-01 ), ( -1.90704772557553e-01 , -9.95624504003784e-02 , -3.81147600804688e-01 ), ( -1.99373035235729e-01 , -9.63580709974224e-02 , -3.13977542407785e-01 ), ( -2.42053536834788e-01 , -1.13276905026004e-01 , -3.40650306216223e-01 ), ( -1.21677080599663e-01 , -7.06672045203527e-02 , -3.21260935674461e-01 ), ( -1.80004324558336e-01 , -8.45025517452499e-02 , -2.56207852610082e-01 ), ( -2.33974007025502e-01 , -1.03987221353875e-01 , -2.69065585766027e-01 ), ( -2.69837044682870e-01 , -1.08561510816550e-01 , -1.86081242494781e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 33, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -4834,10 +7823,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 34, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 34, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 34, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 34, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 34, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 34, atoms_positions[size = 51] = { ( 8.19928248168927e+00 , 4.32426689753966e-02 , -7.06900358608923e-01 ), ( 6.82269070189451e+00 , -6.13764926659809e-01 , -5.16880035718534e-01 ), ( 6.07701132309998e+00 , -3.36705544159249e-01 , 8.16861088770233e-01 ), ( 4.89808556299347e+00 , -1.52047783855024e-01 , 7.60077270528482e-01 ), ( 6.99570786501574e+00 , -2.08476137883713e+00 , -8.43257407036207e-01 ), ( 6.79345392752965e+00 , -3.08580009346970e-01 , 1.96507289322943e+00 ), ( 6.07903706363312e+00 , -2.37011156592875e-01 , 3.22216430071421e+00 ), ( 7.15325739125771e+00 , -3.51156564941396e-01 , 4.40783514370672e+00 ), ( 5.30693357635731e+00 , 1.06450062938171e+00 , 3.36315875996404e+00 ), ( 4.19208799221550e+00 , 1.00306496304032e+00 , 3.82184551922138e+00 ), ( 5.85492400911472e+00 , 2.25160696744740e+00 , 2.96380532347502e+00 ), ( 5.13117200184208e+00 , 3.53045480547987e+00 , 2.86512724648861e+00 ), ( 6.28200019777729e+00 , 4.44691711279416e+00 , 2.28381154465095e+00 ), ( 3.85932041175221e+00 , 3.62721564676007e+00 , 2.01127992536186e+00 ), ( 2.83757715452672e+00 , 4.16153060129455e+00 , 2.41894403045113e+00 ), ( 3.90078613714491e+00 , 3.16133099871682e+00 , 7.66566242117880e-01 ), ( 2.76522915842112e+00 , 3.10922334815726e+00 , -6.99820658943434e-02 ), ( 3.13649903500476e+00 , 2.65420589741729e+00 , -1.53430359023798e+00 ), ( 1.58363709122344e+00 , 2.24965893509786e+00 , 4.34218323836917e-01 ), ( 4.25908640926286e-01 , 2.61461992610346e+00 , 4.37249439916099e-01 ), ( 2.03721554601976e+00 , 1.11739097228770e+00 , 1.04774787933842e+00 ), ( 1.27469598890323e+00 , 1.57857677434009e-01 , 1.66638272373459e+00 ), ( 2.09388972574858e+00 , -1.09389004942111e+00 , 2.03712822296875e+00 ), ( 5.72493319881723e-01 , 6.16953391732061e-01 , 2.93976427211256e+00 ), ( -5.99923271234357e-01 , 3.58096679238054e-01 , 3.19994832001263e+00 ), ( 1.28676895845726e+00 , 1.41926069400591e+00 , 3.77578364299027e+00 ), ( 9.01917625907552e-01 , 1.98139301607146e+00 , 5.04622921438861e+00 ), ( 2.05468060339195e+00 , 2.77175716623085e+00 , 5.72600999785528e+00 ), ( -3.59784887976669e-01 , 2.89346526189633e+00 , 4.93084205638007e+00 ), ( -1.11736388386602e+00 , 3.07085315791936e+00 , 5.89331397417883e+00 ), ( -5.32130846876883e-01 , 3.49239472997256e+00 , 3.74379401902314e+00 ), ( -1.45107255452032e+00 , 4.47553686818780e+00 , 3.41741341749673e+00 ), ( -7.65090001147442e-01 , 5.45860499633047e+00 , 2.48562051225388e+00 ), ( -2.75201405685088e+00 , 3.93474907322799e+00 , 2.73645960600855e+00 ), ( -3.79753418105992e+00 , 4.58901549333180e+00 , 2.81109890187318e+00 ), ( -2.70708351781196e+00 , 2.64312098712079e+00 , 2.35072894724435e+00 ), ( -3.81527726316310e+00 , 1.80992686265173e+00 , 1.99782470976297e+00 ), ( -3.34775320239414e+00 , 8.91359605135749e-01 , 7.79368123263810e-01 ), ( -4.26032807276174e+00 , 1.02602624411697e+00 , 3.24647485168588e+00 ), ( -5.43901038056310e+00 , 7.30996178392527e-01 , 3.34982070449990e+00 ), ( -3.36570977315917e+00 , 7.22044864349293e-01 , 4.16216573739025e+00 ), ( -3.66575877559271e+00 , 6.98030386715717e-02 , 5.47047854661170e+00 ), ( -2.35280113648233e+00 , -2.91430069069599e-01 , 6.12531361013041e+00 ), ( -4.49261716443863e+00 , 9.44801538298533e-01 , 6.42080466597303e+00 ), ( -5.35553307291137e+00 , 5.47922125948171e-01 , 7.18255546743241e+00 ), ( -6.30095269654030e+00 , 3.60728638503266e+00 , 6.76581792426097e+00 ), ( -7.03318933709519e+00 , 4.30033811984162e+00 , 7.51894318036934e+00 ), ( -6.61460457490353e+00 , 3.16848186313731e+00 , 5.55200359987311e+00 ), ( -4.11247216608464e+00 , 2.25364742528459e+00 , 6.41339366894072e+00 ), ( -4.81013341147260e+00 , 3.28475172278346e+00 , 7.21702956500683e+00 ), ( -4.00801121720644e+00 , 4.60191943380506e+00 , 7.27953341872253e+00 ) } +colvars: Step 34, atoms_positions[size = 51] = { ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 ), ( 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 ), ( 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 ), ( 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ), ( 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 ), ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 ), ( 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 ), ( 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 ), ( 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 ), ( 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ), ( 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 ), ( 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 ), ( 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 ), ( 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 ), ( 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 ), ( 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 ), ( 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 ), ( 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 ), ( 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 ), ( 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 ), ( 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 ), ( 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 ), ( 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 ), ( 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 ), ( -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 ), ( 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 ), ( 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 ), ( 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 ), ( -3.59887877851289e-01 , 2.89341210824563e+00 , 4.93080537448977e+00 ), ( -1.11752535128005e+00 , 3.07079403948851e+00 , 5.89323910393435e+00 ), ( -5.32183156670204e-01 , 3.49237702712859e+00 , 3.74376491377976e+00 ), ( -1.45110993394368e+00 , 4.47552471132078e+00 , 3.41735254418937e+00 ), ( -7.65070322521645e-01 , 5.45860851201285e+00 , 2.48561592211971e+00 ), ( -2.75200839518506e+00 , 3.93473792506609e+00 , 2.73631425357401e+00 ), ( -3.79753915657748e+00 , 4.58898675042232e+00 , 2.81090688733797e+00 ), ( -2.70703679486343e+00 , 2.64312058255035e+00 , 2.35056268991001e+00 ), ( -3.81520007124380e+00 , 1.80992449237204e+00 , 1.99756322640363e+00 ), ( -3.34760852615227e+00 , 8.91368221115539e-01 , 7.79124805166928e-01 ), ( -4.26031034996816e+00 , 1.02599952098258e+00 , 3.24616744685834e+00 ), ( -5.43899565340654e+00 , 7.30961009524662e-01 , 3.34945957410753e+00 ), ( -3.36573818489708e+00 , 7.21994493966916e-01 , 4.16188646216874e+00 ), ( -3.66587207559550e+00 , 6.97286392999179e-02 , 5.47015820635550e+00 ), ( -2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 ), ( -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 ), ( -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 ), ( -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 ), ( -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 ), ( -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 ), ( -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 ), ( -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 ), ( -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ) } colvars: Step 34, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 34, atom_groups_ids[size = 0] = @@ -4855,162 +7844,301 @@ colvars: Collective variables module, step no. 34 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.89014188887543e-01 , -1.68855035770422e-02 , 9.57175886862297e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.87157334453261e-01 , -1.65935395079231e-02 , 9.57739693088000e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 , 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 , 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 , 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 , 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 , 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 , 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 , 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 , 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 , 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 , 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 , 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 , 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 , 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 , 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 , 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 , -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 , 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 , 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 , 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 , -3.59887877851289e-01 , 2.89341210824563e+00 , 4.93080537448977e+00 , -1.11752535128005e+00 , 3.07079403948851e+00 , 5.89323910393435e+00 , -5.32183156670204e-01 , 3.49237702712859e+00 , 3.74376491377976e+00 , -1.45110993394368e+00 , 4.47552471132078e+00 , 3.41735254418937e+00 , -7.65070322521645e-01 , 5.45860851201285e+00 , 2.48561592211971e+00 , -2.75200839518506e+00 , 3.93473792506609e+00 , 2.73631425357401e+00 , -3.79753915657748e+00 , 4.58898675042232e+00 , 2.81090688733797e+00 , -2.70703679486343e+00 , 2.64312058255035e+00 , 2.35056268991001e+00 , -3.81520007124380e+00 , 1.80992449237204e+00 , 1.99756322640363e+00 , -3.34760852615227e+00 , 8.91368221115539e-01 , 7.79124805166928e-01 , -4.26031034996816e+00 , 1.02599952098258e+00 , 3.24616744685834e+00 , -5.43899565340654e+00 , 7.30961009524662e-01 , 3.34945957410753e+00 , -3.36573818489708e+00 , 7.21994493966916e-01 , 4.16188646216874e+00 , -3.66587207559550e+00 , 6.97286392999179e-02 , 5.47015820635550e+00 , -2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 , -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 , -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 , -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 , -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 , -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 , -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 , -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 , -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.89014188887543e-01 , -1.68855035770422e-02 , 9.57175886862297e-01 ). +colvars: Colvar "one" has value ( -2.87157334453261e-01 , -1.65935395079231e-02 , 9.57739693088000e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 , 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 , 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 , 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 , 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 , 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 , 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 , 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 , 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 , 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 , 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 , 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 , 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 , 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 , 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 , 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 , -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 , 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 , 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 , 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 , -3.59887877851289e-01 , 2.89341210824563e+00 , 4.93080537448977e+00 , -1.11752535128005e+00 , 3.07079403948851e+00 , 5.89323910393435e+00 , -5.32183156670204e-01 , 3.49237702712859e+00 , 3.74376491377976e+00 , -1.45110993394368e+00 , 4.47552471132078e+00 , 3.41735254418937e+00 , -7.65070322521645e-01 , 5.45860851201285e+00 , 2.48561592211971e+00 , -2.75200839518506e+00 , 3.93473792506609e+00 , 2.73631425357401e+00 , -3.79753915657748e+00 , 4.58898675042232e+00 , 2.81090688733797e+00 , -2.70703679486343e+00 , 2.64312058255035e+00 , 2.35056268991001e+00 , -3.81520007124380e+00 , 1.80992449237204e+00 , 1.99756322640363e+00 , -3.34760852615227e+00 , 8.91368221115539e-01 , 7.79124805166928e-01 , -4.26031034996816e+00 , 1.02599952098258e+00 , 3.24616744685834e+00 , -5.43899565340654e+00 , 7.30961009524662e-01 , 3.34945957410753e+00 , -3.36573818489708e+00 , 7.21994493966916e-01 , 4.16188646216874e+00 , -3.66587207559550e+00 , 6.97286392999179e-02 , 5.47015820635550e+00 , -2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 , -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 , -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 , -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 , -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 , -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 , -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 , -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 , -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.2983 , 2.28951 , -15.2399 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.3236 , 6.53236 , 13.0647 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.2983 , 2.28951 , -15.2399 ) to colvar "one". -colvars: Adding total bias energy: 43.875 +colvars: Adding biasing force ( 65.3236 , 6.53236 , 13.0647 ) to colvar "one". +colvars: Adding total bias energy: 55.5021 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.2983 , 2.28951 , -15.2399 ) +colvars: Force to be applied: ( 65.3236 , 6.53236 , 13.0647 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.94323 , -0.513907 , -1.39039 ) -colvars: ( -4.23882 , -0.440675 , -1.19226 ) -colvars: ( -4.23882 , -0.440675 , -1.19226 ) -colvars: ( -5.64623 , -0.586992 , -1.58812 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17845 , -0.535884 , -1.44577 ) +colvars: ( -4.44052 , -0.45952 , -1.23975 ) +colvars: ( -4.44052 , -0.45952 , -1.23975 ) +colvars: ( -5.9149 , -0.612094 , -1.65138 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.884406 , 0.196339 , 0.602947 ) -colvars: ( 0.767071 , 0.265925 , 0.626335 ) -colvars: ( 0.750853 , 0.259373 , 0.608503 ) -colvars: ( 0.657684 , 0.265854 , 0.56354 ) -colvars: ( 0.646057 , 0.199729 , 0.470735 ) -colvars: ( 0.573052 , 0.341848 , 0.614021 ) -colvars: ( 0.468243 , 0.354901 , 0.570946 ) -colvars: ( 0.3932 , 0.450833 , 0.652897 ) -colvars: ( 0.387943 , 0.310429 , 0.466984 ) -colvars: ( 0.354091 , 0.268811 , 0.393363 ) -colvars: ( 0.358729 , 0.315856 , 0.457308 ) -colvars: ( 0.288649 , 0.273142 , 0.361492 ) -colvars: ( 0.261582 , 0.302142 , 0.383755 ) -colvars: ( 0.349829 , 0.176511 , 0.270683 ) -colvars: ( 0.292336 , 0.13317 , 0.181269 ) -colvars: ( 0.470119 , 0.140537 , 0.292775 ) -colvars: ( 0.541221 , 0.0503403 , 0.216035 ) -colvars: ( 0.668048 , 0.0304258 , 0.262794 ) -colvars: ( 0.550133 , 0.0184546 , 0.179607 ) -colvars: ( 0.534719 , -0.0462008 , 0.0865461 ) -colvars: ( 0.571031 , 0.0658266 , 0.253297 ) -colvars: ( 0.570048 , 0.0494165 , 0.231356 ) -colvars: ( 0.606234 , 0.113586 , 0.335691 ) -colvars: ( 0.448318 , 0.0530013 , 0.166247 ) -colvars: ( 0.441852 , -0.00267842 , 0.0900083 ) -colvars: ( 0.34824 , 0.1176 , 0.193031 ) -colvars: ( 0.22625 , 0.125317 , 0.133156 ) -colvars: ( 0.136407 , 0.209954 , 0.19191 ) -colvars: ( 0.198298 , 0.0522093 , 0.0218975 ) -colvars: ( 0.150226 , 0.0158754 , -0.0529897 ) -colvars: ( 0.230735 , 0.0274071 , 0.00818198 ) -colvars: ( 0.216675 , -0.0443729 , -0.0933839 ) -colvars: ( 0.250718 , -0.0470786 , -0.0773939 ) -colvars: ( 0.290626 , -0.129317 , -0.161648 ) -colvars: ( 0.247514 , -0.182281 , -0.255356 ) -colvars: ( 0.4037 , -0.143636 , -0.115483 ) -colvars: ( 0.479852 , -0.218218 , -0.168988 ) -colvars: ( 0.608503 , -0.220033 , -0.0976057 ) -colvars: ( 0.434016 , -0.223329 , -0.20192 ) -colvars: ( 0.439546 , -0.290895 , -0.286766 ) -colvars: ( 0.38656 , -0.151139 , -0.135083 ) -colvars: ( 0.333887 , -0.145618 , -0.158084 ) -colvars: ( 0.318015 , -0.0599536 , -0.0555897 ) -colvars: ( 0.212993 , -0.155059 , -0.239682 ) -colvars: ( 0.189357 , -0.197081 , -0.307972 ) -colvars: ( 0.0149245 , -0.20111 , -0.413211 ) -colvars: ( -0.0742322 , -0.219305 , -0.488019 ) -colvars: ( 0.112999 , -0.24981 , -0.420432 ) -colvars: ( 0.132454 , -0.11502 , -0.233692 ) -colvars: ( 0.0154263 , -0.120034 , -0.307307 ) -colvars: ( -0.0720213 , -0.0403961 , -0.253691 ) +colvars: ( 0.92526 , 0.205682 , 0.629229 ) +colvars: ( 0.802614 , 0.278379 , 0.653714 ) +colvars: ( 0.785579 , 0.2716 , 0.635157 ) +colvars: ( 0.688312 , 0.278184 , 0.588128 ) +colvars: ( 0.67615 , 0.209017 , 0.491181 ) +colvars: ( 0.599889 , 0.357566 , 0.640873 ) +colvars: ( 0.49038 , 0.371093 , 0.59588 ) +colvars: ( 0.411977 , 0.471342 , 0.681502 ) +colvars: ( 0.406404 , 0.324558 , 0.487333 ) +colvars: ( 0.371045 , 0.280972 , 0.410412 ) +colvars: ( 0.3758 , 0.330284 , 0.47729 ) +colvars: ( 0.3025 , 0.285601 , 0.377255 ) +colvars: ( 0.274139 , 0.315987 , 0.40058 ) +colvars: ( 0.366423 , 0.1846 , 0.282377 ) +colvars: ( 0.306325 , 0.139224 , 0.188987 ) +colvars: ( 0.492139 , 0.147082 , 0.305419 ) +colvars: ( 0.566438 , 0.0528135 , 0.225232 ) +colvars: ( 0.698973 , 0.0321143 , 0.274054 ) +colvars: ( 0.575818 , 0.0193994 , 0.187117 ) +colvars: ( 0.559699 , -0.0482344 , 0.0899044 ) +colvars: ( 0.597729 , 0.0688965 , 0.264043 ) +colvars: ( 0.596771 , 0.051658 , 0.241066 ) +colvars: ( 0.634657 , 0.118742 , 0.350005 ) +colvars: ( 0.469554 , 0.0552899 , 0.173077 ) +colvars: ( 0.462816 , -0.0029768 , 0.0934132 ) +colvars: ( 0.364943 , 0.122788 , 0.201106 ) +colvars: ( 0.237444 , 0.130754 , 0.138594 ) +colvars: ( 0.143528 , 0.219221 , 0.200021 ) +colvars: ( 0.208173 , 0.0543178 , 0.022411 ) +colvars: ( 0.157949 , 0.016251 , -0.0558256 ) +colvars: ( 0.242004 , 0.028477 , 0.00812639 ) +colvars: ( 0.227251 , -0.0465563 , -0.0979338 ) +colvars: ( 0.262757 , -0.0492784 , -0.0811809 ) +colvars: ( 0.304559 , -0.135361 , -0.169292 ) +colvars: ( 0.259487 , -0.190785 , -0.267168 ) +colvars: ( 0.42277 , -0.150273 , -0.121126 ) +colvars: ( 0.502386 , -0.228245 , -0.177071 ) +colvars: ( 0.636868 , -0.230053 , -0.102556 ) +colvars: ( 0.454546 , -0.233701 , -0.211514 ) +colvars: ( 0.460329 , -0.304373 , -0.300162 ) +colvars: ( 0.405002 , -0.158289 , -0.141712 ) +colvars: ( 0.350014 , -0.152626 , -0.165775 ) +colvars: ( 0.333484 , -0.0630974 , -0.0587352 ) +colvars: ( 0.223642 , -0.162587 , -0.250968 ) +colvars: ( 0.198967 , -0.206593 , -0.322328 ) +colvars: ( 0.0164937 , -0.210789 , -0.432086 ) +colvars: ( -0.0767039 , -0.229883 , -0.510199 ) +colvars: ( 0.118957 , -0.261601 , -0.439633 ) +colvars: ( 0.139417 , -0.120727 , -0.244643 ) +colvars: ( 0.0170817 , -0.12605 , -0.321494 ) +colvars: ( -0.074339 , -0.0427993 , -0.265429 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.94323 , 0.513907 , 1.39039 ) -colvars: ( 4.23882 , 0.440675 , 1.19226 ) -colvars: ( 4.23882 , 0.440675 , 1.19226 ) -colvars: ( 5.64623 , 0.586992 , 1.58812 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17845 , 0.535884 , 1.44577 ) +colvars: ( 4.44052 , 0.45952 , 1.23975 ) +colvars: ( 4.44052 , 0.45952 , 1.23975 ) +colvars: ( 5.9149 , 0.612094 , 1.65138 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.610856 , -0.0809681 , -0.357355 ) -colvars: ( -0.550115 , -0.164746 , -0.323994 ) -colvars: ( -0.49799 , -0.142168 , -0.26412 ) -colvars: ( -0.513325 , -0.192581 , -0.296212 ) -colvars: ( -0.503618 , -0.132802 , -0.266681 ) -colvars: ( -0.490795 , -0.285949 , -0.304441 ) -colvars: ( -0.460691 , -0.326845 , -0.287701 ) -colvars: ( -0.440982 , -0.435731 , -0.303899 ) -colvars: ( -0.397415 , -0.290733 , -0.212138 ) -colvars: ( -0.394087 , -0.265082 , -0.200309 ) -colvars: ( -0.346371 , -0.284794 , -0.158854 ) -colvars: ( -0.285319 , -0.247135 , -0.0850164 ) -colvars: ( -0.234913 , -0.26206 , -0.0392741 ) -colvars: ( -0.303298 , -0.142453 , -0.0684687 ) -colvars: ( -0.272665 , -0.112658 , -0.0278152 ) -colvars: ( -0.355711 , -0.0843587 , -0.101951 ) -colvars: ( -0.380876 , 0.0152876 , -0.0942942 ) -colvars: ( -0.428594 , 0.0635029 , -0.126323 ) -colvars: ( -0.420355 , 0.0303503 , -0.129006 ) -colvars: ( -0.40896 , 0.0880099 , -0.098478 ) -colvars: ( -0.466202 , -0.0246841 , -0.193303 ) -colvars: ( -0.502618 , -0.0263429 , -0.230464 ) -colvars: ( -0.553985 , -0.0929311 , -0.304133 ) -colvars: ( -0.452744 , -0.0566793 , -0.190354 ) -colvars: ( -0.460279 , -0.0119836 , -0.183147 ) -colvars: ( -0.398733 , -0.13193 , -0.16094 ) -colvars: ( -0.343046 , -0.163547 , -0.115409 ) -colvars: ( -0.293586 , -0.254914 , -0.0959012 ) -colvars: ( -0.300587 , -0.0894564 , -0.0482148 ) -colvars: ( -0.288689 , -0.0705557 , -0.0300012 ) -colvars: ( -0.278121 , -0.0437755 , -0.0105182 ) -colvars: ( -0.241237 , 0.0322484 , 0.0517098 ) -colvars: ( -0.217187 , 0.0591784 , 0.0847973 ) -colvars: ( -0.284635 , 0.12016 , 0.0371532 ) -colvars: ( -0.258281 , 0.162628 , 0.0776964 ) -colvars: ( -0.35312 , 0.148485 , -0.0223336 ) -colvars: ( -0.401467 , 0.225659 , -0.0454175 ) -colvars: ( -0.471194 , 0.248357 , -0.108014 ) -colvars: ( -0.415724 , 0.205425 , -0.0664434 ) -colvars: ( -0.420237 , 0.267132 , -0.0505718 ) -colvars: ( -0.422578 , 0.117492 , -0.102418 ) -colvars: ( -0.432402 , 0.0867885 , -0.12245 ) -colvars: ( -0.455916 , -0.00803373 , -0.177454 ) -colvars: ( -0.367015 , 0.0755409 , -0.0604303 ) -colvars: ( -0.371543 , 0.1022 , -0.0561652 ) -colvars: ( -0.205068 , 0.109317 , 0.113565 ) -colvars: ( -0.156597 , 0.111353 , 0.162972 ) -colvars: ( -0.228938 , 0.182695 , 0.113835 ) -colvars: ( -0.304297 , 0.0344133 , -0.0109753 ) -colvars: ( -0.238711 , 0.0207904 , 0.0504598 ) -colvars: ( -0.185441 , -0.0633648 , 0.0761839 ) +colvars: ( -0.638885 , -0.0849213 , -0.372115 ) +colvars: ( -0.575488 , -0.172453 , -0.337212 ) +colvars: ( -0.520885 , -0.148907 , -0.274664 ) +colvars: ( -0.537181 , -0.201457 , -0.308278 ) +colvars: ( -0.527032 , -0.138947 , -0.277564 ) +colvars: ( -0.513763 , -0.299003 , -0.316798 ) +colvars: ( -0.482454 , -0.341662 , -0.299373 ) +colvars: ( -0.461972 , -0.455443 , -0.316171 ) +colvars: ( -0.416311 , -0.303885 , -0.220569 ) +colvars: ( -0.412903 , -0.277017 , -0.208325 ) +colvars: ( -0.362872 , -0.297716 , -0.164896 ) +colvars: ( -0.299037 , -0.258333 , -0.0878816 ) +colvars: ( -0.246261 , -0.273984 , -0.0400389 ) +colvars: ( -0.317738 , -0.14893 , -0.0707336 ) +colvars: ( -0.285761 , -0.117739 , -0.0283908 ) +colvars: ( -0.372397 , -0.0882735 , -0.10569 ) +colvars: ( -0.398608 , 0.0158614 , -0.0978112 ) +colvars: ( -0.448331 , 0.0661698 , -0.131209 ) +colvars: ( -0.439973 , 0.0316649 , -0.134148 ) +colvars: ( -0.428064 , 0.0919631 , -0.102394 ) +colvars: ( -0.487986 , -0.0258387 , -0.201228 ) +colvars: ( -0.526162 , -0.027511 , -0.240102 ) +colvars: ( -0.579925 , -0.09711 , -0.316927 ) +colvars: ( -0.474168 , -0.0591348 , -0.198289 ) +colvars: ( -0.482081 , -0.0123747 , -0.19088 ) +colvars: ( -0.417785 , -0.137765 , -0.167504 ) +colvars: ( -0.359698 , -0.170737 , -0.120017 ) +colvars: ( -0.308063 , -0.266227 , -0.0995345 ) +colvars: ( -0.315253 , -0.0932899 , -0.0499706 ) +colvars: ( -0.302894 , -0.0734736 , -0.0310569 ) +colvars: ( -0.291625 , -0.0456078 , -0.0105944 ) +colvars: ( -0.252993 , 0.0338491 , 0.0542775 ) +colvars: ( -0.2277 , 0.0619185 , 0.0888848 ) +colvars: ( -0.298311 , 0.12574 , 0.0389541 ) +colvars: ( -0.270785 , 0.170168 , 0.0811748 ) +colvars: ( -0.369836 , 0.155304 , -0.0231416 ) +colvars: ( -0.420337 , 0.235971 , -0.0473534 ) +colvars: ( -0.493127 , 0.25963 , -0.112658 ) +colvars: ( -0.43539 , 0.214905 , -0.0693822 ) +colvars: ( -0.440108 , 0.279431 , -0.0529318 ) +colvars: ( -0.442689 , 0.123036 , -0.106873 ) +colvars: ( -0.453112 , 0.0910253 , -0.127847 ) +colvars: ( -0.4778 , -0.0080665 , -0.185167 ) +colvars: ( -0.384853 , 0.0793352 , -0.0631615 ) +colvars: ( -0.389655 , 0.107255 , -0.0588148 ) +colvars: ( -0.215552 , 0.114681 , 0.118404 ) +colvars: ( -0.164951 , 0.116862 , 0.169918 ) +colvars: ( -0.240343 , 0.191304 , 0.118675 ) +colvars: ( -0.319297 , 0.0363442 , -0.0114655 ) +colvars: ( -0.25082 , 0.0221642 , 0.0526219 ) +colvars: ( -0.195185 , -0.0657943 , 0.0795931 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 34. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 34. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 34, atoms_new_colvar_forces = { ( -4.66968467730647e+00 , -3.98535764896394e-01 , -1.14479461041868e+00 ), ( -4.02186586847765e+00 , -3.39496664546440e-01 , -8.89915685724953e-01 ), ( -4.09446320674110e+00 , -3.67401420752595e-01 , -9.24928118480411e-01 ), ( -5.50379499139976e+00 , -5.20064962826203e-01 , -1.38406475081348e+00 ), ( 2.52862835477283e-01 , 1.17204291123779e-01 , 3.44382801753356e-01 ), ( 5.02549211289822e+00 , 5.69805601309177e-01 , 1.69996671677032e+00 ), ( 4.24637458075738e+00 , 4.68730693662607e-01 , 1.47550146077075e+00 ), ( -4.77826762691794e-02 , 1.51018406915943e-02 , 3.48997985736102e-01 ), ( 4.22935114677442e+00 , 4.60371048307047e-01 , 1.44710174918278e+00 ), ( 5.60623807569989e+00 , 5.90720588683336e-01 , 1.78117433018362e+00 ), ( 1.23583210274947e-02 , 3.10625175598719e-02 , 2.98453522761200e-01 ), ( 3.32937256284721e-03 , 2.60066305896624e-02 , 2.76475718081853e-01 ), ( 2.66682738421338e-02 , 4.00826650770476e-02 , 3.44481103295033e-01 ), ( 4.65311855232145e-02 , 3.40576859424195e-02 , 2.02214762867393e-01 ), ( 1.96717261233661e-02 , 2.05123269665865e-02 , 1.53453323880322e-01 ), ( 1.14408069799234e-01 , 5.61784555554073e-02 , 1.90824123900925e-01 ), ( 1.60344882671914e-01 , 6.56278969761322e-02 , 1.21740820184294e-01 ), ( 2.39454688381125e-01 , 9.39287530714586e-02 , 1.36470596032705e-01 ), ( 1.29777095602017e-01 , 4.88049277296106e-02 , 5.06012713544814e-02 ), ( 1.25758244751251e-01 , 4.18091399735610e-02 , -1.19319263436668e-02 ), ( 1.04828297798102e-01 , 4.11424993347926e-02 , 5.99934316120360e-02 ), ( 6.74307158151144e-02 , 2.30735869252806e-02 , 8.92324837849123e-04 ), ( 5.22485813188008e-02 , 2.06552450324260e-02 , 3.15580193981421e-02 ), ( -4.42647633581983e-03 , -3.67805829784899e-03 , -2.41074103710462e-02 ), ( -1.84267726514626e-02 , -1.46620019873643e-02 , -9.31387800215068e-02 ), ( -5.04922619256448e-02 , -1.43305662789096e-02 , 3.20911979132146e-02 ), ( -1.16796066394915e-01 , -3.82299637879766e-02 , 1.77473599654943e-02 ), ( -1.57179713700557e-01 , -4.49601392162065e-02 , 9.60091466302025e-02 ), ( -1.02288980792726e-01 , -3.72471605576334e-02 , -2.63173188765250e-02 ), ( -1.38462668260544e-01 , -5.46803596104781e-02 , -8.29909122011471e-02 ), ( -4.73858656743748e-02 , -1.63683457195723e-02 , -2.33617285988538e-03 ), ( -2.45624769203801e-02 , -1.21245386428889e-02 , -4.16740783774202e-02 ), ( 3.35312460520490e-02 , 1.20998749539420e-02 , 7.40339352567526e-03 ), ( 5.99045553348876e-03 , -9.15663385549989e-03 , -1.24494393770357e-01 ), ( -1.07671472680909e-02 , -1.96534698778889e-02 , -1.77659266847587e-01 ), ( 5.05797346371175e-02 , 4.84945799729997e-03 , -1.37817007716939e-01 ), ( 7.83842258201953e-02 , 7.44081322069479e-03 , -2.14405048442866e-01 ), ( 1.37309438586973e-01 , 2.83241572130489e-02 , -2.05619494926364e-01 ), ( 1.82921229476102e-02 , -1.79040872757231e-02 , -2.68363169853558e-01 ), ( 1.93084549023900e-02 , -2.37624063076849e-02 , -3.37338080264935e-01 ), ( -3.60180996619245e-02 , -3.36471058673632e-02 , -2.37500976269758e-01 ), ( -9.85144937590744e-02 , -5.88290225385445e-02 , -2.80533758359584e-01 ), ( -1.37901044314944e-01 , -6.79873512947285e-02 , -2.33043437489882e-01 ), ( -1.54022156249555e-01 , -7.95179237640221e-02 , -3.00112216125075e-01 ), ( -1.82185810088524e-01 , -9.48810688857158e-02 , -3.64136988654834e-01 ), ( -1.90143353503948e-01 , -9.17929585012935e-02 , -2.99645402220216e-01 ), ( -2.30829218684587e-01 , -1.07951603903597e-01 , -3.25047146027383e-01 ), ( -1.15939912742137e-01 , -6.71155963308890e-02 , -3.06597447195414e-01 ), ( -1.71842830975162e-01 , -8.06068647110167e-02 , -2.44667082588142e-01 ), ( -2.23284761602432e-01 , -9.92438254814662e-02 , -2.56847022337407e-01 ), ( -2.57462353602662e-01 , -1.03760832180838e-01 , -1.77507457058724e-01 ) } +colvars: Step 34, atoms_new_colvar_forces = { ( -4.89207790183618e+00 , -4.15122393422152e-01 , -1.18865944944393e+00 ), ( -4.21339656599004e+00 , -3.53593925479209e-01 , -9.23247799910002e-01 ), ( -4.28939089016549e+00 , -3.82793309350308e-01 , -9.59901188084321e-01 ), ( -5.76578470637730e+00 , -5.42023922197129e-01 , -1.43776721768089e+00 ), ( 2.64693961548336e-01 , 1.22693563549609e-01 , 3.60493344381193e-01 ), ( 5.26457783516552e+00 , 5.94447048429273e-01 , 1.76984911150636e+00 ), ( 4.44844802111224e+00 , 4.88951823046885e-01 , 1.53625774796560e+00 ), ( -4.99955465911185e-02 , 1.58996003715131e-02 , 3.65331568545859e-01 ), ( 4.43061438957446e+00 , 4.80193617553499e-01 , 1.50651464907953e+00 ), ( 5.87304597055867e+00 , 6.16049737988205e-01 , 1.85347026095904e+00 ), ( 1.29283499682310e-02 , 3.25684264792283e-02 , 3.12394236530586e-01 ), ( 3.46282923948704e-03 , 2.72676561698180e-02 , 2.89373192147298e-01 ), ( 2.78783281890533e-02 , 4.20032047720394e-02 , 3.60541438087145e-01 ), ( 4.86851167124881e-02 , 3.56695428925346e-02 , 2.11643038440695e-01 ), ( 2.05645813430333e-02 , 2.14855039556672e-02 , 1.60596234655948e-01 ), ( 1.19742571689663e-01 , 5.88082390684821e-02 , 1.99729197953058e-01 ), ( 1.67829283865154e-01 , 6.86749286807425e-02 , 1.27420450066263e-01 ), ( 2.50642695719310e-01 , 9.82841416736648e-02 , 1.42845702609494e-01 ), ( 1.35844833766718e-01 , 5.10642887969307e-02 , 5.29691138827324e-02 ), ( 1.31635563968384e-01 , 4.37287221381917e-02 , -1.24895896717630e-02 ), ( 1.09743220442345e-01 , 4.30577943864882e-02 , 6.28147116457306e-02 ), ( 7.06095024240929e-02 , 2.41470395377948e-02 , 9.64154857561572e-04 ), ( 5.47317076653039e-02 , 2.16318689297221e-02 , 3.30783409709317e-02 ), ( -4.61339196130928e-03 , -3.84495031494735e-03 , -2.52122009401218e-02 ), ( -1.92651819617661e-02 , -1.53514658164406e-02 , -9.74668415745923e-02 ), ( -5.28422936009517e-02 , -1.49766796886275e-02 , 3.36017509450781e-02 ), ( -1.22254091212308e-01 , -3.99831713070345e-02 , 1.85773137146949e-02 ), ( -1.64534546870824e-01 , -4.70058861347695e-02 , 1.00486451106187e-01 ), ( -1.07080634123299e-01 , -3.89721870900899e-02 , -2.75596095017998e-02 ), ( -1.44945385628667e-01 , -5.72226697247052e-02 , -8.68825241028128e-02 ), ( -4.96210210320117e-02 , -1.71308080191692e-02 , -2.46797329567554e-03 ), ( -2.57417833491587e-02 , -1.27072104130814e-02 , -4.36563096528796e-02 ), ( 3.50569488762591e-02 , 1.26401492722969e-02 , 7.70393273253328e-03 ), ( 6.24768816248500e-03 , -9.62139053241703e-03 , -1.30337943322201e-01 ), ( -1.12985180071072e-02 , -2.06177355430267e-02 , -1.85993589056636e-01 ), ( 5.29348141254694e-02 , 5.03138439773476e-03 , -1.44267875163925e-01 ), ( 8.20488240947292e-02 , 7.72564961274524e-03 , -2.24424383109399e-01 ), ( 1.43741200481599e-01 , 2.95776404414769e-02 , -2.15213605094362e-01 ), ( 1.91560122699135e-02 , -1.87960611889979e-02 , -2.80895918416516e-01 ), ( 2.02208567094964e-02 , -2.49419990716658e-02 , -3.53093435084104e-01 ), ( -3.76869002135258e-02 , -3.52523426763374e-02 , -2.48585256624855e-01 ), ( -1.03097299401374e-01 , -6.16010311536067e-02 , -2.93621852395483e-01 ), ( -1.44315955892824e-01 , -7.11639239898008e-02 , -2.43902469408960e-01 ), ( -1.61211568058450e-01 , -8.32521849218474e-02 , -3.14129047786798e-01 ), ( -1.90688403130903e-01 , -9.93378441717621e-02 , -3.81142834348199e-01 ), ( -1.99058749744944e-01 , -9.61082746547262e-02 , -3.13682024238514e-01 ), ( -2.41655340583087e-01 , -1.13020999449668e-01 , -3.40281173242029e-01 ), ( -1.21386618258863e-01 , -7.02975300165448e-02 , -3.20958120944753e-01 ), ( -1.79879455960514e-01 , -8.43825397273040e-02 , -2.56108328278949e-01 ), ( -2.33738308587350e-01 , -1.03885528953455e-01 , -2.68871577117677e-01 ), ( -2.69524049133083e-01 , -1.08593607135721e-01 , -1.85835805291378e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 34, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5048,10 +8176,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 35, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 35, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 35, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 35, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 35, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 35, atoms_positions[size = 51] = { ( 8.18758198097177e+00 , 4.27478682525558e-02 , -7.03073864718682e-01 ), ( 6.81892603616415e+00 , -6.18076415183793e-01 , -5.13546428131625e-01 ), ( 6.06951427437994e+00 , -3.30810763696199e-01 , 8.16350677814167e-01 ), ( 4.89321910407625e+00 , -1.52662587114762e-01 , 7.63913756830912e-01 ), ( 6.99651171726648e+00 , -2.08914407394131e+00 , -8.35214586840129e-01 ), ( 6.78859984438564e+00 , -3.11582634416293e-01 , 1.96328053406074e+00 ), ( 6.07826062298173e+00 , -2.39023088884221e-01 , 3.23575089194013e+00 ), ( 7.15441537341716e+00 , -3.54044338483169e-01 , 4.41288117313694e+00 ), ( 5.30362416804953e+00 , 1.06425780254130e+00 , 3.36191654236819e+00 ), ( 4.19315491042160e+00 , 1.00315119612648e+00 , 3.83299120788568e+00 ), ( 5.85558945301547e+00 , 2.25270701717089e+00 , 2.96144771599686e+00 ), ( 5.12857791808631e+00 , 3.52474021572560e+00 , 2.86019759651651e+00 ), ( 6.27588499529192e+00 , 4.44043001841798e+00 , 2.28405402729534e+00 ), ( 3.85991209859930e+00 , 3.62377298029292e+00 , 2.00807455715279e+00 ), ( 2.84334728192445e+00 , 4.15947479199413e+00 , 2.41535962459290e+00 ), ( 3.89996305372963e+00 , 3.15329603214102e+00 , 7.73224350753064e-01 ), ( 2.76246883684866e+00 , 3.12085996583065e+00 , -7.18906541142714e-02 ), ( 3.14058835980832e+00 , 2.65661167071910e+00 , -1.52946994391430e+00 ), ( 1.59811093466795e+00 , 2.26072624846230e+00 , 4.39253167874339e-01 ), ( 4.28697049253433e-01 , 2.61390503461078e+00 , 4.31331776322257e-01 ), ( 2.03091355842757e+00 , 1.11280160418402e+00 , 1.04589431623526e+00 ), ( 1.28492381556108e+00 , 1.62266000909496e-01 , 1.66403632346912e+00 ), ( 2.09579951205790e+00 , -1.09382170507587e+00 , 2.03477050502121e+00 ), ( 5.71622244880999e-01 , 6.19151258205981e-01 , 2.93627140596799e+00 ), ( -6.03518368501017e-01 , 3.58329528393548e-01 , 3.20444114748897e+00 ), ( 1.28801333045379e+00 , 1.42517414274212e+00 , 3.78033168563557e+00 ), ( 9.08307043256981e-01 , 1.98327309741441e+00 , 5.05045869603861e+00 ), ( 2.04617960728112e+00 , 2.77480964603669e+00 , 5.72590075891612e+00 ), ( -3.58967862256763e-01 , 2.89151536062043e+00 , 4.92549707964069e+00 ), ( -1.11797911682967e+00 , 3.07121399168678e+00 , 5.89564811768541e+00 ), ( -5.27122678693306e-01 , 3.48612701333263e+00 , 3.73494587033308e+00 ), ( -1.45038797102721e+00 , 4.47573847155800e+00 , 3.41610927692764e+00 ), ( -7.70296733412233e-01 , 5.46520426033772e+00 , 2.48693167492189e+00 ), ( -2.75335684941670e+00 , 3.93092928480662e+00 , 2.72741557414028e+00 ), ( -3.79541083274844e+00 , 4.59451203402486e+00 , 2.80964670439779e+00 ), ( -2.70997109251309e+00 , 2.64703993841399e+00 , 2.34914280380566e+00 ), ( -3.81857542077355e+00 , 1.80288221679954e+00 , 1.99462250318659e+00 ), ( -3.34497155680255e+00 , 8.96821350508929e-01 , 7.72904907828611e-01 ), ( -4.26522253219310e+00 , 1.02306043001778e+00 , 3.24435040202505e+00 ), ( -5.43071260761457e+00 , 7.25511300010191e-01 , 3.35306729611027e+00 ), ( -3.36291898738489e+00 , 7.18055332355550e-01 , 4.16430494982979e+00 ), ( -3.66506207886651e+00 , 6.63448298643537e-02 , 5.46387395862483e+00 ), ( -2.34497695303459e+00 , -2.84148804099343e-01 , 6.12630206690102e+00 ), ( -4.49273886878980e+00 , 9.54014263844208e-01 , 6.42078726816540e+00 ), ( -5.35513187654054e+00 , 5.40902278628718e-01 , 7.17814661148211e+00 ), ( -6.29552184861197e+00 , 3.60359691419288e+00 , 6.77228531577779e+00 ), ( -7.03991858334833e+00 , 4.29979172811510e+00 , 7.51877764950065e+00 ), ( -6.61143450534926e+00 , 3.17076314448908e+00 , 5.55566431774449e+00 ), ( -4.11590920405686e+00 , 2.25265547618249e+00 , 6.41738370151145e+00 ), ( -4.80693600371367e+00 , 3.28175856712602e+00 , 7.20769015248805e+00 ), ( -4.00736480079121e+00 , 4.61331469004481e+00 , 7.28079518983349e+00 ) } +colvars: Step 35, atoms_positions[size = 51] = { ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 ), ( 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 ), ( 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 ), ( 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 ), ( 6.99557007941534e+00 , -2.08949019947414e+00 , -8.34982348421562e-01 ), ( 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 ), ( 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 ), ( 7.15684013418872e+00 , -3.54390863773740e-01 , 4.41439619442458e+00 ), ( 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 ), ( 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 ), ( 5.85765441330763e+00 , 2.25357632863418e+00 , 2.96135309177717e+00 ), ( 5.12892956232295e+00 , 3.52475977030786e+00 , 2.86058621031244e+00 ), ( 6.27581259529792e+00 , 4.44068649408999e+00 , 2.28442867565879e+00 ), ( 3.86003778030757e+00 , 3.62365514967571e+00 , 2.00838763634469e+00 ), ( 2.84340461899748e+00 , 4.15942819785390e+00 , 2.41554148010378e+00 ), ( 3.90011501266677e+00 , 3.15331106552999e+00 , 7.73473736426513e-01 ), ( 2.76266377314302e+00 , 3.12093202274932e+00 , -7.17337222929322e-02 ), ( 3.14084718885558e+00 , 2.65670750570764e+00 , -1.52930446548570e+00 ), ( 1.59827200508141e+00 , 2.26078244998539e+00 , 4.39327007224038e-01 ), ( 4.28855127489450e-01 , 2.61395650836417e+00 , 4.31340874109629e-01 ), ( 2.03103823246046e+00 , 1.11283247621894e+00 , 1.04595998456927e+00 ), ( 1.28500694013577e+00 , 1.62305442570039e-01 , 1.66404889101030e+00 ), ( 2.09593707495244e+00 , -1.09369235287619e+00 , 2.03492022443080e+00 ), ( 5.71701501672222e-01 , 6.19146366947443e-01 , 2.93626404368821e+00 ), ( -6.03471256680418e-01 , 3.58340641749683e-01 , 3.20436015880103e+00 ), ( 1.28814514769357e+00 , 1.42513706084500e+00 , 3.78036167098267e+00 ), ( 9.08243457151620e-01 , 1.98320481057185e+00 , 5.05045130621804e+00 ), ( 2.04602747974294e+00 , 2.77475796806591e+00 , 5.72598118253736e+00 ), ( -3.59074828003976e-01 , 2.89145859638115e+00 , 4.92545793713795e+00 ), ( -1.11814862986205e+00 , 3.07115079927318e+00 , 5.89556865291653e+00 ), ( -5.27177213900735e-01 , 3.48610820723234e+00 , 3.73491500917195e+00 ), ( -1.45042715435018e+00 , 4.47572552119355e+00 , 3.41604513508138e+00 ), ( -7.70276122056878e-01 , 5.46520805609154e+00 , 2.48692710701402e+00 ), ( -2.75335044085151e+00 , 3.93091767583567e+00 , 2.72726254319426e+00 ), ( -3.79541596068014e+00 , 4.59448204069508e+00 , 2.80944426413156e+00 ), ( -2.70992237328715e+00 , 2.64703925881070e+00 , 2.34896722069397e+00 ), ( -3.81849439416217e+00 , 1.80287939976997e+00 , 1.99434655132483e+00 ), ( -3.34481882479411e+00 , 8.96831071549861e-01 , 7.72648337869764e-01 ), ( -4.26520399062543e+00 , 1.02303275116830e+00 , 3.24402621763846e+00 ), ( -5.43069766365938e+00 , 7.25474343111396e-01 , 3.35268627716778e+00 ), ( -3.36294899981467e+00 , 7.18002344988279e-01 , 4.16401048308498e+00 ), ( -3.66518114880938e+00 , 6.62673025110593e-02 , 5.46353759127663e+00 ), ( -2.34513938023854e+00 , -2.84218864339135e-01 , 6.12603983596036e+00 ), ( -4.49291987378211e+00 , 9.53913863017457e-01 , 6.42042535520696e+00 ), ( -5.35534261947300e+00 , 5.40785600506347e-01 , 7.17774433235047e+00 ), ( -6.29576538853292e+00 , 3.60348415987392e+00 , 6.77192099230956e+00 ), ( -7.04018281524354e+00 , 4.29966523735166e+00 , 7.51840899176246e+00 ), ( -6.61161190256765e+00 , 3.17067013371524e+00 , 5.55527971765492e+00 ), ( -4.11611022697671e+00 , 2.25256146811143e+00 , 6.41707374462336e+00 ), ( -4.80719704397028e+00 , 3.28162916048152e+00 , 7.20738265589035e+00 ), ( -4.00765081229166e+00 , 4.61319375564242e+00 , 7.28057771414888e+00 ) } colvars: Step 35, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 35, atom_groups_ids[size = 0] = @@ -5069,162 +8197,301 @@ colvars: Collective variables module, step no. 35 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.87142969394406e-01 , -1.75485194704134e-02 , 9.57726978105848e-01 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.85214732151540e-01 , -1.72436288368453e-02 , 9.58308517038361e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". colvars: Calculating fit gradients. +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.99557007941534e+00 , -2.08949019947414e+00 , -8.34982348421562e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 , 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 7.15684013418872e+00 , -3.54390863773740e-01 , 4.41439619442458e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 , 5.85765441330763e+00 , 2.25357632863418e+00 , 2.96135309177717e+00 , 5.12892956232295e+00 , 3.52475977030786e+00 , 2.86058621031244e+00 , 6.27581259529792e+00 , 4.44068649408999e+00 , 2.28442867565879e+00 , 3.86003778030757e+00 , 3.62365514967571e+00 , 2.00838763634469e+00 , 2.84340461899748e+00 , 4.15942819785390e+00 , 2.41554148010378e+00 , 3.90011501266677e+00 , 3.15331106552999e+00 , 7.73473736426513e-01 , 2.76266377314302e+00 , 3.12093202274932e+00 , -7.17337222929322e-02 , 3.14084718885558e+00 , 2.65670750570764e+00 , -1.52930446548570e+00 , 1.59827200508141e+00 , 2.26078244998539e+00 , 4.39327007224038e-01 , 4.28855127489450e-01 , 2.61395650836417e+00 , 4.31340874109629e-01 , 2.03103823246046e+00 , 1.11283247621894e+00 , 1.04595998456927e+00 , 1.28500694013577e+00 , 1.62305442570039e-01 , 1.66404889101030e+00 , 2.09593707495244e+00 , -1.09369235287619e+00 , 2.03492022443080e+00 , 5.71701501672222e-01 , 6.19146366947443e-01 , 2.93626404368821e+00 , -6.03471256680418e-01 , 3.58340641749683e-01 , 3.20436015880103e+00 , 1.28814514769357e+00 , 1.42513706084500e+00 , 3.78036167098267e+00 , 9.08243457151620e-01 , 1.98320481057185e+00 , 5.05045130621804e+00 , 2.04602747974294e+00 , 2.77475796806591e+00 , 5.72598118253736e+00 , -3.59074828003976e-01 , 2.89145859638115e+00 , 4.92545793713795e+00 , -1.11814862986205e+00 , 3.07115079927318e+00 , 5.89556865291653e+00 , -5.27177213900735e-01 , 3.48610820723234e+00 , 3.73491500917195e+00 , -1.45042715435018e+00 , 4.47572552119355e+00 , 3.41604513508138e+00 , -7.70276122056878e-01 , 5.46520805609154e+00 , 2.48692710701402e+00 , -2.75335044085151e+00 , 3.93091767583567e+00 , 2.72726254319426e+00 , -3.79541596068014e+00 , 4.59448204069508e+00 , 2.80944426413156e+00 , -2.70992237328715e+00 , 2.64703925881070e+00 , 2.34896722069397e+00 , -3.81849439416217e+00 , 1.80287939976997e+00 , 1.99434655132483e+00 , -3.34481882479411e+00 , 8.96831071549861e-01 , 7.72648337869764e-01 , -4.26520399062543e+00 , 1.02303275116830e+00 , 3.24402621763846e+00 , -5.43069766365938e+00 , 7.25474343111396e-01 , 3.35268627716778e+00 , -3.36294899981467e+00 , 7.18002344988279e-01 , 4.16401048308498e+00 , -3.66518114880938e+00 , 6.62673025110593e-02 , 5.46353759127663e+00 , -2.34513938023854e+00 , -2.84218864339135e-01 , 6.12603983596036e+00 , -4.49291987378211e+00 , 9.53913863017457e-01 , 6.42042535520696e+00 , -5.35534261947300e+00 , 5.40785600506347e-01 , 7.17774433235047e+00 , -6.29576538853292e+00 , 3.60348415987392e+00 , 6.77192099230956e+00 , -7.04018281524354e+00 , 4.29966523735166e+00 , 7.51840899176246e+00 , -6.61161190256765e+00 , 3.17067013371524e+00 , 5.55527971765492e+00 , -4.11611022697671e+00 , 2.25256146811143e+00 , 6.41707374462336e+00 , -4.80719704397028e+00 , 3.28162916048152e+00 , 7.20738265589035e+00 , -4.00765081229166e+00 , 4.61319375564242e+00 , 7.28057771414888e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.87142969394406e-01 , -1.75485194704134e-02 , 9.57726978105848e-01 ). +colvars: Colvar "one" has value ( -2.85214732151540e-01 , -1.72436288368453e-02 , 9.58308517038361e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.99557007941534e+00 , -2.08949019947414e+00 , -8.34982348421562e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 , 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 7.15684013418872e+00 , -3.54390863773740e-01 , 4.41439619442458e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 , 5.85765441330763e+00 , 2.25357632863418e+00 , 2.96135309177717e+00 , 5.12892956232295e+00 , 3.52475977030786e+00 , 2.86058621031244e+00 , 6.27581259529792e+00 , 4.44068649408999e+00 , 2.28442867565879e+00 , 3.86003778030757e+00 , 3.62365514967571e+00 , 2.00838763634469e+00 , 2.84340461899748e+00 , 4.15942819785390e+00 , 2.41554148010378e+00 , 3.90011501266677e+00 , 3.15331106552999e+00 , 7.73473736426513e-01 , 2.76266377314302e+00 , 3.12093202274932e+00 , -7.17337222929322e-02 , 3.14084718885558e+00 , 2.65670750570764e+00 , -1.52930446548570e+00 , 1.59827200508141e+00 , 2.26078244998539e+00 , 4.39327007224038e-01 , 4.28855127489450e-01 , 2.61395650836417e+00 , 4.31340874109629e-01 , 2.03103823246046e+00 , 1.11283247621894e+00 , 1.04595998456927e+00 , 1.28500694013577e+00 , 1.62305442570039e-01 , 1.66404889101030e+00 , 2.09593707495244e+00 , -1.09369235287619e+00 , 2.03492022443080e+00 , 5.71701501672222e-01 , 6.19146366947443e-01 , 2.93626404368821e+00 , -6.03471256680418e-01 , 3.58340641749683e-01 , 3.20436015880103e+00 , 1.28814514769357e+00 , 1.42513706084500e+00 , 3.78036167098267e+00 , 9.08243457151620e-01 , 1.98320481057185e+00 , 5.05045130621804e+00 , 2.04602747974294e+00 , 2.77475796806591e+00 , 5.72598118253736e+00 , -3.59074828003976e-01 , 2.89145859638115e+00 , 4.92545793713795e+00 , -1.11814862986205e+00 , 3.07115079927318e+00 , 5.89556865291653e+00 , -5.27177213900735e-01 , 3.48610820723234e+00 , 3.73491500917195e+00 , -1.45042715435018e+00 , 4.47572552119355e+00 , 3.41604513508138e+00 , -7.70276122056878e-01 , 5.46520805609154e+00 , 2.48692710701402e+00 , -2.75335044085151e+00 , 3.93091767583567e+00 , 2.72726254319426e+00 , -3.79541596068014e+00 , 4.59448204069508e+00 , 2.80944426413156e+00 , -2.70992237328715e+00 , 2.64703925881070e+00 , 2.34896722069397e+00 , -3.81849439416217e+00 , 1.80287939976997e+00 , 1.99434655132483e+00 , -3.34481882479411e+00 , 8.96831071549861e-01 , 7.72648337869764e-01 , -4.26520399062543e+00 , 1.02303275116830e+00 , 3.24402621763846e+00 , -5.43069766365938e+00 , 7.25474343111396e-01 , 3.35268627716778e+00 , -3.36294899981467e+00 , 7.18002344988279e-01 , 4.16401048308498e+00 , -3.66518114880938e+00 , 6.62673025110593e-02 , 5.46353759127663e+00 , -2.34513938023854e+00 , -2.84218864339135e-01 , 6.12603983596036e+00 , -4.49291987378211e+00 , 9.53913863017457e-01 , 6.42042535520696e+00 , -5.35534261947300e+00 , 5.40785600506347e-01 , 7.17774433235047e+00 , -6.29576538853292e+00 , 3.60348415987392e+00 , 6.77192099230956e+00 , -7.04018281524354e+00 , 4.29966523735166e+00 , 7.51840899176246e+00 , -6.61161190256765e+00 , 3.17067013371524e+00 , 5.55527971765492e+00 , -4.11611022697671e+00 , 2.25256146811143e+00 , 6.41707374462336e+00 , -4.80719704397028e+00 , 3.28162916048152e+00 , 7.20738265589035e+00 , -4.00765081229166e+00 , 4.61319375564242e+00 , 7.28057771414888e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.2609 , 2.30277 , -15.2509 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.2351 , 6.52351 , 13.047 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.2609 , 2.30277 , -15.2509 ) to colvar "one". -colvars: Adding total bias energy: 43.8002 +colvars: Adding biasing force ( 65.2351 , 6.52351 , 13.047 ) to colvar "one". +colvars: Adding total bias energy: 55.3721 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.2609 , 2.30277 , -15.2509 ) +colvars: Force to be applied: ( 65.2351 , 6.52351 , 13.047 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.94669 , -0.5115 , -1.38241 ) -colvars: ( -4.24179 , -0.438611 , -1.18542 ) -colvars: ( -4.24179 , -0.438611 , -1.18542 ) -colvars: ( -5.65019 , -0.584243 , -1.57901 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.17368 , -0.53241 , -1.43468 ) +colvars: ( -4.43643 , -0.456542 , -1.23024 ) +colvars: ( -4.43643 , -0.456542 , -1.23024 ) +colvars: ( -5.90945 , -0.608127 , -1.63872 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.883684 , 0.196443 , 0.601163 ) -colvars: ( 0.766551 , 0.265873 , 0.624526 ) -colvars: ( 0.750303 , 0.259397 , 0.60681 ) -colvars: ( 0.657389 , 0.265683 , 0.561863 ) -colvars: ( 0.645787 , 0.199619 , 0.469274 ) -colvars: ( 0.572927 , 0.341499 , 0.612216 ) -colvars: ( 0.468338 , 0.354415 , 0.569221 ) -colvars: ( 0.393442 , 0.450162 , 0.650976 ) -colvars: ( 0.388161 , 0.309966 , 0.465545 ) -colvars: ( 0.354395 , 0.268335 , 0.392073 ) -colvars: ( 0.35895 , 0.315433 , 0.455957 ) -colvars: ( 0.288969 , 0.272753 , 0.360412 ) -colvars: ( 0.261897 , 0.301774 , 0.382692 ) -colvars: ( 0.350034 , 0.176287 , 0.269814 ) -colvars: ( 0.292651 , 0.132946 , 0.180613 ) -colvars: ( 0.470099 , 0.140458 , 0.291845 ) -colvars: ( 0.54107 , 0.0504231 , 0.215278 ) -colvars: ( 0.667647 , 0.0306573 , 0.261934 ) -colvars: ( 0.550018 , 0.0185095 , 0.178871 ) -colvars: ( 0.534637 , -0.046089 , 0.086027 ) -colvars: ( 0.570919 , 0.065786 , 0.252334 ) -colvars: ( 0.569991 , 0.0493217 , 0.230381 ) -colvars: ( 0.606145 , 0.113396 , 0.334422 ) -colvars: ( 0.448497 , 0.0527864 , 0.165423 ) -colvars: ( 0.442067 , -0.00286504 , 0.0893378 ) -colvars: ( 0.348588 , 0.117251 , 0.192175 ) -colvars: ( 0.226827 , 0.124855 , 0.132449 ) -colvars: ( 0.13713 , 0.209348 , 0.191098 ) -colvars: ( 0.198899 , 0.0518486 , 0.0214911 ) -colvars: ( 0.150937 , 0.0154889 , -0.0532398 ) -colvars: ( 0.231228 , 0.0271684 , 0.00786386 ) -colvars: ( 0.217163 , -0.0444977 , -0.0934235 ) -colvars: ( 0.251089 , -0.0470969 , -0.0774078 ) -colvars: ( 0.291001 , -0.129314 , -0.161561 ) -colvars: ( 0.247969 , -0.182252 , -0.255044 ) -colvars: ( 0.403886 , -0.143552 , -0.115542 ) -colvars: ( 0.479923 , -0.218021 , -0.16896 ) -colvars: ( 0.608347 , -0.219743 , -0.0977721 ) -colvars: ( 0.434223 , -0.223233 , -0.201871 ) -colvars: ( 0.439755 , -0.290733 , -0.286533 ) -colvars: ( 0.386884 , -0.151207 , -0.135224 ) -colvars: ( 0.334356 , -0.145801 , -0.158223 ) -colvars: ( 0.318543 , -0.0602908 , -0.0560066 ) -colvars: ( 0.213679 , -0.155319 , -0.239607 ) -colvars: ( 0.190115 , -0.19735 , -0.307768 ) -colvars: ( 0.0158941 , -0.201365 , -0.412605 ) -colvars: ( -0.0731018 , -0.219605 , -0.487222 ) -colvars: ( 0.113762 , -0.249894 , -0.419789 ) -colvars: ( 0.133251 , -0.115341 , -0.233577 ) -colvars: ( 0.0164282 , -0.120429 , -0.306993 ) -colvars: ( -0.0708842 , -0.0409186 , -0.253463 ) +colvars: ( 0.92296 , 0.205459 , 0.626253 ) +colvars: ( 0.800734 , 0.277868 , 0.650672 ) +colvars: ( 0.783694 , 0.271182 , 0.63227 ) +colvars: ( 0.686863 , 0.277543 , 0.585337 ) +colvars: ( 0.674749 , 0.208556 , 0.488783 ) +colvars: ( 0.598771 , 0.356603 , 0.637858 ) +colvars: ( 0.48968 , 0.369959 , 0.593026 ) +colvars: ( 0.411566 , 0.469844 , 0.678296 ) +colvars: ( 0.405973 , 0.323526 , 0.484968 ) +colvars: ( 0.370767 , 0.279998 , 0.408334 ) +colvars: ( 0.375422 , 0.329285 , 0.475037 ) +colvars: ( 0.302348 , 0.284713 , 0.37546 ) +colvars: ( 0.274028 , 0.315071 , 0.398765 ) +colvars: ( 0.366041 , 0.184056 , 0.280965 ) +colvars: ( 0.30616 , 0.138755 , 0.187961 ) +colvars: ( 0.491308 , 0.146756 , 0.303902 ) +colvars: ( 0.565342 , 0.052818 , 0.224034 ) +colvars: ( 0.697388 , 0.0323139 , 0.272663 ) +colvars: ( 0.574747 , 0.0194281 , 0.186006 ) +colvars: ( 0.558689 , -0.048033 , 0.089187 ) +colvars: ( 0.596626 , 0.0687406 , 0.262559 ) +colvars: ( 0.59573 , 0.0514715 , 0.239607 ) +colvars: ( 0.633521 , 0.118342 , 0.348048 ) +colvars: ( 0.468978 , 0.0549671 , 0.171895 ) +colvars: ( 0.462289 , -0.00317348 , 0.0925278 ) +colvars: ( 0.36472 , 0.12221 , 0.199843 ) +colvars: ( 0.237679 , 0.130039 , 0.137597 ) +colvars: ( 0.144076 , 0.218206 , 0.198809 ) +colvars: ( 0.20848 , 0.0538389 , 0.0219299 ) +colvars: ( 0.158458 , 0.0158065 , -0.0560085 ) +colvars: ( 0.242138 , 0.0281728 , 0.00776365 ) +colvars: ( 0.227403 , -0.0466139 , -0.0978208 ) +colvars: ( 0.262722 , -0.049216 , -0.0810681 ) +colvars: ( 0.30446 , -0.135134 , -0.168925 ) +colvars: ( 0.259549 , -0.19044 , -0.266397 ) +colvars: ( 0.422274 , -0.149934 , -0.120997 ) +colvars: ( 0.501635 , -0.227657 , -0.176757 ) +colvars: ( 0.63565 , -0.229361 , -0.102575 ) +colvars: ( 0.454022 , -0.233213 , -0.21112 ) +colvars: ( 0.459797 , -0.303698 , -0.299422 ) +colvars: ( 0.404687 , -0.158103 , -0.141638 ) +colvars: ( 0.349947 , -0.152574 , -0.165658 ) +colvars: ( 0.333509 , -0.063359 , -0.0590944 ) +colvars: ( 0.224016 , -0.162602 , -0.250478 ) +colvars: ( 0.199459 , -0.206546 , -0.32158 ) +colvars: ( 0.0175125 , -0.210718 , -0.430723 ) +colvars: ( -0.0753586 , -0.22983 , -0.5085 ) +colvars: ( 0.119583 , -0.261262 , -0.438217 ) +colvars: ( 0.140049 , -0.120875 , -0.24412 ) +colvars: ( 0.0181361 , -0.12627 , -0.320627 ) +colvars: ( -0.0729883 , -0.0432945 , -0.264747 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.94669 , 0.5115 , 1.38241 ) -colvars: ( 4.24179 , 0.438611 , 1.18542 ) -colvars: ( 4.24179 , 0.438611 , 1.18542 ) -colvars: ( 5.65019 , 0.584243 , 1.57901 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.17368 , 0.53241 , 1.43468 ) +colvars: ( 4.43643 , 0.456542 , 1.23024 ) +colvars: ( 4.43643 , 0.456542 , 1.23024 ) +colvars: ( 5.90945 , 0.608127 , 1.63872 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.610093 , -0.0809758 , -0.355505 ) -colvars: ( -0.549561 , -0.164729 , -0.321991 ) -colvars: ( -0.497273 , -0.142169 , -0.26208 ) -colvars: ( -0.513053 , -0.19252 , -0.294366 ) -colvars: ( -0.503349 , -0.132731 , -0.265108 ) -colvars: ( -0.490767 , -0.285863 , -0.302419 ) -colvars: ( -0.460956 , -0.326717 , -0.285785 ) -colvars: ( -0.441466 , -0.435584 , -0.301713 ) -colvars: ( -0.397727 , -0.290586 , -0.210451 ) -colvars: ( -0.394521 , -0.264911 , -0.198853 ) -colvars: ( -0.346578 , -0.284658 , -0.15711 ) -colvars: ( -0.285542 , -0.246986 , -0.0834765 ) -colvars: ( -0.235025 , -0.261927 , -0.0375793 ) -colvars: ( -0.30335 , -0.142316 , -0.0672275 ) -colvars: ( -0.272814 , -0.112497 , -0.0268108 ) -colvars: ( -0.355505 , -0.084257 , -0.100705 ) -colvars: ( -0.380491 , 0.015375 , -0.0933141 ) -colvars: ( -0.427904 , 0.0635458 , -0.125252 ) -colvars: ( -0.420107 , 0.0304586 , -0.128209 ) -colvars: ( -0.408723 , 0.0881304 , -0.0979538 ) -colvars: ( -0.466071 , -0.0245699 , -0.192357 ) -colvars: ( -0.50265 , -0.026206 , -0.229653 ) -colvars: ( -0.554097 , -0.0927967 , -0.303084 ) -colvars: ( -0.45305 , -0.0564996 , -0.189687 ) -colvars: ( -0.460644 , -0.0117879 , -0.182732 ) -colvars: ( -0.399208 , -0.131731 , -0.160116 ) -colvars: ( -0.343772 , -0.163309 , -0.114702 ) -colvars: ( -0.29446 , -0.254664 , -0.0949447 ) -colvars: ( -0.301238 , -0.0892146 , -0.0477825 ) -colvars: ( -0.289482 , -0.0702872 , -0.0297926 ) -colvars: ( -0.278542 , -0.043561 , -0.0100782 ) -colvars: ( -0.241552 , 0.0324615 , 0.0518986 ) -colvars: ( -0.217259 , 0.0593593 , 0.0850894 ) -colvars: ( -0.28484 , 0.120367 , 0.0370699 ) -colvars: ( -0.258544 , 0.162852 , 0.077359 ) -colvars: ( -0.353167 , 0.148665 , -0.0223693 ) -colvars: ( -0.401417 , 0.225832 , -0.0456881 ) -colvars: ( -0.470928 , 0.248494 , -0.108157 ) -colvars: ( -0.415921 , 0.205633 , -0.066855 ) -colvars: ( -0.420431 , 0.26735 , -0.0512539 ) -colvars: ( -0.422999 , 0.117721 , -0.102648 ) -colvars: ( -0.433079 , 0.0870524 , -0.122784 ) -colvars: ( -0.456762 , -0.00776047 , -0.177517 ) -colvars: ( -0.367895 , 0.0758405 , -0.0609292 ) -colvars: ( -0.372538 , 0.102522 , -0.056891 ) -colvars: ( -0.206039 , 0.109651 , 0.112772 ) -colvars: ( -0.157716 , 0.111714 , 0.162012 ) -colvars: ( -0.229616 , 0.182991 , 0.113002 ) -colvars: ( -0.305229 , 0.0347197 , -0.0113617 ) -colvars: ( -0.239829 , 0.0211296 , 0.0499341 ) -colvars: ( -0.186681 , -0.0630155 , 0.0758994 ) +colvars: ( -0.637012 , -0.0847962 , -0.36949 ) +colvars: ( -0.573946 , -0.172151 , -0.334485 ) +colvars: ( -0.51926 , -0.148666 , -0.272008 ) +colvars: ( -0.536004 , -0.201058 , -0.30577 ) +colvars: ( -0.525875 , -0.138641 , -0.2754 ) +colvars: ( -0.512888 , -0.298408 , -0.314088 ) +colvars: ( -0.481943 , -0.340946 , -0.296807 ) +colvars: ( -0.46173 , -0.454512 , -0.313288 ) +colvars: ( -0.415963 , -0.303213 , -0.218383 ) +colvars: ( -0.41269 , -0.276364 , -0.206408 ) +colvars: ( -0.362501 , -0.297068 , -0.162747 ) +colvars: ( -0.29879 , -0.257738 , -0.0860838 ) +colvars: ( -0.245984 , -0.273381 , -0.0381594 ) +colvars: ( -0.317277 , -0.148534 , -0.0692831 ) +colvars: ( -0.285459 , -0.11737 , -0.0272661 ) +colvars: ( -0.371569 , -0.0880211 , -0.104173 ) +colvars: ( -0.397545 , 0.0159205 , -0.0965907 ) +colvars: ( -0.446858 , 0.0660931 , -0.129832 ) +colvars: ( -0.438986 , 0.0317213 , -0.13306 ) +colvars: ( -0.427108 , 0.0919305 , -0.101651 ) +colvars: ( -0.487042 , -0.0256772 , -0.199864 ) +colvars: ( -0.525328 , -0.0273204 , -0.238815 ) +colvars: ( -0.579086 , -0.0968031 , -0.315252 ) +colvars: ( -0.473715 , -0.0588422 , -0.197227 ) +colvars: ( -0.481678 , -0.0121435 , -0.1901 ) +colvars: ( -0.417609 , -0.137317 , -0.16633 ) +colvars: ( -0.359886 , -0.170189 , -0.11905 ) +colvars: ( -0.308497 , -0.265502 , -0.0983378 ) +colvars: ( -0.315438 , -0.0928701 , -0.0494177 ) +colvars: ( -0.303251 , -0.0730574 , -0.0307751 ) +colvars: ( -0.291603 , -0.0453005 , -0.0101015 ) +colvars: ( -0.252923 , 0.034019 , 0.0543903 ) +colvars: ( -0.227413 , 0.0620037 , 0.0890476 ) +colvars: ( -0.298047 , 0.125746 , 0.0388042 ) +colvars: ( -0.270629 , 0.170119 , 0.080681 ) +colvars: ( -0.369282 , 0.155231 , -0.0231324 ) +colvars: ( -0.419594 , 0.235753 , -0.0475517 ) +colvars: ( -0.492031 , 0.259332 , -0.112606 ) +colvars: ( -0.434887 , 0.214763 , -0.0696926 ) +colvars: ( -0.439593 , 0.279189 , -0.0535585 ) +colvars: ( -0.442412 , 0.123074 , -0.106925 ) +colvars: ( -0.453091 , 0.0911576 , -0.127973 ) +colvars: ( -0.477918 , -0.0077544 , -0.184906 ) +colvars: ( -0.385164 , 0.0795275 , -0.0635765 ) +colvars: ( -0.390081 , 0.107425 , -0.059479 ) +colvars: ( -0.216246 , 0.114849 , 0.11736 ) +colvars: ( -0.165889 , 0.117058 , 0.168607 ) +colvars: ( -0.240682 , 0.1913 , 0.117589 ) +colvars: ( -0.319774 , 0.0366167 , -0.0118509 ) +colvars: ( -0.251611 , 0.0224974 , 0.0519764 ) +colvars: ( -0.1962 , -0.0653004 , 0.0791571 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 35. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 35. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 35, atoms_new_colvar_forces = { ( -4.67310333701294e+00 , -3.96032869940031e-01 , -1.13675305028486e+00 ), ( -4.02479957028831e+00 , -3.37467689934347e-01 , -8.82882424665855e-01 ), ( -4.09745376704392e+00 , -3.65449000257380e-01 , -9.17919437563292e-01 ), ( -5.50774836181518e+00 , -5.17354476923141e-01 , -1.37484342627038e+00 ), ( 2.53030350518999e-01 , 1.17227596444910e-01 , 3.44729588176145e-01 ), ( 5.02885491171662e+00 , 5.67136221560684e-01 , 1.69220810896820e+00 ), ( 4.24917203563580e+00 , 4.66309522141449e-01 , 1.46885282471950e+00 ), ( -4.80242524581079e-02 , 1.45781511894730e-02 , 3.49262293185711e-01 ), ( 4.23222393718410e+00 , 4.57991206770844e-01 , 1.44051137186065e+00 ), ( 5.61006104746842e+00 , 5.87667202087456e-01 , 1.77222956826844e+00 ), ( 1.23723178987559e-02 , 3.07748147024519e-02 , 2.98846552446167e-01 ), ( 3.42739432270961e-03 , 2.57670842615945e-02 , 2.76935566089332e-01 ), ( 2.68723556617763e-02 , 3.98470279859051e-02 , 3.45113093705503e-01 ), ( 4.66848876722257e-02 , 3.39715386165191e-02 , 2.02586559466735e-01 ), ( 1.98368929854562e-02 , 2.04489747721448e-02 , 1.53802157009476e-01 ), ( 1.14594104233756e-01 , 5.62005173865854e-02 , 1.91139632044393e-01 ), ( 1.60579043884203e-01 , 6.57980516184638e-02 , 1.21964372100301e-01 ), ( 2.39742772996248e-01 , 9.42030829912775e-02 , 1.36681939673041e-01 ), ( 1.29910816783726e-01 , 4.89680709008115e-02 , 5.06622184299092e-02 ), ( 1.25913455107463e-01 , 4.20414027096970e-02 , -1.19268204007757e-02 ), ( 1.04847609558364e-01 , 4.12160899635881e-02 , 5.99771987505697e-02 ), ( 6.73410827361106e-02 , 2.31157352696927e-02 , 7.28103622259585e-04 ), ( 5.20485563198561e-02 , 2.05994314268606e-02 , 3.13379855807844e-02 ), ( -4.55297079334849e-03 , -3.71326528800056e-03 , -2.42634388459483e-02 ), ( -1.85767713735709e-02 , -1.46529696763599e-02 , -9.33942113425376e-02 ), ( -5.06199247262318e-02 , -1.44803594209622e-02 , 3.20582915336324e-02 ), ( -1.16944090443793e-01 , -3.84542482717961e-02 , 1.77474215944577e-02 ), ( -1.57330263863535e-01 , -4.53155236639219e-02 , 9.61537190643975e-02 ), ( -1.02339422117264e-01 , -3.73659870840615e-02 , -2.62913984055313e-02 ), ( -1.38544996413361e-01 , -5.47982872395032e-02 , -8.30324292047760e-02 ), ( -4.73143735272678e-02 , -1.63925143830818e-02 , -2.21433014419287e-03 ), ( -2.43891322746087e-02 , -1.20361919765720e-02 , -4.15249114609246e-02 ), ( 3.38301237189134e-02 , 1.22623486766634e-02 , 7.68164970826732e-03 ), ( 6.16028199457325e-03 , -8.94702602556456e-03 , -1.24491135655574e-01 ), ( -1.05750968292833e-02 , -1.93995854997111e-02 , -1.77684834745378e-01 ), ( 5.07185958852135e-02 , 5.11358691736646e-03 , -1.37911719580562e-01 ), ( 7.85062642577156e-02 , 7.81065713001006e-03 , -2.14648055937921e-01 ), ( 1.37418630195967e-01 , 2.87509036442712e-02 , -2.05928610860533e-01 ), ( 1.83014219457107e-02 , -1.76002080764069e-02 , -2.68726426506252e-01 ), ( 1.93237985701823e-02 , -2.33833163173352e-02 , -3.37786932931459e-01 ), ( -3.61144502819910e-02 , -3.34868527864934e-02 , -2.37872090743582e-01 ), ( -9.87224474023593e-02 , -5.87484647035892e-02 , -2.81006968561271e-01 ), ( -1.38218723413092e-01 , -6.80512651421760e-02 , -2.33523157650282e-01 ), ( -1.54216600811588e-01 , -7.94786656696858e-02 , -3.00536569962526e-01 ), ( -1.82423321499678e-01 , -9.48284207823263e-02 , -3.64658632862215e-01 ), ( -1.90144766825209e-01 , -9.17144630820363e-02 , -2.99832436309255e-01 ), ( -2.30818052273284e-01 , -1.07890787533157e-01 , -3.25210159533535e-01 ), ( -1.15854697122805e-01 , -6.69022906216085e-02 , -3.06786410634412e-01 ), ( -1.71978000601565e-01 , -8.06209422725339e-02 , -2.44938506930591e-01 ), ( -2.23400608647969e-01 , -9.92994026605735e-02 , -2.57058381513554e-01 ), ( -2.57564689392599e-01 , -1.03934143936365e-01 , -1.77563306489887e-01 ) } +colvars: Step 35, atoms_new_colvar_forces = { ( -4.88773041589092e+00 , -4.11747518843095e-01 , -1.17792165613234e+00 ), ( -4.20964083320243e+00 , -3.50825276103993e-01 , -9.14054824244604e-01 ), ( -4.28556963406229e+00 , -3.80056019703401e-01 , -9.50673798522474e-01 ), ( -5.76057780104335e+00 , -5.38211345555065e-01 , -1.42533419000840e+00 ), ( 2.64433777671576e-01 , 1.22516386488947e-01 , 3.60262875102062e-01 ), ( 5.25956196086280e+00 , 5.90605514472119e-01 , 1.75845374595699e+00 ), ( 4.44416553275086e+00 , 4.85554943208970e-01 , 1.52646018403272e+00 ), ( -5.01645356454149e-02 , 1.53312307515041e-02 , 3.65007285136006e-01 ), ( 4.42643918786033e+00 , 4.76853917049569e-01 , 1.49682605555635e+00 ), ( 5.86752780851986e+00 , 6.11760618797509e-01 , 1.84064345203498e+00 ), ( 1.29212468468592e-02 , 3.22170935596684e-02 , 3.12289968770812e-01 ), ( 3.55830990268030e-03 , 2.69748988590546e-02 , 2.89375769967817e-01 ), ( 2.80436349964942e-02 , 4.16903335922004e-02 , 3.60605826785305e-01 ), ( 4.87643819756062e-02 , 3.55218396178170e-02 , 2.11681724122980e-01 ), ( 2.07018237491816e-02 , 2.13846809025174e-02 , 1.60694638770488e-01 ), ( 1.19739051482598e-01 , 5.87346125919219e-02 , 1.99729209947583e-01 ), ( 1.67797025916064e-01 , 6.87384570544897e-02 , 1.27443658948740e-01 ), ( 2.50530742622340e-01 , 9.84069560231624e-02 , 1.42831156975679e-01 ), ( 1.35760965628326e-01 , 5.11494379433253e-02 , 5.29457483579534e-02 ), ( 1.31580943542922e-01 , 4.38974800073435e-02 , -1.24636561763200e-02 ), ( 1.09583519653664e-01 , 4.30633374482006e-02 , 6.26952779110617e-02 ), ( 7.04010630709179e-02 , 2.41510393194242e-02 , 7.92648254228812e-04 ), ( 5.44348328275769e-02 , 2.15385449770796e-02 , 3.27964633753685e-02 ), ( -4.73686647494842e-03 , -3.87511753734138e-03 , -2.53325043703360e-02 ), ( -1.93889253197023e-02 , -1.53169493665381e-02 , -9.75718457958037e-02 ), ( -5.28881246319936e-02 , -1.51072241077729e-02 , 3.35126051890826e-02 ), ( -1.22207388663047e-01 , -4.01498134739777e-02 , 1.85467828808255e-02 ), ( -1.64421376548035e-01 , -4.72967471810293e-02 , 1.00471437819341e-01 ), ( -1.06957594948178e-01 , -3.90312780405301e-02 , -2.74878368456391e-02 ), ( -1.44793325520095e-01 , -5.72508869947707e-02 , -8.67835539894558e-02 ), ( -4.94657279405175e-02 , -1.71277082198067e-02 , -2.33785265957891e-03 ), ( -2.55199857872662e-02 , -1.25948513702735e-02 , -4.34304530799997e-02 ), ( 3.53092271896965e-02 , 1.27876886030257e-02 , 