From 494b751ff8fd4bc3a3ddcc8b824cac31b805b59d Mon Sep 17 00:00:00 2001 From: HanatoK Date: Fri, 13 Sep 2024 11:22:53 -0500 Subject: [PATCH] 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 +}