7.97949528036909e-03 ), ( 6.41360581866401e-03 , -9.38854054791916e-03 , -1.30121257665082e-01 ), ( -1.10807762782602e-02 , -2.03209922034441e-02 , -1.85715696077113e-01 ), ( 5.29922541427579e-02 , 5.29663563833063e-03 , -1.44129760474241e-01 ), ( 8.20412963040485e-02 , 8.09593520773705e-03 , -2.24308593836000e-01 ), ( 1.43619375022329e-01 , 2.99709825523847e-02 , -2.15181243279100e-01 ), ( 1.91346939294886e-02 , -1.84505750720338e-02 , -2.80812320289916e-01 ), ( 2.02041612678813e-02 , -2.45085522620857e-02 , -3.52980310490388e-01 ), ( -3.77246918730068e-02 , -3.50285835670905e-02 , -2.48562761576247e-01 ), ( -1.03143599841225e-01 , -6.14165720153193e-02 , -2.93631469474359e-01 ), ( -1.44408550166542e-01 , -7.11133800420470e-02 , -2.44000259312310e-01 ), ( -1.61148724977604e-01 , -8.30749564303604e-02 , -3.14054608163947e-01 ), ( -1.90621840589093e-01 , -9.91203630109317e-02 , -3.81059508335726e-01 ), ( -1.98733961295644e-01 , -9.58692876794523e-02 , -3.13362647420307e-01 ), ( -2.41247761119296e-01 , -1.12772561806286e-01 , -3.39893461381864e-01 ), ( -1.21099191399720e-01 , -6.99612980240896e-02 , -3.20628712112169e-01 ), ( -1.79724726253634e-01 , -8.42586700062325e-02 , -2.55970522827265e-01 ), ( -2.33475387983648e-01 , -1.03772620881512e-01 , -2.68650775547765e-01 ), ( -2.69188676099671e-01 , -1.08594874619903e-01 , -1.85589931087990e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 35, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5262,10 +8529,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 36, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 36, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 36, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 36, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 36, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 36, atoms_positions[size = 51] = { ( 8.17518917512548e+00 , 4.20932162402850e-02 , -6.99380683784479e-01 ), ( 6.81460123882792e+00 , -6.21522171600354e-01 , -5.09578424489461e-01 ), ( 6.06410997214541e+00 , -3.26043161463894e-01 , 8.14673069718519e-01 ), ( 4.88701023537668e+00 , -1.53027098069873e-01 , 7.67860023067761e-01 ), ( 6.99824440044699e+00 , -2.09382931386667e+00 , -8.27386655102873e-01 ), ( 6.78317908220918e+00 , -3.14047143732065e-01 , 1.96123951362137e+00 ), ( 6.07931470397312e+00 , -2.40626383838944e-01 , 3.24924024298311e+00 ), ( 7.15447925384046e+00 , -3.57234629211548e-01 , 4.41791319142681e+00 ), ( 5.30111987545515e+00 , 1.06423224442739e+00 , 3.36107596992258e+00 ), ( 4.19372091455259e+00 , 1.00359783505039e+00 , 3.84425956338652e+00 ), ( 5.85542179024010e+00 , 2.25412648552387e+00 , 2.95903112006657e+00 ), ( 5.12739809162237e+00 , 3.51940370590129e+00 , 2.85564495005150e+00 ), ( 6.26956012748138e+00 , 4.43421892228316e+00 , 2.28426989991293e+00 ), ( 3.86090195107428e+00 , 3.62051193243425e+00 , 2.00519708133362e+00 ), ( 2.84895138029515e+00 , 4.15738956160830e+00 , 2.41208938018834e+00 ), ( 3.89983954776634e+00 , 3.14513750676237e+00 , 7.79862184348236e-01 ), ( 2.75890327575505e+00 , 3.13290364879249e+00 , -7.48869054177583e-02 ), ( 3.14432045991482e+00 , 2.65919342218048e+00 , -1.52389762352200e+00 ), ( 1.61351123419885e+00 , 2.27114458901352e+00 , 4.45361991052464e-01 ), ( 4.31276139932799e-01 , 2.61317351245067e+00 , 4.25357566582053e-01 ), ( 2.02555983656296e+00 , 1.11000187885621e+00 , 1.04250449293346e+00 ), ( 1.29315621293675e+00 , 1.65377976174572e-01 , 1.66293187119804e+00 ), ( 2.09744766219105e+00 , -1.09363106718668e+00 , 2.03181238049657e+00 ), ( 5.70789693138863e-01 , 6.22350067753368e-01 , 2.93369174430324e+00 ), ( -6.07013237367369e-01 , 3.58467436784136e-01 , 3.20866962649618e+00 ), ( 1.28968641523697e+00 , 1.43025310862581e+00 , 3.78401468528374e+00 ), ( 9.13717777439262e-01 , 1.98562890454697e+00 , 5.05496771534087e+00 ), ( 2.03869413228311e+00 , 2.77793948732377e+00 , 5.72600455843582e+00 ), ( -3.57624002886876e-01 , 2.88949728773538e+00 , 4.92106557794947e+00 ), ( -1.11841225104512e+00 , 3.07152796678649e+00 , 5.89739292844448e+00 ), ( -5.21592068985012e-01 , 3.47895078341291e+00 , 3.72619207610853e+00 ), ( -1.45136143851699e+00 , 4.47658226302127e+00 , 3.41381303059645e+00 ), ( -7.74683171499790e-01 , 5.47233397985892e+00 , 2.48794766162271e+00 ), ( -2.75456271630087e+00 , 3.92758039691698e+00 , 2.72047005088196e+00 ), ( -3.79306389594734e+00 , 4.59966286284149e+00 , 2.80771741377871e+00 ), ( -2.71251020359701e+00 , 2.65077831472665e+00 , 2.34696276135925e+00 ), ( -3.82151457473994e+00 , 1.79539277372270e+00 , 1.99101247269911e+00 ), ( -3.34203536663097e+00 , 9.02876114262936e-01 , 7.66831669818640e-01 ), ( -4.27006467355301e+00 , 1.02049005288999e+00 , 3.24090970652971e+00 ), ( -5.42299517375100e+00 , 7.19851795765019e-01 , 3.35667038536792e+00 ), ( -3.35977181021253e+00 , 7.13481608601062e-01 , 4.16735503723690e+00 ), ( -3.66451828935214e+00 , 6.29393383345861e-02 , 5.45642322517551e+00 ), ( -2.33657262210542e+00 , -2.76730996101650e-01 , 6.12827789323743e+00 ), ( -4.49170751016758e+00 , 9.63528712671481e-01 , 6.42056484459742e+00 ), ( -5.35496151743373e+00 , 5.33639852320449e-01 , 7.17372801345931e+00 ), ( -6.28937224752982e+00 , 3.60062919018572e+00 , 6.78014779680789e+00 ), ( -7.04616889789833e+00 , 4.29854293934481e+00 , 7.51767903209868e+00 ), ( -6.60948320503296e+00 , 3.17316282929707e+00 , 5.55884665002323e+00 ), ( -4.11993287885638e+00 , 2.25188914754568e+00 , 6.42101339223344e+00 ), ( -4.80343157933424e+00 , 3.27792611513744e+00 , 7.19827113426333e+00 ), ( -4.00755025383473e+00 , 4.62458441110233e+00 , 7.28178260714863e+00 ) } +colvars: Step 36, atoms_positions[size = 51] = { ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 ), ( 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 ), ( 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 ), ( 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 ), ( 6.99723356848930e+00 , -2.09419525812471e+00 , -8.27129300320567e-01 ), ( 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 ), ( 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 ), ( 7.15706021666618e+00 , -3.57597425855947e-01 , 4.41945794203117e+00 ), ( 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 ), ( 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 ), ( 5.85758832793169e+00 , 2.25504488524377e+00 , 2.95891408447770e+00 ), ( 5.12779342097314e+00 , 3.51941981343439e+00 , 2.85605341409322e+00 ), ( 6.26948731267596e+00 , 4.43451101750161e+00 , 2.28466092075193e+00 ), ( 3.86104658422879e+00 , 3.62038375789240e+00 , 2.00553047766542e+00 ), ( 2.84901780336858e+00 , 4.15733284514224e+00 , 2.41228272300415e+00 ), ( 3.90000070771336e+00 , 3.14514793484549e+00 , 7.80126214616235e-01 ), ( 2.75910867030025e+00 , 3.13297851157940e+00 , -7.47200298448949e-02 ), ( 3.14459302428540e+00 , 2.65929421023285e+00 , -1.52372351883350e+00 ), ( 1.61368031524600e+00 , 2.27120350503521e+00 , 4.45440350384779e-01 ), ( 4.31443198308536e-01 , 2.61322851488362e+00 , 4.25368395503651e-01 ), ( 2.02568946456082e+00 , 1.11003293167251e+00 , 1.04256934791582e+00 ), ( 1.29324408837554e+00 , 1.65418978524617e-01 , 1.66294534831571e+00 ), ( 2.09759579563072e+00 , -1.09349147718460e+00 , 2.03197610368111e+00 ), ( 5.70875932381883e-01 , 6.22345595517025e-01 , 2.93368466438564e+00 ), ( -6.06959227306262e-01 , 3.58481065283510e-01 , 3.20858547514740e+00 ), ( 1.28982439599295e+00 , 1.43021466496170e+00 , 3.78404569606397e+00 ), ( 9.13653392685198e-01 , 1.98555734869590e+00 , 5.05495946536194e+00 ), ( 2.03853629348129e+00 , 2.77788525774637e+00 , 5.72608999678792e+00 ), ( -3.57734959834092e-01 , 2.88943674699778e+00 , 4.92102384123755e+00 ), ( -1.11858976612841e+00 , 3.07146048554314e+00 , 5.89730870348002e+00 ), ( -5.21648760875345e-01 , 3.47893075978990e+00 , 3.72615940149803e+00 ), ( -1.45140237321515e+00 , 4.47656846776950e+00 , 3.41374554257939e+00 ), ( -7.74661600225245e-01 , 5.47233806133262e+00 , 2.48794318145854e+00 ), ( -2.75455552906930e+00 , 3.92756827594720e+00 , 2.72030917715245e+00 ), ( -3.79306921941895e+00 , 4.59963166833403e+00 , 2.80750434481269e+00 ), ( -2.71245945596158e+00 , 2.65077731215350e+00 , 2.34677756924521e+00 ), ( -3.82142967663025e+00 , 1.79538957524820e+00 , 1.99072186156305e+00 ), ( -3.34187444427744e+00 , 9.02887036972023e-01 , 7.66561654111795e-01 ), ( -4.27004532929729e+00 , 1.02046130461287e+00 , 3.24056835145711e+00 ), ( -5.42297998545340e+00 , 7.19813061559532e-01 , 3.35626899032413e+00 ), ( -3.35980353726781e+00 , 7.13425912407024e-01 , 4.16704508215239e+00 ), ( -3.66464323877533e+00 , 6.28586029648061e-02 , 5.45607066683593e+00 ), ( -2.33674333981043e+00 , -2.76805072869965e-01 , 6.12800241170569e+00 ), ( -4.49189756436332e+00 , 9.63422943902330e-01 , 6.42018477707952e+00 ), ( -5.35518376619704e+00 , 5.33516535464145e-01 , 7.17330430327523e+00 ), ( -6.28962935081183e+00 , 3.60051004574782e+00 , 6.77976422121130e+00 ), ( -7.04644687483213e+00 , 4.29840961125306e+00 , 7.51729040384008e+00 ), ( -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 ), ( -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 ), ( -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 ), ( -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ) } colvars: Step 36, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 36, atom_groups_ids[size = 0] = @@ -5282,163 +8549,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 36 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.85104418391494e-01 , -1.80726295704393e-02 , 9.58326066990801e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.83103690637276e-01 , -1.77547915732536e-02 , 9.58924954166771e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.99723356848930e+00 , -2.09419525812471e+00 , -8.27129300320567e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 , 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 7.15706021666618e+00 , -3.57597425855947e-01 , 4.41945794203117e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 , 5.85758832793169e+00 , 2.25504488524377e+00 , 2.95891408447770e+00 , 5.12779342097314e+00 , 3.51941981343439e+00 , 2.85605341409322e+00 , 6.26948731267596e+00 , 4.43451101750161e+00 , 2.28466092075193e+00 , 3.86104658422879e+00 , 3.62038375789240e+00 , 2.00553047766542e+00 , 2.84901780336858e+00 , 4.15733284514224e+00 , 2.41228272300415e+00 , 3.90000070771336e+00 , 3.14514793484549e+00 , 7.80126214616235e-01 , 2.75910867030025e+00 , 3.13297851157940e+00 , -7.47200298448949e-02 , 3.14459302428540e+00 , 2.65929421023285e+00 , -1.52372351883350e+00 , 1.61368031524600e+00 , 2.27120350503521e+00 , 4.45440350384779e-01 , 4.31443198308536e-01 , 2.61322851488362e+00 , 4.25368395503651e-01 , 2.02568946456082e+00 , 1.11003293167251e+00 , 1.04256934791582e+00 , 1.29324408837554e+00 , 1.65418978524617e-01 , 1.66294534831571e+00 , 2.09759579563072e+00 , -1.09349147718460e+00 , 2.03197610368111e+00 , 5.70875932381883e-01 , 6.22345595517025e-01 , 2.93368466438564e+00 , -6.06959227306262e-01 , 3.58481065283510e-01 , 3.20858547514740e+00 , 1.28982439599295e+00 , 1.43021466496170e+00 , 3.78404569606397e+00 , 9.13653392685198e-01 , 1.98555734869590e+00 , 5.05495946536194e+00 , 2.03853629348129e+00 , 2.77788525774637e+00 , 5.72608999678792e+00 , -3.57734959834092e-01 , 2.88943674699778e+00 , 4.92102384123755e+00 , -1.11858976612841e+00 , 3.07146048554314e+00 , 5.89730870348002e+00 , -5.21648760875345e-01 , 3.47893075978990e+00 , 3.72615940149803e+00 , -1.45140237321515e+00 , 4.47656846776950e+00 , 3.41374554257939e+00 , -7.74661600225245e-01 , 5.47233806133262e+00 , 2.48794318145854e+00 , -2.75455552906930e+00 , 3.92756827594720e+00 , 2.72030917715245e+00 , -3.79306921941895e+00 , 4.59963166833403e+00 , 2.80750434481269e+00 , -2.71245945596158e+00 , 2.65077731215350e+00 , 2.34677756924521e+00 , -3.82142967663025e+00 , 1.79538957524820e+00 , 1.99072186156305e+00 , -3.34187444427744e+00 , 9.02887036972023e-01 , 7.66561654111795e-01 , -4.27004532929729e+00 , 1.02046130461287e+00 , 3.24056835145711e+00 , -5.42297998545340e+00 , 7.19813061559532e-01 , 3.35626899032413e+00 , -3.35980353726781e+00 , 7.13425912407024e-01 , 4.16704508215239e+00 , -3.66464323877533e+00 , 6.28586029648061e-02 , 5.45607066683593e+00 , -2.33674333981043e+00 , -2.76805072869965e-01 , 6.12800241170569e+00 , -4.49189756436332e+00 , 9.63422943902330e-01 , 6.42018477707952e+00 , -5.35518376619704e+00 , 5.33516535464145e-01 , 7.17330430327523e+00 , -6.28962935081183e+00 , 3.60051004574782e+00 , 6.77976422121130e+00 , -7.04644687483213e+00 , 4.29840961125306e+00 , 7.51729040384008e+00 , -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 , -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 , -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 , -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.85104418391494e-01 , -1.80726295704393e-02 , 9.58326066990801e-01 ). +colvars: Colvar "one" has value ( -2.83103690637276e-01 , -1.77547915732536e-02 , 9.58924954166771e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.99723356848930e+00 , -2.09419525812471e+00 , -8.27129300320567e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 , 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 7.15706021666618e+00 , -3.57597425855947e-01 , 4.41945794203117e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 , 5.85758832793169e+00 , 2.25504488524377e+00 , 2.95891408447770e+00 , 5.12779342097314e+00 , 3.51941981343439e+00 , 2.85605341409322e+00 , 6.26948731267596e+00 , 4.43451101750161e+00 , 2.28466092075193e+00 , 3.86104658422879e+00 , 3.62038375789240e+00 , 2.00553047766542e+00 , 2.84901780336858e+00 , 4.15733284514224e+00 , 2.41228272300415e+00 , 3.90000070771336e+00 , 3.14514793484549e+00 , 7.80126214616235e-01 , 2.75910867030025e+00 , 3.13297851157940e+00 , -7.47200298448949e-02 , 3.14459302428540e+00 , 2.65929421023285e+00 , -1.52372351883350e+00 , 1.61368031524600e+00 , 2.27120350503521e+00 , 4.45440350384779e-01 , 4.31443198308536e-01 , 2.61322851488362e+00 , 4.25368395503651e-01 , 2.02568946456082e+00 , 1.11003293167251e+00 , 1.04256934791582e+00 , 1.29324408837554e+00 , 1.65418978524617e-01 , 1.66294534831571e+00 , 2.09759579563072e+00 , -1.09349147718460e+00 , 2.03197610368111e+00 , 5.70875932381883e-01 , 6.22345595517025e-01 , 2.93368466438564e+00 , -6.06959227306262e-01 , 3.58481065283510e-01 , 3.20858547514740e+00 , 1.28982439599295e+00 , 1.43021466496170e+00 , 3.78404569606397e+00 , 9.13653392685198e-01 , 1.98555734869590e+00 , 5.05495946536194e+00 , 2.03853629348129e+00 , 2.77788525774637e+00 , 5.72608999678792e+00 , -3.57734959834092e-01 , 2.88943674699778e+00 , 4.92102384123755e+00 , -1.11858976612841e+00 , 3.07146048554314e+00 , 5.89730870348002e+00 , -5.21648760875345e-01 , 3.47893075978990e+00 , 3.72615940149803e+00 , -1.45140237321515e+00 , 4.47656846776950e+00 , 3.41374554257939e+00 , -7.74661600225245e-01 , 5.47233806133262e+00 , 2.48794318145854e+00 , -2.75455552906930e+00 , 3.92756827594720e+00 , 2.72030917715245e+00 , -3.79306921941895e+00 , 4.59963166833403e+00 , 2.80750434481269e+00 , -2.71245945596158e+00 , 2.65077731215350e+00 , 2.34677756924521e+00 , -3.82142967663025e+00 , 1.79538957524820e+00 , 1.99072186156305e+00 , -3.34187444427744e+00 , 9.02887036972023e-01 , 7.66561654111795e-01 , -4.27004532929729e+00 , 1.02046130461287e+00 , 3.24056835145711e+00 , -5.42297998545340e+00 , 7.19813061559532e-01 , 3.35626899032413e+00 , -3.35980353726781e+00 , 7.13425912407024e-01 , 4.16704508215239e+00 , -3.66464323877533e+00 , 6.28586029648061e-02 , 5.45607066683593e+00 , -2.33674333981043e+00 , -2.76805072869965e-01 , 6.12800241170569e+00 , -4.49189756436332e+00 , 9.63422943902330e-01 , 6.42018477707952e+00 , -5.35518376619704e+00 , 5.33516535464145e-01 , 7.17330430327523e+00 , -6.28962935081183e+00 , 3.60051004574782e+00 , 6.77976422121130e+00 , -7.04644687483213e+00 , 4.29840961125306e+00 , 7.51729040384008e+00 , -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 , -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 , -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 , -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.2201 , 2.31325 , -15.2629 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.1383 , 6.51383 , 13.0277 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.2201 , 2.31325 , -15.2629 ) to colvar "one". -colvars: Adding total bias energy: 43.718 +colvars: Adding biasing force ( 65.1383 , 6.51383 , 13.0277 ) to colvar "one". +colvars: Adding total bias energy: 55.2297 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.2201 , 2.31325 , -15.2629 ) +colvars: Force to be applied: ( 65.1383 , 6.51383 , 13.0277 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.95047 , -0.508986 , -1.37354 ) -colvars: ( -4.24503 , -0.436455 , -1.17781 ) -colvars: ( -4.24503 , -0.436455 , -1.17781 ) -colvars: ( -5.6545 , -0.581371 , -1.56888 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.16842 , -0.528748 , -1.42246 ) +colvars: ( -4.43192 , -0.453401 , -1.21976 ) +colvars: ( -4.43192 , -0.453401 , -1.21976 ) +colvars: ( -5.90344 , -0.603944 , -1.62476 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.882922 , 0.196576 , 0.599212 ) -colvars: ( 0.766003 , 0.265841 , 0.622549 ) -colvars: ( 0.749716 , 0.259448 , 0.604956 ) -colvars: ( 0.657083 , 0.26552 , 0.560031 ) -colvars: ( 0.645508 , 0.199519 , 0.467674 ) -colvars: ( 0.572806 , 0.341148 , 0.610248 ) -colvars: ( 0.468455 , 0.353916 , 0.567341 ) -colvars: ( 0.393719 , 0.449467 , 0.648885 ) -colvars: ( 0.388403 , 0.309488 , 0.463973 ) -colvars: ( 0.354732 , 0.267841 , 0.390662 ) -colvars: ( 0.359189 , 0.315 , 0.454478 ) -colvars: ( 0.289308 , 0.272355 , 0.359225 ) -colvars: ( 0.262225 , 0.301399 , 0.381522 ) -colvars: ( 0.35025 , 0.176062 , 0.268853 ) -colvars: ( 0.292982 , 0.132718 , 0.179883 ) -colvars: ( 0.470073 , 0.140387 , 0.290816 ) -colvars: ( 0.540903 , 0.0505233 , 0.214436 ) -colvars: ( 0.667212 , 0.0309185 , 0.260978 ) -colvars: ( 0.549896 , 0.0185767 , 0.178054 ) -colvars: ( 0.534549 , -0.0459643 , 0.085443 ) -colvars: ( 0.570807 , 0.0657522 , 0.251273 ) -colvars: ( 0.569944 , 0.0492273 , 0.22931 ) -colvars: ( 0.606072 , 0.113202 , 0.333033 ) -colvars: ( 0.448704 , 0.052561 , 0.164517 ) -colvars: ( 0.442313 , -0.00306365 , 0.0885969 ) -colvars: ( 0.348973 , 0.116884 , 0.191233 ) -colvars: ( 0.227457 , 0.124365 , 0.13167 ) -colvars: ( 0.137913 , 0.208707 , 0.190207 ) -colvars: ( 0.199548 , 0.0514644 , 0.0210352 ) -colvars: ( 0.151705 , 0.0150739 , -0.053526 ) -colvars: ( 0.231754 , 0.0269159 , 0.00750072 ) -colvars: ( 0.21768 , -0.0446308 , -0.0934876 ) -colvars: ( 0.251472 , -0.0471137 , -0.0774467 ) -colvars: ( 0.291397 , -0.129313 , -0.161489 ) -colvars: ( 0.248449 , -0.182227 , -0.254729 ) -colvars: ( 0.404084 , -0.143464 , -0.115628 ) -colvars: ( 0.480002 , -0.217816 , -0.168952 ) -colvars: ( 0.608185 , -0.219437 , -0.0979746 ) -colvars: ( 0.434452 , -0.223139 , -0.201839 ) -colvars: ( 0.439987 , -0.290572 , -0.286301 ) -colvars: ( 0.387245 , -0.151288 , -0.135394 ) -colvars: ( 0.334877 , -0.146006 , -0.158389 ) -colvars: ( 0.319132 , -0.0606583 , -0.0564695 ) -colvars: ( 0.214428 , -0.155609 , -0.239541 ) -colvars: ( 0.190943 , -0.197653 , -0.30756 ) -colvars: ( 0.0169329 , -0.201652 , -0.411967 ) -colvars: ( -0.0718932 , -0.219942 , -0.486378 ) -colvars: ( 0.114576 , -0.249996 , -0.419112 ) -colvars: ( 0.134113 , -0.115693 , -0.233467 ) -colvars: ( 0.0175077 , -0.120863 , -0.306667 ) -colvars: ( -0.0696627 , -0.0414862 , -0.25323 ) +colvars: ( 0.920477 , 0.205233 , 0.62301 ) +colvars: ( 0.798702 , 0.277334 , 0.647358 ) +colvars: ( 0.781649 , 0.27075 , 0.629123 ) +colvars: ( 0.685297 , 0.276868 , 0.582298 ) +colvars: ( 0.673233 , 0.208073 , 0.486169 ) +colvars: ( 0.597564 , 0.355583 , 0.634578 ) +colvars: ( 0.488927 , 0.368755 , 0.589924 ) +colvars: ( 0.411126 , 0.468248 , 0.674813 ) +colvars: ( 0.405505 , 0.322428 , 0.482394 ) +colvars: ( 0.370463 , 0.278961 , 0.406072 ) +colvars: ( 0.375004 , 0.328226 , 0.472581 ) +colvars: ( 0.302169 , 0.283772 , 0.373497 ) +colvars: ( 0.273886 , 0.314101 , 0.396779 ) +colvars: ( 0.365612 , 0.183482 , 0.279416 ) +colvars: ( 0.305963 , 0.138259 , 0.18683 ) +colvars: ( 0.490393 , 0.146416 , 0.302239 ) +colvars: ( 0.564141 , 0.0528321 , 0.222715 ) +colvars: ( 0.69566 , 0.0325386 , 0.271133 ) +colvars: ( 0.573578 , 0.0194665 , 0.184782 ) +colvars: ( 0.557586 , -0.047811 , 0.0883896 ) +colvars: ( 0.59543 , 0.0685809 , 0.260935 ) +colvars: ( 0.594606 , 0.0512773 , 0.238013 ) +colvars: ( 0.632302 , 0.117919 , 0.345916 ) +colvars: ( 0.468356 , 0.0546254 , 0.170601 ) +colvars: ( 0.461721 , -0.00338162 , 0.0915566 ) +colvars: ( 0.364478 , 0.121595 , 0.198463 ) +colvars: ( 0.237929 , 0.129277 , 0.136505 ) +colvars: ( 0.144661 , 0.217122 , 0.197486 ) +colvars: ( 0.208803 , 0.053328 , 0.0213949 ) +colvars: ( 0.158999 , 0.0153309 , -0.0562194 ) +colvars: ( 0.242267 , 0.0278504 , 0.0073537 ) +colvars: ( 0.227546 , -0.0466726 , -0.097718 ) +colvars: ( 0.262658 , -0.0491442 , -0.0809689 ) +colvars: ( 0.304336 , -0.13489 , -0.168548 ) +colvars: ( 0.259595 , -0.190069 , -0.265581 ) +colvars: ( 0.421724 , -0.149569 , -0.120877 ) +colvars: ( 0.500813 , -0.227025 , -0.176436 ) +colvars: ( 0.634327 , -0.228616 , -0.102616 ) +colvars: ( 0.453449 , -0.232691 , -0.21071 ) +colvars: ( 0.459216 , -0.302976 , -0.298637 ) +colvars: ( 0.404345 , -0.157904 , -0.141571 ) +colvars: ( 0.349878 , -0.152521 , -0.165543 ) +colvars: ( 0.333544 , -0.0636412 , -0.0594912 ) +colvars: ( 0.224419 , -0.162622 , -0.249958 ) +colvars: ( 0.199992 , -0.2065 , -0.32078 ) +colvars: ( 0.0185975 , -0.210647 , -0.429261 ) +colvars: ( -0.0739237 , -0.229779 , -0.506674 ) +colvars: ( 0.120242 , -0.260901 , -0.436701 ) +colvars: ( 0.140725 , -0.121037 , -0.243565 ) +colvars: ( 0.0192652 , -0.12651 , -0.319701 ) +colvars: ( -0.071542 , -0.0438282 , -0.26402 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.95047 , 0.508986 , 1.37354 ) -colvars: ( 4.24503 , 0.436455 , 1.17781 ) -colvars: ( 4.24503 , 0.436455 , 1.17781 ) -colvars: ( 5.6545 , 0.581371 , 1.56888 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.16842 , 0.528748 , 1.42246 ) +colvars: ( 4.43192 , 0.453401 , 1.21976 ) +colvars: ( 4.43192 , 0.453401 , 1.21976 ) +colvars: ( 5.90344 , 0.603944 , 1.62476 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.60926 , -0.0810102 , -0.353452 ) -colvars: ( -0.548959 , -0.16471 , -0.319797 ) -colvars: ( -0.496515 , -0.142181 , -0.259874 ) -colvars: ( -0.512751 , -0.192439 , -0.292345 ) -colvars: ( -0.503054 , -0.132652 , -0.263378 ) -colvars: ( -0.490725 , -0.285723 , -0.300217 ) -colvars: ( -0.461223 , -0.326511 , -0.2837 ) -colvars: ( -0.441965 , -0.435324 , -0.299346 ) -colvars: ( -0.398058 , -0.290369 , -0.208629 ) -colvars: ( -0.39498 , -0.264671 , -0.197273 ) -colvars: ( -0.346812 , -0.284459 , -0.155254 ) -colvars: ( -0.285806 , -0.246782 , -0.0818589 ) -colvars: ( -0.235185 , -0.261741 , -0.0358225 ) -colvars: ( -0.303433 , -0.142156 , -0.0659207 ) -colvars: ( -0.273007 , -0.112317 , -0.0257631 ) -colvars: ( -0.355309 , -0.0841582 , -0.0993785 ) -colvars: ( -0.380105 , 0.015428 , -0.0922609 ) -colvars: ( -0.427192 , 0.0635293 , -0.12409 ) -colvars: ( -0.419853 , 0.0305356 , -0.127329 ) -colvars: ( -0.408485 , 0.0882064 , -0.0973644 ) -colvars: ( -0.465928 , -0.0244682 , -0.191297 ) -colvars: ( -0.502668 , -0.0260733 , -0.228717 ) -colvars: ( -0.554185 , -0.0926464 , -0.301873 ) -colvars: ( -0.453364 , -0.0563048 , -0.188915 ) -colvars: ( -0.461016 , -0.0115849 , -0.182221 ) -colvars: ( -0.39971 , -0.131492 , -0.159199 ) -colvars: ( -0.344545 , -0.163013 , -0.113923 ) -colvars: ( -0.295398 , -0.254326 , -0.0939201 ) -colvars: ( -0.301945 , -0.0889354 , -0.0473117 ) -colvars: ( -0.290339 , -0.0699795 , -0.0295581 ) -colvars: ( -0.279015 , -0.0433307 , -0.00961442 ) -colvars: ( -0.241925 , 0.0326671 , 0.0520805 ) -colvars: ( -0.217385 , 0.0595147 , 0.0853637 ) -colvars: ( -0.285089 , 0.12054 , 0.0369808 ) -colvars: ( -0.258859 , 0.163036 , 0.0769935 ) -colvars: ( -0.353236 , 0.148799 , -0.0223841 ) -colvars: ( -0.401374 , 0.225937 , -0.0459323 ) -colvars: ( -0.470646 , 0.248548 , -0.108243 ) -colvars: ( -0.416132 , 0.205789 , -0.0672352 ) -colvars: ( -0.420638 , 0.2675 , -0.0519165 ) -colvars: ( -0.423439 , 0.117928 , -0.102828 ) -colvars: ( -0.433783 , 0.0873143 , -0.123063 ) -colvars: ( -0.457634 , -0.00745866 , -0.177497 ) -colvars: ( -0.368824 , 0.0761496 , -0.0614039 ) -colvars: ( -0.373585 , 0.102852 , -0.0575993 ) -colvars: ( -0.2071 , 0.109988 , 0.111925 ) -colvars: ( -0.158943 , 0.112085 , 0.160972 ) -colvars: ( -0.230369 , 0.183261 , 0.112115 ) -colvars: ( -0.306226 , 0.035047 , -0.0117425 ) -colvars: ( -0.241034 , 0.0215009 , 0.0493846 ) -colvars: ( -0.188024 , -0.0626092 , 0.0755846 ) +colvars: ( -0.634968 , -0.0846854 , -0.366603 ) +colvars: ( -0.572265 , -0.17182 , -0.331514 ) +colvars: ( -0.517513 , -0.148414 , -0.269141 ) +colvars: ( -0.534714 , -0.200604 , -0.303037 ) +colvars: ( -0.52461 , -0.138305 , -0.273034 ) +colvars: ( -0.511916 , -0.297709 , -0.311147 ) +colvars: ( -0.48136 , -0.340097 , -0.294024 ) +colvars: ( -0.46143 , -0.453393 , -0.310174 ) +colvars: ( -0.415568 , -0.302421 , -0.216029 ) +colvars: ( -0.412437 , -0.275595 , -0.204333 ) +colvars: ( -0.362101 , -0.296308 , -0.16046 ) +colvars: ( -0.298539 , -0.257046 , -0.0841962 ) +colvars: ( -0.245721 , -0.27268 , -0.0362146 ) +colvars: ( -0.3168 , -0.148092 , -0.0677573 ) +colvars: ( -0.285156 , -0.116963 , -0.0260951 ) +colvars: ( -0.370694 , -0.087758 , -0.10256 ) +colvars: ( -0.396418 , 0.015941 , -0.0952819 ) +colvars: ( -0.445292 , 0.065944 , -0.128345 ) +colvars: ( -0.437925 , 0.0317398 , -0.131866 ) +colvars: ( -0.426085 , 0.0918367 , -0.100825 ) +colvars: ( -0.48601 , -0.0255249 , -0.198353 ) +colvars: ( -0.524398 , -0.0271302 , -0.237362 ) +colvars: ( -0.578132 , -0.0964649 , -0.313362 ) +colvars: ( -0.473195 , -0.0585251 , -0.196027 ) +colvars: ( -0.481206 , -0.0119033 , -0.189191 ) +colvars: ( -0.417392 , -0.136806 , -0.165035 ) +colvars: ( -0.360066 , -0.169554 , -0.117991 ) +colvars: ( -0.308947 , -0.264647 , -0.0970579 ) +colvars: ( -0.315628 , -0.0923976 , -0.0488182 ) +colvars: ( -0.303624 , -0.0725896 , -0.0304621 ) +colvars: ( -0.291589 , -0.0449704 , -0.00958362 ) +colvars: ( -0.252872 , 0.0341752 , 0.0544869 ) +colvars: ( -0.227146 , 0.0620521 , 0.089177 ) +colvars: ( -0.297781 , 0.125697 , 0.0386426 ) +colvars: ( -0.270485 , 0.17 , 0.0801465 ) +colvars: ( -0.368693 , 0.155085 , -0.0230977 ) +colvars: ( -0.418793 , 0.235426 , -0.0477142 ) +colvars: ( -0.490842 , 0.258905 , -0.112478 ) +colvars: ( -0.434329 , 0.214532 , -0.069958 ) +colvars: ( -0.439021 , 0.278833 , -0.0541544 ) +colvars: ( -0.442084 , 0.12307 , -0.106908 ) +colvars: ( -0.453025 , 0.0912728 , -0.128021 ) +colvars: ( -0.477986 , -0.00741222 , -0.184529 ) +colvars: ( -0.385464 , 0.0797162 , -0.0639548 ) +colvars: ( -0.390497 , 0.107586 , -0.0601134 ) +colvars: ( -0.216998 , 0.115002 , 0.116243 ) +colvars: ( -0.166909 , 0.117244 , 0.167188 ) +colvars: ( -0.241059 , 0.191238 , 0.116429 ) +colvars: ( -0.320266 , 0.0369042 , -0.0122275 ) +colvars: ( -0.252451 , 0.0228594 , 0.0512996 ) +colvars: ( -0.19729 , -0.0647379 , 0.0786778 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 36. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 36. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 36, atoms_new_colvar_forces = { ( -4.67680981299801e+00 , -3.93419916334486e-01 , -1.12778318560016e+00 ), ( -4.02798514651675e+00 , -3.35324300766826e-01 , -8.75060941564380e-01 ), ( -4.10069782795079e+00 , -3.63374047640199e-01 , -9.10126025505338e-01 ), ( -5.51204759434347e+00 , -5.14503949669059e-01 , -1.36458418189624e+00 ), ( 2.53201889104779e-01 , 1.17266526636215e-01 , 3.45082379454502e-01 ), ( 5.03255445975864e+00 , 5.64411751762652e-01 , 1.68357415874436e+00 ), ( 4.25226117945735e+00 , 4.63859699208330e-01 , 1.46145420076683e+00 ), ( -4.82458599130015e-02 , 1.41435778571937e-02 , 3.49539244433002e-01 ), ( 4.23537483968622e+00 , 4.55574827155590e-01 , 1.43315658751557e+00 ), ( 5.61425492030036e+00 , 5.84541952670831e-01 , 1.76226904624533e+00 ), ( 1.23775269804394e-02 , 3.05404514231495e-02 , 2.99224754699200e-01 ), ( 3.50277966765278e-03 , 2.55724155068570e-02 , 2.77366022666686e-01 ), ( 2.70390582350280e-02 , 3.96583996008955e-02 , 3.45699491308639e-01 ), ( 4.68162565367057e-02 , 3.39060756844611e-02 , 2.02932223767680e-01 ), ( 1.99751033407011e-02 , 2.04003788145163e-02 , 1.54120009683309e-01 ), ( 1.14763828025389e-01 , 5.62287821693943e-02 , 1.91437924425326e-01 ), ( 1.60798654370062e-01 , 6.59512912585725e-02 , 1.22175503058931e-01 ), ( 2.40019999516228e-01 , 9.44477896663818e-02 , 1.36887169004425e-01 ), ( 1.30042805383875e-01 , 4.91122799905491e-02 , 5.07247209508654e-02 ), ( 1.26064754385581e-01 , 4.22421186779151e-02 , -1.19213659144137e-02 ), ( 1.04878753326529e-01 , 4.12839777406290e-02 , 5.99758822557784e-02 ), ( 6.72759970684957e-02 , 2.31540224131994e-02 , 5.92195849687366e-04 ), ( 5.18869509811863e-02 , 2.05552565174021e-02 , 3.11598614291391e-02 ), ( -4.65982110295154e-03 , -3.74379495012654e-03 , -2.43982955194266e-02 ), ( -1.87037042917493e-02 , -1.46485608145348e-02 , -9.36239450211399e-02 ), ( -5.07366490487596e-02 , -1.46079351699329e-02 , 3.20346436320663e-02 ), ( -1.17088071469363e-01 , -3.86477185652305e-02 , 1.77474629975729e-02 ), ( -1.57485001610508e-01 , -4.56191623608826e-02 , 9.62866167913694e-02 ), ( -1.02397424798874e-01 , -3.74710527330217e-02 , -2.62764450692238e-02 ), ( -1.38634018126673e-01 , -5.49055469670486e-02 , -8.30840938867525e-02 ), ( -4.72614037490586e-02 , -1.64148658586030e-02 , -2.11370006647546e-03 ), ( -2.42454000906378e-02 , -1.19637250350060e-02 , -4.14071703745038e-02 ), ( 3.40876523484299e-02 , 1.24009986279386e-02 , 7.91702180405973e-03 ), ( 6.30824401740210e-03 , -8.77320775895118e-03 , -1.24508403625052e-01 ), ( -1.04094839494642e-02 , -1.91904853948852e-02 , -1.77735294023034e-01 ), ( 5.08478268221022e-02 , 5.33484317368221e-03 , -1.38012201110185e-01 ), ( 7.86278744573657e-02 , 8.12020109017481e-03 , -2.14884607329695e-01 ), ( 1.37538442333592e-01 , 2.91110561140189e-02 , -2.06217724862702e-01 ), ( 1.83198662480812e-02 , -1.73501684897990e-02 , -2.69074034768406e-01 ), ( 1.93494883849533e-02 , -2.30715995812671e-02 , -3.38217460007524e-01 ), ( -3.61947045778886e-02 , -3.33593697512488e-02 , -2.38222634245323e-01 ), ( -9.89056009258076e-02 , -5.86918788434534e-02 , -2.81451636606534e-01 ), ( -1.38502138712054e-01 , -6.81169108964202e-02 , -2.33966571218231e-01 ), ( -1.54396547496042e-01 , -7.94596715048706e-02 , -3.00944805405404e-01 ), ( -1.82642254530010e-01 , -9.48009548315469e-02 , -3.65159513066281e-01 ), ( -1.90167387725943e-01 , -9.16637867674694e-02 , -3.00042470677464e-01 ), ( -2.30835743628847e-01 , -1.07857331891220e-01 , -3.25405165291124e-01 ), ( -1.15792229930688e-01 , -6.67350667777830e-02 , -3.06997356751722e-01 ), ( -1.72112286169905e-01 , -8.06461958226265e-02 , -2.45209961894309e-01 ), ( -2.23526347308519e-01 , -9.93620573571558e-02 , -2.57282706431221e-01 ), ( -2.57686689771386e-01 , -1.04095411226895e-01 , -1.77645223752059e-01 ) } +colvars: Step 36, atoms_new_colvar_forces = { ( -4.88290787959985e+00 , -4.08200374054955e-01 , -1.16605619629334e+00 ), ( -4.20548016891334e+00 , -3.47887950651219e-01 , -9.03918376523148e-01 ), ( -4.28133317148205e+00 , -3.77136784235968e-01 , -9.40500813690554e-01 ), ( -5.75481840725893e+00 , -5.34175996949823e-01 , -1.41162422839094e+00 ), ( 2.64136212576255e-01 , 1.22336397428614e-01 , 3.59981596157192e-01 ), ( 5.25406462462492e+00 , 5.86621840634209e-01 , 1.74589494816703e+00 ), ( 4.43948376393649e+00 , 4.82059265347452e-01 , 1.51566272495863e+00 ), ( -5.03040666377811e-02 , 1.48552310530294e-02 , 3.64638670236814e-01 ), ( 4.42185303103199e+00 , 4.73408400497671e-01 , 1.48612691965680e+00 ), ( 5.86146715504996e+00 , 6.07309596204211e-01 , 1.82649745944155e+00 ), ( 1.29029354738554e-02 , 3.19173781716707e-02 , 3.12120441955794e-01 ), ( 3.62929724733180e-03 , 2.67255802536898e-02 , 2.89301218510092e-01 ), ( 2.81649081397981e-02 , 4.14208231868997e-02 , 3.60564542809657e-01 ), ( 4.88122637735174e-02 , 3.53904866371355e-02 , 2.11659033765666e-01 ), ( 2.08071709543126e-02 , 2.12961419299805e-02 , 1.60734596431752e-01 ), ( 1.19699310346034e-01 , 5.86582555019768e-02 , 1.99679195122940e-01 ), ( 1.67722760500288e-01 , 6.87730799911296e-02 , 1.27433370930817e-01 ), ( 2.50367616662423e-01 , 9.84826443864759e-02 , 1.42787348443313e-01 ), ( 1.35653774193513e-01 , 5.12063332237386e-02 , 5.29155821628234e-02 ), ( 1.31501299079290e-01 , 4.40257174262198e-02 , -1.24354450944110e-02 ), ( 1.09419100990292e-01 , 4.30559922102335e-02 , 6.25817365461039e-02 ), ( 7.02076210386009e-02 , 2.41471186372095e-02 , 6.51122069988325e-04 ), ( 5.41702848644654e-02 , 2.14542111453117e-02 , 3.25539793654729e-02 ), ( -4.83867853065029e-03 , -3.89968113014447e-03 , -2.54262533561946e-02 ), ( -1.94850858323686e-02 , -1.52849045958067e-02 , -9.76340270289430e-02 ), ( -5.29139003296956e-02 , -1.52117330442295e-02 , 3.34280346901958e-02 ), ( -1.22137002841928e-01 , -4.02773087691312e-02 , 1.85133555813677e-02 ), ( -1.64286549852698e-01 , -4.75250698389417e-02 , 1.00428165544681e-01 ), ( -1.06825681469098e-01 , -3.90695463935979e-02 , -2.74233305156697e-02 ), ( -1.44625509671643e-01 , -5.72586807907720e-02 , -8.66815657975791e-02 ), ( -4.93223315313861e-02 , -1.71199718514299e-02 , -2.22991900840161e-03 ), ( -2.53257206748039e-02 , -1.24974058228974e-02 , -4.32311595456356e-02 ), ( 3.55118639307809e-02 , 1.29078301955494e-02 , 8.20812170434740e-03 ), ( 6.55512967237215e-03 , -9.19228409226058e-03 , -1.29905815750122e-01 ), ( -1.08895642309799e-02 , -2.00686786292528e-02 , -1.85434878831553e-01 ), ( 5.30309446781353e-02 , 5.51543872117077e-03 , -1.43974984993789e-01 ), ( 8.20201680367365e-02 , 8.40079875213690e-03 , -2.24150442826249e-01 ), ( 1.43485968790938e-01 , 3.02887459588873e-02 , -2.15093576456319e-01 ), ( 1.91199056930694e-02 , -1.81594217993694e-02 , -2.80667591738177e-01 ), ( 2.01950592746803e-02 , -2.41428714439166e-02 , -3.52791774368278e-01 ), ( -3.77395177613851e-02 , -3.48341122218770e-02 , -2.48478974685638e-01 ), ( -1.03147325075184e-01 , -6.12478506860099e-02 , -2.93564136029933e-01 ), ( -1.44441916425068e-01 , -7.10533735743670e-02 , -2.44020673175622e-01 ), ( -1.61045104498478e-01 , -8.29060934743623e-02 , -3.13913179314616e-01 ), ( -1.90505526545789e-01 , -9.89139305197881e-02 , -3.80893618564478e-01 ), ( -1.98400478959442e-01 , -9.56446980795320e-02 , -3.13018016995541e-01 ), ( -2.40832918734827e-01 , -1.12535358143519e-01 , -3.39485844270407e-01 ), ( -1.20817018294349e-01 , -6.96629991769804e-02 , -3.20271855352053e-01 ), ( -1.79540742003913e-01 , -8.41333214035848e-02 , -2.55792111290274e-01 ), ( -2.33186184157980e-01 , -1.03650786877325e-01 , -2.68401102252966e-01 ), ( -2.68831719246441e-01 , -1.08566119243542e-01 , -1.85342272112195e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 36, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5476,10 +8882,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 37, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 37, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 37, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 37, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 37, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 37, atoms_positions[size = 51] = { ( 8.16221384686843e+00 , 4.13014786872230e-02 , -6.95869465127482e-01 ), ( 6.80958518252857e+00 , -6.24035047837337e-01 , -5.04964972430719e-01 ), ( 6.06079494684484e+00 , -3.22545667083951e-01 , 8.11981869964738e-01 ), ( 4.87946608224906e+00 , -1.53112496283750e-01 , 7.71878512263832e-01 ), ( 7.00078352714887e+00 , -2.09877085823173e+00 , -8.19840147577199e-01 ), ( 6.77720007689676e+00 , -3.15926781875816e-01 , 1.95915457666183e+00 ), ( 6.08220694026630e+00 , -2.41846162620031e-01 , 3.26210281971864e+00 ), ( 7.15352338552264e+00 , -3.60595148601759e-01 , 4.42296851794176e+00 ), ( 5.29942667186752e+00 , 1.06442318130758e+00 , 3.36086393669537e+00 ), ( 4.19382876288619e+00 , 1.00442170620445e+00 , 3.85558490510857e+00 ), ( 5.85440905365025e+00 , 2.25568752711447e+00 , 2.95658460900511e+00 ), ( 5.12743496896675e+00 , 3.51468625382453e+00 , 2.85144103841877e+00 ), ( 6.26310532944841e+00 , 4.42841268469618e+00 , 2.28417907685263e+00 ), ( 3.86243396392037e+00 , 3.61735898954025e+00 , 2.00273107308675e+00 ), ( 2.85429970161286e+00 , 4.15533815267892e+00 , 2.40915508884607e+00 ), ( 3.90028805200589e+00 , 3.13690048343511e+00 , 7.86208055968976e-01 ), ( 2.75505920966684e+00 , 3.14533620009754e+00 , -7.89119396031499e-02 ), ( 3.14765550464798e+00 , 2.66162645196632e+00 , -1.51791246315896e+00 ), ( 1.62884174060956e+00 , 2.28082042718727e+00 , 4.52408139830500e-01 ), ( 4.33947229136713e-01 , 2.61241076171236e+00 , 4.19358483211939e-01 ), ( 2.02146154905566e+00 , 1.10933944749563e+00 , 1.03747347142710e+00 ), ( 1.29905019023886e+00 , 1.66973494111863e-01 , 1.66318925038576e+00 ), ( 2.09891934597921e+00 , -1.09336629375871e+00 , 2.02834132117978e+00 ), ( 5.70021758784393e-01 , 6.26558661209594e-01 , 2.93223567614384e+00 ), ( -6.10263237510015e-01 , 3.58535047388056e-01 , 3.21254611976693e+00 ), ( 1.29176679194291e+00 , 1.43447739519174e+00 , 3.78672618261532e+00 ), ( 9.17953237815866e-01 , 1.98834562347871e+00 , 5.05962679594164e+00 ), ( 2.03247948558527e+00 , 2.78125232226779e+00 , 5.72643872335939e+00 ), ( -3.55771138815002e-01 , 2.88740730470469e+00 , 4.91780379415905e+00 ), ( -1.11856643667602e+00 , 3.07179125326318e+00 , 5.89837009466563e+00 ), ( -5.15786722327386e-01 , 3.47102828849230e+00 , 3.71750773797147e+00 ), ( -1.45388225734082e+00 , 4.47784206387289e+00 , 3.41049560690259e+00 ), ( -7.78199021904833e-01 , 5.47992384229274e+00 , 2.48864337010154e+00 ), ( -2.75562363679492e+00 , 3.92509055318619e+00 , 2.71583357918873e+00 ), ( -3.79047210252953e+00 , 4.60438687176698e+00 , 2.80527800043448e+00 ), ( -2.71480438238707e+00 , 2.65396324850562e+00 , 2.34403103673808e+00 ), ( -3.82393508277507e+00 , 1.78790832685572e+00 , 1.98706744895440e+00 ), ( -3.33895603665298e+00 , 9.09392570698246e-01 , 7.61244875945969e-01 ), ( -4.27422515739842e+00 , 1.01823156606361e+00 , 3.23638416754381e+00 ), ( -5.41619906673795e+00 , 7.13953851763116e-01 , 3.36061517707978e+00 ), ( -3.35646940904617e+00 , 7.08597569109325e-01 , 4.17089315247876e+00 ), ( -3.66414071394427e+00 , 5.98366873055360e-02 , 5.44865864809506e+00 ), ( -2.32771899477028e+00 , -2.69418780756333e-01 , 6.13110451020095e+00 ), ( -4.48955885516758e+00 , 9.72684049461152e-01 , 6.42006993069601e+00 ), ( -5.35494548616549e+00 , 5.26273943951513e-01 , 7.16926044539897e+00 ), ( -6.28289914525333e+00 , 3.59857504559191e+00 , 6.78920310227812e+00 ), ( -7.05179379342705e+00 , 4.29651912581031e+00 , 7.51564897131421e+00 ), ( -6.60857004327578e+00 , 3.17559654682944e+00 , 5.56164275402900e+00 ), ( -4.12440330771683e+00 , 2.25160864170603e+00 , 6.42412050527497e+00 ), ( -4.79989001669577e+00 , 3.27364371953981e+00 , 7.18919260728866e+00 ), ( -4.00836098535606e+00 , 4.63532012837581e+00 , 7.28246892452509e+00 ) } +colvars: Step 37, atoms_positions[size = 51] = { ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 ), ( 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 ), ( 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 ), ( 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ), ( 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 ), ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 ), ( 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 ), ( 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 ), ( 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 ), ( 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ), ( 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 ), ( 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 ), ( 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 ), ( 3.86259944889717e+00 , 3.61722008681940e+00 , 2.00308558020086e+00 ), ( 2.85437670154951e+00 , 4.15527002052534e+00 , 2.40936050794665e+00 ), ( 3.90045897397993e+00 , 3.13690575985605e+00 , 7.86487238395873e-01 ), ( 2.75527536482980e+00 , 3.14541374278433e+00 , -7.87345083063442e-02 ), ( 3.14794216985481e+00 , 2.66173230769858e+00 , -1.51772966163117e+00 ), ( 1.62901901629547e+00 , 2.28088215339071e+00 , 4.52491085121546e-01 ), ( 4.34123539261918e-01 , 2.61246940369668e+00 , 4.19371180847241e-01 ), ( 2.02159602369996e+00 , 1.10937081770796e+00 , 1.03753735465995e+00 ), ( 1.29914298840967e+00 , 1.67015904134200e-01 , 1.66320354438444e+00 ), ( 2.09907830495032e+00 , -1.09321620076143e+00 , 2.02852009135147e+00 ), ( 5.70115136929533e-01 , 6.26554860319424e-01 , 2.93222884904075e+00 ), ( -6.10201928231757e-01 , 3.58551350526315e-01 , 3.21245892405136e+00 ), ( 1.29191109307057e+00 , 1.43443741132798e+00 , 3.78675801241357e+00 ), ( 9.17888105407320e-01 , 1.98827097712886e+00 , 5.05961780707725e+00 ), ( 2.03231605133370e+00 , 2.78119558738282e+00 , 5.72652950117283e+00 ), ( -3.55886113385222e-01 , 2.88734283041279e+00 , 4.91775934200459e+00 ), ( -1.11875187300532e+00 , 3.07171926132761e+00 , 5.89828094798470e+00 ), ( -5.15845484680853e-01 , 3.47100691662013e+00 , 3.71747317327984e+00 ), ( -1.45392488246232e+00 , 4.47782737121568e+00 , 3.41042470589553e+00 ), ( -7.78176466290134e-01 , 5.47992820638078e+00 , 2.48863904731468e+00 ), ( -2.75561566311572e+00 , 3.92507785420583e+00 , 2.71566470414495e+00 ), ( -3.79047766038997e+00 , 4.60435453120212e+00 , 2.80505411222305e+00 ), ( -2.71475155579475e+00 , 2.65396188733802e+00 , 2.34383594524730e+00 ), ( -3.82384628855180e+00 , 1.78790482718998e+00 , 1.98676202535117e+00 ), ( -3.33878680658610e+00 , 9.09404778041523e-01 , 7.60961224505685e-01 ), ( -4.27420503934880e+00 , 1.01820161920294e+00 , 3.23602529439721e+00 ), ( -5.41618360572693e+00 , 7.13913354085080e-01 , 3.36019291686581e+00 ), ( -3.35650294249584e+00 , 7.08539067358897e-01 , 4.17056744070843e+00 ), ( -3.66427165233763e+00 , 5.97526421563971e-02 , 5.44828972260972e+00 ), ( -2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 ), ( -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 ), ( -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 ), ( -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 ), ( -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 ), ( -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 ), ( -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 ), ( -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 ), ( -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ) } colvars: Step 37, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 37, atom_groups_ids[size = 0] = @@ -5497,162 +8903,301 @@ colvars: Collective variables module, step no. 37 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.82901971968914e-01 , -1.84568715824041e-02 , 9.58971229050950e-01 ). +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ). +colvars: Done calculating colvar "group1". +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.80827613502008e-01 , -1.81261010387522e-02 , 9.59587044491483e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 , 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 , 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 , 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 , 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 , 3.86259944889717e+00 , 3.61722008681940e+00 , 2.00308558020086e+00 , 2.85437670154951e+00 , 4.15527002052534e+00 , 2.40936050794665e+00 , 3.90045897397993e+00 , 3.13690575985605e+00 , 7.86487238395873e-01 , 2.75527536482980e+00 , 3.14541374278433e+00 , -7.87345083063442e-02 , 3.14794216985481e+00 , 2.66173230769858e+00 , -1.51772966163117e+00 , 1.62901901629547e+00 , 2.28088215339071e+00 , 4.52491085121546e-01 , 4.34123539261918e-01 , 2.61246940369668e+00 , 4.19371180847241e-01 , 2.02159602369996e+00 , 1.10937081770796e+00 , 1.03753735465995e+00 , 1.29914298840967e+00 , 1.67015904134200e-01 , 1.66320354438444e+00 , 2.09907830495032e+00 , -1.09321620076143e+00 , 2.02852009135147e+00 , 5.70115136929533e-01 , 6.26554860319424e-01 , 2.93222884904075e+00 , -6.10201928231757e-01 , 3.58551350526315e-01 , 3.21245892405136e+00 , 1.29191109307057e+00 , 1.43443741132798e+00 , 3.78675801241357e+00 , 9.17888105407320e-01 , 1.98827097712886e+00 , 5.05961780707725e+00 , 2.03231605133370e+00 , 2.78119558738282e+00 , 5.72652950117283e+00 , -3.55886113385222e-01 , 2.88734283041279e+00 , 4.91775934200459e+00 , -1.11875187300532e+00 , 3.07171926132761e+00 , 5.89828094798470e+00 , -5.15845484680853e-01 , 3.47100691662013e+00 , 3.71747317327984e+00 , -1.45392488246232e+00 , 4.47782737121568e+00 , 3.41042470589553e+00 , -7.78176466290134e-01 , 5.47992820638078e+00 , 2.48863904731468e+00 , -2.75561566311572e+00 , 3.92507785420583e+00 , 2.71566470414495e+00 , -3.79047766038997e+00 , 4.60435453120212e+00 , 2.80505411222305e+00 , -2.71475155579475e+00 , 2.65396188733802e+00 , 2.34383594524730e+00 , -3.82384628855180e+00 , 1.78790482718998e+00 , 1.98676202535117e+00 , -3.33878680658610e+00 , 9.09404778041523e-01 , 7.60961224505685e-01 , -4.27420503934880e+00 , 1.01820161920294e+00 , 3.23602529439721e+00 , -5.41618360572693e+00 , 7.13913354085080e-01 , 3.36019291686581e+00 , -3.35650294249584e+00 , 7.08539067358897e-01 , 4.17056744070843e+00 , -3.66427165233763e+00 , 5.97526421563971e-02 , 5.44828972260972e+00 , -2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 , -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 , -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 , -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 , -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 , -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 , -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 , -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 , -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.82901971968914e-01 , -1.84568715824041e-02 , 9.58971229050950e-01 ). +colvars: Colvar "one" has value ( -2.80827613502008e-01 , -1.81261010387522e-02 , 9.59587044491483e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 , 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 , 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 , 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 , 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 , 3.86259944889717e+00 , 3.61722008681940e+00 , 2.00308558020086e+00 , 2.85437670154951e+00 , 4.15527002052534e+00 , 2.40936050794665e+00 , 3.90045897397993e+00 , 3.13690575985605e+00 , 7.86487238395873e-01 , 2.75527536482980e+00 , 3.14541374278433e+00 , -7.87345083063442e-02 , 3.14794216985481e+00 , 2.66173230769858e+00 , -1.51772966163117e+00 , 1.62901901629547e+00 , 2.28088215339071e+00 , 4.52491085121546e-01 , 4.34123539261918e-01 , 2.61246940369668e+00 , 4.19371180847241e-01 , 2.02159602369996e+00 , 1.10937081770796e+00 , 1.03753735465995e+00 , 1.29914298840967e+00 , 1.67015904134200e-01 , 1.66320354438444e+00 , 2.09907830495032e+00 , -1.09321620076143e+00 , 2.02852009135147e+00 , 5.70115136929533e-01 , 6.26554860319424e-01 , 2.93222884904075e+00 , -6.10201928231757e-01 , 3.58551350526315e-01 , 3.21245892405136e+00 , 1.29191109307057e+00 , 1.43443741132798e+00 , 3.78675801241357e+00 , 9.17888105407320e-01 , 1.98827097712886e+00 , 5.05961780707725e+00 , 2.03231605133370e+00 , 2.78119558738282e+00 , 5.72652950117283e+00 , -3.55886113385222e-01 , 2.88734283041279e+00 , 4.91775934200459e+00 , -1.11875187300532e+00 , 3.07171926132761e+00 , 5.89828094798470e+00 , -5.15845484680853e-01 , 3.47100691662013e+00 , 3.71747317327984e+00 , -1.45392488246232e+00 , 4.47782737121568e+00 , 3.41042470589553e+00 , -7.78176466290134e-01 , 5.47992820638078e+00 , 2.48863904731468e+00 , -2.75561566311572e+00 , 3.92507785420583e+00 , 2.71566470414495e+00 , -3.79047766038997e+00 , 4.60435453120212e+00 , 2.80505411222305e+00 , -2.71475155579475e+00 , 2.65396188733802e+00 , 2.34383594524730e+00 , -3.82384628855180e+00 , 1.78790482718998e+00 , 1.98676202535117e+00 , -3.33878680658610e+00 , 9.09404778041523e-01 , 7.60961224505685e-01 , -4.27420503934880e+00 , 1.01820161920294e+00 , 3.23602529439721e+00 , -5.41618360572693e+00 , 7.13913354085080e-01 , 3.36019291686581e+00 , -3.35650294249584e+00 , 7.08539067358897e-01 , 4.17056744070843e+00 , -3.66427165233763e+00 , 5.97526421563971e-02 , 5.44828972260972e+00 , -2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 , -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 , -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 , -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 , -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 , -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 , -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 , -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 , -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.176 , 2.32094 , -15.2758 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 65.0336 , 6.50336 , 13.0067 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.176 , 2.32094 , -15.2758 ) to colvar "one". -colvars: Adding total bias energy: 43.6285 +colvars: Adding biasing force ( 65.0336 , 6.50336 , 13.0067 ) to colvar "one". +colvars: Adding total bias energy: 55.0754 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.176 , 2.32094 , -15.2758 ) +colvars: Force to be applied: ( 65.0336 , 6.50336 , 13.0067 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.95456 , -0.506389 , -1.36376 ) -colvars: ( -4.24853 , -0.434229 , -1.16943 ) -colvars: ( -4.24853 , -0.434229 , -1.16943 ) -colvars: ( -5.65917 , -0.578405 , -1.55771 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.16274 , -0.524934 , -1.40913 ) +colvars: ( -4.42705 , -0.450131 , -1.20833 ) +colvars: ( -4.42705 , -0.450131 , -1.20833 ) +colvars: ( -5.89696 , -0.599587 , -1.60953 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.882121 , 0.196743 , 0.597088 ) -colvars: ( 0.765428 , 0.265834 , 0.620398 ) -colvars: ( 0.749091 , 0.25953 , 0.602934 ) -colvars: ( 0.656767 , 0.265371 , 0.558038 ) -colvars: ( 0.645219 , 0.199433 , 0.465931 ) -colvars: ( 0.57269 , 0.340802 , 0.60811 ) -colvars: ( 0.468596 , 0.353409 , 0.565301 ) -colvars: ( 0.394033 , 0.448757 , 0.646619 ) -colvars: ( 0.388672 , 0.309002 , 0.462263 ) -colvars: ( 0.355103 , 0.267334 , 0.389127 ) -colvars: ( 0.359447 , 0.314561 , 0.452866 ) -colvars: ( 0.289667 , 0.27195 , 0.357924 ) -colvars: ( 0.262563 , 0.301023 , 0.380236 ) -colvars: ( 0.350473 , 0.175838 , 0.267795 ) -colvars: ( 0.293327 , 0.132487 , 0.179074 ) -colvars: ( 0.47004 , 0.140328 , 0.289685 ) -colvars: ( 0.540719 , 0.0506422 , 0.213505 ) -colvars: ( 0.666739 , 0.0312103 , 0.259921 ) -colvars: ( 0.549766 , 0.0186575 , 0.177152 ) -colvars: ( 0.534454 , -0.0458261 , 0.0847927 ) -colvars: ( 0.570694 , 0.0657274 , 0.250112 ) -colvars: ( 0.569906 , 0.0491358 , 0.22814 ) -colvars: ( 0.606014 , 0.113007 , 0.331525 ) -colvars: ( 0.448938 , 0.0523278 , 0.163526 ) -colvars: ( 0.442589 , -0.00327204 , 0.0877863 ) -colvars: ( 0.349394 , 0.116503 , 0.190205 ) -colvars: ( 0.228138 , 0.12385 , 0.130818 ) -colvars: ( 0.138757 , 0.208035 , 0.189233 ) -colvars: ( 0.200243 , 0.0510586 , 0.0205292 ) -colvars: ( 0.152529 , 0.014632 , -0.0538477 ) -colvars: ( 0.232313 , 0.0266506 , 0.00709116 ) -colvars: ( 0.218221 , -0.0447724 , -0.0935773 ) -colvars: ( 0.251866 , -0.0471296 , -0.077513 ) -colvars: ( 0.291813 , -0.129316 , -0.161432 ) -colvars: ( 0.248953 , -0.182208 , -0.254409 ) -colvars: ( 0.404292 , -0.143374 , -0.11574 ) -colvars: ( 0.480085 , -0.217605 , -0.168962 ) -colvars: ( 0.608014 , -0.219115 , -0.0982113 ) -colvars: ( 0.434702 , -0.223048 , -0.201819 ) -colvars: ( 0.44024 , -0.290413 , -0.286065 ) -colvars: ( 0.387639 , -0.15138 , -0.13559 ) -colvars: ( 0.335449 , -0.146233 , -0.158577 ) -colvars: ( 0.319783 , -0.0610538 , -0.0569749 ) -colvars: ( 0.21524 , -0.155929 , -0.239478 ) -colvars: ( 0.191842 , -0.19799 , -0.307344 ) -colvars: ( 0.0180391 , -0.201971 , -0.411294 ) -colvars: ( -0.0706082 , -0.220319 , -0.485481 ) -colvars: ( 0.11544 , -0.25012 , -0.418399 ) -colvars: ( 0.135042 , -0.116077 , -0.23336 ) -colvars: ( 0.018664 , -0.121336 , -0.306328 ) -colvars: ( -0.0683577 , -0.042098 , -0.25299 ) +colvars: ( 0.917827 , 0.205013 , 0.619508 ) +colvars: ( 0.796532 , 0.276787 , 0.64378 ) +colvars: ( 0.779458 , 0.270312 , 0.625718 ) +colvars: ( 0.683626 , 0.27617 , 0.579018 ) +colvars: ( 0.671614 , 0.207576 , 0.483344 ) +colvars: ( 0.596279 , 0.354519 , 0.631041 ) +colvars: ( 0.488129 , 0.367493 , 0.586579 ) +colvars: ( 0.410666 , 0.466574 , 0.671062 ) +colvars: ( 0.405005 , 0.321278 , 0.479614 ) +colvars: ( 0.370142 , 0.277873 , 0.403628 ) +colvars: ( 0.374551 , 0.327116 , 0.469925 ) +colvars: ( 0.301965 , 0.282785 , 0.37137 ) +colvars: ( 0.273716 , 0.313086 , 0.394622 ) +colvars: ( 0.365141 , 0.182885 , 0.277732 ) +colvars: ( 0.305738 , 0.137743 , 0.185593 ) +colvars: ( 0.489403 , 0.146068 , 0.30043 ) +colvars: ( 0.562844 , 0.0528577 , 0.221275 ) +colvars: ( 0.693798 , 0.0327896 , 0.269463 ) +colvars: ( 0.572322 , 0.019516 , 0.183448 ) +colvars: ( 0.556398 , -0.047569 , 0.0875128 ) +colvars: ( 0.59415 , 0.0684211 , 0.259174 ) +colvars: ( 0.593409 , 0.0510794 , 0.236287 ) +colvars: ( 0.631011 , 0.11748 , 0.343617 ) +colvars: ( 0.467697 , 0.0542687 , 0.1692 ) +colvars: ( 0.46112 , -0.00359885 , 0.0905024 ) +colvars: ( 0.364222 , 0.120948 , 0.196968 ) +colvars: ( 0.238198 , 0.128472 , 0.13532 ) +colvars: ( 0.145286 , 0.215978 , 0.196053 ) +colvars: ( 0.209143 , 0.0527886 , 0.0208062 ) +colvars: ( 0.159573 , 0.0148266 , -0.0564587 ) +colvars: ( 0.242394 , 0.0275118 , 0.00689564 ) +colvars: ( 0.227683 , -0.0467331 , -0.097628 ) +colvars: ( 0.262566 , -0.0490648 , -0.0808868 ) +colvars: ( 0.304187 , -0.13463 , -0.168163 ) +colvars: ( 0.259628 , -0.189678 , -0.264726 ) +colvars: ( 0.421125 , -0.149181 , -0.120767 ) +colvars: ( 0.499926 , -0.226355 , -0.17611 ) +colvars: ( 0.632908 , -0.227825 , -0.102677 ) +colvars: ( 0.452833 , -0.23214 , -0.210283 ) +colvars: ( 0.458592 , -0.302215 , -0.297809 ) +colvars: ( 0.403981 , -0.157695 , -0.141511 ) +colvars: ( 0.34981 , -0.152467 , -0.165427 ) +colvars: ( 0.333595 , -0.0639425 , -0.0599225 ) +colvars: ( 0.224853 , -0.162649 , -0.249408 ) +colvars: ( 0.200567 , -0.20646 , -0.319927 ) +colvars: ( 0.0197462 , -0.21058 , -0.427704 ) +colvars: ( -0.0724034 , -0.229736 , -0.504727 ) +colvars: ( 0.120932 , -0.260526 , -0.435089 ) +colvars: ( 0.141447 , -0.121215 , -0.242979 ) +colvars: ( 0.0204675 , -0.126772 , -0.318716 ) +colvars: ( -0.0700032 , -0.0443999 , -0.263251 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.95456 , 0.506389 , 1.36376 ) -colvars: ( 4.24853 , 0.434229 , 1.16943 ) -colvars: ( 4.24853 , 0.434229 , 1.16943 ) -colvars: ( 5.65917 , 0.578405 , 1.55771 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.16274 , 0.524934 , 1.40913 ) +colvars: ( 4.42705 , 0.450131 , 1.20833 ) +colvars: ( 4.42705 , 0.450131 , 1.20833 ) +colvars: ( 5.89696 , 0.599587 , 1.60953 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.60836 , -0.0810755 , -0.351197 ) -colvars: ( -0.548311 , -0.164692 , -0.317412 ) -colvars: ( -0.495716 , -0.142208 , -0.257501 ) -colvars: ( -0.512422 , -0.192339 , -0.290148 ) -colvars: ( -0.502733 , -0.132569 , -0.26149 ) -colvars: ( -0.490667 , -0.285531 , -0.297832 ) -colvars: ( -0.461493 , -0.326232 , -0.281443 ) -colvars: ( -0.442477 , -0.434954 , -0.296796 ) -colvars: ( -0.398407 , -0.290084 , -0.206673 ) -colvars: ( -0.395461 , -0.264363 , -0.195569 ) -colvars: ( -0.347071 , -0.284199 , -0.153284 ) -colvars: ( -0.28611 , -0.246525 , -0.0801632 ) -colvars: ( -0.235394 , -0.261503 , -0.0340038 ) -colvars: ( -0.303548 , -0.141975 , -0.0645481 ) -colvars: ( -0.273241 , -0.112119 , -0.0246715 ) -colvars: ( -0.355125 , -0.0840638 , -0.0979711 ) -colvars: ( -0.379718 , 0.0154449 , -0.0911346 ) -colvars: ( -0.426457 , 0.0634514 , -0.12284 ) -colvars: ( -0.419595 , 0.0305793 , -0.126365 ) -colvars: ( -0.408244 , 0.0882359 , -0.0967091 ) -colvars: ( -0.465773 , -0.0243815 , -0.190124 ) -colvars: ( -0.502671 , -0.0259478 , -0.227655 ) -colvars: ( -0.55425 , -0.0924842 , -0.3005 ) -colvars: ( -0.453684 , -0.0560974 , -0.188037 ) -colvars: ( -0.461396 , -0.0113773 , -0.181612 ) -colvars: ( -0.400235 , -0.131215 , -0.158185 ) -colvars: ( -0.345364 , -0.162659 , -0.11307 ) -colvars: ( -0.296397 , -0.253904 , -0.0928257 ) -colvars: ( -0.302705 , -0.0886203 , -0.0468007 ) -colvars: ( -0.291257 , -0.0696336 , -0.0292959 ) -colvars: ( -0.279539 , -0.0430858 , -0.00912572 ) -colvars: ( -0.242353 , 0.0328647 , 0.0522563 ) -colvars: ( -0.217563 , 0.0596447 , 0.0856206 ) -colvars: ( -0.285379 , 0.12068 , 0.0368871 ) -colvars: ( -0.259225 , 0.163179 , 0.076601 ) -colvars: ( -0.353327 , 0.148886 , -0.022377 ) -colvars: ( -0.401339 , 0.225971 , -0.0461488 ) -colvars: ( -0.470349 , 0.248516 , -0.108272 ) -colvars: ( -0.416356 , 0.205891 , -0.0675823 ) -colvars: ( -0.420856 , 0.267582 , -0.0525578 ) -colvars: ( -0.423898 , 0.118113 , -0.102957 ) -colvars: ( -0.434512 , 0.087572 , -0.123284 ) -colvars: ( -0.458533 , -0.00713113 , -0.177392 ) -colvars: ( -0.369801 , 0.0764664 , -0.0618515 ) -colvars: ( -0.374683 , 0.103189 , -0.0582871 ) -colvars: ( -0.208249 , 0.110329 , 0.111024 ) -colvars: ( -0.160272 , 0.112466 , 0.159855 ) -colvars: ( -0.231193 , 0.183504 , 0.111175 ) -colvars: ( -0.307286 , 0.035394 , -0.0121154 ) -colvars: ( -0.242324 , 0.0219036 , 0.0488137 ) -colvars: ( -0.189467 , -0.0621461 , 0.0752416 ) +colvars: ( -0.632769 , -0.0845946 , -0.36346 ) +colvars: ( -0.570459 , -0.171467 , -0.328306 ) +colvars: ( -0.515654 , -0.148155 , -0.266071 ) +colvars: ( -0.53332 , -0.200104 , -0.300086 ) +colvars: ( -0.523246 , -0.137947 , -0.270472 ) +colvars: ( -0.510857 , -0.296917 , -0.307982 ) +colvars: ( -0.48071 , -0.339123 , -0.291028 ) +colvars: ( -0.461078 , -0.452097 , -0.306835 ) +colvars: ( -0.415133 , -0.301517 , -0.213511 ) +colvars: ( -0.412149 , -0.274719 , -0.202105 ) +colvars: ( -0.361676 , -0.295443 , -0.15804 ) +colvars: ( -0.298289 , -0.256263 , -0.0822212 ) +colvars: ( -0.245472 , -0.271888 , -0.0342064 ) +colvars: ( -0.316311 , -0.147608 , -0.0661579 ) +colvars: ( -0.284857 , -0.116521 , -0.0248784 ) +colvars: ( -0.369779 , -0.0874875 , -0.100853 ) +colvars: ( -0.395238 , 0.0159218 , -0.0938873 ) +colvars: ( -0.443644 , 0.0657222 , -0.126751 ) +colvars: ( -0.436798 , 0.0317191 , -0.13057 ) +colvars: ( -0.425001 , 0.0916817 , -0.0999188 ) +colvars: ( -0.4849 , -0.025385 , -0.1967 ) +colvars: ( -0.52338 , -0.0269441 , -0.235747 ) +colvars: ( -0.577073 , -0.096101 , -0.311265 ) +colvars: ( -0.472615 , -0.0581874 , -0.194693 ) +colvars: ( -0.480674 , -0.0116573 , -0.188155 ) +colvars: ( -0.417142 , -0.136238 , -0.163619 ) +colvars: ( -0.360241 , -0.168837 , -0.116842 ) +colvars: ( -0.309415 , -0.263667 , -0.0956953 ) +colvars: ( -0.315828 , -0.0918756 , -0.0481717 ) +colvars: ( -0.304015 , -0.0720731 , -0.0301169 ) +colvars: ( -0.291585 , -0.0446194 , -0.00904007 ) +colvars: ( -0.252843 , 0.0343175 , 0.0545689 ) +colvars: ( -0.226902 , 0.0620649 , 0.0892749 ) +colvars: ( -0.297516 , 0.125595 , 0.0384711 ) +colvars: ( -0.270354 , 0.169814 , 0.0795739 ) +colvars: ( -0.368075 , 0.154867 , -0.0230368 ) +colvars: ( -0.417942 , 0.234993 , -0.0478405 ) +colvars: ( -0.489569 , 0.258353 , -0.112274 ) +colvars: ( -0.433723 , 0.214214 , -0.0701779 ) +colvars: ( -0.4384 , 0.278366 , -0.0547183 ) +colvars: ( -0.441713 , 0.123024 , -0.106822 ) +colvars: ( -0.45292 , 0.0913699 , -0.127991 ) +colvars: ( -0.478012 , -0.00704334 , -0.184039 ) +colvars: ( -0.385755 , 0.0799005 , -0.0642944 ) +colvars: ( -0.390908 , 0.107738 , -0.0607156 ) +colvars: ( -0.217806 , 0.115143 , 0.115057 ) +colvars: ( -0.16801 , 0.117424 , 0.16567 ) +colvars: ( -0.241474 , 0.19112 , 0.115202 ) +colvars: ( -0.320776 , 0.0372058 , -0.0125929 ) +colvars: ( -0.25334 , 0.0232496 , 0.0505951 ) +colvars: ( -0.198451 , -0.0641088 , 0.0781593 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 37. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 37. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 37, atoms_new_colvar_forces = { ( -4.68079553249617e+00 , -3.90721895618969e-01 , -1.11787324656340e+00 ), ( -4.03141453603078e+00 , -3.33086813782210e-01 , -8.66442892955978e-01 ), ( -4.10418623448907e+00 , -3.61196511182811e-01 , -9.01538438505066e-01 ), ( -5.51668060541587e+00 , -5.11541154617190e-01 , -1.35327157498399e+00 ), ( 2.53374825165688e-01 , 1.17322169448769e-01 , 3.45433181799156e-01 ), ( 5.03657985327035e+00 , 5.61659960641624e-01 , 1.67404209341983e+00 ), ( 4.25563397348131e+00 , 4.61405922504199e-01 , 1.45328628285756e+00 ), ( -4.84442616610080e-02 , 1.38025975533743e-02 , 3.49823453963319e-01 ), ( 4.23879566335603e+00 , 4.53146327700456e-01 , 1.42501824867508e+00 ), ( 5.61880848900630e+00 , 5.81376086152293e-01 , 1.75127016885759e+00 ), ( 1.23751629209414e-02 , 3.03624050329420e-02 , 2.99582223305569e-01 ), ( 3.55647451650315e-03 , 2.54253041427815e-02 , 2.77761155557903e-01 ), ( 2.71689427313820e-02 , 3.95197786985720e-02 , 3.46232417577520e-01 ), ( 4.69250501267432e-02 , 3.38627285580941e-02 , 2.03246898926615e-01 ), ( 2.00862325737857e-02 , 2.03676767578085e-02 , 1.54402948805392e-01 ), ( 1.14915835889301e-01 , 5.62639135599647e-02 , 1.91714090264702e-01 ), ( 1.61001132407563e-01 , 6.60870744671900e-02 , 1.22370314969212e-01 ), ( 2.40282509037127e-01 , 9.46617001859483e-02 , 1.37081687589387e-01 ), ( 1.30170935491765e-01 , 4.92367151919846e-02 , 5.07868671384857e-02 ), ( 1.26209697484766e-01 , 4.24097939166141e-02 , -1.19163708031666e-02 ), ( 1.04920415505240e-01 , 4.13458390222983e-02 , 5.99880583284731e-02 ), ( 6.72347892241592e-02 , 2.31880262838069e-02 , 4.84986555042671e-04 ), ( 5.17638537920039e-02 , 2.05229437716475e-02 , 3.10240696105379e-02 ), ( -4.74663551212839e-03 , -3.76963808851908e-03 , -2.45108020970518e-02 ), ( -1.88072262373017e-02 , -1.46493220805063e-02 , -9.38253083188769e-02 ), ( -5.08410918623465e-02 , -1.47122946893009e-02 , 3.20204100219570e-02 ), ( -1.17225692763493e-01 , -3.88089109282382e-02 , 1.77481262564441e-02 ), ( -1.57640630657621e-01 , -4.58684192517203e-02 , 9.64070293321571e-02 ), ( -1.02461440260749e-01 , -3.75616505670021e-02 , -2.62715214286438e-02 ), ( -1.38727817224171e-01 , -5.50016507571514e-02 , -8.31436370117906e-02 ), ( -4.72265238926294e-02 , -1.64351362572042e-02 , -2.03456716462021e-03 ), ( -2.41317300224776e-02 , -1.19076615469125e-02 , -4.13209718239030e-02 ), ( 3.43023282685017e-02 , 1.25150853629424e-02 , 8.10765798596971e-03 ), ( 6.43305557384805e-03 , -8.63682620381885e-03 , -1.24544725572984e-01 ), ( -1.02716843777416e-02 , -1.90282633652653e-02 , -1.77808237161421e-01 ), ( 5.09655320331248e-02 , 5.51110593631737e-03 , -1.38116611939811e-01 ), ( 7.87464417376239e-02 , 8.36631309864255e-03 , -2.15111316988457e-01 ), ( 1.37665484322824e-01 , 2.94010824133421e-02 , -2.06483634438232e-01 ), ( 1.83458559865556e-02 , -1.71569406424844e-02 , -2.69400847097267e-01 ), ( 1.93835544705327e-02 , -2.28309663692608e-02 , -3.38623206007411e-01 ), ( -3.62591465777498e-02 , -3.32666481258157e-02 , -2.38547396361860e-01 ), ( -9.90631394023752e-02 , -5.86609636197708e-02 , -2.81861005796358e-01 ), ( -1.38749283366791e-01 , -6.81849563023802e-02 , -2.34367180870072e-01 ), ( -1.54560510038397e-01 , -7.94623831678002e-02 , -3.01329780997028e-01 ), ( -1.82840869088693e-01 , -9.48004587363242e-02 , -3.65630962124531e-01 ), ( -1.90209875224079e-01 , -9.16423897349099e-02 , -3.00269394055042e-01 ), ( -2.30880522584762e-01 , -1.07852628794259e-01 , -3.25625569717512e-01 ), ( -1.15752595115674e-01 , -6.66162568833465e-02 , -3.07224625198104e-01 ), ( -1.72243879691875e-01 , -8.06834379363101e-02 , -2.45475689578199e-01 ), ( -2.23659542413118e-01 , -9.94323139694904e-02 , -2.57514036532548e-01 ), ( -2.57825081966900e-01 , -1.04244057182641e-01 , -1.77748819704570e-01 ) } +colvars: Step 37, atoms_new_colvar_forces = { ( -4.87768340091064e+00 , -4.04515767829389e-01 , -1.15308077989926e+00 ), ( -4.20097681355703e+00 , -3.44810675996169e-01 , -8.92853789587307e-01 ), ( -4.27674390111940e+00 , -3.74064477872092e-01 , -9.29397030160039e-01 ), ( -5.74859063228890e+00 , -5.29958050663217e-01 , -1.39665675402575e+00 ), ( 2.63803073591474e-01 , 1.22156769296109e-01 , 3.59647315946333e-01 ), ( 5.24816274406836e+00 , 5.82536587822630e-01 , 1.73218869553827e+00 ), ( 4.43446889915649e+00 , 4.78500064884967e-01 , 1.50387962233720e+00 ), ( -5.04116713926906e-02 , 1.44761896627373e-02 , 3.64226325004024e-01 ), ( 4.41692168797072e+00 , 4.69891932048396e-01 , 1.47443120504272e+00 ), ( 5.85495080586629e+00 , 6.02741463937726e-01 , 1.81105128190514e+00 ), ( 1.28749576319738e-02 , 3.16727297019153e-02 , 3.11884909766902e-01 ), ( 3.67694080954450e-03 , 2.65227810484956e-02 , 2.89148426393064e-01 ), ( 2.82433742396482e-02 , 4.11983291947543e-02 , 3.60415726827408e-01 ), ( 4.88294417275390e-02 , 3.52775028285380e-02 , 2.11573629907615e-01 ), ( 2.08809568767205e-02 , 2.12213798958254e-02 , 1.60714878406654e-01 ), ( 1.19624009465562e-01 , 5.85808403129090e-02 , 1.99577517515682e-01 ), ( 1.67606734863712e-01 , 6.87794743067848e-02 , 1.27387745429499e-01 ), ( 2.50153639908545e-01 , 9.85117828115238e-02 , 1.42711944173507e-01 ), ( 1.35523380967889e-01 , 5.12350481214440e-02 , 5.28775171111929e-02 ), ( 1.31396350884718e-01 , 4.41127500705837e-02 , -1.24060209174162e-02 ), ( 1.09250435610859e-01 , 4.30361820912343e-02 , 6.24736166561782e-02 ), ( 7.00295966772967e-02 , 2.41352684722350e-02 , 5.39881366658557e-04 ), ( 5.39389527876329e-02 , 2.13794282805596e-02 , 3.23517320504840e-02 ), ( -4.91857376580790e-03 , -3.91871398765551e-03 , -2.54927330783864e-02 ), ( -1.95537264278258e-02 , -1.52561437342837e-02 , -9.76523676273865e-02 ), ( -5.29191645627358e-02 , -1.52895085259884e-02 , 3.33487448423313e-02 ), ( -1.22042627232472e-01 , -4.03649373402419e-02 , 1.84780260128458e-02 ), ( -1.64129427277217e-01 , -4.76891159906219e-02 , 1.00357565236874e-01 ), ( -1.06685087792716e-01 , -3.90869775394688e-02 , -2.73655377503504e-02 ), ( -1.44442405045796e-01 , -5.72465648154617e-02 , -8.65756363523023e-02 ), ( -4.91911623122935e-02 , -1.71076260251905e-02 , -2.14442688614674e-03 ), ( -2.51597903645701e-02 , -1.24155772310293e-02 , -4.30591764368354e-02 ), ( 3.56640469890183e-02 , 1.30001099744317e-02 , 8.38817710329237e-03 ), ( 6.67109880696493e-03 , -9.03436340479885e-03 , -1.29692238036441e-01 ), ( -1.07264236900141e-02 , -1.98631557679952e-02 , -1.85151718794343e-01 ), ( 5.30498429345028e-02 , 5.68583763969494e-03 , -1.43804083361619e-01 ), ( 8.19841057638790e-02 , 8.63734608329719e-03 , -2.23950276315525e-01 ), ( 1.43339855796387e-01 , 3.05280193383436e-02 , -2.14951039351014e-01 ), ( 1.91102547580405e-02 , -1.79258075663515e-02 , -2.80461242310813e-01 ), ( 2.01917810604034e-02 , -2.38489838462535e-02 , -3.52527220572662e-01 ), ( -3.77323966607108e-02 , -3.46714768692280e-02 , -2.48332802200249e-01 ), ( -1.03109504559677e-01 , -6.10975953308200e-02 , -2.93417945581451e-01 ), ( -1.44416579761663e-01 , -7.09858088855299e-02 , -2.43961250544664e-01 ), ( -1.60901994961709e-01 , -8.27484428513748e-02 , -3.13702754209035e-01 ), ( -1.90341009584740e-01 , -9.87220095142527e-02 , -3.80642732473909e-01 ), ( -1.98060257827384e-01 , -9.54375652645738e-02 , -3.12647039402676e-01 ), ( -2.40413024259414e-01 , -1.12312668677671e-01 , -3.39057144551452e-01 ), ( -1.20542203354837e-01 , -6.94060878279039e-02 , -3.19887059849072e-01 ), ( -1.79328721309453e-01 , -8.40087412672682e-02 , -2.55571471275001e-01 ), ( -2.32872144915632e-01 , -1.03522324988299e-01 , -2.68120889649633e-01 ), ( -2.68454324278848e-01 , -1.08508648212007e-01 , -1.85091323373151e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 37, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5690,10 +9235,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 38, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 38, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 38, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 38, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 38, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 38, atoms_positions[size = 51] = { ( 8.14877873702211e+00 , 4.04022721702150e-02 , -6.92577086270675e-01 ), ( 6.80383152526671e+00 , -6.25597810854992e-01 , -4.99771627510369e-01 ), ( 6.05932862659391e+00 , -3.20392500925269e-01 , 8.08487337579745e-01 ), ( 4.87070927794586e+00 , -1.52911259798077e-01 , 7.75927389735424e-01 ), ( 7.00396081156044e+00 , -2.10390864650469e+00 , -8.12611727360559e-01 ), ( 6.77073270899749e+00 , -3.17202239475859e-01 , 1.95721416087662e+00 ), ( 6.08686545431381e+00 , -2.42704371492925e-01 , 3.27386819011241e+00 ), ( 7.15166129400360e+00 , -3.63976099229150e-01 , 4.42806348262264e+00 ), ( 5.29848152657454e+00 , 1.06482932961643e+00 , 3.36150801488537e+00 ), ( 4.19355467261569e+00 , 1.00563379356190e+00 , 3.86689314972318e+00 ), ( 5.85259008782183e+00 , 2.25717099327585e+00 , 2.95413915945799e+00 ), ( 5.12845700669889e+00 , 3.51080158512586e+00 , 2.84751873236696e+00 ), ( 6.25658169578520e+00 , 4.42311314391522e+00 , 2.28353460841378e+00 ), ( 3.86464129015471e+00 , 3.61424732694166e+00 , 2.00074863629636e+00 ), ( 2.85931974231682e+00 , 4.15337731964328e+00 , 2.40657553175952e+00 ), ( 3.90116127535849e+00 , 3.12864077430610e+00 , 7.91981858618513e-01 ), ( 2.75146176774071e+00 , 3.15808893346107e+00 , -8.38524301874596e-02 ), ( 3.15058020779582e+00 , 2.66360425680610e+00 , -1.51187231648151e+00 ), ( 1.64311380419904e+00 , 2.28974777568346e+00 , 4.60145209510769e-01 ), ( 4.37019188271778e-01 , 2.61159587015864e+00 , 4.13388133914335e-01 ), ( 2.01889031571544e+00 , 1.11096194922320e+00 , 1.03081568585815e+00 ), ( 1.30237801467038e+00 , 1.66952552639638e-01 , 1.66483452152124e+00 ), ( 2.10032363952688e+00 , -1.09309550185934e+00 , 2.02445737458888e+00 ), ( 5.69319084217896e-01 , 6.31712977451387e-01 , 2.93204363618353e+00 ), ( -6.13129327738737e-01 , 3.58567830265565e-01 , 3.21600122017048e+00 ), ( 1.29424026004458e+00 , 1.43789524187990e+00 , 3.78845033901546e+00 ), ( 9.20863346462551e-01 , 1.99127820048878e+00 , 5.06428998086043e+00 ), ( 2.02769970654205e+00 , 2.78482427262160e+00 , 5.72727759600340e+00 ), ( -3.53429738457185e-01 , 2.88525141896991e+00 , 4.91587622733329e+00 ), ( -1.11836681366995e+00 , 3.07200369822809e+00 , 5.89844056717887e+00 ), ( -5.09978582591622e-01 , 3.46256168935760e+00 , 3.70887589967705e+00 ), ( -1.45774543366842e+00 , 4.47927258473410e+00 , 3.40618952998717e+00 ), ( -7.80847160084358e-01 , 5.48787734405077e+00 , 2.48901293264984e+00 ), ( -2.75654315918850e+00 , 3.92374661648390e+00 , 2.71362055129860e+00 ), ( -3.78763499735523e+00 , 4.60862489696840e+00 , 2.80231332205132e+00 ), ( -2.71694603742992e+00 , 2.65629449817826e+00 , 2.34023304844123e+00 ), ( -3.82568791162424e+00 , 1.78086501651260e+00 , 1.98285962576433e+00 ), ( -3.33575644565417e+00 , 9.16232299352979e-01 , 7.56233762708860e-01 ), ( -4.27714753389729e+00 , 1.01616214271383e+00 , 3.23106157672000e+00 ), ( -5.41060709338710e+00 , 7.07769419654237e-01 , 3.36487357914603e+00 ), ( -3.35323357058458e+00 , 7.03693457278879e-01 , 4.17446542367788e+00 ), ( -3.66391973477359e+00 , 5.72897449881609e-02 , 5.44112795976568e+00 ), ( -2.31859332615496e+00 , -2.62462774180647e-01 , 6.13459495972546e+00 ), ( -4.48639827864321e+00 , 9.80835634045819e-01 , 6.41926482609842e+00 ), ( -5.35497870111677e+00 , 5.18953963119411e-01 , 7.16468574383976e+00 ), ( -6.27648156798849e+00 , 3.59754886587097e+00 , 6.79912500299058e+00 ), ( -7.05668789292172e+00 , 4.29369310510554e+00 , 7.51274068172582e+00 ), ( -6.60848210980863e+00 , 3.17799348101263e+00 , 5.56419804658952e+00 ), ( -4.12917365884651e+00 , 2.25204464458803e+00 , 6.42656371846837e+00 ), ( -4.79660124309934e+00 , 3.26935026374641e+00 , 7.18090217513124e+00 ), ( -4.00955688686220e+00 , 4.64510175581389e+00 , 7.28286043509099e+00 ) } +colvars: Step 38, atoms_positions[size = 51] = { ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 ), ( 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 ), ( 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 ), ( 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ), ( 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 ), ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 ), ( 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 ), ( 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 ), ( 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 ), ( 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ), ( 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 ), ( 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 ), ( 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 ), ( 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 ), ( 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 ), ( 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 ), ( 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 ), ( 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 ), ( 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 ), ( 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 ), ( 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 ), ( 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 ), ( 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 ), ( 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 ), ( -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 ), ( 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 ), ( 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 ), ( 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 ), ( -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 ), ( -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 ), ( -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 ), ( -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 ), ( -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 ), ( -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 ), ( -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 ), ( -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 ), ( -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 ), ( -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 ), ( -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 ), ( -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 ), ( -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 ), ( -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 ), ( -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 ), ( -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 ), ( -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 ), ( -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 ), ( -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 ), ( -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 ), ( -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 ), ( -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 ), ( -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ) } colvars: Step 38, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 38, atom_groups_ids[size = 0] = @@ -5710,163 +9255,302 @@ colvars: ---------------------------------------------------------------------- colvars: Collective variables module, step no. 38 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. colvars: Calculating colvar "one", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.80541218552965e-01 , -1.87029804430822e-02 , 9.59659743458776e-01 ). +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.78392072118256e-01 , -1.83593331534544e-02 , 9.60292033221074e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 , 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 , 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 , 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 , 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 , 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 , 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 , 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 , 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 , 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 , 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 , 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 , 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 , 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 , 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 , 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 , -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 , 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 , 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 , 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 , -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 , -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 , -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 , -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 , -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 , -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 , -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 , -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 , -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 , -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 , -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 , -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 , -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 , -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 , -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 , -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 , -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 , -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 , -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 , -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 , -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 , -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 , -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ). +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.80541218552965e-01 , -1.87029804430822e-02 , 9.59659743458776e-01 ). +colvars: Colvar "one" has value ( -2.78392072118256e-01 , -1.83593331534544e-02 , 9.60292033221074e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 , 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 , 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 , 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 , 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 , 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 , 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 , 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 , 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 , 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 , 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 , 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 , 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 , 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 , 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 , 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 , -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 , 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 , 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 , 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 , -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 , -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 , -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 , -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 , -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 , -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 , -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 , -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 , -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 , -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 , -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 , -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 , -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 , -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 , -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 , -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 , -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 , -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 , -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 , -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 , -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 , -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 , -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.1288 , 2.32586 , -15.2896 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 64.9214 , 6.49214 , 12.9843 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.1288 , 2.32586 , -15.2896 ) to colvar "one". -colvars: Adding total bias energy: 43.532 +colvars: Adding biasing force ( 64.9214 , 6.49214 , 12.9843 ) to colvar "one". +colvars: Adding total bias energy: 54.9095 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.1288 , 2.32586 , -15.2896 ) +colvars: Force to be applied: ( 64.9214 , 6.49214 , 12.9843 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.95893 , -0.503731 , -1.35307 ) -colvars: ( -4.25228 , -0.431949 , -1.16026 ) -colvars: ( -4.25228 , -0.431949 , -1.16026 ) -colvars: ( -5.66416 , -0.575369 , -1.5455 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.15671 , -0.521 , -1.39471 ) +colvars: ( -4.42188 , -0.446758 , -1.19596 ) +colvars: ( -4.42188 , -0.446758 , -1.19596 ) +colvars: ( -5.89007 , -0.595094 , -1.59306 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.881279 , 0.196945 , 0.594789 ) -colvars: ( 0.764825 , 0.265855 , 0.618068 ) -colvars: ( 0.748426 , 0.259646 , 0.600738 ) -colvars: ( 0.656441 , 0.26524 , 0.55588 ) -colvars: ( 0.64492 , 0.199364 , 0.464042 ) -colvars: ( 0.57258 , 0.340464 , 0.605798 ) -colvars: ( 0.468759 , 0.3529 , 0.563096 ) -colvars: ( 0.394384 , 0.448036 , 0.644174 ) -colvars: ( 0.388965 , 0.30851 , 0.460412 ) -colvars: ( 0.355507 , 0.266817 , 0.387465 ) -colvars: ( 0.359722 , 0.314122 , 0.451115 ) -colvars: ( 0.290043 , 0.271543 , 0.356506 ) -colvars: ( 0.262912 , 0.300648 , 0.37883 ) -colvars: ( 0.350704 , 0.175617 , 0.266637 ) -colvars: ( 0.293686 , 0.132255 , 0.178184 ) -colvars: ( 0.469999 , 0.140281 , 0.288448 ) -colvars: ( 0.540515 , 0.0507802 , 0.212481 ) -colvars: ( 0.666228 , 0.0315327 , 0.258762 ) -colvars: ( 0.549625 , 0.0187526 , 0.176165 ) -colvars: ( 0.534349 , -0.0456746 , 0.0840755 ) -colvars: ( 0.570579 , 0.0657134 , 0.24885 ) -colvars: ( 0.569878 , 0.0490494 , 0.226872 ) -colvars: ( 0.605971 , 0.112816 , 0.329896 ) -colvars: ( 0.449197 , 0.0520892 , 0.162452 ) -colvars: ( 0.442895 , -0.00348821 , 0.0869073 ) -colvars: ( 0.349852 , 0.11611 , 0.18909 ) -colvars: ( 0.228871 , 0.123314 , 0.129893 ) -colvars: ( 0.139661 , 0.207337 , 0.188175 ) -colvars: ( 0.200985 , 0.0506334 , 0.019973 ) -colvars: ( 0.153407 , 0.0141651 , -0.0542042 ) -colvars: ( 0.232902 , 0.026374 , 0.00663461 ) -colvars: ( 0.218786 , -0.0449223 , -0.0936928 ) -colvars: ( 0.252266 , -0.0471453 , -0.0776079 ) -colvars: ( 0.292245 , -0.129324 , -0.161388 ) -colvars: ( 0.249476 , -0.182196 , -0.254084 ) -colvars: ( 0.404508 , -0.143283 , -0.115876 ) -colvars: ( 0.480171 , -0.217388 , -0.168988 ) -colvars: ( 0.607833 , -0.21878 , -0.0984801 ) -colvars: ( 0.43497 , -0.22296 , -0.201808 ) -colvars: ( 0.44051 , -0.290257 , -0.285822 ) -colvars: ( 0.388067 , -0.151483 , -0.135808 ) -colvars: ( 0.33607 , -0.14648 , -0.158782 ) -colvars: ( 0.320495 , -0.0614751 , -0.057519 ) -colvars: ( 0.216114 , -0.156277 , -0.239415 ) -colvars: ( 0.19281 , -0.198359 , -0.307114 ) -colvars: ( 0.0192098 , -0.202324 , -0.410581 ) -colvars: ( -0.0692499 , -0.220735 , -0.484529 ) -colvars: ( 0.11635 , -0.250268 , -0.417647 ) -colvars: ( 0.136034 , -0.116492 , -0.233252 ) -colvars: ( 0.0198949 , -0.121847 , -0.305971 ) -colvars: ( -0.066971 , -0.0427524 , -0.252743 ) +colvars: ( 0.915026 , 0.204804 , 0.615756 ) +colvars: ( 0.794237 , 0.276235 , 0.639946 ) +colvars: ( 0.777132 , 0.269875 , 0.622065 ) +colvars: ( 0.681862 , 0.275456 , 0.575502 ) +colvars: ( 0.669903 , 0.207071 , 0.480315 ) +colvars: ( 0.594926 , 0.353422 , 0.627253 ) +colvars: ( 0.487295 , 0.366185 , 0.583 ) +colvars: ( 0.410193 , 0.464833 , 0.66705 ) +colvars: ( 0.404481 , 0.320085 , 0.476634 ) +colvars: ( 0.369808 , 0.276742 , 0.40101 ) +colvars: ( 0.37407 , 0.325966 , 0.467073 ) +colvars: ( 0.301743 , 0.281763 , 0.369079 ) +colvars: ( 0.273521 , 0.312035 , 0.392296 ) +colvars: ( 0.364631 , 0.182269 , 0.275913 ) +colvars: ( 0.305487 , 0.137209 , 0.184252 ) +colvars: ( 0.488345 , 0.145716 , 0.298478 ) +colvars: ( 0.561458 , 0.0528961 , 0.219716 ) +colvars: ( 0.691812 , 0.033067 , 0.267658 ) +colvars: ( 0.570984 , 0.0195775 , 0.182005 ) +colvars: ( 0.555131 , -0.0473077 , 0.0865582 ) +colvars: ( 0.592796 , 0.0682641 , 0.25728 ) +colvars: ( 0.59215 , 0.0508806 , 0.234434 ) +colvars: ( 0.629659 , 0.117031 , 0.341156 ) +colvars: ( 0.467005 , 0.0539005 , 0.167695 ) +colvars: ( 0.460492 , -0.003823 , 0.0893691 ) +colvars: ( 0.363957 , 0.120276 , 0.195362 ) +colvars: ( 0.238489 , 0.127632 , 0.134046 ) +colvars: ( 0.145952 , 0.214781 , 0.194513 ) +colvars: ( 0.209502 , 0.0522239 , 0.0201649 ) +colvars: ( 0.160181 , 0.0142961 , -0.056726 ) +colvars: ( 0.242521 , 0.0271589 , 0.00638947 ) +colvars: ( 0.227813 , -0.046796 , -0.0975526 ) +colvars: ( 0.262448 , -0.0489789 , -0.0808242 ) +colvars: ( 0.304017 , -0.134358 , -0.167772 ) +colvars: ( 0.259647 , -0.18927 , -0.263833 ) +colvars: ( 0.420481 , -0.148772 , -0.120668 ) +colvars: ( 0.498979 , -0.225653 , -0.175778 ) +colvars: ( 0.631401 , -0.226993 , -0.102759 ) +colvars: ( 0.452179 , -0.231564 , -0.209841 ) +colvars: ( 0.457929 , -0.301422 , -0.296937 ) +colvars: ( 0.4036 , -0.157478 , -0.141456 ) +colvars: ( 0.349749 , -0.152416 , -0.165308 ) +colvars: ( 0.333665 , -0.0642611 , -0.0603849 ) +colvars: ( 0.225321 , -0.162684 , -0.248828 ) +colvars: ( 0.201186 , -0.206427 , -0.319021 ) +colvars: ( 0.0209552 , -0.210521 , -0.426057 ) +colvars: ( -0.0708031 , -0.229704 , -0.502663 ) +colvars: ( 0.121652 , -0.260143 , -0.433385 ) +colvars: ( 0.142214 , -0.121407 , -0.242362 ) +colvars: ( 0.0217403 , -0.127056 , -0.317675 ) +colvars: ( -0.068376 , -0.045008 , -0.262441 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.95893 , 0.503731 , 1.35307 ) -colvars: ( 4.25228 , 0.431949 , 1.16026 ) -colvars: ( 4.25228 , 0.431949 , 1.16026 ) -colvars: ( 5.66416 , 0.575369 , 1.5455 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.15671 , 0.521 , 1.39471 ) +colvars: ( 4.42188 , 0.446758 , 1.19596 ) +colvars: ( 4.42188 , 0.446758 , 1.19596 ) +colvars: ( 5.89007 , 0.595094 , 1.59306 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.607396 , -0.0811741 , -0.34874 ) -colvars: ( -0.547618 , -0.164679 , -0.314838 ) -colvars: ( -0.494879 , -0.14225 , -0.254962 ) -colvars: ( -0.512065 , -0.192224 , -0.287777 ) -colvars: ( -0.502387 , -0.132485 , -0.259446 ) -colvars: ( -0.490595 , -0.285292 , -0.295268 ) -colvars: ( -0.461763 , -0.325881 , -0.279015 ) -colvars: ( -0.443001 , -0.434479 , -0.294063 ) -colvars: ( -0.398773 , -0.289734 , -0.204583 ) -colvars: ( -0.395964 , -0.26399 , -0.19374 ) -colvars: ( -0.347355 , -0.283879 , -0.1512 ) -colvars: ( -0.286453 , -0.246216 , -0.0783894 ) -colvars: ( -0.235648 , -0.261215 , -0.0321233 ) -colvars: ( -0.303693 , -0.141774 , -0.0631096 ) -colvars: ( -0.273515 , -0.111903 , -0.0235359 ) -colvars: ( -0.35495 , -0.0839748 , -0.0964831 ) -colvars: ( -0.37933 , 0.0154252 , -0.0899356 ) -colvars: ( -0.425701 , 0.0633118 , -0.121501 ) -colvars: ( -0.419331 , 0.0305885 , -0.125318 ) -colvars: ( -0.408002 , 0.0882184 , -0.0959881 ) -colvars: ( -0.465607 , -0.0243118 , -0.188837 ) -colvars: ( -0.502661 , -0.0258319 , -0.226466 ) -colvars: ( -0.554292 , -0.0923131 , -0.298966 ) -colvars: ( -0.454011 , -0.0558801 , -0.187053 ) -colvars: ( -0.461783 , -0.0111675 , -0.180904 ) -colvars: ( -0.400784 , -0.130903 , -0.157075 ) -colvars: ( -0.346226 , -0.162251 , -0.112143 ) -colvars: ( -0.297455 , -0.253399 , -0.0916607 ) -colvars: ( -0.303515 , -0.0882709 , -0.0462486 ) -colvars: ( -0.292232 , -0.0692515 , -0.0290047 ) -colvars: ( -0.280111 , -0.0428271 , -0.00861134 ) -colvars: ( -0.242834 , 0.0330542 , 0.052427 ) -colvars: ( -0.217792 , 0.0597498 , 0.0858607 ) -colvars: ( -0.285711 , 0.120785 , 0.0367894 ) -colvars: ( -0.259639 , 0.163282 , 0.0761827 ) -colvars: ( -0.353438 , 0.148924 , -0.0223474 ) -colvars: ( -0.401311 , 0.225935 , -0.0463374 ) -colvars: ( -0.470036 , 0.248399 , -0.108244 ) -colvars: ( -0.416592 , 0.205938 , -0.0678955 ) -colvars: ( -0.421087 , 0.267594 , -0.0531771 ) -colvars: ( -0.424375 , 0.118273 , -0.103034 ) -colvars: ( -0.435265 , 0.0878232 , -0.123448 ) -colvars: ( -0.459454 , -0.00678093 , -0.177201 ) -colvars: ( -0.370822 , 0.0767889 , -0.0622706 ) -colvars: ( -0.375828 , 0.103531 , -0.0589526 ) -colvars: ( -0.209481 , 0.110673 , 0.110073 ) -colvars: ( -0.161701 , 0.112857 , 0.158663 ) -colvars: ( -0.232086 , 0.183721 , 0.110183 ) -colvars: ( -0.308406 , 0.0357591 , -0.0124788 ) -colvars: ( -0.243693 , 0.0223364 , 0.0482234 ) -colvars: ( -0.191006 , -0.0616276 , 0.0748727 ) +colvars: ( -0.630429 , -0.0845273 , -0.360072 ) +colvars: ( -0.568538 , -0.171096 , -0.324869 ) +colvars: ( -0.513695 , -0.147894 , -0.262806 ) +colvars: ( -0.531834 , -0.199563 , -0.296926 ) +colvars: ( -0.521793 , -0.137569 , -0.267722 ) +colvars: ( -0.50972 , -0.296038 , -0.3046 ) +colvars: ( -0.48 , -0.338036 , -0.287827 ) +colvars: ( -0.460679 , -0.450637 , -0.303278 ) +colvars: ( -0.414663 , -0.300509 , -0.210834 ) +colvars: ( -0.411831 , -0.273742 , -0.199729 ) +colvars: ( -0.361231 , -0.294481 , -0.155489 ) +colvars: ( -0.29804 , -0.255395 , -0.0801613 ) +colvars: ( -0.24524 , -0.27101 , -0.0321365 ) +colvars: ( -0.315813 , -0.147085 , -0.0644872 ) +colvars: ( -0.284563 , -0.116047 , -0.023617 ) +colvars: ( -0.36883 , -0.087212 , -0.0990548 ) +colvars: ( -0.394008 , 0.0158627 , -0.0924098 ) +colvars: ( -0.441922 , 0.0654288 , -0.125055 ) +colvars: ( -0.435614 , 0.0316587 , -0.129174 ) +colvars: ( -0.423864 , 0.0914666 , -0.0989346 ) +colvars: ( -0.483718 , -0.0252596 , -0.19491 ) +colvars: ( -0.522283 , -0.026765 , -0.233976 ) +colvars: ( -0.575918 , -0.0957166 , -0.308966 ) +colvars: ( -0.471982 , -0.0578329 , -0.193227 ) +colvars: ( -0.480087 , -0.0114083 , -0.186996 ) +colvars: ( -0.416861 , -0.135617 , -0.162087 ) +colvars: ( -0.360413 , -0.168045 , -0.115605 ) +colvars: ( -0.309902 , -0.26257 , -0.0942516 ) +colvars: ( -0.316038 , -0.0913079 , -0.0474786 ) +colvars: ( -0.304426 , -0.0715114 , -0.0297389 ) +colvars: ( -0.291593 , -0.0442496 , -0.00847057 ) +colvars: ( -0.252836 , 0.0344464 , 0.0546381 ) +colvars: ( -0.226682 , 0.0620436 , 0.0893434 ) +colvars: ( -0.297256 , 0.125443 , 0.0382911 ) +colvars: ( -0.270239 , 0.169565 , 0.0789661 ) +colvars: ( -0.367433 , 0.154579 , -0.0229498 ) +colvars: ( -0.417047 , 0.234457 , -0.047931 ) +colvars: ( -0.488221 , 0.257681 , -0.111996 ) +colvars: ( -0.433075 , 0.213812 , -0.0703527 ) +colvars: ( -0.437736 , 0.277793 , -0.0552503 ) +colvars: ( -0.441305 , 0.122936 , -0.106668 ) +colvars: ( -0.452781 , 0.0914478 , -0.127884 ) +colvars: ( -0.477999 , -0.00665133 , -0.183436 ) +colvars: ( -0.386042 , 0.0800796 , -0.0645949 ) +colvars: ( -0.391316 , 0.10788 , -0.0612847 ) +colvars: ( -0.21867 , 0.115271 , 0.113808 ) +colvars: ( -0.169187 , 0.117597 , 0.164057 ) +colvars: ( -0.241929 , 0.19095 , 0.113911 ) +colvars: ( -0.321304 , 0.0375202 , -0.0129455 ) +colvars: ( -0.254275 , 0.0236664 , 0.0498664 ) +colvars: ( -0.199682 , -0.0634162 , 0.0776055 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 38. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 38. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 38, atoms_new_colvar_forces = { ( -4.68504596593723e+00 , -3.87960044554837e-01 , -1.10702493925305e+00 ), ( -4.03507454616897e+00 , -3.30772868806218e-01 , -8.57030935206698e-01 ), ( -4.10790495556206e+00 , -3.58933917415277e-01 , -8.92158331179923e-01 ), ( -5.52162879898756e+00 , -5.08490065370030e-01 , -1.34090541382355e+00 ), ( 2.53547409807237e-01 , 1.17395343649830e-01 , 3.45775403176845e-01 ), ( 5.04091444867002e+00 , 5.58903662245786e-01 , 1.66360378252024e+00 ), ( 4.25927712420322e+00 , 4.58968120362369e-01 , 1.44434234185778e+00 ), ( -4.86169599682644e-02 , 1.35573361755443e-02 , 3.50110621415940e-01 ), ( 4.24247321253911e+00 , 4.50725540939055e-01 , 1.41609001358819e+00 ), ( 5.62370379124786e+00 , 5.78195336211898e-01 , 1.73922672541253e+00 ), ( 1.23666273463987e-02 , 3.02422454952214e-02 , 2.99914640683939e-01 ), ( 3.58989977694230e-03 , 2.53272254604359e-02 , 2.78116884271365e-01 ), ( 2.72634678160686e-02 , 3.94329001137475e-02 , 3.46706534634495e-01 ), ( 4.70116903514599e-02 , 3.38423850950537e-02 , 2.03527221670406e-01 ), ( 2.01708266466297e-02 , 2.03515991148052e-02 , 1.54648439753815e-01 ), ( 1.15049531051039e-01 , 5.63064566006523e-02 , 1.91964485654303e-01 ), ( 1.61184870150210e-01 , 6.62053769391688e-02 , 1.22545803357855e-01 ), ( 2.40527655710593e-01 , 9.48445406100823e-02 , 1.37261743010277e-01 ), ( 1.30293647844552e-01 , 4.93411042457558e-02 , 5.08469877054185e-02 ), ( 1.26346453868404e-01 , 4.25438295628965e-02 , -1.19126281563288e-02 ), ( 1.04971429695855e-01 , 4.14015704463733e-02 , 6.00122413028724e-02 ), ( 6.72165009221579e-02 , 2.32174900127881e-02 , 4.06207199910719e-04 ), ( 5.16786736507181e-02 , 2.05024805236968e-02 , 3.09301614310952e-02 ), ( -4.81348973304196e-03 , -3.79088971167800e-03 , -2.46004014656881e-02 ), ( -1.88875810881352e-02 , -1.46556633711438e-02 , -9.39966504518929e-02 ), ( -5.09323798536477e-02 , -1.47930398366066e-02 , 3.20156209176616e-02 ), ( -1.17355219398364e-01 , -3.89372323921185e-02 , 1.77500594058494e-02 ), ( -1.57794431188953e-01 , -4.60621112272657e-02 , 9.65147346148430e-02 ), ( -1.02530163051209e-01 , -3.76375000794702e-02 , -2.62755864450294e-02 ), ( -1.38824877862961e-01 , -5.50864743684770e-02 , -8.32089577353211e-02 ), ( -4.72090688131942e-02 , -1.64531555692097e-02 , -1.97673131999296e-03 ), ( -2.40479788659493e-02 , -1.18681527321205e-02 , -4.12658442023945e-02 ), ( 3.44737419770871e-02 , 1.26044700774544e-02 , 8.25280977670068e-03 ), ( 6.53398962619500e-03 , -8.53860662145461e-03 , -1.24598629209296e-01 ), ( -1.01624664771037e-02 , -1.89138686042996e-02 , -1.77901375590074e-01 ), ( 5.10702798626905e-02 , 5.64140043345243e-03 , -1.38223502965335e-01 ), ( 7.88597348547954e-02 , 8.54749130007304e-03 , -2.15325787422210e-01 ), ( 1.37796735547282e-01 , 2.96192904115347e-02 , -2.06724388549256e-01 ), ( 1.83777162934834e-02 , -1.70220590215046e-02 , -2.69703184484445e-01 ), ( 1.94239440017776e-02 , -2.26633310832260e-02 , -3.38999530485407e-01 ), ( -3.63085283047891e-02 , -3.32098185281161e-02 , -2.38842661451588e-01 ), ( -9.91951666535170e-02 , -5.86568132718223e-02 , -2.82230221411499e-01 ), ( -1.38959462318140e-01 , -6.82560615145092e-02 , -2.34720410979020e-01 ), ( -1.54707908207242e-01 , -7.94877772935072e-02 , -3.01686063575200e-01 ), ( -1.83018527797304e-01 , -9.48281363681882e-02 , -3.66066412603138e-01 ), ( -1.90271117983092e-01 , -9.16511265324128e-02 , -3.00507860855284e-01 ), ( -2.30950834508462e-01 , -1.07877507039663e-01 , -3.25865450825500e-01 ), ( -1.15735761416530e-01 , -6.65470676589007e-02 , -3.07463332151836e-01 ), ( -1.72371650621547e-01 , -8.07332797727855e-02 , -2.45731027583700e-01 ), ( -2.23798397383055e-01 , -9.95106432150125e-02 , -2.57747268007509e-01 ), ( -2.57977165311456e-01 , -1.04379984067821e-01 , -1.77869935972177e-01 ) } +colvars: Step 38, atoms_new_colvar_forces = { ( -4.87211628471813e+00 , -4.00723696435930e-01 , -1.13902559685542e+00 ), ( -4.19618112062730e+00 , -3.41618652775116e-01 , -8.80886640494536e-01 ), ( -4.27185249304519e+00 , -3.70864683261145e-01 , -9.17387542307019e-01 ), ( -5.74196285124811e+00 , -5.25592613345036e-01 , -1.38046516841937e+00 ), ( 2.63436695172010e-01 , 1.21980183873108e-01 , 3.59258822687694e-01 ), ( 5.24191905370620e+00 , 5.78383900025139e-01 , 1.71736382057580e+00 ), ( 4.42917469889649e+00 , 4.74906575536316e-01 , 1.49113614173051e+00 ), ( -5.04856316323478e-02 , 1.41960855031390e-02 , 3.63771460263893e-01 ), ( 4.41169880812001e+00 , 4.66333549843916e-01 , 1.46176418728760e+00 ), ( 5.84804936609122e+00 , 5.98093948311445e-01 , 1.79433848850076e+00 ), ( 1.28390258135648e-02 , 3.14849985990572e-02 , 3.11583875992712e-01 ), ( 3.70289354056513e-03 , 2.63682143155367e-02 , 2.88917857719304e-01 ), ( 2.82811857352332e-02 , 4.10250507590758e-02 , 3.60159740153088e-01 ), ( 4.88172382287936e-02 , 3.51842526209211e-02 , 2.11425482513839e-01 ), ( 2.09242125707623e-02 , 2.11614057207995e-02 , 1.60635538220059e-01 ), ( 1.19514499385215e-01 , 5.85038153619524e-02 , 1.99423621621964e-01 ), ( 1.67449994282037e-01 , 6.87587757502283e-02 , 1.27305729225293e-01 ), ( 2.49890063073903e-01 , 9.84957788584253e-02 , 1.42603323462884e-01 ), ( 1.35370312059017e-01 , 5.12361986108216e-02 , 5.28306435895485e-02 ), ( 1.31266286226148e-01 , 4.41588078367218e-02 , -1.23764059304486e-02 ), ( 1.09077979208189e-01 , 4.30045041094490e-02 , 6.23702845380885e-02 ), ( 6.98669807188264e-02 , 2.41156230644165e-02 , 4.58514556624962e-04 ), ( 5.37408900422847e-02 , 2.13144634124023e-02 , 3.21895567314332e-02 ), ( -4.97680321526328e-03 , -3.93239731200813e-03 , -2.55318716107590e-02 ), ( -1.95955224962919e-02 , -1.52313040682568e-02 , -9.76268191527637e-02 ), ( -5.29038951167375e-02 , -1.53404889564458e-02 , 3.32752471439421e-02 ), ( -1.21924401426481e-01 , -4.04128727814948e-02 , 1.84417597620489e-02 ), ( -1.63949746135120e-01 , -4.77886697639920e-02 , 1.00261047281662e-01 ), ( -1.06536103855439e-01 , -3.90839635592086e-02 , -2.73137530310096e-02 ), ( -1.44244684364032e-01 , -5.72153615265834e-02 , -8.64648961120009e-02 ), ( -4.90722160147482e-02 , -1.70907738552945e-02 , -2.08109649362115e-03 ), ( -2.50223025757974e-02 , -1.23496395013128e-02 , -4.29145362918981e-02 ), ( 3.57661110053366e-02 , 1.30647037335049e-02 , 8.51922866820989e-03 ), ( 6.76096283443661e-03 , -8.91549215319049e-03 , -1.29480937298523e-01 ), ( -1.05922023196020e-02 , -1.97054936783417e-02 , -1.84866633030489e-01 ), ( 5.30483383961673e-02 , 5.80712809585909e-03 , -1.43617788492431e-01 ), ( 8.19320773382444e-02 , 8.80446263001067e-03 , -2.23709166098813e-01 ), ( 1.43180098258807e-01 , 3.06878669656324e-02 , -2.14755093475696e-01 ), ( 1.91042482792362e-02 , -1.77513282747287e-02 , -2.80193948256684e-01 ), ( 2.01924497840280e-02 , -2.36289028306198e-02 , -3.52187475693729e-01 ), ( -3.77047905553755e-02 , -3.45422233218000e-02 , -2.48124399881779e-01 ), ( -1.03032000452791e-01 , -6.09677714260224e-02 , -2.93192620152274e-01 ), ( -1.44334266803832e-01 , -7.09124683497476e-02 , -2.43821262073845e-01 ), ( -1.60721410136378e-01 , -8.26042071975248e-02 , -3.13422711508172e-01 ), ( -1.90130730016332e-01 , -9.85472626624001e-02 , -3.80306128235332e-01 ), ( -1.97715174740678e-01 , -9.52501299041566e-02 , -3.12248973167422e-01 ), ( -2.39990125847505e-01 , -1.12106974818264e-01 , -3.38606393215890e-01 ), ( -1.20276516750188e-01 , -6.91926694174377e-02 , -3.19474183656651e-01 ), ( -1.79090329393824e-01 , -8.38868210874086e-02 , -2.55307785632367e-01 ), ( -2.32535036301363e-01 , -1.03389308783731e-01 , -2.67808995162089e-01 ), ( -2.68057828977866e-01 , -1.08424122490680e-01 , -1.84835550495924e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 38, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -5904,10 +9588,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 39, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 39, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 39, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 39, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 39, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 39, atoms_positions[size = 51] = { ( 8.13501525759879e+00 , 3.94301437201377e-02 , -6.89525118168788e-01 ), ( 6.79737406289504e+00 , -6.26242921438514e-01 , -4.94139159645281e-01 ), ( 6.05925587723481e+00 , -3.19591065981759e-01 , 8.04449984366639e-01 ), ( 4.86096696215647e+00 , -1.52434410451711e-01 , 7.79960468702964e-01 ), ( 7.00757152055447e+00 , -2.10916947785025e+00 , -8.05703765902434e-01 ), ( 6.76390357467338e+00 , -3.17885143998751e-01 , 1.95557875649197e+00 ), ( 6.09313497227905e+00 , -2.43218284076312e-01 , 3.28415217784596e+00 ), ( 7.14903957909723e+00 , -3.67219896303452e-01 , 4.43319355840772e+00 ), ( 5.29816852780219e+00 , 1.06544532202552e+00 , 3.36322307375322e+00 ), ( 4.19300058306129e+00 , 1.00723876295409e+00 , 3.87810648871806e+00 ), ( 5.85004057706449e+00 , 2.25833157077558e+00 , 2.95172641623963e+00 ), ( 5.13022679803697e+00 , 3.50791439777201e+00 , 2.84379152633758e+00 ), ( 6.25002502961042e+00 , 4.41838871842487e+00 , 2.28213293111414e+00 ), ( 3.86762467160158e+00 , 3.61112430358377e+00 , 1.99930532274789e+00 ), ( 2.86396181294268e+00 , 4.15155375400149e+00 , 2.40436550760949e+00 ), ( 3.90230863312830e+00 , 3.12042543592870e+00 , 7.96912654362322e-01 ), ( 2.74858853518684e+00 , 3.17104178934016e+00 , -8.95446414171198e-02 ), ( 3.15311824947009e+00 , 2.66485814787895e+00 , -1.50613180371636e+00 ), ( 1.65544040594615e+00 , 2.29799485442806e+00 , 4.68225471915235e-01 ), ( 4.40768580680346e-01 , 2.61071078748745e+00 , 4.07520387417323e-01 ), ( 2.01807257960741e+00 , 1.11481109030766e+00 , 1.02266699128096e+00 ), ( 1.30303799677655e+00 , 1.65345710704498e-01 , 1.66779133679323e+00 ), ( 2.10178587628848e+00 , -1.09290224130655e+00 , 2.02027483147359e+00 ), ( 5.68660695442402e-01 , 6.37676733633720e-01 , 2.93317950514362e+00 ), ( -6.15484185506568e-01 , 3.58610951757020e-01 , 3.21898741594644e+00 ), ( 1.29709335507056e+00 , 1.44061775520531e+00 , 3.78925943748216e+00 ), ( 9.22351265956098e-01 , 1.99426240830054e+00 , 5.06880552607546e+00 ), ( 2.02442768164686e+00 , 2.78869245086042e+00 , 5.72854810117999e+00 ), ( -3.50622535899037e-01 , 2.88304906050733e+00 , 4.91533596090805e+00 ), ( -1.11776468139881e+00 , 3.07216942105024e+00 , 5.89751320452373e+00 ), ( -5.04448951998347e-01 , 3.45377628926940e+00 , 3.70029845630575e+00 ), ( -1.46266588566389e+00 , 4.48062897336731e+00 , 3.40098346263665e+00 ), ( -7.82680278322045e-01 , 5.49607569209838e+00 , 2.48906666761961e+00 ), ( -2.75733130889330e+00 , 3.92370376616143e+00 , 2.71383902844605e+00 ), ( -3.78457733504229e+00 , 4.61234595519783e+00 , 2.79882796855850e+00 ), ( -2.71900328656696e+00 , 2.65757234810844e+00 , 2.33550480644871e+00 ), ( -3.82665257343246e+00 , 1.77465978260212e+00 , 1.97845524345337e+00 ), ( -3.33247112892680e+00 , 9.23256509077847e-01 , 7.51871898070328e-01 ), ( -4.27840057343480e+00 , 1.01412722932380e+00 , 3.22525925468793e+00 ), ( -5.40641953384532e+00 , 7.01271558429892e-01 , 3.36940403470712e+00 ), ( -3.35028167834817e+00 , 6.99054643628883e-01 , 4.17763098059498e+00 ), ( -3.66382024617179e+00 , 5.55391358636345e-02 , 5.43434836263815e+00 ), ( -2.30941607457838e+00 , -2.56106232906855e-01 , 6.13852807308339e+00 ), ( -4.48238857897561e+00 , 9.87402879999148e-01 , 6.41814265630123e+00 ), ( -5.35493720737201e+00 , 5.11829946319280e-01 , 7.15993460884329e+00 ), ( -6.27045762569907e+00 , 3.59758060766193e+00 , 6.80948482476097e+00 ), ( -7.06079560794194e+00 , 4.29008647703466e+00 , 7.50905685615827e+00 ), ( -6.60899199977438e+00 , 3.18029928965737e+00 , 5.56669433576142e+00 ), ( -4.13409708582981e+00 , 2.25337631161557e+00 , 6.42822554641307e+00 ), ( -4.79385256846801e+00 , 3.26551090628151e+00 , 7.17384911190218e+00 ), ( -4.01088640611851e+00 , 4.65351479489929e+00 , 7.28298517741049e+00 ) } +colvars: Step 39, atoms_positions[size = 51] = { ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 ), ( 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 ), ( 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 ), ( 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ), ( 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 ), ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 ), ( 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 ), ( 7.15209468106941e+00 , -3.67624117504530e-01 , 4.43478070280023e+00 ), ( 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 ), ( 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ), ( 5.85248794713263e+00 , 2.25938076251533e+00 , 2.95153690628167e+00 ), ( 5.13075591770814e+00 , 3.50792385890992e+00 , 2.84425719233370e+00 ), ( 6.24995676938641e+00 , 4.41880966581118e+00 , 2.28256973292094e+00 ), ( 3.86783704089829e+00 , 3.61096286566776e+00 , 1.99970444568263e+00 ), ( 2.86406518132278e+00 , 4.15145858317519e+00 , 2.40459705297965e+00 ), ( 3.90250111205385e+00 , 3.12041888120911e+00 , 7.97223726672285e-01 ), ( 2.74882732907450e+00 , 3.17112421441466e+00 , -8.93440550655717e-02 ), ( 3.15343423214524e+00 , 2.66497450487673e+00 , -1.50593128968213e+00 ), ( 1.65563470587165e+00 , 2.29806247818938e+00 , 4.68317536017901e-01 ), ( 4.40964171499351e-01 , 2.61077705421038e+00 , 4.07537300936663e-01 ), ( 2.01821656468275e+00 , 1.11484345357438e+00 , 1.02272875349485e+00 ), ( 1.30314111019426e+00 , 1.65390561871593e-01 , 1.66780700656013e+00 ), ( 2.10196684283618e+00 , -1.09273041986010e+00 , 2.02048684397801e+00 ), ( 5.68768745235939e-01 , 6.37675112563199e-01 , 2.93317291449566e+00 ), ( -6.15407244554440e-01 , 3.58633018326628e-01 , 3.21889462115816e+00 ), ( 1.29725121846989e+00 , 1.44057397906235e+00 , 3.78929213200849e+00 ), ( 9.22284891708561e-01 , 1.99418215931574e+00 , 5.06879541844135e+00 ), ( 2.02425336785241e+00 , 2.78863082044487e+00 , 5.72865046142383e+00 ), ( -3.50745637122294e-01 , 2.88297630164963e+00 , 4.91528578031121e+00 ), ( -1.11796558039258e+00 , 3.07208771619379e+00 , 5.89741374769812e+00 ), ( -5.04511543035556e-01 , 3.45375176842667e+00 , 3.70025979089654e+00 ), ( -1.46271168084986e+00 , 4.48061232010830e+00 , 3.40090560148433e+00 ), ( -7.82655702934262e-01 , 5.49608057962156e+00 , 2.48906287015350e+00 ), ( -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 ), ( -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 ), ( -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 ), ( -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 ), ( -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 ), ( -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 ), ( -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 ), ( -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 ), ( -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 ), ( -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 ), ( -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 ), ( -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 ), ( -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 ), ( -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 ), ( -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 ), ( -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 ), ( -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 ), ( -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ) } colvars: Step 39, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 39, atom_groups_ids[size = 0] = @@ -5925,162 +9609,301 @@ colvars: Collective variables module, step no. 39 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Done calculating gradients of colvar "group1". +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Done calculating colvar "group1". colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.78029409440391e-01 , -1.88154958979349e-02 , 9.60388267629474e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.75804320334978e-01 , -1.84590719592386e-02 , 9.61036544334795e-01 ). colvars: Calculating gradients of colvar "one". colvars: Calculating fit gradients. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 , 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 7.15209468106941e+00 , -3.67624117504530e-01 , 4.43478070280023e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 , 5.85248794713263e+00 , 2.25938076251533e+00 , 2.95153690628167e+00 , 5.13075591770814e+00 , 3.50792385890992e+00 , 2.84425719233370e+00 , 6.24995676938641e+00 , 4.41880966581118e+00 , 2.28256973292094e+00 , 3.86783704089829e+00 , 3.61096286566776e+00 , 1.99970444568263e+00 , 2.86406518132278e+00 , 4.15145858317519e+00 , 2.40459705297965e+00 , 3.90250111205385e+00 , 3.12041888120911e+00 , 7.97223726672285e-01 , 2.74882732907450e+00 , 3.17112421441466e+00 , -8.93440550655717e-02 , 3.15343423214524e+00 , 2.66497450487673e+00 , -1.50593128968213e+00 , 1.65563470587165e+00 , 2.29806247818938e+00 , 4.68317536017901e-01 , 4.40964171499351e-01 , 2.61077705421038e+00 , 4.07537300936663e-01 , 2.01821656468275e+00 , 1.11484345357438e+00 , 1.02272875349485e+00 , 1.30314111019426e+00 , 1.65390561871593e-01 , 1.66780700656013e+00 , 2.10196684283618e+00 , -1.09273041986010e+00 , 2.02048684397801e+00 , 5.68768745235939e-01 , 6.37675112563199e-01 , 2.93317291449566e+00 , -6.15407244554440e-01 , 3.58633018326628e-01 , 3.21889462115816e+00 , 1.29725121846989e+00 , 1.44057397906235e+00 , 3.78929213200849e+00 , 9.22284891708561e-01 , 1.99418215931574e+00 , 5.06879541844135e+00 , 2.02425336785241e+00 , 2.78863082044487e+00 , 5.72865046142383e+00 , -3.50745637122294e-01 , 2.88297630164963e+00 , 4.91528578031121e+00 , -1.11796558039258e+00 , 3.07208771619379e+00 , 5.89741374769812e+00 , -5.04511543035556e-01 , 3.45375176842667e+00 , 3.70025979089654e+00 , -1.46271168084986e+00 , 4.48061232010830e+00 , 3.40090560148433e+00 , -7.82655702934262e-01 , 5.49608057962156e+00 , 2.48906287015350e+00 , -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 , -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 , -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 , -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 , -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 , -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 , -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 , -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 , -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 , -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 , -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 , -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 , -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 , -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 , -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 , -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 , -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 , -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.78029409440391e-01 , -1.88154958979349e-02 , 9.60388267629474e-01 ). +colvars: Colvar "one" has value ( -2.75804320334978e-01 , -1.84590719592386e-02 , 9.61036544334795e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 , 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 7.15209468106941e+00 , -3.67624117504530e-01 , 4.43478070280023e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 , 5.85248794713263e+00 , 2.25938076251533e+00 , 2.95153690628167e+00 , 5.13075591770814e+00 , 3.50792385890992e+00 , 2.84425719233370e+00 , 6.24995676938641e+00 , 4.41880966581118e+00 , 2.28256973292094e+00 , 3.86783704089829e+00 , 3.61096286566776e+00 , 1.99970444568263e+00 , 2.86406518132278e+00 , 4.15145858317519e+00 , 2.40459705297965e+00 , 3.90250111205385e+00 , 3.12041888120911e+00 , 7.97223726672285e-01 , 2.74882732907450e+00 , 3.17112421441466e+00 , -8.93440550655717e-02 , 3.15343423214524e+00 , 2.66497450487673e+00 , -1.50593128968213e+00 , 1.65563470587165e+00 , 2.29806247818938e+00 , 4.68317536017901e-01 , 4.40964171499351e-01 , 2.61077705421038e+00 , 4.07537300936663e-01 , 2.01821656468275e+00 , 1.11484345357438e+00 , 1.02272875349485e+00 , 1.30314111019426e+00 , 1.65390561871593e-01 , 1.66780700656013e+00 , 2.10196684283618e+00 , -1.09273041986010e+00 , 2.02048684397801e+00 , 5.68768745235939e-01 , 6.37675112563199e-01 , 2.93317291449566e+00 , -6.15407244554440e-01 , 3.58633018326628e-01 , 3.21889462115816e+00 , 1.29725121846989e+00 , 1.44057397906235e+00 , 3.78929213200849e+00 , 9.22284891708561e-01 , 1.99418215931574e+00 , 5.06879541844135e+00 , 2.02425336785241e+00 , 2.78863082044487e+00 , 5.72865046142383e+00 , -3.50745637122294e-01 , 2.88297630164963e+00 , 4.91528578031121e+00 , -1.11796558039258e+00 , 3.07208771619379e+00 , 5.89741374769812e+00 , -5.04511543035556e-01 , 3.45375176842667e+00 , 3.70025979089654e+00 , -1.46271168084986e+00 , 4.48061232010830e+00 , 3.40090560148433e+00 , -7.82655702934262e-01 , 5.49608057962156e+00 , 2.48906287015350e+00 , -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 , -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 , -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 , -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 , -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 , -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 , -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 , -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 , -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 , -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 , -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 , -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 , -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 , -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 , -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 , -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 , -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 , -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.0786 , 2.32811 , -15.3042 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 64.802 , 6.4802 , 12.9604 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.0786 , 2.32811 , -15.3042 ) to colvar "one". -colvars: Adding total bias energy: 43.4287 +colvars: Adding biasing force ( 64.802 , 6.4802 , 12.9604 ) to colvar "one". +colvars: Adding total bias energy: 54.7326 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.0786 , 2.32811 , -15.3042 ) +colvars: Force to be applied: ( 64.802 , 6.4802 , 12.9604 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.96357 , -0.501028 , -1.34148 ) -colvars: ( -4.25626 , -0.429631 , -1.15032 ) -colvars: ( -4.25626 , -0.429631 , -1.15032 ) -colvars: ( -5.66946 , -0.572281 , -1.53226 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.15038 , -0.516971 , -1.37925 ) +colvars: ( -4.41645 , -0.443303 , -1.1827 ) +colvars: ( -4.41645 , -0.443303 , -1.1827 ) +colvars: ( -5.88283 , -0.590492 , -1.5754 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.880397 , 0.197185 , 0.592315 ) -colvars: ( 0.764194 , 0.265906 , 0.61556 ) -colvars: ( 0.747723 , 0.259796 , 0.598367 ) -colvars: ( 0.656105 , 0.265128 , 0.553558 ) -colvars: ( 0.644611 , 0.199313 , 0.462008 ) -colvars: ( 0.572474 , 0.340138 , 0.603312 ) -colvars: ( 0.468947 , 0.352393 , 0.560728 ) -colvars: ( 0.394772 , 0.447311 , 0.641549 ) -colvars: ( 0.389284 , 0.308017 , 0.458419 ) -colvars: ( 0.355944 , 0.266293 , 0.385677 ) -colvars: ( 0.360015 , 0.313683 , 0.449225 ) -colvars: ( 0.290437 , 0.271136 , 0.354969 ) -colvars: ( 0.26327 , 0.300275 , 0.377301 ) -colvars: ( 0.350942 , 0.1754 , 0.265378 ) -colvars: ( 0.294056 , 0.132023 , 0.177212 ) -colvars: ( 0.469949 , 0.140248 , 0.287103 ) -colvars: ( 0.54029 , 0.0509371 , 0.211365 ) -colvars: ( 0.665678 , 0.0318848 , 0.2575 ) -colvars: ( 0.549473 , 0.0188622 , 0.175092 ) -colvars: ( 0.534232 , -0.0455099 , 0.083292 ) -colvars: ( 0.570461 , 0.065711 , 0.247486 ) -colvars: ( 0.569857 , 0.0489694 , 0.225508 ) -colvars: ( 0.605942 , 0.112629 , 0.328149 ) -colvars: ( 0.449481 , 0.051847 , 0.161297 ) -colvars: ( 0.443229 , -0.00371055 , 0.0859621 ) -colvars: ( 0.350344 , 0.115707 , 0.187889 ) -colvars: ( 0.229653 , 0.122759 , 0.128895 ) -colvars: ( 0.140623 , 0.206615 , 0.187035 ) -colvars: ( 0.20177 , 0.0501904 , 0.0193677 ) -colvars: ( 0.154338 , 0.0136751 , -0.0545941 ) -colvars: ( 0.23352 , 0.0260869 , 0.00613145 ) -colvars: ( 0.219372 , -0.0450804 , -0.0938341 ) -colvars: ( 0.252671 , -0.0471612 , -0.0777321 ) -colvars: ( 0.292691 , -0.129336 , -0.161357 ) -colvars: ( 0.250017 , -0.182191 , -0.253752 ) -colvars: ( 0.404729 , -0.143189 , -0.116036 ) -colvars: ( 0.480255 , -0.217166 , -0.169028 ) -colvars: ( 0.607638 , -0.218431 , -0.098779 ) -colvars: ( 0.435253 , -0.222876 , -0.201804 ) -colvars: ( 0.440796 , -0.290106 , -0.285569 ) -colvars: ( 0.388524 , -0.151596 , -0.136047 ) -colvars: ( 0.336737 , -0.146746 , -0.159003 ) -colvars: ( 0.321265 , -0.0619198 , -0.0580986 ) -colvars: ( 0.217046 , -0.156651 , -0.239349 ) -colvars: ( 0.193843 , -0.19876 , -0.306866 ) -colvars: ( 0.0204417 , -0.202711 , -0.409826 ) -colvars: ( -0.067822 , -0.22119 , -0.483519 ) -colvars: ( 0.117303 , -0.250438 , -0.416852 ) -colvars: ( 0.137087 , -0.116936 , -0.233141 ) -colvars: ( 0.0211973 , -0.122395 , -0.305594 ) -colvars: ( -0.0655056 , -0.0434473 , -0.252485 ) +colvars: ( 0.912086 , 0.204609 , 0.611764 ) +colvars: ( 0.791829 , 0.275683 , 0.635866 ) +colvars: ( 0.774684 , 0.269442 , 0.618171 ) +colvars: ( 0.680013 , 0.274732 , 0.571762 ) +colvars: ( 0.668109 , 0.206562 , 0.477089 ) +colvars: ( 0.593515 , 0.352298 , 0.623226 ) +colvars: ( 0.48643 , 0.36484 , 0.579196 ) +colvars: ( 0.409713 , 0.463039 , 0.662789 ) +colvars: ( 0.403938 , 0.318856 , 0.473463 ) +colvars: ( 0.369466 , 0.275577 , 0.398223 ) +colvars: ( 0.373566 , 0.324784 , 0.464034 ) +colvars: ( 0.301503 , 0.28071 , 0.366631 ) +colvars: ( 0.273306 , 0.310954 , 0.389806 ) +colvars: ( 0.364087 , 0.181638 , 0.273963 ) +colvars: ( 0.305213 , 0.13666 , 0.18281 ) +colvars: ( 0.487223 , 0.145361 , 0.296388 ) +colvars: ( 0.55999 , 0.0529475 , 0.21804 ) +colvars: ( 0.689712 , 0.0333701 , 0.265721 ) +colvars: ( 0.569573 , 0.0196513 , 0.180458 ) +colvars: ( 0.553791 , -0.0470284 , 0.0855282 ) +colvars: ( 0.591373 , 0.0681115 , 0.255258 ) +colvars: ( 0.590833 , 0.0506831 , 0.232462 ) +colvars: ( 0.628251 , 0.116575 , 0.338541 ) +colvars: ( 0.466286 , 0.0535234 , 0.166091 ) +colvars: ( 0.459841 , -0.00405233 , 0.0881609 ) +colvars: ( 0.363686 , 0.119583 , 0.193651 ) +colvars: ( 0.238801 , 0.12676 , 0.132687 ) +colvars: ( 0.146659 , 0.21354 , 0.19287 ) +colvars: ( 0.209881 , 0.0516369 , 0.0194726 ) +colvars: ( 0.160823 , 0.0137419 , -0.0570202 ) +colvars: ( 0.242648 , 0.0267932 , 0.00583616 ) +colvars: ( 0.227938 , -0.0468617 , -0.0974928 ) +colvars: ( 0.262305 , -0.048888 , -0.0807827 ) +colvars: ( 0.303826 , -0.134076 , -0.167376 ) +colvars: ( 0.259653 , -0.18885 , -0.262905 ) +colvars: ( 0.419796 , -0.148346 , -0.12058 ) +colvars: ( 0.497976 , -0.224921 , -0.175442 ) +colvars: ( 0.629811 , -0.226123 , -0.102859 ) +colvars: ( 0.451491 , -0.230966 , -0.209384 ) +colvars: ( 0.457229 , -0.300599 , -0.296024 ) +colvars: ( 0.403203 , -0.157254 , -0.141406 ) +colvars: ( 0.349694 , -0.152366 , -0.165187 ) +colvars: ( 0.333755 , -0.0645952 , -0.0608753 ) +colvars: ( 0.22582 , -0.162727 , -0.248217 ) +colvars: ( 0.201846 , -0.206402 , -0.318064 ) +colvars: ( 0.0222204 , -0.210471 , -0.424323 ) +colvars: ( -0.0691285 , -0.229685 , -0.500489 ) +colvars: ( 0.122399 , -0.259753 , -0.431593 ) +colvars: ( 0.143024 , -0.121615 , -0.241717 ) +colvars: ( 0.0230795 , -0.127361 , -0.316581 ) +colvars: ( -0.0666655 , -0.0456504 , -0.261593 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.96357 , 0.501028 , 1.34148 ) -colvars: ( 4.25626 , 0.429631 , 1.15032 ) -colvars: ( 4.25626 , 0.429631 , 1.15032 ) -colvars: ( 5.66946 , 0.572281 , 1.53226 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.15038 , 0.516971 , 1.37925 ) +colvars: ( 4.41645 , 0.443303 , 1.1827 ) +colvars: ( 4.41645 , 0.443303 , 1.1827 ) +colvars: ( 5.88283 , 0.590492 , 1.5754 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.606369 , -0.0813065 , -0.346087 ) -colvars: ( -0.546882 , -0.16467 , -0.312079 ) -colvars: ( -0.494004 , -0.142309 , -0.252263 ) -colvars: ( -0.511681 , -0.192096 , -0.285236 ) -colvars: ( -0.502018 , -0.132401 , -0.257249 ) -colvars: ( -0.490507 , -0.285008 , -0.292527 ) -colvars: ( -0.462034 , -0.325465 , -0.276419 ) -colvars: ( -0.443535 , -0.433903 , -0.291151 ) -colvars: ( -0.399154 , -0.289323 , -0.20236 ) -colvars: ( -0.396488 , -0.263557 , -0.191787 ) -colvars: ( -0.347662 , -0.283503 , -0.149005 ) -colvars: ( -0.286832 , -0.245857 , -0.0765381 ) -colvars: ( -0.235945 , -0.260877 , -0.0301812 ) -colvars: ( -0.303865 , -0.141555 , -0.061606 ) -colvars: ( -0.273826 , -0.11167 , -0.0223563 ) -colvars: ( -0.354783 , -0.0838916 , -0.0949159 ) -colvars: ( -0.37894 , 0.0153696 , -0.0886653 ) -colvars: ( -0.424924 , 0.0631122 , -0.120075 ) -colvars: ( -0.419063 , 0.0305636 , -0.124188 ) -colvars: ( -0.407758 , 0.0881545 , -0.0952028 ) -colvars: ( -0.46543 , -0.0242597 , -0.187439 ) -colvars: ( -0.502637 , -0.025727 , -0.225153 ) -colvars: ( -0.554312 , -0.0921356 , -0.297272 ) -colvars: ( -0.454342 , -0.0556548 , -0.185964 ) -colvars: ( -0.462175 , -0.0109573 , -0.1801 ) -colvars: ( -0.401354 , -0.130558 , -0.155869 ) -colvars: ( -0.347128 , -0.161792 , -0.111142 ) -colvars: ( -0.298568 , -0.252815 , -0.0904252 ) -colvars: ( -0.304373 , -0.0878892 , -0.0456553 ) -colvars: ( -0.293262 , -0.0688353 , -0.0286842 ) -colvars: ( -0.280728 , -0.0425557 , -0.00807094 ) -colvars: ( -0.243365 , 0.0332355 , 0.0525935 ) -colvars: ( -0.218068 , 0.0598309 , 0.0860851 ) -colvars: ( -0.28608 , 0.120858 , 0.0366886 ) -colvars: ( -0.260099 , 0.163344 , 0.0757397 ) -colvars: ( -0.353568 , 0.148915 , -0.0222955 ) -colvars: ( -0.401289 , 0.22583 , -0.0464984 ) -colvars: ( -0.469708 , 0.248197 , -0.10816 ) -colvars: ( -0.416839 , 0.20593 , -0.0681754 ) -colvars: ( -0.421327 , 0.267538 , -0.0537746 ) -colvars: ( -0.424868 , 0.118407 , -0.10306 ) -colvars: ( -0.43604 , 0.0880662 , -0.123554 ) -colvars: ( -0.460398 , -0.00641104 , -0.176925 ) -colvars: ( -0.371885 , 0.0771152 , -0.0626612 ) -colvars: ( -0.377019 , 0.103875 , -0.0595956 ) -colvars: ( -0.210792 , 0.11102 , 0.109073 ) -colvars: ( -0.163223 , 0.113258 , 0.157399 ) -colvars: ( -0.233044 , 0.183911 , 0.109143 ) -colvars: ( -0.309582 , 0.0361404 , -0.0128318 ) -colvars: ( -0.245139 , 0.0227973 , 0.0476154 ) -colvars: ( -0.192635 , -0.0610563 , 0.0744798 ) +colvars: ( -0.627959 , -0.0844848 , -0.35645 ) +colvars: ( -0.566512 , -0.170711 , -0.321215 ) +colvars: ( -0.511644 , -0.147634 , -0.259355 ) +colvars: ( -0.530263 , -0.198987 , -0.293566 ) +colvars: ( -0.520259 , -0.137177 , -0.264791 ) +colvars: ( -0.508512 , -0.295081 , -0.301011 ) +colvars: ( -0.479237 , -0.336843 , -0.284431 ) +colvars: ( -0.460238 , -0.449025 , -0.299513 ) +colvars: ( -0.414161 , -0.299405 , -0.208005 ) +colvars: ( -0.411487 , -0.272674 , -0.197211 ) +colvars: ( -0.360769 , -0.293429 , -0.152814 ) +colvars: ( -0.297794 , -0.254448 , -0.0780193 ) +colvars: ( -0.245025 , -0.270052 , -0.0300066 ) +colvars: ( -0.315309 , -0.146527 , -0.0627475 ) +colvars: ( -0.284275 , -0.115544 , -0.0223119 ) +colvars: ( -0.36785 , -0.0869328 , -0.0971696 ) +colvars: ( -0.392736 , 0.0157651 , -0.0908531 ) +colvars: ( -0.440133 , 0.0650667 , -0.12326 ) +colvars: ( -0.434377 , 0.0315596 , -0.127683 ) +colvars: ( -0.42268 , 0.0911935 , -0.0978757 ) +colvars: ( -0.482471 , -0.0251498 , -0.192987 ) +colvars: ( -0.521113 , -0.0265947 , -0.232056 ) +colvars: ( -0.574676 , -0.0953155 , -0.306475 ) +colvars: ( -0.471301 , -0.0574644 , -0.191636 ) +colvars: ( -0.479452 , -0.0111585 , -0.185719 ) +colvars: ( -0.416555 , -0.134948 , -0.160443 ) +colvars: ( -0.360584 , -0.167182 , -0.114281 ) +colvars: ( -0.310407 , -0.261365 , -0.0927293 ) +colvars: ( -0.31626 , -0.0906982 , -0.0467398 ) +colvars: ( -0.304856 , -0.0709081 , -0.0293284 ) +colvars: ( -0.291613 , -0.0438628 , -0.00787526 ) +colvars: ( -0.252851 , 0.0345623 , 0.0546963 ) +colvars: ( -0.226485 , 0.0619904 , 0.0893849 ) +colvars: ( -0.297001 , 0.125241 , 0.0381039 ) +colvars: ( -0.27014 , 0.169255 , 0.0783257 ) +colvars: ( -0.366769 , 0.154226 , -0.0228374 ) +colvars: ( -0.416113 , 0.233824 , -0.047987 ) +colvars: ( -0.486805 , 0.256893 , -0.111649 ) +colvars: ( -0.43239 , 0.21333 , -0.070484 ) +colvars: ( -0.437034 , 0.277117 , -0.0557512 ) +colvars: ( -0.440862 , 0.122807 , -0.106449 ) +colvars: ( -0.452612 , 0.0915062 , -0.127703 ) +colvars: ( -0.477953 , -0.00623967 , -0.182727 ) +colvars: ( -0.386326 , 0.0802523 , -0.0648572 ) +colvars: ( -0.391723 , 0.10801 , -0.0618212 ) +colvars: ( -0.219587 , 0.115387 , 0.1125 ) +colvars: ( -0.170437 , 0.117766 , 0.162356 ) +colvars: ( -0.24242 , 0.19073 , 0.112559 ) +colvars: ( -0.321851 , 0.0378456 , -0.0132846 ) +colvars: ( -0.255256 , 0.0241077 , 0.049116 ) +colvars: ( -0.200978 , -0.0626641 , 0.0770197 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 39. colvars: colvarmodule::write_traj_files() colvars: Using colvarproxy_namd::output_stream() colvars: colvarmodule::end_of_step(), step = 39. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 39, atoms_new_colvar_forces = { ( -4.68954119047701e+00 , -3.85149724894070e-01 , -1.09525402232860e+00 ), ( -4.03894739503836e+00 , -3.28395697579528e-01 , -8.46839141921896e-01 ), ( -4.11183566162515e+00 , -3.56599657591745e-01 , -8.81998947583959e-01 ), ( -5.52686777124093e+00 , -5.05368468946877e-01 , -1.32750154128391e+00 ), ( 2.53718766023828e-01 , 1.17486469897245e-01 , 3.46104292120658e-01 ), ( 5.04553629527217e+00 , 5.56158317413406e-01 , 1.65226684793111e+00 ), ( 4.26317238704944e+00 , 4.56559334622244e-01 , 1.43462913794130e+00 ), ( -4.87624794298556e-02 , 1.34072186325228e-02 , 3.50397711199689e-01 ), ( 4.24638961908121e+00 , 4.48325620682142e-01 , 1.40637926803101e+00 ), ( 5.62891661354505e+00 , 5.75017243947897e-01 , 1.72614998039327e+00 ), ( 1.23533589188348e-02 , 3.01798934975890e-02 , 3.00219552681599e-01 ), ( 3.60483316666277e-03 , 2.52782325660993e-02 , 2.78431275904403e-01 ), ( 2.73248780575444e-02 , 3.93979863742646e-02 , 3.47119459388892e-01 ), ( 4.70772234125372e-02 , 3.38452650549425e-02 , 2.03771588358902e-01 ), ( 2.02300781732224e-02 , 2.03523723913996e-02 , 1.54855569729158e-01 ), ( 1.15165136335723e-01 , 5.63567640425060e-02 , 1.92187018719023e-01 ), ( 1.61349319706483e-01 , 6.63067071145899e-02 , 1.22700114093274e-01 ), ( 2.40754141612545e-01 , 9.49969894515954e-02 , 1.37424738931895e-01 ), ( 1.30410028913662e-01 , 4.94257881605713e-02 , 5.09037929291311e-02 ), ( 1.26473924482915e-01 , 4.26446206098426e-02 , -1.19108247164042e-02 ), ( 1.05030804314861e-01 , 4.14512984492250e-02 , 6.00469667202549e-02 ), ( 6.72198933172334e-02 , 2.32423466184547e-02 , 3.54904215881441e-04 ), ( 5.16300913153956e-02 , 2.04935944620715e-02 , 3.08767541824016e-02 ), ( -4.86095333326475e-03 , -3.80774743249413e-03 , -2.46672436484585e-02 ), ( -1.89456051778193e-02 , -1.46678089418535e-02 , -9.41375044331503e-02 ), ( -5.10101901904896e-02 , -1.48504441014234e-02 , 3.20201355732448e-02 ), ( -1.17475611531463e-01 , -3.90330585698587e-02 , 1.77538354151428e-02 ), ( -1.57944436853938e-01 , -4.62006940530025e-02 , 9.66100785696662e-02 ), ( -1.02602584369978e-01 , -3.76987875748095e-02 , -2.62875637930174e-02 ), ( -1.38924135643100e-01 , -5.51602740603401e-02 , -8.32782652662297e-02 ), ( -4.72081429702560e-02 , -1.64688624861600e-02 , -1.93948289092324e-03 ), ( -2.39933500713810e-02 , -1.18449335598510e-02 , -4.12406820793752e-02 ), ( 3.46026790678287e-02 , 1.26696650526816e-02 , 8.35299547683815e-03 ), ( 6.61099790286646e-03 , -8.47822285746856e-03 , -1.24668666134085e-01 ), ( -1.00818450242713e-02 , -1.88469378746466e-02 , -1.78012603048105e-01 ), ( 5.11612433368664e-02 , 5.72605910654783e-03 , -1.38331859343317e-01 ), ( 7.89660975446043e-02 , 8.66410248820965e-03 , -2.15526723541092e-01 ), ( 1.37929758977092e-01 , 2.97660898000908e-02 , -2.06939389288260e-01 ), ( 1.84138537434986e-02 , -1.69453840340082e-02 , -2.69979066918451e-01 ), ( 1.94687170202535e-02 , -2.25685165960764e-02 , -3.39343896595633e-01 ), ( -3.63439889633463e-02 , -3.31889835654128e-02 , -2.39106475208884e-01 ), ( -9.93026663182876e-02 , -5.86797627539019e-02 , -2.82556703646834e-01 ), ( -1.39133331405120e-01 , -6.83307997173733e-02 , -2.35024001069001e-01 ), ( -1.54839043094663e-01 , -7.95362226189403e-02 , -3.02010322409087e-01 ), ( -1.83175664045330e-01 , -9.48844323358188e-02 , -3.66461874899253e-01 ), ( -1.90350171977169e-01 , -9.16900988761847e-02 , -3.00753594623707e-01 ), ( -2.31045281665251e-01 , -1.07932084547541e-01 , -3.26119885692409e-01 ), ( -1.15741452536877e-01 , -6.65273756963924e-02 , -3.07709622182550e-01 ), ( -1.72495142798950e-01 , -8.07960371360381e-02 , -2.45972727412390e-01 ), ( -2.23941765568113e-01 , -9.95973836571451e-02 , -2.57978483112888e-01 ), ( -2.58140878941947e-01 , -1.04503578377180e-01 , -1.78004903434872e-01 ) } +colvars: Step 39, atoms_new_colvar_forces = { ( -4.86624888188174e+00 , -3.96846870810409e-01 , -1.12393283910536e+00 ), ( -4.19112890348070e+00 , -3.38331517233914e-01 , -8.68052342709592e-01 ), ( -4.26669521102572e+00 , -3.67557643479787e-01 , -9.04507382720872e-01 ), ( -5.73498403444011e+00 , -5.21106874330410e-01 , -1.36309638276026e+00 ), ( 2.63039719328412e-01 , 1.21808606746486e-01 , 3.58816049029923e-01 ), ( 5.23537853780408e+00 , 5.74188625236823e-01 , 1.70146163887394e+00 ), ( 4.42363942606241e+00 , 4.71299483584489e-01 , 1.47746818775184e+00 ), ( -5.05252225535211e-02 , 1.40139555680489e-02 , 3.63275791484696e-01 ), ( 4.40622288551885e+00 , 4.62753988587406e-01 , 1.44816210595151e+00 ), ( 5.84081329579396e+00 , 5.93394527303759e-01 , 1.77640673879265e+00 ), ( 1.27968526509231e-02 , 3.13541852328310e-02 , 3.11219118021952e-01 ), ( 3.70917523991948e-03 , 2.62619996992839e-02 , 2.88611609060987e-01 ), ( 2.82812640814406e-02 , 4.09014620763242e-02 , 3.59799278659715e-01 ), ( 4.87775267289722e-02 , 3.51112982228473e-02 , 2.11215959969178e-01 ), ( 2.09386115151937e-02 , 2.11166378679873e-02 , 1.60497998048344e-01 ), ( 1.19372725886971e-01 , 5.84282841160213e-02 , 1.99218157241819e-01 ), ( 1.67254327445789e-01 , 6.87125317282526e-02 , 1.27187213018348e-01 ), ( 2.49578995784398e-01 , 9.84368335739027e-02 , 1.42460782216679e-01 ), ( 1.35195468618677e-01 , 5.12109402703477e-02 , 5.27743403932174e-02 ), ( 1.31111771450573e-01 , 4.41650867263977e-02 , -1.23474749183609e-02 ), ( 1.08902116868153e-01 , 4.29617013130471e-02 , 6.22709859610579e-02 ), ( 6.97192969986092e-02 , 2.40884641687701e-02 , 4.05873732892692e-04 ), ( 5.35752380407125e-02 , 2.12592535748896e-02 , 3.20662093135859e-02 ), ( -5.01413743191209e-03 , -3.94101361003935e-03 , -2.55442982851857e-02 ), ( -1.96117385202164e-02 , -1.52107871956150e-02 , -9.75583784328992e-02 ), ( -5.28685391564081e-02 , -1.53652998345423e-02 , 3.32077892656157e-02 ), ( -1.21782927083157e-01 , -4.04222364071606e-02 , 1.84053946066618e-02 ), ( -1.63747672167038e-01 , -4.78251673446656e-02 , 1.00140392817315e-01 ), ( -1.06379087298422e-01 , -3.90613070346572e-02 , -2.72671718419319e-02 ), ( -1.44033164146982e-01 , -5.71661682147888e-02 , -8.63486103204718e-02 ), ( -4.89651244709921e-02 , -1.70695951364150e-02 , -2.03909618221090e-03 ), ( -2.49126009154574e-02 , -1.22993890853467e-02 , -4.27964892910963e-02 ), ( 3.58195935432474e-02 , 1.31024577418579e-02 , 8.60218814107983e-03 ), ( 6.82489061115937e-03 , -8.83523074512255e-03 , -1.29272047426560e-01 ), ( -1.04869053564732e-02 , -1.95953026501091e-02 , -1.84579800551297e-01 ), ( 5.30263513415448e-02 , 5.87999973341891e-03 , -1.43416961499342e-01 ), ( 8.18634837905476e-02 , 8.90302520024833e-03 , -2.23428842175944e-01 ), ( 1.43006056251065e-01 , 3.07695439429659e-02 , -2.14508147633802e-01 ), ( 1.91004446781697e-02 , -1.76357354096791e-02 , -2.79867555273676e-01 ), ( 2.01952733562084e-02 , -2.34823339925463e-02 , -3.51774801986377e-01 ), ( -3.76584821190159e-02 , -3.44467091087731e-02 , -2.47855237136219e-01 ), ( -1.02917371001586e-01 , -6.08593832803947e-02 , -2.92889644212754e-01 ), ( -1.44197811938873e-01 , -7.08348737155169e-02 , -2.43601901479221e-01 ), ( -1.60505924946831e-01 , -8.24747399491582e-02 , -3.13073960838549e-01 ), ( -1.89877822052170e-01 , -9.83913028876804e-02 , -3.79884970331958e-01 ), ( -1.97366811362835e-01 , -9.50835974358932e-02 , -3.11823499450721e-01 ), ( -2.39565864837849e-01 , -1.11919728153128e-01 , -3.38132907776551e-01 ), ( -1.20021171512207e-01 , -6.90232539396338e-02 , -3.19033444303139e-01 ), ( -1.78827528193025e-01 , -8.37689366093193e-02 , -2.55001164246048e-01 ), ( -2.32176768406599e-01 , -1.03253425804644e-01 , -2.67464930231412e-01 ), ( -2.67643623090158e-01 , -1.08314468817058e-01 , -1.84573519231204e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 39, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- @@ -6118,10 +9941,10 @@ colvars: Updating group positions arrays. colvars: Updating grid objects. colvars: ---------------------------------------------------------------------- colvars: Step 40, atoms_ids[size = 51] = { 0, 3, 9, 10, 5, 11, 13, 15, 19, 20, 21, 23, 25, 29, 30, 31, 33, 35, 39, 40, 41, 43, 45, 49, 50, 51, 53, 55, 59, 60, 61, 63, 65, 69, 70, 71, 73, 75, 79, 80, 81, 83, 85, 89, 90, 91, 92, 93, 96, 98, 100 } -colvars: Step 40, atoms_refcount[size = 51] = { 3, 3, 3, 3, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 40, atoms_refcount[size = 51] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } colvars: Step 40, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } colvars: Step 40, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } -colvars: Step 40, atoms_positions[size = 51] = { ( 8.12105901178684e+00 , 3.84226283907114e-02 , -6.86717885048334e-01 ), ( 6.79031524301517e+00 , -6.26050504072990e-01 , -4.88274685603578e-01 ), ( 6.05995211580310e+00 , -3.20085794055288e-01 , 8.00170068632393e-01 ), ( 4.85054921410866e+00 , -1.51708376423104e-01 , 7.83927579783448e-01 ), ( 7.01138742580607e+00 , -2.11446858072754e+00 , -7.99083136874665e-01 ), ( 6.75688571289485e+00 , -3.18020767235407e-01 , 1.95437180756530e+00 ), ( 6.10077878305847e+00 , -2.43397095496519e-01 , 3.29267868076293e+00 ), ( 7.14583106110183e+00 , -3.70172886093937e-01 , 4.43833555648328e+00 ), ( 5.29833883198606e+00 , 1.06625811215479e+00 , 3.36619681421965e+00 ), ( 4.19228440064791e+00 , 1.00923478775605e+00 , 3.88914924887784e+00 ), ( 5.84685642653782e+00 , 2.25891568630460e+00 , 2.94937774317570e+00 ), ( 5.13252402954428e+00 , 3.50612309515531e+00 , 2.84017930938219e+00 ), ( 6.24344427519495e+00 , 4.41426944231342e+00 , 2.27981822599335e+00 ), ( 3.87143338382539e+00 , 3.60795730140310e+00 , 1.99843462826635e+00 ), ( 2.86820328051534e+00 , 4.14990122379047e+00 , 2.40253508354811e+00 ), ( 3.90359165474461e+00 , 3.11233173226373e+00 , 8.00756320838139e-01 ), ( 2.74682823285188e+00 , 3.18403024342829e+00 , -9.57831846352821e-02 ), ( 3.15533221828101e+00 , 2.66517251318307e+00 , -1.50100632762412e+00 ), ( 1.66512306771901e+00 , 2.30568485079699e+00 , 4.76221142802963e-01 ), ( 4.45402504043012e-01 , 2.60974796336796e+00 , 4.01843763817422e-01 ), ( 2.01917037167459e+00 , 1.12063296128010e+00 , 1.01328106062490e+00 ), ( 1.30105928161206e+00 , 1.62311836724961e-01 , 1.67187984927862e+00 ), ( 2.10343630165357e+00 , -1.09287845043043e+00 , 2.01592429128284e+00 ), ( 5.68011572073184e-01 , 6.44248180171018e-01 , 2.93562930904170e+00 ), ( -6.17218642168799e-01 , 3.58717315596372e-01 , 3.22148163939923e+00 ), ( 1.30030456484385e+00 , 1.44280744325559e+00 , 3.78930477101615e+00 ), ( 9.22378520478911e-01 , 1.99712651411855e+00 , 5.07302735114155e+00 ), ( 2.02264712416081e+00 , 2.79285061496176e+00 , 5.73022970446251e+00 ), ( -3.47376027355219e-01 , 2.88083606144856e+00 , 4.91611465581226e+00 ), ( -1.11673949208574e+00 , 3.07229694576606e+00 , 5.89554932337739e+00 ), ( -4.99471962080539e-01 , 3.44490303313808e+00 , 3.69180412368484e+00 ), ( -1.46829772733846e+00 , 4.48168554569302e+00 , 3.39501400705136e+00 ), ( -7.83794803040324e-01 , 5.50438459908698e+00 , 2.48882738957871e+00 ), ( -2.75800104042783e+00 , 3.92496746891646e+00 , 2.71638667872342e+00 ), ( -3.78135058786988e+00 , 4.61555058188124e+00 , 2.79484660644305e+00 ), ( -2.72101007952248e+00 , 2.65771618414932e+00 , 2.32983712611732e+00 ), ( -3.82675332822892e+00 , 1.76963084128839e+00 , 1.97391075134387e+00 ), ( -3.32914723792086e+00 , 9.30331970886669e-01 , 7.48209808092791e-01 ), ( -4.27771848726241e+00 , 1.01195061406328e+00 , 3.21929726464452e+00 ), ( -5.40373708027661e+00 , 6.94458199866029e-01 , 3.37415144200379e+00 ), ( -3.34779907680153e+00 , 6.94943417684864e-01 , 4.18000273089232e+00 ), ( -3.66378416447534e+00 , 5.47958850223550e-02 , 5.42876490230581e+00 ), ( -2.30044147106763e+00 , -2.50568962720670e-01 , 6.14266632592068e+00 ), ( -4.47773362413644e+00 , 9.91914202203342e-01 , 6.41672486665103e+00 ), ( -5.35468974719743e+00 , 5.05041768878412e-01 , 7.15493552115057e+00 ), ( -6.26510458721272e+00 , 3.59861756350138e+00 , 6.81978333230359e+00 ), ( -7.06411553698509e+00 , 4.28576896347840e+00 , 7.50474367817482e+00 ), ( -6.60987420839401e+00 , 3.18247523255589e+00 , 5.56932785453876e+00 ), ( -4.13903219713242e+00 , 2.25571592522886e+00 , 6.42901319882496e+00 ), ( -4.79190564018779e+00 , 3.26258861232214e+00 , 7.16845632251530e+00 ), ( -4.01210959687813e+00 , 4.66018193684896e+00 , 7.28287892592627e+00 ) } +colvars: Step 40, atoms_positions[size = 51] = { ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 ), ( 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 ), ( 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 ), ( 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ), ( 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 ), ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 ), ( 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 ), ( 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 ), ( 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 ), ( 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ), ( 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 ), ( 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 ), ( 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 ), ( 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 ), ( 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 ), ( 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 ), ( 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 ), ( 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 ), ( 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 ), ( 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 ), ( 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 ), ( 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 ), ( 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 ), ( 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 ), ( -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 ), ( 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 ), ( 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 ), ( 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 ), ( -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 ), ( -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 ), ( -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 ), ( -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 ), ( -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 ), ( -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 ), ( -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 ), ( -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 ), ( -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 ), ( -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 ), ( -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 ), ( -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 ), ( -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 ), ( -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 ), ( -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 ), ( -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 ), ( -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 ), ( -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 ), ( -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 ), ( -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 ), ( -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 ), ( -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 ), ( -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ) } colvars: Step 40, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } colvars: ---------------------------------------------------------------------- colvars: Step 40, atom_groups_ids[size = 0] = @@ -6139,154 +9962,290 @@ colvars: Collective variables module, step no. 40 colvars: Calculating collective variables. colvars: [0/4]: calc_colvars_items_smp(), first = 0, last = 0, cv = one, cvc = 0 colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. colvars: Calculating colvar components. -colvars: Colvar component no. 1 within colvar "one" has value ( -2.75375163222155e-01 , -1.88018998907846e-02 , 9.61152957671602e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.73073003055543e-01 , -1.84328428660908e-02 , 9.61816700471613e-01 ). colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ). +colvars: Calculating gradients of colvar "group1". colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 , 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 , 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 , 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 , 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 , 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 , 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 , 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 , 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 , 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 , 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 , 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 , 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 , 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 , 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 , 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 , -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 , 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 , 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 , 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 , -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 , -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 , -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 , -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 , -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 , -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 , -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 , -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 , -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 , -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 , -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 , -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 , -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 , -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 , -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 , -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 , -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 , -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 , -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 , -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 , -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 , -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 , -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) colvars: Done calculating fit gradients. colvars: Done calculating gradients of colvar "one". colvars: Done calculating colvar "one". colvars: Calculating colvar "one"'s properties. -colvars: Colvar "one" has value ( -2.75375163222155e-01 , -1.88018998907846e-02 , 9.61152957671602e-01 ). +colvars: Colvar "one" has value ( -2.73073003055543e-01 , -1.84328428660908e-02 , 9.61816700471613e-01 ). colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 , 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 , 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 , 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 , 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 , 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 , 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 , 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 , 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 , 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 , 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 , 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 , 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 , 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 , 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 , 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 , -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 , 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 , 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 , 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 , -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 , -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 , -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 , -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 , -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 , -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 , -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 , -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 , -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 , -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 , -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 , -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 , -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 , -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 , -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 , -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 , -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 , -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 , -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 , -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 , -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 , -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 , -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. colvars: Updating collective variable biases. colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 colvars: Updating the harmonic bias "harmonic1". colvars: Done updating the restraint bias "harmonic1". -colvars: Current forces for the restraint bias "harmonic1": { ( 25.0255 , 2.32784 , -15.3195 ) }. +colvars: Current forces for the restraint bias "harmonic1": { ( 64.6761 , 6.46761 , 12.9352 ) }. colvars: Collecting forces from all biases. colvars: Communicating a force to colvar "one". -colvars: Adding biasing force ( 25.0255 , 2.32784 , -15.3195 ) to colvar "one". -colvars: Adding total bias energy: 43.319 +colvars: Adding biasing force ( 64.6761 , 6.46761 , 12.9352 ) to colvar "one". +colvars: Adding total bias energy: 54.5456 colvars: Updating the internal degrees of freedom of colvars (if they have any). colvars: Updating colvar "one". colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". colvars: Adding total colvar energy: 0 colvars: Communicating forces from the colvars to the atoms. colvars: Communicating forces from colvar "one". -colvars: Force to be applied: ( 25.0255 , 2.32784 , -15.3195 ) +colvars: Force to be applied: ( 64.6761 , 6.46761 , 12.9352 ) colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( -4.96845 , -0.498288 , -1.32901 ) -colvars: ( -4.26044 , -0.427282 , -1.13963 ) -colvars: ( -4.26044 , -0.427282 , -1.13963 ) -colvars: ( -5.67503 , -0.569152 , -1.51802 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( -5.14375 , -0.512863 , -1.36279 ) +colvars: ( -4.41077 , -0.43978 , -1.16859 ) +colvars: ( -4.41077 , -0.43978 , -1.16859 ) +colvars: ( -5.87527 , -0.5858 , -1.5566 ) colvars: Applying force on the fitting group of main group: -colvars: ( 0.879475 , 0.19746 , 0.589668 ) -colvars: ( 0.763537 , 0.265986 , 0.612876 ) -colvars: ( 0.746982 , 0.259979 , 0.595824 ) -colvars: ( 0.655758 , 0.265036 , 0.551074 ) -colvars: ( 0.64429 , 0.199281 , 0.45983 ) -colvars: ( 0.572374 , 0.339824 , 0.600655 ) -colvars: ( 0.469157 , 0.351888 , 0.558199 ) -colvars: ( 0.395198 , 0.446581 , 0.638748 ) -colvars: ( 0.389628 , 0.307523 , 0.456287 ) -colvars: ( 0.356411 , 0.265765 , 0.383765 ) -colvars: ( 0.360325 , 0.313246 , 0.447198 ) -colvars: ( 0.290847 , 0.270728 , 0.353316 ) -colvars: ( 0.263638 , 0.299906 , 0.37565 ) -colvars: ( 0.351185 , 0.175187 , 0.264019 ) -colvars: ( 0.294437 , 0.131791 , 0.176159 ) -colvars: ( 0.469888 , 0.140228 , 0.285653 ) -colvars: ( 0.540044 , 0.0511119 , 0.210158 ) -colvars: ( 0.665088 , 0.0322651 , 0.256135 ) -colvars: ( 0.549308 , 0.0189857 , 0.173935 ) -colvars: ( 0.534103 , -0.0453327 , 0.0824438 ) -colvars: ( 0.570338 , 0.0657203 , 0.246025 ) -colvars: ( 0.569843 , 0.0488962 , 0.22405 ) -colvars: ( 0.605925 , 0.112449 , 0.326288 ) -colvars: ( 0.449787 , 0.0516022 , 0.160062 ) -colvars: ( 0.443589 , -0.00393792 , 0.0849533 ) -colvars: ( 0.350868 , 0.115297 , 0.186605 ) -colvars: ( 0.230482 , 0.122188 , 0.127828 ) -colvars: ( 0.141642 , 0.205871 , 0.185814 ) -colvars: ( 0.202596 , 0.0497313 , 0.0187152 ) -colvars: ( 0.155318 , 0.0131637 , -0.0550156 ) -colvars: ( 0.234164 , 0.0257902 , 0.00558312 ) -colvars: ( 0.219976 , -0.0452463 , -0.0940002 ) -colvars: ( 0.25308 , -0.0471777 , -0.0778849 ) -colvars: ( 0.293149 , -0.129353 , -0.161338 ) -colvars: ( 0.250572 , -0.182194 , -0.253413 ) -colvars: ( 0.404953 , -0.143094 , -0.116219 ) -colvars: ( 0.480337 , -0.21694 , -0.169081 ) -colvars: ( 0.607428 , -0.21807 , -0.0991062 ) -colvars: ( 0.435549 , -0.222795 , -0.201805 ) -colvars: ( 0.441093 , -0.289959 , -0.285304 ) -colvars: ( 0.389008 , -0.151718 , -0.136303 ) -colvars: ( 0.337447 , -0.147029 , -0.159235 ) -colvars: ( 0.322088 , -0.0623854 , -0.0587106 ) -colvars: ( 0.218032 , -0.157051 , -0.239277 ) -colvars: ( 0.194937 , -0.199189 , -0.306599 ) -colvars: ( 0.0217305 , -0.203128 , -0.40903 ) -colvars: ( -0.0663289 , -0.221682 , -0.482451 ) -colvars: ( 0.118294 , -0.25063 , -0.416016 ) -colvars: ( 0.138196 , -0.117408 , -0.233025 ) -colvars: ( 0.0225668 , -0.122976 , -0.305196 ) -colvars: ( -0.0639655 , -0.0441802 , -0.252215 ) +colvars: ( 0.909017 , 0.20443 , 0.607544 ) +colvars: ( 0.789318 , 0.275132 , 0.631553 ) +colvars: ( 0.772123 , 0.269017 , 0.614048 ) +colvars: ( 0.678088 , 0.274001 , 0.567808 ) +colvars: ( 0.666238 , 0.206052 , 0.473678 ) +colvars: ( 0.59205 , 0.351153 , 0.618972 ) +colvars: ( 0.48554 , 0.363463 , 0.575179 ) +colvars: ( 0.409228 , 0.461198 , 0.658292 ) +colvars: ( 0.403378 , 0.317597 , 0.470111 ) +colvars: ( 0.369117 , 0.27438 , 0.395276 ) +colvars: ( 0.373041 , 0.323572 , 0.460815 ) +colvars: ( 0.301249 , 0.279631 , 0.364032 ) +colvars: ( 0.273071 , 0.309845 , 0.387158 ) +colvars: ( 0.363511 , 0.180995 , 0.27189 ) +colvars: ( 0.304919 , 0.136099 , 0.18127 ) +colvars: ( 0.486043 , 0.145005 , 0.294165 ) +colvars: ( 0.558446 , 0.0530113 , 0.216254 ) +colvars: ( 0.687506 , 0.0336974 , 0.263657 ) +colvars: ( 0.568092 , 0.0197369 , 0.178811 ) +colvars: ( 0.552385 , -0.0467322 , 0.0844263 ) +colvars: ( 0.589888 , 0.0679639 , 0.253115 ) +colvars: ( 0.589463 , 0.0504879 , 0.230375 ) +colvars: ( 0.626794 , 0.116114 , 0.335782 ) +colvars: ( 0.465543 , 0.0531392 , 0.164394 ) +colvars: ( 0.459168 , -0.0042856 , 0.0868822 ) +colvars: ( 0.36341 , 0.11887 , 0.191839 ) +colvars: ( 0.239134 , 0.12586 , 0.131246 ) +colvars: ( 0.147406 , 0.212258 , 0.191129 ) +colvars: ( 0.210277 , 0.0510297 , 0.0187322 ) +colvars: ( 0.161495 , 0.0131664 , -0.0573398 ) +colvars: ( 0.242776 , 0.026416 , 0.00523774 ) +colvars: ( 0.228057 , -0.0469302 , -0.0974483 ) +colvars: ( 0.262137 , -0.0487927 , -0.0807623 ) +colvars: ( 0.303616 , -0.133786 , -0.166976 ) +colvars: ( 0.259646 , -0.188419 , -0.261946 ) +colvars: ( 0.419071 , -0.147905 , -0.120502 ) +colvars: ( 0.496921 , -0.224164 , -0.175101 ) +colvars: ( 0.628144 , -0.22522 , -0.102978 ) +colvars: ( 0.450769 , -0.230349 , -0.20891 ) +colvars: ( 0.456495 , -0.299752 , -0.29507 ) +colvars: ( 0.402793 , -0.157023 , -0.141359 ) +colvars: ( 0.349646 , -0.152317 , -0.16506 ) +colvars: ( 0.333865 , -0.0649427 , -0.061391 ) +colvars: ( 0.226349 , -0.162778 , -0.247576 ) +colvars: ( 0.202543 , -0.206384 , -0.317056 ) +colvars: ( 0.0235368 , -0.21043 , -0.422507 ) +colvars: ( -0.0673859 , -0.22968 , -0.498209 ) +colvars: ( 0.12317 , -0.25936 , -0.429718 ) +colvars: ( 0.143874 , -0.121836 , -0.241042 ) +colvars: ( 0.0244801 , -0.127687 , -0.315435 ) +colvars: ( -0.0648778 , -0.0463245 , -0.260709 ) +colvars: Done applying force on the fitting group of main group: colvars: Communicating a colvar force from atom group to the MD engine. colvars: Applying force on main group : -colvars: ( 4.96845 , 0.498288 , 1.32901 ) -colvars: ( 4.26044 , 0.427282 , 1.13963 ) -colvars: ( 4.26044 , 0.427282 , 1.13963 ) -colvars: ( 5.67503 , 0.569152 , 1.51802 ) -colvars: Calculating fit forces. -colvars: Done calculating fit forces. +colvars: ( 5.14375 , 0.512863 , 1.36279 ) +colvars: ( 4.41077 , 0.43978 , 1.16859 ) +colvars: ( 4.41077 , 0.43978 , 1.16859 ) +colvars: ( 5.87527 , 0.5858 , 1.5566 ) colvars: Applying force on the fitting group of main group: -colvars: ( -0.605283 , -0.0814713 , -0.343245 ) -colvars: ( -0.546104 , -0.164667 , -0.30914 ) -colvars: ( -0.493093 , -0.142383 , -0.249407 ) -colvars: ( -0.511271 , -0.191956 , -0.28253 ) -colvars: ( -0.501624 , -0.132316 , -0.254904 ) -colvars: ( -0.490404 , -0.284682 , -0.289614 ) -colvars: ( -0.462304 , -0.324985 , -0.273661 ) -colvars: ( -0.444078 , -0.433233 , -0.288065 ) -colvars: ( -0.399548 , -0.288853 , -0.200008 ) -colvars: ( -0.397029 , -0.263067 , -0.189715 ) -colvars: ( -0.347989 , -0.283073 , -0.146701 ) -colvars: ( -0.287244 , -0.245451 , -0.0746108 ) -colvars: ( -0.236282 , -0.260492 , -0.028178 ) -colvars: ( -0.304062 , -0.141317 , -0.0600384 ) -colvars: ( -0.274171 , -0.111421 , -0.0211333 ) -colvars: ( -0.354625 , -0.0838134 , -0.0932714 ) -colvars: ( -0.378549 , 0.0152802 , -0.0873257 ) -colvars: ( -0.424126 , 0.0628556 , -0.118566 ) -colvars: ( -0.418788 , 0.0305061 , -0.122979 ) -colvars: ( -0.407511 , 0.0880463 , -0.0943553 ) -colvars: ( -0.465241 , -0.0242249 , -0.185934 ) -colvars: ( -0.502599 , -0.0256335 , -0.22372 ) -colvars: ( -0.554309 , -0.0919531 , -0.295426 ) -colvars: ( -0.454677 , -0.0554227 , -0.184774 ) -colvars: ( -0.462572 , -0.0107479 , -0.179202 ) -colvars: ( -0.401943 , -0.130182 , -0.154572 ) -colvars: ( -0.348068 , -0.161285 , -0.110068 ) -colvars: ( -0.299731 , -0.252158 , -0.0891205 ) -colvars: ( -0.305274 , -0.0874775 , -0.0450216 ) -colvars: ( -0.294343 , -0.0683874 , -0.0283346 ) -colvars: ( -0.281387 , -0.0422725 , -0.0075047 ) -colvars: ( -0.243943 , 0.033409 , 0.0527565 ) -colvars: ( -0.218389 , 0.0598896 , 0.0862951 ) -colvars: ( -0.286484 , 0.120899 , 0.0365849 ) -colvars: ( -0.260601 , 0.163369 , 0.075273 ) -colvars: ( -0.353715 , 0.148861 , -0.022222 ) -colvars: ( -0.401272 , 0.225658 , -0.0466333 ) -colvars: ( -0.469366 , 0.247914 , -0.108023 ) -colvars: ( -0.417096 , 0.20587 , -0.0684236 ) -colvars: ( -0.421577 , 0.267415 , -0.0543518 ) -colvars: ( -0.425375 , 0.118515 , -0.103036 ) -colvars: ( -0.436835 , 0.0882998 , -0.123605 ) -colvars: ( -0.461361 , -0.00602419 , -0.176568 ) -colvars: ( -0.372987 , 0.0774436 , -0.0630242 ) -colvars: ( -0.378251 , 0.10422 , -0.0602171 ) -colvars: ( -0.212177 , 0.111369 , 0.108026 ) -colvars: ( -0.164834 , 0.113666 , 0.156066 ) -colvars: ( -0.234063 , 0.184075 , 0.108055 ) -colvars: ( -0.310811 , 0.0365359 , -0.0131747 ) -colvars: ( -0.246656 , 0.0232837 , 0.0469907 ) -colvars: ( -0.194349 , -0.0604355 , 0.0740647 ) +colvars: ( -0.625368 , -0.0844664 , -0.35261 ) +colvars: ( -0.564389 , -0.170315 , -0.317356 ) +colvars: ( -0.509508 , -0.147373 , -0.255728 ) +colvars: ( -0.528612 , -0.198378 , -0.290017 ) +colvars: ( -0.518649 , -0.136771 , -0.26169 ) +colvars: ( -0.507237 , -0.294051 , -0.297227 ) +colvars: ( -0.478424 , -0.335553 , -0.280849 ) +colvars: ( -0.459758 , -0.447272 , -0.295551 ) +colvars: ( -0.413631 , -0.298213 , -0.205031 ) +colvars: ( -0.411117 , -0.271521 , -0.194558 ) +colvars: ( -0.360291 , -0.292294 , -0.150021 ) +colvars: ( -0.297551 , -0.253428 , -0.0757988 ) +colvars: ( -0.244824 , -0.269019 , -0.0278188 ) +colvars: ( -0.314798 , -0.145936 , -0.0609419 ) +colvars: ( -0.283992 , -0.115013 , -0.0209648 ) +colvars: ( -0.366841 , -0.0866503 , -0.0952017 ) +colvars: ( -0.391423 , 0.0156314 , -0.0892212 ) +colvars: ( -0.438282 , 0.0646406 , -0.121372 ) +colvars: ( -0.433092 , 0.031424 , -0.126102 ) +colvars: ( -0.421451 , 0.090866 , -0.0967462 ) +colvars: ( -0.481165 , -0.0250553 , -0.190941 ) +colvars: ( -0.519878 , -0.0264336 , -0.229995 ) +colvars: ( -0.573354 , -0.0949003 , -0.303803 ) +colvars: ( -0.470575 , -0.0570841 , -0.189926 ) +colvars: ( -0.478772 , -0.0109091 , -0.184331 ) +colvars: ( -0.416224 , -0.134236 , -0.158693 ) +colvars: ( -0.360754 , -0.166255 , -0.112877 ) +colvars: ( -0.31093 , -0.26006 , -0.0911316 ) +colvars: ( -0.316492 , -0.0900499 , -0.0459571 ) +colvars: ( -0.305303 , -0.0702667 , -0.0288864 ) +colvars: ( -0.291645 , -0.0434603 , -0.00725477 ) +colvars: ( -0.252887 , 0.0346661 , 0.0547448 ) +colvars: ( -0.22631 , 0.0619076 , 0.0894017 ) +colvars: ( -0.296752 , 0.124994 , 0.0379104 ) +colvars: ( -0.270056 , 0.168889 , 0.0776549 ) +colvars: ( -0.366086 , 0.153811 , -0.0227007 ) +colvars: ( -0.415142 , 0.2331 , -0.0480107 ) +colvars: ( -0.485326 , 0.255996 , -0.111236 ) +colvars: ( -0.431671 , 0.212772 , -0.0705746 ) +colvars: ( -0.436297 , 0.276346 , -0.0562233 ) +colvars: ( -0.440388 , 0.122639 , -0.106169 ) +colvars: ( -0.452415 , 0.0915445 , -0.127452 ) +colvars: ( -0.477876 , -0.00581152 , -0.181915 ) +colvars: ( -0.386607 , 0.0804178 , -0.065083 ) +colvars: ( -0.392129 , 0.10813 , -0.0623269 ) +colvars: ( -0.220553 , 0.115492 , 0.111136 ) +colvars: ( -0.171755 , 0.117928 , 0.160573 ) +colvars: ( -0.242947 , 0.190464 , 0.111153 ) +colvars: ( -0.322416 , 0.0381802 , -0.0136105 ) +colvars: ( -0.256279 , 0.024571 , 0.0483461 ) +colvars: ( -0.202335 , -0.0618573 , 0.0764049 ) +colvars: Done applying force on the fitting group of main group: colvars: Done communicating forces from colvar "one". colvars: colvarmodule::analyze(), step = 40. colvars: colvarmodule::write_traj_files() @@ -6297,8 +10256,11 @@ colvars: Using colvarproxy_namd::output_stream() colvars: Writing formatted state for bias "harmonic1" colvars: colvarmodule::end_of_step(), step = 40. colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". colvars: ---------------------------------------------------------------------- -colvars: Step 40, atoms_new_colvar_forces = { ( -4.69425621928030e+00 , -3.82299293531605e-01 , -1.08259138985050e+00 ), ( -4.04301104341328e+00 , -3.25963208101038e-01 , -8.35893878661085e-01 ), ( -4.11595607698720e+00 , -3.54202091663012e-01 , -8.71086049655236e-01 ), ( -5.53236771588536e+00 , -5.02186714644302e-01 , -1.31309315973091e+00 ), ( 2.53888846719415e-01 , 1.17595525457716e-01 , 3.46417250400701e-01 ), ( 5.05041829897174e+00 , 5.53430773090023e-01 , 1.64005611225967e+00 ), ( 4.26729665699043e+00 , 4.54184594630911e-01 , 1.42416813087359e+00 ), ( -4.88806078491699e-02 , 1.33487489633205e-02 , 3.50683065016341e-01 ), ( 4.25052245994865e+00 , 4.45951931194706e-01 , 1.39590834641362e+00 ), ( 5.63441670782379e+00 , 5.71849738829720e-01 , 1.71207020437378e+00 ), ( 1.23366993044769e-02 , 3.01734792405036e-02 , 3.00496560792935e-01 ), ( 3.60330382822177e-03 , 2.52768315020174e-02 , 2.78704756676739e-01 ), ( 2.73561002156189e-02 , 3.94136106638130e-02 , 3.47472063103420e-01 ), ( 4.71232770937250e-02 , 3.38708564598179e-02 , 2.03980348396035e-01 ), ( 2.02658012733531e-02 , 2.03696695196413e-02 , 1.55025212261148e-01 ), ( 1.15263686220147e-01 , 5.64149706436544e-02 , 1.92381357469619e-01 ), ( 1.61495044376692e-01 , 6.63921394750813e-02 , 1.22832733602513e-01 ), ( 2.40962099296910e-01 , 9.51207430915074e-02 , 1.37569466093544e-01 ), ( 1.30519861097751e-01 , 4.94917657810325e-02 , 5.09564742764324e-02 ), ( 1.26591825707300e-01 , 4.27136321467979e-02 , -1.19114698073206e-02 ), ( 1.05097731844517e-01 , 4.14953960140019e-02 , 6.00908493172415e-02 ), ( 6.72434452314901e-02 , 2.32627372292199e-02 , 3.29411571107774e-04 ), ( 5.16160106797033e-02 , 2.04957380611913e-02 , 3.08614760964039e-02 ), ( -4.89011140648138e-03 , -3.82051532300732e-03 , -2.47122525670103e-02 ), ( -1.89827265351792e-02 , -1.46857755478728e-02 , -9.42487078872073e-02 ), ( -5.10748135423793e-02 , -1.48855039510186e-02 , 3.20336041855653e-02 ), ( -1.17586606502013e-01 , -3.90978081951123e-02 , 1.77598887431232e-02 ), ( -1.58089567227928e-01 , -4.62863930833078e-02 , 9.66939541792814e-02 ), ( -1.02678024282419e-01 , -3.77462019687896e-02 , -2.63063912756204e-02 ), ( -1.39025002292574e-01 , -5.52237131152498e-02 , -8.33501808145621e-02 ), ( -4.72226162435921e-02 , -1.64823154225552e-02 , -1.92158104703002e-03 ), ( -2.39663382418125e-02 , -1.18372933854927e-02 , -4.12437048147867e-02 ), ( 3.46912021407856e-02 , 1.27118771004866e-02 , 8.41013004242197e-03 ), ( 6.66481432988858e-03 , -8.45421436963140e-03 , -1.24753419439499e-01 ), ( -1.00289522664995e-02 , -1.88256908193125e-02 , -1.78140029209524e-01 ), ( 5.12383161124934e-02 , 5.76682664923539e-03 , -1.38441123385543e-01 ), ( 7.90646052522583e-02 , 8.71853503463832e-03 , -2.15714006408506e-01 ), ( 1.38062868973438e-01 , 2.98441641896576e-02 , -2.07129458099311e-01 ), ( 1.84528915679896e-02 , -1.69249601769574e-02 , -2.70228373715246e-01 ), ( 1.95162161633862e-02 , -2.25440771252065e-02 , -3.39656071605553e-01 ), ( -3.63669778407855e-02 , -3.32031259312454e-02 , -2.39338835403575e-01 ), ( -9.93874519156564e-02 , -5.87293132402941e-02 , -2.82840417994324e-01 ), ( -1.39272909769278e-01 , -6.84096349353490e-02 , -2.35278296104018e-01 ), ( -1.54955051902739e-01 , -7.96074177852305e-02 , -3.02301613111528e-01 ), ( -1.83313726057656e-01 , -9.49689547058241e-02 , -3.66816281783523e-01 ), ( -1.90446178428819e-01 , -9.17585877080269e-02 , -3.01003597891805e-01 ), ( -2.31162538711229e-01 , -1.08015703657244e-01 , -3.26385175995963e-01 ), ( -1.15769016831794e-01 , -6.65556151205041e-02 , -3.07960838121793e-01 ), ( -1.72614546231601e-01 , -8.08716967814934e-02 , -2.46199182186840e-01 ), ( -2.24089127527084e-01 , -9.96927216164915e-02 , -2.58205183976685e-01 ), ( -2.58314823991350e-01 , -1.04615743063521e-01 , -1.78150725600739e-01 ) } +colvars: Step 40, atoms_new_colvar_forces = { ( -4.86010500487513e+00 , -3.92899476781565e-01 , -1.10785721873104e+00 ), ( -4.18584012135942e+00 , -3.34962322561261e-01 , -8.54396583409615e-01 ), ( -4.26129258537055e+00 , -3.64157246411969e-01 , -8.90801999102965e-01 ), ( -5.72768189464099e+00 , -5.16518692575566e-01 , -1.34461147393970e+00 ), ( 2.62614933737386e-01 , 1.21643196582163e-01 , 3.58320228267059e-01 ), ( 5.22856653164363e+00 , 5.69964893972689e-01 , 1.68453660030878e+00 ), ( 4.41788419879669e+00 , 4.67689682026466e-01 , 1.46292282216087e+00 ), ( -5.05309252132559e-02 , 1.39257115269364e-02 , 3.62741493084848e-01 ), ( 4.40051564040493e+00 , 4.59164448844135e-01 , 1.43367269992625e+00 ), ( 5.83327082858468e+00 , 5.88658850729039e-01 , 1.75731846986772e+00 ), ( 1.27500039872741e-02 , 3.12783106080479e-02 , 3.10793732251512e-01 ), ( 3.69805211512170e-03 , 2.62025486681574e-02 , 2.88233477601792e-01 ), ( 2.82471623542027e-02 , 4.08261801951898e-02 , 3.59339489691045e-01 ), ( 4.87126546060106e-02 , 3.50583306953602e-02 , 2.10947915841365e-01 ), ( 2.09264208987602e-02 , 2.10868507446829e-02 , 1.60305126941948e-01 ), ( 1.19201158802730e-01 , 5.83549571087401e-02 , 1.98963090804411e-01 ), ( 1.67022234450991e-01 , 6.86426967088851e-02 , 1.27033160175296e-01 ), ( 2.49223370441218e-01 , 9.83379500123318e-02 , 1.42284699220159e-01 ), ( 1.35000114916889e-01 , 5.11609815544152e-02 , 5.27083545084148e-02 ), ( 1.30933975271148e-01 , 4.41337908242187e-02 , -1.23198772055619e-02 ), ( 1.08723128264765e-01 , 4.29086581040898e-02 , 6.21748839294782e-02 ), ( 6.95855807919954e-02 , 2.40542268943943e-02 , 3.80060658965092e-04 ), ( 5.34401709694688e-02 , 2.12133864559464e-02 , 3.19793165209076e-02 ), ( -5.03187648228520e-03 , -3.94494665803143e-03 , -2.55313892881111e-02 ), ( -1.96042067736224e-02 , -1.51947328419243e-02 , -9.74491528415509e-02 ), ( -5.28140476899892e-02 , -1.53652878309355e-02 , 3.31463057759504e-02 ), ( -1.21619293554667e-01 , -4.03951395042048e-02 , 1.83695676879411e-02 ), ( -1.63523861300645e-01 , -4.78017821499703e-02 , 9.99976808830524e-02 ), ( -1.06214451109011e-01 , -3.90202332767928e-02 , -2.72249337865024e-02 ), ( -1.43808766912087e-01 , -5.71003535725851e-02 , -8.62262480146662e-02 ), ( -4.88691380386168e-02 , -1.70443490260226e-02 , -2.01703003472374e-03 ), ( -2.48292115802329e-02 , -1.22641177815657e-02 , -4.27034572360182e-02 ), ( 3.58272815045241e-02 , 1.31149152258394e-02 , 8.63941847240535e-03 ), ( 6.86386165582842e-03 , -8.79191657407025e-03 , -1.29065382176512e-01 ), ( -1.04095724900709e-02 , -1.95306413489265e-02 , -1.84291124342117e-01 ), ( 5.29844218525999e-02 , 5.90661814191340e-03 , -1.43202552188758e-01 ), ( 8.17782812299959e-02 , 8.93602219704753e-03 , -2.23111662214294e-01 ), ( 1.42817498250238e-01 , 3.07766230419280e-02 , -2.14213517111727e-01 ), ( 1.90975872719274e-02 , -1.75768123337172e-02 , -2.79485105483733e-01 ), ( 2.01987133536012e-02 , -2.34065200978483e-02 , -3.51292930914822e-01 ), ( -3.75954707463619e-02 , -3.43840123366401e-02 , -2.47528167059879e-01 ), ( -1.02768759885532e-01 , -6.07723846491564e-02 , -2.92512391019645e-01 ), ( -1.44011086499806e-01 , -7.07542340805300e-02 , -2.43306450783254e-01 ), ( -1.60258548256346e-01 , -8.23604570604809e-02 , -3.12659079784094e-01 ), ( -1.89585960104167e-01 , -9.82545854569550e-02 , -3.79382475231133e-01 ), ( -1.97016290220132e-01 , -9.49380420681069e-02 , -3.11370803813321e-01 ), ( -2.39141293687696e-01 , -1.11751250135048e-01 , -3.37636382369183e-01 ), ( -1.19776646754559e-01 , -6.88966356000031e-02 , -3.18565456170577e-01 ), ( -1.78542464818243e-01 , -8.36558831046468e-02 , -2.54652758549066e-01 ), ( -2.31799270250000e-01 , -1.03115915983205e-01 , -2.67088981711532e-01 ), ( -2.67213057543186e-01 , -1.08181859060886e-01 , -1.84304010066073e-01 ) } colvars: ---------------------------------------------------------------------- colvars: Step 40, atom_groups_new_colvar_forces = colvars: ---------------------------------------------------------------------- diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped index defd4fc4a..946d37af4 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,22 @@ configuration { colvar { name one - x ( -0.27537516322216 , -0.018801899890785 , 0.9611529576716 ) + x ( -0.27307300305554 , -0.018432842866091 , 0.96181670047161 ) +} + +colvar { + name group1 + x ( 8.1149547406244 , 0.039025973728438 , -0.6883939751094 , 6.7853094963308 , -0.62690773735816 , -0.48927248081367 , 6.0570819222823 , -0.3204984026977 , 0.79983438945443 , 4.8474758357047 , -0.15265005661356 , 0.78539193495272 ) +} + +colvar { + name group2 + x ( 6.7569195116675 , -0.31726772022198 , 1.9526785556885 , 6.1045094882016 , -0.24248172346477 , 3.2933184881202 , 5.3025069575603 , 1.0670731950028 , 3.3674918263121 , 4.1976525207215 , 1.0093055490164 , 3.8928528477676 ) +} + +colvar { + name fitting_group1 + x ( 8.1149547406244 , 0.039025973728438 , -0.6883939751094 , 6.7853094963308 , -0.62690773735816 , -0.48927248081367 , 7.010066781814 , -2.1149340872622 , -0.79871868234416 , 6.0570819222823 , -0.3204984026977 , 0.79983438945443 , 4.8474758357047 , -0.15265005661356 , 0.78539193495272 , 6.7569195116675 , -0.31726772022198 , 1.9526785556885 , 6.1045094882016 , -0.24248172346477 , 3.2933184881202 , 7.1490449752629 , -0.37058757233971 , 4.4399196197799 , 5.3025069575603 , 1.0670731950028 , 3.3674918263121 , 4.1976525207215 , 1.0093055490164 , 3.8928528477676 , 5.8493891412547 , 2.259999877851 , 2.9491637404497 , 5.1330973450144 , 3.5061330235678 , 2.8406622822242 , 6.2433790945366 , 4.4147409098211 , 2.2802690895513 , 3.8716714078007 , 3.6077840924352 , 1.9988572259436 , 2.8683227898067 , 4.1497902846583 , 2.4027808174741 , 3.9037961131111 , 3.1123185616756 , 0.8010841726464 , 2.7470790455553 , 3.1841148212122 , -0.09556990656272 , 3.1556634001638 , 2.6652943276712 , -1.5007967041156 , 1.6653262429665 , 2.3057555454737 , 0.47631763100361 , 0.44560810177051 , 2.6098182262123 , 0.40186304979305 , 2.0193190829342 , 1.1206659142018 , 1.0133417993941 , 1.3011677521639 , 0.1623577837318 , 1.6718961286692 , 2.103628243052 , -1.0926954426178 , 2.0161544932039 , 0.56812713179284 , 0.64424808838615 , 2.935622587854 , -0.61713346155249 , 0.3587424368388 , 3.2213863603549 , 1.3004699607377 , 1.4427613668925 , 3.7893374633666 , 0.92231170569283 , 1.9970437445982 , 5.0730168340908 , 2.022467523431 , 2.7927865699648 , 5.7303382474983 , -0.34750321982683 , 2.8807589865422 , 4.916061499821 , -1.1169478598693 , 3.072210023565 , 5.8954444765507 , -0.49953629598684 , 3.4448766860833 , 3.6917631985707 , -1.4683449913708 , 4.4816678223792 , 3.3949326423562 , -0.78376920558253 , 5.504389713531 , 2.4888239527826 , -2.7579909921335 , 3.9249525693942 , 2.7161928948191 , -3.7813569682913 , 4.6155151357506 , 2.794589224195 , -2.7209505257799 , 2.6577136814415 , 2.3296106064383 , -3.8266527670617 , 1.7696270105557 , 1.9735601737672 , -3.3289525461208 , 0.93034839318414 , 0.74788408689063 , -4.277696268604 , 1.0119162061298 , 3.2188841996731 , -5.4037207127892 , 0.69441249408377 , 3.3736636976958 , -3.3478383186157 , 0.69487591672332 , 4.1796284021595 , -3.6639337506895 , 0.054701081155268 , 5.4283456514115 , -2.3006455799535 , -0.25065988383128 , 6.1423365190653 , -4.4779626075131 , 0.99178687455206 , 6.416269786801 , -5.3549594957076 , 0.50489047118977 , 7.1544211891747 , -6.2654163308751 , 3.5984702819319 , 6.8193217922678 , -7.0644511389725 , 4.2856069056051 , 7.5042704740056 , -6.6100994654206 , 3.1823589471874 , 5.5688401074549 , -4.1392877914223 , 2.2555968316084 , 6.4286170126916 , -4.7922326877167 , 3.2624257062394 , 7.1680690755413 , -4.012470999143 , 4.6600285619364 , 7.2826034153248 ) } restraint { diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj index dd9505092..b1cdf8add 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ -# step one fa_one - 20 ( -3.04541710533304e-01 , -1.99152414877620e-04 , 9.52498979990932e-01 ) ( 2.56088356696367e+01 , 1.95578319419462e+00 , -1.51463793080245e+01 ) - 21 ( -3.03300920671651e-01 , -1.24565183823531e-03 , 9.52894012926530e-01 ) ( 2.55840198724037e+01 , 1.97671318266177e+00 , -1.51542799667365e+01 ) - 22 ( -3.02208395802458e-01 , -2.38936177499928e-03 , 9.53238887402740e-01 ) ( 2.55621693750198e+01 , 1.99958738139705e+00 , -1.51611774562607e+01 ) - 23 ( -3.01235983053210e-01 , -3.61953298784803e-03 , 9.53542752840645e-01 ) ( 2.55427211200349e+01 , 2.02419080565403e+00 , -1.51672547650188e+01 ) - 24 ( -3.00350438745275e-01 , -4.92097847437880e-03 , 9.53816228587234e-01 ) ( 2.55250102338762e+01 , 2.05021971538464e+00 , -1.51727242799506e+01 ) - 25 ( -2.99515551202827e-01 , -6.27415312265916e-03 , 9.54070788563543e-01 ) ( 2.55083124830272e+01 , 2.07728320835025e+00 , -1.51778154794767e+01 ) - 26 ( -2.98694198360127e-01 , -7.65591975074812e-03 , 9.54318166419759e-01 ) ( 2.54918854261732e+01 , 2.10491854091203e+00 , -1.51827630366011e+01 ) - 27 ( -2.97850201345680e-01 , -9.04087721924012e-03 , 9.54569808917841e-01 ) ( 2.54750054858843e+01 , 2.13261769028187e+00 , -1.51877958865627e+01 ) - 28 ( -2.96949879926448e-01 , -1.04029858363134e-02 , 9.54836397870000e-01 ) ( 2.54569990574996e+01 , 2.15985986262333e+00 , -1.51931276656059e+01 ) - 29 ( -2.95963250214387e-01 , -1.17171742424022e-02 , 9.55127458693503e-01 ) ( 2.54372664632584e+01 , 2.18614363074511e+00 , -1.51989488820759e+01 ) - 30 ( -2.94864820949374e-01 , -1.29606427096605e-02 , 9.55451076249876e-01 ) ( 2.54152978779581e+01 , 2.21101300009028e+00 , -1.52054212332034e+01 ) - 31 ( -2.93633996751009e-01 , -1.41137029745784e-02 , 9.55813726277445e-01 ) ( 2.53906813939908e+01 , 2.23407420538864e+00 , -1.52126742337548e+01 ) - 32 ( -2.92255140925596e-01 , -1.51601432225139e-02 , 9.56220216613324e-01 ) ( 2.53631042774826e+01 , 2.25500301034735e+00 , -1.52208040404724e+01 ) - 33 ( -2.90717372797486e-01 , -1.60872298396465e-02 , 9.56673721908266e-01 ) ( 2.53323489149204e+01 , 2.27354474269000e+00 , -1.52298741463712e+01 ) - 34 ( -2.89014188887543e-01 , -1.68855035770422e-02 , 9.57175886862297e-01 ) ( 2.52982852367215e+01 , 2.28951021743791e+00 , -1.52399174454518e+01 ) - 35 ( -2.87142969394406e-01 , -1.75485194704134e-02 , 9.57726978105848e-01 ) ( 2.52608608468588e+01 , 2.30277053530534e+00 , -1.52509392703228e+01 ) - 36 ( -2.85104418391494e-01 , -1.80726295704393e-02 , 9.58326066990801e-01 ) ( 2.52200898268005e+01 , 2.31325273730585e+00 , -1.52629210480219e+01 ) - 37 ( -2.82901971968914e-01 , -1.84568715824041e-02 , 9.58971229050950e-01 ) ( 2.51760408983489e+01 , 2.32093757754515e+00 , -1.52758242892249e+01 ) - 38 ( -2.80541218552965e-01 , -1.87029804430822e-02 , 9.59659743458776e-01 ) ( 2.51288258300300e+01 , 2.32585975475871e+00 , -1.52895945773814e+01 ) - 39 ( -2.78029409440391e-01 , -1.88154958979349e-02 , 9.60388267629474e-01 ) ( 2.50785896477785e+01 , 2.32811006385576e+00 , -1.53041650607953e+01 ) - 40 ( -2.75375163222155e-01 , -1.88018998907846e-02 , 9.61152957671602e-01 ) ( 2.50255047234138e+01 , 2.32783814371276e+00 , -1.53194588616379e+01 ) +# step one fa_one group1 group2 fitting_group1 E_harmonic1 + 20 ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ) ( 6.60362557644092e+01 , 6.60362557644092e+00 , 1.32072511528818e+01 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ) ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) 5.65386573831414e+01 + 21 ( -3.02299978352974e-01 , -1.10908187249818e-03 , 9.53212197270467e-01 ) ( 6.59775965870217e+01 , 6.59775965870217e+00 , 1.31955193174043e+01 ) ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ) ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ) ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 , 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 , 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 , 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 , 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 , 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 , 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 , 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 , 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 , 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 , 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 , 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 , 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 , 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 , 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 , 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 , -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 , 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 , 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 , 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 , -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 , -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 , -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 , -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 , -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 , -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 , -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 , -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 , -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 , -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 , -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 , -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 , -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 , -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 , -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 , -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 , -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 , -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 , -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 , -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 , -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 , -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 , -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ) 5.64539548629295e+01 + 22 ( -3.01144188109486e-01 , -2.24212177402314e-03 , 9.53575980642250e-01 ) ( 6.59267215416616e+01 , 6.59267215416616e+00 , 1.31853443083323e+01 ) ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ) ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ) ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 , 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 , 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 , 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 , 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 , 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 , 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 , 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 , 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 , 3.06614504628802e+00 , 2.69347985600063e+00 , 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-2.73073003055543e-01 , -1.84328428660908e-02 , 9.61816700471613e-01 ) ( 6.46761268758138e+01 , 6.46761268758138e+00 , 1.29352253751628e+01 ) ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ) ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ) ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 , 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 , 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 , 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 , 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 , 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 , 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 , 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 , 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 , 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 , 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 , 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 , 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 , 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 , 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 , 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 , -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 , 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 , 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 , 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 , -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 , -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 , -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 , -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 , -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 , -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 , -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 , -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 , -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 , -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 , -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 , -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 , -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 , -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 , -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 , -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 , -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 , -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 , -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 , -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 , -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 , -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 , -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ) 5.45455543522492e+01 diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py new file mode 100644 index 000000000..86b7620e4 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py @@ -0,0 +1,262 @@ +#!/usr/bin/env python3 +import torch +import re +import numpy as np + +torch.set_printoptions(precision=10) + + +# function to extract grad +def set_grad(var): + def hook(grad): + var.grad = grad + return hook + +mass1 = torch.tensor([14.0070, 12.0110, 12.0110, 15.999], dtype=torch.float64) + +mass2 = torch.tensor([14.0070, 12.0110, 12.0110, 15.999], dtype=torch.float64) + +ref_fitting_group = torch.tensor( + [[ 5.69469 , -1.80418 , -5.22382 ], + [ 6.37169 , -1.08118 , -4.10382 ], + [ 6.61169 , 0.365824 , -4.58082 ], + [ 5.62269 , -1.09518 , -2.77982 ], + [ 4.39969 , -0.986176 , -2.72882 ], + [ 6.36569 , -1.21018 , -1.66282 ], + [ 5.83469 , -1.37018 , -0.318824 ], + [ 7.00969 , -1.45018 , 0.678176 ], + [ 4.84269 , -0.296176 , 0.126176 ], + [ 3.77369 , -0.596176 , 0.648176 ], + [ 5.15669 , 0.991824 , -0.113824 ], + [ 4.27869 , 2.10682 , 0.190176 ], + [ 5.03669 , 3.42282 , -0.0748235 ], + [ 2.96669 , 2.09282 , -0.596824 ], + [ 1.89969 , 2.39182 , -0.0678235 ], + [ 3.01469 , 1.69682 , -1.88382 ], + [ 1.84869 , 1.57082 , -2.73482 ], + [ 2.30269 , 1.40782 , -4.19882 ], + [ 0.962686 , 0.399824 , -2.31982 ], + [-0.255314 , 0.522824 , -2.22882 ], + [ 1.57569 , -0.758176 , -2.00882 ], + [ 0.900686 , -1.92218 , -1.46882 ], + [ 1.91969 , -3.07218 , -1.33582 ], + [ 0.223686 , -1.65518 , -0.123824 ], + [-0.930314 , -2.01818 , 0.0891765 ], + [ 0.918686 , -0.964176 , 0.800176 ], + [ 0.372686 , -0.514176 , 2.06618 ], + [ 1.49069 , 0.164824 , 2.88418 ], + [-0.814314 , 0.435824 , 1.92118 ], + [-1.84631 , 0.257824 , 2.56118 ], + [-0.707314 , 1.45482 , 1.04518 ], + [-1.78431 , 2.37982 , 0.745176 ], + [-1.24331 , 3.48882 , -0.178824 ], + [-3.00931 , 1.72082 , 0.109176 ], + [-4.14731 , 2.02882 , 0.455176 ], + [-2.80331 , 0.769824 , -0.821824 ], + [-3.86731 , -0.00917647, -1.42282 ], + [-3.28731 , -0.820176 , -2.59882 ], + [-4.57231 , -0.946176 , -0.440824 ], + [-5.78931 , -1.10018 , -0.475824 ], + [-3.81431 , -1.58718 , 0.469176 ], + [-4.35131 , -2.44718 , 1.50418 ], + [-3.19331 , -3.25818 , 2.12018 ], + [-5.10031 , -1.70118 , 2.61018 ], + [-6.15131 , -2.13818 , 3.07218 ], + [-6.33131 , 1.19882 , 3.62918 ], + [-7.08531 , 1.74482 , 4.44018 ], + [-6.45431 , 1.44382 , 2.30618 ], + [-4.56431 , -0.557176 , 3.07518 ], + [-5.19131 , 0.240824 , 4.11318 ], + [-4.10131 , 1.05882 , 4.83518 ]], dtype=torch.float64) + +# fitting_group = atom_positions +# main_group = atom_positions[[0, 1, 2, 3]] + + +def get_optimal_rotation(fitting_atoms: torch.tensor, reference_atoms: torch.tensor): + fitting_atoms_centered = fitting_atoms - fitting_atoms.mean(dim=0) + reference_atoms_centered = reference_atoms - reference_atoms.mean(dim=0) + mat_R = torch.linalg.matmul(fitting_atoms_centered.T, reference_atoms_centered) + F00 = mat_R[0][0] + mat_R[1][1] + mat_R[2][2] + F01 = mat_R[1][2] - mat_R[2][1] + F02 = mat_R[2][0] - mat_R[0][2] + F03 = mat_R[0][1] - mat_R[1][0] + F10 = F01 + F11 = mat_R[0][0] - mat_R[1][1] - mat_R[2][2] + F12 = mat_R[0][1] + mat_R[1][0] + F13 = mat_R[0][2] + mat_R[2][0] + F20 = F02 + F21 = F12 + F22 = -mat_R[0][0] + mat_R[1][1] - mat_R[2][2] + F23 = mat_R[1][2] + mat_R[2][1] + F30 = F03 + F31 = F13 + F32 = F23 + F33 = -mat_R[0][0] - mat_R[1][1] + mat_R[2][2] + row0 = torch.stack((F00, F01, F02, F03)) + row1 = torch.stack((F10, F11, F12, F13)) + row2 = torch.stack((F20, F21, F22, F23)) + row3 = torch.stack((F30, F31, F32, F33)) + F = torch.stack((row0, row1, row2, row3)) + w, v = torch.linalg.eigh(F) + q = v[:, -1] + q.register_hook(set_grad(q)) + R00 = q[0] * q[0] + q[1] * q[1] - q[2] * q[2] - q[3] * q[3] + R01 = 2.0 * (q[1] * q[2] - q[0] * q[3]) + R02 = 2.0 * (q[1] * q[3] + q[0] * q[2]) + R10 = 2.0 * (q[1] * q[2] + q[0] * q[3]) + R11 = q[0] * q[0] - q[1] * q[1] + q[2] * q[2] - q[3] * q[3] + R12 = 2.0 * (q[2] * q[3] - q[0] * q[1]) + R20 = 2.0 * (q[1] * q[3] - q[0] * q[2]) + R21 = 2.0 * (q[2] * q[3] + q[0] * q[1]) + R22 = q[0] * q[0] - q[1] * q[1] - q[2] * q[2] + q[3] * q[3] + row0 = torch.stack((R00, R01, R02)) + row1 = torch.stack((R10, R11, R12)) + row2 = torch.stack((R20, R21, R22)) + R = torch.stack((row0, row1, row2)) + return w, v, R, q + + +def center_of_mass(pos, mass): + return torch.sum(pos * mass[:, None], dim=0) / torch.sum(mass) + + +def read_data_from_traj(filename): + group1_positions = [] + group2_positions = [] + fitting_group1_positions = [] + fitting_group2_positions = [] + forces = [] + with open(filename, 'r') as f_input: + for line in f_input: + s = line.strip() + if s.startswith('#'): + # skip comment lines + continue + if len(s) > 0: + # skip empty lines + # match the data in parentheses + result = re.findall(r'\(([^)]+)\)', s) + # get the force applied on the orientation + forces.append(torch.tensor(list(map(float, result[1].split(','))), dtype=torch.float64)) + # get the group1 position + tmp = np.array(list(map(float, result[2].split(',')))).reshape(-1, 3) + group1_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + # get the group2 position + tmp = np.array(list(map(float, result[3].split(',')))).reshape(-1, 3) + group2_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + # get the fitting group1 position + tmp = np.array(list(map(float, result[4].split(',')))).reshape(-1, 3) + fitting_group1_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + fitting_group2_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + return forces, group1_positions, group2_positions, fitting_group1_positions, fitting_group2_positions + + +# Use Colvars definition: the distance between two unit vectors is angle between them +def dist2_distance_dir(v1, v2): + v1_normalized = v1 / torch.linalg.norm(v1) + v2_normalized = v2 / torch.linalg.norm(v2) + dist = torch.acos(torch.sum(v1_normalized * v2_normalized)) + return dist * dist + + +def scan_force_from_log(filename): + main_group_forces = [] + fitting_group_forces = [] + with open(filename, 'r') as f_input: + new_main_group_started = False + main_group_force = [] + new_fitting_group_started = False + fitting_group_force = [] + for line in f_input: + if new_main_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + main_group_force.append(list(map(float, result[0].split(',')))) + else: + new_main_group_started = False + main_group_forces.append(np.array(main_group_force)) + main_group_force = [] + if new_fitting_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + fitting_group_force.append(list(map(float, result[0].split(',')))) + else: + new_fitting_group_started = False + fitting_group_forces.append(np.array(fitting_group_force)) + fitting_group_force = [] + if line.startswith('colvars: Applying force on the fitting group of main group:'): + new_fitting_group_started = True + continue + if line.startswith('colvars: Applying force on main group'): + new_main_group_started = True + continue + return main_group_forces, fitting_group_forces + + +def test(group1, group2, fitting_group_1, fitting_group_2): + # Fit group 1 + w1, v1, R1, q1 = get_optimal_rotation(fitting_group_1, ref_fitting_group) + rpg_cog1 = fitting_group_1.mean(dim=0) + # group1_c = group1.mean(dim=0) + group1_centered = group1 - rpg_cog1 + group1_rotated = (R1 @ group1_centered.T).T + # Fit group 2 + w2, v2, R2, q2 = get_optimal_rotation(fitting_group_2, ref_fitting_group) + rpg_cog2 = fitting_group_2.mean(dim=0) + # group2_c = group2.mean(dim=0) + group2_centered = group2 - rpg_cog2 + group2_rotated = (R2 @ group2_centered.T).T + # distanceDir + c2 = center_of_mass(group2_rotated, mass2) + c1 = center_of_mass(group1_rotated, mass1) + d = c2 - c1 + d_dir = d / torch.linalg.norm(d) + ref = torch.tensor([1.0, 0.1, 0.2], dtype=torch.float64) + energy = 0.5 * 10.0 * dist2_distance_dir(d_dir, ref) / 0.25 + energy.backward(retain_graph=True) + return -group1.grad.cpu().detach().numpy(), -group2.grad.cpu().detach().numpy(), \ + -fitting_group_1.grad.cpu().detach().numpy(), -fitting_group_2.grad.cpu().detach().numpy() + + +if __name__ == '__main__': + print('Compare AutoDiff/test.colvars.traj and AutoDiff/test.colvars.out') + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.colvars.out') + group1_forces_colvars = main_group_forces_colvars[::2] + group2_forces_colvars = main_group_forces_colvars[1::2] + fitting_group1_forces_colvars = fitting_group_forces_colvars[::2] + fitting_group2_forces_colvars = fitting_group_forces_colvars[1::2] + # read the positions from .colvars.traj + _, group1_positions, group2_positions, fitting_group1_positions, fitting_group2_positions = read_data_from_traj('AutoDiff/test.colvars.traj') + for i in range(len(group1_positions)): + # calculate forces from pytorch + gf1_pytorch, gf2_pytorch, fgf1_pytorch, fgf2_pytorch = test( + group1_positions[i], group2_positions[i], fitting_group1_positions[i], fitting_group2_positions[i]) + # error with respect to colvars + error_group1 = np.mean(np.abs(group1_forces_colvars[i] - gf1_pytorch) / np.abs(gf1_pytorch)) + error_group2 = np.mean(np.abs(group2_forces_colvars[i] - gf2_pytorch) / np.abs(gf2_pytorch)) + error_fitting_group1 = np.mean(np.abs(fitting_group1_forces_colvars[i] - fgf1_pytorch) / np.abs(fgf1_pytorch)) + error_fitting_group2 = np.mean(np.abs(fitting_group2_forces_colvars[i] - fgf2_pytorch) / np.abs(fgf2_pytorch)) + print(f'Error of forces: group1 = {error_group1:12.5e}, group2 = {error_group2:12.5e}, fitting_group1 = {error_fitting_group1:12.5e}, fitting_group2 = {error_fitting_group2:12.5e}') + + # Do the same thing with the restart file + print('Compare AutoDiff/test.restart.colvars.traj and AutoDiff/test.restart.colvars.out') + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.restart.colvars.out') + group1_forces_colvars = main_group_forces_colvars[::2] + group2_forces_colvars = main_group_forces_colvars[1::2] + fitting_group1_forces_colvars = fitting_group_forces_colvars[::2] + fitting_group2_forces_colvars = fitting_group_forces_colvars[1::2] + # read the positions from .colvars.traj + _, group1_positions, group2_positions, fitting_group1_positions, fitting_group2_positions = read_data_from_traj('AutoDiff/test.restart.colvars.traj') + for i in range(len(group1_positions)): + # calculate forces from pytorch + gf1_pytorch, gf2_pytorch, fgf1_pytorch, fgf2_pytorch = test( + group1_positions[i], group2_positions[i], fitting_group1_positions[i], fitting_group2_positions[i]) + # error with respect to colvars + error_group1 = np.mean(np.abs(group1_forces_colvars[i] - gf1_pytorch) / np.abs(gf1_pytorch)) + error_group2 = np.mean(np.abs(group2_forces_colvars[i] - gf2_pytorch) / np.abs(gf2_pytorch)) + error_fitting_group1 = np.mean(np.abs(fitting_group1_forces_colvars[i] - fgf1_pytorch) / np.abs(fgf1_pytorch)) + error_fitting_group2 = np.mean(np.abs(fitting_group2_forces_colvars[i] - fgf2_pytorch) / np.abs(fgf2_pytorch)) + print(f'Error of forces: group1 = {error_group1:12.5e}, group2 = {error_group2:12.5e}, fitting_group1 = {error_fitting_group1:12.5e}, fitting_group2 = {error_fitting_group2:12.5e}') diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt index e1d311c69..73471c571 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt @@ -1,3 +1,3 @@ Info: NAMD 3.1alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2024-06-04. -colvars: Using NAMD interface, version "2023-12-05". +colvars: Initializing the collective variables module, version 2024-10-11. +colvars: Using NAMD interface, version "2024-10-05". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in index dff68dbf5..59aca6398 100644 --- a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in @@ -15,7 +15,6 @@ colvar { indexGroup group1 centerToReference yes rotateToReference yes - #enableFitGradients no fittingGroup { indexGroup heavy_atoms } @@ -25,17 +24,44 @@ colvar { indexGroup group2 centerToReference yes rotateToReference yes - #enableFitGradients no fittingGroup { indexGroup heavy_atoms } refPositionsFile heavy_atoms_refpos.xyz } } -} +} + +colvar { + name group1 + cartesian { + atoms { + indexGroup group1 + } + } +} + +colvar { + name group2 + cartesian { + atoms { + indexGroup group2 + } + } +} + +colvar { + name fitting_group1 + cartesian { + atoms { + indexGroup heavy_atoms + } + } +} harmonic { colvars one centers (1.0, 0.1, 0.2) forceConstant 10.0 + outputEnergy on } From a395a04973c143ca49dcfb84d827fa2d14943dd8 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 11 Oct 2024 16:45:15 -0500 Subject: [PATCH 13/14] chore: add more comments about the group_forces in atom_group For the time being this field is only used for storing the main group forces of non-scalable components with fitting groups. --- src/colvaratoms.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/colvaratoms.h b/src/colvaratoms.h index bb1c10ed5..1493046e0 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -257,7 +257,9 @@ class colvarmodule::atom_group /// \brief Index in the colvarproxy arrays (if the group is scalable) int index; - /// \brief The forces acting on the group atoms (stored mainly used for calculating the fitting group forces) + /// \brief The temporary forces acting on the main group atoms. + /// Currently this is only used for calculating the fitting group forces for + /// non-scalar components. std::vector group_forces; public: From 748cb510e35e169fbc255d15445e2945709b7632 Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 11 Oct 2024 16:59:41 -0500 Subject: [PATCH 14/14] refactor: revert cvm::atom_group::do_feature_side_effects --- src/colvaratoms.cpp | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index 917e0397a..745cb0328 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -921,6 +921,15 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) void cvm::atom_group::do_feature_side_effects(int id) { + // If enabled features are changed upstream, the features below should be refreshed + switch (id) { + case f_ag_fit_gradients: + if (is_enabled(f_ag_center) || is_enabled(f_ag_rotate)) { + atom_group *group_for_fit = fitting_group ? fitting_group : this; + group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::atom_pos(0.0, 0.0, 0.0)); + } + break; + } } @@ -1209,14 +1218,9 @@ void cvm::atom_group::calc_fit_gradients() cvm::log("Calculating fit gradients.\n"); cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; - if (group_for_fit->fit_gradients.size() != group_for_fit->size()) { - group_for_fit->fit_gradients.assign(group_for_fit->size(), 0); - } else { - std::fill(group_for_fit->fit_gradients.begin(), - group_for_fit->fit_gradients.end(), 0); - } + auto accessor_main = [this](size_t i){return atoms[i].grad;}; - auto accessor_fitting = [&group_for_fit](size_t j, const cvm::rvector& grad){group_for_fit->fit_gradients[j] += grad;}; + auto accessor_fitting = [&group_for_fit](size_t j, const cvm::rvector& grad){group_for_fit->fit_gradients[j] = grad;}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) calc_fit_forces_impl(accessor_main, accessor_fitting); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate))