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..56e5917b5 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.out @@ -0,0 +1,10164 @@ +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: - Multiple replicas: enabled (replica number 1 of 1) +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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Initializing a new "distanceDir" component, with configuration: +colvars: +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: 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 value = "off". +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = off +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: 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: 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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group1 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group1" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group1 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group1 +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group1 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group1 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group1 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group1 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group1 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group1 +colvars: DEPS: colvar group1 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group1 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group1 testing "linear" +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group1". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group2" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group2 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group2" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group2 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group2 +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: feature "linear" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group2 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group2 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group2 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group2 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group2 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group2 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group2 +colvars: DEPS: colvar group2 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group2 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group2 testing "linear" +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group2". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting_group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting_group1 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting_group1 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting_group1 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting_group1 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar fitting_group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting_group1 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar fitting_group1 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting_group1 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar fitting_group1 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar fitting_group1 testing "linear" +colvars: DEPS: colvar fitting_group1 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar fitting_group1 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "fitting_group1". +colvars: Configuration string for "colvar": " +colvars: +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 4 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: outputEnergy on +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 value = "on". +colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword "outputEnergy" not found. +colvars: # outputEnergy = on +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 +colvars: - scalable_calculation +colvars: - 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: outputEnergy on +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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: outputEnergy on +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +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: - cartesian colvar component: +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: Re-initialized atom group for variable "group1":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "group2":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "fitting_group1":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 0 +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 0, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 0, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 0, atoms_positions[size = 51] = { ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 ), ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 ), ( 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 ), ( 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ), ( 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 ), ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 ), ( 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 ), ( 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 ), ( 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 ), ( 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ), ( 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 ), ( 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 ), ( 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 ), ( 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 ), ( 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 ), ( 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 ), ( 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 ), ( 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 ), ( 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 ), ( 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 ), ( 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 ), ( 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 ), ( 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 ), ( 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 ), ( -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 ), ( 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 ), ( 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 ), ( 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 ), ( -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 ), ( -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 ), ( -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 ), ( -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 ), ( -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 ), ( -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 ), ( -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 ), ( -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 ), ( -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 ), ( -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 ), ( -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 ), ( -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 ), ( -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 ), ( -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 ), ( -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 ), ( -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 ), ( -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 ), ( -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 ), ( -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 ), ( -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 ), ( -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 ), ( -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ), ( -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) } +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.8285 , 6.78285 , 13.5657 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.8285 , 6.78285 , 13.5657 ) to colvar "one". +colvars: Adding total bias energy: 59.0741 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.8285 , 6.78285 , 13.5657 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.24283 , -0.621686 , -1.74324 ) +colvars: ( -4.49572 , -0.533095 , -1.49482 ) +colvars: ( -4.49572 , -0.533095 , -1.49482 ) +colvars: ( -5.98843 , -0.710098 , -1.99115 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.980525 , 0.208361 , 0.707889 ) +colvars: ( 0.847187 , 0.286419 , 0.7363 ) +colvars: ( 0.831964 , 0.278148 , 0.715627 ) +colvars: ( 0.721144 , 0.289021 , 0.66407 ) +colvars: ( 0.707924 , 0.217011 , 0.555875 ) +colvars: ( 0.623477 , 0.374153 , 0.723797 ) +colvars: ( 0.502375 , 0.391122 , 0.674537 ) +colvars: ( 0.415863 , 0.497748 , 0.770897 ) +colvars: ( 0.41239 , 0.343411 , 0.553969 ) +colvars: ( 0.372619 , 0.29912 , 0.468382 ) +colvars: ( 0.381832 , 0.348698 , 0.54294 ) +colvars: ( 0.303719 , 0.302613 , 0.43178 ) +colvars: ( 0.275733 , 0.333551 , 0.458004 ) +colvars: ( 0.374035 , 0.19566 , 0.325218 ) +colvars: ( 0.308466 , 0.149439 , 0.221418 ) +colvars: ( 0.511606 , 0.153877 , 0.349848 ) +colvars: ( 0.593091 , 0.0538224 , 0.25961 ) +colvars: ( 0.738774 , 0.0291662 , 0.312961 ) +colvars: ( 0.600507 , 0.0200257 , 0.217028 ) +colvars: ( 0.582961 , -0.0503026 , 0.108571 ) +colvars: ( 0.621867 , 0.0724375 , 0.30284 ) +colvars: ( 0.617923 , 0.0557667 , 0.27726 ) +colvars: ( 0.656934 , 0.126134 , 0.398688 ) +colvars: ( 0.47834 , 0.0623652 , 0.202443 ) +colvars: ( 0.469948 , 0.00212506 , 0.113539 ) +colvars: ( 0.364797 , 0.134592 , 0.234653 ) +colvars: ( 0.225359 , 0.145517 , 0.165945 ) +colvars: ( 0.123604 , 0.239381 , 0.235366 ) +colvars: ( 0.195341 , 0.0654024 , 0.03636 ) +colvars: ( 0.13949 , 0.0270989 , -0.0505699 ) +colvars: ( 0.235117 , 0.0364732 , 0.0200283 ) +colvars: ( 0.221044 , -0.0425041 , -0.0983778 ) +colvars: ( 0.262915 , -0.0474471 , -0.0800596 ) +colvars: ( 0.30454 , -0.136337 , -0.178744 ) +colvars: ( 0.255545 , -0.193422 , -0.287693 ) +colvars: ( 0.432497 , -0.153726 , -0.125944 ) +colvars: ( 0.518254 , -0.236176 , -0.189105 ) +colvars: ( 0.664508 , -0.240442 , -0.107027 ) +colvars: ( 0.4632 , -0.239658 , -0.227084 ) +colvars: ( 0.469112 , -0.313383 , -0.326152 ) +colvars: ( 0.407091 , -0.159032 , -0.14862 ) +colvars: ( 0.34436 , -0.150822 , -0.174944 ) +colvars: ( 0.324244 , -0.0560804 , -0.055169 ) +colvars: ( 0.206872 , -0.158964 , -0.269019 ) +colvars: ( 0.178541 , -0.203801 , -0.348481 ) +colvars: ( -0.0144018 , -0.207442 , -0.469665 ) +colvars: ( -0.115821 , -0.225702 , -0.556117 ) +colvars: ( 0.0990981 , -0.263246 , -0.479038 ) +colvars: ( 0.11689 , -0.114495 , -0.26127 ) +colvars: ( -0.0160137 , -0.117953 , -0.346065 ) +colvars: ( -0.114683 , -0.0297495 , -0.282666 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.24283 , 0.621686 , 1.74324 ) +colvars: ( 4.49572 , 0.533095 , 1.49482 ) +colvars: ( 4.49572 , 0.533095 , 1.49482 ) +colvars: ( 5.98843 , 0.710098 , 1.99115 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.6815 , -0.0870646 , -0.438519 ) +colvars: ( -0.610334 , -0.175958 , -0.409522 ) +colvars: ( -0.560732 , -0.152516 , -0.348217 ) +colvars: ( -0.562005 , -0.206019 , -0.375247 ) +colvars: ( -0.551575 , -0.143387 , -0.33459 ) +colvars: ( -0.530032 , -0.304649 , -0.390463 ) +colvars: ( -0.488409 , -0.348368 , -0.369523 ) +colvars: ( -0.460313 , -0.463211 , -0.39645 ) +colvars: ( -0.419939 , -0.311191 , -0.282579 ) +colvars: ( -0.412296 , -0.284511 , -0.262032 ) +colvars: ( -0.369557 , -0.305297 , -0.228931 ) +colvars: ( -0.3045 , -0.26642 , -0.144612 ) +colvars: ( -0.254997 , -0.282406 , -0.102379 ) +colvars: ( -0.329137 , -0.156089 , -0.116367 ) +colvars: ( -0.29345 , -0.125296 , -0.0655582 ) +colvars: ( -0.393142 , -0.0941533 , -0.151115 ) +colvars: ( -0.425665 , 0.0109803 , -0.133324 ) +colvars: ( -0.486297 , 0.0625799 , -0.169643 ) +colvars: ( -0.462764 , 0.0269574 , -0.163051 ) +colvars: ( -0.450285 , 0.0873345 , -0.121412 ) +colvars: ( -0.507307 , -0.0305329 , -0.235639 ) +colvars: ( -0.540279 , -0.032181 , -0.269684 ) +colvars: ( -0.591927 , -0.101677 , -0.355214 ) +colvars: ( -0.478375 , -0.0649877 , -0.22304 ) +colvars: ( -0.484329 , -0.0181032 , -0.206483 ) +colvars: ( -0.415674 , -0.144795 , -0.198208 ) +colvars: ( -0.348452 , -0.178964 , -0.146854 ) +colvars: ( -0.291288 , -0.275603 , -0.135706 ) +colvars: ( -0.30602 , -0.101513 , -0.0667915 ) +colvars: ( -0.288652 , -0.0820378 , -0.0399035 ) +colvars: ( -0.289997 , -0.0534103 , -0.0274846 ) +colvars: ( -0.254525 , 0.0261796 , 0.0465887 ) +colvars: ( -0.237288 , 0.0546097 , 0.0776541 ) +colvars: ( -0.304016 , 0.119067 , 0.041374 ) +colvars: ( -0.274172 , 0.16327 , 0.0927428 ) +colvars: ( -0.38166 , 0.149755 , -0.0221654 ) +colvars: ( -0.435953 , 0.231401 , -0.0376328 ) +colvars: ( -0.51685 , 0.256293 , -0.107241 ) +colvars: ( -0.44268 , 0.209891 , -0.0547671 ) +colvars: ( -0.447514 , 0.274703 , -0.0284547 ) +colvars: ( -0.44248 , 0.1173 , -0.0991214 ) +colvars: ( -0.44425 , 0.0847434 , -0.116572 ) +colvars: ( -0.463499 , -0.0148166 , -0.183894 ) +colvars: ( -0.368351 , 0.0719336 , -0.0461905 ) +colvars: ( -0.369239 , 0.0997629 , -0.0336948 ) +colvars: ( -0.194146 , 0.105585 , 0.145693 ) +colvars: ( -0.137942 , 0.106979 , 0.203047 ) +colvars: ( -0.229174 , 0.18333 , 0.147777 ) +colvars: ( -0.300383 , 0.0280482 , 0.00123885 ) +colvars: ( -0.22483 , 0.0127714 , 0.0700847 ) +colvars: ( -0.164527 , -0.0762928 , 0.0880445 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 0. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 0. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atoms_new_colvar_forces = { ( -4.94380109020736e+00 , -5.00388904640502e-01 , -1.47386559815863e+00 ), ( -4.25887034346859e+00 , -4.22634331302087e-01 , -1.16804598817012e+00 ), ( -4.33658351120613e+00 , -4.50092951033408e-01 , -1.20600109185253e+00 ), ( -5.83208455846301e+00 , -6.36474758865210e-01 , -1.76986309115155e+00 ), ( 2.71232531748555e-01 , 1.25632048086319e-01 , 3.67409255074628e-01 ), ( 5.33627146515550e+00 , 6.91190199802536e-01 , 2.07656909073876e+00 ), ( 4.50968880718936e+00 , 5.75848803067544e-01 , 1.79983797012281e+00 ), ( -4.44501052695659e-02 , 3.45377122156243e-02 , 3.74447254352333e-01 ), ( 4.48817355031418e+00 , 5.65314954451102e-01 , 1.76621340521082e+00 ), ( 5.94875680298447e+00 , 7.24707761830127e-01 , 2.19749895846013e+00 ), ( 1.22753001388897e-02 , 4.34017304887051e-02 , 3.14008822405178e-01 ), ( -7.80697849611267e-04 , 3.61932412570256e-02 , 2.87168384711426e-01 ), ( 2.07361033473052e-02 , 5.11451171492998e-02 , 3.55624446863570e-01 ), ( 4.48981036871490e-02 , 3.95707933953106e-02 , 2.08850570890745e-01 ), ( 1.50159624716962e-02 , 2.41427303559141e-02 , 1.55859612872436e-01 ), ( 1.18463692969193e-01 , 5.97239231052729e-02 , 1.98732940462020e-01 ), ( 1.67425756640778e-01 , 6.48027016473707e-02 , 1.26285440252794e-01 ), ( 2.52476962283068e-01 , 9.17460657890331e-02 , 1.43318430504137e-01 ), ( 1.37743878011550e-01 , 4.69830445208921e-02 , 5.39772464142627e-02 ), ( 1.32675758834949e-01 , 3.70319044311048e-02 , -1.28407988568328e-02 ), ( 1.14559902356933e-01 , 4.19045677827880e-02 , 6.72008825996200e-02 ), ( 7.76445955145584e-02 , 2.35857857533280e-02 , 7.57631932046199e-03 ), ( 6.50078200994428e-02 , 2.44563690553224e-02 , 4.34741760720458e-02 ), ( -3.52924814698841e-05 , -2.62247362813921e-03 , -2.05964658376968e-02 ), ( -1.43804694810325e-02 , -1.59781771824823e-02 , -9.29442152582067e-02 ), ( -5.08770104951550e-02 , -1.02029133458509e-02 , 3.64446437587760e-02 ), ( -1.23092373357461e-01 , -3.34467449133838e-02 , 1.90906572366346e-02 ), ( -1.67684565489913e-01 , -3.62222146197359e-02 , 9.96592102664404e-02 ), ( -1.10679336183364e-01 , -3.61104510979557e-02 , -3.04314790816462e-02 ), ( -1.49161855665883e-01 , -5.49388369767760e-02 , -9.04734047750292e-02 ), ( -5.48798679042043e-02 , -1.69371419508729e-02 , -7.45633898018655e-03 ), ( -3.34817413245006e-02 , -1.63245354811410e-02 , -5.17891871208446e-02 ), ( 2.56279270454741e-02 , 7.16265511734566e-03 , -2.40548975951840e-03 ), ( 5.24011831872395e-04 , -1.72695796190696e-02 , -1.37370276016371e-01 ), ( -1.86268060074735e-02 , -3.01525977674522e-02 , -1.94949856296420e-01 ), ( 5.08365486515878e-02 , -3.97098722060221e-03 , -1.48109358926904e-01 ), ( 8.23006804426702e-02 , -4.77487898187540e-03 , -2.26738014259551e-01 ), ( 1.47658217162366e-01 , 1.58512609294484e-02 , -2.14267730284841e-01 ), ( 2.05204286258686e-02 , -2.97669344400476e-02 , -2.81851418440884e-01 ), ( 2.15981054298106e-02 , -3.86802829304581e-02 , -3.54606960554895e-01 ), ( -3.53890024292071e-02 , -4.17323039104114e-02 , -2.47741104198243e-01 ), ( -9.98896207864740e-02 , -6.60790513521777e-02 , -2.91516258512565e-01 ), ( -1.39254212665718e-01 , -7.08969819297212e-02 , -2.39062632972191e-01 ), ( -1.61479102641855e-01 , -8.70305677041763e-02 , -3.15209319593768e-01 ), ( -1.90698023720256e-01 , -1.04037830628658e-01 , -3.82175651846584e-01 ), ( -2.08547889799338e-01 , -1.01857291465968e-01 , -3.23971823679259e-01 ), ( -2.53762785465945e-01 , -1.18722910421569e-01 , -3.53069902704324e-01 ), ( -1.30076081210408e-01 , -7.99158043524913e-02 , -3.31260946756196e-01 ), ( -1.83492900055176e-01 , -8.64470461357563e-02 , -2.60030769910419e-01 ), ( -2.40844087307098e-01 , -1.05181536366297e-01 , -2.75980792341469e-01 ), ( -2.79209582001028e-01 , -1.06042349967139e-01 , -1.94621752292357e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 1, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 1, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 1, atoms_positions[size = 51] = { ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 ), ( 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 ), ( 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 ), ( 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ), ( 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 ), ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 ), ( 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 ), ( 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 ), ( 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 ), ( 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ), ( 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 ), ( 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 ), ( 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 ), ( 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 ), ( 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 ), ( 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 ), ( 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 ), ( 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 ), ( 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 ), ( 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 ), ( 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 ), ( 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 ), ( 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 ), ( 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 ), ( -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 ), ( 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 ), ( 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 ), ( 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 ), ( -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 ), ( -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 ), ( -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 ), ( -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 ), ( -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 ), ( -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 ), ( -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 ), ( -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 ), ( -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 ), ( -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 ), ( -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 ), ( -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 ), ( -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 ), ( -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 ), ( -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 ), ( -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 ), ( -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 ), ( -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 ), ( -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 ), ( -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 ), ( -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 ), ( -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 ), ( -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ) } +colvars: Step 1, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ). +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.39355617493064e-01 , 6.97292683121385e-03 , 9.40632310293086e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 , 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 , 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 , 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 , 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 , 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 , 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 , 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 , 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 , 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 , 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 , 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 , 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 , 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 , 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 , 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 , -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 , 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 , 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 , 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 , -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 , -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 , -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 , -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 , -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 , -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 , -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 , -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 , -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 , -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 , -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 , -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 , -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 , -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 , -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 , -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 , -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 , -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 , -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 , -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 , -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 , -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 , -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.39355617493064e-01 , 6.97292683121385e-03 , 9.40632310293086e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 , 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 , 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 , 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 , 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 , 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 , 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 , 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 , 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 , 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 , 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 , 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 , 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 , 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 , 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 , 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 , -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 , 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 , 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 , 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 , -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 , -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 , -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 , -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 , -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 , -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 , -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 , -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 , -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 , -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 , -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 , -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 , -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 , -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 , -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 , -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 , -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 , -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 , -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 , -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 , -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 , -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 , -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.8087 , 6.78087 , 13.5617 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.8087 , 6.78087 , 13.5617 ) to colvar "one". +colvars: Adding total bias energy: 59.0466 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.8087 , 6.78087 , 13.5617 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.24407 , -0.621478 , -1.74192 ) +colvars: ( -4.49679 , -0.532917 , -1.4937 ) +colvars: ( -4.49679 , -0.532917 , -1.4937 ) +colvars: ( -5.98986 , -0.709861 , -1.98965 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.980103 , 0.208479 , 0.707343 ) +colvars: ( 0.84685 , 0.286561 , 0.735623 ) +colvars: ( 0.831565 , 0.278265 , 0.714895 ) +colvars: ( 0.720936 , 0.28916 , 0.663439 ) +colvars: ( 0.707733 , 0.21711 , 0.555381 ) +colvars: ( 0.623363 , 0.374334 , 0.723051 ) +colvars: ( 0.502391 , 0.391309 , 0.673817 ) +colvars: ( 0.415958 , 0.497988 , 0.770015 ) +colvars: ( 0.412445 , 0.343553 , 0.553318 ) +colvars: ( 0.372737 , 0.299243 , 0.467848 ) +colvars: ( 0.381846 , 0.348825 , 0.542224 ) +colvars: ( 0.303758 , 0.302697 , 0.431124 ) +colvars: ( 0.275723 , 0.333631 , 0.457231 ) +colvars: ( 0.374017 , 0.195691 , 0.324736 ) +colvars: ( 0.308504 , 0.149439 , 0.221034 ) +colvars: ( 0.511475 , 0.153898 , 0.34941 ) +colvars: ( 0.592898 , 0.0537961 , 0.259335 ) +colvars: ( 0.738445 , 0.0291354 , 0.312683 ) +colvars: ( 0.600376 , 0.0199986 , 0.216876 ) +colvars: ( 0.58285 , -0.0503686 , 0.108553 ) +colvars: ( 0.621771 , 0.0724549 , 0.302641 ) +colvars: ( 0.617897 , 0.0557918 , 0.277156 ) +colvars: ( 0.656922 , 0.126213 , 0.398496 ) +colvars: ( 0.47844 , 0.0623842 , 0.202369 ) +colvars: ( 0.470085 , 0.00211752 , 0.113601 ) +colvars: ( 0.364965 , 0.134634 , 0.234452 ) +colvars: ( 0.225643 , 0.145553 , 0.165756 ) +colvars: ( 0.123941 , 0.239451 , 0.235005 ) +colvars: ( 0.195614 , 0.0653818 , 0.0362843 ) +colvars: ( 0.139834 , 0.0270587 , -0.0505412 ) +colvars: ( 0.235297 , 0.0364249 , 0.0199373 ) +colvars: ( 0.221197 , -0.0426071 , -0.0983626 ) +colvars: ( 0.262966 , -0.0475665 , -0.0801105 ) +colvars: ( 0.304657 , -0.136476 , -0.178551 ) +colvars: ( 0.255703 , -0.193597 , -0.287388 ) +colvars: ( 0.432539 , -0.153855 , -0.125719 ) +colvars: ( 0.518262 , -0.236333 , -0.188718 ) +colvars: ( 0.664413 , -0.240584 , -0.106649 ) +colvars: ( 0.463317 , -0.239806 , -0.226619 ) +colvars: ( 0.469241 , -0.313568 , -0.325542 ) +colvars: ( 0.40729 , -0.159132 , -0.14825 ) +colvars: ( 0.344669 , -0.150909 , -0.174519 ) +colvars: ( 0.324605 , -0.0561066 , -0.0548723 ) +colvars: ( 0.20728 , -0.159071 , -0.268562 ) +colvars: ( 0.179009 , -0.203925 , -0.347905 ) +colvars: ( -0.0139216 , -0.207624 , -0.46918 ) +colvars: ( -0.115265 , -0.225905 , -0.555586 ) +colvars: ( 0.0994568 , -0.263455 , -0.478507 ) +colvars: ( 0.117321 , -0.114598 , -0.260921 ) +colvars: ( -0.0154909 , -0.118075 , -0.345699 ) +colvars: ( -0.114117 , -0.029841 , -0.282469 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.24407 , 0.621478 , 1.74192 ) +colvars: ( 4.49679 , 0.532917 , 1.4937 ) +colvars: ( 4.49679 , 0.532917 , 1.4937 ) +colvars: ( 5.98986 , 0.709861 , 1.98965 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.681278 , -0.0870714 , -0.438179 ) +colvars: ( -0.610149 , -0.176111 , -0.408961 ) +colvars: ( -0.560375 , -0.152583 , -0.34748 ) +colvars: ( -0.561943 , -0.206245 , -0.374716 ) +colvars: ( -0.551508 , -0.143509 , -0.334194 ) +colvars: ( -0.530082 , -0.30506 , -0.3898 ) +colvars: ( -0.488596 , -0.34888 , -0.368879 ) +colvars: ( -0.460599 , -0.463931 , -0.395623 ) +colvars: ( -0.420071 , -0.31162 , -0.281911 ) +colvars: ( -0.412502 , -0.284913 , -0.261506 ) +colvars: ( -0.369551 , -0.305677 , -0.228086 ) +colvars: ( -0.304423 , -0.266712 , -0.14373 ) +colvars: ( -0.254778 , -0.282684 , -0.101263 ) +colvars: ( -0.328989 , -0.156186 , -0.115686 ) +colvars: ( -0.293324 , -0.125343 , -0.0649488 ) +colvars: ( -0.392913 , -0.0941361 , -0.150536 ) +colvars: ( -0.425369 , 0.0111821 , -0.132945 ) +colvars: ( -0.485882 , 0.062888 , -0.169297 ) +colvars: ( -0.46261 , 0.0271465 , -0.162897 ) +colvars: ( -0.450129 , 0.0876247 , -0.12139 ) +colvars: ( -0.507286 , -0.0304751 , -0.23553 ) +colvars: ( -0.54041 , -0.0321668 , -0.269768 ) +colvars: ( -0.592173 , -0.101811 , -0.355301 ) +colvars: ( -0.478606 , -0.0650441 , -0.223112 ) +colvars: ( -0.484612 , -0.018096 , -0.206729 ) +colvars: ( -0.415928 , -0.144981 , -0.198069 ) +colvars: ( -0.348781 , -0.179216 , -0.146669 ) +colvars: ( -0.291631 , -0.27601 , -0.135265 ) +colvars: ( -0.306251 , -0.101609 , -0.0666492 ) +colvars: ( -0.288957 , -0.0821179 , -0.0398784 ) +colvars: ( -0.290057 , -0.0533843 , -0.0272524 ) +colvars: ( -0.254475 , 0.0263669 , 0.0467815 ) +colvars: ( -0.237054 , 0.05489 , 0.0779985 ) +colvars: ( -0.303967 , 0.119401 , 0.0413084 ) +colvars: ( -0.274127 , 0.163678 , 0.0925894 ) +colvars: ( -0.381611 , 0.150129 , -0.0223614 ) +colvars: ( -0.435919 , 0.2319 , -0.0380797 ) +colvars: ( -0.51678 , 0.256832 , -0.107767 ) +colvars: ( -0.442818 , 0.210312 , -0.0553629 ) +colvars: ( -0.447663 , 0.275227 , -0.0292202 ) +colvars: ( -0.44276 , 0.117535 , -0.0996548 ) +colvars: ( -0.4447 , 0.0848834 , -0.117222 ) +colvars: ( -0.464078 , -0.0148733 , -0.184466 ) +colvars: ( -0.368836 , 0.0720531 , -0.0467928 ) +colvars: ( -0.369806 , 0.0999082 , -0.0344554 ) +colvars: ( -0.194465 , 0.10582 , 0.145326 ) +colvars: ( -0.138286 , 0.107217 , 0.20269 ) +colvars: ( -0.229351 , 0.183723 , 0.14736 ) +colvars: ( -0.300809 , 0.0281182 , 0.000858489 ) +colvars: ( -0.225279 , 0.0128195 , 0.06977 ) +colvars: ( -0.164968 , -0.076382 , 0.0879943 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 1. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 1. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atoms_new_colvar_forces = { ( -4.94524752703150e+00 , -5.00070478706819e-01 , -1.47275647312878e+00 ), ( -4.26009131684454e+00 , -4.22467159035450e-01 , -1.16703423693781e+00 ), ( -4.33779800471171e+00 , -4.50002583986641e-01 , -1.20497275307046e+00 ), ( -5.83363187452853e+00 , -6.36259583558461e-01 , -1.76846030974805e+00 ), ( 2.71190015483635e-01 , 1.25681762375493e-01 , 3.67414267382630e-01 ), ( 5.33735414735488e+00 , 6.90751295593571e-01 , 2.07517161763720e+00 ), ( 4.51058662070597e+00 , 5.75345653833406e-01 , 1.79863383269542e+00 ), ( -4.46408275205372e-02 , 3.40569702021636e-02 , 3.74391940973145e-01 ), ( 4.48916537934960e+00 , 5.64850532194998e-01 , 1.76510354545200e+00 ), ( 5.95009180286499e+00 , 7.24190384703997e-01 , 2.19598868309754e+00 ), ( 1.22949080365150e-02 , 4.31475303857823e-02 , 3.14138299966590e-01 ), ( -6.65082887394586e-04 , 3.59849096022542e-02 , 2.87394147806122e-01 ), ( 2.09454431592941e-02 , 5.09470381688317e-02 , 3.55967803435473e-01 ), ( 4.50276732595528e-02 , 3.95050702537192e-02 , 2.09049454974075e-01 ), ( 1.51802648863201e-02 , 2.40955261372282e-02 , 1.56085385382948e-01 ), ( 1.18562776981734e-01 , 5.97616492017114e-02 , 1.98873784794414e-01 ), ( 1.67528528090387e-01 , 6.49782066429318e-02 , 1.26389616432355e-01 ), ( 2.52562895437471e-01 , 9.20233604106910e-02 , 1.43385334010810e-01 ), ( 1.37765499890022e-01 , 4.71451801693997e-02 , 5.39782543565037e-02 ), ( 1.32720403241798e-01 , 3.72561466313631e-02 , -1.28377211574611e-02 ), ( 1.14484776500457e-01 , 4.19797663850426e-02 , 6.71108044658936e-02 ), ( 7.74864448064505e-02 , 2.36249234418552e-02 , 7.38778540003382e-03 ), ( 6.47491303559717e-02 , 2.44020990549570e-02 , 4.31954803199882e-02 ), ( -1.65996344847597e-04 , -2.65988605064772e-03 , -2.07426523928385e-02 ), ( -1.45266011426173e-02 , -1.59784925856758e-02 , -9.31283714811172e-02 ), ( -5.09624157039873e-02 , -1.03461898436014e-02 , 3.63822086561157e-02 ), ( -1.23137558839672e-01 , -3.36628074369859e-02 , 1.90863694359183e-02 ), ( -1.67690024220711e-01 , -3.65584088695555e-02 , 9.97392996339642e-02 ), ( -1.10637609383330e-01 , -3.62270759413579e-02 , -3.03648856269820e-02 ), ( -1.49122820034138e-01 , -5.50591676751083e-02 , -9.04196191188827e-02 ), ( -5.47598464287284e-02 , -1.69594129214750e-02 , -7.31508188067119e-03 ), ( -3.32778789705395e-02 , -1.62401947888544e-02 , -5.15811466436443e-02 ), ( 2.59122622261631e-02 , 7.32352281212509e-03 , -2.11201683056700e-03 ), ( 6.90782403088619e-04 , -1.70749634648680e-02 , -1.37242435415941e-01 ), ( -1.84237103006750e-02 , -2.99190152647431e-02 , -1.94798292468153e-01 ), ( 5.09278555322116e-02 , -3.72550751223835e-03 , -1.48080588220414e-01 ), ( 8.23437845427731e-02 , -4.43378522041665e-03 , -2.26797996663325e-01 ), ( 1.47632691579756e-01 , 1.62473698427204e-02 , -2.14415728561813e-01 ), ( 2.04981810854328e-02 , -2.94946983223998e-02 , -2.81982021639434e-01 ), ( 2.15774723237853e-02 , -3.83407955579049e-02 , -3.54762198175992e-01 ), ( -3.54698833919641e-02 , -4.15971863107600e-02 , -2.47905033768520e-01 ), ( -1.00031783639185e-01 , -6.60251552771045e-02 , -2.91741615166040e-01 ), ( -1.39472463045771e-01 , -7.09798775635357e-02 , -2.39338250043644e-01 ), ( -1.61555754569422e-01 , -8.70174905659755e-02 , -3.15355116544667e-01 ), ( -1.90797127483342e-01 , -1.04017177822925e-01 , -3.82360498044434e-01 ), ( -2.08386671206907e-01 , -1.01803638409611e-01 , -3.23853995585936e-01 ), ( -2.53551331972853e-01 , -1.18687855692914e-01 , -3.52895579795768e-01 ), ( -1.29893744126556e-01 , -7.97320503419824e-02 , -3.31146804351725e-01 ), ( -1.83487110521711e-01 , -8.64802309664682e-02 , -2.60062666463744e-01 ), ( -2.40770073694591e-01 , -1.05255110618706e-01 , -2.75928747265521e-01 ), ( -2.79084701552500e-01 , -1.06222917731058e-01 , -1.94475080116808e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 2, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 2, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 2, atoms_positions[size = 51] = { ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 ), ( 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 ), ( 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 ), ( 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ), ( 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 ), ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 ), ( 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 ), ( 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 ), ( 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 ), ( 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ), ( 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 ), ( 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 ), ( 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 ), ( 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 ), ( 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 ), ( 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 ), ( 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 ), ( 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 ), ( 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 ), ( 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 ), ( 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 ), ( 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 ), ( 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 ), ( 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 ), ( -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 ), ( 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 ), ( 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 ), ( 2.07182033199839e+00 , 2.58031779371270e+00 , 5.62057469557046e+00 ), ( -3.51857196195411e-01 , 2.92077044604945e+00 , 4.98737377407843e+00 ), ( -1.18280243435512e+00 , 3.01570859553755e+00 , 5.89917024566929e+00 ), ( -3.87794524035796e-01 , 3.70427740475066e+00 , 3.87474106468534e+00 ), ( -1.45631659311092e+00 , 4.61459312113414e+00 , 3.53258748757127e+00 ), ( -7.71525128042554e-01 , 5.37658887799748e+00 , 2.40420582867879e+00 ), ( -2.70490428589622e+00 , 3.89833430415539e+00 , 2.94596647609308e+00 ), ( -3.85265660442606e+00 , 4.40316710638716e+00 , 2.87069731043829e+00 ), ( -2.55585188833545e+00 , 2.62089196733170e+00 , 2.50849763245218e+00 ), ( -3.73243849554280e+00 , 1.88635394790118e+00 , 2.08117836350766e+00 ), ( -3.40440071450160e+00 , 7.90661562036665e-01 , 1.01489640110740e+00 ), ( -4.34244212012249e+00 , 1.12117982289474e+00 , 3.21348229313481e+00 ), ( -5.52935789612539e+00 , 9.45030885109751e-01 , 3.35102540103283e+00 ), ( -3.48508756370938e+00 , 6.29272994238064e-01 , 4.17781951543363e+00 ), ( -3.75586862376688e+00 , 1.04520414973514e-01 , 5.46864407236529e+00 ), ( -2.44525530896877e+00 , -4.36565885647881e-01 , 6.12524526296224e+00 ), ( -4.45857858178953e+00 , 1.01874210402695e+00 , 6.41862089191568e+00 ), ( -5.32722382061257e+00 , 5.89222135203817e-01 , 7.17650607594958e+00 ), ( -6.29286070068146e+00 , 3.54731394746929e+00 , 6.69277654767522e+00 ), ( -6.92914021657276e+00 , 4.31545509454118e+00 , 7.41850395505831e+00 ), ( -6.76638550864120e+00 , 3.20728475580864e+00 , 5.49812607601866e+00 ), ( -4.07643555217667e+00 , 2.29036116971940e+00 , 6.47113605156518e+00 ), ( -4.91331270399169e+00 , 3.24680915830551e+00 , 7.21653797742536e+00 ), ( -4.05853070415384e+00 , 4.48539472961622e+00 , 7.26244219143046e+00 ) } +colvars: Step 2, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.38665979440331e-01 , 6.30649599530219e-03 , 9.40885531017447e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 , 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 , 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 , 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 , 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 , 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 , 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 , 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 , 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 , 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 , 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 , 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 , 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 , 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 , 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 , 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 , -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 , 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 , 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 , 2.07182033199839e+00 , 2.58031779371270e+00 , 5.62057469557046e+00 , -3.51857196195411e-01 , 2.92077044604945e+00 , 4.98737377407843e+00 , -1.18280243435512e+00 , 3.01570859553755e+00 , 5.89917024566929e+00 , -3.87794524035796e-01 , 3.70427740475066e+00 , 3.87474106468534e+00 , -1.45631659311092e+00 , 4.61459312113414e+00 , 3.53258748757127e+00 , -7.71525128042554e-01 , 5.37658887799748e+00 , 2.40420582867879e+00 , -2.70490428589622e+00 , 3.89833430415539e+00 , 2.94596647609308e+00 , -3.85265660442606e+00 , 4.40316710638716e+00 , 2.87069731043829e+00 , -2.55585188833545e+00 , 2.62089196733170e+00 , 2.50849763245218e+00 , -3.73243849554280e+00 , 1.88635394790118e+00 , 2.08117836350766e+00 , -3.40440071450160e+00 , 7.90661562036665e-01 , 1.01489640110740e+00 , -4.34244212012249e+00 , 1.12117982289474e+00 , 3.21348229313481e+00 , -5.52935789612539e+00 , 9.45030885109751e-01 , 3.35102540103283e+00 , -3.48508756370938e+00 , 6.29272994238064e-01 , 4.17781951543363e+00 , -3.75586862376688e+00 , 1.04520414973514e-01 , 5.46864407236529e+00 , -2.44525530896877e+00 , -4.36565885647881e-01 , 6.12524526296224e+00 , -4.45857858178953e+00 , 1.01874210402695e+00 , 6.41862089191568e+00 , -5.32722382061257e+00 , 5.89222135203817e-01 , 7.17650607594958e+00 , -6.29286070068146e+00 , 3.54731394746929e+00 , 6.69277654767522e+00 , -6.92914021657276e+00 , 4.31545509454118e+00 , 7.41850395505831e+00 , -6.76638550864120e+00 , 3.20728475580864e+00 , 5.49812607601866e+00 , -4.07643555217667e+00 , 2.29036116971940e+00 , 6.47113605156518e+00 , -4.91331270399169e+00 , 3.24680915830551e+00 , 7.21653797742536e+00 , -4.05853070415384e+00 , 4.48539472961622e+00 , 7.26244219143046e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.38665979440331e-01 , 6.30649599530219e-03 , 9.40885531017447e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 7.03875551839640e+00 , -2.01024025165437e+00 , -1.03297589247868e+00 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 6.45320367305775e-01 , 6.90730405468658e+00 , -2.68406076628325e-01 , 1.78554030655546e+00 , 6.17987000003956e+00 , -1.29065346014296e-01 , 3.04265160592337e+00 , 7.19403094938619e+00 , -3.17368076603133e-01 , 4.30321050023964e+00 , 5.30494001847566e+00 , 1.13376473110554e+00 , 3.26705973154811e+00 , 4.08869234207102e+00 , 1.07659501955135e+00 , 3.60872276359474e+00 , 5.87394225687174e+00 , 2.33800769487248e+00 , 2.95025984749482e+00 , 5.23075713697808e+00 , 3.59958457214155e+00 , 2.87916109872632e+00 , 6.32630924917659e+00 , 4.63549159888322e+00 , 2.47116623313691e+00 , 3.90153104354634e+00 , 3.69481392219336e+00 , 2.02631942741481e+00 , 2.92849874345353e+00 , 4.11702547093943e+00 , 2.57104401947607e+00 , 3.81753100629896e+00 , 3.24384600622391e+00 , 7.83692227051668e-01 , 2.66012783014539e+00 , 3.20111607321956e+00 , -6.85997060770361e-02 , 3.04893204122928e+00 , 2.73309527666146e+00 , -1.57997320681501e+00 , 1.64934034739335e+00 , 2.16482459909592e+00 , 5.69612967517946e-01 , 4.24922530643620e-01 , 2.42605388958177e+00 , 5.70944302575278e-01 , 1.98623200571213e+00 , 9.97646157021839e-01 , 1.06028428925596e+00 , 1.12204264907651e+00 , 1.47143645460771e-02 , 1.68718093608555e+00 , 2.01639837322967e+00 , -1.20568281198686e+00 , 2.02326720420533e+00 , 4.98103216334056e-01 , 5.80679809398376e-01 , 3.01308835064376e+00 , -6.84829735061026e-01 , 3.90833014408853e-01 , 3.19685907790461e+00 , 1.27431993992135e+00 , 1.30473010211987e+00 , 3.82336714821545e+00 , 8.08600751270380e-01 , 1.88137193204971e+00 , 5.08538334416430e+00 , 2.07182033199839e+00 , 2.58031779371270e+00 , 5.62057469557046e+00 , -3.51857196195411e-01 , 2.92077044604945e+00 , 4.98737377407843e+00 , -1.18280243435512e+00 , 3.01570859553755e+00 , 5.89917024566929e+00 , -3.87794524035796e-01 , 3.70427740475066e+00 , 3.87474106468534e+00 , -1.45631659311092e+00 , 4.61459312113414e+00 , 3.53258748757127e+00 , -7.71525128042554e-01 , 5.37658887799748e+00 , 2.40420582867879e+00 , -2.70490428589622e+00 , 3.89833430415539e+00 , 2.94596647609308e+00 , -3.85265660442606e+00 , 4.40316710638716e+00 , 2.87069731043829e+00 , -2.55585188833545e+00 , 2.62089196733170e+00 , 2.50849763245218e+00 , -3.73243849554280e+00 , 1.88635394790118e+00 , 2.08117836350766e+00 , -3.40440071450160e+00 , 7.90661562036665e-01 , 1.01489640110740e+00 , -4.34244212012249e+00 , 1.12117982289474e+00 , 3.21348229313481e+00 , -5.52935789612539e+00 , 9.45030885109751e-01 , 3.35102540103283e+00 , -3.48508756370938e+00 , 6.29272994238064e-01 , 4.17781951543363e+00 , -3.75586862376688e+00 , 1.04520414973514e-01 , 5.46864407236529e+00 , -2.44525530896877e+00 , -4.36565885647881e-01 , 6.12524526296224e+00 , -4.45857858178953e+00 , 1.01874210402695e+00 , 6.41862089191568e+00 , -5.32722382061257e+00 , 5.89222135203817e-01 , 7.17650607594958e+00 , -6.29286070068146e+00 , 3.54731394746929e+00 , 6.69277654767522e+00 , -6.92914021657276e+00 , 4.31545509454118e+00 , 7.41850395505831e+00 , -6.76638550864120e+00 , 3.20728475580864e+00 , 5.49812607601866e+00 , -4.07643555217667e+00 , 2.29036116971940e+00 , 6.47113605156518e+00 , -4.91331270399169e+00 , 3.24680915830551e+00 , 7.21653797742536e+00 , -4.05853070415384e+00 , 4.48539472961622e+00 , 7.26244219143046e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.7758 , 6.77758 , 13.5552 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.7758 , 6.77758 , 13.5552 ) to colvar "one". +colvars: Adding total bias energy: 59.0009 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.7758 , 6.77758 , 13.5552 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.24396 , -0.620729 , -1.73858 ) +colvars: ( -4.4967 , -0.532275 , -1.49083 ) +colvars: ( -4.4967 , -0.532275 , -1.49083 ) +colvars: ( -5.98973 , -0.709005 , -1.98583 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.979291 , 0.208554 , 0.706289 ) +colvars: ( 0.84619 , 0.286615 , 0.734433 ) +colvars: ( 0.830841 , 0.27831 , 0.713677 ) +colvars: ( 0.720472 , 0.28919 , 0.66234 ) +colvars: ( 0.707289 , 0.217131 , 0.554478 ) +colvars: ( 0.623047 , 0.374354 , 0.721806 ) +colvars: ( 0.502269 , 0.391308 , 0.672626 ) +colvars: ( 0.415964 , 0.49798 , 0.76861 ) +colvars: ( 0.4124 , 0.343527 , 0.552278 ) +colvars: ( 0.372777 , 0.299206 , 0.466968 ) +colvars: ( 0.38177 , 0.348788 , 0.541138 ) +colvars: ( 0.303737 , 0.302636 , 0.430174 ) +colvars: ( 0.275662 , 0.333563 , 0.456164 ) +colvars: ( 0.3739 , 0.195634 , 0.324016 ) +colvars: ( 0.308474 , 0.149365 , 0.220475 ) +colvars: ( 0.511175 , 0.153865 , 0.348713 ) +colvars: ( 0.59249 , 0.0537709 , 0.258846 ) +colvars: ( 0.737825 , 0.0291363 , 0.312154 ) +colvars: ( 0.600032 , 0.0199766 , 0.216521 ) +colvars: ( 0.582532 , -0.0504006 , 0.108393 ) +colvars: ( 0.621459 , 0.0724462 , 0.30218 ) +colvars: ( 0.617665 , 0.0557857 , 0.276792 ) +colvars: ( 0.656694 , 0.126225 , 0.397964 ) +colvars: ( 0.478406 , 0.0623511 , 0.202083 ) +colvars: ( 0.470092 , 0.00207906 , 0.113497 ) +colvars: ( 0.365056 , 0.134583 , 0.234031 ) +colvars: ( 0.22592 , 0.145474 , 0.165395 ) +colvars: ( 0.124323 , 0.239359 , 0.234443 ) +colvars: ( 0.195886 , 0.0652868 , 0.0361188 ) +colvars: ( 0.140208 , 0.0269505 , -0.0505543 ) +colvars: ( 0.235449 , 0.0363307 , 0.0197749 ) +colvars: ( 0.221322 , -0.0427146 , -0.0983437 ) +colvars: ( 0.262958 , -0.0476711 , -0.0801578 ) +colvars: ( 0.304703 , -0.136573 , -0.178318 ) +colvars: ( 0.255811 , -0.19371 , -0.286979 ) +colvars: ( 0.432448 , -0.153926 , -0.125499 ) +colvars: ( 0.518095 , -0.236392 , -0.188311 ) +colvars: ( 0.664071 , -0.240612 , -0.106308 ) +colvars: ( 0.463292 , -0.239872 , -0.226121 ) +colvars: ( 0.469224 , -0.313638 , -0.324845 ) +colvars: ( 0.407383 , -0.159198 , -0.147896 ) +colvars: ( 0.34491 , -0.150983 , -0.174102 ) +colvars: ( 0.324918 , -0.0561727 , -0.0546567 ) +colvars: ( 0.207689 , -0.159174 , -0.268049 ) +colvars: ( 0.179492 , -0.204037 , -0.347232 ) +colvars: ( -0.0133458 , -0.207786 , -0.468491 ) +colvars: ( -0.114565 , -0.22609 , -0.554794 ) +colvars: ( 0.0998483 , -0.263602 , -0.477768 ) +colvars: ( 0.117794 , -0.11472 , -0.260506 ) +colvars: ( -0.0148628 , -0.118225 , -0.345206 ) +colvars: ( -0.113396 , -0.0300056 , -0.28217 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.24396 , 0.620729 , 1.73858 ) +colvars: ( 4.4967 , 0.532275 , 1.49083 ) +colvars: ( 4.4967 , 0.532275 , 1.49083 ) +colvars: ( 5.98973 , 0.709005 , 1.98583 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.680694 , -0.087056 , -0.437362 ) +colvars: ( -0.609666 , -0.176178 , -0.407936 ) +colvars: ( -0.559734 , -0.152587 , -0.346326 ) +colvars: ( -0.561635 , -0.206355 , -0.373758 ) +colvars: ( -0.551201 , -0.143552 , -0.333422 ) +colvars: ( -0.529929 , -0.305283 , -0.388688 ) +colvars: ( -0.48863 , -0.349163 , -0.367811 ) +colvars: ( -0.460769 , -0.464342 , -0.394334 ) +colvars: ( -0.420095 , -0.311842 , -0.280902 ) +colvars: ( -0.412615 , -0.28512 , -0.26067 ) +colvars: ( -0.36946 , -0.30586 , -0.226938 ) +colvars: ( -0.3043 , -0.26683 , -0.142626 ) +colvars: ( -0.254534 , -0.282784 , -0.0999484 ) +colvars: ( -0.328764 , -0.156185 , -0.114824 ) +colvars: ( -0.29315 , -0.125308 , -0.0642132 ) +colvars: ( -0.392544 , -0.0940704 , -0.149748 ) +colvars: ( -0.424897 , 0.0113595 , -0.132386 ) +colvars: ( -0.485227 , 0.0631266 , -0.168736 ) +colvars: ( -0.46227 , 0.0273082 , -0.162553 ) +colvars: ( -0.449793 , 0.0878505 , -0.121227 ) +colvars: ( -0.507061 , -0.0304032 , -0.235163 ) +colvars: ( -0.540332 , -0.0321297 , -0.269576 ) +colvars: ( -0.592186 , -0.101874 , -0.355028 ) +colvars: ( -0.478688 , -0.0650453 , -0.222954 ) +colvars: ( -0.484746 , -0.0180598 , -0.206775 ) +colvars: ( -0.416087 , -0.145054 , -0.197711 ) +colvars: ( -0.349077 , -0.179324 , -0.146314 ) +colvars: ( -0.291991 , -0.276207 , -0.134647 ) +colvars: ( -0.306468 , -0.101613 , -0.0664171 ) +colvars: ( -0.289271 , -0.0821123 , -0.0397993 ) +colvars: ( -0.290093 , -0.0533073 , -0.0269604 ) +colvars: ( -0.254412 , 0.0265505 , 0.0469599 ) +colvars: ( -0.236797 , 0.0551376 , 0.0783111 ) +colvars: ( -0.303863 , 0.119669 , 0.0412157 ) +colvars: ( -0.27405 , 0.163996 , 0.0923521 ) +colvars: ( -0.381446 , 0.150413 , -0.0225305 ) +colvars: ( -0.435726 , 0.232253 , -0.0385019 ) +colvars: ( -0.516485 , 0.257201 , -0.108205 ) +colvars: ( -0.442817 , 0.210612 , -0.0559301 ) +colvars: ( -0.447668 , 0.27559 , -0.0299949 ) +colvars: ( -0.442919 , 0.117717 , -0.100114 ) +colvars: ( -0.445052 , 0.0850025 , -0.117791 ) +colvars: ( -0.464562 , -0.0148811 , -0.184887 ) +colvars: ( -0.369286 , 0.0721681 , -0.0473807 ) +colvars: ( -0.370345 , 0.100037 , -0.0352261 ) +colvars: ( -0.194862 , 0.106032 , 0.144803 ) +colvars: ( -0.138755 , 0.107437 , 0.20212 ) +colvars: ( -0.229557 , 0.184032 , 0.146784 ) +colvars: ( -0.301245 , 0.0282123 , 0.000461777 ) +colvars: ( -0.225801 , 0.0129088 , 0.0693751 ) +colvars: ( -0.165531 , -0.0763699 , 0.0878645 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 2. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 2. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atoms_new_colvar_forces = { ( -4.94536484424471e+00 , -4.99230329339275e-01 , -1.46965138667428e+00 ), ( -4.26017169338647e+00 , -4.21837885497957e-01 , -1.16433344372845e+00 ), ( -4.33785972011736e+00 , -4.49439154598515e-01 , -1.20224951005482e+00 ), ( -5.83364162440807e+00 , -6.35425752643177e-01 , -1.76477374399873e+00 ), ( 2.71106477651610e-01 , 1.25722479883961e-01 , 3.67351443020935e-01 ), ( 5.33708059316313e+00 , 6.89799349662734e-01 , 2.07169601164356e+00 ), ( 4.51033556629133e+00 , 5.74419693366348e-01 , 1.79564555246299e+00 ), ( -4.48047999794275e-02 , 3.36388133054046e-02 , 3.74276559888785e-01 ), ( 4.48900187903556e+00 , 5.63959538908433e-01 , 1.76220658873513e+00 ), ( 5.94989167637375e+00 , 7.23091482993244e-01 , 2.19212860059994e+00 ), ( 1.23095353487825e-02 , 4.29279321141343e-02 , 3.14199957428508e-01 ), ( -5.62532568835983e-04 , 3.58064304664043e-02 , 2.87547664585458e-01 ), ( 2.11279362215647e-02 , 5.07786372071457e-02 , 3.56215326332885e-01 ), ( 4.51353870465388e-02 , 3.94498239469809e-02 , 2.09191993135665e-01 ), ( 1.53240403624194e-02 , 2.40569741006357e-02 , 1.56261841838829e-01 ), ( 1.18631213357434e-01 , 5.97949668988609e-02 , 1.98964911025173e-01 ), ( 1.67592406930671e-01 , 6.51304136706980e-02 , 1.26459852680159e-01 ), ( 2.52597717509630e-01 , 9.22628218633901e-02 , 1.43418033557420e-01 ), ( 1.37762014245814e-01 , 4.72848444314161e-02 , 5.39682796902565e-02 ), ( 1.32738485105735e-01 , 3.74498751149277e-02 , -1.28340241241104e-02 ), ( 1.14398700280755e-01 , 4.20430110654893e-02 , 6.70164300705228e-02 ), ( 7.73324842683294e-02 , 2.36560215455751e-02 , 7.21530116826130e-03 ), ( 6.45073992803266e-02 , 2.43510635340137e-02 , 4.29353375260687e-02 ), ( -2.82611138640421e-04 , -2.69411093985940e-03 , -2.08711298473133e-02 ), ( -1.46544324307763e-02 , -1.59807735460644e-02 , -9.32782921275177e-02 ), ( -5.10303929134580e-02 , -1.04709934114900e-02 , 3.63198957179338e-02 ), ( -1.23157715921451e-01 , -3.38495294483925e-02 , 1.90803829080292e-02 ), ( -1.67667609162110e-01 , -3.68481648406214e-02 , 9.97958424624752e-02 ), ( -1.10582086245515e-01 , -3.63266443574183e-02 , -3.02982381308109e-02 ), ( -1.49063210094619e-01 , -5.51617435820511e-02 , -9.03535974195620e-02 ), ( -5.46436650728548e-02 , -1.69766128267981e-02 , -7.18557018089740e-03 ), ( -3.30902501543696e-02 , -1.61641368762427e-02 , -5.13837073628916e-02 ), ( 2.61618773729005e-02 , 7.46654549545343e-03 , -1.84665973786238e-03 ), ( 8.39944953888894e-04 , -1.69042916182381e-02 , -1.37102762169889e-01 ), ( -1.82388158934780e-02 , -2.97140112926790e-02 , -1.94626862762827e-01 ), ( 5.10014130804014e-02 , -3.51224489192514e-03 , -1.48029058791080e-01 ), ( 8.23693559692558e-02 , -4.13873007770021e-03 , -2.26813159187842e-01 ), ( 1.47586222339250e-01 , 1.65886115570443e-02 , -2.14513279691095e-01 ), ( 2.04757191889185e-02 , -2.92597430710658e-02 , -2.82050682998041e-01 ), ( 2.15564734451574e-02 , -3.80476722220259e-02 , -3.54840336799863e-01 ), ( -3.55355903107537e-02 , -4.14812950402868e-02 , -2.48009242898295e-01 ), ( -1.00141474779805e-01 , -6.59799797980471e-02 , -2.91892981680507e-01 ), ( -1.39643749627078e-01 , -7.10538351169382e-02 , -2.39543859667753e-01 ), ( -1.61596777723409e-01 , -8.70062941269483e-02 , -3.15429800338440e-01 ), ( -1.90853207439237e-01 , -1.03999574012606e-01 , -3.82458396448231e-01 ), ( -2.08207591594682e-01 , -1.01753656038357e-01 , -3.23688440661073e-01 ), ( -2.53319897531783e-01 , -1.18652957765828e-01 , -3.52673399626206e-01 ), ( -1.29708690061578e-01 , -7.95697482525082e-02 , -3.30984091985120e-01 ), ( -1.83451072437040e-01 , -8.65077194601226e-02 , -2.60043906098063e-01 ), ( -2.40663663419215e-01 , -1.05316193775053e-01 , -2.75830749010938e-01 ), ( -2.78926800166438e-01 , -1.06375552664104e-01 , -1.94305492276471e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 3, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 3, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 3, atoms_positions[size = 51] = { ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 ), ( 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 ), ( 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 ), ( 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ), ( 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 ), ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 ), ( 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 ), ( 7.18887438592740e+00 , -3.18190538896136e-01 , 4.30240438250701e+00 ), ( 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 ), ( 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ), ( 5.87428924915182e+00 , 2.33046858202937e+00 , 2.95718817842218e+00 ), ( 5.22756354085870e+00 , 3.59806563949040e+00 , 2.87989840364726e+00 ), ( 6.33004327971406e+00 , 4.62660866005681e+00 , 2.46802543565857e+00 ), ( 3.89875294604380e+00 , 3.70379107545018e+00 , 2.02347367014388e+00 ), ( 2.92333166283481e+00 , 4.11580409777728e+00 , 2.56498566370563e+00 ), ( 3.81870402884775e+00 , 3.24371757057811e+00 , 7.82494662400517e-01 ), ( 2.66311149915854e+00 , 3.19306435678778e+00 , -7.50205577463578e-02 ), ( 3.04938916927457e+00 , 2.72951079865366e+00 , -1.58743520554313e+00 ), ( 1.64233040103771e+00 , 2.15864553679670e+00 , 5.75793583272084e-01 ), ( 4.27090638049903e-01 , 2.43325492205922e+00 , 5.66066171000393e-01 ), ( 1.98044204554190e+00 , 1.00388530801315e+00 , 1.05723759401865e+00 ), ( 1.12901973159542e+00 , 1.29167416517915e-02 , 1.68724137458764e+00 ), ( 2.01590257389253e+00 , -1.19931623024337e+00 , 2.02325134846391e+00 ), ( 5.02873252997144e-01 , 5.87789122186409e-01 , 3.01035401048538e+00 ), ( -6.81444799066583e-01 , 3.85824301681720e-01 , 3.19254195491642e+00 ), ( 1.28185433712608e+00 , 1.30770649318966e+00 , 3.82341417641572e+00 ), ( 8.15485986974327e-01 , 1.88749888489650e+00 , 5.08218920724669e+00 ), ( 2.06838974384938e+00 , 2.58346613036847e+00 , 5.62073972587495e+00 ), ( -3.54753217917702e-01 , 2.92076530153912e+00 , 4.98647989495056e+00 ), ( -1.18059860901710e+00 , 3.01914604664074e+00 , 5.90115755916543e+00 ), ( -3.94243204894331e-01 , 3.70183869752321e+00 , 3.87005048430333e+00 ), ( -1.46136791229833e+00 , 4.60679178565910e+00 , 3.53446291377488e+00 ), ( -7.67375356843104e-01 , 5.37852593586357e+00 , 2.40557758311810e+00 ), ( -2.70861285809934e+00 , 3.89781582916249e+00 , 2.94244555060088e+00 ), ( -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 ), ( -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 ), ( -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 ), ( -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 ), ( -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 ), ( -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 ), ( -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 ), ( -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 ), ( -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 ), ( -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 ), ( -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 ), ( -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 ), ( -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 ), ( -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 ), ( -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 ), ( -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 ), ( -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ) } +colvars: Step 3, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar "one", components 0 through 1. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.37727237769795e-01 , 5.76269013801485e-03 , 9.41226383114476e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 , 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 7.18887438592740e+00 , -3.18190538896136e-01 , 4.30240438250701e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 , 5.87428924915182e+00 , 2.33046858202937e+00 , 2.95718817842218e+00 , 5.22756354085870e+00 , 3.59806563949040e+00 , 2.87989840364726e+00 , 6.33004327971406e+00 , 4.62660866005681e+00 , 2.46802543565857e+00 , 3.89875294604380e+00 , 3.70379107545018e+00 , 2.02347367014388e+00 , 2.92333166283481e+00 , 4.11580409777728e+00 , 2.56498566370563e+00 , 3.81870402884775e+00 , 3.24371757057811e+00 , 7.82494662400517e-01 , 2.66311149915854e+00 , 3.19306435678778e+00 , -7.50205577463578e-02 , 3.04938916927457e+00 , 2.72951079865366e+00 , -1.58743520554313e+00 , 1.64233040103771e+00 , 2.15864553679670e+00 , 5.75793583272084e-01 , 4.27090638049903e-01 , 2.43325492205922e+00 , 5.66066171000393e-01 , 1.98044204554190e+00 , 1.00388530801315e+00 , 1.05723759401865e+00 , 1.12901973159542e+00 , 1.29167416517915e-02 , 1.68724137458764e+00 , 2.01590257389253e+00 , -1.19931623024337e+00 , 2.02325134846391e+00 , 5.02873252997144e-01 , 5.87789122186409e-01 , 3.01035401048538e+00 , -6.81444799066583e-01 , 3.85824301681720e-01 , 3.19254195491642e+00 , 1.28185433712608e+00 , 1.30770649318966e+00 , 3.82341417641572e+00 , 8.15485986974327e-01 , 1.88749888489650e+00 , 5.08218920724669e+00 , 2.06838974384938e+00 , 2.58346613036847e+00 , 5.62073972587495e+00 , -3.54753217917702e-01 , 2.92076530153912e+00 , 4.98647989495056e+00 , -1.18059860901710e+00 , 3.01914604664074e+00 , 5.90115755916543e+00 , -3.94243204894331e-01 , 3.70183869752321e+00 , 3.87005048430333e+00 , -1.46136791229833e+00 , 4.60679178565910e+00 , 3.53446291377488e+00 , -7.67375356843104e-01 , 5.37852593586357e+00 , 2.40557758311810e+00 , -2.70861285809934e+00 , 3.89781582916249e+00 , 2.94244555060088e+00 , -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 , -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 , -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 , -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 , -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 , -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 , -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 , -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 , -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 , -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 , -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 , -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 , -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 , -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 , -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 , -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 , -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.37727237769795e-01 , 5.76269013801485e-03 , 9.41226383114476e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 , 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 7.18887438592740e+00 , -3.18190538896136e-01 , 4.30240438250701e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 , 5.87428924915182e+00 , 2.33046858202937e+00 , 2.95718817842218e+00 , 5.22756354085870e+00 , 3.59806563949040e+00 , 2.87989840364726e+00 , 6.33004327971406e+00 , 4.62660866005681e+00 , 2.46802543565857e+00 , 3.89875294604380e+00 , 3.70379107545018e+00 , 2.02347367014388e+00 , 2.92333166283481e+00 , 4.11580409777728e+00 , 2.56498566370563e+00 , 3.81870402884775e+00 , 3.24371757057811e+00 , 7.82494662400517e-01 , 2.66311149915854e+00 , 3.19306435678778e+00 , -7.50205577463578e-02 , 3.04938916927457e+00 , 2.72951079865366e+00 , -1.58743520554313e+00 , 1.64233040103771e+00 , 2.15864553679670e+00 , 5.75793583272084e-01 , 4.27090638049903e-01 , 2.43325492205922e+00 , 5.66066171000393e-01 , 1.98044204554190e+00 , 1.00388530801315e+00 , 1.05723759401865e+00 , 1.12901973159542e+00 , 1.29167416517915e-02 , 1.68724137458764e+00 , 2.01590257389253e+00 , -1.19931623024337e+00 , 2.02325134846391e+00 , 5.02873252997144e-01 , 5.87789122186409e-01 , 3.01035401048538e+00 , -6.81444799066583e-01 , 3.85824301681720e-01 , 3.19254195491642e+00 , 1.28185433712608e+00 , 1.30770649318966e+00 , 3.82341417641572e+00 , 8.15485986974327e-01 , 1.88749888489650e+00 , 5.08218920724669e+00 , 2.06838974384938e+00 , 2.58346613036847e+00 , 5.62073972587495e+00 , -3.54753217917702e-01 , 2.92076530153912e+00 , 4.98647989495056e+00 , -1.18059860901710e+00 , 3.01914604664074e+00 , 5.90115755916543e+00 , -3.94243204894331e-01 , 3.70183869752321e+00 , 3.87005048430333e+00 , -1.46136791229833e+00 , 4.60679178565910e+00 , 3.53446291377488e+00 , -7.67375356843104e-01 , 5.37852593586357e+00 , 2.40557758311810e+00 , -2.70861285809934e+00 , 3.89781582916249e+00 , 2.94244555060088e+00 , -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 , -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 , -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 , -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 , -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 , -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 , -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 , -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 , -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 , -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 , -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 , -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 , -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 , -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 , -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 , -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 , -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.7293 , 6.77293 , 13.5459 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.7293 , 6.77293 , 13.5459 ) to colvar "one". +colvars: Adding total bias energy: 58.9364 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.7293 , 6.77293 , 13.5459 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.24245 , -0.619393 , -1.73315 ) +colvars: ( -4.4954 , -0.531129 , -1.48618 ) +colvars: ( -4.4954 , -0.531129 , -1.48618 ) +colvars: ( -5.988 , -0.70748 , -1.97963 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.978076 , 0.208579 , 0.704715 ) +colvars: ( 0.845198 , 0.286571 , 0.73272 ) +colvars: ( 0.829782 , 0.278273 , 0.711963 ) +colvars: ( 0.719742 , 0.289103 , 0.660762 ) +colvars: ( 0.706584 , 0.217067 , 0.55316 ) +colvars: ( 0.622523 , 0.374202 , 0.72005 ) +colvars: ( 0.502006 , 0.391108 , 0.670955 ) +colvars: ( 0.415878 , 0.497712 , 0.766674 ) +colvars: ( 0.412254 , 0.343321 , 0.550839 ) +colvars: ( 0.372736 , 0.299001 , 0.465737 ) +colvars: ( 0.381599 , 0.348578 , 0.539675 ) +colvars: ( 0.303656 , 0.302424 , 0.428922 ) +colvars: ( 0.275547 , 0.333338 , 0.454796 ) +colvars: ( 0.37368 , 0.195485 , 0.323053 ) +colvars: ( 0.308374 , 0.149212 , 0.219736 ) +colvars: ( 0.5107 , 0.153775 , 0.347749 ) +colvars: ( 0.59186 , 0.0537435 , 0.258138 ) +colvars: ( 0.736906 , 0.0291659 , 0.31137 ) +colvars: ( 0.599468 , 0.0199567 , 0.215958 ) +colvars: ( 0.582001 , -0.0504 , 0.108088 ) +colvars: ( 0.620927 , 0.0724069 , 0.301449 ) +colvars: ( 0.617221 , 0.0557437 , 0.27616 ) +colvars: ( 0.656243 , 0.126163 , 0.397082 ) +colvars: ( 0.478233 , 0.0622615 , 0.201579 ) +colvars: ( 0.469965 , 0.00200631 , 0.113222 ) +colvars: ( 0.365068 , 0.134434 , 0.233387 ) +colvars: ( 0.226189 , 0.145276 , 0.164857 ) +colvars: ( 0.124752 , 0.239097 , 0.233677 ) +colvars: ( 0.196159 , 0.0651142 , 0.0358609 ) +colvars: ( 0.140611 , 0.026772 , -0.050611 ) +colvars: ( 0.235571 , 0.0361886 , 0.0195385 ) +colvars: ( 0.221416 , -0.0428267 , -0.0983218 ) +colvars: ( 0.262891 , -0.0477602 , -0.0802021 ) +colvars: ( 0.304675 , -0.136627 , -0.178048 ) +colvars: ( 0.255867 , -0.193758 , -0.286466 ) +colvars: ( 0.43222 , -0.153936 , -0.125284 ) +colvars: ( 0.517748 , -0.236348 , -0.187886 ) +colvars: ( 0.663475 , -0.240523 , -0.106009 ) +colvars: ( 0.463123 , -0.239851 , -0.225591 ) +colvars: ( 0.469058 , -0.313589 , -0.324064 ) +colvars: ( 0.407368 , -0.15923 , -0.147559 ) +colvars: ( 0.345084 , -0.151044 , -0.173694 ) +colvars: ( 0.325182 , -0.0562811 , -0.0545258 ) +colvars: ( 0.208097 , -0.159275 , -0.26748 ) +colvars: ( 0.179992 , -0.204133 , -0.346463 ) +colvars: ( -0.0126718 , -0.207924 , -0.467596 ) +colvars: ( -0.113717 , -0.226252 , -0.553737 ) +colvars: ( 0.100274 , -0.26368 , -0.476817 ) +colvars: ( 0.118308 , -0.114859 , -0.260023 ) +colvars: ( -0.0141262 , -0.118403 , -0.344586 ) +colvars: ( -0.112516 , -0.0302437 , -0.281767 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.24245 , 0.619393 , 1.73315 ) +colvars: ( 4.4954 , 0.531129 , 1.48618 ) +colvars: ( 4.4954 , 0.531129 , 1.48618 ) +colvars: ( 5.988 , 0.70748 , 1.97963 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.679737 , -0.0870137 , -0.436053 ) +colvars: ( -0.608874 , -0.176153 , -0.406435 ) +colvars: ( -0.558802 , -0.152523 , -0.344743 ) +colvars: ( -0.561074 , -0.20634 , -0.372365 ) +colvars: ( -0.550646 , -0.143511 , -0.332264 ) +colvars: ( -0.529565 , -0.305307 , -0.387119 ) +colvars: ( -0.488507 , -0.349205 , -0.36631 ) +colvars: ( -0.46082 , -0.464428 , -0.392574 ) +colvars: ( -0.420008 , -0.311847 , -0.279546 ) +colvars: ( -0.412632 , -0.285121 , -0.259518 ) +colvars: ( -0.36928 , -0.305836 , -0.225483 ) +colvars: ( -0.30413 , -0.266767 , -0.141296 ) +colvars: ( -0.254266 , -0.2827 , -0.0984329 ) +colvars: ( -0.32846 , -0.156081 , -0.113777 ) +colvars: ( -0.292928 , -0.125186 , -0.0633496 ) +colvars: ( -0.392032 , -0.0939533 , -0.148744 ) +colvars: ( -0.424245 , 0.0115129 , -0.131642 ) +colvars: ( -0.484326 , 0.0632946 , -0.167953 ) +colvars: ( -0.461736 , 0.0274434 , -0.16201 ) +colvars: ( -0.449272 , 0.0880112 , -0.120917 ) +colvars: ( -0.506626 , -0.0303141 , -0.23453 ) +colvars: ( -0.540038 , -0.0320652 , -0.2691 ) +colvars: ( -0.591959 , -0.10186 , -0.354386 ) +colvars: ( -0.478618 , -0.0649862 , -0.22256 ) +colvars: ( -0.484728 , -0.0179905 , -0.206614 ) +colvars: ( -0.416148 , -0.14501 , -0.197129 ) +colvars: ( -0.349341 , -0.179282 , -0.145785 ) +colvars: ( -0.292369 , -0.276187 , -0.13385 ) +colvars: ( -0.306671 , -0.101522 , -0.0660933 ) +colvars: ( -0.289593 , -0.0820165 , -0.039665 ) +colvars: ( -0.290103 , -0.0531769 , -0.0266075 ) +colvars: ( -0.254336 , 0.0267304 , 0.0471237 ) +colvars: ( -0.236516 , 0.0553508 , 0.078591 ) +colvars: ( -0.303704 , 0.119869 , 0.0410966 ) +colvars: ( -0.27394 , 0.16422 , 0.0920304 ) +colvars: ( -0.381163 , 0.150604 , -0.0226701 ) +colvars: ( -0.43537 , 0.232458 , -0.0388958 ) +colvars: ( -0.515956 , 0.257397 , -0.108549 ) +colvars: ( -0.442669 , 0.21079 , -0.0564647 ) +colvars: ( -0.447522 , 0.275789 , -0.0307751 ) +colvars: ( -0.442953 , 0.117847 , -0.100493 ) +colvars: ( -0.4453 , 0.0851032 , -0.118274 ) +colvars: ( -0.464948 , -0.0148347 , -0.185152 ) +colvars: ( -0.369698 , 0.0722808 , -0.0479517 ) +colvars: ( -0.370856 , 0.100152 , -0.0360047 ) +colvars: ( -0.195338 , 0.10622 , 0.14412 ) +colvars: ( -0.139351 , 0.107638 , 0.201333 ) +colvars: ( -0.229794 , 0.184253 , 0.146045 ) +colvars: ( -0.301692 , 0.0283331 , 4.94566e-05 ) +colvars: ( -0.226397 , 0.0130417 , 0.0688985 ) +colvars: ( -0.166219 , -0.0762527 , 0.0876522 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 3. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 3. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atoms_new_colvar_forces = { ( -4.94411184671079e+00 , -4.97827513445736e-01 , -1.46449135037820e+00 ), ( -4.25907640521865e+00 , -4.20711456786056e-01 , -1.15989394156424e+00 ), ( -4.33673317769691e+00 , -4.48366501363439e-01 , -1.19778202100695e+00 ), ( -5.83206630045447e+00 , -6.33924119977363e-01 , -1.75873742632449e+00 ), ( 2.70980020612708e-01 , 1.25749755944837e-01 , 3.67220461302410e-01 ), ( 5.33540843769253e+00 , 6.88287635230181e-01 , 2.06608439293031e+00 ), ( 4.50889974963906e+00 , 5.73031757721403e-01 , 1.79082311728939e+00 ), ( -4.49416315065174e-02 , 3.32833456980806e-02 , 3.74099563837129e-01 ), ( 4.48764679167200e+00 , 5.62602923523582e-01 , 1.75747196273388e+00 ), ( 5.94810856283136e+00 , 7.21359809854066e-01 , 2.18585209845762e+00 ), ( 1.23182431151496e-02 , 4.27418719254232e-02 , 3.14191620291453e-01 ), ( -4.74416193415428e-04 , 3.56567177610567e-02 , 2.87626199467661e-01 ), ( 2.12814041388975e-02 , 5.06380997492398e-02 , 3.56363328527525e-01 ), ( 4.52197772755877e-02 , 3.94035396542006e-02 , 2.09276201599730e-01 ), ( 1.54458868355712e-02 , 2.40259994114552e-02 , 1.56386914327082e-01 ), ( 1.18667398254240e-01 , 5.98215048345298e-02 , 1.99005120483717e-01 ), ( 1.67615720865544e-01 , 6.52564920828010e-02 , 1.26495754888538e-01 ), ( 2.52579421928450e-01 , 9.24605005403267e-02 , 1.43416723091599e-01 ), ( 1.37732531939567e-01 , 4.74000180514384e-02 , 5.39477638410795e-02 ), ( 1.32729168872771e-01 , 3.76112537757227e-02 , -1.28290054297651e-02 ), ( 1.14301418742866e-01 , 4.20928208462876e-02 , 6.69186082022440e-02 ), ( 7.71832550686790e-02 , 2.36784766810483e-02 , 7.06042771512738e-03 ), ( 6.42837202712789e-02 , 2.43030078484564e-02 , 4.26956614103106e-02 ), ( -3.84329372512093e-04 , -2.72472916439909e-03 , -2.09808707804465e-02 ), ( -1.47628235207854e-02 , -1.59841739107175e-02 , -9.33924543843910e-02 ), ( -5.10803034919172e-02 , -1.05765153684527e-02 , 3.62576862219569e-02 ), ( -1.23152065175043e-01 , -3.40052163812419e-02 , 1.90720230464335e-02 ), ( -1.67616763767845e-01 , -3.70895287307892e-02 , 9.98270398312682e-02 ), ( -1.10512426265833e-01 , -3.64077329425433e-02 , -3.02323805237733e-02 ), ( -1.48982346206602e-01 , -5.52444650887813e-02 , -9.02760252414938e-02 ), ( -5.45317489037881e-02 , -1.69883324043285e-02 , -7.06894903341551e-03 ), ( -3.29197549988429e-02 , -1.60963474146286e-02 , -5.11981358015210e-02 ), ( 2.63750143131919e-02 , 7.59060243351772e-03 , -1.61115692641367e-03 ), ( 9.70867813391729e-04 , -1.67576633972936e-02 , -1.36951455760848e-01 ), ( -1.80727359462569e-02 , -2.95373785036137e-02 , -1.94435756236881e-01 ), ( 5.10568221807806e-02 , -3.33172246149266e-03 , -1.47954036182704e-01 ), ( 8.23773230277767e-02 , -3.89030474462265e-03 , -2.26781689509279e-01 ), ( 1.47518804880217e-01 , 1.68736913838752e-02 , -2.14557736824648e-01 ), ( 2.04537680097125e-02 , -2.90615161904835e-02 , -2.82055200722617e-01 ), ( 2.15359977798839e-02 , -3.78001826957295e-02 , -3.54838685488566e-01 ), ( -3.55848857133958e-02 , -4.13832707320046e-02 , -2.48051749485939e-01 ), ( -1.00216698830745e-01 , -6.59410279588554e-02 , -2.91968109753298e-01 ), ( -1.39765584367239e-01 , -7.11157696196284e-02 , -2.39677324262951e-01 ), ( -1.61600215592381e-01 , -8.69937885828269e-02 , -3.15431833916719e-01 ), ( -1.90863879034194e-01 , -1.03981201565893e-01 , -3.82467406313103e-01 ), ( -2.08009834583172e-01 , -1.01704171955603e-01 , -3.23475504908314e-01 ), ( -2.53067678027391e-01 , -1.18614509952742e-01 , -3.52404165644519e-01 ), ( -1.29520566963423e-01 , -7.94267978023419e-02 , -3.30772706408666e-01 ), ( -1.83383340883908e-01 , -8.65264099464878e-02 , -2.59974038061368e-01 ), ( -2.40523504544333e-01 , -1.05361075555689e-01 , -2.75687099588435e-01 ), ( -2.78734843790854e-01 , -1.06496400307745e-01 , -1.94114453032528e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 4, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 4, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 4, atoms_positions[size = 51] = { ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 ), ( 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 ), ( 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 ), ( 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ), ( 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 ), ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 ), ( 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 ), ( 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 ), ( 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 ), ( 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ), ( 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 ), ( 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 ), ( 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 ), ( 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 ), ( 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 ), ( 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 ), ( 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 ), ( 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 ), ( 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 ), ( 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 ), ( 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 ), ( 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 ), ( 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 ), ( 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 ), ( -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 ), ( 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 ), ( 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 ), ( 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 ), ( -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 ), ( -1.17836558276957e+00 , 3.02261104816295e+00 , 5.90276840372370e+00 ), ( -4.01302424179341e-01 , 3.69849881712387e+00 , 3.86545342166451e+00 ), ( -1.46590890439991e+00 , 4.59865695705450e+00 , 3.53615846971960e+00 ), ( -7.63233646113516e-01 , 5.38072830628868e+00 , 2.40731483544891e+00 ), ( -2.71331069598888e+00 , 3.89707509031229e+00 , 2.93922305454171e+00 ), ( -3.85425548868909e+00 , 4.41458054455749e+00 , 2.85996693260786e+00 ), ( -2.56891242118530e+00 , 2.61382706053113e+00 , 2.50018071521494e+00 ), ( -3.72280812663129e+00 , 1.90195999542730e+00 , 2.07499278897672e+00 ), ( -3.40867725952187e+00 , 7.99802561950416e-01 , 1.00115557235893e+00 ), ( -4.32545280821172e+00 , 1.10899537342912e+00 , 3.22039502470298e+00 ), ( -5.53351177439246e+00 , 9.30423737330286e-01 , 3.34743812026931e+00 ), ( -3.47526232399215e+00 , 6.31186205193408e-01 , 4.16470361442067e+00 ), ( -3.76916231092019e+00 , 1.03560723559009e-01 , 5.47574864057925e+00 ), ( -2.42579604390000e+00 , -4.19510894178595e-01 , 6.13327314251220e+00 ), ( -4.46410817799216e+00 , 1.00718933605956e+00 , 6.41670516158355e+00 ), ( -5.32471542662051e+00 , 5.95665490335250e-01 , 7.18047316154811e+00 ), ( -6.29683784304267e+00 , 3.54743931376085e+00 , 6.69752696916196e+00 ), ( -6.91966222332481e+00 , 4.30777465539821e+00 , 7.41749594212074e+00 ), ( -6.75473280268310e+00 , 3.20844297878927e+00 , 5.50482041882141e+00 ), ( -4.08020191955437e+00 , 2.29656035348140e+00 , 6.47726737906147e+00 ), ( -4.91288479652016e+00 , 3.24197930773862e+00 , 7.21486048527815e+00 ), ( -4.06885606267348e+00 , 4.49555323945452e+00 , 7.26530353283818e+00 ) } +colvars: Step 4, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 , 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 , 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 , 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 , 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 , 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 , 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 , 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 , 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 , 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 , 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 , 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 , 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 , 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 , 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 , 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 , -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 , 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 , 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 , 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 , -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 , -1.17836558276957e+00 , 3.02261104816295e+00 , 5.90276840372370e+00 , -4.01302424179341e-01 , 3.69849881712387e+00 , 3.86545342166451e+00 , -1.46590890439991e+00 , 4.59865695705450e+00 , 3.53615846971960e+00 , -7.63233646113516e-01 , 5.38072830628868e+00 , 2.40731483544891e+00 , -2.71331069598888e+00 , 3.89707509031229e+00 , 2.93922305454171e+00 , -3.85425548868909e+00 , 4.41458054455749e+00 , 2.85996693260786e+00 , -2.56891242118530e+00 , 2.61382706053113e+00 , 2.50018071521494e+00 , -3.72280812663129e+00 , 1.90195999542730e+00 , 2.07499278897672e+00 , -3.40867725952187e+00 , 7.99802561950416e-01 , 1.00115557235893e+00 , -4.32545280821172e+00 , 1.10899537342912e+00 , 3.22039502470298e+00 , -5.53351177439246e+00 , 9.30423737330286e-01 , 3.34743812026931e+00 , -3.47526232399215e+00 , 6.31186205193408e-01 , 4.16470361442067e+00 , -3.76916231092019e+00 , 1.03560723559009e-01 , 5.47574864057925e+00 , -2.42579604390000e+00 , -4.19510894178595e-01 , 6.13327314251220e+00 , -4.46410817799216e+00 , 1.00718933605956e+00 , 6.41670516158355e+00 , -5.32471542662051e+00 , 5.95665490335250e-01 , 7.18047316154811e+00 , -6.29683784304267e+00 , 3.54743931376085e+00 , 6.69752696916196e+00 , -6.91966222332481e+00 , 4.30777465539821e+00 , 7.41749594212074e+00 , -6.75473280268310e+00 , 3.20844297878927e+00 , 5.50482041882141e+00 , -4.08020191955437e+00 , 2.29656035348140e+00 , 6.47726737906147e+00 , -4.91288479652016e+00 , 3.24197930773862e+00 , 7.21486048527815e+00 , -4.06885606267348e+00 , 4.49555323945452e+00 , 7.26530353283818e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.36535507777281e-01 , 5.34093077602620e-03 , 9.41655630505937e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.36535507777281e-01 , 5.34093077602620e-03 , 9.41655630505937e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 , 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 , 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 , 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 , 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 , 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 , 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 , 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 , 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 , 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 , 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 , 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 , 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 , 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 , 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 , 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 , -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 , 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 , 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 , 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 , -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 , -1.17836558276957e+00 , 3.02261104816295e+00 , 5.90276840372370e+00 , -4.01302424179341e-01 , 3.69849881712387e+00 , 3.86545342166451e+00 , -1.46590890439991e+00 , 4.59865695705450e+00 , 3.53615846971960e+00 , -7.63233646113516e-01 , 5.38072830628868e+00 , 2.40731483544891e+00 , -2.71331069598888e+00 , 3.89707509031229e+00 , 2.93922305454171e+00 , -3.85425548868909e+00 , 4.41458054455749e+00 , 2.85996693260786e+00 , -2.56891242118530e+00 , 2.61382706053113e+00 , 2.50018071521494e+00 , -3.72280812663129e+00 , 1.90195999542730e+00 , 2.07499278897672e+00 , -3.40867725952187e+00 , 7.99802561950416e-01 , 1.00115557235893e+00 , -4.32545280821172e+00 , 1.10899537342912e+00 , 3.22039502470298e+00 , -5.53351177439246e+00 , 9.30423737330286e-01 , 3.34743812026931e+00 , -3.47526232399215e+00 , 6.31186205193408e-01 , 4.16470361442067e+00 , -3.76916231092019e+00 , 1.03560723559009e-01 , 5.47574864057925e+00 , -2.42579604390000e+00 , -4.19510894178595e-01 , 6.13327314251220e+00 , -4.46410817799216e+00 , 1.00718933605956e+00 , 6.41670516158355e+00 , -5.32471542662051e+00 , 5.95665490335250e-01 , 7.18047316154811e+00 , -6.29683784304267e+00 , 3.54743931376085e+00 , 6.69752696916196e+00 , -6.91966222332481e+00 , 4.30777465539821e+00 , 7.41749594212074e+00 , -6.75473280268310e+00 , 3.20844297878927e+00 , 5.50482041882141e+00 , -4.08020191955437e+00 , 2.29656035348140e+00 , 6.47726737906147e+00 , -4.91288479652016e+00 , 3.24197930773862e+00 , 7.21486048527815e+00 , -4.06885606267348e+00 , 4.49555323945452e+00 , 7.26530353283818e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.6692 , 6.76692 , 13.5338 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.6692 , 6.76692 , 13.5338 ) to colvar "one". +colvars: Adding total bias energy: 58.8527 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.6692 , 6.76692 , 13.5338 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.23957 , -0.61745 , -1.72566 ) +colvars: ( -4.49293 , -0.529463 , -1.47975 ) +colvars: ( -4.49293 , -0.529463 , -1.47975 ) +colvars: ( -5.98471 , -0.705261 , -1.97107 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.976464 , 0.208547 , 0.702628 ) +colvars: ( 0.843878 , 0.286424 , 0.730489 ) +colvars: ( 0.828394 , 0.278149 , 0.70976 ) +colvars: ( 0.718751 , 0.288893 , 0.658711 ) +colvars: ( 0.705622 , 0.216911 , 0.551429 ) +colvars: ( 0.621792 , 0.373873 , 0.717791 ) +colvars: ( 0.501603 , 0.390705 , 0.668811 ) +colvars: ( 0.415703 , 0.497178 , 0.764213 ) +colvars: ( 0.412007 , 0.342932 , 0.549009 ) +colvars: ( 0.372617 , 0.298625 , 0.464159 ) +colvars: ( 0.381335 , 0.348192 , 0.53784 ) +colvars: ( 0.303514 , 0.302058 , 0.427375 ) +colvars: ( 0.275379 , 0.332955 , 0.453133 ) +colvars: ( 0.373359 , 0.19524 , 0.32185 ) +colvars: ( 0.308203 , 0.148979 , 0.21882 ) +colvars: ( 0.510051 , 0.153623 , 0.346523 ) +colvars: ( 0.591012 , 0.0537111 , 0.257212 ) +colvars: ( 0.73569 , 0.0292204 , 0.310332 ) +colvars: ( 0.59869 , 0.0199359 , 0.215188 ) +colvars: ( 0.581261 , -0.050369 , 0.107638 ) +colvars: ( 0.620177 , 0.0723336 , 0.300452 ) +colvars: ( 0.616569 , 0.0556627 , 0.275264 ) +colvars: ( 0.655572 , 0.126024 , 0.395856 ) +colvars: ( 0.477925 , 0.062113 , 0.20086 ) +colvars: ( 0.469708 , 0.0018974 , 0.112776 ) +colvars: ( 0.365002 , 0.134183 , 0.23252 ) +colvars: ( 0.226453 , 0.144958 , 0.164145 ) +colvars: ( 0.125227 , 0.238664 , 0.23271 ) +colvars: ( 0.196432 , 0.0648636 , 0.0355108 ) +colvars: ( 0.141045 , 0.0265233 , -0.050712 ) +colvars: ( 0.235666 , 0.0359979 , 0.0192281 ) +colvars: ( 0.221481 , -0.0429434 , -0.0982988 ) +colvars: ( 0.262764 , -0.0478342 , -0.0802453 ) +colvars: ( 0.304575 , -0.136638 , -0.177742 ) +colvars: ( 0.255874 , -0.193739 , -0.285853 ) +colvars: ( 0.431857 , -0.153888 , -0.125077 ) +colvars: ( 0.517223 , -0.236204 , -0.187445 ) +colvars: ( 0.662629 , -0.240319 , -0.105754 ) +colvars: ( 0.462811 , -0.239746 , -0.225032 ) +colvars: ( 0.468745 , -0.313423 , -0.323201 ) +colvars: ( 0.407248 , -0.159229 , -0.147241 ) +colvars: ( 0.345191 , -0.151094 , -0.173297 ) +colvars: ( 0.3254 , -0.0564323 , -0.0544799 ) +colvars: ( 0.208508 , -0.159371 , -0.266858 ) +colvars: ( 0.180511 , -0.204213 , -0.3456 ) +colvars: ( -0.0118988 , -0.208037 , -0.466498 ) +colvars: ( -0.112719 , -0.226389 , -0.552422 ) +colvars: ( 0.100734 , -0.263689 , -0.475662 ) +colvars: ( 0.118867 , -0.115016 , -0.259477 ) +colvars: ( -0.0132805 , -0.118606 , -0.343842 ) +colvars: ( -0.111477 , -0.0305532 , -0.281262 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.23957 , 0.61745 , 1.72566 ) +colvars: ( 4.49293 , 0.529463 , 1.47975 ) +colvars: ( 4.49293 , 0.529463 , 1.47975 ) +colvars: ( 5.98471 , 0.705261 , 1.97107 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.678413 , -0.0869414 , -0.434258 ) +colvars: ( -0.607779 , -0.176034 , -0.404464 ) +colvars: ( -0.557584 , -0.152389 , -0.342737 ) +colvars: ( -0.560265 , -0.206199 , -0.370541 ) +colvars: ( -0.549849 , -0.143384 , -0.330724 ) +colvars: ( -0.528996 , -0.305131 , -0.385097 ) +colvars: ( -0.488229 , -0.349007 , -0.364383 ) +colvars: ( -0.460755 , -0.464191 , -0.390352 ) +colvars: ( -0.419812 , -0.311635 , -0.277848 ) +colvars: ( -0.412554 , -0.284915 , -0.258055 ) +colvars: ( -0.369014 , -0.305605 , -0.223727 ) +colvars: ( -0.303915 , -0.266524 , -0.139746 ) +colvars: ( -0.253974 , -0.282433 , -0.0967209 ) +colvars: ( -0.328079 , -0.155876 , -0.112548 ) +colvars: ( -0.292658 , -0.124978 , -0.0623596 ) +colvars: ( -0.39138 , -0.093784 , -0.147528 ) +colvars: ( -0.423414 , 0.0116438 , -0.130714 ) +colvars: ( -0.483183 , 0.063394 , -0.166949 ) +colvars: ( -0.461013 , 0.027554 , -0.161271 ) +colvars: ( -0.448569 , 0.0881091 , -0.12046 ) +colvars: ( -0.505985 , -0.0302053 , -0.233634 ) +colvars: ( -0.53953 , -0.0319706 , -0.26834 ) +colvars: ( -0.591494 , -0.101766 , -0.353379 ) +colvars: ( -0.478396 , -0.0648645 , -0.221932 ) +colvars: ( -0.48456 , -0.0178852 , -0.206247 ) +colvars: ( -0.416114 , -0.144846 , -0.196325 ) +colvars: ( -0.349574 , -0.179088 , -0.145085 ) +colvars: ( -0.292765 , -0.275947 , -0.132877 ) +colvars: ( -0.306861 , -0.101333 , -0.0656787 ) +colvars: ( -0.289925 , -0.0818295 , -0.0394757 ) +colvars: ( -0.29009 , -0.0529923 , -0.0261937 ) +colvars: ( -0.254247 , 0.0269071 , 0.0472739 ) +colvars: ( -0.236212 , 0.0555298 , 0.0788397 ) +colvars: ( -0.303491 , 0.120004 , 0.0409534 ) +colvars: ( -0.273799 , 0.164352 , 0.0916275 ) +colvars: ( -0.380763 , 0.150705 , -0.022778 ) +colvars: ( -0.434854 , 0.232517 , -0.0392581 ) +colvars: ( -0.515198 , 0.257423 , -0.108795 ) +colvars: ( -0.442378 , 0.210849 , -0.0569636 ) +colvars: ( -0.447228 , 0.275828 , -0.0315567 ) +colvars: ( -0.442866 , 0.117928 , -0.100792 ) +colvars: ( -0.445448 , 0.0851888 , -0.11867 ) +colvars: ( -0.465238 , -0.0147308 , -0.185259 ) +colvars: ( -0.370074 , 0.0723941 , -0.0485041 ) +colvars: ( -0.371339 , 0.100255 , -0.0367886 ) +colvars: ( -0.195894 , 0.106385 , 0.143282 ) +colvars: ( -0.140075 , 0.10782 , 0.200332 ) +colvars: ( -0.230063 , 0.184389 , 0.145148 ) +colvars: ( -0.30215 , 0.0284824 , -0.000376771 ) +colvars: ( -0.227069 , 0.0132196 , 0.0683424 ) +colvars: ( -0.167032 , -0.0760299 , 0.0873589 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 4. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 4. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atoms_new_colvar_forces = { ( -4.94151873108853e+00 , -4.95844394742801e-01 , -1.45728843242111e+00 ), ( -4.25683152929605e+00 , -4.19073570429103e-01 , -1.15372614016457e+00 ), ( -4.33444438845863e+00 , -4.46769799211681e-01 , -1.19158111943272e+00 ), ( -5.82894022039823e+00 , -6.31733357552042e-01 , -1.75036623073903e+00 ), ( 2.70809952346392e-01 , 1.25759659929497e-01 , 3.67022957097078e-01 ), ( 5.33236665680773e+00 , 6.86192275166386e-01 , 2.05835151414738e+00 ), ( 4.50630396391752e+00 , 5.71161364447410e-01 , 1.78417888002817e+00 ), ( -4.50521064735852e-02 , 3.29873596199127e-02 , 3.73861120665321e-01 ), ( 4.48512499842786e+00 , 5.60760529967644e-01 , 1.75091180485056e+00 ), ( 5.94477590622766e+00 , 7.18969977626746e-01 , 2.17717508972119e+00 ), ( 1.23204279884955e-02 , 4.25864921143228e-02 , 3.14113516873341e-01 ), ( -4.01260714282592e-04 , 3.55331586591927e-02 , 2.87629810528536e-01 ), ( 2.14052148191664e-02 , 5.05221201997225e-02 , 3.56411931734833e-01 ), ( 4.52804785364694e-02 , 3.93641970626369e-02 , 2.09302312339995e-01 ), ( 1.55455475389473e-02 , 2.40011187840913e-02 , 1.56460619817514e-01 ), ( 1.18670986750850e-01 , 5.98391688943326e-02 , 1.98995041694911e-01 ), ( 1.67598272749677e-01 , 6.53548826711292e-02 , 1.26498155048923e-01 ), ( 2.52507784367427e-01 , 9.26144883813088e-02 , 1.43382693002266e-01 ), ( 1.37676970832130e-01 , 4.74898849057159e-02 , 5.39174198038382e-02 ), ( 1.32692507809491e-01 , 3.77400726622781e-02 , -1.28220381118743e-02 ), ( 1.14192795160641e-01 , 4.21283427876479e-02 , 6.68180303148438e-02 ), ( 7.70387094492635e-02 , 2.36920825383860e-02 , 6.92370981846402e-03 ), ( 6.40779472015232e-02 , 2.42574612242072e-02 , 4.24770456540305e-02 ), ( -4.71146217026763e-04 , -2.75151840879517e-03 , -2.10717675375920e-02 ), ( -1.48516349236037e-02 , -1.59877827070383e-02 , -9.34708518249164e-02 ), ( -5.11122474941834e-02 , -1.06629392444262e-02 , 3.61954208352342e-02 ), ( -1.23120670979236e-01 , -3.41297369124331e-02 , 1.90607158308125e-02 ), ( -1.67537703748154e-01 , -3.72829997464116e-02 , 9.98321014309942e-02 ), ( -1.10428572677273e-01 , -3.64698190250280e-02 , -3.01679323445352e-02 ), ( -1.48880060390512e-01 , -5.53061782201492e-02 , -9.01877507098243e-02 ), ( -5.44240578645827e-02 , -1.69944092753382e-02 , -6.96561227952253e-03 ), ( -3.27662421073514e-02 , -1.60363396419879e-02 , -5.10248197226018e-02 ), ( 2.65517574135329e-02 , 7.69557423923618e-03 , -1.40564014935160e-03 ), ( 1.08386285815548e-03 , -1.66338922359559e-02 , -1.36788746907841e-01 ), ( -1.79250392762637e-02 , -2.93873777960727e-02 , -1.94225368128489e-01 ), ( 5.10944014416220e-02 , -3.18275430613568e-03 , -1.47855432047221e-01 ), ( 8.23681479943154e-02 , -3.68667686980284e-03 , -2.26703340912932e-01 ), ( 1.47430866801357e-01 , 1.71041949493687e-02 , -2.14548450271599e-01 ), ( 2.04328717296331e-02 , -2.88975256565817e-02 , -2.81995614928140e-01 ), ( 2.15167314441352e-02 , -3.75951838175833e-02 , -3.54757322940780e-01 ), ( -3.56173143482683e-02 , -4.13007796309533e-02 , -2.48032804522046e-01 ), ( -1.00256939903858e-01 , -6.59054030137752e-02 , -2.91967548149587e-01 ), ( -1.39837578616564e-01 , -7.11631415690601e-02 , -2.39739292495174e-01 ), ( -1.61565496181255e-01 , -8.69767375581534e-02 , -3.15362153547064e-01 ), ( -1.90828449787856e-01 , -1.03958146781982e-01 , -3.82388631261111e-01 ), ( -2.07792752897369e-01 , -1.01651827484115e-01 , -3.23216587535757e-01 ), ( -2.52793961676474e-01 , -1.18568799618888e-01 , -3.52089570352585e-01 ), ( -1.29328698069343e-01 , -7.92999657404734e-02 , -3.30513670981765e-01 ), ( -1.83283431592216e-01 , -8.65335336324582e-02 , -2.59854154010991e-01 ), ( -2.40349070486967e-01 , -1.05386727914137e-01 , -2.75499254537413e-01 ), ( -2.78508454946323e-01 , -1.06583088087811e-01 , -1.93903612270080e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 5, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 5, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 5, atoms_positions[size = 51] = { ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 ), ( 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 ), ( 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 ), ( 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 ), ( 7.04065873224138e+00 , -2.01833296981288e+00 , -1.01693732833577e+00 ), ( 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 ), ( 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 ), ( 7.17538034267917e+00 , -3.21242762016170e-01 , 4.29855168076096e+00 ), ( 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 ), ( 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 ), ( 5.87539806276546e+00 , 2.31240985061275e+00 , 2.97014834098906e+00 ), ( 5.22045541044482e+00 , 3.59634000902379e+00 , 2.88135009450921e+00 ), ( 6.33556840963606e+00 , 4.60687122456596e+00 , 2.46154267623522e+00 ), ( 3.89733976249443e+00 , 3.71958370766481e+00 , 2.02069126404248e+00 ), ( 2.90986850355711e+00 , 4.11525694547682e+00 , 2.55392862424380e+00 ), ( 3.82402284814097e+00 , 3.24274713169095e+00 , 7.77218893145038e-01 ), ( 2.66883306741140e+00 , 3.17373864836739e+00 , -8.63413721619713e-02 ), ( 3.04772299627009e+00 , 2.72379039269836e+00 , -1.59629179777349e+00 ), ( 1.62300540102769e+00 , 2.15239416279852e+00 , 5.82564492602534e-01 ), ( 4.32825535551040e-01 , 2.44780015548533e+00 , 5.56964034822003e-01 ), ( 1.97246218522001e+00 , 1.01153306857404e+00 , 1.05347641473001e+00 ), ( 1.14378372746903e+00 , 1.32534609583773e-02 , 1.68846439706830e+00 ), ( 2.01515655210737e+00 , -1.18697389770786e+00 , 2.02187581765090e+00 ), ( 5.13510127632644e-01 , 5.99454044877085e-01 , 2.99941462155069e+00 ), ( -6.75609219672412e-01 , 3.76332979525036e-01 , 3.18545149481743e+00 ), ( 1.29542103087650e+00 , 1.31432316768908e+00 , 3.82604811682509e+00 ), ( 8.29530569093443e-01 , 1.90017975542296e+00 , 5.07401910024172e+00 ), ( 2.05855836566831e+00 , 2.58942481763467e+00 , 5.62179715274072e+00 ), ( -3.58863638717831e-01 , 2.92014509118021e+00 , 4.98512619418679e+00 ), ( -1.17613148004942e+00 , 3.02607864337171e+00 , 5.90402719946517e+00 ), ( -4.08863122404988e-01 , 3.69412576843576e+00 , 3.86107585574595e+00 ), ( -1.46993194559316e+00 , 4.59050309281920e+00 , 3.53747996998097e+00 ), ( -7.59060233310232e-01 , 5.38308614886267e+00 , 2.40952223666742e+00 ), ( -2.71897816745416e+00 , 3.89602862252007e+00 , 2.93626096222774e+00 ), ( -3.85356112454900e+00 , 4.42028273573898e+00 , 2.85514318192395e+00 ), ( -2.57516756309611e+00 , 2.61161657288815e+00 , 2.49527550724508e+00 ), ( -3.71923167479111e+00 , 1.90738885494446e+00 , 2.07103256252133e+00 ), ( -3.41086011185269e+00 , 8.05653207893339e-01 , 9.93701643727931e-01 ), ( -4.31702988150970e+00 , 1.10221101723040e+00 , 3.22563146928878e+00 ), ( -5.53582719469801e+00 , 9.23269046977417e-01 , 3.34543241383312e+00 ), ( -3.46995162329921e+00 , 6.33934339046132e-01 , 4.15752819281306e+00 ), ( -3.77419638808229e+00 , 1.00547898851902e-01 , 5.47894501126548e+00 ), ( -2.41708935603261e+00 , -4.09548047162091e-01 , 6.13751734042486e+00 ), ( -4.46670493814301e+00 , 1.00204671894782e+00 , 6.41688790074973e+00 ), ( -5.32379297742663e+00 , 5.98704129809046e-01 , 7.18236872886878e+00 ), ( -6.29750134152972e+00 , 3.54903094952594e+00 , 6.69964903296575e+00 ), ( -6.91624712767947e+00 , 4.30428715900772e+00 , 7.41754976068118e+00 ), ( -6.75004367444995e+00 , 3.20870713576147e+00 , 5.50822758656231e+00 ), ( -4.08349872089577e+00 , 2.29945633007041e+00 , 6.47978428488058e+00 ), ( -4.91013406314155e+00 , 3.23789768567445e+00 , 7.21413013421060e+00 ), ( -4.07392760517108e+00 , 4.50301612731662e+00 , 7.26796286445452e+00 ) } +colvars: Step 5, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.35094576448585e-01 , 5.03425973663854e-03 , 9.42171046606532e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 7.04065873224138e+00 , -2.01833296981288e+00 , -1.01693732833577e+00 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 , 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 7.17538034267917e+00 , -3.21242762016170e-01 , 4.29855168076096e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 , 5.87539806276546e+00 , 2.31240985061275e+00 , 2.97014834098906e+00 , 5.22045541044482e+00 , 3.59634000902379e+00 , 2.88135009450921e+00 , 6.33556840963606e+00 , 4.60687122456596e+00 , 2.46154267623522e+00 , 3.89733976249443e+00 , 3.71958370766481e+00 , 2.02069126404248e+00 , 2.90986850355711e+00 , 4.11525694547682e+00 , 2.55392862424380e+00 , 3.82402284814097e+00 , 3.24274713169095e+00 , 7.77218893145038e-01 , 2.66883306741140e+00 , 3.17373864836739e+00 , -8.63413721619713e-02 , 3.04772299627009e+00 , 2.72379039269836e+00 , -1.59629179777349e+00 , 1.62300540102769e+00 , 2.15239416279852e+00 , 5.82564492602534e-01 , 4.32825535551040e-01 , 2.44780015548533e+00 , 5.56964034822003e-01 , 1.97246218522001e+00 , 1.01153306857404e+00 , 1.05347641473001e+00 , 1.14378372746903e+00 , 1.32534609583773e-02 , 1.68846439706830e+00 , 2.01515655210737e+00 , -1.18697389770786e+00 , 2.02187581765090e+00 , 5.13510127632644e-01 , 5.99454044877085e-01 , 2.99941462155069e+00 , -6.75609219672412e-01 , 3.76332979525036e-01 , 3.18545149481743e+00 , 1.29542103087650e+00 , 1.31432316768908e+00 , 3.82604811682509e+00 , 8.29530569093443e-01 , 1.90017975542296e+00 , 5.07401910024172e+00 , 2.05855836566831e+00 , 2.58942481763467e+00 , 5.62179715274072e+00 , -3.58863638717831e-01 , 2.92014509118021e+00 , 4.98512619418679e+00 , -1.17613148004942e+00 , 3.02607864337171e+00 , 5.90402719946517e+00 , -4.08863122404988e-01 , 3.69412576843576e+00 , 3.86107585574595e+00 , -1.46993194559316e+00 , 4.59050309281920e+00 , 3.53747996998097e+00 , -7.59060233310232e-01 , 5.38308614886267e+00 , 2.40952223666742e+00 , -2.71897816745416e+00 , 3.89602862252007e+00 , 2.93626096222774e+00 , -3.85356112454900e+00 , 4.42028273573898e+00 , 2.85514318192395e+00 , -2.57516756309611e+00 , 2.61161657288815e+00 , 2.49527550724508e+00 , -3.71923167479111e+00 , 1.90738885494446e+00 , 2.07103256252133e+00 , -3.41086011185269e+00 , 8.05653207893339e-01 , 9.93701643727931e-01 , -4.31702988150970e+00 , 1.10221101723040e+00 , 3.22563146928878e+00 , -5.53582719469801e+00 , 9.23269046977417e-01 , 3.34543241383312e+00 , -3.46995162329921e+00 , 6.33934339046132e-01 , 4.15752819281306e+00 , -3.77419638808229e+00 , 1.00547898851902e-01 , 5.47894501126548e+00 , -2.41708935603261e+00 , -4.09548047162091e-01 , 6.13751734042486e+00 , -4.46670493814301e+00 , 1.00204671894782e+00 , 6.41688790074973e+00 , -5.32379297742663e+00 , 5.98704129809046e-01 , 7.18236872886878e+00 , -6.29750134152972e+00 , 3.54903094952594e+00 , 6.69964903296575e+00 , -6.91624712767947e+00 , 4.30428715900772e+00 , 7.41754976068118e+00 , -6.75004367444995e+00 , 3.20870713576147e+00 , 5.50822758656231e+00 , -4.08349872089577e+00 , 2.29945633007041e+00 , 6.47978428488058e+00 , -4.91013406314155e+00 , 3.23789768567445e+00 , 7.21413013421060e+00 , -4.07392760517108e+00 , 4.50301612731662e+00 , 7.26796286445452e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.35094576448585e-01 , 5.03425973663854e-03 , 9.42171046606532e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.38812555635156e+00 , 4.32705508836218e-02 , -7.54716113397584e-01 , 6.99388060283788e+00 , -4.98830753972824e-01 , -6.55447578824873e-01 , 7.04065873224138e+00 , -2.01833296981288e+00 , -1.01693732833577e+00 , 6.25540296936181e+00 , -2.59151141423199e-01 , 6.59027986625355e-01 , 5.00226628693023e+00 , -2.07796280221137e-01 , 6.62267249707252e-01 , 6.90408665234348e+00 , -2.69605719769045e-01 , 1.80748769966000e+00 , 6.17702149943405e+00 , -1.22426392234786e-01 , 3.06349309525987e+00 , 7.17538034267917e+00 , -3.21242762016170e-01 , 4.29855168076096e+00 , 5.30568505228566e+00 , 1.11991445264153e+00 , 3.28564058909634e+00 , 4.08856559252705e+00 , 1.06803054001519e+00 , 3.62080305003688e+00 , 5.87539806276546e+00 , 2.31240985061275e+00 , 2.97014834098906e+00 , 5.22045541044482e+00 , 3.59634000902379e+00 , 2.88135009450921e+00 , 6.33556840963606e+00 , 4.60687122456596e+00 , 2.46154267623522e+00 , 3.89733976249443e+00 , 3.71958370766481e+00 , 2.02069126404248e+00 , 2.90986850355711e+00 , 4.11525694547682e+00 , 2.55392862424380e+00 , 3.82402284814097e+00 , 3.24274713169095e+00 , 7.77218893145038e-01 , 2.66883306741140e+00 , 3.17373864836739e+00 , -8.63413721619713e-02 , 3.04772299627009e+00 , 2.72379039269836e+00 , -1.59629179777349e+00 , 1.62300540102769e+00 , 2.15239416279852e+00 , 5.82564492602534e-01 , 4.32825535551040e-01 , 2.44780015548533e+00 , 5.56964034822003e-01 , 1.97246218522001e+00 , 1.01153306857404e+00 , 1.05347641473001e+00 , 1.14378372746903e+00 , 1.32534609583773e-02 , 1.68846439706830e+00 , 2.01515655210737e+00 , -1.18697389770786e+00 , 2.02187581765090e+00 , 5.13510127632644e-01 , 5.99454044877085e-01 , 2.99941462155069e+00 , -6.75609219672412e-01 , 3.76332979525036e-01 , 3.18545149481743e+00 , 1.29542103087650e+00 , 1.31432316768908e+00 , 3.82604811682509e+00 , 8.29530569093443e-01 , 1.90017975542296e+00 , 5.07401910024172e+00 , 2.05855836566831e+00 , 2.58942481763467e+00 , 5.62179715274072e+00 , -3.58863638717831e-01 , 2.92014509118021e+00 , 4.98512619418679e+00 , -1.17613148004942e+00 , 3.02607864337171e+00 , 5.90402719946517e+00 , -4.08863122404988e-01 , 3.69412576843576e+00 , 3.86107585574595e+00 , -1.46993194559316e+00 , 4.59050309281920e+00 , 3.53747996998097e+00 , -7.59060233310232e-01 , 5.38308614886267e+00 , 2.40952223666742e+00 , -2.71897816745416e+00 , 3.89602862252007e+00 , 2.93626096222774e+00 , -3.85356112454900e+00 , 4.42028273573898e+00 , 2.85514318192395e+00 , -2.57516756309611e+00 , 2.61161657288815e+00 , 2.49527550724508e+00 , -3.71923167479111e+00 , 1.90738885494446e+00 , 2.07103256252133e+00 , -3.41086011185269e+00 , 8.05653207893339e-01 , 9.93701643727931e-01 , -4.31702988150970e+00 , 1.10221101723040e+00 , 3.22563146928878e+00 , -5.53582719469801e+00 , 9.23269046977417e-01 , 3.34543241383312e+00 , -3.46995162329921e+00 , 6.33934339046132e-01 , 4.15752819281306e+00 , -3.77419638808229e+00 , 1.00547898851902e-01 , 5.47894501126548e+00 , -2.41708935603261e+00 , -4.09548047162091e-01 , 6.13751734042486e+00 , -4.46670493814301e+00 , 1.00204671894782e+00 , 6.41688790074973e+00 , -5.32379297742663e+00 , 5.98704129809046e-01 , 7.18236872886878e+00 , -6.29750134152972e+00 , 3.54903094952594e+00 , 6.69964903296575e+00 , -6.91624712767947e+00 , 4.30428715900772e+00 , 7.41754976068118e+00 , -6.75004367444995e+00 , 3.20870713576147e+00 , 5.50822758656231e+00 , -4.08349872089577e+00 , 2.29945633007041e+00 , 6.47978428488058e+00 , -4.91013406314155e+00 , 3.23789768567445e+00 , 7.21413013421060e+00 , -4.07392760517108e+00 , 4.50301612731662e+00 , 7.26796286445452e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.5957 , 6.75957 , 13.5191 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.5957 , 6.75957 , 13.5191 ) to colvar "one". +colvars: Adding total bias energy: 58.7504 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.5957 , 6.75957 , 13.5191 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.23542 , -0.614906 , -1.71618 ) +colvars: ( -4.48937 , -0.527282 , -1.47163 ) +colvars: ( -4.48937 , -0.527282 , -1.47163 ) +colvars: ( -5.97997 , -0.702355 , -1.96025 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.974477 , 0.208456 , 0.700053 ) +colvars: ( 0.842247 , 0.286172 , 0.727769 ) +colvars: ( 0.826692 , 0.277938 , 0.707092 ) +colvars: ( 0.717514 , 0.288561 , 0.656212 ) +colvars: ( 0.704417 , 0.216666 , 0.549309 ) +colvars: ( 0.620868 , 0.373372 , 0.715055 ) +colvars: ( 0.501069 , 0.390104 , 0.666218 ) +colvars: ( 0.415445 , 0.496388 , 0.761257 ) +colvars: ( 0.411666 , 0.342367 , 0.546806 ) +colvars: ( 0.372425 , 0.298083 , 0.462251 ) +colvars: ( 0.380984 , 0.347635 , 0.535653 ) +colvars: ( 0.303316 , 0.301542 , 0.425547 ) +colvars: ( 0.275161 , 0.332419 , 0.451189 ) +colvars: ( 0.372944 , 0.194902 , 0.320418 ) +colvars: ( 0.307968 , 0.148668 , 0.217734 ) +colvars: ( 0.50924 , 0.153411 , 0.345046 ) +colvars: ( 0.589957 , 0.0536714 , 0.256079 ) +colvars: ( 0.734195 , 0.0292958 , 0.309051 ) +colvars: ( 0.597707 , 0.019912 , 0.214221 ) +colvars: ( 0.580324 , -0.0503113 , 0.107049 ) +colvars: ( 0.619223 , 0.0722252 , 0.2992 ) +colvars: ( 0.615722 , 0.0555417 , 0.274116 ) +colvars: ( 0.654697 , 0.125806 , 0.394302 ) +colvars: ( 0.477491 , 0.0619063 , 0.199936 ) +colvars: ( 0.46933 , 0.00175207 , 0.112168 ) +colvars: ( 0.364865 , 0.133835 , 0.231442 ) +colvars: ( 0.226714 , 0.144524 , 0.163267 ) +colvars: ( 0.125749 , 0.238068 , 0.23155 ) +colvars: ( 0.19671 , 0.0645378 , 0.0350719 ) +colvars: ( 0.141511 , 0.0262074 , -0.0508564 ) +colvars: ( 0.235737 , 0.0357602 , 0.018846 ) +colvars: ( 0.22152 , -0.0430649 , -0.0982764 ) +colvars: ( 0.262582 , -0.0478942 , -0.0802893 ) +colvars: ( 0.304408 , -0.136607 , -0.177405 ) +colvars: ( 0.255835 , -0.193658 , -0.285147 ) +colvars: ( 0.431369 , -0.153783 , -0.124881 ) +colvars: ( 0.516531 , -0.235964 , -0.186992 ) +colvars: ( 0.661548 , -0.240008 , -0.105542 ) +colvars: ( 0.462368 , -0.239561 , -0.224449 ) +colvars: ( 0.468296 , -0.313145 , -0.322263 ) +colvars: ( 0.407032 , -0.159197 , -0.146943 ) +colvars: ( 0.34524 , -0.151134 , -0.172914 ) +colvars: ( 0.325577 , -0.0566256 , -0.0545162 ) +colvars: ( 0.208925 , -0.159463 , -0.266188 ) +colvars: ( 0.181052 , -0.204277 , -0.344651 ) +colvars: ( -0.0110289 , -0.208124 , -0.465212 ) +colvars: ( -0.111578 , -0.2265 , -0.550864 ) +colvars: ( 0.101231 , -0.26363 , -0.474315 ) +colvars: ( 0.119471 , -0.115188 , -0.258873 ) +colvars: ( -0.0123278 , -0.118833 , -0.342983 ) +colvars: ( -0.110283 , -0.0309296 , -0.280664 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.23542 , 0.614906 , 1.71618 ) +colvars: ( 4.48937 , 0.527282 , 1.47163 ) +colvars: ( 4.48937 , 0.527282 , 1.47163 ) +colvars: ( 5.97997 , 0.702355 , 1.96025 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.676743 , -0.0868383 , -0.432001 ) +colvars: ( -0.606398 , -0.175823 , -0.402048 ) +colvars: ( -0.556095 , -0.152189 , -0.340329 ) +colvars: ( -0.559222 , -0.205937 , -0.368308 ) +colvars: ( -0.548823 , -0.143174 , -0.328821 ) +colvars: ( -0.528234 , -0.304763 , -0.382648 ) +colvars: ( -0.487808 , -0.348577 , -0.362053 ) +colvars: ( -0.460583 , -0.463644 , -0.387694 ) +colvars: ( -0.419516 , -0.311215 , -0.275827 ) +colvars: ( -0.412391 , -0.284513 , -0.256299 ) +colvars: ( -0.368669 , -0.305178 , -0.221684 ) +colvars: ( -0.303659 , -0.266111 , -0.137985 ) +colvars: ( -0.253661 , -0.281993 , -0.0948231 ) +colvars: ( -0.327626 , -0.155573 , -0.111145 ) +colvars: ( -0.292344 , -0.124687 , -0.0612491 ) +colvars: ( -0.390597 , -0.0935645 , -0.146109 ) +colvars: ( -0.422416 , 0.0117541 , -0.12961 ) +colvars: ( -0.481811 , 0.0634295 , -0.165733 ) +colvars: ( -0.460111 , 0.027643 , -0.160343 ) +colvars: ( -0.447695 , 0.0881492 , -0.119861 ) +colvars: ( -0.50515 , -0.0300757 , -0.232485 ) +colvars: ( -0.538824 , -0.0318446 , -0.267311 ) +colvars: ( -0.590808 , -0.101593 , -0.352023 ) +colvars: ( -0.478035 , -0.0646808 , -0.22108 ) +colvars: ( -0.484252 , -0.0177428 , -0.205684 ) +colvars: ( -0.415992 , -0.144566 , -0.19531 ) +colvars: ( -0.349778 , -0.178748 , -0.144221 ) +colvars: ( -0.293181 , -0.275499 , -0.131738 ) +colvars: ( -0.307041 , -0.101051 , -0.0651772 ) +colvars: ( -0.290268 , -0.0815542 , -0.0392334 ) +colvars: ( -0.290057 , -0.0527551 , -0.0257211 ) +colvars: ( -0.254149 , 0.0270817 , 0.0474133 ) +colvars: ( -0.235888 , 0.0556767 , 0.0790609 ) +colvars: ( -0.303228 , 0.120077 , 0.0407899 ) +colvars: ( -0.273629 , 0.164398 , 0.0911506 ) +colvars: ( -0.380254 , 0.150721 , -0.0228531 ) +colvars: ( -0.434188 , 0.232441 , -0.0395872 ) +colvars: ( -0.514225 , 0.257292 , -0.108945 ) +colvars: ( -0.441955 , 0.210798 , -0.0574257 ) +colvars: ( -0.446797 , 0.275718 , -0.0323361 ) +colvars: ( -0.442665 , 0.117966 , -0.101012 ) +colvars: ( -0.445504 , 0.0852636 , -0.118981 ) +colvars: ( -0.465439 , -0.0145686 , -0.185217 ) +colvars: ( -0.370419 , 0.0725111 , -0.0490366 ) +colvars: ( -0.3718 , 0.100351 , -0.0375754 ) +colvars: ( -0.196527 , 0.106531 , 0.142298 ) +colvars: ( -0.140921 , 0.107988 , 0.199132 ) +colvars: ( -0.230363 , 0.184445 , 0.144105 ) +colvars: ( -0.302623 , 0.0286614 , -0.000814407 ) +colvars: ( -0.227813 , 0.0134423 , 0.0677126 ) +colvars: ( -0.167965 , -0.0757054 , 0.0869896 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 5. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 5. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atoms_new_colvar_forces = { ( -4.93768494226984e+00 , -4.93288890120217e-01 , -1.44813121666665e+00 ), ( -4.25352244045865e+00 , -4.16932622912841e-01 , -1.14590509214404e+00 ), ( -4.33107906543258e+00 , -4.44657599180775e-01 , -1.18372237480152e+00 ), ( -5.82437716510441e+00 , -6.28862714358498e-01 , -1.73976202698154e+00 ), ( 2.70597007471361e-01 , 1.25749083418850e-01 , 3.66762712094374e-01 ), ( 5.32805357607444e+00 , 6.83514841741323e-01 , 2.04859034711696e+00 ), ( 4.50263191825848e+00 , 5.68808850993012e-01 , 1.77579237717863e+00 ), ( -4.51382818778515e-02 , 3.27442119592583e-02 , 3.73563356008317e-01 ), ( 4.48152078257820e+00 , 5.58433238338579e-01 , 1.74260582654412e+00 ), ( 5.94000610865309e+00 , 7.15925282711389e-01 , 2.16620236805264e+00 ), ( 1.23158819761253e-02 , 4.24571519063832e-02 , 3.13968587103605e-01 ), ( -3.42648006105506e-04 , 3.54316380041383e-02 , 2.87561707841683e-01 ), ( 2.15004642581194e-02 , 5.04259784843997e-02 , 3.56365547326197e-01 ), ( 4.53183625143250e-02 , 3.93293574566300e-02 , 2.09273044603217e-01 ), ( 1.56240373387013e-02 , 2.39805029931352e-02 , 1.56485320228507e-01 ), ( 1.18643062750990e-01 , 5.98463107270278e-02 , 1.98937335082845e-01 ), ( 1.67541539661773e-01 , 6.54255296348837e-02 , 1.26469225808406e-01 ), ( 2.52384616803299e-01 , 9.27252495603290e-02 , 1.43318408152354e-01 ), ( 1.37596176637766e-01 , 4.75550056436365e-02 , 5.38782333859945e-02 ), ( 1.32629566187619e-01 , 3.78379244128352e-02 , -1.28126143201877e-02 ), ( 1.14072860060252e-01 , 4.21494678827976e-02 , 6.67151860121063e-02 ), ( 7.68981766913132e-02 , 2.36970776153220e-02 , 6.80453237339584e-03 ), ( 6.38885969511801e-02 , 2.42137378221992e-02 , 4.22785885005952e-02 ), ( -5.43938299810420e-04 , -2.77449159653712e-03 , -2.11447458474619e-02 ), ( -1.49218348929824e-02 , -1.59906824553589e-02 , -9.35151814964226e-02 ), ( -5.11271463814839e-02 , -1.07315298382845e-02 , 3.61327974958587e-02 ), ( -1.23064556176147e-01 , -3.42246880068121e-02 , 1.90460325794582e-02 ), ( -1.67431531351463e-01 , -3.74317405334914e-02 , 9.98114173401053e-02 ), ( -1.10330813486318e-01 , -3.65134029501701e-02 , -3.01052348849448e-02 ), ( -1.48756794797632e-01 , -5.53468429960343e-02 , -9.00897716356312e-02 ), ( -5.43200581784176e-02 , -1.69949591558956e-02 , -6.87509706350081e-03 ), ( -3.26284208685158e-02 , -1.59831328795033e-02 , -5.08631551834695e-02 ), ( 2.66942179180675e-02 , 7.78245929666979e-03 , -1.22844473176587e-03 ), ( 1.18026594086185e-03 , -1.65304508485450e-02 , -1.36614909479677e-01 ), ( -1.77941700646179e-02 , -2.92606942760620e-02 , -1.93996331615999e-01 ), ( 5.11152593622973e-02 , -3.06235115996423e-03 , -1.47733904656736e-01 ), ( 8.23428845352939e-02 , -3.52346953015942e-03 , -2.26579657776115e-01 ), ( 1.47323334991899e-01 , 1.72847684719611e-02 , -2.14487061656851e-01 ), ( 2.04133605463603e-02 , -2.87633124040187e-02 , -2.81874503252225e-01 ), ( 2.14991172292727e-02 , -3.74270878535857e-02 , -3.54599462106207e-01 ), ( -3.56333073901528e-02 , -4.12305732399287e-02 , -2.47955170408784e-01 ), ( -1.00263354533243e-01 , -6.58699640719693e-02 , -2.91894976071863e-01 ), ( -1.39861702854053e-01 , -7.11941852439772e-02 , -2.39733518258875e-01 ), ( -1.61493635100085e-01 , -8.69520689517708e-02 , -3.15224448305118e-01 ), ( -1.90748165374756e-01 , -1.03926651134371e-01 , -3.82226565007153e-01 ), ( -2.07555968566540e-01 , -1.01593274904900e-01 , -3.22914235361790e-01 ), ( -2.52498236898942e-01 , -1.18512344933050e-01 , -3.51732259815879e-01 ), ( -1.29132112882627e-01 , -7.91849803206830e-02 , -3.30209259457896e-01 ), ( -1.83151985289478e-01 , -8.65268695798549e-02 , -2.59687044895439e-01 ), ( -2.40140828851289e-01 , -1.05391069455491e-01 , -2.75269918588568e-01 ), ( -2.78248070003092e-01 , -1.06635024182009e-01 , -1.93674768357050e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 6, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 6, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 6, atoms_positions[size = 51] = { ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 ), ( 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 ), ( 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 ), ( 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 ), ( 7.04201555099061e+00 , -2.02050568202986e+00 , -1.01095918508983e+00 ), ( 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 ), ( 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 ), ( 7.16724600547698e+00 , -3.23457816615841e-01 , 4.29584430367597e+00 ), ( 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 ), ( 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 ), ( 5.87593597617318e+00 , 2.30253862916233e+00 , 2.97597265646037e+00 ), ( 5.21721353076129e+00 , 3.59597007511603e+00 , 2.88232644638125e+00 ), ( 6.33732844472895e+00 , 4.59629505881425e+00 , 2.45821720058526e+00 ), ( 3.89841886989411e+00 , 3.72602515256593e+00 , 2.02060672375480e+00 ), ( 2.90163859561185e+00 , 4.11598692141058e+00 , 2.54894451315239e+00 ), ( 3.82825409784994e+00 , 3.24208459259053e+00 , 7.73406194586500e-01 ), ( 2.67105524123482e+00 , 3.16251906451889e+00 , -9.10730059314331e-02 ), ( 3.04590999511220e+00 , 2.72187692027414e+00 , -1.59753086769456e+00 ), ( 1.61200628352592e+00 , 2.15269472340813e+00 , 5.82544644062388e-01 ), ( 4.35756748777557e-01 , 2.45515633198171e+00 , 5.52825059613988e-01 ), ( 1.97037235331458e+00 , 1.01273541810539e+00 , 1.05319421577032e+00 ), ( 1.15110600864534e+00 , 1.59866561905923e-02 , 1.68932994796430e+00 ), ( 2.01512013916619e+00 , -1.18091084465548e+00 , 2.02057579533244e+00 ), ( 5.19105469798803e-01 , 6.03751696402325e-01 , 2.99163142287312e+00 ), ( -6.72886836516355e-01 , 3.71983893027156e-01 , 3.18262255084290e+00 ), ( 1.30138914203718e+00 , 1.31799129123245e+00 , 3.82827939703354e+00 ), ( 8.36256674898712e-01 , 1.90659029059265e+00 , 5.06918877544204e+00 ), ( 2.05272041220510e+00 , 2.59248976061916e+00 , 5.62269186133449e+00 ), ( -3.59898534695024e-01 , 2.91963356273390e+00 , 4.98445621212317e+00 ), ( -1.17391800038070e+00 , 3.02952158168549e+00 , 5.90495963634345e+00 ), ( -4.16792067248368e-01 , 3.68860565679751e+00 , 3.85705103294777e+00 ), ( -1.47348778711130e+00 , 4.58263272771055e+00 , 3.53822775040597e+00 ), ( -7.54820296625674e-01 , 5.38550393877410e+00 , 2.41225622261323e+00 ), ( -2.72548458263952e+00 , 3.89460490153238e+00 , 2.93351632047225e+00 ), ( -3.85198578444575e+00 , 4.42597054842895e+00 , 2.85065485184329e+00 ), ( -2.58093832643556e+00 , 2.61071833644784e+00 , 2.49004186169887e+00 ), ( -3.71682803626518e+00 , 1.91061829197026e+00 , 2.06641130275165e+00 ), ( -3.41289478688424e+00 , 8.12252048203337e-01 , 9.85888091499494e-01 ), ( -4.30942983875831e+00 , 1.09534931485942e+00 , 3.23136276915903e+00 ), ( -5.53785606211609e+00 , 9.16209594457123e-01 , 3.34332710128568e+00 ), ( -3.46429988873949e+00 , 6.37592796519501e-01 , 4.15072862341052e+00 ), ( -3.77775300960228e+00 , 9.59573757368899e-02 , 5.48140295359406e+00 ), ( -2.40926491947795e+00 , -3.98894890699091e-01 , 6.14185569677671e+00 ), ( -4.46908951835721e+00 , 9.97820565764761e-01 , 6.41785913641396e+00 ), ( -5.32321822477403e+00 , 6.01481105198029e-01 , 7.18427723959524e+00 ), ( -6.29686369435140e+00 , 3.55126815673210e+00 , 6.70151222217351e+00 ), ( -6.91389609509752e+00 , 4.30123221834033e+00 , 7.41815348169977e+00 ), ( -6.74629806351582e+00 , 3.20880069721169e+00 , 5.51154954373544e+00 ), ( -4.08755630619893e+00 , 2.30172816421519e+00 , 6.48163985555273e+00 ), ( -4.90581235595044e+00 , 3.23289872377110e+00 , 7.21352814018328e+00 ), ( -4.07874815839021e+00 , 4.51178048034416e+00 , 7.27131933992993e+00 ) } +colvars: Step 6, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 ). +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.33416359589612e-01 , 4.82914602417237e-03 , 9.42767315145518e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 7.04201555099061e+00 , -2.02050568202986e+00 , -1.01095918508983e+00 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 , 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 7.16724600547698e+00 , -3.23457816615841e-01 , 4.29584430367597e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 , 5.87593597617318e+00 , 2.30253862916233e+00 , 2.97597265646037e+00 , 5.21721353076129e+00 , 3.59597007511603e+00 , 2.88232644638125e+00 , 6.33732844472895e+00 , 4.59629505881425e+00 , 2.45821720058526e+00 , 3.89841886989411e+00 , 3.72602515256593e+00 , 2.02060672375480e+00 , 2.90163859561185e+00 , 4.11598692141058e+00 , 2.54894451315239e+00 , 3.82825409784994e+00 , 3.24208459259053e+00 , 7.73406194586500e-01 , 2.67105524123482e+00 , 3.16251906451889e+00 , -9.10730059314331e-02 , 3.04590999511220e+00 , 2.72187692027414e+00 , -1.59753086769456e+00 , 1.61200628352592e+00 , 2.15269472340813e+00 , 5.82544644062388e-01 , 4.35756748777557e-01 , 2.45515633198171e+00 , 5.52825059613988e-01 , 1.97037235331458e+00 , 1.01273541810539e+00 , 1.05319421577032e+00 , 1.15110600864534e+00 , 1.59866561905923e-02 , 1.68932994796430e+00 , 2.01512013916619e+00 , -1.18091084465548e+00 , 2.02057579533244e+00 , 5.19105469798803e-01 , 6.03751696402325e-01 , 2.99163142287312e+00 , -6.72886836516355e-01 , 3.71983893027156e-01 , 3.18262255084290e+00 , 1.30138914203718e+00 , 1.31799129123245e+00 , 3.82827939703354e+00 , 8.36256674898712e-01 , 1.90659029059265e+00 , 5.06918877544204e+00 , 2.05272041220510e+00 , 2.59248976061916e+00 , 5.62269186133449e+00 , -3.59898534695024e-01 , 2.91963356273390e+00 , 4.98445621212317e+00 , -1.17391800038070e+00 , 3.02952158168549e+00 , 5.90495963634345e+00 , -4.16792067248368e-01 , 3.68860565679751e+00 , 3.85705103294777e+00 , -1.47348778711130e+00 , 4.58263272771055e+00 , 3.53822775040597e+00 , -7.54820296625674e-01 , 5.38550393877410e+00 , 2.41225622261323e+00 , -2.72548458263952e+00 , 3.89460490153238e+00 , 2.93351632047225e+00 , -3.85198578444575e+00 , 4.42597054842895e+00 , 2.85065485184329e+00 , -2.58093832643556e+00 , 2.61071833644784e+00 , 2.49004186169887e+00 , -3.71682803626518e+00 , 1.91061829197026e+00 , 2.06641130275165e+00 , -3.41289478688424e+00 , 8.12252048203337e-01 , 9.85888091499494e-01 , -4.30942983875831e+00 , 1.09534931485942e+00 , 3.23136276915903e+00 , -5.53785606211609e+00 , 9.16209594457123e-01 , 3.34332710128568e+00 , -3.46429988873949e+00 , 6.37592796519501e-01 , 4.15072862341052e+00 , -3.77775300960228e+00 , 9.59573757368899e-02 , 5.48140295359406e+00 , -2.40926491947795e+00 , -3.98894890699091e-01 , 6.14185569677671e+00 , -4.46908951835721e+00 , 9.97820565764761e-01 , 6.41785913641396e+00 , -5.32321822477403e+00 , 6.01481105198029e-01 , 7.18427723959524e+00 , -6.29686369435140e+00 , 3.55126815673210e+00 , 6.70151222217351e+00 , -6.91389609509752e+00 , 4.30123221834033e+00 , 7.41815348169977e+00 , -6.74629806351582e+00 , 3.20880069721169e+00 , 5.51154954373544e+00 , -4.08755630619893e+00 , 2.30172816421519e+00 , 6.48163985555273e+00 , -4.90581235595044e+00 , 3.23289872377110e+00 , 7.21352814018328e+00 , -4.07874815839021e+00 , 4.51178048034416e+00 , 7.27131933992993e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.33416359589612e-01 , 4.82914602417237e-03 , 9.42767315145518e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.38001520093994e+00 , 4.35365966130729e-02 , -7.57173139428919e-01 , 6.99242452405203e+00 , -5.04838432007226e-01 , -6.50502307145267e-01 , 7.04201555099061e+00 , -2.02050568202986e+00 , -1.01095918508983e+00 , 6.25505789577293e+00 , -2.63687463251509e-01 , 6.65146630639674e-01 , 4.99669068861688e+00 , -2.06654452084439e-01 , 6.67577859773879e-01 , 6.90342743334272e+00 , -2.69542318403298e-01 , 1.81495378669923e+00 , 6.17734955212912e+00 , -1.20494091054508e-01 , 3.07455576407274e+00 , 7.16724600547698e+00 , -3.23457816615841e-01 , 4.29584430367597e+00 , 5.30392428485857e+00 , 1.11716832591936e+00 , 3.29124895034911e+00 , 4.09146351396268e+00 , 1.06503749349131e+00 , 3.62458285467521e+00 , 5.87593597617318e+00 , 2.30253862916233e+00 , 2.97597265646037e+00 , 5.21721353076129e+00 , 3.59597007511603e+00 , 2.88232644638125e+00 , 6.33732844472895e+00 , 4.59629505881425e+00 , 2.45821720058526e+00 , 3.89841886989411e+00 , 3.72602515256593e+00 , 2.02060672375480e+00 , 2.90163859561185e+00 , 4.11598692141058e+00 , 2.54894451315239e+00 , 3.82825409784994e+00 , 3.24208459259053e+00 , 7.73406194586500e-01 , 2.67105524123482e+00 , 3.16251906451889e+00 , -9.10730059314331e-02 , 3.04590999511220e+00 , 2.72187692027414e+00 , -1.59753086769456e+00 , 1.61200628352592e+00 , 2.15269472340813e+00 , 5.82544644062388e-01 , 4.35756748777557e-01 , 2.45515633198171e+00 , 5.52825059613988e-01 , 1.97037235331458e+00 , 1.01273541810539e+00 , 1.05319421577032e+00 , 1.15110600864534e+00 , 1.59866561905923e-02 , 1.68932994796430e+00 , 2.01512013916619e+00 , -1.18091084465548e+00 , 2.02057579533244e+00 , 5.19105469798803e-01 , 6.03751696402325e-01 , 2.99163142287312e+00 , -6.72886836516355e-01 , 3.71983893027156e-01 , 3.18262255084290e+00 , 1.30138914203718e+00 , 1.31799129123245e+00 , 3.82827939703354e+00 , 8.36256674898712e-01 , 1.90659029059265e+00 , 5.06918877544204e+00 , 2.05272041220510e+00 , 2.59248976061916e+00 , 5.62269186133449e+00 , -3.59898534695024e-01 , 2.91963356273390e+00 , 4.98445621212317e+00 , -1.17391800038070e+00 , 3.02952158168549e+00 , 5.90495963634345e+00 , -4.16792067248368e-01 , 3.68860565679751e+00 , 3.85705103294777e+00 , -1.47348778711130e+00 , 4.58263272771055e+00 , 3.53822775040597e+00 , -7.54820296625674e-01 , 5.38550393877410e+00 , 2.41225622261323e+00 , -2.72548458263952e+00 , 3.89460490153238e+00 , 2.93351632047225e+00 , -3.85198578444575e+00 , 4.42597054842895e+00 , 2.85065485184329e+00 , -2.58093832643556e+00 , 2.61071833644784e+00 , 2.49004186169887e+00 , -3.71682803626518e+00 , 1.91061829197026e+00 , 2.06641130275165e+00 , -3.41289478688424e+00 , 8.12252048203337e-01 , 9.85888091499494e-01 , -4.30942983875831e+00 , 1.09534931485942e+00 , 3.23136276915903e+00 , -5.53785606211609e+00 , 9.16209594457123e-01 , 3.34332710128568e+00 , -3.46429988873949e+00 , 6.37592796519501e-01 , 4.15072862341052e+00 , -3.77775300960228e+00 , 9.59573757368899e-02 , 5.48140295359406e+00 , -2.40926491947795e+00 , -3.98894890699091e-01 , 6.14185569677671e+00 , -4.46908951835721e+00 , 9.97820565764761e-01 , 6.41785913641396e+00 , -5.32321822477403e+00 , 6.01481105198029e-01 , 7.18427723959524e+00 , -6.29686369435140e+00 , 3.55126815673210e+00 , 6.70151222217351e+00 , -6.91389609509752e+00 , 4.30123221834033e+00 , 7.41815348169977e+00 , -6.74629806351582e+00 , 3.20880069721169e+00 , 5.51154954373544e+00 , -4.08755630619893e+00 , 2.30172816421519e+00 , 6.48163985555273e+00 , -4.90581235595044e+00 , 3.23289872377110e+00 , 7.21352814018328e+00 , -4.07874815839021e+00 , 4.51178048034416e+00 , 7.27131933992993e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.5097 , 6.75097 , 13.5019 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.5097 , 6.75097 , 13.5019 ) to colvar "one". +colvars: Adding total bias energy: 58.6303 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.5097 , 6.75097 , 13.5019 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.23016 , -0.611795 , -1.7049 ) +colvars: ( -4.48486 , -0.524614 , -1.46195 ) +colvars: ( -4.48486 , -0.524614 , -1.46195 ) +colvars: ( -5.97397 , -0.698801 , -1.94736 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.972151 , 0.208306 , 0.697037 ) +colvars: ( 0.840336 , 0.285822 , 0.724605 ) +colvars: ( 0.824708 , 0.277643 , 0.704003 ) +colvars: ( 0.716055 , 0.288116 , 0.653307 ) +colvars: ( 0.702995 , 0.216335 , 0.546834 ) +colvars: ( 0.619771 , 0.372709 , 0.711888 ) +colvars: ( 0.50042 , 0.38932 , 0.66322 ) +colvars: ( 0.415115 , 0.495361 , 0.757852 ) +colvars: ( 0.411244 , 0.341637 , 0.544266 ) +colvars: ( 0.37217 , 0.297387 , 0.460046 ) +colvars: ( 0.380558 , 0.346921 , 0.533146 ) +colvars: ( 0.30307 , 0.300889 , 0.423463 ) +colvars: ( 0.2749 , 0.331741 , 0.448989 ) +colvars: ( 0.372446 , 0.194478 , 0.318779 ) +colvars: ( 0.307677 , 0.148284 , 0.216494 ) +colvars: ( 0.508283 , 0.153141 , 0.343342 ) +colvars: ( 0.588718 , 0.053623 , 0.254756 ) +colvars: ( 0.732448 , 0.0293876 , 0.30755 ) +colvars: ( 0.596544 , 0.0198831 , 0.213074 ) +colvars: ( 0.579211 , -0.0502308 , 0.106332 ) +colvars: ( 0.618086 , 0.0720823 , 0.297718 ) +colvars: ( 0.614701 , 0.0553818 , 0.272738 ) +colvars: ( 0.653639 , 0.125515 , 0.392451 ) +colvars: ( 0.476947 , 0.0616445 , 0.198823 ) +colvars: ( 0.468846 , 0.00157184 , 0.111411 ) +colvars: ( 0.364667 , 0.133395 , 0.230172 ) +colvars: ( 0.226976 , 0.143982 , 0.162237 ) +colvars: ( 0.126317 , 0.23732 , 0.230216 ) +colvars: ( 0.196994 , 0.0641426 , 0.0345513 ) +colvars: ( 0.14201 , 0.0258295 , -0.0510417 ) +colvars: ( 0.235788 , 0.0354787 , 0.0183974 ) +colvars: ( 0.221539 , -0.043191 , -0.0982568 ) +colvars: ( 0.262353 , -0.0479419 , -0.0803363 ) +colvars: ( 0.304184 , -0.13654 , -0.177041 ) +colvars: ( 0.255758 , -0.19352 , -0.28436 ) +colvars: ( 0.430771 , -0.153629 , -0.124695 ) +colvars: ( 0.515693 , -0.235639 , -0.186531 ) +colvars: ( 0.660258 , -0.239599 , -0.105372 ) +colvars: ( 0.461809 , -0.239303 , -0.223846 ) +colvars: ( 0.467728 , -0.312765 , -0.321262 ) +colvars: ( 0.406732 , -0.159138 , -0.146666 ) +colvars: ( 0.345241 , -0.151164 , -0.172544 ) +colvars: ( 0.325723 , -0.0568582 , -0.0546286 ) +colvars: ( 0.209352 , -0.159552 , -0.265476 ) +colvars: ( 0.181617 , -0.204328 , -0.343627 ) +colvars: ( -0.0100666 , -0.208187 , -0.463758 ) +colvars: ( -0.110301 , -0.226585 , -0.54909 ) +colvars: ( 0.101764 , -0.263508 , -0.472797 ) +colvars: ( 0.120119 , -0.115375 , -0.258217 ) +colvars: ( -0.0112737 , -0.119081 , -0.342021 ) +colvars: ( -0.108947 , -0.0313666 , -0.279983 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.23016 , 0.611795 , 1.7049 ) +colvars: ( 4.48486 , 0.524614 , 1.46195 ) +colvars: ( 4.48486 , 0.524614 , 1.46195 ) +colvars: ( 5.97397 , 0.698801 , 1.94736 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.674764 , -0.0867058 , -0.429325 ) +colvars: ( -0.604763 , -0.175528 , -0.399227 ) +colvars: ( -0.554365 , -0.151927 , -0.337557 ) +colvars: ( -0.557971 , -0.205564 , -0.365705 ) +colvars: ( -0.547594 , -0.142886 , -0.326589 ) +colvars: ( -0.527301 , -0.304222 , -0.379813 ) +colvars: ( -0.48726 , -0.347939 , -0.359358 ) +colvars: ( -0.460318 , -0.462817 , -0.384642 ) +colvars: ( -0.419132 , -0.310607 , -0.273513 ) +colvars: ( -0.412152 , -0.283931 , -0.254276 ) +colvars: ( -0.368253 , -0.304574 , -0.219383 ) +colvars: ( -0.303367 , -0.265542 , -0.136035 ) +colvars: ( -0.25333 , -0.281398 , -0.0927564 ) +colvars: ( -0.32711 , -0.155181 , -0.109585 ) +colvars: ( -0.291993 , -0.124322 , -0.060028 ) +colvars: ( -0.389697 , -0.0932992 , -0.144505 ) +colvars: ( -0.421269 , 0.011847 , -0.128343 ) +colvars: ( -0.480234 , 0.0634082 , -0.164322 ) +colvars: ( -0.459052 , 0.0277143 , -0.159243 ) +colvars: ( -0.446669 , 0.088139 , -0.119132 ) +colvars: ( -0.504144 , -0.0299254 , -0.231108 ) +colvars: ( -0.537941 , -0.0316877 , -0.266037 ) +colvars: ( -0.589927 , -0.101344 , -0.350353 ) +colvars: ( -0.477551 , -0.0644384 , -0.220025 ) +colvars: ( -0.483822 , -0.0175638 , -0.20494 ) +colvars: ( -0.415794 , -0.14418 , -0.194103 ) +colvars: ( -0.349962 , -0.178275 , -0.14321 ) +colvars: ( -0.293618 , -0.274862 , -0.130449 ) +colvars: ( -0.307214 , -0.100683 , -0.0645956 ) +colvars: ( -0.290623 , -0.0811972 , -0.0389415 ) +colvars: ( -0.290007 , -0.0524691 , -0.0251934 ) +colvars: ( -0.254043 , 0.0272558 , 0.0475453 ) +colvars: ( -0.235547 , 0.0557954 , 0.0792603 ) +colvars: ( -0.302922 , 0.120097 , 0.040611 ) +colvars: ( -0.273436 , 0.164368 , 0.0906101 ) +colvars: ( -0.37965 , 0.150664 , -0.0228955 ) +colvars: ( -0.43339 , 0.232245 , -0.0398829 ) +colvars: ( -0.51306 , 0.257022 , -0.109006 ) +colvars: ( -0.441414 , 0.210651 , -0.0578512 ) +colvars: ( -0.446245 , 0.275478 , -0.0331099 ) +colvars: ( -0.442366 , 0.117969 , -0.101158 ) +colvars: ( -0.44548 , 0.0853325 , -0.119214 ) +colvars: ( -0.465566 , -0.0143499 , -0.185038 ) +colvars: ( -0.370739 , 0.072635 , -0.0495491 ) +colvars: ( -0.372244 , 0.100444 , -0.0383625 ) +colvars: ( -0.197233 , 0.106661 , 0.141186 ) +colvars: ( -0.141879 , 0.108143 , 0.197754 ) +colvars: ( -0.230694 , 0.184432 , 0.142934 ) +colvars: ( -0.30311 , 0.0288702 , -0.00126033 ) +colvars: ( -0.228627 , 0.0137081 , 0.0670182 ) +colvars: ( -0.169008 , -0.075287 , 0.0865533 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 6. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 6. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atoms_new_colvar_forces = { ( -4.93277292055766e+00 , -4.90194513271413e-01 , -1.43718383333350e+00 ), ( -4.24928844495011e+00 , -4.14319730328549e-01 , -1.13656961900244e+00 ), ( -4.32677727761942e+00 , -4.42061894343978e-01 , -1.17434520382541e+00 ), ( -5.81856326291688e+00 , -6.25352159657104e-01 , -1.72711250346991e+00 ), ( 2.70343425805526e-01 , 1.25715952073241e-01 , 3.66445668373938e-01 ), ( 5.32263066066988e+00 , 6.80282678401000e-01 , 2.03697104157011e+00 ), ( 4.49802088896574e+00 , 5.65995619089272e-01 , 1.76580945083832e+00 ), ( -4.52035265146508e-02 , 3.25438648520574e-02 , 3.73210410765344e-01 ), ( 4.47697249662949e+00 , 5.55643205079631e-01 , 1.73270046685604e+00 ), ( 5.93398341449267e+00 , 7.12257975911161e-01 , 2.15312644673420e+00 ), ( 1.23048167143113e-02 , 4.23475122450560e-02 , 3.13762582844874e-01 ), ( -2.97171646727656e-04 , 3.53466248661184e-02 , 2.87428385601990e-01 ), ( 2.15700519999917e-02 , 5.03436675814751e-02 , 3.56233058093854e-01 ), ( 4.53355923905861e-02 , 3.92962552243516e-02 , 2.09193704051278e-01 ), ( 1.56836952509605e-02 , 2.39620465464446e-02 , 1.56465827499981e-01 ), ( 1.18586204326617e-01 , 5.98418472976366e-02 , 1.98836754857717e-01 ), ( 1.67448748047038e-01 , 6.54700065207059e-02 , 1.26412506316467e-01 ), ( 2.52213861342067e-01 , 9.27957885803099e-02 , 1.43227506416146e-01 ), ( 1.37491966621685e-01 , 4.75973997241057e-02 , 5.38314454658977e-02 ), ( 1.32542463896655e-01 , 3.79082711831248e-02 , -1.28003734385221e-02 ), ( 1.13941825729200e-01 , 4.21568906295997e-02 , 6.66103202097719e-02 ), ( 7.67603445059466e-02 , 2.36941602198378e-02 , 6.70103940096495e-03 ), ( 6.37128045711135e-02 , 2.41709392214954e-02 , 4.20977889768344e-02 ), ( -6.04497053169673e-04 , -2.79392161927046e-03 , -2.12018202273477e-02 ), ( -1.49755440332211e-02 , -1.59920005743246e-02 , -9.35289229831404e-02 ), ( -5.11267753565900e-02 , -1.07846615639152e-02 , 3.60693662718652e-02 ), ( -1.22985744019474e-01 , -3.42934558425949e-02 , 1.90277168373195e-02 ), ( -1.67300274843786e-01 , -3.75416338873689e-02 , 9.97666384062255e-02 ), ( -1.10219801322070e-01 , -3.65400619460836e-02 , -3.00443107593338e-02 ), ( -1.48613635269094e-01 , -5.53676205887283e-02 , -8.99832027239536e-02 ), ( -5.42187072697088e-02 , -1.69903857255689e-02 , -6.79602414139265e-03 ), ( -3.25038224479355e-02 , -1.59352502622686e-02 , -5.07114756277418e-02 ), ( 2.68066106451045e-02 , 7.85342832467995e-03 , -1.07601146900668e-03 ), ( 1.26247108743466e-03 , -1.64434790416789e-02 , -1.36430240369820e-01 ), ( -1.76774126169826e-02 , -2.91524626528663e-02 , -1.93749495888178e-01 ), ( 5.11213223315123e-02 , -2.96571820449221e-03 , -1.47590885938418e-01 ), ( 8.23031978551875e-02 , -3.39377031822058e-03 , -2.26414054631252e-01 ), ( 1.47197656354189e-01 , 1.74231335128101e-02 , -2.14377625068559e-01 ), ( 2.03953358800427e-02 , -2.86525120856640e-02 , -2.81697082376507e-01 ), ( 2.14833367169718e-02 , -3.72879411012616e-02 , -3.54371573849421e-01 ), ( -3.56342243788104e-02 , -4.11685773495180e-02 , -2.47824216738292e-01 ), ( -1.00238847665071e-01 , -6.58314657400450e-02 , -2.91757315536222e-01 ), ( -1.39842388910251e-01 , -7.12080659211185e-02 , -2.39666973315091e-01 ), ( -1.61387312507324e-01 , -8.69170398054735e-02 , -3.15025236157483e-01 ), ( -1.90626303123439e-01 , -1.03883309669788e-01 , -3.81989187490294e-01 ), ( -2.07299403741781e-01 , -1.01525330995274e-01 , -3.22572117774458e-01 ), ( -2.52180223912891e-01 , -1.18442069433478e-01 , -3.51335784780881e-01 ), ( -1.28929552893268e-01 , -7.90766459788611e-02 , -3.29862989467372e-01 ), ( -1.82990827114357e-01 , -8.65048942820909e-02 , -2.59477222294974e-01 ), ( -2.39900299630396e-01 , -1.05373135934358e-01 , -2.75003028614189e-01 ), ( -2.77954990514854e-01 , -1.06653558958758e-01 , -1.93429795096022e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 7, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 7, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 7, atoms_positions[size = 51] = { ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 ), ( 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 ), ( 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 ), ( 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 ), ( 7.04360578585032e+00 , -2.02253210321486e+00 , -1.00475508697818e+00 ), ( 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 ), ( 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 ), ( 7.15839369415653e+00 , -3.26081276239317e-01 , 4.29289707258867e+00 ), ( 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 ), ( 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 ), ( 5.87628142275448e+00 , 2.29260416098295e+00 , 2.98123131140797e+00 ), ( 5.21461212463495e+00 , 3.59576743915649e+00 , 2.88362406780732e+00 ), ( 6.33841023238199e+00 , 4.58549633824642e+00 , 2.45478769693888e+00 ), ( 3.90032731528937e+00 , 3.73133228488110e+00 , 2.02125381715923e+00 ), ( 2.89255651494714e+00 , 4.11737441114465e+00 , 2.54429236626012e+00 ), ( 3.83356882425037e+00 , 3.24142730507447e+00 , 7.69061966445767e-01 ), ( 2.67252484262143e+00 , 3.15034995420553e+00 , -9.51496895508225e-02 ), ( 3.04369939118193e+00 , 2.72067318755565e+00 , -1.59666058085304e+00 ), ( 1.60113592967078e+00 , 2.15519099674224e+00 , 5.80071804456076e-01 ), ( 4.38240041119901e-01 , 2.46262336976879e+00 , 5.48980991334079e-01 ), ( 1.96959368088953e+00 , 1.01234376536455e+00 , 1.05408760152221e+00 ), ( 1.15807993418597e+00 , 2.06042343395636e-02 , 1.69020108367558e+00 ), ( 2.01540951886049e+00 , -1.17487180030149e+00 , 2.01894428622946e+00 ), ( 5.24663015581007e-01 , 6.06965654388053e-01 , 2.98277511565960e+00 ), ( -6.70091636820477e-01 , 3.67973696398877e-01 , 3.18020094552207e+00 ), ( 1.30678882139017e+00 , 1.32183553100694e+00 , 3.83074937761609e+00 ), ( 8.42480492065935e-01 , 1.91297367485748e+00 , 5.06403257253622e+00 ), ( 2.04676600763386e+00 , 2.59577116983262e+00 , 5.62384874446350e+00 ), ( -3.60187962065452e-01 , 2.91906438707605e+00 , 4.98365392120015e+00 ), ( -1.17173739380431e+00 , 3.03291119872267e+00 , 5.90558861048476e+00 ), ( -4.24942864299879e-01 , 3.68185527221630e+00 , 3.85350813056666e+00 ), ( -1.47667798663298e+00 , 4.57531645519427e+00 , 3.53820386981816e+00 ), ( -7.50485901509571e-01 , 5.38790647509149e+00 , 2.41552070759660e+00 ), ( -2.73259922857375e+00 , 3.89276029477454e+00 , 2.93094623652956e+00 ), ( -3.84966920894560e+00 , 4.43165634430076e+00 , 2.84648308433646e+00 ), ( -2.58607921786046e+00 , 2.61135604056535e+00 , 2.48458862212576e+00 ), ( -3.71575189353043e+00 , 1.91132888948723e+00 , 2.06114453689343e+00 ), ( -3.41464867152714e+00 , 8.19463186795656e-01 , 9.77744520824400e-01 ), ( -4.30317263798616e+00 , 1.08870954003847e+00 , 3.23703847428725e+00 ), ( -5.53930210531588e+00 , 9.09235310273094e-01 , 3.34117073165080e+00 ), ( -3.45825411873271e+00 , 6.41907326842739e-01 , 4.14489107139214e+00 ), ( -3.77964154389490e+00 , 8.99884693047571e-02 , 5.48280131463119e+00 ), ( -2.40241948018949e+00 , -3.87812824665575e-01 , 6.14622445774217e+00 ), ( -4.47118005780455e+00 , 9.94760153779481e-01 , 6.41957195336128e+00 ), ( -5.32307757703637e+00 , 6.03902619770999e-01 , 7.18625074294096e+00 ), ( -6.29473276809766e+00 , 3.55390365365507e+00 , 6.70309262515356e+00 ), ( -6.91269406186489e+00 , 4.29872080475097e+00 , 7.41940655795881e+00 ), ( -6.74359627925831e+00 , 3.20873680426871e+00 , 5.51467328326202e+00 ), ( -4.09220742797595e+00 , 2.30305792852368e+00 , 6.48263397793547e+00 ), ( -4.90008080100881e+00 , 3.22721176264580e+00 , 7.21307955904248e+00 ), ( -4.08321878774328e+00 , 4.52152209517614e+00 , 7.27520162172180e+00 ) } +colvars: Step 7, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.31520710742130e-01 , 4.70585069947745e-03 , 9.43436205219106e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 7.04360578585032e+00 , -2.02253210321486e+00 , -1.00475508697818e+00 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 , 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 7.15839369415653e+00 , -3.26081276239317e-01 , 4.29289707258867e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 , 5.87628142275448e+00 , 2.29260416098295e+00 , 2.98123131140797e+00 , 5.21461212463495e+00 , 3.59576743915649e+00 , 2.88362406780732e+00 , 6.33841023238199e+00 , 4.58549633824642e+00 , 2.45478769693888e+00 , 3.90032731528937e+00 , 3.73133228488110e+00 , 2.02125381715923e+00 , 2.89255651494714e+00 , 4.11737441114465e+00 , 2.54429236626012e+00 , 3.83356882425037e+00 , 3.24142730507447e+00 , 7.69061966445767e-01 , 2.67252484262143e+00 , 3.15034995420553e+00 , -9.51496895508225e-02 , 3.04369939118193e+00 , 2.72067318755565e+00 , -1.59666058085304e+00 , 1.60113592967078e+00 , 2.15519099674224e+00 , 5.80071804456076e-01 , 4.38240041119901e-01 , 2.46262336976879e+00 , 5.48980991334079e-01 , 1.96959368088953e+00 , 1.01234376536455e+00 , 1.05408760152221e+00 , 1.15807993418597e+00 , 2.06042343395636e-02 , 1.69020108367558e+00 , 2.01540951886049e+00 , -1.17487180030149e+00 , 2.01894428622946e+00 , 5.24663015581007e-01 , 6.06965654388053e-01 , 2.98277511565960e+00 , -6.70091636820477e-01 , 3.67973696398877e-01 , 3.18020094552207e+00 , 1.30678882139017e+00 , 1.32183553100694e+00 , 3.83074937761609e+00 , 8.42480492065935e-01 , 1.91297367485748e+00 , 5.06403257253622e+00 , 2.04676600763386e+00 , 2.59577116983262e+00 , 5.62384874446350e+00 , -3.60187962065452e-01 , 2.91906438707605e+00 , 4.98365392120015e+00 , -1.17173739380431e+00 , 3.03291119872267e+00 , 5.90558861048476e+00 , -4.24942864299879e-01 , 3.68185527221630e+00 , 3.85350813056666e+00 , -1.47667798663298e+00 , 4.57531645519427e+00 , 3.53820386981816e+00 , -7.50485901509571e-01 , 5.38790647509149e+00 , 2.41552070759660e+00 , -2.73259922857375e+00 , 3.89276029477454e+00 , 2.93094623652956e+00 , -3.84966920894560e+00 , 4.43165634430076e+00 , 2.84648308433646e+00 , -2.58607921786046e+00 , 2.61135604056535e+00 , 2.48458862212576e+00 , -3.71575189353043e+00 , 1.91132888948723e+00 , 2.06114453689343e+00 , -3.41464867152714e+00 , 8.19463186795656e-01 , 9.77744520824400e-01 , -4.30317263798616e+00 , 1.08870954003847e+00 , 3.23703847428725e+00 , -5.53930210531588e+00 , 9.09235310273094e-01 , 3.34117073165080e+00 , -3.45825411873271e+00 , 6.41907326842739e-01 , 4.14489107139214e+00 , -3.77964154389490e+00 , 8.99884693047571e-02 , 5.48280131463119e+00 , -2.40241948018949e+00 , -3.87812824665575e-01 , 6.14622445774217e+00 , -4.47118005780455e+00 , 9.94760153779481e-01 , 6.41957195336128e+00 , -5.32307757703637e+00 , 6.03902619770999e-01 , 7.18625074294096e+00 , -6.29473276809766e+00 , 3.55390365365507e+00 , 6.70309262515356e+00 , -6.91269406186489e+00 , 4.29872080475097e+00 , 7.41940655795881e+00 , -6.74359627925831e+00 , 3.20873680426871e+00 , 5.51467328326202e+00 , -4.09220742797595e+00 , 2.30305792852368e+00 , 6.48263397793547e+00 , -4.90008080100881e+00 , 3.22721176264580e+00 , 7.21307955904248e+00 , -4.08321878774328e+00 , 4.52152209517614e+00 , 7.27520162172180e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.31520710742130e-01 , 4.70585069947745e-03 , 9.43436205219106e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.37190106763982e+00 , 4.37561116084561e-02 , -7.59489305159392e-01 , 6.99146655294224e+00 , -5.11033157667386e-01 , -6.45977286460864e-01 , 7.04360578585032e+00 , -2.02253210321486e+00 , -1.00475508697818e+00 , 6.25196208599282e+00 , -2.69117916729808e-01 , 6.70520250332210e-01 , 4.99199738915039e+00 , -2.05118307397508e-01 , 6.72732800889520e-01 , 6.90292565485735e+00 , -2.69294104018625e-01 , 1.82226498360330e+00 , 6.17819997066727e+00 , -1.18922585352062e-01 , 3.08730409705415e+00 , 7.15839369415653e+00 , -3.26081276239317e-01 , 4.29289707258867e+00 , 5.30140732164225e+00 , 1.11525760659848e+00 , 3.29660832093321e+00 , 4.09563360084175e+00 , 1.06198925177721e+00 , 3.62828711379519e+00 , 5.87628142275448e+00 , 2.29260416098295e+00 , 2.98123131140797e+00 , 5.21461212463495e+00 , 3.59576743915649e+00 , 2.88362406780732e+00 , 6.33841023238199e+00 , 4.58549633824642e+00 , 2.45478769693888e+00 , 3.90032731528937e+00 , 3.73133228488110e+00 , 2.02125381715923e+00 , 2.89255651494714e+00 , 4.11737441114465e+00 , 2.54429236626012e+00 , 3.83356882425037e+00 , 3.24142730507447e+00 , 7.69061966445767e-01 , 2.67252484262143e+00 , 3.15034995420553e+00 , -9.51496895508225e-02 , 3.04369939118193e+00 , 2.72067318755565e+00 , -1.59666058085304e+00 , 1.60113592967078e+00 , 2.15519099674224e+00 , 5.80071804456076e-01 , 4.38240041119901e-01 , 2.46262336976879e+00 , 5.48980991334079e-01 , 1.96959368088953e+00 , 1.01234376536455e+00 , 1.05408760152221e+00 , 1.15807993418597e+00 , 2.06042343395636e-02 , 1.69020108367558e+00 , 2.01540951886049e+00 , -1.17487180030149e+00 , 2.01894428622946e+00 , 5.24663015581007e-01 , 6.06965654388053e-01 , 2.98277511565960e+00 , -6.70091636820477e-01 , 3.67973696398877e-01 , 3.18020094552207e+00 , 1.30678882139017e+00 , 1.32183553100694e+00 , 3.83074937761609e+00 , 8.42480492065935e-01 , 1.91297367485748e+00 , 5.06403257253622e+00 , 2.04676600763386e+00 , 2.59577116983262e+00 , 5.62384874446350e+00 , -3.60187962065452e-01 , 2.91906438707605e+00 , 4.98365392120015e+00 , -1.17173739380431e+00 , 3.03291119872267e+00 , 5.90558861048476e+00 , -4.24942864299879e-01 , 3.68185527221630e+00 , 3.85350813056666e+00 , -1.47667798663298e+00 , 4.57531645519427e+00 , 3.53820386981816e+00 , -7.50485901509571e-01 , 5.38790647509149e+00 , 2.41552070759660e+00 , -2.73259922857375e+00 , 3.89276029477454e+00 , 2.93094623652956e+00 , -3.84966920894560e+00 , 4.43165634430076e+00 , 2.84648308433646e+00 , -2.58607921786046e+00 , 2.61135604056535e+00 , 2.48458862212576e+00 , -3.71575189353043e+00 , 1.91132888948723e+00 , 2.06114453689343e+00 , -3.41464867152714e+00 , 8.19463186795656e-01 , 9.77744520824400e-01 , -4.30317263798616e+00 , 1.08870954003847e+00 , 3.23703847428725e+00 , -5.53930210531588e+00 , 9.09235310273094e-01 , 3.34117073165080e+00 , -3.45825411873271e+00 , 6.41907326842739e-01 , 4.14489107139214e+00 , -3.77964154389490e+00 , 8.99884693047571e-02 , 5.48280131463119e+00 , -2.40241948018949e+00 , -3.87812824665575e-01 , 6.14622445774217e+00 , -4.47118005780455e+00 , 9.94760153779481e-01 , 6.41957195336128e+00 , -5.32307757703637e+00 , 6.03902619770999e-01 , 7.18625074294096e+00 , -6.29473276809766e+00 , 3.55390365365507e+00 , 6.70309262515356e+00 , -6.91269406186489e+00 , 4.29872080475097e+00 , 7.41940655795881e+00 , -6.74359627925831e+00 , 3.20873680426871e+00 , 5.51467328326202e+00 , -4.09220742797595e+00 , 2.30305792852368e+00 , 6.48263397793547e+00 , -4.90008080100881e+00 , 3.22721176264580e+00 , 7.21307955904248e+00 , -4.08321878774328e+00 , 4.52152209517614e+00 , 7.27520162172180e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.4123 , 6.74123 , 13.4825 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.4123 , 6.74123 , 13.4825 ) to colvar "one". +colvars: Adding total bias energy: 58.4943 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.4123 , 6.74123 , 13.4825 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.22401 , -0.608175 , -1.69203 ) +colvars: ( -4.47959 , -0.52151 , -1.45092 ) +colvars: ( -4.47959 , -0.52151 , -1.45092 ) +colvars: ( -5.96694 , -0.694666 , -1.93266 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.969539 , 0.208103 , 0.693641 ) +colvars: ( 0.838189 , 0.285384 , 0.72106 ) +colvars: ( 0.822485 , 0.277273 , 0.700551 ) +colvars: ( 0.714411 , 0.287569 , 0.650053 ) +colvars: ( 0.701391 , 0.215928 , 0.544054 ) +colvars: ( 0.618529 , 0.371905 , 0.70835 ) +colvars: ( 0.499675 , 0.388375 , 0.659873 ) +colvars: ( 0.414726 , 0.494126 , 0.754062 ) +colvars: ( 0.410754 , 0.340762 , 0.541435 ) +colvars: ( 0.371865 , 0.296557 , 0.457583 ) +colvars: ( 0.380069 , 0.346068 , 0.530364 ) +colvars: ( 0.302786 , 0.300114 , 0.42116 ) +colvars: ( 0.274604 , 0.330939 , 0.446571 ) +colvars: ( 0.371879 , 0.193977 , 0.316959 ) +colvars: ( 0.307341 , 0.147836 , 0.215119 ) +colvars: ( 0.507205 , 0.15282 , 0.341441 ) +colvars: ( 0.587324 , 0.0535654 , 0.253269 ) +colvars: ( 0.730489 , 0.0294919 , 0.305857 ) +colvars: ( 0.595229 , 0.0198484 , 0.211771 ) +colvars: ( 0.577952 , -0.0501319 , 0.105502 ) +colvars: ( 0.616797 , 0.0719077 , 0.296035 ) +colvars: ( 0.613536 , 0.0551863 , 0.271162 ) +colvars: ( 0.65243 , 0.125158 , 0.390343 ) +colvars: ( 0.476312 , 0.0613334 , 0.197549 ) +colvars: ( 0.468277 , 0.00135988 , 0.110525 ) +colvars: ( 0.364422 , 0.132876 , 0.228735 ) +colvars: ( 0.227244 , 0.143346 , 0.161076 ) +colvars: ( 0.12693 , 0.236441 , 0.22873 ) +colvars: ( 0.197289 , 0.0636863 , 0.0339587 ) +colvars: ( 0.142542 , 0.0253974 , -0.051264 ) +colvars: ( 0.235828 , 0.0351586 , 0.0178898 ) +colvars: ( 0.221545 , -0.0433218 , -0.0982416 ) +colvars: ( 0.262089 , -0.0479795 , -0.0803878 ) +colvars: ( 0.303916 , -0.136442 , -0.176658 ) +colvars: ( 0.255654 , -0.193332 , -0.283505 ) +colvars: ( 0.430083 , -0.153433 , -0.124522 ) +colvars: ( 0.514734 , -0.23524 , -0.186065 ) +colvars: ( 0.658793 , -0.239108 , -0.105241 ) +colvars: ( 0.461157 , -0.238983 , -0.223229 ) +colvars: ( 0.467064 , -0.312298 , -0.320208 ) +colvars: ( 0.406366 , -0.159055 , -0.146409 ) +colvars: ( 0.345206 , -0.151188 , -0.172188 ) +colvars: ( 0.325848 , -0.0571261 , -0.0548084 ) +colvars: ( 0.209793 , -0.159639 , -0.264731 ) +colvars: ( 0.182211 , -0.204366 , -0.34254 ) +colvars: ( -0.00901934 , -0.208228 , -0.462163 ) +colvars: ( -0.108902 , -0.226648 , -0.547132 ) +colvars: ( 0.102335 , -0.263333 , -0.471135 ) +colvars: ( 0.120813 , -0.115575 , -0.25752 ) +colvars: ( -0.0101266 , -0.119347 , -0.340975 ) +colvars: ( -0.107481 , -0.0318559 , -0.279233 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.22401 , 0.608175 , 1.69203 ) +colvars: ( 4.47959 , 0.52151 , 1.45092 ) +colvars: ( 4.47959 , 0.52151 , 1.45092 ) +colvars: ( 5.96694 , 0.694666 , 1.93266 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.672527 , -0.0865473 , -0.42629 ) +colvars: ( -0.602916 , -0.175161 , -0.39606 ) +colvars: ( -0.552432 , -0.151613 , -0.334472 ) +colvars: ( -0.556549 , -0.205096 , -0.362785 ) +colvars: ( -0.546196 , -0.142532 , -0.324075 ) +colvars: ( -0.526227 , -0.303532 , -0.376647 ) +colvars: ( -0.48661 , -0.347122 , -0.356352 ) +colvars: ( -0.459978 , -0.461752 , -0.381254 ) +colvars: ( -0.418678 , -0.309839 , -0.270948 ) +colvars: ( -0.411853 , -0.283195 , -0.252025 ) +colvars: ( -0.367782 , -0.303818 , -0.21686 ) +colvars: ( -0.303048 , -0.264843 , -0.13392 ) +colvars: ( -0.252986 , -0.280671 , -0.0905431 ) +colvars: ( -0.326543 , -0.154715 , -0.107887 ) +colvars: ( -0.291613 , -0.123893 , -0.0587098 ) +colvars: ( -0.3887 , -0.0929944 , -0.142741 ) +colvars: ( -0.419999 , 0.0119261 , -0.126936 ) +colvars: ( -0.478487 , 0.0633397 , -0.162743 ) +colvars: ( -0.457862 , 0.0277721 , -0.157992 ) +colvars: ( -0.445518 , 0.0880883 , -0.118288 ) +colvars: ( -0.502997 , -0.0297556 , -0.229532 ) +colvars: ( -0.536913 , -0.0315019 , -0.264552 ) +colvars: ( -0.588884 , -0.10103 , -0.348412 ) +colvars: ( -0.476968 , -0.0641437 , -0.218795 ) +colvars: ( -0.483293 , -0.0173508 , -0.204042 ) +colvars: ( -0.415536 , -0.143701 , -0.192731 ) +colvars: ( -0.350131 , -0.177687 , -0.14207 ) +colvars: ( -0.294076 , -0.274062 , -0.12903 ) +colvars: ( -0.307385 , -0.100239 , -0.0639435 ) +colvars: ( -0.290994 , -0.0807683 , -0.0386053 ) +colvars: ( -0.289947 , -0.05214 , -0.0246159 ) +colvars: ( -0.253934 , 0.027431 , 0.0476745 ) +colvars: ( -0.235193 , 0.0558913 , 0.0794448 ) +colvars: ( -0.302582 , 0.120074 , 0.0404226 ) +colvars: ( -0.273225 , 0.164276 , 0.0900191 ) +colvars: ( -0.378968 , 0.150547 , -0.0229066 ) +colvars: ( -0.432483 , 0.231952 , -0.0401464 ) +colvars: ( -0.511737 , 0.256637 , -0.108986 ) +colvars: ( -0.440778 , 0.210426 , -0.0582424 ) +colvars: ( -0.445595 , 0.275131 , -0.0338755 ) +colvars: ( -0.441988 , 0.117945 , -0.101239 ) +colvars: ( -0.445394 , 0.085401 , -0.119376 ) +colvars: ( -0.465634 , -0.0140789 , -0.184741 ) +colvars: ( -0.371044 , 0.0727693 , -0.0500422 ) +colvars: ( -0.372679 , 0.100541 , -0.0391477 ) +colvars: ( -0.198004 , 0.106783 , 0.139968 ) +colvars: ( -0.142938 , 0.108293 , 0.196227 ) +colvars: ( -0.231054 , 0.184364 , 0.141655 ) +colvars: ( -0.303616 , 0.029108 , -0.00171098 ) +colvars: ( -0.229503 , 0.0140142 , 0.0662712 ) +colvars: ( -0.170151 , -0.0747861 , 0.0860621 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 7. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 7. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atoms_new_colvar_forces = { ( -4.92699883197614e+00 , -4.86618724078052e-01 , -1.42467913094181e+00 ), ( -4.24431483555213e+00 , -4.11287219671329e-01 , -1.12591650522093e+00 ), ( -4.32172548846806e+00 , -4.39036591639196e-01 , -1.16364704256842e+00 ), ( -5.81174639582869e+00 , -6.21270459094370e-01 , -1.71268334398654e+00 ), ( 2.70052898658315e-01 , 1.25659362376525e-01 , 3.66079747178291e-01 ), ( 5.31631328128861e+00 , 6.76547546607386e-01 , 2.02373389034186e+00 ), ( 4.49265382843113e+00 , 5.62763039892953e-01 , 1.75443622150832e+00 ), ( -4.52524431744932e-02 , 3.23732624357328e-02 , 3.72808324782638e-01 ), ( 4.47166464129130e+00 , 5.52432741893097e-01 , 1.72140285504558e+00 ), ( 5.92695336328533e+00 , 7.08027654029380e-01 , 2.13821958782846e+00 ), ( 1.22878489801734e-02 , 4.22497951376943e-02 , 3.13503913694177e-01 ), ( -2.62484217107173e-04 , 3.52714054790649e-02 , 2.87239453324821e-01 ), ( 2.16185923554538e-02 , 5.02681587839578e-02 , 3.56027588063913e-01 ), ( 4.53355603635980e-02 , 3.92619305021430e-02 , 2.09072043074313e-01 ), ( 1.57281166857478e-02 , 2.39434706755070e-02 , 1.56409280914787e-01 ), ( 1.18504415282576e-01 , 5.98253385749289e-02 , 1.98700017301344e-01 ), ( 1.67324793120046e-01 , 6.54914977375688e-02 , 1.26332799629771e-01 ), ( 2.52001495399523e-01 , 9.28315906323536e-02 , 1.43114686396074e-01 ), ( 1.37367087737100e-01 , 4.76204952545460e-02 , 5.37785095330312e-02 ), ( 1.32434327972042e-01 , 3.79563375141697e-02 , -1.27851195363125e-02 ), ( 1.13800086301131e-01 , 4.21520983496086e-02 , 6.65034147195922e-02 ), ( 7.66233001267707e-02 , 2.36844621949030e-02 , 6.61017092669614e-03 ), ( 6.35464049324757e-02 , 2.41279804304955e-02 , 4.19305974577354e-02 ), ( -6.55479027328432e-04 , -2.81034241410720e-03 , -2.12460458791061e-02 ), ( -1.50159753928555e-02 , -1.59909609765167e-02 , -9.35172506680649e-02 ), ( -5.11137193793151e-02 , -1.08257415609619e-02 , 3.60045413260593e-02 ), ( -1.22887211874929e-01 , -3.43411097624845e-02 , 1.90056983032946e-02 ), ( -1.67146847611439e-01 , -3.76210820417883e-02 , 9.97006441348429e-02 ), ( -1.10096542309538e-01 , -3.65524061995518e-02 , -2.99848532408046e-02 ), ( -1.48452289187343e-01 , -5.53708545005314e-02 , -8.98692329159941e-02 ), ( -5.41184858954967e-02 , -1.69813649118323e-02 , -6.72612538257950e-03 ), ( -3.23888681510061e-02 , -1.58907664148986e-02 , -5.05670848859939e-02 ), ( 2.68951404023747e-02 , 7.91176868470593e-03 , -9.42971094339551e-04 ), ( 1.33386914111683e-03 , -1.63679234867106e-02 , -1.36235044052652e-01 ), ( -1.75709611069120e-02 , -2.90564481287763e-02 , -1.93485892842965e-01 ), ( 5.11152898928713e-02 , -2.88642876811310e-03 , -1.47428542727451e-01 ), ( 8.22513316859267e-02 , -3.28838801100539e-03 , -2.26211728774532e-01 ), ( 1.47055774923415e-01 , 1.75298052307391e-02 , -2.14226510447514e-01 ), ( 2.03786775835960e-02 , -2.85571087585229e-02 , -2.81471070714635e-01 ), ( 2.14693175798356e-02 , -3.71677411212247e-02 , -3.54083216026652e-01 ), ( -3.56223109084824e-02 , -4.11100708189845e-02 , -2.47647777397812e-01 ), ( -1.00187991162661e-01 , -6.57867228273436e-02 , -2.91564544866084e-01 ), ( -1.39786410977202e-01 , -7.12049629450578e-02 , -2.39549659977143e-01 ), ( -1.61250801320601e-01 , -8.68693877612319e-02 , -3.14773680781064e-01 ), ( -1.90468083862388e-01 , -1.03825257324807e-01 , -3.81687741360248e-01 ), ( -2.07023287438830e-01 , -1.01445134203992e-01 , -3.22194905697269e-01 ), ( -2.51839889257839e-01 , -1.18355459820924e-01 , -3.50904477214909e-01 ), ( -1.28719504995320e-01 , -7.89690629367549e-02 , -3.29479510394179e-01 ), ( -1.82802921447344e-01 , -8.64668811244112e-02 , -2.59230783675944e-01 ), ( -2.39630021885021e-01 , -1.05333163037167e-01 , -2.74703626973197e-01 ), ( -2.77631361011988e-01 , -1.06641978076813e-01 , -1.93170565240454e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 8, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 8, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 8, atoms_positions[size = 51] = { ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 ), ( 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 ), ( 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 ), ( 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 ), ( 7.04534836653206e+00 , -2.02448407054308e+00 , -9.98404589097309e-01 ), ( 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 ), ( 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 ), ( 7.14902591067445e+00 , -3.29049307138878e-01 , 4.28994950397455e+00 ), ( 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 ), ( 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 ), ( 5.87629272107495e+00 , 2.28299099600567e+00 , 2.98584493482321e+00 ), ( 5.21291617904918e+00 , 3.59559442159943e+00 , 2.88533141464119e+00 ), ( 6.33882182249135e+00 , 4.57468922568852e+00 , 2.45117186603165e+00 ), ( 3.90270903183939e+00 , 3.73544171710473e+00 , 2.02251051274607e+00 ), ( 2.88279978105576e+00 , 4.11937815033797e+00 , 2.53992315236496e+00 ), ( 3.83995777165251e+00 , 3.24086082368063e+00 , 7.64404324467284e-01 ), ( 2.67305748498782e+00 , 3.13734293346480e+00 , -9.85910588833170e-02 ), ( 3.04129456288167e+00 , 2.72016520151402e+00 , -1.59377513008085e+00 ), ( 1.59116028395355e+00 , 2.15957458460487e+00 , 5.75180933236148e-01 ), ( 4.39907657454557e-01 , 2.47026745569223e+00 , 5.45422219368124e-01 ), ( 1.97014376172849e+00 , 1.01068814224053e+00 , 1.05609809458750e+00 ), ( 1.16448374596575e+00 , 2.70512316447285e-02 , 1.69098165565567e+00 ), ( 2.01606322025152e+00 , -1.16883486837498e+00 , 2.01706394316924e+00 ), ( 5.30011405833675e-01 , 6.09134351990563e-01 , 2.97330241396327e+00 ), ( -6.67074004134921e-01 , 3.64344491997748e-01 , 3.17811611541346e+00 ), ( 1.31160462125396e+00 , 1.32575550905386e+00 , 3.83311107606156e+00 ), ( 8.47983856956386e-01 , 1.91928984360101e+00 , 5.05871618317316e+00 ), ( 2.04112429756780e+00 , 2.59938027721393e+00 , 5.62530545703922e+00 ), ( -3.59731401881105e-01 , 2.91849204256345e+00 , 4.98263934846755e+00 ), ( -1.16959039530870e+00 , 3.03621836564236e+00 , 5.90593087889633e+00 ), ( -4.33167500245590e-01 , 3.67383388380730e+00 , 3.85055944875870e+00 ), ( -1.47964036329859e+00 , 4.56877461658980e+00 , 3.53722022403730e+00 ), ( -7.46037561806663e-01 , 5.39024276065731e+00 , 2.41926930155664e+00 ), ( -2.74001319544020e+00 , 3.89049308176989e+00 , 2.92851186870193e+00 ), ( -3.84678155103800e+00 , 4.43736309769519e+00 , 2.84260902125762e+00 ), ( -2.59051556066129e+00 , 2.61364264511348e+00 , 2.47899855467404e+00 ), ( -3.71606996116065e+00 , 1.90935949382654e+00 , 2.05530426056400e+00 ), ( -3.41600082364528e+00 , 8.27113821984746e-01 , 9.69311501518656e-01 ), ( -4.29866877430971e+00 , 1.08257130745408e+00 , 3.24213293255095e+00 ), ( -5.53992830490405e+00 , 9.02331427755674e-01 , 3.33902124343832e+00 ), ( -3.45177922141792e+00 , 6.46615632694836e-01 , 4.14053791760893e+00 ), ( -3.77976929413120e+00 , 8.29295553901299e-02 , 5.48290176368017e+00 ), ( -2.39661097592831e+00 , -3.76598220818232e-01 , 6.15054540772288e+00 ), ( -4.47289527207232e+00 , 9.92990867028161e-01 , 6.42192392244427e+00 ), ( -5.32344337905715e+00 , 6.05889648480862e-01 , 7.18833411462202e+00 ), ( -6.29103911668904e+00 , 3.55674366561199e+00 , 6.70440856281332e+00 ), ( -6.91267479614233e+00 , 4.29682099619191e+00 , 7.42137030682990e+00 ), ( -6.74199032214353e+00 , 3.20851202494557e+00 , 5.51747586064245e+00 ), ( -4.09726679864892e+00 , 2.30320061945396e+00 , 6.48259584656277e+00 ), ( -4.89314801165446e+00 , 3.22111514411689e+00 , 7.21280775033448e+00 ), ( -4.08728743975958e+00 , 4.53185546978033e+00 , 7.27937324449132e+00 ) } +colvars: Step 8, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 7.04534836653206e+00 , -2.02448407054308e+00 , -9.98404589097309e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 , 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 7.14902591067445e+00 , -3.29049307138878e-01 , 4.28994950397455e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 , 5.87629272107495e+00 , 2.28299099600567e+00 , 2.98584493482321e+00 , 5.21291617904918e+00 , 3.59559442159943e+00 , 2.88533141464119e+00 , 6.33882182249135e+00 , 4.57468922568852e+00 , 2.45117186603165e+00 , 3.90270903183939e+00 , 3.73544171710473e+00 , 2.02251051274607e+00 , 2.88279978105576e+00 , 4.11937815033797e+00 , 2.53992315236496e+00 , 3.83995777165251e+00 , 3.24086082368063e+00 , 7.64404324467284e-01 , 2.67305748498782e+00 , 3.13734293346480e+00 , -9.85910588833170e-02 , 3.04129456288167e+00 , 2.72016520151402e+00 , -1.59377513008085e+00 , 1.59116028395355e+00 , 2.15957458460487e+00 , 5.75180933236148e-01 , 4.39907657454557e-01 , 2.47026745569223e+00 , 5.45422219368124e-01 , 1.97014376172849e+00 , 1.01068814224053e+00 , 1.05609809458750e+00 , 1.16448374596575e+00 , 2.70512316447285e-02 , 1.69098165565567e+00 , 2.01606322025152e+00 , -1.16883486837498e+00 , 2.01706394316924e+00 , 5.30011405833675e-01 , 6.09134351990563e-01 , 2.97330241396327e+00 , -6.67074004134921e-01 , 3.64344491997748e-01 , 3.17811611541346e+00 , 1.31160462125396e+00 , 1.32575550905386e+00 , 3.83311107606156e+00 , 8.47983856956386e-01 , 1.91928984360101e+00 , 5.05871618317316e+00 , 2.04112429756780e+00 , 2.59938027721393e+00 , 5.62530545703922e+00 , -3.59731401881105e-01 , 2.91849204256345e+00 , 4.98263934846755e+00 , -1.16959039530870e+00 , 3.03621836564236e+00 , 5.90593087889633e+00 , -4.33167500245590e-01 , 3.67383388380730e+00 , 3.85055944875870e+00 , -1.47964036329859e+00 , 4.56877461658980e+00 , 3.53722022403730e+00 , -7.46037561806663e-01 , 5.39024276065731e+00 , 2.41926930155664e+00 , -2.74001319544020e+00 , 3.89049308176989e+00 , 2.92851186870193e+00 , -3.84678155103800e+00 , 4.43736309769519e+00 , 2.84260902125762e+00 , -2.59051556066129e+00 , 2.61364264511348e+00 , 2.47899855467404e+00 , -3.71606996116065e+00 , 1.90935949382654e+00 , 2.05530426056400e+00 , -3.41600082364528e+00 , 8.27113821984746e-01 , 9.69311501518656e-01 , -4.29866877430971e+00 , 1.08257130745408e+00 , 3.24213293255095e+00 , -5.53992830490405e+00 , 9.02331427755674e-01 , 3.33902124343832e+00 , -3.45177922141792e+00 , 6.46615632694836e-01 , 4.14053791760893e+00 , -3.77976929413120e+00 , 8.29295553901299e-02 , 5.48290176368017e+00 , -2.39661097592831e+00 , -3.76598220818232e-01 , 6.15054540772288e+00 , -4.47289527207232e+00 , 9.92990867028161e-01 , 6.42192392244427e+00 , -5.32344337905715e+00 , 6.05889648480862e-01 , 7.18833411462202e+00 , -6.29103911668904e+00 , 3.55674366561199e+00 , 6.70440856281332e+00 , -6.91267479614233e+00 , 4.29682099619191e+00 , 7.42137030682990e+00 , -6.74199032214353e+00 , 3.20851202494557e+00 , 5.51747586064245e+00 , -4.09726679864892e+00 , 2.30320061945396e+00 , 6.48259584656277e+00 , -4.89314801165446e+00 , 3.22111514411689e+00 , 7.21280775033448e+00 , -4.08728743975958e+00 , 4.53185546978033e+00 , 7.27937324449132e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.29434737593730e-01 , 4.63948372091272e-03 , 9.44166949674343e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.29434737593730e-01 , 4.63948372091272e-03 , 9.44166949674343e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.36380148584633e+00 , 4.39061391653765e-02 , -7.61565889180621e-01 , 6.99090347971702e+00 , -5.17205687669704e-01 , -6.41814118827945e-01 , 7.04534836653206e+00 , -2.02448407054308e+00 , -9.98404589097309e-01 , 6.24611624405088e+00 , -2.75355508143864e-01 , 6.75237715535789e-01 , 4.98825510188857e+00 , -2.03217727679501e-01 , 6.77731615963053e-01 , 6.90248968807012e+00 , -2.68879634309547e-01 , 1.82933785588394e+00 , 6.17945405952814e+00 , -1.17847766608153e-01 , 3.10133380017129e+00 , 7.14902591067445e+00 , -3.29049307138878e-01 , 4.28994950397455e+00 , 5.29842920421599e+00 , 1.11403514066913e+00 , 3.30174526439615e+00 , 4.10085967460815e+00 , 1.05890309358596e+00 , 3.63196301028956e+00 , 5.87629272107495e+00 , 2.28299099600567e+00 , 2.98584493482321e+00 , 5.21291617904918e+00 , 3.59559442159943e+00 , 2.88533141464119e+00 , 6.33882182249135e+00 , 4.57468922568852e+00 , 2.45117186603165e+00 , 3.90270903183939e+00 , 3.73544171710473e+00 , 2.02251051274607e+00 , 2.88279978105576e+00 , 4.11937815033797e+00 , 2.53992315236496e+00 , 3.83995777165251e+00 , 3.24086082368063e+00 , 7.64404324467284e-01 , 2.67305748498782e+00 , 3.13734293346480e+00 , -9.85910588833170e-02 , 3.04129456288167e+00 , 2.72016520151402e+00 , -1.59377513008085e+00 , 1.59116028395355e+00 , 2.15957458460487e+00 , 5.75180933236148e-01 , 4.39907657454557e-01 , 2.47026745569223e+00 , 5.45422219368124e-01 , 1.97014376172849e+00 , 1.01068814224053e+00 , 1.05609809458750e+00 , 1.16448374596575e+00 , 2.70512316447285e-02 , 1.69098165565567e+00 , 2.01606322025152e+00 , -1.16883486837498e+00 , 2.01706394316924e+00 , 5.30011405833675e-01 , 6.09134351990563e-01 , 2.97330241396327e+00 , -6.67074004134921e-01 , 3.64344491997748e-01 , 3.17811611541346e+00 , 1.31160462125396e+00 , 1.32575550905386e+00 , 3.83311107606156e+00 , 8.47983856956386e-01 , 1.91928984360101e+00 , 5.05871618317316e+00 , 2.04112429756780e+00 , 2.59938027721393e+00 , 5.62530545703922e+00 , -3.59731401881105e-01 , 2.91849204256345e+00 , 4.98263934846755e+00 , -1.16959039530870e+00 , 3.03621836564236e+00 , 5.90593087889633e+00 , -4.33167500245590e-01 , 3.67383388380730e+00 , 3.85055944875870e+00 , -1.47964036329859e+00 , 4.56877461658980e+00 , 3.53722022403730e+00 , -7.46037561806663e-01 , 5.39024276065731e+00 , 2.41926930155664e+00 , -2.74001319544020e+00 , 3.89049308176989e+00 , 2.92851186870193e+00 , -3.84678155103800e+00 , 4.43736309769519e+00 , 2.84260902125762e+00 , -2.59051556066129e+00 , 2.61364264511348e+00 , 2.47899855467404e+00 , -3.71606996116065e+00 , 1.90935949382654e+00 , 2.05530426056400e+00 , -3.41600082364528e+00 , 8.27113821984746e-01 , 9.69311501518656e-01 , -4.29866877430971e+00 , 1.08257130745408e+00 , 3.24213293255095e+00 , -5.53992830490405e+00 , 9.02331427755674e-01 , 3.33902124343832e+00 , -3.45177922141792e+00 , 6.46615632694836e-01 , 4.14053791760893e+00 , -3.77976929413120e+00 , 8.29295553901299e-02 , 5.48290176368017e+00 , -2.39661097592831e+00 , -3.76598220818232e-01 , 6.15054540772288e+00 , -4.47289527207232e+00 , 9.92990867028161e-01 , 6.42192392244427e+00 , -5.32344337905715e+00 , 6.05889648480862e-01 , 7.18833411462202e+00 , -6.29103911668904e+00 , 3.55674366561199e+00 , 6.70440856281332e+00 , -6.91267479614233e+00 , 4.29682099619191e+00 , 7.42137030682990e+00 , -6.74199032214353e+00 , 3.20851202494557e+00 , 5.51747586064245e+00 , -4.09726679864892e+00 , 2.30320061945396e+00 , 6.48259584656277e+00 , -4.89314801165446e+00 , 3.22111514411689e+00 , 7.21280775033448e+00 , -4.08728743975958e+00 , 4.53185546978033e+00 , 7.27937324449132e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.3053 , 6.73053 , 13.4611 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.3053 , 6.73053 , 13.4611 ) to colvar "one". +colvars: Adding total bias energy: 58.3443 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.3053 , 6.73053 , 13.4611 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.21723 , -0.604127 , -1.67788 ) +colvars: ( -4.47377 , -0.518039 , -1.43878 ) +colvars: ( -4.47377 , -0.518039 , -1.43878 ) +colvars: ( -5.9592 , -0.690043 , -1.9165 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.966702 , 0.207855 , 0.689941 ) +colvars: ( 0.835857 , 0.284872 , 0.717209 ) +colvars: ( 0.820076 , 0.27684 , 0.696811 ) +colvars: ( 0.712623 , 0.286937 , 0.64652 ) +colvars: ( 0.699645 , 0.215457 , 0.54103 ) +colvars: ( 0.617177 , 0.370983 , 0.704515 ) +colvars: ( 0.49886 , 0.387298 , 0.656246 ) +colvars: ( 0.414295 , 0.49272 , 0.749964 ) +colvars: ( 0.410217 , 0.339769 , 0.538373 ) +colvars: ( 0.371526 , 0.295616 , 0.454914 ) +colvars: ( 0.379536 , 0.345101 , 0.527362 ) +colvars: ( 0.302476 , 0.299241 , 0.41868 ) +colvars: ( 0.274287 , 0.330036 , 0.443976 ) +colvars: ( 0.371263 , 0.193413 , 0.314995 ) +colvars: ( 0.306976 , 0.147336 , 0.213636 ) +colvars: ( 0.506035 , 0.152456 , 0.339381 ) +colvars: ( 0.585811 , 0.0534993 , 0.251649 ) +colvars: ( 0.728365 , 0.029605 , 0.304011 ) +colvars: ( 0.593799 , 0.0198077 , 0.21034 ) +colvars: ( 0.576581 , -0.0500194 , 0.104582 ) +colvars: ( 0.615392 , 0.071706 , 0.294192 ) +colvars: ( 0.612262 , 0.0549605 , 0.269426 ) +colvars: ( 0.651105 , 0.124746 , 0.388028 ) +colvars: ( 0.475612 , 0.0609809 , 0.196143 ) +colvars: ( 0.467646 , 0.00112084 , 0.109533 ) +colvars: ( 0.364145 , 0.132289 , 0.227163 ) +colvars: ( 0.227522 , 0.142632 , 0.159808 ) +colvars: ( 0.127583 , 0.235453 , 0.227123 ) +colvars: ( 0.197599 , 0.0631797 , 0.0333066 ) +colvars: ( 0.143108 , 0.0249203 , -0.051518 ) +colvars: ( 0.235865 , 0.0348063 , 0.0173332 ) +colvars: ( 0.221547 , -0.043457 , -0.098232 ) +colvars: ( 0.261801 , -0.0480094 , -0.080445 ) +colvars: ( 0.30362 , -0.136319 , -0.176261 ) +colvars: ( 0.255535 , -0.193105 , -0.2826 ) +colvars: ( 0.42933 , -0.153203 , -0.124361 ) +colvars: ( 0.513685 , -0.234782 , -0.185599 ) +colvars: ( 0.657196 , -0.23855 , -0.105143 ) +colvars: ( 0.460437 , -0.238614 , -0.222603 ) +colvars: ( 0.46633 , -0.311761 , -0.319115 ) +colvars: ( 0.405955 , -0.158956 , -0.146171 ) +colvars: ( 0.345149 , -0.151207 , -0.171847 ) +colvars: ( 0.325963 , -0.0574239 , -0.0550448 ) +colvars: ( 0.210253 , -0.159724 , -0.263964 ) +colvars: ( 0.182834 , -0.204395 , -0.341407 ) +colvars: ( -0.00789679 , -0.208252 , -0.460458 ) +colvars: ( -0.107399 , -0.226693 , -0.545031 ) +colvars: ( 0.102943 , -0.263114 , -0.469362 ) +colvars: ( 0.121549 , -0.115786 , -0.256793 ) +colvars: ( -0.00889815 , -0.119629 , -0.339863 ) +colvars: ( -0.105904 , -0.0323883 , -0.27843 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.21723 , 0.604127 , 1.67788 ) +colvars: ( 4.47377 , 0.518039 , 1.43878 ) +colvars: ( 4.47377 , 0.518039 , 1.43878 ) +colvars: ( 5.9592 , 0.690043 , 1.9165 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.670093 , -0.0863681 , -0.422968 ) +colvars: ( -0.600907 , -0.17474 , -0.392618 ) +colvars: ( -0.550346 , -0.151261 , -0.331136 ) +colvars: ( -0.554996 , -0.204553 , -0.359612 ) +colvars: ( -0.544672 , -0.142126 , -0.321336 ) +colvars: ( -0.525048 , -0.302727 , -0.373217 ) +colvars: ( -0.485884 , -0.346166 , -0.353099 ) +colvars: ( -0.459586 , -0.460503 , -0.3776 ) +colvars: ( -0.418173 , -0.308946 , -0.268184 ) +colvars: ( -0.411513 , -0.28234 , -0.249592 ) +colvars: ( -0.36727 , -0.302945 , -0.214159 ) +colvars: ( -0.302712 , -0.264042 , -0.131673 ) +colvars: ( -0.252634 , -0.279844 , -0.0882105 ) +colvars: ( -0.325941 , -0.154189 , -0.106077 ) +colvars: ( -0.291214 , -0.123413 , -0.0573111 ) +colvars: ( -0.387632 , -0.0926585 , -0.140846 ) +colvars: ( -0.418635 , 0.0119953 , -0.125413 ) +colvars: ( -0.47661 , 0.0632353 , -0.161025 ) +colvars: ( -0.456573 , 0.0278213 , -0.156619 ) +colvars: ( -0.444272 , 0.0880081 , -0.117349 ) +colvars: ( -0.501743 , -0.0295687 , -0.227797 ) +colvars: ( -0.535778 , -0.0312911 , -0.262898 ) +colvars: ( -0.587721 , -0.100663 , -0.346256 ) +colvars: ( -0.476312 , -0.0638054 , -0.217424 ) +colvars: ( -0.482693 , -0.0171078 , -0.203019 ) +colvars: ( -0.415236 , -0.143148 , -0.191226 ) +colvars: ( -0.350295 , -0.177006 , -0.140827 ) +colvars: ( -0.294558 , -0.273134 , -0.127506 ) +colvars: ( -0.307561 , -0.0997336 , -0.0632329 ) +colvars: ( -0.291383 , -0.0802803 , -0.0382311 ) +colvars: ( -0.289882 , -0.0517751 , -0.0239956 ) +colvars: ( -0.253826 , 0.0276095 , 0.0478056 ) +colvars: ( -0.234833 , 0.0559711 , 0.0796225 ) +colvars: ( -0.302221 , 0.120021 , 0.0402311 ) +colvars: ( -0.273005 , 0.16414 , 0.0893929 ) +colvars: ( -0.378229 , 0.150387 , -0.0228888 ) +colvars: ( -0.431495 , 0.231586 , -0.0403806 ) +colvars: ( -0.510296 , 0.256168 , -0.108899 ) +colvars: ( -0.440074 , 0.210147 , -0.058603 ) +colvars: ( -0.444874 , 0.274706 , -0.0346312 ) +colvars: ( -0.441555 , 0.117906 , -0.101264 ) +colvars: ( -0.445266 , 0.0854742 , -0.119482 ) +colvars: ( -0.465665 , -0.0137622 , -0.184349 ) +colvars: ( -0.371343 , 0.0729169 , -0.0505175 ) +colvars: ( -0.373114 , 0.100645 , -0.039929 ) +colvars: ( -0.198831 , 0.106902 , 0.138669 ) +colvars: ( -0.144079 , 0.108443 , 0.194588 ) +colvars: ( -0.231443 , 0.184258 , 0.140297 ) +colvars: ( -0.304141 , 0.0293729 , -0.00216246 ) +colvars: ( -0.230435 , 0.0143563 , 0.0654858 ) +colvars: ( -0.171376 , -0.074217 , 0.0855308 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 8. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 8. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atoms_new_colvar_forces = { ( -4.92062102276460e+00 , -4.82640086402408e-01 , -1.41090709788162e+00 ), ( -4.23882300605358e+00 , -4.07905998443878e-01 , -1.11419071648431e+00 ), ( -4.31614662308449e+00 , -4.35654787495289e-01 , -1.15187353857763e+00 ), ( -5.80422300642920e+00 , -6.16711741355150e-01 , -1.69680505101877e+00 ), ( 2.69730415475049e-01 , 1.25579660928816e-01 , 3.65674486085080e-01 ), ( 5.30935930421059e+00 , 6.72383167042985e-01 , 2.00917749325564e+00 ), ( 4.48674966182718e+00 , 5.59170530438994e-01 , 1.74192893872839e+00 ), ( -4.52906298257705e-02 , 3.22171503858267e-02 , 3.72364783352675e-01 ), ( 4.46581806624927e+00 , 5.48862333806290e-01 , 1.70897058867861e+00 ), ( 5.91920974857694e+00 , 7.03318412070536e-01 , 2.12182035960104e+00 ), ( 1.22659525918241e-02 , 4.21552798374245e-02 , 3.13203231438047e-01 ), ( -2.35449825619849e-04 , 3.51985139700656e-02 , 2.87007138398798e-01 ), ( 2.16521316420076e-02 , 5.01918575449373e-02 , 3.55765812291965e-01 ), ( 4.53226913390948e-02 , 3.92234256799797e-02 , 2.08917853504543e-01 ), ( 1.57619387743165e-02 , 2.39224751759000e-02 , 1.56324760053555e-01 ), ( 1.18402915597713e-01 , 5.97970291228929e-02 , 1.98535455383764e-01 ), ( 1.67175995244537e-01 , 6.54946140811529e-02 , 1.26235922817558e-01 ), ( 2.51755249276545e-01 , 9.28402975914267e-02 , 1.42985471270553e-01 ), ( 1.37225093985104e-01 , 4.76289236613890e-02 , 5.37210230860738e-02 ), ( 1.32309149368861e-01 , 3.79887911644722e-02 , -1.27668340774620e-02 ), ( 1.13648225863308e-01 , 4.21372838913594e-02 , 6.63942130256543e-02 ), ( 7.64846659166681e-02 , 2.36694781705501e-02 , 6.52785402352585e-03 ), ( 6.33841952374116e-02 , 2.40836554961314e-02 , 4.17716779614807e-02 ), ( -7.00248608696719e-04 , -2.82451954875375e-03 , -2.12813385831128e-02 ), ( -1.50472452036515e-02 , -1.59869396997441e-02 , -9.34867470803088e-02 ), ( -5.10912382790079e-02 , -1.08590004350120e-02 , 3.59376467537308e-02 ), ( -1.22772754211688e-01 , -3.43740921663118e-02 , 1.89801000449557e-02 ), ( -1.66974932373970e-01 , -3.76804871495528e-02 , 9.96173937663538e-02 ), ( -1.09962368821707e-01 , -3.65539210011210e-02 , -2.99262571378577e-02 ), ( -1.48275025635186e-01 , -5.53599330649248e-02 , -8.97490845489287e-02 ), ( -5.40175037301750e-02 , -1.69688024866761e-02 , -6.66238588198451e-03 ), ( -3.22790874989935e-02 , -1.58474256704186e-02 , -5.04264386623485e-02 ), ( 2.69676448462849e-02 , 7.96168744989820e-03 , -8.22472164126120e-04 ), ( 1.39865524379135e-03 , -1.62978531419949e-02 , -1.36029656644145e-01 ), ( -1.74701394458462e-02 , -2.89654373170617e-02 , -1.93206735091724e-01 ), ( 5.11004986260297e-02 , -2.81682533688396e-03 , -1.47249689247549e-01 ), ( 8.21900123767041e-02 , -3.19642828593120e-03 , -2.25979411403335e-01 ), ( 1.46900072719255e-01 , 1.76174357491722e-02 , -2.14042077672817e-01 ), ( 2.03630711473856e-02 , -2.84679434628290e-02 , -2.81206304273171e-01 ), ( 2.14567618961489e-02 , -3.70550714493615e-02 , -3.53746559626665e-01 ), ( -3.56005649721288e-02 , -4.10499915429206e-02 , -2.47435750153755e-01 ), ( -1.00116770630907e-01 , -6.57328263410535e-02 , -2.91329182539394e-01 ), ( -1.39702517366954e-01 , -7.11860778591733e-02 , -2.39394078165158e-01 ), ( -1.61089749065314e-01 , -8.68074914211787e-02 , -3.14481134001435e-01 ), ( -1.90280403524510e-01 , -1.03750370890082e-01 , -3.81336169015597e-01 ), ( -2.06728189061952e-01 , -1.01350338916010e-01 , -3.21788092155524e-01 ), ( -2.51477506982419e-01 , -1.18250740234853e-01 , -3.50443301704092e-01 ), ( -1.28500313421132e-01 , -7.88560071267686e-02 , -3.29064425604893e-01 ), ( -1.82592240115323e-01 , -8.64129621561250e-02 , -2.58955125406175e-01 ), ( -2.39333463508562e-01 , -1.05272589551821e-01 , -2.74377645288446e-01 ), ( -2.77280117590632e-01 , -1.06605313306912e-01 , -1.92898903429652e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 9, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 9, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 9, atoms_positions[size = 51] = { ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 ), ( 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 ), ( 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 ), ( 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 ), ( 7.04716055156384e+00 , -2.02642724541937e+00 , -9.91996217526734e-01 ), ( 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 ), ( 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 ), ( 7.13937501148286e+00 , -3.32281007196666e-01 , 4.28724944051132e+00 ), ( 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 ), ( 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 ), ( 5.87584240605616e+00 , 2.27406079439535e+00 , 2.98975335414505e+00 ), ( 5.21231076724505e+00 , 3.59532021733656e+00 , 2.88750725412396e+00 ), ( 6.33859306036526e+00 , 4.56409445599567e+00 , 2.44725866444525e+00 ), ( 3.90518088129681e+00 , 3.73833202821970e+00 , 2.02424928541876e+00 ), ( 2.87258675504871e+00 , 4.12193535116982e+00 , 2.53577331855110e+00 ), ( 3.84736969212799e+00 , 3.24045587181967e+00 , 7.59651605650163e-01 ), ( 2.67255189423094e+00 , 3.12365193022208e+00 , -1.01439806041565e-01 ), ( 3.03889129974584e+00 , 2.72026741320911e+00 , -1.58903460828758e+00 ), ( 1.58275888302685e+00 , 2.16537626786957e+00 , 5.68033334049131e-01 ), ( 4.40434598356364e-01 , 2.47816226156406e+00 , 5.42124173255944e-01 ), ( 1.97201951582835e+00 , 1.00824717188618e+00 , 1.05906022437336e+00 ), ( 1.17011266336580e+00 , 3.51272591235100e-02 , 1.69160000001138e+00 ), ( 2.01708799463464e+00 , -1.16279170265369e+00 , 2.01503314553798e+00 ), ( 5.34997134557080e-01 , 6.10358093113758e-01 , 2.96371481860032e+00 ), ( -6.63701749479078e-01 , 3.61125539662574e-01 , 3.17629043775601e+00 ), ( 1.31581612316446e+00 , 1.32962185090911e+00 , 3.83499611283094e+00 ), ( 8.52576343402521e-01 , 1.92550867614467e+00 , 5.05341694767528e+00 ), ( 2.03622843302767e+00 , 2.60342277714730e+00 , 5.62712163754377e+00 ), ( -3.58569781342234e-01 , 2.91796222083163e+00 , 4.98136460221299e+00 ), ( -1.16746538661149e+00 , 3.03941451175296e+00 , 5.90599491867180e+00 ), ( -4.41327274576360e-01 , 3.66455315494170e+00 , 3.84828734308887e+00 ), ( -1.48252901462828e+00 , 4.56316209173146e+00 , 3.53510885209680e+00 ), ( -7.41466556365248e-01 , 5.39248711418538e+00 , 2.42341371144279e+00 ), ( -2.74736907658648e+00 , 3.88785416209683e+00 , 2.92618062941570e+00 ), ( -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 ), ( -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 ), ( -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 ), ( -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 ), ( -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 ), ( -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 ), ( -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 ), ( -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 ), ( -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 ), ( -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 ), ( -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 ), ( -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 ), ( -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 ), ( -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 ), ( -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 ), ( -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 ), ( -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ) } +colvars: Step 9, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.27191798357385e-01 , 4.60173684513572e-03 , 9.44946745116183e-01 ). +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 ). +colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating gradients of colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 7.04716055156384e+00 , -2.02642724541937e+00 , -9.91996217526734e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 , 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 7.13937501148286e+00 , -3.32281007196666e-01 , 4.28724944051132e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 , 5.87584240605616e+00 , 2.27406079439535e+00 , 2.98975335414505e+00 , 5.21231076724505e+00 , 3.59532021733656e+00 , 2.88750725412396e+00 , 6.33859306036526e+00 , 4.56409445599567e+00 , 2.44725866444525e+00 , 3.90518088129681e+00 , 3.73833202821970e+00 , 2.02424928541876e+00 , 2.87258675504871e+00 , 4.12193535116982e+00 , 2.53577331855110e+00 , 3.84736969212799e+00 , 3.24045587181967e+00 , 7.59651605650163e-01 , 2.67255189423094e+00 , 3.12365193022208e+00 , -1.01439806041565e-01 , 3.03889129974584e+00 , 2.72026741320911e+00 , -1.58903460828758e+00 , 1.58275888302685e+00 , 2.16537626786957e+00 , 5.68033334049131e-01 , 4.40434598356364e-01 , 2.47816226156406e+00 , 5.42124173255944e-01 , 1.97201951582835e+00 , 1.00824717188618e+00 , 1.05906022437336e+00 , 1.17011266336580e+00 , 3.51272591235100e-02 , 1.69160000001138e+00 , 2.01708799463464e+00 , -1.16279170265369e+00 , 2.01503314553798e+00 , 5.34997134557080e-01 , 6.10358093113758e-01 , 2.96371481860032e+00 , -6.63701749479078e-01 , 3.61125539662574e-01 , 3.17629043775601e+00 , 1.31581612316446e+00 , 1.32962185090911e+00 , 3.83499611283094e+00 , 8.52576343402521e-01 , 1.92550867614467e+00 , 5.05341694767528e+00 , 2.03622843302767e+00 , 2.60342277714730e+00 , 5.62712163754377e+00 , -3.58569781342234e-01 , 2.91796222083163e+00 , 4.98136460221299e+00 , -1.16746538661149e+00 , 3.03941451175296e+00 , 5.90599491867180e+00 , -4.41327274576360e-01 , 3.66455315494170e+00 , 3.84828734308887e+00 , -1.48252901462828e+00 , 4.56316209173146e+00 , 3.53510885209680e+00 , -7.41466556365248e-01 , 5.39248711418538e+00 , 2.42341371144279e+00 , -2.74736907658648e+00 , 3.88785416209683e+00 , 2.92618062941570e+00 , -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 , -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 , -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 , -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 , -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 , -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 , -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 , -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 , -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 , -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 , -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 , -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 , -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 , -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 , -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 , -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 , -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.27191798357385e-01 , 4.60173684513572e-03 , 9.44946745116183e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.35574200449490e+00 , 4.39675546981018e-02 , -7.63317212544130e-01 , 6.99054837237979e+00 , -5.23144389332198e-01 , -6.37914443339441e-01 , 7.04716055156384e+00 , -2.02642724541937e+00 , -9.91996217526734e-01 , 6.23777819863291e+00 , -2.82307577486665e-01 , 6.79417005097865e-01 , 4.98541559951068e+00 , -2.00985952636184e-01 , 6.82568822504010e-01 , 6.90199933858766e+00 , -2.68317098210572e-01 , 1.83613097050216e+00 , 6.18097416720584e+00 , -1.17395409526563e-01 , 3.11614785564356e+00 , 7.13937501148286e+00 , -3.32281007196666e-01 , 4.28724944051132e+00 , 5.29534427577585e+00 , 1.11331676850587e+00 , 3.30668471368515e+00 , 4.10688090706510e+00 , 1.05579993709584e+00 , 3.63566705631447e+00 , 5.87584240605616e+00 , 2.27406079439535e+00 , 2.98975335414505e+00 , 5.21231076724505e+00 , 3.59532021733656e+00 , 2.88750725412396e+00 , 6.33859306036526e+00 , 4.56409445599567e+00 , 2.44725866444525e+00 , 3.90518088129681e+00 , 3.73833202821970e+00 , 2.02424928541876e+00 , 2.87258675504871e+00 , 4.12193535116982e+00 , 2.53577331855110e+00 , 3.84736969212799e+00 , 3.24045587181967e+00 , 7.59651605650163e-01 , 2.67255189423094e+00 , 3.12365193022208e+00 , -1.01439806041565e-01 , 3.03889129974584e+00 , 2.72026741320911e+00 , -1.58903460828758e+00 , 1.58275888302685e+00 , 2.16537626786957e+00 , 5.68033334049131e-01 , 4.40434598356364e-01 , 2.47816226156406e+00 , 5.42124173255944e-01 , 1.97201951582835e+00 , 1.00824717188618e+00 , 1.05906022437336e+00 , 1.17011266336580e+00 , 3.51272591235100e-02 , 1.69160000001138e+00 , 2.01708799463464e+00 , -1.16279170265369e+00 , 2.01503314553798e+00 , 5.34997134557080e-01 , 6.10358093113758e-01 , 2.96371481860032e+00 , -6.63701749479078e-01 , 3.61125539662574e-01 , 3.17629043775601e+00 , 1.31581612316446e+00 , 1.32962185090911e+00 , 3.83499611283094e+00 , 8.52576343402521e-01 , 1.92550867614467e+00 , 5.05341694767528e+00 , 2.03622843302767e+00 , 2.60342277714730e+00 , 5.62712163754377e+00 , -3.58569781342234e-01 , 2.91796222083163e+00 , 4.98136460221299e+00 , -1.16746538661149e+00 , 3.03941451175296e+00 , 5.90599491867180e+00 , -4.41327274576360e-01 , 3.66455315494170e+00 , 3.84828734308887e+00 , -1.48252901462828e+00 , 4.56316209173146e+00 , 3.53510885209680e+00 , -7.41466556365248e-01 , 5.39248711418538e+00 , 2.42341371144279e+00 , -2.74736907658648e+00 , 3.88785416209683e+00 , 2.92618062941570e+00 , -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 , -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 , -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 , -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 , -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 , -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 , -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 , -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 , -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 , -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 , -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 , -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 , -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 , -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 , -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 , -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 , -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.1907 , 6.71907 , 13.4381 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.1907 , 6.71907 , 13.4381 ) to colvar "one". +colvars: Adding total bias energy: 58.1833 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.1907 , 6.71907 , 13.4381 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.21011 , -0.599752 , -1.66278 ) +colvars: ( -4.46767 , -0.514287 , -1.42583 ) +colvars: ( -4.46767 , -0.514287 , -1.42583 ) +colvars: ( -5.95106 , -0.685045 , -1.89925 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.963712 , 0.207573 , 0.686021 ) +colvars: ( 0.833401 , 0.284306 , 0.713138 ) +colvars: ( 0.81754 , 0.276361 , 0.692862 ) +colvars: ( 0.710739 , 0.286244 , 0.642785 ) +colvars: ( 0.697806 , 0.214939 , 0.537829 ) +colvars: ( 0.615751 , 0.369975 , 0.700468 ) +colvars: ( 0.498 , 0.386123 , 0.652419 ) +colvars: ( 0.413841 , 0.491188 , 0.745646 ) +colvars: ( 0.409652 , 0.338688 , 0.535144 ) +colvars: ( 0.37117 , 0.294592 , 0.452096 ) +colvars: ( 0.378978 , 0.344049 , 0.524202 ) +colvars: ( 0.302155 , 0.298293 , 0.416074 ) +colvars: ( 0.273959 , 0.329057 , 0.441256 ) +colvars: ( 0.37062 , 0.192802 , 0.312926 ) +colvars: ( 0.306596 , 0.146796 , 0.212074 ) +colvars: ( 0.504807 , 0.152059 , 0.337208 ) +colvars: ( 0.584222 , 0.0534264 , 0.249932 ) +colvars: ( 0.726131 , 0.0297241 , 0.302052 ) +colvars: ( 0.592294 , 0.0197618 , 0.208817 ) +colvars: ( 0.57514 , -0.0498975 , 0.103594 ) +colvars: ( 0.613911 , 0.0714834 , 0.29223 ) +colvars: ( 0.610919 , 0.0547113 , 0.267572 ) +colvars: ( 0.649707 , 0.124292 , 0.385563 ) +colvars: ( 0.474873 , 0.0605968 , 0.19464 ) +colvars: ( 0.466979 , 0.000860634 , 0.108462 ) +colvars: ( 0.363854 , 0.131653 , 0.225493 ) +colvars: ( 0.227816 , 0.141861 , 0.158461 ) +colvars: ( 0.128273 , 0.234386 , 0.225427 ) +colvars: ( 0.197927 , 0.0626348 , 0.0326096 ) +colvars: ( 0.143705 , 0.0244091 , -0.0517976 ) +colvars: ( 0.235907 , 0.0344294 , 0.0167392 ) +colvars: ( 0.221554 , -0.0435962 , -0.0982291 ) +colvars: ( 0.261505 , -0.0480343 , -0.0805084 ) +colvars: ( 0.303312 , -0.136178 , -0.175857 ) +colvars: ( 0.255414 , -0.19285 , -0.281661 ) +colvars: ( 0.428539 , -0.15295 , -0.124212 ) +colvars: ( 0.512582 , -0.234282 , -0.185136 ) +colvars: ( 0.655513 , -0.237945 , -0.105074 ) +colvars: ( 0.459679 , -0.238211 , -0.221976 ) +colvars: ( 0.465557 , -0.311174 , -0.318 ) +colvars: ( 0.40552 , -0.158845 , -0.145951 ) +colvars: ( 0.345088 , -0.151225 , -0.17152 ) +colvars: ( 0.32608 , -0.0577453 , -0.0553256 ) +colvars: ( 0.210737 , -0.159811 , -0.263183 ) +colvars: ( 0.183488 , -0.20442 , -0.340246 ) +colvars: ( -0.00671073 , -0.208265 , -0.458678 ) +colvars: ( -0.10581 , -0.226727 , -0.542833 ) +colvars: ( 0.103587 , -0.262864 , -0.467513 ) +colvars: ( 0.122325 , -0.116007 , -0.256048 ) +colvars: ( -0.00760195 , -0.119923 , -0.338709 ) +colvars: ( -0.104241 , -0.0329536 , -0.277592 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.21011 , 0.599752 , 1.66278 ) +colvars: ( 4.46767 , 0.514287 , 1.42583 ) +colvars: ( 4.46767 , 0.514287 , 1.42583 ) +colvars: ( 5.95106 , 0.685045 , 1.89925 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.66753 , -0.0861754 , -0.419444 ) +colvars: ( -0.598793 , -0.174281 , -0.388979 ) +colvars: ( -0.548158 , -0.150883 , -0.327622 ) +colvars: ( -0.553361 , -0.203962 , -0.35626 ) +colvars: ( -0.543067 , -0.141684 , -0.318436 ) +colvars: ( -0.523804 , -0.301845 , -0.369602 ) +colvars: ( -0.485115 , -0.345117 , -0.34967 ) +colvars: ( -0.459165 , -0.459129 , -0.373757 ) +colvars: ( -0.41764 , -0.307967 , -0.265277 ) +colvars: ( -0.411152 , -0.281402 , -0.247028 ) +colvars: ( -0.366738 , -0.301994 , -0.211329 ) +colvars: ( -0.302367 , -0.263173 , -0.129328 ) +colvars: ( -0.252281 , -0.27895 , -0.085789 ) +colvars: ( -0.325318 , -0.153624 , -0.104184 ) +colvars: ( -0.290805 , -0.122899 , -0.055851 ) +colvars: ( -0.386519 , -0.0923014 , -0.138855 ) +colvars: ( -0.417212 , 0.0120587 , -0.123804 ) +colvars: ( -0.474647 , 0.063107 , -0.159207 ) +colvars: ( -0.455224 , 0.0278664 , -0.155157 ) +colvars: ( -0.442968 , 0.0879107 , -0.116339 ) +colvars: ( -0.500424 , -0.0293682 , -0.225948 ) +colvars: ( -0.534577 , -0.0310604 , -0.261123 ) +colvars: ( -0.586486 , -0.100256 , -0.343948 ) +colvars: ( -0.475616 , -0.0634342 , -0.215952 ) +colvars: ( -0.482053 , -0.0168402 , -0.201907 ) +colvars: ( -0.414917 , -0.142542 , -0.189625 ) +colvars: ( -0.350463 , -0.176261 , -0.139509 ) +colvars: ( -0.295062 , -0.272117 , -0.125905 ) +colvars: ( -0.307746 , -0.0991835 , -0.0624773 ) +colvars: ( -0.29179 , -0.0797481 , -0.0378264 ) +colvars: ( -0.289821 , -0.0513831 , -0.0233405 ) +colvars: ( -0.253724 , 0.0277934 , 0.0479436 ) +colvars: ( -0.234472 , 0.0560423 , 0.0798017 ) +colvars: ( -0.30185 , 0.119951 , 0.0400426 ) +colvars: ( -0.272784 , 0.163978 , 0.0887478 ) +colvars: ( -0.377458 , 0.150201 , -0.022846 ) +colvars: ( -0.430459 , 0.231176 , -0.0405895 ) +colvars: ( -0.508779 , 0.255645 , -0.10876 ) +colvars: ( -0.439331 , 0.209835 , -0.0589382 ) +colvars: ( -0.444112 , 0.274236 , -0.0353756 ) +colvars: ( -0.441093 , 0.117862 , -0.101249 ) +colvars: ( -0.44512 , 0.0855573 , -0.119545 ) +colvars: ( -0.465681 , -0.0134083 , -0.183889 ) +colvars: ( -0.371648 , 0.0730804 , -0.0509772 ) +colvars: ( -0.37356 , 0.100763 , -0.0407045 ) +colvars: ( -0.199704 , 0.107026 , 0.13732 ) +colvars: ( -0.145284 , 0.1086 , 0.192875 ) +colvars: ( -0.231857 , 0.184133 , 0.138889 ) +colvars: ( -0.304689 , 0.0296625 , -0.00261076 ) +colvars: ( -0.231413 , 0.0147291 , 0.0646776 ) +colvars: ( -0.172664 , -0.0735964 , 0.0849759 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 9. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 9. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atoms_new_colvar_forces = { ( -4.91392645926424e+00 , -4.78354531687070e-01 , -1.39619988059762e+00 ), ( -4.23305884780525e+00 , -4.04262063894514e-01 , -1.10167278383500e+00 ), ( -4.31028839697398e+00 , -4.32005112276300e-01 , -1.13930590856027e+00 ), ( -5.79632262732491e+00 , -6.11790903768499e-01 , -1.67985596207422e+00 ), ( 2.69382053999768e-01 , 1.25478466987595e-01 , 3.65240538808074e-01 ), ( 5.30205583008023e+00 , 6.67881948967973e-01 , 1.99364353829785e+00 ), ( 4.48055204292375e+00 , 5.55293047410926e-01 , 1.72858092947742e+00 ), ( -4.53242727510913e-02 , 3.20593150676229e-02 , 3.71888776093524e-01 ), ( 4.45967856098579e+00 , 5.45008042861195e-01 , 1.69569854356309e+00 ), ( 5.91107943140383e+00 , 6.98235090240089e-01 , 2.10431632234368e+00 ), ( 1.22403891305727e-02 , 4.20550206168737e-02 , 3.12872795008926e-01 ), ( -2.12391322996941e-04 , 3.51203463737099e-02 , 2.86745499073317e-01 ), ( 2.16776872887153e-02 , 5.01072337327672e-02 , 3.55466855085267e-01 ), ( 4.53021258186663e-02 , 3.91780386785694e-02 , 2.08742319671006e-01 ), ( 1.57904867750500e-02 , 2.38969326720686e-02 , 1.56222654966668e-01 ), ( 1.18287811551815e-01 , 5.97578523001544e-02 , 1.98352484870876e-01 ), ( 1.67009717114514e-01 , 6.54850482940890e-02 , 1.26128324451353e-01 ), ( 2.51484170048454e-01 , 9.28311309487453e-02 , 1.42845864193466e-01 ), ( 1.37070160525086e-01 , 4.76281665264511e-02 , 5.36606379111071e-02 ), ( 1.32171559729858e-01 , 3.80132223916730e-02 , -1.27456875581090e-02 ), ( 1.13487049449578e-01 , 4.21151863718765e-02 , 6.62822948290591e-02 ), ( 7.63418376715962e-02 , 2.36509551170928e-02 , 6.44934673773689e-03 ), ( 6.32203858685036e-02 , 2.40367443921425e-02 , 4.16148852737993e-02 ), ( -7.42614556335675e-04 , -2.83738966827861e-03 , -2.13121661541531e-02 ), ( -1.50740598991539e-02 , -1.59795212905273e-02 , -9.34449304075277e-02 ), ( -5.10630458821023e-02 , -1.08891564905611e-02 , 3.58680014850378e-02 ), ( -1.22646768338075e-01 , -3.43997144551907e-02 , 1.89512433421106e-02 ), ( -1.66788805970042e-01 , -3.77314303498387e-02 , 9.95216766404465e-02 ), ( -1.09818909430557e-01 , -3.65487013332218e-02 , -2.98676931507554e-02 ), ( -1.48084597629049e-01 , -5.53390393636705e-02 , -8.96239836590932e-02 ), ( -5.39136842169272e-02 , -1.69537682150749e-02 , -6.60130000650828e-03 ), ( -3.21694905209136e-02 , -1.58028299577319e-02 , -5.02854795889152e-02 ), ( 2.70329980947698e-02 , 8.00797613028162e-03 , -7.06751342333167e-04 ), ( 1.46150130702782e-03 , -1.62269426707087e-02 , -1.35814526781097e-01 ), ( -1.73697791017358e-02 , -2.88718298453524e-02 , -1.92913469723319e-01 ), ( 5.10806956956508e-02 , -2.74863623601343e-03 , -1.47057670884840e-01 ), ( 8.21222916884362e-02 , -3.10617064293883e-03 , -2.25724988678412e-01 ), ( 1.46733283375062e-01 , 1.76998043841258e-02 , -2.13834152603038e-01 ), ( 2.03480472695023e-02 , -2.83754617248093e-02 , -2.80914143807489e-01 ), ( 2.14451854438670e-02 , -3.69380339824519e-02 , -3.53375659821508e-01 ), ( -3.55725250144994e-02 , -4.09833596594847e-02 , -2.47199471705149e-01 ), ( -1.00032182737161e-01 , -6.56674034689093e-02 , -2.91065479520581e-01 ), ( -1.39600838208372e-01 , -7.11535661152981e-02 , -2.39214377766981e-01 ), ( -1.60910842962379e-01 , -8.67305353722443e-02 , -3.14160443699850e-01 ), ( -1.90071419859278e-01 , -1.03657481132018e-01 , -3.80950258633566e-01 ), ( -2.06415112665146e-01 , -1.01239344797800e-01 , -3.21357793188336e-01 ), ( -2.51093806299783e-01 , -1.18127062642584e-01 , -3.49957723265751e-01 ), ( -1.28270395442697e-01 , -7.87314622598084e-02 , -3.28624089938550e-01 ), ( -1.82363573694134e-01 , -8.63441521289618e-02 , -2.58658535128284e-01 ), ( -2.39014910464563e-01 , -1.05193984024581e-01 , -2.74031630992006e-01 ), ( -2.76904944904725e-01 , -1.06549981011579e-01 , -1.92616589050566e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 10, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 10, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 10, atoms_positions[size = 51] = { ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 ), ( 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 ), ( 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 ), ( 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ), ( 7.04895826785284e+00 , -2.02841613924265e+00 , -9.85620442392675e-01 ), ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 ), ( 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 ), ( 7.12969433751879e+00 , -3.35680652336380e-01 , 4.28503772503019e+00 ), ( 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 ), ( 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ), ( 5.87483291148707e+00 , 2.26612775399137e+00 , 2.99291808497733e+00 ), ( 5.21288218233115e+00 , 3.59483636987744e+00 , 2.89017476261959e+00 ), ( 6.33778269382874e+00 , 4.55392840471158e+00 , 2.44292221389244e+00 ), ( 3.90736828557834e+00 , 3.74001732699088e+00 , 2.02634249627287e+00 ), ( 2.86216241234034e+00 , 4.12496626340601e+00 , 2.53177091658216e+00 ), ( 3.85570437251192e+00 , 3.24026057383498e+00 , 7.55004313381073e-01 ), ( 2.67101051130264e+00 , 3.10947735928082e+00 , -1.03748879769602e-01 ), ( 3.03667107279091e+00 , 2.72082034295573e+00 , -1.58267128144666e+00 ), ( 1.57645987327715e+00 , 2.17201170366100e+00 , 5.58898221912687e-01 ), ( 4.39572022444068e-01 , 2.48637696550970e+00 , 5.39052019817798e-01 ), ( 1.97518629797634e+00 , 1.00561062528445e+00 , 1.06271551157552e+00 ), ( 1.17478869838474e+00 , 4.45031176098170e-02 , 1.69201496031117e+00 ), ( 2.01846155214988e+00 , -1.15674706353646e+00 , 2.01296064067269e+00 ), ( 5.39500145364343e-01 , 6.10790093980941e-01 , 2.95452140096997e+00 ), ( -6.59871345662798e-01 , 3.58332426277972e-01 , 3.17464616891419e+00 ), ( 1.31939486528605e+00 , 1.33329077272868e+00 , 3.83604631037267e+00 ), ( 8.56110299823718e-01 , 1.93160690859167e+00 , 5.04830818361770e+00 ), ( 2.03247776335589e+00 , 2.60799796092075e+00 , 5.62937340995863e+00 ), ( -3.56784467007829e-01 , 2.91750779164715e+00 , 4.97982149780186e+00 ), ( -1.16533896424590e+00 , 3.04247270492991e+00 , 5.90578034932131e+00 ), ( -4.49302128018119e-01 , 3.65408419381410e+00 , 3.84673249600533e+00 ), ( -1.48549160764506e+00 , 4.55855770175891e+00 , 3.53173500540108e+00 ), ( -7.36778602155233e-01 , 5.39463728504328e+00 , 2.42783652284936e+00 ), ( -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 ), ( -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 ), ( -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 ), ( -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 ), ( -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 ), ( -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 ), ( -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 ), ( -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 ), ( -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 ), ( -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 ), ( -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 ), ( -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 ), ( -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 ), ( -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 ), ( -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 ), ( -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 ), ( -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 ), ( -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ) } +colvars: Step 10, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.24830306441272e-01 , 4.56308785799901e-03 , 9.45761307226337e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 7.04895826785284e+00 , -2.02841613924265e+00 , -9.85620442392675e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 , 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 7.12969433751879e+00 , -3.35680652336380e-01 , 4.28503772503019e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 , 5.87483291148707e+00 , 2.26612775399137e+00 , 2.99291808497733e+00 , 5.21288218233115e+00 , 3.59483636987744e+00 , 2.89017476261959e+00 , 6.33778269382874e+00 , 4.55392840471158e+00 , 2.44292221389244e+00 , 3.90736828557834e+00 , 3.74001732699088e+00 , 2.02634249627287e+00 , 2.86216241234034e+00 , 4.12496626340601e+00 , 2.53177091658216e+00 , 3.85570437251192e+00 , 3.24026057383498e+00 , 7.55004313381073e-01 , 2.67101051130264e+00 , 3.10947735928082e+00 , -1.03748879769602e-01 , 3.03667107279091e+00 , 2.72082034295573e+00 , -1.58267128144666e+00 , 1.57645987327715e+00 , 2.17201170366100e+00 , 5.58898221912687e-01 , 4.39572022444068e-01 , 2.48637696550970e+00 , 5.39052019817798e-01 , 1.97518629797634e+00 , 1.00561062528445e+00 , 1.06271551157552e+00 , 1.17478869838474e+00 , 4.45031176098170e-02 , 1.69201496031117e+00 , 2.01846155214988e+00 , -1.15674706353646e+00 , 2.01296064067269e+00 , 5.39500145364343e-01 , 6.10790093980941e-01 , 2.95452140096997e+00 , -6.59871345662798e-01 , 3.58332426277972e-01 , 3.17464616891419e+00 , 1.31939486528605e+00 , 1.33329077272868e+00 , 3.83604631037267e+00 , 8.56110299823718e-01 , 1.93160690859167e+00 , 5.04830818361770e+00 , 2.03247776335589e+00 , 2.60799796092075e+00 , 5.62937340995863e+00 , -3.56784467007829e-01 , 2.91750779164715e+00 , 4.97982149780186e+00 , -1.16533896424590e+00 , 3.04247270492991e+00 , 5.90578034932131e+00 , -4.49302128018119e-01 , 3.65408419381410e+00 , 3.84673249600533e+00 , -1.48549160764506e+00 , 4.55855770175891e+00 , 3.53173500540108e+00 , -7.36778602155233e-01 , 5.39463728504328e+00 , 2.42783652284936e+00 , -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 , -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 , -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 , -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 , -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 , -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 , -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 , -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 , -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 , -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 , -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 , -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 , -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 , -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 , -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 , -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 , -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 , -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.24830306441272e-01 , 4.56308785799901e-03 , 9.45761307226337e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 7.04895826785284e+00 , -2.02841613924265e+00 , -9.85620442392675e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 , 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 7.12969433751879e+00 , -3.35680652336380e-01 , 4.28503772503019e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 , 5.87483291148707e+00 , 2.26612775399137e+00 , 2.99291808497733e+00 , 5.21288218233115e+00 , 3.59483636987744e+00 , 2.89017476261959e+00 , 6.33778269382874e+00 , 4.55392840471158e+00 , 2.44292221389244e+00 , 3.90736828557834e+00 , 3.74001732699088e+00 , 2.02634249627287e+00 , 2.86216241234034e+00 , 4.12496626340601e+00 , 2.53177091658216e+00 , 3.85570437251192e+00 , 3.24026057383498e+00 , 7.55004313381073e-01 , 2.67101051130264e+00 , 3.10947735928082e+00 , -1.03748879769602e-01 , 3.03667107279091e+00 , 2.72082034295573e+00 , -1.58267128144666e+00 , 1.57645987327715e+00 , 2.17201170366100e+00 , 5.58898221912687e-01 , 4.39572022444068e-01 , 2.48637696550970e+00 , 5.39052019817798e-01 , 1.97518629797634e+00 , 1.00561062528445e+00 , 1.06271551157552e+00 , 1.17478869838474e+00 , 4.45031176098170e-02 , 1.69201496031117e+00 , 2.01846155214988e+00 , -1.15674706353646e+00 , 2.01296064067269e+00 , 5.39500145364343e-01 , 6.10790093980941e-01 , 2.95452140096997e+00 , -6.59871345662798e-01 , 3.58332426277972e-01 , 3.17464616891419e+00 , 1.31939486528605e+00 , 1.33329077272868e+00 , 3.83604631037267e+00 , 8.56110299823718e-01 , 1.93160690859167e+00 , 5.04830818361770e+00 , 2.03247776335589e+00 , 2.60799796092075e+00 , 5.62937340995863e+00 , -3.56784467007829e-01 , 2.91750779164715e+00 , 4.97982149780186e+00 , -1.16533896424590e+00 , 3.04247270492991e+00 , 5.90578034932131e+00 , -4.49302128018119e-01 , 3.65408419381410e+00 , 3.84673249600533e+00 , -1.48549160764506e+00 , 4.55855770175891e+00 , 3.53173500540108e+00 , -7.36778602155233e-01 , 5.39463728504328e+00 , 2.42783652284936e+00 , -2.75429493601640e+00 , 3.88495310831184e+00 , 2.92392603038740e+00 , -3.84004300593541e+00 , 4.44894809174040e+00 , 2.83567925268557e+00 , -2.59730901504765e+00 , 2.62297594102584e+00 , 2.46757898386656e+00 , -3.72073899481800e+00 , 1.89762666622178e+00 , 2.04241256570179e+00 , -3.41711338214382e+00 , 8.42924467140121e-01 , 9.51820920540742e-01 , -4.29578488467706e+00 , 1.07269310551473e+00 , 3.24883841176961e+00 , -5.53817460298205e+00 , 8.88660537135122e-01 , 3.33499180466238e+00 , -3.43753839468245e+00 , 6.56253856247153e-01 , 4.13779791848132e+00 , -3.77484953192977e+00 , 6.70651498660891e-02 , 5.47879973382342e+00 , -2.38816632628263e+00 , -3.55037752169867e-01 , 6.15868154173364e+00 , -4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 , -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 , -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 , -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 , -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 , -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 , -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 , -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 67.0705 , 6.70705 , 13.4141 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 67.0705 , 6.70705 , 13.4141 ) to colvar "one". +colvars: Adding total bias energy: 58.0141 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 67.0705 , 6.70705 , 13.4141 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.20295 , -0.595163 , -1.64708 ) +colvars: ( -4.46153 , -0.510352 , -1.41237 ) +colvars: ( -4.46153 , -0.510352 , -1.41237 ) +colvars: ( -5.94288 , -0.679804 , -1.88132 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.960645 , 0.20727 , 0.681975 ) +colvars: ( 0.830884 , 0.283707 , 0.70894 ) +colvars: ( 0.814942 , 0.275855 , 0.688794 ) +colvars: ( 0.708811 , 0.285512 , 0.638933 ) +colvars: ( 0.695925 , 0.214392 , 0.534525 ) +colvars: ( 0.614294 , 0.368914 , 0.696296 ) +colvars: ( 0.497125 , 0.384887 , 0.648476 ) +colvars: ( 0.413383 , 0.48958 , 0.7412 ) +colvars: ( 0.409082 , 0.337554 , 0.531817 ) +colvars: ( 0.370815 , 0.293518 , 0.44919 ) +colvars: ( 0.378416 , 0.342947 , 0.52095 ) +colvars: ( 0.301837 , 0.297301 , 0.413393 ) +colvars: ( 0.273635 , 0.328033 , 0.438462 ) +colvars: ( 0.369971 , 0.192162 , 0.310795 ) +colvars: ( 0.306219 , 0.146232 , 0.210464 ) +colvars: ( 0.503556 , 0.151643 , 0.334966 ) +colvars: ( 0.5826 , 0.0533491 , 0.248158 ) +colvars: ( 0.723846 , 0.029847 , 0.300027 ) +colvars: ( 0.590758 , 0.0197121 , 0.207238 ) +colvars: ( 0.57367 , -0.0497709 , 0.102563 ) +colvars: ( 0.6124 , 0.0712476 , 0.290198 ) +colvars: ( 0.609547 , 0.0544469 , 0.265647 ) +colvars: ( 0.648277 , 0.123812 , 0.383008 ) +colvars: ( 0.474125 , 0.0601924 , 0.193077 ) +colvars: ( 0.466305 , 0.000586045 , 0.107342 ) +colvars: ( 0.363565 , 0.130986 , 0.223763 ) +colvars: ( 0.228131 , 0.141053 , 0.157065 ) +colvars: ( 0.128996 , 0.233268 , 0.223677 ) +colvars: ( 0.198279 , 0.0620654 , 0.0318832 ) +colvars: ( 0.144334 , 0.0238752 , -0.0520959 ) +colvars: ( 0.235965 , 0.0340363 , 0.0161204 ) +colvars: ( 0.221577 , -0.0437392 , -0.0982334 ) +colvars: ( 0.261215 , -0.0480571 , -0.0805785 ) +colvars: ( 0.30301 , -0.136029 , -0.175454 ) +colvars: ( 0.255306 , -0.19258 , -0.280708 ) +colvars: ( 0.427739 , -0.152684 , -0.124074 ) +colvars: ( 0.51146 , -0.233759 , -0.184679 ) +colvars: ( 0.653794 , -0.237313 , -0.105025 ) +colvars: ( 0.458912 , -0.237788 , -0.221353 ) +colvars: ( 0.464775 , -0.310559 , -0.316877 ) +colvars: ( 0.405086 , -0.158729 , -0.145745 ) +colvars: ( 0.345036 , -0.151244 , -0.171207 ) +colvars: ( 0.326212 , -0.0580833 , -0.0556372 ) +colvars: ( 0.211248 , -0.159901 , -0.262401 ) +colvars: ( 0.184175 , -0.204445 , -0.339074 ) +colvars: ( -0.00547473 , -0.208274 , -0.45686 ) +colvars: ( -0.10416 , -0.226756 , -0.540583 ) +colvars: ( 0.104265 , -0.262599 , -0.465626 ) +colvars: ( 0.123138 , -0.116236 , -0.255298 ) +colvars: ( -0.00625371 , -0.120228 , -0.337536 ) +colvars: ( -0.102514 , -0.0335414 , -0.27674 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.20295 , 0.595163 , 1.64708 ) +colvars: ( 4.46153 , 0.510352 , 1.41237 ) +colvars: ( 4.46153 , 0.510352 , 1.41237 ) +colvars: ( 5.94288 , 0.679804 , 1.88132 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.664913 , -0.0859778 , -0.415805 ) +colvars: ( -0.596637 , -0.173807 , -0.38523 ) +colvars: ( -0.545927 , -0.150496 , -0.324005 ) +colvars: ( -0.551694 , -0.203347 , -0.352805 ) +colvars: ( -0.541432 , -0.141225 , -0.315444 ) +colvars: ( -0.522538 , -0.300927 , -0.365881 ) +colvars: ( -0.484335 , -0.344022 , -0.346143 ) +colvars: ( -0.458742 , -0.457696 , -0.36981 ) +colvars: ( -0.417104 , -0.306948 , -0.262287 ) +colvars: ( -0.410792 , -0.280424 , -0.24439 ) +colvars: ( -0.366203 , -0.301006 , -0.208424 ) +colvars: ( -0.302027 , -0.262272 , -0.126923 ) +colvars: ( -0.251932 , -0.278026 , -0.0833115 ) +colvars: ( -0.324691 , -0.153039 , -0.102238 ) +colvars: ( -0.290399 , -0.122366 , -0.0543501 ) +colvars: ( -0.38539 , -0.091934 , -0.136805 ) +colvars: ( -0.415766 , 0.01212 , -0.122141 ) +colvars: ( -0.472648 , 0.0629672 , -0.157325 ) +colvars: ( -0.453851 , 0.027912 , -0.153639 ) +colvars: ( -0.441643 , 0.0878083 , -0.115285 ) +colvars: ( -0.499083 , -0.0291587 , -0.224031 ) +colvars: ( -0.533355 , -0.0308162 , -0.259278 ) +colvars: ( -0.585228 , -0.0998259 , -0.341555 ) +colvars: ( -0.474911 , -0.0630423 , -0.21442 ) +colvars: ( -0.481406 , -0.0165546 , -0.200741 ) +colvars: ( -0.414598 , -0.141907 , -0.187968 ) +colvars: ( -0.350645 , -0.175478 , -0.138145 ) +colvars: ( -0.295589 , -0.271054 , -0.124258 ) +colvars: ( -0.307947 , -0.0986065 , -0.0616914 ) +colvars: ( -0.292218 , -0.0791881 , -0.0373993 ) +colvars: ( -0.28977 , -0.0509737 , -0.0226596 ) +colvars: ( -0.253632 , 0.0279845 , 0.0480933 ) +colvars: ( -0.234115 , 0.0561127 , 0.0799906 ) +colvars: ( -0.301483 , 0.11988 , 0.0398636 ) +colvars: ( -0.272571 , 0.163811 , 0.0881004 ) +colvars: ( -0.37668 , 0.15001 , -0.0227826 ) +colvars: ( -0.429409 , 0.230753 , -0.0407782 ) +colvars: ( -0.507236 , 0.255104 , -0.108588 ) +colvars: ( -0.438579 , 0.209517 , -0.0592538 ) +colvars: ( -0.443341 , 0.273754 , -0.0361082 ) +colvars: ( -0.440628 , 0.117823 , -0.101205 ) +colvars: ( -0.444978 , 0.0856549 , -0.119581 ) +colvars: ( -0.465704 , -0.013027 , -0.183388 ) +colvars: ( -0.37197 , 0.0732619 , -0.0514237 ) +colvars: ( -0.374025 , 0.100898 , -0.0414726 ) +colvars: ( -0.200611 , 0.107163 , 0.13595 ) +colvars: ( -0.146531 , 0.108771 , 0.19113 ) +colvars: ( -0.232294 , 0.184008 , 0.137461 ) +colvars: ( -0.30526 , 0.0299734 , -0.00305187 ) +colvars: ( -0.232426 , 0.0151267 , 0.0638633 ) +colvars: ( -0.173996 , -0.0729419 , 0.0844146 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 10. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atoms_new_colvar_forces = { ( -4.90721521818644e+00 , -4.73870786712652e-01 , -1.38091477818025e+00 ), ( -4.22727947915419e+00 , -4.00452243715495e-01 , -1.08866450508672e+00 ), ( -4.30440996742968e+00 , -4.28187255104780e-01 , -1.12624661622607e+00 ), ( -5.78839020894122e+00 , -6.06637961847330e-01 , -1.66224301649813e+00 ), ( 2.69014751613858e-01 , 1.25358618238813e-01 , 3.64789105177912e-01 ), ( 5.29470412581475e+00 , 6.63150876426976e-01 , 1.97749961084672e+00 ), ( 4.47431659059565e+00 , 5.51217931478780e-01 , 1.71470785458333e+00 ), ( -4.53596158039452e-02 , 3.18840627601026e-02 , 3.71390215390095e-01 ), ( 4.45350387722105e+00 , 5.40958244259191e-01 , 1.68190394486273e+00 ), ( 5.90290505873046e+00 , 6.92898590570129e-01 , 2.08612444512667e+00 ), ( 1.22126331866665e-02 , 4.19406780340398e-02 , 3.12525703172802e-01 ), ( -1.89394613707761e-04 , 3.50298648912931e-02 , 2.86469456014899e-01 ), ( 2.17026752784405e-02 , 5.00075282522233e-02 , 3.55150927912739e-01 ), ( 4.52793272988443e-02 , 3.91235906882275e-02 , 2.08557220462046e-01 ), ( 1.58193300286871e-02 , 2.38650932441996e-02 , 1.56113879996155e-01 ), ( 1.18165693090680e-01 , 5.97093876394846e-02 , 1.98160954730796e-01 ), ( 1.66833895016226e-01 , 6.54691100847247e-02 , 1.26016621253944e-01 ), ( 2.51198093154190e-01 , 9.28141306260056e-02 , 1.42701941432096e-01 ), ( 1.36906860890021e-01 , 4.76240982493063e-02 , 5.35989609398464e-02 ), ( 1.32026557753796e-01 , 3.80374903598184e-02 , -1.27220490949054e-02 ), ( 1.13317635725557e-01 , 4.20888774190430e-02 , 6.61671896305862e-02 ), ( 7.61922963739712e-02 , 2.36307558005545e-02 , 6.36968734366083e-03 ), ( 6.30491839407602e-02 , 2.39861444751687e-02 , 4.14538911418829e-02 ), ( -7.86494290214823e-04 , -2.84997613756573e-03 , -2.13431538111226e-02 ), ( -1.51013213602507e-02 , -1.59685447206908e-02 , -9.33996609892180e-02 ), ( -5.10330310243135e-02 , -1.09209992052759e-02 , 3.57950318514191e-02 ), ( -1.22513991104271e-01 , -3.44255258188375e-02 , 1.89196500716248e-02 ), ( -1.66593126748012e-01 , -3.77856611671253e-02 , 9.94187969247893e-02 ), ( -1.09668061787916e-01 , -3.65411120110773e-02 , -2.98082150050602e-02 ), ( -1.47884159951637e-01 , -5.53128169067022e-02 , -8.94951448539763e-02 ), ( -5.38050059720047e-02 , -1.69374144538034e-02 , -6.53920598676141e-03 ), ( -3.20550484318294e-02 , -1.57546688528021e-02 , -5.01400797346093e-02 ), ( 2.71003511424442e-02 , 8.05558174944536e-03 , -5.87867940786607e-04 ), ( 1.52713215699579e-03 , -1.61490539427529e-02 , -1.35590342281533e-01 ), ( -1.72647112458419e-02 , -2.87683438518996e-02 , -1.92607880448279e-01 ), ( 5.10597482439506e-02 , -2.67372040503736e-03 , -1.46856235504666e-01 ), ( 8.20513443320531e-02 , -3.00612150775692e-03 , -2.25457045193199e-01 ), ( 1.46558386589924e-01 , 1.77905963189787e-02 , -2.13613377753834e-01 ), ( 2.03330229305949e-02 , -2.82705894952819e-02 , -2.80606754848932e-01 ), ( 2.14339555948247e-02 , -3.68053410607088e-02 , -3.52985572218408e-01 ), ( -3.55420123674877e-02 , -4.09057515777496e-02 , -2.46950953915162e-01 ), ( -9.99417416209531e-02 , -6.55888745871515e-02 , -2.90788430582709e-01 ), ( -1.39492151096945e-01 , -7.11103908817001e-02 , -2.39025312091656e-01 ), ( -1.60721409442294e-01 , -8.66386440202250e-02 , -3.13825121559050e-01 ), ( -1.89850057174861e-01 , -1.03546550046362e-01 , -3.80546615670789e-01 ), ( -2.06085649306466e-01 , -1.01111515874264e-01 , -3.20910555605155e-01 ), ( -2.50690197418701e-01 , -1.17984671586598e-01 , -3.49453608696638e-01 ), ( -1.28028542025109e-01 , -7.85902187842150e-02 , -3.28165409791750e-01 ), ( -1.82122317573020e-01 , -8.62623196497184e-02 , -2.58349718696580e-01 ), ( -2.38679358248130e-01 , -1.05100891525063e-01 , -2.73672453172879e-01 ), ( -2.76510254384952e-01 , -1.06483286115883e-01 , -1.92325407427920e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 11, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 11, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 11, atoms_positions[size = 51] = { ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 ), ( 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 ), ( 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 ), ( 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 ), ( 7.05065634311566e+00 , -2.03049004075621e+00 , -9.79362510556569e-01 ), ( 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 ), ( 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 ), ( 7.12024786069621e+00 , -3.39139905946113e-01 , 4.28353219426788e+00 ), ( 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 ), ( 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 ), ( 5.87320938131017e+00 , 2.25943775728641e+00 , 2.99532323655327e+00 ), ( 5.21460824073739e+00 , 3.59406844683129e+00 , 2.89331623199200e+00 ), ( 6.33648153033934e+00 , 4.54439309911936e+00 , 2.43803927314067e+00 ), ( 3.90893824316231e+00 , 3.74054027462900e+00 , 2.02866662801620e+00 ), ( 2.85178279175922e+00 , 4.12837904124339e+00 , 2.52784179556043e+00 ), ( 3.86480984721616e+00 , 3.24029379334385e+00 , 7.50630541184627e-01 ), ( 2.66855007312622e+00 , 3.09506737302471e+00 , -1.05570547346993e-01 ), ( 3.03480083010960e+00 , 2.72160086873890e+00 , -1.57499534729745e+00 ), ( 1.57258918789361e+00 , 2.17883844709657e+00 , 5.48129606098152e-01 ), ( 4.37174994281082e-01 , 2.49496443849042e+00 , 5.36164612719916e-01 ), ( 1.97956860962535e+00 , 1.00342808156705e+00 , 1.06673411380361e+00 ), ( 1.17837235004353e+00 , 5.47484601953032e-02 , 1.69222321530186e+00 ), ( 2.02013932698568e+00 , -1.15071693488931e+00 , 2.01095937665247e+00 ), ( 5.43445388214036e-01 , 6.10623613737296e-01 , 2.94620123320234e+00 ), ( -6.55516802788368e-01 , 3.55967038646797e-01 , 3.17311244502176e+00 ), ( 1.32230539727642e+00 , 1.33662047778142e+00 , 3.83594474675778e+00 ), ( 8.58493041787829e-01 , 1.93756430053514e+00 , 5.04354534429340e+00 ), ( 2.03020280879893e+00 , 2.61319458720498e+00 , 5.63214215280723e+00 ), ( -3.54493344367681e-01 , 2.91714629572789e+00 , 4.97804445234563e+00 ), ( -1.16317793575365e+00 , 3.04536875480708e+00 , 5.90527907810562e+00 ), ( -4.56997665157424e-01 , 3.64256089882158e+00 , 3.84588521388551e+00 ), ( -1.48864716069633e+00 , 4.55495951618193e+00 , 3.52701224906812e+00 ), ( -7.31998500857074e-01 , 5.39670953743225e+00 , 2.43240573927225e+00 ), ( -2.76043877081303e+00 , 3.88195838914561e+00 , 2.92172497691190e+00 ), ( -3.83655800207824e+00 , 4.45487150145009e+00 , 2.83258820678848e+00 ), ( -2.59982512815912e+00 , 2.62960582150409e+00 , 2.46175627757411e+00 ), ( -3.72483017568435e+00 , 1.88842108509526e+00 , 2.03569362921275e+00 ), ( -3.41674062596946e+00 , 8.50658448856212e-01 , 9.42931751107171e-01 ), ( -4.29738088737320e+00 , 1.06924065433557e+00 , 3.24986009184129e+00 ), ( -5.53574944736067e+00 , 8.81853210644467e-01 , 3.33322930420472e+00 ), ( -3.42985203154369e+00 , 6.60805330089051e-01 , 4.13978457976856e+00 ), ( -3.77006292042066e+00 , 5.91423770166127e-02 , 5.47469431926495e+00 ), ( -2.38548666440762e+00 , -3.45313164861201e-01 , 6.16230742959650e+00 ), ( -4.47512784749258e+00 , 9.94701715919259e-01 , 6.43113361680443e+00 ), ( -5.32797291281713e+00 , 6.08780004872583e-01 , 7.19550451845062e+00 ), ( -6.27190177315000e+00 , 3.56557744419283e+00 , 6.70756545526345e+00 ), ( -6.91922175772896e+00 , 4.29474385581630e+00 , 7.43148031565427e+00 ), ( -6.74325099782148e+00 , 3.20658513246779e+00 , 5.52273116069913e+00 ), ( -4.11289081713227e+00 , 2.29553198796951e+00 , 6.47520971040690e+00 ), ( -4.86771915066433e+00 , 3.20343344496405e+00 , 7.21347983898504e+00 ), ( -4.09714919691758e+00 , 4.56216329369550e+00 , 7.29069443330947e+00 ) } +colvars: Step 11, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.22392395713355e-01 , 4.49513088585881e-03 , 9.46595445258703e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 7.05065634311566e+00 , -2.03049004075621e+00 , -9.79362510556569e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 , 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 7.12024786069621e+00 , -3.39139905946113e-01 , 4.28353219426788e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 , 5.87320938131017e+00 , 2.25943775728641e+00 , 2.99532323655327e+00 , 5.21460824073739e+00 , 3.59406844683129e+00 , 2.89331623199200e+00 , 6.33648153033934e+00 , 4.54439309911936e+00 , 2.43803927314067e+00 , 3.90893824316231e+00 , 3.74054027462900e+00 , 2.02866662801620e+00 , 2.85178279175922e+00 , 4.12837904124339e+00 , 2.52784179556043e+00 , 3.86480984721616e+00 , 3.24029379334385e+00 , 7.50630541184627e-01 , 2.66855007312622e+00 , 3.09506737302471e+00 , -1.05570547346993e-01 , 3.03480083010960e+00 , 2.72160086873890e+00 , -1.57499534729745e+00 , 1.57258918789361e+00 , 2.17883844709657e+00 , 5.48129606098152e-01 , 4.37174994281082e-01 , 2.49496443849042e+00 , 5.36164612719916e-01 , 1.97956860962535e+00 , 1.00342808156705e+00 , 1.06673411380361e+00 , 1.17837235004353e+00 , 5.47484601953032e-02 , 1.69222321530186e+00 , 2.02013932698568e+00 , -1.15071693488931e+00 , 2.01095937665247e+00 , 5.43445388214036e-01 , 6.10623613737296e-01 , 2.94620123320234e+00 , -6.55516802788368e-01 , 3.55967038646797e-01 , 3.17311244502176e+00 , 1.32230539727642e+00 , 1.33662047778142e+00 , 3.83594474675778e+00 , 8.58493041787829e-01 , 1.93756430053514e+00 , 5.04354534429340e+00 , 2.03020280879893e+00 , 2.61319458720498e+00 , 5.63214215280723e+00 , -3.54493344367681e-01 , 2.91714629572789e+00 , 4.97804445234563e+00 , -1.16317793575365e+00 , 3.04536875480708e+00 , 5.90527907810562e+00 , -4.56997665157424e-01 , 3.64256089882158e+00 , 3.84588521388551e+00 , -1.48864716069633e+00 , 4.55495951618193e+00 , 3.52701224906812e+00 , -7.31998500857074e-01 , 5.39670953743225e+00 , 2.43240573927225e+00 , -2.76043877081303e+00 , 3.88195838914561e+00 , 2.92172497691190e+00 , -3.83655800207824e+00 , 4.45487150145009e+00 , 2.83258820678848e+00 , -2.59982512815912e+00 , 2.62960582150409e+00 , 2.46175627757411e+00 , -3.72483017568435e+00 , 1.88842108509526e+00 , 2.03569362921275e+00 , -3.41674062596946e+00 , 8.50658448856212e-01 , 9.42931751107171e-01 , -4.29738088737320e+00 , 1.06924065433557e+00 , 3.24986009184129e+00 , -5.53574944736067e+00 , 8.81853210644467e-01 , 3.33322930420472e+00 , -3.42985203154369e+00 , 6.60805330089051e-01 , 4.13978457976856e+00 , -3.77006292042066e+00 , 5.91423770166127e-02 , 5.47469431926495e+00 , -2.38548666440762e+00 , -3.45313164861201e-01 , 6.16230742959650e+00 , -4.47512784749258e+00 , 9.94701715919259e-01 , 6.43113361680443e+00 , -5.32797291281713e+00 , 6.08780004872583e-01 , 7.19550451845062e+00 , -6.27190177315000e+00 , 3.56557744419283e+00 , 6.70756545526345e+00 , -6.91922175772896e+00 , 4.29474385581630e+00 , 7.43148031565427e+00 , -6.74325099782148e+00 , 3.20658513246779e+00 , 5.52273116069913e+00 , -4.11289081713227e+00 , 2.29553198796951e+00 , 6.47520971040690e+00 , -4.86771915066433e+00 , 3.20343344496405e+00 , 7.21347983898504e+00 , -4.09714919691758e+00 , 4.56216329369550e+00 , 7.29069443330947e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.22392395713355e-01 , 4.49513088585881e-03 , 9.46595445258703e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 7.05065634311566e+00 , -2.03049004075621e+00 , -9.79362510556569e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 6.91717886073371e-01 , 6.90030778768189e+00 , -2.66843270521422e-01 , 1.84891147568226e+00 , 6.18422920482057e+00 , -1.18746306728174e-01 , 3.14586292085145e+00 , 7.12024786069621e+00 , -3.39139905946113e-01 , 4.28353219426788e+00 , 5.29035739768275e+00 , 1.11257765822196e+00 , 3.31605860203451e+00 , 4.12015961033106e+00 , 1.04963184027854e+00 , 3.64341243715756e+00 , 5.87320938131017e+00 , 2.25943775728641e+00 , 2.99532323655327e+00 , 5.21460824073739e+00 , 3.59406844683129e+00 , 2.89331623199200e+00 , 6.33648153033934e+00 , 4.54439309911936e+00 , 2.43803927314067e+00 , 3.90893824316231e+00 , 3.74054027462900e+00 , 2.02866662801620e+00 , 2.85178279175922e+00 , 4.12837904124339e+00 , 2.52784179556043e+00 , 3.86480984721616e+00 , 3.24029379334385e+00 , 7.50630541184627e-01 , 2.66855007312622e+00 , 3.09506737302471e+00 , -1.05570547346993e-01 , 3.03480083010960e+00 , 2.72160086873890e+00 , -1.57499534729745e+00 , 1.57258918789361e+00 , 2.17883844709657e+00 , 5.48129606098152e-01 , 4.37174994281082e-01 , 2.49496443849042e+00 , 5.36164612719916e-01 , 1.97956860962535e+00 , 1.00342808156705e+00 , 1.06673411380361e+00 , 1.17837235004353e+00 , 5.47484601953032e-02 , 1.69222321530186e+00 , 2.02013932698568e+00 , -1.15071693488931e+00 , 2.01095937665247e+00 , 5.43445388214036e-01 , 6.10623613737296e-01 , 2.94620123320234e+00 , -6.55516802788368e-01 , 3.55967038646797e-01 , 3.17311244502176e+00 , 1.32230539727642e+00 , 1.33662047778142e+00 , 3.83594474675778e+00 , 8.58493041787829e-01 , 1.93756430053514e+00 , 5.04354534429340e+00 , 2.03020280879893e+00 , 2.61319458720498e+00 , 5.63214215280723e+00 , -3.54493344367681e-01 , 2.91714629572789e+00 , 4.97804445234563e+00 , -1.16317793575365e+00 , 3.04536875480708e+00 , 5.90527907810562e+00 , -4.56997665157424e-01 , 3.64256089882158e+00 , 3.84588521388551e+00 , -1.48864716069633e+00 , 4.55495951618193e+00 , 3.52701224906812e+00 , -7.31998500857074e-01 , 5.39670953743225e+00 , 2.43240573927225e+00 , -2.76043877081303e+00 , 3.88195838914561e+00 , 2.92172497691190e+00 , -3.83655800207824e+00 , 4.45487150145009e+00 , 2.83258820678848e+00 , -2.59982512815912e+00 , 2.62960582150409e+00 , 2.46175627757411e+00 , -3.72483017568435e+00 , 1.88842108509526e+00 , 2.03569362921275e+00 , -3.41674062596946e+00 , 8.50658448856212e-01 , 9.42931751107171e-01 , -4.29738088737320e+00 , 1.06924065433557e+00 , 3.24986009184129e+00 , -5.53574944736067e+00 , 8.81853210644467e-01 , 3.33322930420472e+00 , -3.42985203154369e+00 , 6.60805330089051e-01 , 4.13978457976856e+00 , -3.77006292042066e+00 , 5.91423770166127e-02 , 5.47469431926495e+00 , -2.38548666440762e+00 , -3.45313164861201e-01 , 6.16230742959650e+00 , -4.47512784749258e+00 , 9.94701715919259e-01 , 6.43113361680443e+00 , -5.32797291281713e+00 , 6.08780004872583e-01 , 7.19550451845062e+00 , -6.27190177315000e+00 , 3.56557744419283e+00 , 6.70756545526345e+00 , -6.91922175772896e+00 , 4.29474385581630e+00 , 7.43148031565427e+00 , -6.74325099782148e+00 , 3.20658513246779e+00 , 5.52273116069913e+00 , -4.11289081713227e+00 , 2.29553198796951e+00 , 6.47520971040690e+00 , -4.86771915066433e+00 , 3.20343344496405e+00 , 7.21347983898504e+00 , -4.09714919691758e+00 , 4.56216329369550e+00 , 7.29069443330947e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.9473 , 6.69473 , 13.3895 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.9473 , 6.69473 , 13.3895 ) to colvar "one". +colvars: Adding total bias energy: 57.84 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.9473 , 6.69473 , 13.3895 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.19605 , -0.590483 , -1.63117 ) +colvars: ( -4.45561 , -0.506339 , -1.39873 ) +colvars: ( -4.45561 , -0.506339 , -1.39873 ) +colvars: ( -5.935 , -0.674459 , -1.86314 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.957579 , 0.206963 , 0.677893 ) +colvars: ( 0.82837 , 0.2831 , 0.704709 ) +colvars: ( 0.812345 , 0.275342 , 0.684693 ) +colvars: ( 0.70689 , 0.28477 , 0.63505 ) +colvars: ( 0.694052 , 0.213836 , 0.531192 ) +colvars: ( 0.612848 , 0.367838 , 0.692092 ) +colvars: ( 0.496265 , 0.383633 , 0.6445 ) +colvars: ( 0.412941 , 0.487947 , 0.736719 ) +colvars: ( 0.408528 , 0.336402 , 0.528462 ) +colvars: ( 0.370478 , 0.292427 , 0.446259 ) +colvars: ( 0.377869 , 0.341828 , 0.517672 ) +colvars: ( 0.301538 , 0.296295 , 0.410691 ) +colvars: ( 0.273329 , 0.326996 , 0.435649 ) +colvars: ( 0.369338 , 0.191513 , 0.308646 ) +colvars: ( 0.305861 , 0.145659 , 0.208839 ) +colvars: ( 0.502318 , 0.151221 , 0.332704 ) +colvars: ( 0.580989 , 0.0532704 , 0.246365 ) +colvars: ( 0.721568 , 0.0299716 , 0.297982 ) +colvars: ( 0.589235 , 0.0196607 , 0.205639 ) +colvars: ( 0.572214 , -0.0496437 , 0.101516 ) +colvars: ( 0.610902 , 0.0710068 , 0.288144 ) +colvars: ( 0.60819 , 0.0541764 , 0.263699 ) +colvars: ( 0.646861 , 0.123322 , 0.380426 ) +colvars: ( 0.473395 , 0.0597794 , 0.191494 ) +colvars: ( 0.465651 , 0.000304383 , 0.106202 ) +colvars: ( 0.363298 , 0.130306 , 0.222012 ) +colvars: ( 0.228471 , 0.14023 , 0.155652 ) +colvars: ( 0.129745 , 0.232132 , 0.221908 ) +colvars: ( 0.198656 , 0.0614855 , 0.0311433 ) +colvars: ( 0.144991 , 0.0233311 , -0.0524055 ) +colvars: ( 0.236047 , 0.033636 , 0.0154899 ) +colvars: ( 0.221623 , -0.0438856 , -0.0982455 ) +colvars: ( 0.260948 , -0.0480808 , -0.0806554 ) +colvars: ( 0.302731 , -0.135879 , -0.175058 ) +colvars: ( 0.255222 , -0.192307 , -0.279759 ) +colvars: ( 0.42696 , -0.152416 , -0.123946 ) +colvars: ( 0.510357 , -0.23323 , -0.184232 ) +colvars: ( 0.65209 , -0.236675 , -0.10499 ) +colvars: ( 0.458167 , -0.237362 , -0.22074 ) +colvars: ( 0.464016 , -0.309939 , -0.315763 ) +colvars: ( 0.404675 , -0.158615 , -0.145553 ) +colvars: ( 0.345011 , -0.151267 , -0.170907 ) +colvars: ( 0.326371 , -0.0584309 , -0.0559652 ) +colvars: ( 0.211789 , -0.159996 , -0.261629 ) +colvars: ( 0.184894 , -0.204475 , -0.33791 ) +colvars: ( -0.00420391 , -0.208287 , -0.455043 ) +colvars: ( -0.102471 , -0.226789 , -0.538331 ) +colvars: ( 0.104975 , -0.262332 , -0.463739 ) +colvars: ( 0.123982 , -0.116472 , -0.254555 ) +colvars: ( -0.00487049 , -0.12054 , -0.336366 ) +colvars: ( -0.100751 , -0.0341408 , -0.275891 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.19605 , 0.590483 , 1.63117 ) +colvars: ( 4.45561 , 0.506339 , 1.39873 ) +colvars: ( 4.45561 , 0.506339 , 1.39873 ) +colvars: ( 5.935 , 0.674459 , 1.86314 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.662314 , -0.0857846 , -0.412142 ) +colvars: ( -0.594498 , -0.17334 , -0.381457 ) +colvars: ( -0.543709 , -0.150118 , -0.320362 ) +colvars: ( -0.550047 , -0.202737 , -0.349328 ) +colvars: ( -0.539817 , -0.140768 , -0.31243 ) +colvars: ( -0.521292 , -0.300015 , -0.362138 ) +colvars: ( -0.483578 , -0.342932 , -0.342594 ) +colvars: ( -0.458343 , -0.45627 , -0.36584 ) +colvars: ( -0.416589 , -0.305932 , -0.259277 ) +colvars: ( -0.410453 , -0.279445 , -0.241731 ) +colvars: ( -0.365685 , -0.300023 , -0.205497 ) +colvars: ( -0.3017 , -0.261374 , -0.124497 ) +colvars: ( -0.251594 , -0.277108 , -0.0808113 ) +colvars: ( -0.324079 , -0.152455 , -0.100272 ) +colvars: ( -0.290007 , -0.121833 , -0.0528296 ) +colvars: ( -0.384275 , -0.0915677 , -0.134734 ) +colvars: ( -0.414332 , 0.0121828 , -0.120458 ) +colvars: ( -0.470661 , 0.0628277 , -0.155422 ) +colvars: ( -0.452495 , 0.0279618 , -0.152102 ) +colvars: ( -0.440334 , 0.0877128 , -0.114213 ) +colvars: ( -0.49776 , -0.0289453 , -0.222095 ) +colvars: ( -0.532156 , -0.0305656 , -0.257415 ) +colvars: ( -0.583996 , -0.0993912 , -0.339143 ) +colvars: ( -0.47423 , -0.0626427 , -0.212872 ) +colvars: ( -0.480784 , -0.0162585 , -0.19956 ) +colvars: ( -0.414303 , -0.141265 , -0.186294 ) +colvars: ( -0.35085 , -0.174689 , -0.136766 ) +colvars: ( -0.296138 , -0.269986 , -0.122594 ) +colvars: ( -0.308168 , -0.0980209 , -0.0608902 ) +colvars: ( -0.292668 , -0.0786171 , -0.0369583 ) +colvars: ( -0.289736 , -0.0505569 , -0.0219625 ) +colvars: ( -0.253555 , 0.0281846 , 0.048259 ) +colvars: ( -0.233769 , 0.0561899 , 0.080197 ) +colvars: ( -0.301131 , 0.11982 , 0.0396995 ) +colvars: ( -0.272372 , 0.163659 , 0.0874669 ) +colvars: ( -0.375918 , 0.149831 , -0.0227038 ) +colvars: ( -0.428377 , 0.230344 , -0.0409524 ) +colvars: ( -0.505712 , 0.254577 , -0.108401 ) +colvars: ( -0.437849 , 0.209216 , -0.0595566 ) +colvars: ( -0.442594 , 0.273292 , -0.0368289 ) +colvars: ( -0.440188 , 0.117802 , -0.101149 ) +colvars: ( -0.444864 , 0.0857708 , -0.119606 ) +colvars: ( -0.465758 , -0.0126292 , -0.182876 ) +colvars: ( -0.372318 , 0.073463 , -0.05186 ) +colvars: ( -0.374519 , 0.101056 , -0.0422317 ) +colvars: ( -0.201538 , 0.10732 , 0.13459 ) +colvars: ( -0.147798 , 0.108964 , 0.189393 ) +colvars: ( -0.23275 , 0.183904 , 0.136043 ) +colvars: ( -0.305856 , 0.0303019 , -0.00348203 ) +colvars: ( -0.233462 , 0.0155426 , 0.0630591 ) +colvars: ( -0.17535 , -0.072272 , 0.0838643 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 11. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 11. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atoms_new_colvar_forces = { ( -4.90078343283082e+00 , -4.69304939716054e-01 , -1.36541654232102e+00 ), ( -4.22173864945088e+00 , -3.96579211311637e-01 , -1.07547405982912e+00 ), ( -4.29876725746840e+00 , -4.24306744780342e-01 , -1.11300446941000e+00 ), ( -5.78076668885247e+00 , -6.01391375743044e-01 , -1.64438175232614e+00 ), ( 2.68636078315130e-01 , 1.25224014736973e-01 , 3.64331369994507e-01 ), ( 5.28760305095590e+00 , 6.58306388945491e-01 , 1.96112134983409e+00 ), ( 4.46829684153746e+00 , 5.47040898538111e-01 , 1.70063240131138e+00 ), ( -4.54023956339813e-02 , 3.16776544920516e-02 , 3.70879550465582e-01 ), ( 4.44754945706128e+00 , 5.36809513694409e-01 , 1.66791086412683e+00 ), ( 5.89502605346830e+00 , 6.87440092337066e-01 , 2.06767076232209e+00 ), ( 1.21843034227425e-02 , 4.18052959825408e-02 , 3.12175108656937e-01 ), ( -1.62618102043321e-04 , 3.49212496434206e-02 , 2.86193795220697e-01 ), ( 2.17343226901442e-02 , 4.98873878221798e-02 , 3.54837926670121e-01 ), ( 4.52596785697127e-02 , 3.90586460782221e-02 , 2.08374109794610e-01 ), ( 1.58538228914107e-02 , 2.38257529877301e-02 , 1.56009062475107e-01 ), ( 1.18043219659774e-01 , 5.96537616383347e-02 , 1.97970486543308e-01 ), ( 1.66656553754429e-01 , 6.54532082555734e-02 , 1.25907131884304e-01 ), ( 2.50907095860839e-01 , 9.27993251652997e-02 , 1.42559451292976e-01 ), ( 1.36739936503245e-01 , 4.76224964818958e-02 , 5.35374623532944e-02 ), ( 1.31879223673249e-01 , 3.80690478972656e-02 , -1.26964879861136e-02 ), ( 1.13141394409887e-01 , 4.20615216140231e-02 , 6.60485051673235e-02 ), ( 7.60339342339692e-02 , 2.36107162974138e-02 , 6.28416739353432e-03 ), ( 6.28654041122315e-02 , 2.39309972060159e-02 , 4.12828419792915e-02 ), ( -8.35563968785369e-04 , -2.86329479710402e-03 , -2.13786742540487e-02 ), ( -1.51337174937063e-02 , -1.59541245139078e-02 , -9.33585281143269e-02 ), ( -5.10049654171213e-02 , -1.09589661405002e-02 , 3.57183867004734e-02 ), ( -1.22379223950270e-01 , -3.44586629208166e-02 , 1.88860376509928e-02 ), ( -1.66392710395628e-01 , -3.78540757063262e-02 , 9.93142380172693e-02 ), ( -1.09511965645556e-01 , -3.65354269878942e-02 , -2.97468795261682e-02 ), ( -1.47677186588062e-01 , -5.52859983018182e-02 , -8.93637689973341e-02 ), ( -5.36897552770025e-02 , -1.69208906193615e-02 , -6.47263810149609e-03 ), ( -3.19311971427954e-02 , -1.57009459162498e-02 , -4.99865053421004e-02 ), ( 2.71783388133797e-02 , 8.10915997456257e-03 , -4.58466748998743e-04 ), ( 1.59987902378828e-03 , -1.60588035212056e-02 , -1.35358167121535e-01 ), ( -1.71502863079521e-02 , -2.86486967752420e-02 , -1.92292202522445e-01 ), ( 5.10413359017399e-02 , -2.58480080072415e-03 , -1.46649401714235e-01 ), ( 8.19802503728982e-02 , -2.88604582924412e-03 , -2.25184391896305e-01 ), ( 1.46378492350565e-01 , 1.79021935732166e-02 , -2.13390534719039e-01 ), ( 2.03173362292667e-02 , -2.81455653081005e-02 , -2.80296367683953e-01 ), ( 2.14223207336109e-02 , -3.66473521516703e-02 , -3.52591445070795e-01 ), ( -3.55128696236089e-02 , -4.08137237993783e-02 , -2.46702100673147e-01 ), ( -9.98529723625791e-02 , -6.54966394007973e-02 , -2.90512763082388e-01 ), ( -1.39387121834031e-01 , -7.10601043642288e-02 , -2.38841167077406e-01 ), ( -1.60529005762194e-01 , -8.65329339682001e-02 , -3.13488499661599e-01 ), ( -1.89625501057259e-01 , -1.03418749868344e-01 , -3.80141619715457e-01 ), ( -2.05742146333561e-01 , -1.00967320951149e-01 , -3.20453183152707e-01 ), ( -2.50269018572833e-01 , -1.17824980701032e-01 , -3.48937154277653e-01 ), ( -1.27774241837926e-01 , -7.84284067810070e-02 , -3.27695656311434e-01 ), ( -1.81874256847324e-01 , -8.61700864243677e-02 , -2.58037329988097e-01 ), ( -2.38332407520861e-01 , -1.04997600001132e-01 , -2.73307023037450e-01 ), ( -2.76101168267298e-01 , -1.06412855260919e-01 , -1.92027229192213e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 12, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 12, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 12, atoms_positions[size = 51] = { ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 ), ( 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 ), ( 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 ), ( 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 ), ( 7.05216884472931e+00 , -2.03267024040295e+00 , -9.73295825255848e-01 ), ( 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 ), ( 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 ), ( 7.11129887748832e+00 , -3.42540715561059e-01 , 4.28291306597860e+00 ), ( 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 ), ( 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 ), ( 5.87096740802154e+00 , 2.25415274518504e+00 , 2.99697544006320e+00 ), ( 5.21735848461560e+00 , 3.59298233811180e+00 , 2.89686929389489e+00 ), ( 6.33480970096802e+00 , 4.53566617377819e+00 , 2.43250728524615e+00 ), ( 3.90962688169957e+00 , 3.73996516051568e+00 , 2.03110560361885e+00 ), ( 2.84169952185721e+00 , 4.13207466760969e+00 , 2.52391525387548e+00 ), ( 3.87448379573895e+00 , 3.24054073488516e+00 , 7.46656271121759e-01 ), ( 2.66540088662928e+00 , 3.08071427694430e+00 , -1.06948776577169e-01 ), ( 3.03343586756372e+00 , 2.72234638656259e+00 , -1.56639273202783e+00 ), ( 1.57123880468663e+00 , 2.18521828854670e+00 , 5.36140700280098e-01 ), ( 4.33221607223244e-01 , 2.50395086530901e+00 , 5.33416986325957e-01 ), ( 1.98504702243356e+00 , 1.00234847816603e+00 , 1.07074354564732e+00 ), ( 1.18077541027169e+00 , 6.53689673177442e-02 , 1.69226430609757e+00 ), ( 2.02206467836376e+00 , -1.14472594761737e+00 , 2.00914031973690e+00 ), ( 5.46808959195410e-01 , 6.10075626469495e-01 , 2.93916872266926e+00 ), ( -6.50615460135450e-01 , 3.54018439017094e-01 , 3.17163168329279e+00 ), ( 1.32451023183092e+00 , 1.33948783531163e+00 , 3.83444335546463e+00 ), ( 8.59694930478069e-01 , 1.94335942266418e+00 , 5.03925529093421e+00 ), ( 2.02963863244139e+00 , 2.61908349136240e+00 , 5.63550046903603e+00 ), ( -3.51844184523290e-01 , 2.91687912000407e+00 , 4.97610808070261e+00 ), ( -1.16094265390643e+00 , 3.04808227265965e+00 , 5.90447813097405e+00 ), ( -4.64349504781026e-01 , 3.63017888319001e+00 , 3.84568116619849e+00 ), ( -1.49206739475396e+00 , 4.55228680080772e+00 , 3.52091755495627e+00 ), ( -7.27174485366121e-01 , 5.39873112983284e+00 , 2.43698850432327e+00 ), ( -2.76549994203998e+00 , 3.87909092947422e+00 , 2.91955278431552e+00 ), ( -3.83320694871914e+00 , 4.46089668565823e+00 , 2.82972610602657e+00 ), ( -2.60193378324243e+00 , 2.63707500181704e+00 , 2.45582159900282e+00 ), ( -3.72981911892557e+00 , 1.87760712012116e+00 , 2.02904580470210e+00 ), ( -3.41570312436543e+00 , 8.58003564587794e-01 , 9.34084900309542e-01 ), ( -4.30067653974697e+00 , 1.06684783467702e+00 , 3.24916609074616e+00 ), ( -5.53241246992859e+00 , 8.75038253548931e-01 , 3.33169955912849e+00 ), ( -3.42189965148397e+00 , 6.65020150722877e-01 , 4.14396823941459e+00 ), ( -3.76400342980764e+00 , 5.18364871068631e-02 , 5.46948036416195e+00 ), ( -2.38376264792475e+00 , -3.36662883499113e-01 , 6.16551886812340e+00 ), ( -4.47478519017763e+00 , 9.96780026303595e-01 , 6.43424940827949e+00 ), ( -5.33061567930435e+00 , 6.08703030602428e-01 , 7.19820914998331e+00 ), ( -6.26390807988011e+00 , 3.56865160210561e+00 , 6.70876978233037e+00 ), ( -6.92318478431468e+00 , 4.29502014255646e+00 , 7.43603016595229e+00 ), ( -6.74513867300062e+00 , 3.20536849185209e+00 , 5.52310114289021e+00 ), ( -4.11757953139702e+00 , 2.29049008233997e+00 , 6.47023954517971e+00 ), ( -4.85863836232743e+00 , 3.19870850025164e+00 , 7.21444112192501e+00 ), ( -4.09973971458373e+00 , 4.57064905249189e+00 , 7.29314379280119e+00 ) } +colvars: Step 12, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.19922434142702e-01 , 4.37264221813040e-03 , 9.47433647350695e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Calculating fit gradients. +colvars: Done calculating colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 7.05216884472931e+00 , -2.03267024040295e+00 , -9.73295825255848e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 , 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 7.11129887748832e+00 , -3.42540715561059e-01 , 4.28291306597860e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 , 5.87096740802154e+00 , 2.25415274518504e+00 , 2.99697544006320e+00 , 5.21735848461560e+00 , 3.59298233811180e+00 , 2.89686929389489e+00 , 6.33480970096802e+00 , 4.53566617377819e+00 , 2.43250728524615e+00 , 3.90962688169957e+00 , 3.73996516051568e+00 , 2.03110560361885e+00 , 2.84169952185721e+00 , 4.13207466760969e+00 , 2.52391525387548e+00 , 3.87448379573895e+00 , 3.24054073488516e+00 , 7.46656271121759e-01 , 2.66540088662928e+00 , 3.08071427694430e+00 , -1.06948776577169e-01 , 3.03343586756372e+00 , 2.72234638656259e+00 , -1.56639273202783e+00 , 1.57123880468663e+00 , 2.18521828854670e+00 , 5.36140700280098e-01 , 4.33221607223244e-01 , 2.50395086530901e+00 , 5.33416986325957e-01 , 1.98504702243356e+00 , 1.00234847816603e+00 , 1.07074354564732e+00 , 1.18077541027169e+00 , 6.53689673177442e-02 , 1.69226430609757e+00 , 2.02206467836376e+00 , -1.14472594761737e+00 , 2.00914031973690e+00 , 5.46808959195410e-01 , 6.10075626469495e-01 , 2.93916872266926e+00 , -6.50615460135450e-01 , 3.54018439017094e-01 , 3.17163168329279e+00 , 1.32451023183092e+00 , 1.33948783531163e+00 , 3.83444335546463e+00 , 8.59694930478069e-01 , 1.94335942266418e+00 , 5.03925529093421e+00 , 2.02963863244139e+00 , 2.61908349136240e+00 , 5.63550046903603e+00 , -3.51844184523290e-01 , 2.91687912000407e+00 , 4.97610808070261e+00 , -1.16094265390643e+00 , 3.04808227265965e+00 , 5.90447813097405e+00 , -4.64349504781026e-01 , 3.63017888319001e+00 , 3.84568116619849e+00 , -1.49206739475396e+00 , 4.55228680080772e+00 , 3.52091755495627e+00 , -7.27174485366121e-01 , 5.39873112983284e+00 , 2.43698850432327e+00 , -2.76549994203998e+00 , 3.87909092947422e+00 , 2.91955278431552e+00 , -3.83320694871914e+00 , 4.46089668565823e+00 , 2.82972610602657e+00 , -2.60193378324243e+00 , 2.63707500181704e+00 , 2.45582159900282e+00 , -3.72981911892557e+00 , 1.87760712012116e+00 , 2.02904580470210e+00 , -3.41570312436543e+00 , 8.58003564587794e-01 , 9.34084900309542e-01 , -4.30067653974697e+00 , 1.06684783467702e+00 , 3.24916609074616e+00 , -5.53241246992859e+00 , 8.75038253548931e-01 , 3.33169955912849e+00 , -3.42189965148397e+00 , 6.65020150722877e-01 , 4.14396823941459e+00 , -3.76400342980764e+00 , 5.18364871068631e-02 , 5.46948036416195e+00 , -2.38376264792475e+00 , -3.36662883499113e-01 , 6.16551886812340e+00 , -4.47478519017763e+00 , 9.96780026303595e-01 , 6.43424940827949e+00 , -5.33061567930435e+00 , 6.08703030602428e-01 , 7.19820914998331e+00 , -6.26390807988011e+00 , 3.56865160210561e+00 , 6.70876978233037e+00 , -6.92318478431468e+00 , 4.29502014255646e+00 , 7.43603016595229e+00 , -6.74513867300062e+00 , 3.20536849185209e+00 , 5.52310114289021e+00 , -4.11757953139702e+00 , 2.29049008233997e+00 , 6.47023954517971e+00 , -4.85863836232743e+00 , 3.19870850025164e+00 , 7.21444112192501e+00 , -4.09973971458373e+00 , 4.57064905249189e+00 , 7.29314379280119e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.19922434142702e-01 , 4.37264221813040e-03 , 9.47433647350695e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.33221458616166e+00 , 4.35240194596424e-02 , -7.66030780479140e-01 , 6.98806425757258e+00 , -5.37810311097262e-01 , -6.26349647331231e-01 , 7.05216884472931e+00 , -2.03267024040295e+00 , -9.73295825255848e-01 , 6.20348614978163e+00 , -3.06508109468488e-01 , 6.90173411870864e-01 , 4.98036901916146e+00 , -1.92631738004506e-01 , 6.96004385678091e-01 , 6.89883683926379e+00 , -2.65998242898190e-01 , 1.85500090020127e+00 , 6.18567860587742e+00 , -1.20661274862779e-01 , 3.15959980871046e+00 , 7.11129887748832e+00 , -3.42540715561059e-01 , 4.28291306597860e+00 , 5.28914294283639e+00 , 1.11216297431019e+00 , 3.32053027954548e+00 , 4.12685137907208e+00 , 1.04660829171537e+00 , 3.64758189867345e+00 , 5.87096740802154e+00 , 2.25415274518504e+00 , 2.99697544006320e+00 , 5.21735848461560e+00 , 3.59298233811180e+00 , 2.89686929389489e+00 , 6.33480970096802e+00 , 4.53566617377819e+00 , 2.43250728524615e+00 , 3.90962688169957e+00 , 3.73996516051568e+00 , 2.03110560361885e+00 , 2.84169952185721e+00 , 4.13207466760969e+00 , 2.52391525387548e+00 , 3.87448379573895e+00 , 3.24054073488516e+00 , 7.46656271121759e-01 , 2.66540088662928e+00 , 3.08071427694430e+00 , -1.06948776577169e-01 , 3.03343586756372e+00 , 2.72234638656259e+00 , -1.56639273202783e+00 , 1.57123880468663e+00 , 2.18521828854670e+00 , 5.36140700280098e-01 , 4.33221607223244e-01 , 2.50395086530901e+00 , 5.33416986325957e-01 , 1.98504702243356e+00 , 1.00234847816603e+00 , 1.07074354564732e+00 , 1.18077541027169e+00 , 6.53689673177442e-02 , 1.69226430609757e+00 , 2.02206467836376e+00 , -1.14472594761737e+00 , 2.00914031973690e+00 , 5.46808959195410e-01 , 6.10075626469495e-01 , 2.93916872266926e+00 , -6.50615460135450e-01 , 3.54018439017094e-01 , 3.17163168329279e+00 , 1.32451023183092e+00 , 1.33948783531163e+00 , 3.83444335546463e+00 , 8.59694930478069e-01 , 1.94335942266418e+00 , 5.03925529093421e+00 , 2.02963863244139e+00 , 2.61908349136240e+00 , 5.63550046903603e+00 , -3.51844184523290e-01 , 2.91687912000407e+00 , 4.97610808070261e+00 , -1.16094265390643e+00 , 3.04808227265965e+00 , 5.90447813097405e+00 , -4.64349504781026e-01 , 3.63017888319001e+00 , 3.84568116619849e+00 , -1.49206739475396e+00 , 4.55228680080772e+00 , 3.52091755495627e+00 , -7.27174485366121e-01 , 5.39873112983284e+00 , 2.43698850432327e+00 , -2.76549994203998e+00 , 3.87909092947422e+00 , 2.91955278431552e+00 , -3.83320694871914e+00 , 4.46089668565823e+00 , 2.82972610602657e+00 , -2.60193378324243e+00 , 2.63707500181704e+00 , 2.45582159900282e+00 , -3.72981911892557e+00 , 1.87760712012116e+00 , 2.02904580470210e+00 , -3.41570312436543e+00 , 8.58003564587794e-01 , 9.34084900309542e-01 , -4.30067653974697e+00 , 1.06684783467702e+00 , 3.24916609074616e+00 , -5.53241246992859e+00 , 8.75038253548931e-01 , 3.33169955912849e+00 , -3.42189965148397e+00 , 6.65020150722877e-01 , 4.14396823941459e+00 , -3.76400342980764e+00 , 5.18364871068631e-02 , 5.46948036416195e+00 , -2.38376264792475e+00 , -3.36662883499113e-01 , 6.16551886812340e+00 , -4.47478519017763e+00 , 9.96780026303595e-01 , 6.43424940827949e+00 , -5.33061567930435e+00 , 6.08703030602428e-01 , 7.19820914998331e+00 , -6.26390807988011e+00 , 3.56865160210561e+00 , 6.70876978233037e+00 , -6.92318478431468e+00 , 4.29502014255646e+00 , 7.43603016595229e+00 , -6.74513867300062e+00 , 3.20536849185209e+00 , 5.52310114289021e+00 , -4.11757953139702e+00 , 2.29049008233997e+00 , 6.47023954517971e+00 , -4.85863836232743e+00 , 3.19870850025164e+00 , 7.21444112192501e+00 , -4.09973971458373e+00 , 4.57064905249189e+00 , 7.29314379280119e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.8232 , 6.68232 , 13.3646 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.8232 , 6.68232 , 13.3646 ) to colvar "one". +colvars: Adding total bias energy: 57.6644 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.8232 , 6.68232 , 13.3646 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.18969 , -0.585835 , -1.61538 ) +colvars: ( -4.45016 , -0.502354 , -1.38519 ) +colvars: ( -4.45016 , -0.502354 , -1.38519 ) +colvars: ( -5.92774 , -0.66915 , -1.84512 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.954588 , 0.206666 , 0.673866 ) +colvars: ( 0.825922 , 0.282508 , 0.700532 ) +colvars: ( 0.809815 , 0.274843 , 0.680647 ) +colvars: ( 0.705027 , 0.284043 , 0.631216 ) +colvars: ( 0.692237 , 0.213291 , 0.527901 ) +colvars: ( 0.611451 , 0.366782 , 0.687941 ) +colvars: ( 0.495446 , 0.382401 , 0.640575 ) +colvars: ( 0.412534 , 0.486343 , 0.732296 ) +colvars: ( 0.408012 , 0.33527 , 0.525148 ) +colvars: ( 0.370176 , 0.291353 , 0.443362 ) +colvars: ( 0.377358 , 0.340729 , 0.514434 ) +colvars: ( 0.301269 , 0.295306 , 0.40802 ) +colvars: ( 0.273051 , 0.325976 , 0.432867 ) +colvars: ( 0.368743 , 0.190875 , 0.30652 ) +colvars: ( 0.305537 , 0.145094 , 0.207228 ) +colvars: ( 0.501127 , 0.150807 , 0.330468 ) +colvars: ( 0.579432 , 0.0531935 , 0.244591 ) +colvars: ( 0.719352 , 0.0300962 , 0.29596 ) +colvars: ( 0.587767 , 0.0196095 , 0.204058 ) +colvars: ( 0.570812 , -0.0495204 , 0.100478 ) +colvars: ( 0.609458 , 0.0707695 , 0.286113 ) +colvars: ( 0.606887 , 0.0539088 , 0.261773 ) +colvars: ( 0.645501 , 0.12284 , 0.377875 ) +colvars: ( 0.47271 , 0.0593701 , 0.189927 ) +colvars: ( 0.465042 , 2.30471e-05 , 0.105072 ) +colvars: ( 0.363068 , 0.129634 , 0.220279 ) +colvars: ( 0.228839 , 0.139417 , 0.154251 ) +colvars: ( 0.130515 , 0.23101 , 0.220157 ) +colvars: ( 0.199061 , 0.0609095 , 0.0304057 ) +colvars: ( 0.145672 , 0.0227888 , -0.0527192 ) +colvars: ( 0.236159 , 0.0332374 , 0.01486 ) +colvars: ( 0.221701 , -0.044035 , -0.0982658 ) +colvars: ( 0.260714 , -0.0481082 , -0.0807397 ) +colvars: ( 0.302489 , -0.135737 , -0.174675 ) +colvars: ( 0.255174 , -0.192046 , -0.278831 ) +colvars: ( 0.426226 , -0.152157 , -0.123826 ) +colvars: ( 0.509307 , -0.232715 , -0.183798 ) +colvars: ( 0.650449 , -0.236051 , -0.10496 ) +colvars: ( 0.45747 , -0.23695 , -0.220141 ) +colvars: ( 0.463307 , -0.309337 , -0.314669 ) +colvars: ( 0.404308 , -0.158511 , -0.145369 ) +colvars: ( 0.345026 , -0.151299 , -0.170617 ) +colvars: ( 0.326567 , -0.0587806 , -0.0562952 ) +colvars: ( 0.212362 , -0.1601 , -0.260874 ) +colvars: ( 0.185643 , -0.204516 , -0.33677 ) +colvars: ( -0.00291463 , -0.208311 , -0.45326 ) +colvars: ( -0.10077 , -0.226834 , -0.53612 ) +colvars: ( 0.105712 , -0.26208 , -0.461887 ) +colvars: ( 0.124851 , -0.116714 , -0.253832 ) +colvars: ( -0.00347029 , -0.120859 , -0.335222 ) +colvars: ( -0.0989785 , -0.0347412 , -0.275065 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.18969 , 0.585835 , 1.61538 ) +colvars: ( 4.45016 , 0.502354 , 1.38519 ) +colvars: ( 4.45016 , 0.502354 , 1.38519 ) +colvars: ( 5.92774 , 0.66915 , 1.84512 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.659805 , -0.0856054 , -0.408542 ) +colvars: ( -0.592436 , -0.1729 , -0.377742 ) +colvars: ( -0.541561 , -0.149764 , -0.316769 ) +colvars: ( -0.548468 , -0.202158 , -0.345904 ) +colvars: ( -0.538268 , -0.140332 , -0.309462 ) +colvars: ( -0.520108 , -0.299149 , -0.35845 ) +colvars: ( -0.482874 , -0.341894 , -0.339097 ) +colvars: ( -0.457991 , -0.454914 , -0.361929 ) +colvars: ( -0.416115 , -0.304962 , -0.256305 ) +colvars: ( -0.410156 , -0.278508 , -0.239107 ) +colvars: ( -0.365201 , -0.299085 , -0.2026 ) +colvars: ( -0.301398 , -0.260515 , -0.122087 ) +colvars: ( -0.251272 , -0.276233 , -0.0783211 ) +colvars: ( -0.323495 , -0.151892 , -0.0983161 ) +colvars: ( -0.289638 , -0.121315 , -0.0513105 ) +colvars: ( -0.3832 , -0.0912138 , -0.132678 ) +colvars: ( -0.412946 , 0.0122499 , -0.118786 ) +colvars: ( -0.468731 , 0.0626997 , -0.153536 ) +colvars: ( -0.451193 , 0.0280191 , -0.15058 ) +colvars: ( -0.439077 , 0.0876347 , -0.113148 ) +colvars: ( -0.496498 , -0.0287334 , -0.220187 ) +colvars: ( -0.531022 , -0.0303162 , -0.255585 ) +colvars: ( -0.582836 , -0.0989689 , -0.336778 ) +colvars: ( -0.473603 , -0.0622484 , -0.211349 ) +colvars: ( -0.480218 , -0.0159597 , -0.198401 ) +colvars: ( -0.41405 , -0.140641 , -0.184641 ) +colvars: ( -0.351087 , -0.173922 , -0.135399 ) +colvars: ( -0.296707 , -0.268956 , -0.120943 ) +colvars: ( -0.308414 , -0.097445 , -0.0600886 ) +colvars: ( -0.29314 , -0.0780518 , -0.0365119 ) +colvars: ( -0.289726 , -0.0501427 , -0.0212587 ) +colvars: ( -0.253496 , 0.0283949 , 0.048444 ) +colvars: ( -0.23344 , 0.0562809 , 0.0804273 ) +colvars: ( -0.300806 , 0.119785 , 0.0395552 ) +colvars: ( -0.272196 , 0.163538 , 0.0868623 ) +colvars: ( -0.375197 , 0.149681 , -0.0226153 ) +colvars: ( -0.427395 , 0.229978 , -0.0411181 ) +colvars: ( -0.504252 , 0.254095 , -0.108216 ) +colvars: ( -0.43717 , 0.208956 , -0.0598532 ) +colvars: ( -0.441898 , 0.27288 , -0.0375383 ) +colvars: ( -0.439797 , 0.117805 , -0.101095 ) +colvars: ( -0.444799 , 0.085908 , -0.119635 ) +colvars: ( -0.465863 , -0.0122259 , -0.18238 ) +colvars: ( -0.372703 , 0.0736841 , -0.0522888 ) +colvars: ( -0.37505 , 0.101239 , -0.0429806 ) +colvars: ( -0.202473 , 0.107503 , 0.133268 ) +colvars: ( -0.149063 , 0.109183 , 0.187705 ) +colvars: ( -0.23322 , 0.183837 , 0.134665 ) +colvars: ( -0.306477 , 0.0306434 , -0.00389796 ) +colvars: ( -0.23451 , 0.01597 , 0.0622802 ) +colvars: ( -0.176705 , -0.0716049 , 0.083341 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 12. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 12. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atoms_new_colvar_forces = { ( -4.89490574889113e+00 , -4.64774252641731e-01 , -1.35006023160969e+00 ), ( -4.21667171666565e+00 , -3.92745935728585e-01 , -1.06240156560237e+00 ), ( -4.29359785587889e+00 , -4.20469184921439e-01 , -1.09988016615827e+00 ), ( -5.77376897192617e+00 , -5.96190549932710e-01 , -1.62667691433255e+00 ), ( 2.68254009642205e-01 , 1.25079351029727e-01 , 3.63878023447364e-01 ), ( 5.28103187483856e+00 , 6.53468241162387e-01 , 1.94487516194241e+00 ), ( 4.46272966411243e+00 , 5.42861093800513e-01 , 1.68666944573490e+00 ), ( -4.54573561845573e-02 , 3.14293983525731e-02 , 3.70367397645178e-01 ), ( 4.44205365781094e+00 , 5.32661605360381e-01 , 1.65403521844747e+00 ), ( 5.88775893813820e+00 , 6.81994156523306e-01 , 2.04937066321476e+00 ), ( 1.21571008088405e-02 , 4.16438537525102e-02 , 3.11833525414787e-01 ), ( -1.28558119093569e-04 , 3.47903538534744e-02 , 2.85932299166015e-01 ), ( 2.17791621243190e-02 , 4.97432814457449e-02 , 3.54546217085878e-01 ), ( 4.52481308887325e-02 , 3.89826259618592e-02 , 2.08203610691296e-01 ), ( 1.58987103728810e-02 , 2.37783431230710e-02 , 1.55917845951448e-01 ), ( 1.17926751938918e-01 , 5.95934911655521e-02 , 1.97789911765121e-01 ), ( 1.66485372508838e-01 , 6.54433615727072e-02 , 1.25805491016107e-01 ), ( 2.50621000683816e-01 , 9.27959688237679e-02 , 1.42423490979841e-01 ), ( 1.36574083657088e-01 , 4.76286029298191e-02 , 5.34774085413792e-02 ), ( 1.31734460156563e-01 , 3.81143676165490e-02 , -1.26697582429871e-02 ), ( 1.12960101651388e-01 , 4.20361460399759e-02 , 6.59260414106081e-02 ), ( 7.58653239458306e-02 , 2.35925197995797e-02 , 6.18873743058740e-03 ), ( 6.26649822284892e-02 , 2.38707788780387e-02 , 4.10969144218748e-02 ), ( -8.92959680793504e-04 , -2.87826672277569e-03 , -2.14225009843340e-02 ), ( -1.51753706219444e-02 , -1.59366362085343e-02 , -9.33283264047111e-02 ), ( -5.09822485294129e-02 , -1.10067941638486e-02 , 3.56380243051370e-02 ), ( -1.22247083974906e-01 , -3.45052996690010e-02 , 1.88512984490016e-02 ), ( -1.66192319555690e-01 , -3.79458769336318e-02 , 9.92133503535462e-02 ), ( -1.09352966810302e-01 , -3.65355087010639e-02 , -2.96828571144716e-02 ), ( -1.47467382472801e-01 , -5.52630536494705e-02 , -8.92310488465498e-02 ), ( -5.35667351986572e-02 , -1.69052661733132e-02 , -6.39862819504183e-03 ), ( -3.17942629359031e-02 , -1.56401522438041e-02 , -4.98218056743984e-02 ), ( 2.72743998191535e-02 , 8.17269516888103e-03 , -3.12415826215579e-04 ), ( 1.68329897527458e-03 , -1.59519978436565e-02 , -1.35119541705500e-01 ), ( -1.70228143957742e-02 , -2.85081164231803e-02 , -1.91969200515544e-01 ), ( 5.10286830970168e-02 , -2.47603852696932e-03 , -1.46441326330843e-01 ), ( 8.19118009903109e-02 , -2.73776863389308e-03 , -2.24915635454790e-01 ), ( 1.46196725947246e-01 , 1.80447162321154e-02 , -2.13175934601129e-01 ), ( 2.03002750710456e-02 , -2.79945513141760e-02 , -2.79994622801097e-01 ), ( 2.14094345429477e-02 , -3.64568337373448e-02 , -3.52207715795593e-01 ), ( -3.54887320110356e-02 , -4.07050867573193e-02 , -2.46464027267080e-01 ), ( -9.97729655908142e-02 , -6.53911315690126e-02 , -2.90252067443280e-01 ), ( -1.39295638967675e-01 , -7.10065750701262e-02 , -2.38674851929840e-01 ), ( -1.60341051122720e-01 , -8.64154448082740e-02 , -3.13163006600101e-01 ), ( -1.89406743056207e-01 , -1.03276392503134e-01 , -3.79750528934929e-01 ), ( -2.05387826104413e-01 , -1.00808334778545e-01 , -3.19992579801541e-01 ), ( -2.49833715710703e-01 , -1.17650508088223e-01 , -3.48414816503726e-01 ), ( -1.27507941145204e-01 , -7.82438307878345e-02 , -3.27222287886911e-01 ), ( -1.81625360124679e-01 , -8.60706461792183e-02 , -2.57729569122441e-01 ), ( -2.37980145706232e-01 , -1.04888838911070e-01 , -2.72942057278126e-01 ), ( -2.75683472569685e-01 , -1.06346078970650e-01 , -1.91724088450644e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 13, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 13, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 13, atoms_positions[size = 51] = { ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 ), ( 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 ), ( 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 ), ( 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 ), ( 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 ), ( 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 ), ( 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 ), ( 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 ), ( 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 ), ( 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 ), ( 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 ), ( 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 ), ( 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 ), ( 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 ), ( 2.83214575810826e+00 , 4.13595170834672e+00 , 2.51992869876098e+00 ), ( 3.88447884319767e+00 , 3.24095178677905e+00 , 7.43161138393898e-01 ), ( 2.66189458936046e+00 , 3.06674501687041e+00 , -1.07915315664321e-01 ), ( 3.03272107178712e+00 , 2.72278863903895e+00 , -1.55730911754205e+00 ), ( 1.57225734397424e+00 , 2.19057818008372e+00 , 5.23377682763401e-01 ), ( 4.27821186858660e-01 , 2.51332776145223e+00 , 5.30761279881784e-01 ), ( 1.99146378967290e+00 , 1.00295776233815e+00 , 1.07436273138212e+00 ), ( 1.18197300708239e+00 , 7.58502845988991e-02 , 1.69221931299880e+00 ), ( 2.02418101326422e+00 , -1.13880506272946e+00 , 2.00760706123916e+00 ), ( 5.49618108438383e-01 , 6.09368087019359e-01 , 2.93374468907765e+00 ), ( -6.45190245409923e-01 , 3.52464608156817e-01 , 3.17016475896813e+00 ), ( 1.32597733453506e+00 , 1.34180367960609e+00 , 3.83138482698476e+00 ), ( 8.59752646405481e-01 , 1.94896559215968e+00 , 5.03552931652643e+00 ), ( 2.03090979027595e+00 , 2.62570821811796e+00 , 5.63949869801013e+00 ), ( -3.49005720764981e-01 , 2.91669232246480e+00 , 4.97411954802775e+00 ), ( -1.15859126627669e+00 , 3.05059754241338e+00 , 5.90336377131071e+00 ), ( -4.71324849253532e-01 , 3.61718950042861e+00 , 3.84600236908586e+00 ), ( -1.49576392608207e+00 , 4.55038851624654e+00 , 3.51350351544032e+00 ), ( -7.22380687986103e-01 , 5.40073126999859e+00 , 2.44146217134017e+00 ), ( -2.76925466861065e+00 , 3.87661075599847e+00 , 2.91737661568981e+00 ), ( -3.83010802920451e+00 , 4.46701830454351e+00 , 2.82708188305086e+00 ), ( -2.60380816777968e+00 , 2.64492492063907e+00 , 2.44973080554366e+00 ), ( -3.73544928409753e+00 , 1.86577757211119e+00 , 2.02266810954733e+00 ), ( -3.41399991375659e+00 , 8.64775140375181e-01 , 9.25392368021579e-01 ), ( -4.30522154846684e+00 , 1.06547244135007e+00 , 3.24682101086543e+00 ), ( -5.52835078590118e+00 , 8.68197671934854e-01 , 3.33043603374501e+00 ), ( -3.41380912283504e+00 , 6.68858792934437e-01 , 4.15009982032347e+00 ), ( -3.75692856388351e+00 , 4.55701681879979e-02 , 5.46348028888173e+00 ), ( -2.38291005376584e+00 , -3.29306560614546e-01 , 6.16823880404895e+00 ), ( -4.47391676453799e+00 , 9.98985309012160e-01 , 6.43705901718938e+00 ), ( -5.33373979385291e+00 , 6.08169813898481e-01 , 7.20103084854860e+00 ), ( -6.25588657480039e+00 , 3.57192302949498e+00 , 6.71028547717466e+00 ), ( -6.92772939382645e+00 , 4.29558076535878e+00 , 7.44097322494073e+00 ), ( -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 ), ( -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 ), ( -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 ), ( -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ) } +colvars: Step 13, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.17465326396842e-01 , 4.17503558318963e-03 , 9.48260689691198e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 , 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 , 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 , 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 , 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 , 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 , 2.83214575810826e+00 , 4.13595170834672e+00 , 2.51992869876098e+00 , 3.88447884319767e+00 , 3.24095178677905e+00 , 7.43161138393898e-01 , 2.66189458936046e+00 , 3.06674501687041e+00 , -1.07915315664321e-01 , 3.03272107178712e+00 , 2.72278863903895e+00 , -1.55730911754205e+00 , 1.57225734397424e+00 , 2.19057818008372e+00 , 5.23377682763401e-01 , 4.27821186858660e-01 , 2.51332776145223e+00 , 5.30761279881784e-01 , 1.99146378967290e+00 , 1.00295776233815e+00 , 1.07436273138212e+00 , 1.18197300708239e+00 , 7.58502845988991e-02 , 1.69221931299880e+00 , 2.02418101326422e+00 , -1.13880506272946e+00 , 2.00760706123916e+00 , 5.49618108438383e-01 , 6.09368087019359e-01 , 2.93374468907765e+00 , -6.45190245409923e-01 , 3.52464608156817e-01 , 3.17016475896813e+00 , 1.32597733453506e+00 , 1.34180367960609e+00 , 3.83138482698476e+00 , 8.59752646405481e-01 , 1.94896559215968e+00 , 5.03552931652643e+00 , 2.03090979027595e+00 , 2.62570821811796e+00 , 5.63949869801013e+00 , -3.49005720764981e-01 , 2.91669232246480e+00 , 4.97411954802775e+00 , -1.15859126627669e+00 , 3.05059754241338e+00 , 5.90336377131071e+00 , -4.71324849253532e-01 , 3.61718950042861e+00 , 3.84600236908586e+00 , -1.49576392608207e+00 , 4.55038851624654e+00 , 3.51350351544032e+00 , -7.22380687986103e-01 , 5.40073126999859e+00 , 2.44146217134017e+00 , -2.76925466861065e+00 , 3.87661075599847e+00 , 2.91737661568981e+00 , -3.83010802920451e+00 , 4.46701830454351e+00 , 2.82708188305086e+00 , -2.60380816777968e+00 , 2.64492492063907e+00 , 2.44973080554366e+00 , -3.73544928409753e+00 , 1.86577757211119e+00 , 2.02266810954733e+00 , -3.41399991375659e+00 , 8.64775140375181e-01 , 9.25392368021579e-01 , -4.30522154846684e+00 , 1.06547244135007e+00 , 3.24682101086543e+00 , -5.52835078590118e+00 , 8.68197671934854e-01 , 3.33043603374501e+00 , -3.41380912283504e+00 , 6.68858792934437e-01 , 4.15009982032347e+00 , -3.75692856388351e+00 , 4.55701681879979e-02 , 5.46348028888173e+00 , -2.38291005376584e+00 , -3.29306560614546e-01 , 6.16823880404895e+00 , -4.47391676453799e+00 , 9.98985309012160e-01 , 6.43705901718938e+00 , -5.33373979385291e+00 , 6.08169813898481e-01 , 7.20103084854860e+00 , -6.25588657480039e+00 , 3.57192302949498e+00 , 6.71028547717466e+00 , -6.92772939382645e+00 , 4.29558076535878e+00 , 7.44097322494073e+00 , -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 , -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 , -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 , -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.17465326396842e-01 , 4.17503558318963e-03 , 9.48260689691198e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.32477746355595e+00 , 4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 , 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 , 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 , 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 , 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 , 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 , 2.83214575810826e+00 , 4.13595170834672e+00 , 2.51992869876098e+00 , 3.88447884319767e+00 , 3.24095178677905e+00 , 7.43161138393898e-01 , 2.66189458936046e+00 , 3.06674501687041e+00 , -1.07915315664321e-01 , 3.03272107178712e+00 , 2.72278863903895e+00 , -1.55730911754205e+00 , 1.57225734397424e+00 , 2.19057818008372e+00 , 5.23377682763401e-01 , 4.27821186858660e-01 , 2.51332776145223e+00 , 5.30761279881784e-01 , 1.99146378967290e+00 , 1.00295776233815e+00 , 1.07436273138212e+00 , 1.18197300708239e+00 , 7.58502845988991e-02 , 1.69221931299880e+00 , 2.02418101326422e+00 , -1.13880506272946e+00 , 2.00760706123916e+00 , 5.49618108438383e-01 , 6.09368087019359e-01 , 2.93374468907765e+00 , -6.45190245409923e-01 , 3.52464608156817e-01 , 3.17016475896813e+00 , 1.32597733453506e+00 , 1.34180367960609e+00 , 3.83138482698476e+00 , 8.59752646405481e-01 , 1.94896559215968e+00 , 5.03552931652643e+00 , 2.03090979027595e+00 , 2.62570821811796e+00 , 5.63949869801013e+00 , -3.49005720764981e-01 , 2.91669232246480e+00 , 4.97411954802775e+00 , -1.15859126627669e+00 , 3.05059754241338e+00 , 5.90336377131071e+00 , -4.71324849253532e-01 , 3.61718950042861e+00 , 3.84600236908586e+00 , -1.49576392608207e+00 , 4.55038851624654e+00 , 3.51350351544032e+00 , -7.22380687986103e-01 , 5.40073126999859e+00 , 2.44146217134017e+00 , -2.76925466861065e+00 , 3.87661075599847e+00 , 2.91737661568981e+00 , -3.83010802920451e+00 , 4.46701830454351e+00 , 2.82708188305086e+00 , -2.60380816777968e+00 , 2.64492492063907e+00 , 2.44973080554366e+00 , -3.73544928409753e+00 , 1.86577757211119e+00 , 2.02266810954733e+00 , -3.41399991375659e+00 , 8.64775140375181e-01 , 9.25392368021579e-01 , -4.30522154846684e+00 , 1.06547244135007e+00 , 3.24682101086543e+00 , -5.52835078590118e+00 , 8.68197671934854e-01 , 3.33043603374501e+00 , -3.41380912283504e+00 , 6.68858792934437e-01 , 4.15009982032347e+00 , -3.75692856388351e+00 , 4.55701681879979e-02 , 5.46348028888173e+00 , -2.38291005376584e+00 , -3.29306560614546e-01 , 6.16823880404895e+00 , -4.47391676453799e+00 , 9.98985309012160e-01 , 6.43705901718938e+00 , -5.33373979385291e+00 , 6.08169813898481e-01 , 7.20103084854860e+00 , -6.25588657480039e+00 , 3.57192302949498e+00 , 6.71028547717466e+00 , -6.92772939382645e+00 , 4.29558076535878e+00 , 7.44097322494073e+00 , -6.74729414515726e+00 , 3.20377928416455e+00 , 5.52270066700848e+00 , -4.12170722674839e+00 , 2.28456099496655e+00 , 6.46413790042736e+00 , -4.84972269563592e+00 , 3.19497064559602e+00 , 7.21592491896093e+00 , -4.10196360342451e+00 , 4.57770989967242e+00 , 7.29461799618519e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.7009 , 6.67009 , 13.3402 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.7009 , 6.67009 , 13.3402 ) to colvar "one". +colvars: Adding total bias energy: 57.4906 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.7009 , 6.67009 , 13.3402 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.18411 , -0.581337 , -1.60007 ) +colvars: ( -4.44538 , -0.498496 , -1.37206 ) +colvars: ( -4.44538 , -0.498496 , -1.37206 ) +colvars: ( -5.92137 , -0.664012 , -1.82762 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.951742 , 0.206395 , 0.669976 ) +colvars: ( 0.823598 , 0.281953 , 0.696495 ) +colvars: ( 0.807407 , 0.274379 , 0.676732 ) +colvars: ( 0.703269 , 0.283357 , 0.627508 ) +colvars: ( 0.690526 , 0.212778 , 0.524718 ) +colvars: ( 0.610142 , 0.365782 , 0.683925 ) +colvars: ( 0.494697 , 0.381231 , 0.636776 ) +colvars: ( 0.412181 , 0.484819 , 0.728013 ) +colvars: ( 0.407552 , 0.334192 , 0.521938 ) +colvars: ( 0.369926 , 0.290328 , 0.440556 ) +colvars: ( 0.3769 , 0.339683 , 0.511294 ) +colvars: ( 0.301044 , 0.294362 , 0.405425 ) +colvars: ( 0.272813 , 0.325005 , 0.430163 ) +colvars: ( 0.368204 , 0.190265 , 0.304454 ) +colvars: ( 0.305259 , 0.144552 , 0.205661 ) +colvars: ( 0.500013 , 0.150414 , 0.328299 ) +colvars: ( 0.577965 , 0.0531211 , 0.242872 ) +colvars: ( 0.717251 , 0.0302189 , 0.294003 ) +colvars: ( 0.58639 , 0.0195602 , 0.202526 ) +colvars: ( 0.5695 , -0.0494051 , 0.0994725 ) +colvars: ( 0.608107 , 0.0705437 , 0.284148 ) +colvars: ( 0.605676 , 0.0536527 , 0.259913 ) +colvars: ( 0.644236 , 0.12238 , 0.375411 ) +colvars: ( 0.472096 , 0.058976 , 0.188411 ) +colvars: ( 0.464503 , -0.000250906 , 0.103981 ) +colvars: ( 0.36289 , 0.128989 , 0.2186 ) +colvars: ( 0.229238 , 0.138634 , 0.15289 ) +colvars: ( 0.131299 , 0.229934 , 0.218453 ) +colvars: ( 0.199494 , 0.0603511 , 0.0296852 ) +colvars: ( 0.146374 , 0.0222602 , -0.0530299 ) +colvars: ( 0.236307 , 0.0328493 , 0.0142427 ) +colvars: ( 0.221815 , -0.0441871 , -0.0982948 ) +colvars: ( 0.260524 , -0.0481423 , -0.0808319 ) +colvars: ( 0.302298 , -0.135613 , -0.174311 ) +colvars: ( 0.255169 , -0.19181 , -0.277941 ) +colvars: ( 0.425561 , -0.151919 , -0.123714 ) +colvars: ( 0.508339 , -0.232233 , -0.183377 ) +colvars: ( 0.648912 , -0.235461 , -0.104928 ) +colvars: ( 0.456848 , -0.236568 , -0.219562 ) +colvars: ( 0.462673 , -0.308775 , -0.31361 ) +colvars: ( 0.404004 , -0.158421 , -0.14519 ) +colvars: ( 0.345093 , -0.151342 , -0.170336 ) +colvars: ( 0.32681 , -0.0591255 , -0.0566127 ) +colvars: ( 0.212966 , -0.160214 , -0.260146 ) +colvars: ( 0.186419 , -0.204572 , -0.335668 ) +colvars: ( -0.00162404 , -0.208354 , -0.451546 ) +colvars: ( -0.0990831 , -0.226899 , -0.533993 ) +colvars: ( 0.106468 , -0.261859 , -0.460104 ) +colvars: ( 0.125739 , -0.116961 , -0.253137 ) +colvars: ( -0.00207154 , -0.121181 , -0.334124 ) +colvars: ( -0.0972232 , -0.035332 , -0.274277 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.18411 , 0.581337 , 1.60007 ) +colvars: ( 4.44538 , 0.498496 , 1.37206 ) +colvars: ( 4.44538 , 0.498496 , 1.37206 ) +colvars: ( 5.92137 , 0.664012 , 1.82762 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.657448 , -0.0854485 , -0.405083 ) +colvars: ( -0.590503 , -0.172507 , -0.374162 ) +colvars: ( -0.53953 , -0.149449 , -0.313293 ) +colvars: ( -0.546999 , -0.201635 , -0.342603 ) +colvars: ( -0.536827 , -0.139934 , -0.306601 ) +colvars: ( -0.519022 , -0.298367 , -0.354892 ) +colvars: ( -0.482251 , -0.340952 , -0.335722 ) +colvars: ( -0.457708 , -0.453687 , -0.358149 ) +colvars: ( -0.415704 , -0.304077 , -0.253425 ) +colvars: ( -0.409917 , -0.277649 , -0.236567 ) +colvars: ( -0.364767 , -0.298229 , -0.199781 ) +colvars: ( -0.301128 , -0.259727 , -0.119728 ) +colvars: ( -0.250971 , -0.275431 , -0.0758715 ) +colvars: ( -0.322955 , -0.151369 , -0.0963992 ) +colvars: ( -0.289302 , -0.120829 , -0.0498127 ) +colvars: ( -0.382191 , -0.0908824 , -0.130672 ) +colvars: ( -0.411638 , 0.0123237 , -0.117155 ) +colvars: ( -0.466902 , 0.0625931 , -0.151704 ) +colvars: ( -0.449976 , 0.0280866 , -0.149107 ) +colvars: ( -0.437903 , 0.0875837 , -0.112115 ) +colvars: ( -0.495331 , -0.0285283 , -0.218348 ) +colvars: ( -0.52999 , -0.0300751 , -0.253833 ) +colvars: ( -0.581791 , -0.0985751 , -0.334519 ) +colvars: ( -0.473057 , -0.0618716 , -0.209889 ) +colvars: ( -0.479733 , -0.0156658 , -0.197295 ) +colvars: ( -0.413857 , -0.140057 , -0.183046 ) +colvars: ( -0.35136 , -0.173204 , -0.134073 ) +colvars: ( -0.297295 , -0.268002 , -0.119332 ) +colvars: ( -0.308688 , -0.0968957 , -0.0593007 ) +colvars: ( -0.293633 , -0.0775081 , -0.0360683 ) +colvars: ( -0.289743 , -0.0497408 , -0.0205576 ) +colvars: ( -0.253457 , 0.0286157 , 0.0486508 ) +colvars: ( -0.23313 , 0.0563915 , 0.0806867 ) +colvars: ( -0.300518 , 0.119787 , 0.0394344 ) +colvars: ( -0.272049 , 0.163467 , 0.0862993 ) +colvars: ( -0.374537 , 0.149575 , -0.0225226 ) +colvars: ( -0.426491 , 0.229678 , -0.0412815 ) +colvars: ( -0.502895 , 0.253687 , -0.108051 ) +colvars: ( -0.436566 , 0.208754 , -0.0601502 ) +colvars: ( -0.441279 , 0.272545 , -0.0382371 ) +colvars: ( -0.439477 , 0.117842 , -0.101056 ) +colvars: ( -0.444801 , 0.0860681 , -0.119682 ) +colvars: ( -0.466036 , -0.0118282 , -0.181925 ) +colvars: ( -0.373131 , 0.0739249 , -0.0527134 ) +colvars: ( -0.375622 , 0.101449 , -0.0437187 ) +colvars: ( -0.203403 , 0.107717 , 0.13201 ) +colvars: ( -0.150306 , 0.109435 , 0.186099 ) +colvars: ( -0.233699 , 0.183823 , 0.133351 ) +colvars: ( -0.30712 , 0.0309932 , -0.00429714 ) +colvars: ( -0.235557 , 0.0164018 , 0.0615402 ) +colvars: ( -0.17804 , -0.0709576 , 0.082859 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 13. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 13. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atoms_new_colvar_forces = { ( -4.88981896196504e+00 , -4.60390551723254e-01 , -1.33517556811277e+00 ), ( -4.21228162928695e+00 , -3.89049902129704e-01 , -1.04972585545871e+00 ), ( -4.28910692410658e+00 , -4.16774313998016e-01 , -1.08715306920586e+00 ), ( -5.76767119194412e+00 , -5.91167953139013e-01 , -1.60950471137606e+00 ), ( 2.67876680524958e-01 , 1.24929752216452e-01 , 3.63438904895691e-01 ), ( 5.27523399227998e+00 , 6.48752607816794e-01 , 1.92910237707154e+00 ), ( 4.45782140789246e+00 , 5.38775378359889e-01 , 1.67311243783968e+00 ), ( -4.55279460566612e-02 , 3.11321705147235e-02 , 3.69864187073456e-01 ), ( 4.43722378982507e+00 , 5.28611708271286e-01 , 1.64057106278070e+00 ), ( 5.88137875686962e+00 , 6.76691019162951e-01 , 2.03161084176304e+00 ), ( 1.21327495420109e-02 , 4.14534690353304e-02 , 3.11512309172057e-01 ), ( -8.42319167825289e-05 , 3.46348595636129e-02 , 2.85697126200144e-01 ), ( 2.18426861463246e-02 , 4.95735984439514e-02 , 3.54291786058363e-01 ), ( 4.52489567860466e-02 , 3.88957799718568e-02 , 2.08054927761938e-01 ), ( 1.59578651818409e-02 , 2.37229136416288e-02 , 1.55848419325201e-01 ), ( 1.17822071543679e-01 , 5.95312822654525e-02 , 1.97626888946625e-01 ), ( 1.66327351419946e-01 , 6.54448163200975e-02 , 1.25716406855178e-01 ), ( 2.50348975389216e-01 , 9.28119703385379e-02 , 1.42298313485828e-01 ), ( 1.36413773283859e-01 , 4.76468082553589e-02 , 5.34198309692146e-02 ), ( 1.31596787808496e-01 , 3.81785730709885e-02 , -1.26427591612700e-02 ), ( 1.12775883922173e-01 , 4.20154527965672e-02 , 6.57998608481610e-02 ), ( 7.56858654316191e-02 , 2.35776056205410e-02 , 6.08026662443523e-03 ), ( 6.24452792462686e-02 , 2.38053309565956e-02 , 4.08926522131212e-02 ), ( -9.61086682672252e-04 , -2.89565406751356e-03 , -2.14775907665281e-02 ), ( -1.52296050911035e-02 , -1.59166635104930e-02 , -9.33147102978675e-02 ), ( -5.09677319010105e-02 , -1.10673114533446e-02 , 3.55542436727819e-02 ), ( -1.22121809149347e-01 , -3.45702970881061e-02 , 1.88164571166034e-02 ), ( -1.65996483973189e-01 , -3.80680744946709e-02 , 9.91210968432649e-02 ), ( -1.09193558771200e-01 , -3.65445810195318e-02 , -2.96155108704943e-02 ), ( -1.47258577096358e-01 , -5.52479126945070e-02 , -8.90981727184671e-02 ), ( -5.34353811403274e-02 , -1.68914730059245e-02 , -6.31489749812243e-03 ), ( -3.16417197793630e-02 , -1.55713484237388e-02 , -4.96440396384484e-02 ), ( 2.73943373716786e-02 , 8.24926005665480e-03 , -1.45188845464467e-04 ), ( 1.77994020406858e-03 , -1.58258443290363e-02 , -1.34876499903599e-01 ), ( -1.68798291810008e-02 , -2.83435715816595e-02 , -1.91642157004365e-01 ), ( 5.10243811266533e-02 , -2.34333172226778e-03 , -1.46236166494363e-01 ), ( 8.18483615665809e-02 , -2.55558445760179e-03 , -2.24658827699174e-01 ), ( 1.46016120702545e-01 , 1.82255016213926e-02 , -2.12978949787339e-01 ), ( 2.02811035476966e-02 , -2.78138914247876e-02 , -2.79712078538106e-01 ), ( 2.13943829889179e-02 , -3.62292780674321e-02 , -3.51847504541956e-01 ), ( -3.54728586973324e-02 , -4.05789606437091e-02 , -2.46246573978784e-01 ), ( -9.97080491558552e-02 , -6.52737100745764e-02 , -2.90018194421679e-01 ), ( -1.39226336381453e-01 , -7.09536931282848e-02 , -2.38537296583322e-01 ), ( -1.60164526816236e-01 , -8.62889353775075e-02 , -3.12859657823101e-01 ), ( -1.89202213571486e-01 , -1.03122691420405e-01 , -3.79386850276111e-01 ), ( -2.05026780807315e-01 , -1.00637069523100e-01 , -3.19535591632303e-01 ), ( -2.49388860668061e-01 , -1.17464648436431e-01 , -3.47893206719193e-01 ), ( -1.27231151927321e-01 , -7.80360159431520e-02 , -3.26752761726856e-01 ), ( -1.81381579036729e-01 , -8.59675133319940e-02 , -2.57433890746736e-01 ), ( -2.37628983834062e-01 , -1.04779438973798e-01 , -2.72583892963877e-01 ), ( -2.75263491664155e-01 , -1.06289643117102e-01 , -1.91418222726097e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 14, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 14, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 14, atoms_positions[size = 51] = { ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 ), ( 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 ), ( 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 ), ( 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ), ( 7.05429385254313e+00 , -2.03733971095845e+00 , -9.61939487520703e-01 ), ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 ), ( 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 ), ( 7.09587417768813e+00 , -3.48673267580415e-01 , 4.28480410351882e+00 ), ( 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 ), ( 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 ), ( 5.86486454274355e+00 , 2.24797767579896e+00 , 2.99815671646628e+00 ), ( 5.22493545201210e+00 , 3.58991729210236e+00 , 2.90473741736489e+00 ), ( 6.33092192081317e+00 , 4.52116236648895e+00 , 2.41927485778368e+00 ), ( 3.90776010512297e+00 , 3.73584825978615e+00 , 2.03591493688509e+00 ), ( 2.82332465249931e+00 , 4.13991068119476e+00 , 2.51583104327529e+00 ), ( 3.89451144592941e+00 , 3.24144516682814e+00 , 7.40179485370264e-01 ), ( 2.65844106989744e+00 , 3.05350593383516e+00 , -1.08488981331887e-01 ), ( 3.03278747309343e+00 , 2.72268879368398e+00 , -1.54821987670355e+00 ), ( 1.57526439270054e+00 , 2.19446358993994e+00 , 5.10294119197168e-01 ), ( 4.21210277979123e-01 , 2.52304701718955e+00 , 5.28146554175524e-01 ), ( 1.99863625271151e+00 , 1.00572236418968e+00 , 1.07723828604057e+00 ), ( 1.18201227767348e+00 , 8.57044788501173e-02 , 1.69220053554445e+00 ), ( 2.02644354157259e+00 , -1.13299047266892e+00 , 2.00645171537107e+00 ), ( 5.51945150516580e-01 , 6.08708404493696e-01 , 2.93013538978696e+00 ), ( -6.39308246883680e-01 , 3.51274880191373e-01 , 3.16869445588155e+00 ), ( 1.32668812244549e+00 , 1.34352515560620e+00 , 3.82671742359831e+00 ), ( 8.58767606428859e-01 , 1.95434757556696e+00 , 5.03241999566417e+00 ), ( 2.03402657414422e+00 , 2.63307566831980e+00 , 5.64415447011505e+00 ), ( -3.46157050289023e-01 , 2.91655892147137e+00 , 4.97220637353131e+00 ), ( -1.15608468363693e+00 , 3.05290417480726e+00 , 5.90192658127788e+00 ), ( -4.77921309709439e-01 , 3.60388884533245e+00 , 3.84668343251162e+00 ), ( -1.49968243814569e+00 , 4.54905744339707e+00 , 3.50490478092210e+00 ), ( -7.17716458963084e-01 , 5.40273226525777e+00 , 2.44572191675940e+00 ), ( -2.77157354783216e+00 , 3.87479723188297e+00 , 2.91514834348317e+00 ), ( -3.82733991171425e+00 , 4.47321707177170e+00 , 2.82464889913065e+00 ), ( -2.60563833123193e+00 , 2.65265449319031e+00 , 2.44344010564801e+00 ), ( -3.74144641201036e+00 , 1.85357458698069e+00 , 2.01675445782806e+00 ), ( -3.41165642068151e+00 , 8.70813218294187e-01 , 9.16959236491071e-01 ), ( -4.31044435731333e+00 , 1.06500473684454e+00 , 3.24302990936214e+00 ), ( -5.52380553228657e+00 , 8.61315661384654e-01 , 3.32945844168612e+00 ), ( -3.40574236242845e+00 , 6.72342519459051e-01 , 4.15777520505137e+00 ), ( -3.74911277543839e+00 , 4.06956805094106e-02 , 5.45709004439605e+00 ), ( -2.38282299687553e+00 , -3.23399386002607e-01 , 6.17040458948034e+00 ), ( -4.47258552805660e+00 , 1.00088178449150e+00 , 6.43940071021629e+00 ), ( -5.33724838402981e+00 , 6.07253695391686e-01 , 7.20391804672296e+00 ), ( -6.24838121141889e+00 , 3.57550015605705e+00 , 6.71223354327823e+00 ), ( -6.93264006079421e+00 , 4.29628442025119e+00 , 7.44616335288087e+00 ), ( -6.74935856072400e+00 , 3.20178040778415e+00 , 5.52156016554329e+00 ), ( -4.12513552072745e+00 , 2.27807008788324e+00 , 6.45708129476173e+00 ), ( -4.84122820244433e+00 , 3.19240161416128e+00 , 7.21801211044439e+00 ), ( -4.10372836840617e+00 , 4.58305518886815e+00 , 7.29506732137016e+00 ) } +colvars: Step 14, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.15064599275101e-01 , 3.88700842418579e-03 , 9.49062268478276e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 7.05429385254313e+00 , -2.03733971095845e+00 , -9.61939487520703e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 , 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 7.09587417768813e+00 , -3.48673267580415e-01 , 4.28480410351882e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 , 5.86486454274355e+00 , 2.24797767579896e+00 , 2.99815671646628e+00 , 5.22493545201210e+00 , 3.58991729210236e+00 , 2.90473741736489e+00 , 6.33092192081317e+00 , 4.52116236648895e+00 , 2.41927485778368e+00 , 3.90776010512297e+00 , 3.73584825978615e+00 , 2.03591493688509e+00 , 2.82332465249931e+00 , 4.13991068119476e+00 , 2.51583104327529e+00 , 3.89451144592941e+00 , 3.24144516682814e+00 , 7.40179485370264e-01 , 2.65844106989744e+00 , 3.05350593383516e+00 , -1.08488981331887e-01 , 3.03278747309343e+00 , 2.72268879368398e+00 , -1.54821987670355e+00 , 1.57526439270054e+00 , 2.19446358993994e+00 , 5.10294119197168e-01 , 4.21210277979123e-01 , 2.52304701718955e+00 , 5.28146554175524e-01 , 1.99863625271151e+00 , 1.00572236418968e+00 , 1.07723828604057e+00 , 1.18201227767348e+00 , 8.57044788501173e-02 , 1.69220053554445e+00 , 2.02644354157259e+00 , -1.13299047266892e+00 , 2.00645171537107e+00 , 5.51945150516580e-01 , 6.08708404493696e-01 , 2.93013538978696e+00 , -6.39308246883680e-01 , 3.51274880191373e-01 , 3.16869445588155e+00 , 1.32668812244549e+00 , 1.34352515560620e+00 , 3.82671742359831e+00 , 8.58767606428859e-01 , 1.95434757556696e+00 , 5.03241999566417e+00 , 2.03402657414422e+00 , 2.63307566831980e+00 , 5.64415447011505e+00 , -3.46157050289023e-01 , 2.91655892147137e+00 , 4.97220637353131e+00 , -1.15608468363693e+00 , 3.05290417480726e+00 , 5.90192658127788e+00 , -4.77921309709439e-01 , 3.60388884533245e+00 , 3.84668343251162e+00 , -1.49968243814569e+00 , 4.54905744339707e+00 , 3.50490478092210e+00 , -7.17716458963084e-01 , 5.40273226525777e+00 , 2.44572191675940e+00 , -2.77157354783216e+00 , 3.87479723188297e+00 , 2.91514834348317e+00 , -3.82733991171425e+00 , 4.47321707177170e+00 , 2.82464889913065e+00 , -2.60563833123193e+00 , 2.65265449319031e+00 , 2.44344010564801e+00 , -3.74144641201036e+00 , 1.85357458698069e+00 , 2.01675445782806e+00 , -3.41165642068151e+00 , 8.70813218294187e-01 , 9.16959236491071e-01 , -4.31044435731333e+00 , 1.06500473684454e+00 , 3.24302990936214e+00 , -5.52380553228657e+00 , 8.61315661384654e-01 , 3.32945844168612e+00 , -3.40574236242845e+00 , 6.72342519459051e-01 , 4.15777520505137e+00 , -3.74911277543839e+00 , 4.06956805094106e-02 , 5.45709004439605e+00 , -2.38282299687553e+00 , -3.23399386002607e-01 , 6.17040458948034e+00 , -4.47258552805660e+00 , 1.00088178449150e+00 , 6.43940071021629e+00 , -5.33724838402981e+00 , 6.07253695391686e-01 , 7.20391804672296e+00 , -6.24838121141889e+00 , 3.57550015605705e+00 , 6.71223354327823e+00 , -6.93264006079421e+00 , 4.29628442025119e+00 , 7.44616335288087e+00 , -6.74935856072400e+00 , 3.20178040778415e+00 , 5.52156016554329e+00 , -4.12513552072745e+00 , 2.27807008788324e+00 , 6.45708129476173e+00 , -4.84122820244433e+00 , 3.19240161416128e+00 , 7.21801211044439e+00 , -4.10372836840617e+00 , 4.58305518886815e+00 , 7.29506732137016e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.15064599275101e-01 , 3.88700842418579e-03 , 9.49062268478276e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.31765332420999e+00 , 4.27481212181510e-02 , -7.65484553946056e-01 , 6.98238250019389e+00 , -5.44071667342557e-01 , -6.17156972011467e-01 , 7.05429385254313e+00 , -2.03733971095845e+00 , -9.61939487520703e-01 , 6.18040482097983e+00 , -3.24480798925024e-01 , 6.97400500598580e-01 , 4.97701153735991e+00 , -1.85956956378352e-01 , 7.03938590732581e-01 , 6.89409368595230e+00 , -2.64314180409713e-01 , 1.86701189801053e+00 , 6.18755853833973e+00 , -1.26974905877546e-01 , 3.18221815415460e+00 , 7.09587417768813e+00 , -3.48673267580415e-01 , 4.28480410351882e+00 , 5.29047084423862e+00 , 1.11045275712342e+00 , 3.32911873296211e+00 , 4.13915055187918e+00 , 1.04076082667140e+00 , 3.65679841554952e+00 , 5.86486454274355e+00 , 2.24797767579896e+00 , 2.99815671646628e+00 , 5.22493545201210e+00 , 3.58991729210236e+00 , 2.90473741736489e+00 , 6.33092192081317e+00 , 4.52116236648895e+00 , 2.41927485778368e+00 , 3.90776010512297e+00 , 3.73584825978615e+00 , 2.03591493688509e+00 , 2.82332465249931e+00 , 4.13991068119476e+00 , 2.51583104327529e+00 , 3.89451144592941e+00 , 3.24144516682814e+00 , 7.40179485370264e-01 , 2.65844106989744e+00 , 3.05350593383516e+00 , -1.08488981331887e-01 , 3.03278747309343e+00 , 2.72268879368398e+00 , -1.54821987670355e+00 , 1.57526439270054e+00 , 2.19446358993994e+00 , 5.10294119197168e-01 , 4.21210277979123e-01 , 2.52304701718955e+00 , 5.28146554175524e-01 , 1.99863625271151e+00 , 1.00572236418968e+00 , 1.07723828604057e+00 , 1.18201227767348e+00 , 8.57044788501173e-02 , 1.69220053554445e+00 , 2.02644354157259e+00 , -1.13299047266892e+00 , 2.00645171537107e+00 , 5.51945150516580e-01 , 6.08708404493696e-01 , 2.93013538978696e+00 , -6.39308246883680e-01 , 3.51274880191373e-01 , 3.16869445588155e+00 , 1.32668812244549e+00 , 1.34352515560620e+00 , 3.82671742359831e+00 , 8.58767606428859e-01 , 1.95434757556696e+00 , 5.03241999566417e+00 , 2.03402657414422e+00 , 2.63307566831980e+00 , 5.64415447011505e+00 , -3.46157050289023e-01 , 2.91655892147137e+00 , 4.97220637353131e+00 , -1.15608468363693e+00 , 3.05290417480726e+00 , 5.90192658127788e+00 , -4.77921309709439e-01 , 3.60388884533245e+00 , 3.84668343251162e+00 , -1.49968243814569e+00 , 4.54905744339707e+00 , 3.50490478092210e+00 , -7.17716458963084e-01 , 5.40273226525777e+00 , 2.44572191675940e+00 , -2.77157354783216e+00 , 3.87479723188297e+00 , 2.91514834348317e+00 , -3.82733991171425e+00 , 4.47321707177170e+00 , 2.82464889913065e+00 , -2.60563833123193e+00 , 2.65265449319031e+00 , 2.44344010564801e+00 , -3.74144641201036e+00 , 1.85357458698069e+00 , 2.01675445782806e+00 , -3.41165642068151e+00 , 8.70813218294187e-01 , 9.16959236491071e-01 , -4.31044435731333e+00 , 1.06500473684454e+00 , 3.24302990936214e+00 , -5.52380553228657e+00 , 8.61315661384654e-01 , 3.32945844168612e+00 , -3.40574236242845e+00 , 6.72342519459051e-01 , 4.15777520505137e+00 , -3.74911277543839e+00 , 4.06956805094106e-02 , 5.45709004439605e+00 , -2.38282299687553e+00 , -3.23399386002607e-01 , 6.17040458948034e+00 , -4.47258552805660e+00 , 1.00088178449150e+00 , 6.43940071021629e+00 , -5.33724838402981e+00 , 6.07253695391686e-01 , 7.20391804672296e+00 , -6.24838121141889e+00 , 3.57550015605705e+00 , 6.71223354327823e+00 , -6.93264006079421e+00 , 4.29628442025119e+00 , 7.44616335288087e+00 , -6.74935856072400e+00 , 3.20178040778415e+00 , 5.52156016554329e+00 , -4.12513552072745e+00 , 2.27807008788324e+00 , 6.45708129476173e+00 , -4.84122820244433e+00 , 3.19240161416128e+00 , 7.21801211044439e+00 , -4.10372836840617e+00 , 4.58305518886815e+00 , 7.29506732137016e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.5823 , 6.65823 , 13.3165 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.5823 , 6.65823 , 13.3165 ) to colvar "one". +colvars: Adding total bias energy: 57.3219 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.5823 , 6.65823 , 13.3165 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17951 , -0.577094 , -1.58552 ) +colvars: ( -4.44143 , -0.494858 , -1.35958 ) +colvars: ( -4.44143 , -0.494858 , -1.35958 ) +colvars: ( -5.91612 , -0.659165 , -1.811 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.949101 , 0.206161 , 0.666297 ) +colvars: ( 0.821447 , 0.281457 , 0.692669 ) +colvars: ( 0.805171 , 0.273966 , 0.673017 ) +colvars: ( 0.701654 , 0.282736 , 0.623993 ) +colvars: ( 0.688957 , 0.212312 , 0.521702 ) +colvars: ( 0.608953 , 0.36487 , 0.680115 ) +colvars: ( 0.494037 , 0.380158 , 0.633169 ) +colvars: ( 0.411895 , 0.483418 , 0.723944 ) +colvars: ( 0.407164 , 0.3332 , 0.518885 ) +colvars: ( 0.369738 , 0.289383 , 0.437888 ) +colvars: ( 0.376509 , 0.33872 , 0.508304 ) +colvars: ( 0.30087 , 0.293491 , 0.402949 ) +colvars: ( 0.272622 , 0.324109 , 0.427578 ) +colvars: ( 0.367734 , 0.189701 , 0.302483 ) +colvars: ( 0.305038 , 0.144047 , 0.204161 ) +colvars: ( 0.499001 , 0.150052 , 0.326234 ) +colvars: ( 0.576622 , 0.0530556 , 0.241236 ) +colvars: ( 0.715306 , 0.0303374 , 0.292145 ) +colvars: ( 0.585136 , 0.0195142 , 0.201074 ) +colvars: ( 0.568308 , -0.049302 , 0.0985199 ) +colvars: ( 0.606881 , 0.0703363 , 0.282289 ) +colvars: ( 0.604586 , 0.0534159 , 0.258156 ) +colvars: ( 0.643099 , 0.121959 , 0.373085 ) +colvars: ( 0.471571 , 0.0586073 , 0.186978 ) +colvars: ( 0.464052 , -0.000511152 , 0.102952 ) +colvars: ( 0.362775 , 0.128388 , 0.217006 ) +colvars: ( 0.229669 , 0.137901 , 0.151594 ) +colvars: ( 0.13209 , 0.22893 , 0.216827 ) +colvars: ( 0.199955 , 0.0598229 , 0.0289948 ) +colvars: ( 0.14709 , 0.0217562 , -0.053331 ) +colvars: ( 0.236494 , 0.0324794 , 0.0136481 ) +colvars: ( 0.221967 , -0.0443413 , -0.0983329 ) +colvars: ( 0.260385 , -0.0481855 , -0.0809328 ) +colvars: ( 0.302165 , -0.135512 , -0.173971 ) +colvars: ( 0.255213 , -0.19161 , -0.277103 ) +colvars: ( 0.424983 , -0.15171 , -0.123607 ) +colvars: ( 0.507479 , -0.2318 , -0.182973 ) +colvars: ( 0.647514 , -0.234925 , -0.104887 ) +colvars: ( 0.456317 , -0.23623 , -0.219004 ) +colvars: ( 0.462135 , -0.308273 , -0.312596 ) +colvars: ( 0.403777 , -0.158353 , -0.145014 ) +colvars: ( 0.345221 , -0.151398 , -0.17006 ) +colvars: ( 0.327105 , -0.059459 , -0.0569043 ) +colvars: ( 0.2136 , -0.160341 , -0.259451 ) +colvars: ( 0.187219 , -0.204648 , -0.334616 ) +colvars: ( -0.000349529 , -0.208422 , -0.449926 ) +colvars: ( -0.0974344 , -0.226991 , -0.531985 ) +colvars: ( 0.107237 , -0.26168 , -0.458417 ) +colvars: ( 0.126636 , -0.11721 , -0.252479 ) +colvars: ( -0.000692436 , -0.121505 , -0.333088 ) +colvars: ( -0.0955107 , -0.0359033 , -0.273542 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17951 , 0.577094 , 1.58552 ) +colvars: ( 4.44143 , 0.494858 , 1.35958 ) +colvars: ( 4.44143 , 0.494858 , 1.35958 ) +colvars: ( 5.91612 , 0.659165 , 1.811 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.655297 , -0.0853211 , -0.401835 ) +colvars: ( -0.588743 , -0.172177 , -0.370783 ) +colvars: ( -0.537659 , -0.149185 , -0.309994 ) +colvars: ( -0.545678 , -0.201188 , -0.339484 ) +colvars: ( -0.535531 , -0.139589 , -0.303901 ) +colvars: ( -0.518063 , -0.297699 , -0.351524 ) +colvars: ( -0.481732 , -0.340143 , -0.332526 ) +colvars: ( -0.457511 , -0.452636 , -0.354564 ) +colvars: ( -0.415371 , -0.30331 , -0.250686 ) +colvars: ( -0.40975 , -0.276899 , -0.234153 ) +colvars: ( -0.364396 , -0.297487 , -0.197082 ) +colvars: ( -0.300897 , -0.259037 , -0.11745 ) +colvars: ( -0.250693 , -0.27473 , -0.0734898 ) +colvars: ( -0.322469 , -0.150902 , -0.0945471 ) +colvars: ( -0.289003 , -0.120387 , -0.048354 ) +colvars: ( -0.381267 , -0.0905823 , -0.128746 ) +colvars: ( -0.410433 , 0.0124063 , -0.115593 ) +colvars: ( -0.465207 , 0.0625162 , -0.149958 ) +colvars: ( -0.448873 , 0.0281663 , -0.147709 ) +colvars: ( -0.436838 , 0.0875673 , -0.111136 ) +colvars: ( -0.49429 , -0.0283346 , -0.216618 ) +colvars: ( -0.529091 , -0.0298488 , -0.252199 ) +colvars: ( -0.580894 , -0.0982238 , -0.332417 ) +colvars: ( -0.472613 , -0.0615233 , -0.208524 ) +colvars: ( -0.479351 , -0.0153838 , -0.196274 ) +colvars: ( -0.413738 , -0.139531 , -0.181539 ) +colvars: ( -0.351676 , -0.172558 , -0.132811 ) +colvars: ( -0.297899 , -0.267155 , -0.117785 ) +colvars: ( -0.308991 , -0.096388 , -0.0585392 ) +colvars: ( -0.294145 , -0.077 , -0.0356353 ) +colvars: ( -0.28979 , -0.0493597 , -0.019868 ) +colvars: ( -0.25344 , 0.0288471 , 0.0488806 ) +colvars: ( -0.232843 , 0.0565264 , 0.0809789 ) +colvars: ( -0.300274 , 0.119833 , 0.0393395 ) +colvars: ( -0.271933 , 0.163456 , 0.0857883 ) +colvars: ( -0.373953 , 0.149526 , -0.0224313 ) +colvars: ( -0.425687 , 0.229464 , -0.0414481 ) +colvars: ( -0.501675 , 0.253374 , -0.107921 ) +colvars: ( -0.436058 , 0.208628 , -0.0604538 ) +colvars: ( -0.440758 , 0.27231 , -0.0389264 ) +colvars: ( -0.439245 , 0.117917 , -0.101044 ) +colvars: ( -0.444884 , 0.0862516 , -0.119761 ) +colvars: ( -0.466291 , -0.011446 , -0.181533 ) +colvars: ( -0.373606 , 0.074184 , -0.0531369 ) +colvars: ( -0.376239 , 0.101686 , -0.0444456 ) +colvars: ( -0.204314 , 0.107965 , 0.130837 ) +colvars: ( -0.151506 , 0.10972 , 0.184606 ) +colvars: ( -0.234183 , 0.183874 , 0.132123 ) +colvars: ( -0.307785 , 0.0313461 , -0.004678 ) +colvars: ( -0.236593 , 0.0168307 , 0.0608499 ) +colvars: ( -0.179337 , -0.0703459 , 0.0824296 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 14. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 14. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atoms_new_colvar_forces = { ( -4.88570851171614e+00 , -4.56253773604222e-01 , -1.32105352356695e+00 ), ( -4.20872734720022e+00 , -3.85577613582362e-01 , -1.03769308681141e+00 ), ( -4.28545554283310e+00 , -4.13310422094279e-01 , -1.07506981499262e+00 ), ( -5.76268914269491e+00 , -5.86441559791649e-01 , -1.59319752412968e+00 ), ( 2.67512102221459e-01 , 1.24780358318433e-01 , 3.63022771990672e-01 ), ( 5.27040311425189e+00 , 6.44265037876371e-01 , 1.91410551223546e+00 ), ( 4.45373613235302e+00 , 5.34872338551382e-01 , 1.66022158070880e+00 ), ( -4.56162545283365e-02 , 3.07822880510977e-02 , 3.69379816749984e-01 ), ( 4.43322433359100e+00 , 5.24748477029104e-01 , 1.62777876693457e+00 ), ( 5.87610342295328e+00 , 6.71648743826014e-01 , 2.01473368668632e+00 ), ( 1.21129363114962e-02 , 4.12332214763805e-02 , 3.11221341098453e-01 ), ( -2.72594888404143e-05 , 3.44541115508831e-02 , 2.85498488619319e-01 ), ( 2.19292006304853e-02 , 4.93784141234822e-02 , 3.54087834954247e-01 ), ( 4.52656312081194e-02 , 3.87990197041604e-02 , 2.07935621960817e-01 ), ( 1.60341902337049e-02 , 2.36600144308958e-02 , 1.55807321364653e-01 ), ( 1.17734207293443e-01 , 5.94698107445170e-02 , 1.97487731813883e-01 ), ( 1.66188600935006e-01 , 6.54618221384618e-02 , 1.25643584368926e-01 ), ( 2.50099248022815e-01 , 9.28535899253148e-02 , 1.42187278413497e-01 ), ( 1.36263108376236e-01 , 4.76805032052302e-02 , 5.33655307421763e-02 ), ( 1.31470207380580e-01 , 3.82653253584018e-02 , -1.26164721125454e-02 ), ( 1.12591132066163e-01 , 4.20016978708232e-02 , 6.56702954911367e-02 ), ( 7.54957736633364e-02 , 2.35671232324818e-02 , 5.95661542695908e-03 ), ( 6.22051143747376e-02 , 2.37348216717266e-02 , 4.06680244553650e-02 ), ( -1.04156663180405e-03 , -2.91602931812204e-03 , -2.15460267798273e-02 ), ( -1.52988657110378e-02 , -1.58949153969860e-02 , -9.33220667363659e-02 ), ( -5.09636443969827e-02 , -1.11423999111707e-02 , 3.54676473714911e-02 ), ( -1.22007129997978e-01 , -3.46571012622777e-02 , 1.87826057448190e-02 ), ( -1.65809356973343e-01 , -3.82253925041095e-02 , 9.90418747629360e-02 ), ( -1.09036292463458e-01 , -3.65651253925265e-02 , -2.95444296338051e-02 ), ( -1.47054589715852e-01 , -5.52437965616422e-02 , -8.89663143807316e-02 ), ( -5.32957551050355e-02 , -1.68802731208616e-02 , -6.21990813741620e-03 ), ( -3.14722294827953e-02 , -1.54941403179506e-02 , -4.94522956387948e-02 ), ( 2.75421871166536e-02 , 8.34095154176619e-03 , 4.60709069004805e-05 ), ( 1.89129609959227e-03 , -1.56789060797776e-02 , -1.34631476306283e-01 ), ( -1.67201223624295e-02 , -2.81536860558904e-02 , -1.91314740817814e-01 ), ( 5.10303260942475e-02 , -2.18429606248802e-03 , -1.46037931519005e-01 ), ( 8.17918095188016e-02 , -2.33621650666099e-03 , -2.24421210018944e-01 ), ( 1.45839520074683e-01 , 1.84490934142702e-02 , -2.12807721141153e-01 ), ( 2.02590891265704e-02 , -2.76019791361587e-02 , -2.79457910987898e-01 ), ( 2.13762196086749e-02 , -3.59627343913501e-02 , -3.51522240654599e-01 ), ( -3.54680361374518e-02 , -4.04356042436027e-02 , -2.46058050575770e-01 ), ( -9.96636026791784e-02 , -6.51464009076693e-02 , -2.89820968951444e-01 ), ( -1.39186349422021e-01 , -7.09050939470902e-02 , -2.38437216008359e-01 ), ( -1.60005755834681e-01 , -8.61565706229697e-02 , -3.12587792726267e-01 ), ( -1.89019516974402e-01 , -1.02961385390356e-01 , -3.79062016598802e-01 ), ( -2.04663798434532e-01 , -1.00456653359914e-01 , -3.19088822976699e-01 ), ( -2.48939950746201e-01 , -1.17271305621107e-01 , -3.47378913111159e-01 ), ( -1.26946357370064e-01 , -7.78059529956875e-02 , -3.26294311463582e-01 ), ( -1.81148646425748e-01 , -8.58642323381825e-02 , -2.57156829928261e-01 ), ( -2.37285425767131e-01 , -1.04673994747542e-01 , -2.72238343238541e-01 ), ( -2.74847852412318e-01 , -1.06249208776591e-01 , -1.91112042856661e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 15, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 15, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 15, atoms_positions[size = 51] = { ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 ), ( 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 ), ( 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 ), ( 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 ), ( 7.05473892361697e+00 , -2.03978069585531e+00 , -9.56696656116159e-01 ), ( 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 ), ( 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 ), ( 7.08982096830755e+00 , -3.51166956940753e-01 , 4.28741001920924e+00 ), ( 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 ), ( 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 ), ( 5.86122840089223e+00 , 2.24694565302836e+00 , 2.99780509390531e+00 ), ( 5.22908745139920e+00 , 3.58804864345765e+00 , 2.90872115379629e+00 ), ( 6.32898826127183e+00 , 4.51552495482869e+00 , 2.41157873756936e+00 ), ( 3.90515470301220e+00 , 3.73248962779382e+00 , 2.03810827469954e+00 ), ( 2.81540114626890e+00 , 4.14385783489665e+00 , 2.51158474333925e+00 ), ( 3.90427408855215e+00 , 3.24191332378665e+00 , 7.37705952617010e-01 ), ( 2.65549606729918e+00 , 3.04134331251243e+00 , -1.08677222532784e-01 ), ( 3.03374418258581e+00 , 2.72186464645366e+00 , -1.53959171143427e+00 ), ( 1.57968791847728e+00 , 2.19657951904758e+00 , 4.97326997898410e-01 ), ( 4.13736379675307e-01 , 2.53301933374089e+00 , 5.25518331164459e-01 ), ( 2.00637403029016e+00 , 1.01094458268083e+00 , 1.07907903832468e+00 ), ( 1.18101528704331e+00 , 9.45136804738401e-02 , 1.69233228752184e+00 ), ( 2.02882813167391e+00 , -1.12732424294064e+00 , 2.00575221268911e+00 ), ( 5.53896090649999e-01 , 6.08271107573916e-01 , 2.92842091817883e+00 ), ( -6.33075809288131e-01 , 3.50412805654254e-01 , 3.16722686530329e+00 ), ( 1.32664395338748e+00 , 1.34466383120341e+00 , 3.82050202372060e+00 ), ( 8.56900020281219e-01 , 1.95945966251021e+00 , 5.02994153920588e+00 ), ( 2.03888961235672e+00 , 2.64114884413221e+00 , 5.64944655306628e+00 ), ( -3.43476150263057e-01 , 2.91644234646218e+00 , 4.97050093225404e+00 ), ( -1.15339178958262e+00 , 3.05499745666966e+00 , 5.90016689498669e+00 ), ( -4.84163074687500e-01 , 3.59060214801384e+00 , 3.84752234703474e+00 ), ( -1.50370391596201e+00 , 4.54804841951908e+00 , 3.49533660645804e+00 ), ( -7.13302044273382e-01 , 5.40474294273752e+00 , 2.44968501069186e+00 ), ( -2.77242998921563e+00 , 3.87392423478275e+00 , 2.91279805481020e+00 ), ( -3.82494033075986e+00 , 4.47946128165195e+00 , 2.82242534232936e+00 ), ( -2.60761860638666e+00 , 2.65976206398845e+00 , 2.43691711549907e+00 ), ( -3.74754034078466e+00 , 1.84164235626245e+00 , 2.01148186853148e+00 ), ( -3.40872433891289e+00 , 8.75986337224676e-01 , 9.08870838393818e-01 ), ( -4.31570343382940e+00 , 1.06527902394077e+00 , 3.23811722831961e+00 ), ( -5.51904595554738e+00 , 8.54379198401675e-01 , 3.32877288881578e+00 ), ( -3.39789087362984e+00 , 6.75544372858960e-01 , 4.16646799533518e+00 ), ( -3.74083287107551e+00 , 3.74649832889368e-02 , 5.45074936620928e+00 ), ( -2.38337571287417e+00 , -3.19020711104221e-01 , 6.17196940319086e+00 ), ( -4.47088777474719e+00 , 1.00204341019923e+00 , 6.44114945541213e+00 ), ( -5.34102035078252e+00 , 6.06039466412292e-01 , 7.20680167942385e+00 ), ( -6.24192748330466e+00 , 3.57947773859450e+00 , 6.71469633163971e+00 ), ( -6.93770493403295e+00 , 4.29699569742557e+00 , 7.45145361667983e+00 ), ( -6.75095708241872e+00 , 3.19935601312637e+00 , 5.51977222423106e+00 ), ( -4.12776835616795e+00 , 2.27137817021339e+00 , 6.44930464900907e+00 ), ( -4.83338156729211e+00 , 3.19114462708207e+00 , 7.22074730215993e+00 ), ( -4.10488051315969e+00 , 4.58647369597667e+00 , 7.29453646157747e+00 ) } +colvars: Step 15, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.12760327150548e-01 , 3.49835932914566e-03 , 9.49825636231559e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 7.05473892361697e+00 , -2.03978069585531e+00 , -9.56696656116159e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 , 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 7.08982096830755e+00 , -3.51166956940753e-01 , 4.28741001920924e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 , 5.86122840089223e+00 , 2.24694565302836e+00 , 2.99780509390531e+00 , 5.22908745139920e+00 , 3.58804864345765e+00 , 2.90872115379629e+00 , 6.32898826127183e+00 , 4.51552495482869e+00 , 2.41157873756936e+00 , 3.90515470301220e+00 , 3.73248962779382e+00 , 2.03810827469954e+00 , 2.81540114626890e+00 , 4.14385783489665e+00 , 2.51158474333925e+00 , 3.90427408855215e+00 , 3.24191332378665e+00 , 7.37705952617010e-01 , 2.65549606729918e+00 , 3.04134331251243e+00 , -1.08677222532784e-01 , 3.03374418258581e+00 , 2.72186464645366e+00 , -1.53959171143427e+00 , 1.57968791847728e+00 , 2.19657951904758e+00 , 4.97326997898410e-01 , 4.13736379675307e-01 , 2.53301933374089e+00 , 5.25518331164459e-01 , 2.00637403029016e+00 , 1.01094458268083e+00 , 1.07907903832468e+00 , 1.18101528704331e+00 , 9.45136804738401e-02 , 1.69233228752184e+00 , 2.02882813167391e+00 , -1.12732424294064e+00 , 2.00575221268911e+00 , 5.53896090649999e-01 , 6.08271107573916e-01 , 2.92842091817883e+00 , -6.33075809288131e-01 , 3.50412805654254e-01 , 3.16722686530329e+00 , 1.32664395338748e+00 , 1.34466383120341e+00 , 3.82050202372060e+00 , 8.56900020281219e-01 , 1.95945966251021e+00 , 5.02994153920588e+00 , 2.03888961235672e+00 , 2.64114884413221e+00 , 5.64944655306628e+00 , -3.43476150263057e-01 , 2.91644234646218e+00 , 4.97050093225404e+00 , -1.15339178958262e+00 , 3.05499745666966e+00 , 5.90016689498669e+00 , -4.84163074687500e-01 , 3.59060214801384e+00 , 3.84752234703474e+00 , -1.50370391596201e+00 , 4.54804841951908e+00 , 3.49533660645804e+00 , -7.13302044273382e-01 , 5.40474294273752e+00 , 2.44968501069186e+00 , -2.77242998921563e+00 , 3.87392423478275e+00 , 2.91279805481020e+00 , -3.82494033075986e+00 , 4.47946128165195e+00 , 2.82242534232936e+00 , -2.60761860638666e+00 , 2.65976206398845e+00 , 2.43691711549907e+00 , -3.74754034078466e+00 , 1.84164235626245e+00 , 2.01148186853148e+00 , -3.40872433891289e+00 , 8.75986337224676e-01 , 9.08870838393818e-01 , -4.31570343382940e+00 , 1.06527902394077e+00 , 3.23811722831961e+00 , -5.51904595554738e+00 , 8.54379198401675e-01 , 3.32877288881578e+00 , -3.39789087362984e+00 , 6.75544372858960e-01 , 4.16646799533518e+00 , -3.74083287107551e+00 , 3.74649832889368e-02 , 5.45074936620928e+00 , -2.38337571287417e+00 , -3.19020711104221e-01 , 6.17196940319086e+00 , -4.47088777474719e+00 , 1.00204341019923e+00 , 6.44114945541213e+00 , -5.34102035078252e+00 , 6.06039466412292e-01 , 7.20680167942385e+00 , -6.24192748330466e+00 , 3.57947773859450e+00 , 6.71469633163971e+00 , -6.93770493403295e+00 , 4.29699569742557e+00 , 7.45145361667983e+00 , -6.75095708241872e+00 , 3.19935601312637e+00 , 5.51977222423106e+00 , -4.12776835616795e+00 , 2.27137817021339e+00 , 6.44930464900907e+00 , -4.83338156729211e+00 , 3.19114462708207e+00 , 7.22074730215993e+00 , -4.10488051315969e+00 , 4.58647369597667e+00 , 7.29453646157747e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.12760327150548e-01 , 3.49835932914566e-03 , 9.49825636231559e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.31090685983303e+00 , 4.22720758119583e-02 , -7.64532499164663e-01 , 6.97763866184435e+00 , -5.46188078036356e-01 , -6.11741794555155e-01 , 7.05473892361697e+00 , -2.03978069585531e+00 , -9.56696656116159e-01 , 6.17096437238088e+00 , -3.33707243507338e-01 , 7.01461796571725e-01 , 4.97447222365494e+00 , -1.82358799466446e-01 , 7.07567436948592e-01 , 6.89068369846962e+00 , -2.63580043786017e-01 , 1.87313810722543e+00 , 6.18774462217059e+00 , -1.31280791613858e-01 , 3.19031282476682e+00 , 7.08982096830755e+00 , -3.51166956940753e-01 , 4.28741001920924e+00 , 5.29319119118013e+00 , 1.10896102544117e+00 , 3.33325867409280e+00 , 4.14443370209072e+00 , 1.03795554149972e+00 , 3.66193082527524e+00 , 5.86122840089223e+00 , 2.24694565302836e+00 , 2.99780509390531e+00 , 5.22908745139920e+00 , 3.58804864345765e+00 , 2.90872115379629e+00 , 6.32898826127183e+00 , 4.51552495482869e+00 , 2.41157873756936e+00 , 3.90515470301220e+00 , 3.73248962779382e+00 , 2.03810827469954e+00 , 2.81540114626890e+00 , 4.14385783489665e+00 , 2.51158474333925e+00 , 3.90427408855215e+00 , 3.24191332378665e+00 , 7.37705952617010e-01 , 2.65549606729918e+00 , 3.04134331251243e+00 , -1.08677222532784e-01 , 3.03374418258581e+00 , 2.72186464645366e+00 , -1.53959171143427e+00 , 1.57968791847728e+00 , 2.19657951904758e+00 , 4.97326997898410e-01 , 4.13736379675307e-01 , 2.53301933374089e+00 , 5.25518331164459e-01 , 2.00637403029016e+00 , 1.01094458268083e+00 , 1.07907903832468e+00 , 1.18101528704331e+00 , 9.45136804738401e-02 , 1.69233228752184e+00 , 2.02882813167391e+00 , -1.12732424294064e+00 , 2.00575221268911e+00 , 5.53896090649999e-01 , 6.08271107573916e-01 , 2.92842091817883e+00 , -6.33075809288131e-01 , 3.50412805654254e-01 , 3.16722686530329e+00 , 1.32664395338748e+00 , 1.34466383120341e+00 , 3.82050202372060e+00 , 8.56900020281219e-01 , 1.95945966251021e+00 , 5.02994153920588e+00 , 2.03888961235672e+00 , 2.64114884413221e+00 , 5.64944655306628e+00 , -3.43476150263057e-01 , 2.91644234646218e+00 , 4.97050093225404e+00 , -1.15339178958262e+00 , 3.05499745666966e+00 , 5.90016689498669e+00 , -4.84163074687500e-01 , 3.59060214801384e+00 , 3.84752234703474e+00 , -1.50370391596201e+00 , 4.54804841951908e+00 , 3.49533660645804e+00 , -7.13302044273382e-01 , 5.40474294273752e+00 , 2.44968501069186e+00 , -2.77242998921563e+00 , 3.87392423478275e+00 , 2.91279805481020e+00 , -3.82494033075986e+00 , 4.47946128165195e+00 , 2.82242534232936e+00 , -2.60761860638666e+00 , 2.65976206398845e+00 , 2.43691711549907e+00 , -3.74754034078466e+00 , 1.84164235626245e+00 , 2.01148186853148e+00 , -3.40872433891289e+00 , 8.75986337224676e-01 , 9.08870838393818e-01 , -4.31570343382940e+00 , 1.06527902394077e+00 , 3.23811722831961e+00 , -5.51904595554738e+00 , 8.54379198401675e-01 , 3.32877288881578e+00 , -3.39789087362984e+00 , 6.75544372858960e-01 , 4.16646799533518e+00 , -3.74083287107551e+00 , 3.74649832889368e-02 , 5.45074936620928e+00 , -2.38337571287417e+00 , -3.19020711104221e-01 , 6.17196940319086e+00 , -4.47088777474719e+00 , 1.00204341019923e+00 , 6.44114945541213e+00 , -5.34102035078252e+00 , 6.06039466412292e-01 , 7.20680167942385e+00 , -6.24192748330466e+00 , 3.57947773859450e+00 , 6.71469633163971e+00 , -6.93770493403295e+00 , 4.29699569742557e+00 , 7.45145361667983e+00 , -6.75095708241872e+00 , 3.19935601312637e+00 , 5.51977222423106e+00 , -4.12776835616795e+00 , 2.27137817021339e+00 , 6.44930464900907e+00 , -4.83338156729211e+00 , 3.19114462708207e+00 , 7.22074730215993e+00 , -4.10488051315969e+00 , 4.58647369597667e+00 , 7.29453646157747e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.4696 , 6.64696 , 13.2939 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.4696 , 6.64696 , 13.2939 ) to colvar "one". +colvars: Adding total bias energy: 57.161 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.4696 , 6.64696 , 13.2939 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17602 , -0.573193 , -1.57197 ) +colvars: ( -4.43844 , -0.491513 , -1.34796 ) +colvars: ( -4.43844 , -0.491513 , -1.34796 ) +colvars: ( -5.91212 , -0.65471 , -1.79553 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.946712 , 0.205975 , 0.662886 ) +colvars: ( 0.819508 , 0.281034 , 0.689114 ) +colvars: ( 0.803148 , 0.273617 , 0.669559 ) +colvars: ( 0.700214 , 0.282196 , 0.620725 ) +colvars: ( 0.68756 , 0.211908 , 0.518899 ) +colvars: ( 0.607907 , 0.36407 , 0.676568 ) +colvars: ( 0.493485 , 0.379209 , 0.629809 ) +colvars: ( 0.411689 , 0.482179 , 0.72015 ) +colvars: ( 0.40686 , 0.33232 , 0.516037 ) +colvars: ( 0.369622 , 0.28854 , 0.435399 ) +colvars: ( 0.376195 , 0.337866 , 0.505506 ) +colvars: ( 0.300753 , 0.292714 , 0.400624 ) +colvars: ( 0.272483 , 0.323311 , 0.425143 ) +colvars: ( 0.367344 , 0.189196 , 0.300633 ) +colvars: ( 0.304877 , 0.14359 , 0.202749 ) +colvars: ( 0.49811 , 0.149732 , 0.324302 ) +colvars: ( 0.575424 , 0.0529983 , 0.23971 ) +colvars: ( 0.713552 , 0.0304494 , 0.290417 ) +colvars: ( 0.584028 , 0.0194723 , 0.199725 ) +colvars: ( 0.567259 , -0.0492145 , 0.0976371 ) +colvars: ( 0.605804 , 0.0701527 , 0.280565 ) +colvars: ( 0.603642 , 0.0532042 , 0.256533 ) +colvars: ( 0.642115 , 0.121586 , 0.370937 ) +colvars: ( 0.47115 , 0.0582724 , 0.185652 ) +colvars: ( 0.463702 , -0.000752424 , 0.102007 ) +colvars: ( 0.36273 , 0.127845 , 0.215524 ) +colvars: ( 0.230128 , 0.137235 , 0.150384 ) +colvars: ( 0.13288 , 0.228023 , 0.215301 ) +colvars: ( 0.200439 , 0.0593355 , 0.0283459 ) +colvars: ( 0.147814 , 0.0212863 , -0.0536166 ) +colvars: ( 0.23672 , 0.0321345 , 0.0130851 ) +colvars: ( 0.222158 , -0.0444971 , -0.0983801 ) +colvars: ( 0.260299 , -0.0482397 , -0.0810428 ) +colvars: ( 0.302095 , -0.135441 , -0.173659 ) +colvars: ( 0.255306 , -0.191455 , -0.276327 ) +colvars: ( 0.424505 , -0.151539 , -0.123504 ) +colvars: ( 0.506743 , -0.231429 , -0.182586 ) +colvars: ( 0.646283 , -0.234456 , -0.104831 ) +colvars: ( 0.455892 , -0.235947 , -0.21847 ) +colvars: ( 0.461704 , -0.307847 , -0.311634 ) +colvars: ( 0.403636 , -0.15831 , -0.144835 ) +colvars: ( 0.345413 , -0.15147 , -0.169787 ) +colvars: ( 0.327456 , -0.0597754 , -0.0571584 ) +colvars: ( 0.21426 , -0.160481 , -0.258793 ) +colvars: ( 0.188036 , -0.204746 , -0.333624 ) +colvars: ( 0.00089215 , -0.208518 , -0.448424 ) +colvars: ( -0.0958473 , -0.227114 , -0.530125 ) +colvars: ( 0.108008 , -0.261554 , -0.45685 ) +colvars: ( 0.127535 , -0.117461 , -0.251864 ) +colvars: ( 0.000649719 , -0.121827 , -0.332128 ) +colvars: ( -0.093864 , -0.036446 , -0.272869 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17602 , 0.573193 , 1.57197 ) +colvars: ( 4.43844 , 0.491513 , 1.34796 ) +colvars: ( 4.43844 , 0.491513 , 1.34796 ) +colvars: ( 5.91212 , 0.65471 , 1.79553 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.653392 , -0.0852277 , -0.398852 ) +colvars: ( -0.587189 , -0.171921 , -0.367658 ) +colvars: ( -0.53598 , -0.148981 , -0.306921 ) +colvars: ( -0.544531 , -0.200832 , -0.336597 ) +colvars: ( -0.534404 , -0.139307 , -0.301405 ) +colvars: ( -0.517253 , -0.297169 , -0.3484 ) +colvars: ( -0.481333 , -0.339496 , -0.329558 ) +colvars: ( -0.457412 , -0.451801 , -0.351227 ) +colvars: ( -0.415127 , -0.302686 , -0.248124 ) +colvars: ( -0.409664 , -0.276283 , -0.231901 ) +colvars: ( -0.364096 , -0.296882 , -0.194537 ) +colvars: ( -0.300709 , -0.258465 , -0.11528 ) +colvars: ( -0.250441 , -0.274152 , -0.0711987 ) +colvars: ( -0.322044 , -0.150503 , -0.0927811 ) +colvars: ( -0.288748 , -0.119999 , -0.0469496 ) +colvars: ( -0.380442 , -0.0903201 , -0.126924 ) +colvars: ( -0.40935 , 0.0124993 , -0.114121 ) +colvars: ( -0.463673 , 0.062476 , -0.148324 ) +colvars: ( -0.447902 , 0.0282598 , -0.14641 ) +colvars: ( -0.435901 , 0.0875914 , -0.110229 ) +colvars: ( -0.493396 , -0.028156 , -0.215027 ) +colvars: ( -0.528347 , -0.0296422 , -0.250716 ) +colvars: ( -0.580171 , -0.097926 , -0.330515 ) +colvars: ( -0.472286 , -0.0612122 , -0.207281 ) +colvars: ( -0.479087 , -0.0151197 , -0.19536 ) +colvars: ( -0.413702 , -0.139078 , -0.180145 ) +colvars: ( -0.352035 , -0.172003 , -0.131633 ) +colvars: ( -0.298515 , -0.266443 , -0.116322 ) +colvars: ( -0.309323 , -0.0959344 , -0.0578153 ) +colvars: ( -0.294673 , -0.0765394 , -0.03522 ) +colvars: ( -0.289869 , -0.0490068 , -0.0191979 ) +colvars: ( -0.253443 , 0.0290885 , 0.0491336 ) +colvars: ( -0.232578 , 0.0566887 , 0.0813056 ) +colvars: ( -0.300077 , 0.119931 , 0.0392716 ) +colvars: ( -0.27185 , 0.163517 , 0.0853366 ) +colvars: ( -0.373457 , 0.149541 , -0.0223465 ) +colvars: ( -0.424999 , 0.229351 , -0.0416234 ) +colvars: ( -0.500614 , 0.253174 , -0.107838 ) +colvars: ( -0.435659 , 0.208588 , -0.0607695 ) +colvars: ( -0.44035 , 0.272189 , -0.0396079 ) +colvars: ( -0.439113 , 0.118034 , -0.10107 ) +colvars: ( -0.445057 , 0.086458 , -0.119882 ) +colvars: ( -0.466637 , -0.0110886 , -0.181223 ) +colvars: ( -0.37413 , 0.0744591 , -0.0535623 ) +colvars: ( -0.376901 , 0.10195 , -0.0451618 ) +colvars: ( -0.205196 , 0.108248 , 0.129765 ) +colvars: ( -0.152646 , 0.11004 , 0.183247 ) +colvars: ( -0.234664 , 0.183999 , 0.130996 ) +colvars: ( -0.308466 , 0.031697 , -0.00504002 ) +colvars: ( -0.237605 , 0.0172501 , 0.060217 ) +colvars: ( -0.180579 , -0.0697833 , 0.082061 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 15. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 15. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atoms_new_colvar_forces = { ( -4.88269920507628e+00 , -4.52446296131558e-01 , -1.30793548225431e+00 ), ( -4.20611587681103e+00 , -3.82399893859511e-01 , -1.02650748532271e+00 ), ( -4.28275267144583e+00 , -4.10149646689628e-01 , -1.06383505425101e+00 ), ( -5.75896944246471e+00 , -5.82108338049370e-01 , -1.57803144821227e+00 ), ( 2.67167838331193e-01 , 1.24635912226521e-01 , 3.62637157105136e-01 ), ( 5.26667330554919e+00 , 6.40093984399705e-01 , 1.90013694587171e+00 ), ( 4.45058709416635e+00 , 5.31226649470670e-01 , 1.64821406679998e+00 ), ( -4.57231772146376e-02 , 3.03788119582362e-02 , 3.68923300930360e-01 ), ( 4.43016851438168e+00 , 5.21146462072069e-01 , 1.61587533915400e+00 ), ( 5.87208256040792e+00 , 6.66966037131744e-01 , 1.99902447209852e+00 ), ( 1.20992510865886e-02 , 4.09836572718097e-02 , 3.10968892154521e-01 ), ( 4.41576239948449e-05 , 3.42486843759318e-02 , 2.85344604846735e-01 ), ( 2.20418775550471e-02 , 4.91589889477537e-02 , 3.53944779970346e-01 ), ( 4.53008401131758e-02 , 3.86936503603045e-02 , 2.07851624900147e-01 ), ( 1.61296855682379e-02 , 2.35905015140426e-02 , 1.55799501443613e-01 ), ( 1.17667364997870e-01 , 5.94115147834406e-02 , 1.97377423365764e-01 ), ( 1.66074248252500e-01 , 6.54975790518631e-02 , 1.25589791146712e-01 ), ( 2.49878928883532e-01 , 9.29254155549144e-02 , 1.42092918383800e-01 ), ( 1.36125714727971e-01 , 4.77320975442177e-02 , 5.33151062366599e-02 ), ( 1.31358123360124e-01 , 3.83769537146051e-02 , -1.25918825871648e-02 ), ( 1.12408343580062e-01 , 4.19966431490401e-02 , 6.55378831375178e-02 ), ( 7.52959074036862e-02 , 2.35619297623028e-02 , 5.81652390007492e-03 ), ( 6.19445296609211e-02 , 2.36596463126856e-02 , 4.04222111122794e-02 ), ( -1.13532110248166e-03 , -2.93978045519981e-03 , -2.16291147558315e-02 ), ( -1.53847854912670e-02 , -1.58721287379464e-02 , -9.33535919889726e-02 ), ( -5.09716149404266e-02 , -1.12331166127158e-02 , 3.53790405616591e-02 ), ( -1.21906202655111e-01 , -3.47678772676525e-02 , 1.87508249365284e-02 ), ( -1.65634601266584e-01 , -3.84205550864689e-02 , 9.89794175263195e-02 ), ( -1.08883651419844e-01 , -3.65988996337234e-02 , -2.94694085072222e-02 ), ( -1.46859062817992e-01 , -5.52531677969171e-02 , -8.88365963969102e-02 ), ( -5.31484187072113e-02 , -1.68722510187382e-02 , -6.11277646832457e-03 ), ( -3.12854672664357e-02 , -1.54085590957590e-02 , -4.92465091713178e-02 ), ( 2.77203872094699e-02 , 8.44899722432180e-03 , 2.62789756932502e-04 ), ( 2.01794387650917e-03 , -1.55108290900512e-02 , -1.34387102720003e-01 ), ( -1.65435535450074e-02 , -2.79383755473416e-02 , -1.90990750694173e-01 ), ( 5.10477677815733e-02 , -1.99796019264700e-03 , -1.45850322064685e-01 ), ( 8.17435406255514e-02 , -2.07837568905500e-03 , -2.24209044576675e-01 ), ( 1.45669481857759e-01 , 1.87176896380716e-02 , -2.12669033776203e-01 ), ( 2.02335267984439e-02 , -2.73587912813237e-02 , -2.79239787620972e-01 ), ( 2.13540042872654e-02 , -3.56572232534428e-02 , -3.51241498814213e-01 ), ( -3.54765541163397e-02 , -4.02760621005897e-02 , -2.45905189320064e-01 ), ( -9.96440130627073e-02 , -6.50115381496472e-02 , -2.89668188567758e-01 ), ( -1.39181299517898e-01 , -7.08639356256818e-02 , -2.38381206857471e-01 ), ( -1.59870259209741e-01 , -8.60215496701822e-02 , -3.12355024514433e-01 ), ( -1.88865265737409e-01 , -1.02796285654035e-01 , -3.78785329546590e-01 ), ( -2.04304019274105e-01 , -1.00270408319716e-01 , -3.18658401055721e-01 ), ( -2.48492988643436e-01 , -1.17074441350643e-01 , -3.46878222183423e-01 ), ( -1.26656717155222e-01 , -7.75556009689559e-02 , -3.25853670132928e-01 ), ( -1.80931870289518e-01 , -8.57640870766624e-02 , -2.56903918050239e-01 ), ( -2.36955766172313e-01 , -1.04576569693729e-01 , -2.71910565139110e-01 ), ( -2.74443132683073e-01 , -1.06229262365360e-01 , -1.90808009788618e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 16, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 16, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 16, atoms_positions[size = 51] = { ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 ), ( 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 ), ( 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 ), ( 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 ), ( 7.05466781602202e+00 , -2.04223860168671e+00 , -9.51736464236291e-01 ), ( 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 ), ( 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 ), ( 7.08509320289695e+00 , -3.53142554632854e-01 , 4.29109682955083e+00 ), ( 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 ), ( 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 ), ( 5.85739937943113e+00 , 2.24705372923822e+00 , 2.99693495627931e+00 ), ( 5.23296605450751e+00 , 3.58606110840864e+00 , 2.91247709599507e+00 ), ( 6.32721498626626e+00 , 4.51096054330538e+00 , 2.40323812095780e+00 ), ( 3.90156078362489e+00 , 3.72839123981515e+00 , 2.04006304240512e+00 ), ( 2.80849747987868e+00 , 4.14770815693897e+00 , 2.50716653162687e+00 ), ( 3.91345048213876e+00 , 3.24223237482255e+00 , 7.35704502186487e-01 ), ( 2.65352192938508e+00 , 3.03058219725472e+00 , -1.08478988734758e-01 ), ( 3.03566821421468e+00 , 2.72020402497637e+00 , -1.53184494858950e+00 ), ( 1.58482182237910e+00 , 2.19681594444141e+00 , 4.84874977263818e-01 ), ( 4.05830752628882e-01 , 2.54311622034941e+00 , 5.22818761318913e-01 ), ( 2.01449434615761e+00 , 1.01873319035267e+00 , 1.07968478091619e+00 ), ( 1.17917508255272e+00 , 1.01965607587946e-01 , 1.69272590185043e+00 ), ( 2.03133511102619e+00 , -1.12185634481181e+00 , 2.00557055177542e+00 ), ( 5.55595461399606e-01 , 6.08182757174921e-01 , 2.92855358667179e+00 ), ( -6.26630685382450e-01 , 3.49839117918140e-01 , 3.16579064902669e+00 ), ( 1.32586966564794e+00 , 1.34528872112012e+00 , 3.81291116809697e+00 ), ( 8.54359432097506e-01 , 1.96424557858562e+00 , 5.02807312514457e+00 ), ( 2.04529922472684e+00 , 2.64984360296788e+00 , 5.65531328010371e+00 ), ( -3.41128378670846e-01 , 2.91630064517151e+00 , 4.96912331758290e+00 ), ( -1.15049440600122e+00 , 3.05687835727132e+00 , 5.89809994139646e+00 ), ( -4.90094551484171e-01 , 3.57766459827628e+00 , 3.84829453823356e+00 ), ( -1.50765232127455e+00 , 4.54709892177202e+00 , 3.48508471341254e+00 ), ( -7.09271116590437e-01 , 5.40675620645661e+00 , 2.45329243023343e+00 ), ( -2.77189930799630e+00 , 3.87423248244704e+00 , 2.91022951952803e+00 ), ( -3.82290860556533e+00 , 4.48571014839430e+00 , 2.82041394135468e+00 ), ( -2.60993400144245e+00 , 2.66578802597967e+00 , 2.43015018541631e+00 ), ( -3.75348641347962e+00 , 1.83058299040785e+00 , 2.00699787203871e+00 ), ( -3.40528105969574e+00 , 8.80194500244144e-01 , 9.01181203965098e-01 ), ( -4.32034616015787e+00 , 1.06608828721428e+00 , 3.23249604753155e+00 ), ( -5.51434095786223e+00 , 8.47378908615441e-01 , 3.32837306747542e+00 ), ( -3.39046668325370e+00 , 6.78575600903094e-01 , 4.17557341126074e+00 ), ( -3.73235707258592e+00 , 3.60092331314798e-02 , 5.44490895554789e+00 ), ( -2.38442507637343e+00 , -3.16166941813654e-01 , 6.17290186463125e+00 ), ( -4.46894807425871e+00 , 1.00208941164697e+00 , 6.44222120545526e+00 ), ( -5.34491764662130e+00 , 6.04613365323989e-01 , 7.20959762112996e+00 ), ( -6.23700731007577e+00 , 3.58391531958642e+00 , 6.71770325102584e+00 ), ( -6.94273363851727e+00 , 4.29759822630906e+00 , 7.45670916706203e+00 ), ( -6.75173034342212e+00 , 3.19651736390297e+00 , 5.51748939476038e+00 ), ( -4.12955702796124e+00 , 2.26484894211344e+00 , 6.44108485141110e+00 ), ( -4.82637252427413e+00 , 3.19130489622522e+00 , 7.22412139903855e+00 ), ( -4.10522391931655e+00 , 4.58785764103600e+00 , 7.29314746797526e+00 ) } +colvars: Step 16, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.10587038251228e-01 , 3.00315024001721e-03 , 9.50540200495995e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 7.05466781602202e+00 , -2.04223860168671e+00 , -9.51736464236291e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 , 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 7.08509320289695e+00 , -3.53142554632854e-01 , 4.29109682955083e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 , 5.85739937943113e+00 , 2.24705372923822e+00 , 2.99693495627931e+00 , 5.23296605450751e+00 , 3.58606110840864e+00 , 2.91247709599507e+00 , 6.32721498626626e+00 , 4.51096054330538e+00 , 2.40323812095780e+00 , 3.90156078362489e+00 , 3.72839123981515e+00 , 2.04006304240512e+00 , 2.80849747987868e+00 , 4.14770815693897e+00 , 2.50716653162687e+00 , 3.91345048213876e+00 , 3.24223237482255e+00 , 7.35704502186487e-01 , 2.65352192938508e+00 , 3.03058219725472e+00 , -1.08478988734758e-01 , 3.03566821421468e+00 , 2.72020402497637e+00 , -1.53184494858950e+00 , 1.58482182237910e+00 , 2.19681594444141e+00 , 4.84874977263818e-01 , 4.05830752628882e-01 , 2.54311622034941e+00 , 5.22818761318913e-01 , 2.01449434615761e+00 , 1.01873319035267e+00 , 1.07968478091619e+00 , 1.17917508255272e+00 , 1.01965607587946e-01 , 1.69272590185043e+00 , 2.03133511102619e+00 , -1.12185634481181e+00 , 2.00557055177542e+00 , 5.55595461399606e-01 , 6.08182757174921e-01 , 2.92855358667179e+00 , -6.26630685382450e-01 , 3.49839117918140e-01 , 3.16579064902669e+00 , 1.32586966564794e+00 , 1.34528872112012e+00 , 3.81291116809697e+00 , 8.54359432097506e-01 , 1.96424557858562e+00 , 5.02807312514457e+00 , 2.04529922472684e+00 , 2.64984360296788e+00 , 5.65531328010371e+00 , -3.41128378670846e-01 , 2.91630064517151e+00 , 4.96912331758290e+00 , -1.15049440600122e+00 , 3.05687835727132e+00 , 5.89809994139646e+00 , -4.90094551484171e-01 , 3.57766459827628e+00 , 3.84829453823356e+00 , -1.50765232127455e+00 , 4.54709892177202e+00 , 3.48508471341254e+00 , -7.09271116590437e-01 , 5.40675620645661e+00 , 2.45329243023343e+00 , -2.77189930799630e+00 , 3.87423248244704e+00 , 2.91022951952803e+00 , -3.82290860556533e+00 , 4.48571014839430e+00 , 2.82041394135468e+00 , -2.60993400144245e+00 , 2.66578802597967e+00 , 2.43015018541631e+00 , -3.75348641347962e+00 , 1.83058299040785e+00 , 2.00699787203871e+00 , -3.40528105969574e+00 , 8.80194500244144e-01 , 9.01181203965098e-01 , -4.32034616015787e+00 , 1.06608828721428e+00 , 3.23249604753155e+00 , -5.51434095786223e+00 , 8.47378908615441e-01 , 3.32837306747542e+00 , -3.39046668325370e+00 , 6.78575600903094e-01 , 4.17557341126074e+00 , -3.73235707258592e+00 , 3.60092331314798e-02 , 5.44490895554789e+00 , -2.38442507637343e+00 , -3.16166941813654e-01 , 6.17290186463125e+00 , -4.46894807425871e+00 , 1.00208941164697e+00 , 6.44222120545526e+00 , -5.34491764662130e+00 , 6.04613365323989e-01 , 7.20959762112996e+00 , -6.23700731007577e+00 , 3.58391531958642e+00 , 6.71770325102584e+00 , -6.94273363851727e+00 , 4.29759822630906e+00 , 7.45670916706203e+00 , -6.75173034342212e+00 , 3.19651736390297e+00 , 5.51748939476038e+00 , -4.12955702796124e+00 , 2.26484894211344e+00 , 6.44108485141110e+00 , -4.82637252427413e+00 , 3.19130489622522e+00 , 7.22412139903855e+00 , -4.10522391931655e+00 , 4.58785764103600e+00 , 7.29314746797526e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.10587038251228e-01 , 3.00315024001721e-03 , 9.50540200495995e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.30459187186392e+00 , 4.17784235750708e-02 , -7.63175318074913e-01 , 6.97145806042175e+00 , -5.47768022934804e-01 , -6.05719448356618e-01 , 7.05466781602202e+00 , -2.04223860168671e+00 , -9.51736464236291e-01 , 6.16357891206737e+00 , -3.42920721595124e-01 , 7.05976540138249e-01 , 4.97110005202337e+00 , -1.78623192105419e-01 , 7.10964470389451e-01 , 6.88654785464238e+00 , -2.62991898417013e-01 , 1.87947162567863e+00 , 6.18727500597095e+00 , -1.36256465298287e-01 , 3.19594425709688e+00 , 7.08509320289695e+00 , -3.53142554632854e-01 , 4.29109682955083e+00 , 5.29720916728201e+00 , 1.10699113985169e+00 , 3.33730556931626e+00 , 4.14902705247327e+00 , 1.03523464272692e+00 , 3.66744922185933e+00 , 5.85739937943113e+00 , 2.24705372923822e+00 , 2.99693495627931e+00 , 5.23296605450751e+00 , 3.58606110840864e+00 , 2.91247709599507e+00 , 6.32721498626626e+00 , 4.51096054330538e+00 , 2.40323812095780e+00 , 3.90156078362489e+00 , 3.72839123981515e+00 , 2.04006304240512e+00 , 2.80849747987868e+00 , 4.14770815693897e+00 , 2.50716653162687e+00 , 3.91345048213876e+00 , 3.24223237482255e+00 , 7.35704502186487e-01 , 2.65352192938508e+00 , 3.03058219725472e+00 , -1.08478988734758e-01 , 3.03566821421468e+00 , 2.72020402497637e+00 , -1.53184494858950e+00 , 1.58482182237910e+00 , 2.19681594444141e+00 , 4.84874977263818e-01 , 4.05830752628882e-01 , 2.54311622034941e+00 , 5.22818761318913e-01 , 2.01449434615761e+00 , 1.01873319035267e+00 , 1.07968478091619e+00 , 1.17917508255272e+00 , 1.01965607587946e-01 , 1.69272590185043e+00 , 2.03133511102619e+00 , -1.12185634481181e+00 , 2.00557055177542e+00 , 5.55595461399606e-01 , 6.08182757174921e-01 , 2.92855358667179e+00 , -6.26630685382450e-01 , 3.49839117918140e-01 , 3.16579064902669e+00 , 1.32586966564794e+00 , 1.34528872112012e+00 , 3.81291116809697e+00 , 8.54359432097506e-01 , 1.96424557858562e+00 , 5.02807312514457e+00 , 2.04529922472684e+00 , 2.64984360296788e+00 , 5.65531328010371e+00 , -3.41128378670846e-01 , 2.91630064517151e+00 , 4.96912331758290e+00 , -1.15049440600122e+00 , 3.05687835727132e+00 , 5.89809994139646e+00 , -4.90094551484171e-01 , 3.57766459827628e+00 , 3.84829453823356e+00 , -1.50765232127455e+00 , 4.54709892177202e+00 , 3.48508471341254e+00 , -7.09271116590437e-01 , 5.40675620645661e+00 , 2.45329243023343e+00 , -2.77189930799630e+00 , 3.87423248244704e+00 , 2.91022951952803e+00 , -3.82290860556533e+00 , 4.48571014839430e+00 , 2.82041394135468e+00 , -2.60993400144245e+00 , 2.66578802597967e+00 , 2.43015018541631e+00 , -3.75348641347962e+00 , 1.83058299040785e+00 , 2.00699787203871e+00 , -3.40528105969574e+00 , 8.80194500244144e-01 , 9.01181203965098e-01 , -4.32034616015787e+00 , 1.06608828721428e+00 , 3.23249604753155e+00 , -5.51434095786223e+00 , 8.47378908615441e-01 , 3.32837306747542e+00 , -3.39046668325370e+00 , 6.78575600903094e-01 , 4.17557341126074e+00 , -3.73235707258592e+00 , 3.60092331314798e-02 , 5.44490895554789e+00 , -2.38442507637343e+00 , -3.16166941813654e-01 , 6.17290186463125e+00 , -4.46894807425871e+00 , 1.00208941164697e+00 , 6.44222120545526e+00 , -5.34491764662130e+00 , 6.04613365323989e-01 , 7.20959762112996e+00 , -6.23700731007577e+00 , 3.58391531958642e+00 , 6.71770325102584e+00 , -6.94273363851727e+00 , 4.29759822630906e+00 , 7.45670916706203e+00 , -6.75173034342212e+00 , 3.19651736390297e+00 , 5.51748939476038e+00 , -4.12955702796124e+00 , 2.26484894211344e+00 , 6.44108485141110e+00 , -4.82637252427413e+00 , 3.19130489622522e+00 , 7.22412139903855e+00 , -4.10522391931655e+00 , 4.58785764103600e+00 , 7.29314746797526e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.3644 , 6.63644 , 13.2729 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.3644 , 6.63644 , 13.2729 ) to colvar "one". +colvars: Adding total bias energy: 57.0105 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.3644 , 6.63644 , 13.2729 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.1737 , -0.569699 , -1.55962 ) +colvars: ( -4.43645 , -0.488516 , -1.33737 ) +colvars: ( -4.43645 , -0.488516 , -1.33737 ) +colvars: ( -5.90947 , -0.650718 , -1.78142 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.944607 , 0.20584 , 0.659788 ) +colvars: ( 0.81781 , 0.280695 , 0.685873 ) +colvars: ( 0.801363 , 0.273342 , 0.666398 ) +colvars: ( 0.69897 , 0.28175 , 0.617744 ) +colvars: ( 0.686355 , 0.211574 , 0.516346 ) +colvars: ( 0.607022 , 0.3634 , 0.673328 ) +colvars: ( 0.49305 , 0.378406 , 0.626738 ) +colvars: ( 0.411569 , 0.481128 , 0.716676 ) +colvars: ( 0.406645 , 0.331569 , 0.513426 ) +colvars: ( 0.369581 , 0.287816 , 0.43312 ) +colvars: ( 0.375965 , 0.337137 , 0.502933 ) +colvars: ( 0.300696 , 0.292045 , 0.398477 ) +colvars: ( 0.272397 , 0.322626 , 0.422886 ) +colvars: ( 0.36704 , 0.18876 , 0.298925 ) +colvars: ( 0.304781 , 0.143189 , 0.20144 ) +colvars: ( 0.497351 , 0.149458 , 0.322526 ) +colvars: ( 0.574389 , 0.05295 , 0.238312 ) +colvars: ( 0.712009 , 0.0305527 , 0.288838 ) +colvars: ( 0.583081 , 0.019435 , 0.198497 ) +colvars: ( 0.566366 , -0.0491453 , 0.0968372 ) +colvars: ( 0.604892 , 0.0699965 , 0.278999 ) +colvars: ( 0.602858 , 0.0530218 , 0.255068 ) +colvars: ( 0.641301 , 0.12127 , 0.368997 ) +colvars: ( 0.470842 , 0.0579777 , 0.184454 ) +colvars: ( 0.463462 , -0.000970741 , 0.101161 ) +colvars: ( 0.36276 , 0.127369 , 0.214173 ) +colvars: ( 0.230615 , 0.136648 , 0.149276 ) +colvars: ( 0.133662 , 0.227228 , 0.213895 ) +colvars: ( 0.200944 , 0.0588968 , 0.0277473 ) +colvars: ( 0.148538 , 0.0208576 , -0.0538817 ) +colvars: ( 0.236983 , 0.0318197 , 0.0125609 ) +colvars: ( 0.222384 , -0.0446536 , -0.0984358 ) +colvars: ( 0.260266 , -0.0483063 , -0.0811615 ) +colvars: ( 0.302089 , -0.135405 , -0.173376 ) +colvars: ( 0.255448 , -0.191351 , -0.275622 ) +colvars: ( 0.424132 , -0.151411 , -0.123404 ) +colvars: ( 0.506141 , -0.23113 , -0.182216 ) +colvars: ( 0.645235 , -0.234067 , -0.104755 ) +colvars: ( 0.45558 , -0.235727 , -0.217962 ) +colvars: ( 0.461388 , -0.307508 , -0.31073 ) +colvars: ( 0.403585 , -0.158296 , -0.144652 ) +colvars: ( 0.345671 , -0.151557 , -0.169513 ) +colvars: ( 0.327862 , -0.0600698 , -0.057366 ) +colvars: ( 0.214939 , -0.160634 , -0.258174 ) +colvars: ( 0.188861 , -0.204867 , -0.332696 ) +colvars: ( 0.00208578 , -0.208646 , -0.447054 ) +colvars: ( -0.0943418 , -0.227271 , -0.528434 ) +colvars: ( 0.108771 , -0.261487 , -0.455418 ) +colvars: ( 0.128424 , -0.117711 , -0.251296 ) +colvars: ( 0.00193934 , -0.122144 , -0.331251 ) +colvars: ( -0.0923028 , -0.0369526 , -0.272266 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.1737 , 0.569699 , 1.55962 ) +colvars: ( 4.43645 , 0.488516 , 1.33737 ) +colvars: ( 4.43645 , 0.488516 , 1.33737 ) +colvars: ( 5.90947 , 0.650718 , 1.78142 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.65176 , -0.0851704 , -0.396176 ) +colvars: ( -0.585863 , -0.171747 , -0.364826 ) +colvars: ( -0.534513 , -0.148841 , -0.30411 ) +colvars: ( -0.543576 , -0.200578 , -0.333977 ) +colvars: ( -0.533465 , -0.139096 , -0.299145 ) +colvars: ( -0.516607 , -0.296793 , -0.345555 ) +colvars: ( -0.481063 , -0.339028 , -0.326853 ) +colvars: ( -0.457418 , -0.451205 , -0.348174 ) +colvars: ( -0.414977 , -0.302224 , -0.245771 ) +colvars: ( -0.409663 , -0.275818 , -0.229836 ) +colvars: ( -0.363872 , -0.296431 , -0.192171 ) +colvars: ( -0.300565 , -0.258026 , -0.113235 ) +colvars: ( -0.250214 , -0.273709 , -0.0690157 ) +colvars: ( -0.321684 , -0.150179 , -0.0911177 ) +colvars: ( -0.288536 , -0.119674 , -0.0456116 ) +colvars: ( -0.379726 , -0.0901 , -0.125227 ) +colvars: ( -0.4084 , 0.0126043 , -0.112755 ) +colvars: ( -0.462315 , 0.0624779 , -0.146821 ) +colvars: ( -0.447076 , 0.0283682 , -0.145228 ) +colvars: ( -0.435103 , 0.08766 , -0.109407 ) +colvars: ( -0.492662 , -0.0279949 , -0.213596 ) +colvars: ( -0.527771 , -0.0294592 , -0.249409 ) +colvars: ( -0.579636 , -0.0976893 , -0.328842 ) +colvars: ( -0.472085 , -0.0609448 , -0.206182 ) +colvars: ( -0.47895 , -0.0148782 , -0.194572 ) +colvars: ( -0.413753 , -0.138709 , -0.178884 ) +colvars: ( -0.352436 , -0.171552 , -0.130554 ) +colvars: ( -0.299137 , -0.265883 , -0.114958 ) +colvars: ( -0.309681 , -0.0955438 , -0.0571377 ) +colvars: ( -0.295213 , -0.0761353 , -0.0348284 ) +colvars: ( -0.289977 , -0.0486875 , -0.018554 ) +colvars: ( -0.253466 , 0.0293387 , 0.0494086 ) +colvars: ( -0.232336 , 0.0568803 , 0.0816669 ) +colvars: ( -0.299929 , 0.120083 , 0.0392305 ) +colvars: ( -0.271799 , 0.163652 , 0.0849483 ) +colvars: ( -0.373055 , 0.149627 , -0.0222728 ) +colvars: ( -0.424437 , 0.229348 , -0.0418119 ) +colvars: ( -0.499727 , 0.253099 , -0.107813 ) +colvars: ( -0.435376 , 0.208642 , -0.0611021 ) +colvars: ( -0.440061 , 0.272194 , -0.0402834 ) +colvars: ( -0.439085 , 0.118195 , -0.101142 ) +colvars: ( -0.445324 , 0.0866856 , -0.120053 ) +colvars: ( -0.467077 , -0.010763 , -0.181008 ) +colvars: ( -0.374702 , 0.0747471 , -0.0539929 ) +colvars: ( -0.377606 , 0.102236 , -0.0458685 ) +colvars: ( -0.206038 , 0.108564 , 0.128805 ) +colvars: ( -0.153712 , 0.110393 , 0.182037 ) +colvars: ( -0.235137 , 0.1842 , 0.129981 ) +colvars: ( -0.30916 , 0.0320409 , -0.00538378 ) +colvars: ( -0.238585 , 0.0176534 , 0.0596462 ) +colvars: ( -0.181753 , -0.0692805 , 0.0817579 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 16. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 16. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atoms_new_colvar_forces = { ( -4.88085068907305e+00 , -4.49028551929164e-01 , -1.29600505074684e+00 ), ( -4.20449836752702e+00 , -3.79568369070789e-01 , -1.01632430649201e+00 ), ( -4.28105116741037e+00 , -4.07344508252640e-01 , -1.05360440146138e+00 ), ( -5.75658405057599e+00 , -5.78239321822000e-01 , -1.56421676933607e+00 ), ( 2.66850654120383e-01 , 1.24500399472507e-01 , 3.62288258170644e-01 ), ( 5.26411349601398e+00 , 6.36305546643621e-01 , 1.88739008042324e+00 ), ( 4.44843204232688e+00 , 5.27894380406265e-01 , 1.63725644529032e+00 ), ( -4.58487427383804e-02 , 2.99224912067624e-02 , 3.68502409691058e-01 ), ( 4.42811375763588e+00 , 5.17861510298295e-01 , 1.60502694631232e+00 ), ( 5.86939152786686e+00 , 6.62716429830793e-01 , 1.98470143797970e+00 ), ( 1.20931357692768e-02 , 4.07061075669419e-02 , 3.10761607549823e-01 ), ( 1.31340163474214e-04 , 3.40197974706165e-02 , 2.85241839288116e-01 ), ( 2.21829629885617e-02 , 4.89171257411371e-02 , 3.53870531155421e-01 ), ( 4.53565873031619e-02 , 3.85810582605524e-02 , 2.07807414821818e-01 ), ( 1.62456401933390e-02 , 2.35153115016368e-02 , 1.55828556996292e-01 ), ( 1.17624936312603e-01 , 5.93584234737399e-02 , 1.97299748725069e-01 ), ( 1.65988430475053e-01 , 6.55543247547084e-02 , 1.25557009390830e-01 ), ( 2.49693910649660e-01 , 9.30305591635169e-02 , 1.42017065999787e-01 ), ( 1.36004655248192e-01 , 4.78031666460733e-02 , 5.32689860115979e-02 ), ( 1.31263310514551e-01 , 3.85147594908248e-02 , -1.25699010391985e-02 ), ( 1.12229911337970e-01 , 4.20015694953329e-02 , 6.54032439735829e-02 ), ( 7.50874790384561e-02 , 2.35626187995924e-02 , 5.65936400585526e-03 ), ( 6.16643556147614e-02 , 2.35802880442146e-02 , 4.01551900984536e-02 ), ( -1.24275646121408e-03 , -2.96714532752347e-03 , -2.17275868271735e-02 ), ( -1.54883657321769e-02 , -1.58489738486194e-02 , -9.34115097600717e-02 ), ( -5.09927657674062e-02 , -1.13399247924184e-02 , 3.52892877895157e-02 ), ( -1.21821584896125e-01 , -3.49038099162917e-02 , 1.87221033278634e-02 ), ( -1.65475291476308e-01 , -3.86548292634590e-02 , 9.89367627981799e-02 ), ( -1.08737900127232e-01 , -3.66470484735752e-02 , -2.93903836734535e-02 ), ( -1.46675271595853e-01 , -5.52777771765367e-02 , -8.87100220773765e-02 ), ( -5.29942156615225e-02 , -1.68678241372460e-02 , -5.99308463064763e-03 ), ( -3.10817890375260e-02 , -1.53148785160445e-02 , -4.90271339168488e-02 ), ( 2.79301716201383e-02 , 8.57398547511687e-03 , 5.05415453358665e-04 ), ( 2.15981680450927e-03 , -1.53219240057637e-02 , -1.34145923449791e-01 ), ( -1.63506978351837e-02 , -2.76983110422327e-02 , -1.90673765340870e-01 ), ( 5.10774365366631e-02 , -1.78427629910211e-03 , -1.45676560806550e-01 ), ( 8.17045196869475e-02 , -1.78206317383400e-03 , -2.24027507928624e-01 ), ( 1.45508176742863e-01 , 1.90318905822752e-02 , -2.12568317990047e-01 ), ( 2.02037544016062e-02 , -2.70852204318984e-02 , -2.79063859139157e-01 ), ( 2.13268364197606e-02 , -3.53138998393175e-02 , -3.51012977347652e-01 ), ( -3.55002405032920e-02 , -4.01017152862368e-02 , -2.45793237538160e-01 ), ( -9.96527391486413e-02 , -6.48713729919172e-02 , -2.89565809604738e-01 ), ( -1.39215450944104e-01 , -7.08327482746793e-02 , -2.38374063955150e-01 ), ( -1.59762673449301e-01 , -8.58867346246306e-02 , -3.12167322151533e-01 ), ( -1.88744993147753e-01 , -1.02630820233226e-01 , -3.78564068420618e-01 ), ( -2.03952470610454e-01 , -1.00081398696425e-01 , -3.18249682314534e-01 ), ( -2.48053903344336e-01 , -1.16877610053149e-01 , -3.46396743410593e-01 ), ( -1.26365629683014e-01 , -7.72872597662565e-02 , -3.25436738108755e-01 ), ( -1.80735927282973e-01 , -8.56698452581875e-02 , -2.56679643610762e-01 ), ( -2.36645737830085e-01 , -1.04490468464590e-01 , -2.71604912806018e-01 ), ( -2.74055423926221e-01 , -1.06233113356772e-01 , -1.90508421368227e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 17, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 17, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 17, atoms_positions[size = 51] = { ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 ), ( 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 ), ( 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 ), ( 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 ), ( 7.05401205499525e+00 , -2.04466496196176e+00 , -9.47025224643584e-01 ), ( 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 ), ( 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 ), ( 7.08180008292897e+00 , -3.54527947160232e-01 , 4.29578748165592e+00 ), ( 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 ), ( 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 ), ( 5.85353964216460e+00 , 2.24805367878793e+00 , 2.99564529754523e+00 ), ( 5.23617716524237e+00 , 3.58403856898060e+00 , 2.91580391446837e+00 ), ( 6.32567014767930e+00 , 4.50739171941522e+00 , 2.39434985203635e+00 ), ( 3.89717224079018e+00 , 3.72364808759139e+00 , 2.04172037680312e+00 ), ( 2.80269239899311e+00 , 4.15138746672595e+00 , 2.50256701998378e+00 ), ( 3.92173322094697e+00 , 3.24227328210126e+00 , 7.34119595710529e-01 ), ( 2.65294502133193e+00 , 3.02150622781071e+00 , -1.07888117039870e-01 ), ( 3.03859524831226e+00 , 2.71766366155127e+00 , -1.52532419541117e+00 ), ( 1.58989830929609e+00 , 2.19525577378701e+00 , 4.73279518474310e-01 ), ( 3.97972879861437e-01 , 2.55317558768447e+00 , 5.19988069580460e-01 ), ( 2.02283025509722e+00 , 1.02899009908521e+00 , 1.07896597392129e+00 ), ( 1.17674558381348e+00 , 1.07877021809743e-01 , 1.69345406222270e+00 ), ( 2.03398696349812e+00 , -1.11664678353804e+00 , 2.00595125140644e+00 ), ( 5.57169446916974e-01 , 6.08511901276892e-01 , 2.93036595334865e+00 ), ( -6.20132087452973e-01 , 3.49514498441553e-01 , 3.16443432152830e+00 ), ( 1.32441366100069e+00 , 1.34552384914899e+00 , 3.80422012118166e+00 ), ( 8.51392719277319e-01 , 1.96864047989828e+00 , 5.02676461538075e+00 ), ( 2.05296717375719e+00 , 2.65903093218392e+00 , 5.66165528212752e+00 ), ( -3.39255843615151e-01 , 2.91609096609937e+00 , 4.96816447095012e+00 ), ( -1.14739149507487e+00 , 3.05855318833902e+00 , 5.89576004198849e+00 ), ( -4.95771802962824e-01 , 3.56540022601166e+00 , 3.84876866783091e+00 ), ( -1.51130776109123e+00 , 4.54595027404692e+00 , 3.47448716055517e+00 ), ( -7.05761485073891e-01 , 5.40875166463922e+00 , 2.45650875447642e+00 ), ( -2.77014896565513e+00 , 3.87590188849051e+00 , 2.90731888751016e+00 ), ( -3.82121150232841e+00 , 4.49191857250776e+00 , 2.81862093367446e+00 ), ( -2.61274613472344e+00 , 2.67035355842889e+00 , 2.42315521373217e+00 ), ( -3.75908420821069e+00 , 1.82091842133627e+00 , 2.00340852740520e+00 ), ( -3.40142771648094e+00 , 8.83372833544946e-01 , 8.93904987990678e-01 ), ( -4.32376956288346e+00 , 1.06720052773644e+00 , 3.22663102893285e+00 ), ( -5.50993104352038e+00 , 8.40310379958154e-01 , 3.32824213757474e+00 ), ( -3.38368770649199e+00 , 6.81568860254830e-01 , 4.18445906796119e+00 ), ( -3.72393675184907e+00 , 3.63303732430072e-02 , 5.43999666145482e+00 ), ( -2.38581451310621e+00 , -3.14749731928899e-01 , 6.17318424960760e+00 ), ( -4.46691229519516e+00 , 1.00071778705061e+00 , 6.44257521748917e+00 ), ( -5.34879366000581e+00 , 6.03054059269892e-01 , 7.21221079627413e+00 ), ( -6.23400738802797e+00 , 3.58882051711940e+00 , 6.72122229308845e+00 ), ( -6.94757329189829e+00 , 4.29800521007193e+00 , 7.46181835839354e+00 ), ( -6.75136403999623e+00 , 3.19330560929844e+00 , 5.51491429812448e+00 ), ( -4.13049910086630e+00 , 2.25881881766199e+00 , 6.43272068120323e+00 ), ( -4.82034787571045e+00 , 3.19294621544736e+00 , 7.22806234855601e+00 ), ( -4.10455323138208e+00 , 4.58722558592033e+00 , 7.29107578696250e+00 ) } +colvars: Step 17, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -3.08571789563032e-01 , 2.39854344479993e-03 , 9.51198032838174e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 7.05401205499525e+00 , -2.04466496196176e+00 , -9.47025224643584e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 , 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 7.08180008292897e+00 , -3.54527947160232e-01 , 4.29578748165592e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 , 5.85353964216460e+00 , 2.24805367878793e+00 , 2.99564529754523e+00 , 5.23617716524237e+00 , 3.58403856898060e+00 , 2.91580391446837e+00 , 6.32567014767930e+00 , 4.50739171941522e+00 , 2.39434985203635e+00 , 3.89717224079018e+00 , 3.72364808759139e+00 , 2.04172037680312e+00 , 2.80269239899311e+00 , 4.15138746672595e+00 , 2.50256701998378e+00 , 3.92173322094697e+00 , 3.24227328210126e+00 , 7.34119595710529e-01 , 2.65294502133193e+00 , 3.02150622781071e+00 , -1.07888117039870e-01 , 3.03859524831226e+00 , 2.71766366155127e+00 , -1.52532419541117e+00 , 1.58989830929609e+00 , 2.19525577378701e+00 , 4.73279518474310e-01 , 3.97972879861437e-01 , 2.55317558768447e+00 , 5.19988069580460e-01 , 2.02283025509722e+00 , 1.02899009908521e+00 , 1.07896597392129e+00 , 1.17674558381348e+00 , 1.07877021809743e-01 , 1.69345406222270e+00 , 2.03398696349812e+00 , -1.11664678353804e+00 , 2.00595125140644e+00 , 5.57169446916974e-01 , 6.08511901276892e-01 , 2.93036595334865e+00 , -6.20132087452973e-01 , 3.49514498441553e-01 , 3.16443432152830e+00 , 1.32441366100069e+00 , 1.34552384914899e+00 , 3.80422012118166e+00 , 8.51392719277319e-01 , 1.96864047989828e+00 , 5.02676461538075e+00 , 2.05296717375719e+00 , 2.65903093218392e+00 , 5.66165528212752e+00 , -3.39255843615151e-01 , 2.91609096609937e+00 , 4.96816447095012e+00 , -1.14739149507487e+00 , 3.05855318833902e+00 , 5.89576004198849e+00 , -4.95771802962824e-01 , 3.56540022601166e+00 , 3.84876866783091e+00 , -1.51130776109123e+00 , 4.54595027404692e+00 , 3.47448716055517e+00 , -7.05761485073891e-01 , 5.40875166463922e+00 , 2.45650875447642e+00 , -2.77014896565513e+00 , 3.87590188849051e+00 , 2.90731888751016e+00 , -3.82121150232841e+00 , 4.49191857250776e+00 , 2.81862093367446e+00 , -2.61274613472344e+00 , 2.67035355842889e+00 , 2.42315521373217e+00 , -3.75908420821069e+00 , 1.82091842133627e+00 , 2.00340852740520e+00 , -3.40142771648094e+00 , 8.83372833544946e-01 , 8.93904987990678e-01 , -4.32376956288346e+00 , 1.06720052773644e+00 , 3.22663102893285e+00 , -5.50993104352038e+00 , 8.40310379958154e-01 , 3.32824213757474e+00 , -3.38368770649199e+00 , 6.81568860254830e-01 , 4.18445906796119e+00 , -3.72393675184907e+00 , 3.63303732430072e-02 , 5.43999666145482e+00 , -2.38581451310621e+00 , -3.14749731928899e-01 , 6.17318424960760e+00 , -4.46691229519516e+00 , 1.00071778705061e+00 , 6.44257521748917e+00 , -5.34879366000581e+00 , 6.03054059269892e-01 , 7.21221079627413e+00 , -6.23400738802797e+00 , 3.58882051711940e+00 , 6.72122229308845e+00 , -6.94757329189829e+00 , 4.29800521007193e+00 , 7.46181835839354e+00 , -6.75136403999623e+00 , 3.19330560929844e+00 , 5.51491429812448e+00 , -4.13049910086630e+00 , 2.25881881766199e+00 , 6.43272068120323e+00 , -4.82034787571045e+00 , 3.19294621544736e+00 , 7.22806234855601e+00 , -4.10455323138208e+00 , 4.58722558592033e+00 , 7.29107578696250e+00 ). +colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.08571789563032e-01 , 2.39854344479993e-03 , 9.51198032838174e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.29874382253677e+00 , 4.13030426769156e-02 , -7.61460580789011e-01 , 6.96381325887758e+00 , -5.48959332712714e-01 , -5.99118278252740e-01 , 7.05401205499525e+00 , -2.04466496196176e+00 , -9.47025224643584e-01 , 6.15846866566074e+00 , -3.51959132417230e-01 , 7.11031022182484e-01 , 4.96681579764352e+00 , -1.74789110208474e-01 , 7.14131147820063e-01 , 6.88170935956013e+00 , -2.62606154703331e-01 , 1.88608204868155e+00 , 6.18604353354936e+00 , -1.41816510606084e-01 , 3.19904948584051e+00 , 7.08180008292897e+00 , -3.54527947160232e-01 , 4.29578748165592e+00 , 5.30232984838912e+00 , 1.10455866913550e+00 , 3.34126013208179e+00 , 4.15292658802712e+00 , 1.03259786386465e+00 , 3.67336523051127e+00 , 5.85353964216460e+00 , 2.24805367878793e+00 , 2.99564529754523e+00 , 5.23617716524237e+00 , 3.58403856898060e+00 , 2.91580391446837e+00 , 6.32567014767930e+00 , 4.50739171941522e+00 , 2.39434985203635e+00 , 3.89717224079018e+00 , 3.72364808759139e+00 , 2.04172037680312e+00 , 2.80269239899311e+00 , 4.15138746672595e+00 , 2.50256701998378e+00 , 3.92173322094697e+00 , 3.24227328210126e+00 , 7.34119595710529e-01 , 2.65294502133193e+00 , 3.02150622781071e+00 , -1.07888117039870e-01 , 3.03859524831226e+00 , 2.71766366155127e+00 , -1.52532419541117e+00 , 1.58989830929609e+00 , 2.19525577378701e+00 , 4.73279518474310e-01 , 3.97972879861437e-01 , 2.55317558768447e+00 , 5.19988069580460e-01 , 2.02283025509722e+00 , 1.02899009908521e+00 , 1.07896597392129e+00 , 1.17674558381348e+00 , 1.07877021809743e-01 , 1.69345406222270e+00 , 2.03398696349812e+00 , -1.11664678353804e+00 , 2.00595125140644e+00 , 5.57169446916974e-01 , 6.08511901276892e-01 , 2.93036595334865e+00 , -6.20132087452973e-01 , 3.49514498441553e-01 , 3.16443432152830e+00 , 1.32441366100069e+00 , 1.34552384914899e+00 , 3.80422012118166e+00 , 8.51392719277319e-01 , 1.96864047989828e+00 , 5.02676461538075e+00 , 2.05296717375719e+00 , 2.65903093218392e+00 , 5.66165528212752e+00 , -3.39255843615151e-01 , 2.91609096609937e+00 , 4.96816447095012e+00 , -1.14739149507487e+00 , 3.05855318833902e+00 , 5.89576004198849e+00 , -4.95771802962824e-01 , 3.56540022601166e+00 , 3.84876866783091e+00 , -1.51130776109123e+00 , 4.54595027404692e+00 , 3.47448716055517e+00 , -7.05761485073891e-01 , 5.40875166463922e+00 , 2.45650875447642e+00 , -2.77014896565513e+00 , 3.87590188849051e+00 , 2.90731888751016e+00 , -3.82121150232841e+00 , 4.49191857250776e+00 , 2.81862093367446e+00 , -2.61274613472344e+00 , 2.67035355842889e+00 , 2.42315521373217e+00 , -3.75908420821069e+00 , 1.82091842133627e+00 , 2.00340852740520e+00 , -3.40142771648094e+00 , 8.83372833544946e-01 , 8.93904987990678e-01 , -4.32376956288346e+00 , 1.06720052773644e+00 , 3.22663102893285e+00 , -5.50993104352038e+00 , 8.40310379958154e-01 , 3.32824213757474e+00 , -3.38368770649199e+00 , 6.81568860254830e-01 , 4.18445906796119e+00 , -3.72393675184907e+00 , 3.63303732430072e-02 , 5.43999666145482e+00 , -2.38581451310621e+00 , -3.14749731928899e-01 , 6.17318424960760e+00 , -4.46691229519516e+00 , 1.00071778705061e+00 , 6.44257521748917e+00 , -5.34879366000581e+00 , 6.03054059269892e-01 , 7.21221079627413e+00 , -6.23400738802797e+00 , 3.58882051711940e+00 , 6.72122229308845e+00 , -6.94757329189829e+00 , 4.29800521007193e+00 , 7.46181835839354e+00 , -6.75136403999623e+00 , 3.19330560929844e+00 , 5.51491429812448e+00 , -4.13049910086630e+00 , 2.25881881766199e+00 , 6.43272068120323e+00 , -4.82034787571045e+00 , 3.19294621544736e+00 , 7.22806234855601e+00 , -4.10455323138208e+00 , 4.58722558592033e+00 , 7.29107578696250e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.2679 , 6.62679 , 13.2536 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.2679 , 6.62679 , 13.2536 ) to colvar "one". +colvars: Adding total bias energy: 56.8721 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.2679 , 6.62679 , 13.2536 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17255 , -0.566649 , -1.54858 ) +colvars: ( -4.43546 , -0.485901 , -1.32791 ) +colvars: ( -4.43546 , -0.485901 , -1.32791 ) +colvars: ( -5.90816 , -0.647234 , -1.76881 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.942806 , 0.205761 , 0.657029 ) +colvars: ( 0.816365 , 0.280444 , 0.682975 ) +colvars: ( 0.799832 , 0.273143 , 0.663561 ) +colvars: ( 0.697932 , 0.281403 , 0.615076 ) +colvars: ( 0.685352 , 0.211315 , 0.514064 ) +colvars: ( 0.606305 , 0.362869 , 0.670421 ) +colvars: ( 0.492736 , 0.377759 , 0.623981 ) +colvars: ( 0.411536 , 0.480277 , 0.713551 ) +colvars: ( 0.406522 , 0.330957 , 0.511075 ) +colvars: ( 0.369616 , 0.287221 , 0.43107 ) +colvars: ( 0.375819 , 0.336543 , 0.500605 ) +colvars: ( 0.300699 , 0.291494 , 0.396524 ) +colvars: ( 0.272364 , 0.322063 , 0.420823 ) +colvars: ( 0.366823 , 0.188398 , 0.297374 ) +colvars: ( 0.304748 , 0.14285 , 0.200245 ) +colvars: ( 0.49673 , 0.149236 , 0.320922 ) +colvars: ( 0.573522 , 0.0529108 , 0.237054 ) +colvars: ( 0.710691 , 0.0306454 , 0.287424 ) +colvars: ( 0.582302 , 0.0194021 , 0.197402 ) +colvars: ( 0.565635 , -0.0490957 , 0.0961282 ) +colvars: ( 0.604151 , 0.0698694 , 0.277608 ) +colvars: ( 0.60224 , 0.052871 , 0.253776 ) +colvars: ( 0.640662 , 0.121015 , 0.367284 ) +colvars: ( 0.470647 , 0.0577265 , 0.183396 ) +colvars: ( 0.46333 , -0.00116355 , 0.100423 ) +colvars: ( 0.362862 , 0.126967 , 0.212967 ) +colvars: ( 0.231122 , 0.136147 , 0.14828 ) +colvars: ( 0.134429 , 0.226557 , 0.212619 ) +colvars: ( 0.201462 , 0.0585118 , 0.0272056 ) +colvars: ( 0.149254 , 0.0204749 , -0.0541222 ) +colvars: ( 0.237279 , 0.0315381 , 0.0120808 ) +colvars: ( 0.222642 , -0.0448099 , -0.0984984 ) +colvars: ( 0.260286 , -0.0483854 , -0.0812874 ) +colvars: ( 0.302144 , -0.135403 , -0.173125 ) +colvars: ( 0.255635 , -0.1913 , -0.274991 ) +colvars: ( 0.423867 , -0.151329 , -0.123305 ) +colvars: ( 0.505677 , -0.230907 , -0.181863 ) +colvars: ( 0.644377 , -0.233762 , -0.104658 ) +colvars: ( 0.455381 , -0.235574 , -0.217479 ) +colvars: ( 0.461187 , -0.307261 , -0.309887 ) +colvars: ( 0.403622 , -0.158311 , -0.144461 ) +colvars: ( 0.345991 , -0.15166 , -0.169237 ) +colvars: ( 0.328318 , -0.0603387 , -0.0575217 ) +colvars: ( 0.215631 , -0.160799 , -0.257598 ) +colvars: ( 0.189687 , -0.205011 , -0.331836 ) +colvars: ( 0.00321864 , -0.208804 , -0.445827 ) +colvars: ( -0.0929334 , -0.227459 , -0.526923 ) +colvars: ( 0.109519 , -0.261482 , -0.454131 ) +colvars: ( 0.129296 , -0.117957 , -0.250777 ) +colvars: ( 0.00316332 , -0.122453 , -0.330463 ) +colvars: ( -0.0908424 , -0.0374179 , -0.271737 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17255 , 0.566649 , 1.54858 ) +colvars: ( 4.43546 , 0.485901 , 1.32791 ) +colvars: ( 4.43546 , 0.485901 , 1.32791 ) +colvars: ( 5.90816 , 0.647234 , 1.76881 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.650412 , -0.0851487 , -0.393828 ) +colvars: ( -0.584774 , -0.171656 , -0.362311 ) +colvars: ( -0.533266 , -0.148767 , -0.30158 ) +colvars: ( -0.542818 , -0.200428 , -0.331645 ) +colvars: ( -0.532719 , -0.138957 , -0.297141 ) +colvars: ( -0.51613 , -0.296577 , -0.343011 ) +colvars: ( -0.480925 , -0.338751 , -0.324432 ) +colvars: ( -0.457529 , -0.450862 , -0.345428 ) +colvars: ( -0.414923 , -0.30193 , -0.243641 ) +colvars: ( -0.409748 , -0.275511 , -0.227976 ) +colvars: ( -0.363723 , -0.296141 , -0.190001 ) +colvars: ( -0.300464 , -0.257726 , -0.111329 ) +colvars: ( -0.25001 , -0.273408 , -0.0669523 ) +colvars: ( -0.321388 , -0.149935 , -0.0895674 ) +colvars: ( -0.288366 , -0.119414 , -0.0443482 ) +colvars: ( -0.379121 , -0.0899235 , -0.123665 ) +colvars: ( -0.407588 , 0.0127227 , -0.111507 ) +colvars: ( -0.461142 , 0.0625256 , -0.145463 ) +colvars: ( -0.4464 , 0.0284925 , -0.144175 ) +colvars: ( -0.434447 , 0.0877751 , -0.108679 ) +colvars: ( -0.492093 , -0.0278521 , -0.212341 ) +colvars: ( -0.527368 , -0.0293015 , -0.248291 ) +colvars: ( -0.579296 , -0.0975175 , -0.327417 ) +colvars: ( -0.472011 , -0.0607248 , -0.205238 ) +colvars: ( -0.47894 , -0.0146624 , -0.193921 ) +colvars: ( -0.413889 , -0.13843 , -0.177767 ) +colvars: ( -0.352877 , -0.171212 , -0.129583 ) +colvars: ( -0.299762 , -0.265486 , -0.113703 ) +colvars: ( -0.310063 , -0.0952221 , -0.0565129 ) +colvars: ( -0.29576 , -0.0757936 , -0.0344652 ) +colvars: ( -0.290113 , -0.0484053 , -0.0179415 ) +colvars: ( -0.253504 , 0.0295965 , 0.0497036 ) +colvars: ( -0.232114 , 0.0571015 , 0.0820614 ) +colvars: ( -0.299828 , 0.120291 , 0.0392144 ) +colvars: ( -0.271777 , 0.163866 , 0.0846245 ) +colvars: ( -0.372747 , 0.149785 , -0.0222142 ) +colvars: ( -0.424001 , 0.229459 , -0.0420176 ) +colvars: ( -0.499019 , 0.253153 , -0.107852 ) +colvars: ( -0.435211 , 0.208792 , -0.0614555 ) +colvars: ( -0.439893 , 0.272327 , -0.0409552 ) +colvars: ( -0.439163 , 0.118397 , -0.101265 ) +colvars: ( -0.445683 , 0.0869319 , -0.120281 ) +colvars: ( -0.46761 , -0.0104746 , -0.180897 ) +colvars: ( -0.375318 , 0.0750445 , -0.0544314 ) +colvars: ( -0.37835 , 0.102543 , -0.0465675 ) +colvars: ( -0.206832 , 0.108912 , 0.12796 ) +colvars: ( -0.154695 , 0.110775 , 0.180984 ) +colvars: ( -0.235595 , 0.184479 , 0.129083 ) +colvars: ( -0.30986 , 0.0323734 , -0.00571091 ) +colvars: ( -0.239523 , 0.0180352 , 0.0591387 ) +colvars: ( -0.182847 , -0.0688451 , 0.0815215 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 17. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 17. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atoms_new_colvar_forces = { ( -4.88015736595259e+00 , -4.46036198466336e-01 , -1.28538242749713e+00 ), ( -4.20387001123164e+00 , -3.77113297704594e-01 , -1.00724497223348e+00 ), ( -4.28034760920542e+00 , -4.04925824031137e-01 , -1.04447955016954e+00 ), ( -5.75552983118959e+00 , -5.74876520659967e-01 , -1.55189131627040e+00 ), ( 2.66566163465579e-01 , 1.24376770580220e-01 , 3.61980821479692e-01 ), ( 5.26272633610233e+00 , 6.32939844268853e-01 , 1.87599298139621e+00 ), ( 4.44727222712034e+00 , 5.24909665742374e-01 , 1.62745911753024e+00 ), ( -4.59924977081408e-02 , 2.94146333875059e-02 , 3.68123311003704e-01 ), ( 4.42706088684963e+00 , 5.14927536420531e-01 , 1.59534358645283e+00 ), ( 5.86803042983167e+00 , 6.58944285120950e-01 , 1.97190872671386e+00 ), ( 1.20958419018421e-02 , 4.04019894378879e-02 , 3.10604533441209e-01 ), ( 2.35273637626099e-04 , 3.37687214393134e-02 , 2.85194908722332e-01 ), ( 2.23540544025670e-02 , 4.86545337689300e-02 , 3.53870868081869e-01 ), ( 4.54343450249216e-02 , 3.84624174007937e-02 , 2.07806245999574e-01 ), ( 1.63828773126952e-02 , 2.34352507899631e-02 , 1.55897031745500e-01 ), ( 1.17609543873743e-01 , 5.93120332139072e-02 , 1.97257460581520e-01 ), ( 1.65934326070678e-01 , 6.56334972416600e-02 , 1.25546604874536e-01 ), ( 2.49548804174806e-01 , 9.31709615394787e-02 , 1.41960982152818e-01 ), ( 1.35902355594962e-01 , 4.78946561276440e-02 , 5.32274527181748e-02 ), ( 1.31187898310386e-01 , 3.86793842526439e-02 , -1.25512940907047e-02 ), ( 1.12057892619085e-01 , 4.20173245501222e-02 , 6.52669276381761e-02 ), ( 7.48717170204336e-02 , 2.35695622374883e-02 , 5.48483858983992e-03 ), ( 6.13656977317324e-02 , 2.34971707001845e-02 , 3.98672506841835e-02 ), ( -1.36399002557974e-03 , -2.99826090073294e-03 , -2.18418427601044e-02 ), ( -1.56102032596058e-02 , -1.58259772689461e-02 , -9.34973375290691e-02 ), ( -5.10278337643778e-02 , -1.14629605756471e-02 , 3.51991594606000e-02 ), ( -1.21755229879134e-01 , -3.50654650420195e-02 , 1.86972666066966e-02 ), ( -1.65333822554622e-01 , -3.89286491415851e-02 , 9.89162576270934e-02 ), ( -1.08600922782521e-01 , -3.67102543226608e-02 , -2.93073426226554e-02 ), ( -1.46505926294895e-01 , -5.53187629098834e-02 , -8.85873850071875e-02 ), ( -5.28340182021141e-02 , -1.68672612934411e-02 , -5.86065249106413e-03 ), ( -3.08618359440838e-02 , -1.52134167946242e-02 , -4.87947597045069e-02 ), ( 2.81720536253082e-02 , 8.71614272212562e-03 , 7.73940470895157e-04 ), ( 2.31652781295405e-03 , -1.51127155601899e-02 , -1.33910083243585e-01 ), ( -1.61424316645498e-02 , -2.74343489564569e-02 , -1.90366760629126e-01 ), ( 5.11196992026257e-02 , -1.54358524293582e-03 , -1.45519225047703e-01 ), ( 8.16753453628619e-02 , -1.44781366450614e-03 , -2.23880614084183e-01 ), ( 1.45357281505606e-01 , 1.93915246217626e-02 , -2.12509706563197e-01 ), ( 2.01691592912764e-02 , -2.67823785971957e-02 , -2.78934795395103e-01 ), ( 2.12938793740244e-02 , -3.49341821079345e-02 , -3.50842529360566e-01 ), ( -3.55405244895096e-02 , -3.99138378223871e-02 , -2.45726096946784e-01 ), ( -9.96924264046057e-02 , -6.47277205650604e-02 , -2.89518191861758e-01 ), ( -1.39291942293498e-01 , -7.08133520162364e-02 , -2.38419162901851e-01 ), ( -1.59686699407018e-01 , -8.57543336741377e-02 , -3.12029126662255e-01 ), ( -1.88663105921427e-01 , -1.02467642653652e-01 , -3.78403643139270e-01 ), ( -2.03613559494271e-01 , -9.98920233820327e-02 , -3.17866923464479e-01 ), ( -2.47627914849571e-01 , -1.16683548586711e-01 , -3.45938981774479e-01 ), ( -1.26076243452396e-01 , -7.70029494703876e-02 , -3.25048223242792e-01 ), ( -1.80564661927748e-01 , -8.55835606815858e-02 , -2.56487415131268e-01 ), ( -2.36360145018347e-01 , -1.04418081972694e-01 , -2.71324767663208e-01 ), ( -2.73689864302419e-01 , -1.06262981498663e-01 , -1.90215146484118e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 18, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 18, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 18, atoms_positions[size = 51] = { ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 ), ( 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 ), ( 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 ), ( 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 ), ( 7.05271607976549e+00 , -2.04701294245329e+00 , -9.42509469880201e-01 ), ( 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 ), ( 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 ), ( 7.08000330134620e+00 , -3.55284910533089e-01 , 4.30137053149054e+00 ), ( 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 ), ( 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 ), ( 5.84980798357323e+00 , 2.24966439635277e+00 , 2.99404129701435e+00 ), ( 5.23835337285908e+00 , 3.58205403294845e+00 , 2.91851704152070e+00 ), ( 6.32437505535570e+00 , 4.50468705973972e+00 , 2.38502757286954e+00 ), ( 3.89223690233319e+00 , 3.71835333345391e+00 , 2.04303158103372e+00 ), ( 2.79802365953788e+00 , 4.15483351289799e+00 , 2.49778941064640e+00 ), ( 3.92884294881576e+00 , 3.24191316831157e+00 , 7.32888194378791e-01 ), ( 2.65411407264995e+00 , 3.01434081602324e+00 , -1.06896703721620e-01 ), ( 3.04251330256935e+00 , 2.71425750935877e+00 , -1.52028070078280e+00 ), ( 1.59416792303023e+00 , 2.19216481262863e+00 , 4.62809499393612e-01 ), ( 3.90650117951124e-01 , 2.56301077867888e+00 , 5.16967514650667e-01 ), ( 2.03122863395248e+00 , 1.04141285375615e+00 , 1.07695231315893e+00 ), ( 1.17402749138365e+00 , 1.12203382713304e-01 , 1.69452997945191e+00 ), ( 2.03682040442338e+00 , -1.11176603037732e+00 , 2.00691923601827e+00 ), ( 5.58729567815095e-01 , 6.09265222101686e-01 , 2.93358745222653e+00 ), ( -6.13749682045257e-01 , 3.49401893418533e-01 , 3.16322193706003e+00 ), ( 1.32234499813337e+00 , 1.34554049175721e+00 , 3.79479022984922e+00 ), ( 8.48270476285389e-01 , 1.97257500422287e+00 , 5.02594407760662e+00 ), ( 2.06153029458319e+00 , 2.66854561045493e+00 , 5.66834200488296e+00 ), ( -3.37968453786755e-01 , 2.91577381023611e+00 , 4.96767152152444e+00 ), ( -1.14410211403567e+00 , 3.06003295903836e+00 , 5.89320327706122e+00 ), ( -5.01252397644797e-01 , 3.55410076723207e+00 , 3.84872265133012e+00 ), ( -1.51442408648012e+00 , 4.54436794679331e+00 , 3.46391022195393e+00 ), ( -7.02905739367337e-01 , 5.41070286617546e+00 , 2.45932126291340e+00 ), ( -2.76742104498482e+00 , 3.87902722252102e+00 , 2.90391761406626e+00 ), ( -3.81979153228129e+00 , 4.49804278244187e+00 , 2.81705435893745e+00 ), ( -2.61618004736925e+00 , 2.67319162189029e+00 , 2.41597950443951e+00 ), ( -3.76419154983186e+00 , 1.81305967817032e+00 , 2.00076893150958e+00 ), ( -3.39728475255780e+00 , 8.85496773526211e-01 , 8.87014667580360e-01 ), ( -4.32547677394703e+00 , 1.06837556076424e+00 , 3.22099878492571e+00 ), ( -5.50600355198686e+00 , 8.33175855060729e-01 , 3.32835499000222e+00 ), ( -3.37775813338197e+00 , 6.84659597766296e-01 , 4.19251734685362e+00 ), ( -3.71579947164811e+00 , 3.83055166333904e-02 , 5.43638450809476e+00 ), ( -2.38737980508660e+00 , -3.14600305794011e-01 , 6.17281002928248e+00 ), ( -4.46493940928512e+00 , 9.97734180499877e-01 , 6.44221479322284e+00 ), ( -5.35250204695175e+00 , 6.01425334398934e-01 , 7.21454062498389e+00 ), ( -6.23318516478668e+00 , 3.59413898038086e+00 , 6.72515897775978e+00 ), ( -6.95212090530336e+00 , 4.29816642791007e+00 , 7.46670089388892e+00 ), ( -6.74961276587329e+00 , 3.18979119729720e+00 , 5.51228345741242e+00 ), ( -4.13063161466044e+00 , 2.25357244122872e+00 , 6.42451233409495e+00 ), ( -4.81540752225174e+00 , 3.19608420035191e+00 , 7.23243596757610e+00 ), ( -4.10269470555908e+00 , 4.58473628518885e+00 , 7.28852513722620e+00 ) } +colvars: Step 18, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.06732608270377e-01 , 1.68371747048719e-03 , 9.51794238330497e-01 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 7.05271607976549e+00 , -2.04701294245329e+00 , -9.42509469880201e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 , 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 7.08000330134620e+00 , -3.55284910533089e-01 , 4.30137053149054e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 , 5.84980798357323e+00 , 2.24966439635277e+00 , 2.99404129701435e+00 , 5.23835337285908e+00 , 3.58205403294845e+00 , 2.91851704152070e+00 , 6.32437505535570e+00 , 4.50468705973972e+00 , 2.38502757286954e+00 , 3.89223690233319e+00 , 3.71835333345391e+00 , 2.04303158103372e+00 , 2.79802365953788e+00 , 4.15483351289799e+00 , 2.49778941064640e+00 , 3.92884294881576e+00 , 3.24191316831157e+00 , 7.32888194378791e-01 , 2.65411407264995e+00 , 3.01434081602324e+00 , -1.06896703721620e-01 , 3.04251330256935e+00 , 2.71425750935877e+00 , -1.52028070078280e+00 , 1.59416792303023e+00 , 2.19216481262863e+00 , 4.62809499393612e-01 , 3.90650117951124e-01 , 2.56301077867888e+00 , 5.16967514650667e-01 , 2.03122863395248e+00 , 1.04141285375615e+00 , 1.07695231315893e+00 , 1.17402749138365e+00 , 1.12203382713304e-01 , 1.69452997945191e+00 , 2.03682040442338e+00 , -1.11176603037732e+00 , 2.00691923601827e+00 , 5.58729567815095e-01 , 6.09265222101686e-01 , 2.93358745222653e+00 , -6.13749682045257e-01 , 3.49401893418533e-01 , 3.16322193706003e+00 , 1.32234499813337e+00 , 1.34554049175721e+00 , 3.79479022984922e+00 , 8.48270476285389e-01 , 1.97257500422287e+00 , 5.02594407760662e+00 , 2.06153029458319e+00 , 2.66854561045493e+00 , 5.66834200488296e+00 , -3.37968453786755e-01 , 2.91577381023611e+00 , 4.96767152152444e+00 , -1.14410211403567e+00 , 3.06003295903836e+00 , 5.89320327706122e+00 , -5.01252397644797e-01 , 3.55410076723207e+00 , 3.84872265133012e+00 , -1.51442408648012e+00 , 4.54436794679331e+00 , 3.46391022195393e+00 , -7.02905739367337e-01 , 5.41070286617546e+00 , 2.45932126291340e+00 , -2.76742104498482e+00 , 3.87902722252102e+00 , 2.90391761406626e+00 , -3.81979153228129e+00 , 4.49804278244187e+00 , 2.81705435893745e+00 , -2.61618004736925e+00 , 2.67319162189029e+00 , 2.41597950443951e+00 , -3.76419154983186e+00 , 1.81305967817032e+00 , 2.00076893150958e+00 , -3.39728475255780e+00 , 8.85496773526211e-01 , 8.87014667580360e-01 , -4.32547677394703e+00 , 1.06837556076424e+00 , 3.22099878492571e+00 , -5.50600355198686e+00 , 8.33175855060729e-01 , 3.32835499000222e+00 , -3.37775813338197e+00 , 6.84659597766296e-01 , 4.19251734685362e+00 , -3.71579947164811e+00 , 3.83055166333904e-02 , 5.43638450809476e+00 , -2.38737980508660e+00 , -3.14600305794011e-01 , 6.17281002928248e+00 , -4.46493940928512e+00 , 9.97734180499877e-01 , 6.44221479322284e+00 , -5.35250204695175e+00 , 6.01425334398934e-01 , 7.21454062498389e+00 , -6.23318516478668e+00 , 3.59413898038086e+00 , 6.72515897775978e+00 , -6.95212090530336e+00 , 4.29816642791007e+00 , 7.46670089388892e+00 , -6.74961276587329e+00 , 3.18979119729720e+00 , 5.51228345741242e+00 , -4.13063161466044e+00 , 2.25357244122872e+00 , 6.42451233409495e+00 , -4.81540752225174e+00 , 3.19608420035191e+00 , 7.23243596757610e+00 , -4.10269470555908e+00 , 4.58473628518885e+00 , 7.28852513722620e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.06732608270377e-01 , 1.68371747048719e-03 , 9.51794238330497e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.29337330492886e+00 , 4.08824008899196e-02 , -7.59440566896583e-01 , 6.95476172050392e+00 , -5.49928361848478e-01 , -5.92026629408205e-01 , 7.05271607976549e+00 , -2.04701294245329e+00 , -9.42509469880201e-01 , 6.15561026903625e+00 , -3.60629265702461e-01 , 7.16682322072443e-01 , 4.96164425932544e+00 , -1.70910204089273e-01 , 7.17074961713416e-01 , 6.87623165071441e+00 , -2.62478965883063e-01 , 1.89300538417743e+00 , 6.18395503718775e+00 , -1.47872106583385e-01 , 3.19971495589543e+00 , 7.08000330134620e+00 , -3.55284910533089e-01 , 4.30137053149054e+00 , 5.30826303243494e+00 , 1.10171718489902e+00 , 3.34511514919655e+00 , 4.15618660047194e+00 , 1.03004255241929e+00 , 3.67967913489386e+00 , 5.84980798357323e+00 , 2.24966439635277e+00 , 2.99404129701435e+00 , 5.23835337285908e+00 , 3.58205403294845e+00 , 2.91851704152070e+00 , 6.32437505535570e+00 , 4.50468705973972e+00 , 2.38502757286954e+00 , 3.89223690233319e+00 , 3.71835333345391e+00 , 2.04303158103372e+00 , 2.79802365953788e+00 , 4.15483351289799e+00 , 2.49778941064640e+00 , 3.92884294881576e+00 , 3.24191316831157e+00 , 7.32888194378791e-01 , 2.65411407264995e+00 , 3.01434081602324e+00 , -1.06896703721620e-01 , 3.04251330256935e+00 , 2.71425750935877e+00 , -1.52028070078280e+00 , 1.59416792303023e+00 , 2.19216481262863e+00 , 4.62809499393612e-01 , 3.90650117951124e-01 , 2.56301077867888e+00 , 5.16967514650667e-01 , 2.03122863395248e+00 , 1.04141285375615e+00 , 1.07695231315893e+00 , 1.17402749138365e+00 , 1.12203382713304e-01 , 1.69452997945191e+00 , 2.03682040442338e+00 , -1.11176603037732e+00 , 2.00691923601827e+00 , 5.58729567815095e-01 , 6.09265222101686e-01 , 2.93358745222653e+00 , -6.13749682045257e-01 , 3.49401893418533e-01 , 3.16322193706003e+00 , 1.32234499813337e+00 , 1.34554049175721e+00 , 3.79479022984922e+00 , 8.48270476285389e-01 , 1.97257500422287e+00 , 5.02594407760662e+00 , 2.06153029458319e+00 , 2.66854561045493e+00 , 5.66834200488296e+00 , -3.37968453786755e-01 , 2.91577381023611e+00 , 4.96767152152444e+00 , -1.14410211403567e+00 , 3.06003295903836e+00 , 5.89320327706122e+00 , -5.01252397644797e-01 , 3.55410076723207e+00 , 3.84872265133012e+00 , -1.51442408648012e+00 , 4.54436794679331e+00 , 3.46391022195393e+00 , -7.02905739367337e-01 , 5.41070286617546e+00 , 2.45932126291340e+00 , -2.76742104498482e+00 , 3.87902722252102e+00 , 2.90391761406626e+00 , -3.81979153228129e+00 , 4.49804278244187e+00 , 2.81705435893745e+00 , -2.61618004736925e+00 , 2.67319162189029e+00 , 2.41597950443951e+00 , -3.76419154983186e+00 , 1.81305967817032e+00 , 2.00076893150958e+00 , -3.39728475255780e+00 , 8.85496773526211e-01 , 8.87014667580360e-01 , -4.32547677394703e+00 , 1.06837556076424e+00 , 3.22099878492571e+00 , -5.50600355198686e+00 , 8.33175855060729e-01 , 3.32835499000222e+00 , -3.37775813338197e+00 , 6.84659597766296e-01 , 4.19251734685362e+00 , -3.71579947164811e+00 , 3.83055166333904e-02 , 5.43638450809476e+00 , -2.38737980508660e+00 , -3.14600305794011e-01 , 6.17281002928248e+00 , -4.46493940928512e+00 , 9.97734180499877e-01 , 6.44221479322284e+00 , -5.35250204695175e+00 , 6.01425334398934e-01 , 7.21454062498389e+00 , -6.23318516478668e+00 , 3.59413898038086e+00 , 6.72515897775978e+00 , -6.95212090530336e+00 , 4.29816642791007e+00 , 7.46670089388892e+00 , -6.74961276587329e+00 , 3.18979119729720e+00 , 5.51228345741242e+00 , -4.13063161466044e+00 , 2.25357244122872e+00 , 6.42451233409495e+00 , -4.81540752225174e+00 , 3.19608420035191e+00 , 7.23243596757610e+00 , -4.10269470555908e+00 , 4.58473628518885e+00 , 7.28852513722620e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.181 , 6.6181 , 13.2362 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.181 , 6.6181 , 13.2362 ) to colvar "one". +colvars: Adding total bias energy: 56.7471 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.181 , 6.6181 , 13.2362 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17251 , -0.564055 , -1.53892 ) +colvars: ( -4.43543 , -0.483677 , -1.31963 ) +colvars: ( -4.43543 , -0.483677 , -1.31963 ) +colvars: ( -5.90812 , -0.644271 , -1.75778 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.941307 , 0.205735 , 0.654619 ) +colvars: ( 0.815175 , 0.280281 , 0.680429 ) +colvars: ( 0.798556 , 0.27302 , 0.661057 ) +colvars: ( 0.697098 , 0.281156 , 0.612729 ) +colvars: ( 0.68455 , 0.21113 , 0.512062 ) +colvars: ( 0.605754 , 0.362475 , 0.667859 ) +colvars: ( 0.49254 , 0.377268 , 0.621548 ) +colvars: ( 0.411587 , 0.479628 , 0.710786 ) +colvars: ( 0.406486 , 0.330484 , 0.508992 ) +colvars: ( 0.369721 , 0.286756 , 0.429257 ) +colvars: ( 0.375754 , 0.336083 , 0.498533 ) +colvars: ( 0.300757 , 0.291061 , 0.394774 ) +colvars: ( 0.272383 , 0.32162 , 0.418963 ) +colvars: ( 0.366689 , 0.188109 , 0.295985 ) +colvars: ( 0.304776 , 0.142571 , 0.19917 ) +colvars: ( 0.496246 , 0.149063 , 0.319496 ) +colvars: ( 0.572824 , 0.0528804 , 0.235941 ) +colvars: ( 0.709597 , 0.0307268 , 0.286179 ) +colvars: ( 0.581689 , 0.0193738 , 0.196445 ) +colvars: ( 0.565064 , -0.0490656 , 0.0955139 ) +colvars: ( 0.603578 , 0.0697717 , 0.276395 ) +colvars: ( 0.601783 , 0.0527522 , 0.25266 ) +colvars: ( 0.640194 , 0.120821 , 0.365803 ) +colvars: ( 0.47056 , 0.0575198 , 0.182482 ) +colvars: ( 0.463303 , -0.00132976 , 0.0997985 ) +colvars: ( 0.36303 , 0.12664 , 0.21191 ) +colvars: ( 0.231643 , 0.135733 , 0.147402 ) +colvars: ( 0.135172 , 0.22601 , 0.211482 ) +colvars: ( 0.201987 , 0.0581821 , 0.0267243 ) +colvars: ( 0.149955 , 0.0201401 , -0.0543355 ) +colvars: ( 0.237603 , 0.031291 , 0.0116486 ) +colvars: ( 0.222926 , -0.0449648 , -0.0985654 ) +colvars: ( 0.260353 , -0.0484762 , -0.0814178 ) +colvars: ( 0.302256 , -0.135436 , -0.172902 ) +colvars: ( 0.25586 , -0.191302 , -0.274434 ) +colvars: ( 0.423703 , -0.151291 , -0.123206 ) +colvars: ( 0.505345 , -0.23076 , -0.181528 ) +colvars: ( 0.643704 , -0.23354 , -0.104538 ) +colvars: ( 0.455288 , -0.235486 , -0.217023 ) +colvars: ( 0.461095 , -0.307105 , -0.309108 ) +colvars: ( 0.403741 , -0.158354 , -0.144264 ) +colvars: ( 0.346363 , -0.151775 , -0.168959 ) +colvars: ( 0.328815 , -0.0605802 , -0.0576239 ) +colvars: ( 0.216326 , -0.160973 , -0.257063 ) +colvars: ( 0.190503 , -0.205174 , -0.331046 ) +colvars: ( 0.00428134 , -0.208989 , -0.444743 ) +colvars: ( -0.0916322 , -0.227677 , -0.525594 ) +colvars: ( 0.110242 , -0.261535 , -0.45299 ) +colvars: ( 0.13014 , -0.118197 , -0.250306 ) +colvars: ( 0.00431179 , -0.122752 , -0.329765 ) +colvars: ( -0.0894927 , -0.0378388 , -0.271279 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17251 , 0.564055 , 1.53892 ) +colvars: ( 4.43543 , 0.483677 , 1.31963 ) +colvars: ( 4.43543 , 0.483677 , 1.31963 ) +colvars: ( 5.90812 , 0.644271 , 1.75778 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.649345 , -0.0851595 , -0.391818 ) +colvars: ( -0.583919 , -0.171647 , -0.360118 ) +colvars: ( -0.532237 , -0.148753 , -0.299339 ) +colvars: ( -0.542254 , -0.200381 , -0.329609 ) +colvars: ( -0.532162 , -0.138891 , -0.295399 ) +colvars: ( -0.515816 , -0.296521 , -0.340776 ) +colvars: ( -0.480915 , -0.338661 , -0.3223 ) +colvars: ( -0.45774 , -0.450772 , -0.342996 ) +colvars: ( -0.414959 , -0.301806 , -0.241742 ) +colvars: ( -0.409914 , -0.275364 , -0.226324 ) +colvars: ( -0.363646 , -0.296011 , -0.188032 ) +colvars: ( -0.300401 , -0.257564 , -0.109567 ) +colvars: ( -0.249827 , -0.273248 , -0.0650135 ) +colvars: ( -0.321154 , -0.14977 , -0.0881351 ) +colvars: ( -0.288234 , -0.11922 , -0.0431636 ) +colvars: ( -0.378623 , -0.0897894 , -0.122243 ) +colvars: ( -0.40691 , 0.0128555 , -0.110382 ) +colvars: ( -0.46015 , 0.0626209 , -0.144254 ) +colvars: ( -0.445869 , 0.0286332 , -0.143254 ) +colvars: ( -0.433931 , 0.0879368 , -0.10805 ) +colvars: ( -0.491684 , -0.0277273 , -0.211266 ) +colvars: ( -0.527134 , -0.0291693 , -0.247367 ) +colvars: ( -0.579145 , -0.0974105 , -0.326245 ) +colvars: ( -0.472059 , -0.060553 , -0.204454 ) +colvars: ( -0.479053 , -0.0144737 , -0.193411 ) +colvars: ( -0.414107 , -0.138243 , -0.1768 ) +colvars: ( -0.353352 , -0.170987 , -0.128725 ) +colvars: ( -0.300384 , -0.265252 , -0.112562 ) +colvars: ( -0.310461 , -0.094971 , -0.0559445 ) +colvars: ( -0.296308 , -0.0755168 , -0.0341337 ) +colvars: ( -0.290271 , -0.0481617 , -0.0173639 ) +colvars: ( -0.253553 , 0.0298604 , 0.0500156 ) +colvars: ( -0.231907 , 0.0573518 , 0.0824862 ) +colvars: ( -0.299769 , 0.120552 , 0.0392208 ) +colvars: ( -0.27178 , 0.164155 , 0.0843627 ) +colvars: ( -0.372529 , 0.150015 , -0.0221739 ) +colvars: ( -0.423688 , 0.229684 , -0.0422434 ) +colvars: ( -0.498487 , 0.253337 , -0.107958 ) +colvars: ( -0.435159 , 0.209035 , -0.0618327 ) +colvars: ( -0.439841 , 0.272585 , -0.0416259 ) +colvars: ( -0.43934 , 0.118641 , -0.101443 ) +colvars: ( -0.446128 , 0.0871937 , -0.120569 ) +colvars: ( -0.468228 , -0.0102267 , -0.180895 ) +colvars: ( -0.375971 , 0.0753477 , -0.0548807 ) +colvars: ( -0.379126 , 0.102866 , -0.0472612 ) +colvars: ( -0.207572 , 0.109286 , 0.12723 ) +colvars: ( -0.155587 , 0.111183 , 0.180086 ) +colvars: ( -0.236033 , 0.184831 , 0.128299 ) +colvars: ( -0.310561 , 0.0326909 , -0.00602394 ) +colvars: ( -0.240414 , 0.0183914 , 0.0586924 ) +colvars: ( -0.183858 , -0.0684813 , 0.0813497 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 18. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 18. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atoms_new_colvar_forces = { ( -4.88055193397894e+00 , -4.43478910108217e-01 , -1.27612127602987e+00 ), ( -4.20417305438709e+00 , -3.75042739796872e-01 , -9.99314366272996e-01 ), ( -4.28058523683773e+00 , -4.02901954553682e-01 , -1.03650554418330e+00 ), ( -5.75573229032827e+00 , -5.72031674256922e-01 , -1.54111669298228e+00 ), ( 2.66318501216363e-01 , 1.24266758922591e-01 , 3.61718003296263e-01 ), ( 5.26245078426296e+00 , 6.30009218048564e-01 , 1.86600457302523e+00 ), ( 4.44705461385751e+00 , 5.22282976675805e-01 , 1.61887303421573e+00 ), ( -4.61538444750539e-02 , 2.88561944776561e-02 , 3.67790243298683e-01 ), ( 4.42695650367718e+00 , 5.12354875967253e-01 , 1.58687593843419e+00 ), ( 5.86792736008040e+00 , 6.55662845665289e-01 , 1.96071222741343e+00 ), ( 1.21083892763216e-02 , 4.00722555898481e-02 , 3.10501115119141e-01 ), ( 3.56729122269750e-04 , 3.34963142396088e-02 , 2.85207034264299e-01 ), ( 2.25563370014032e-02 , 4.83723396037330e-02 , 3.53949728091593e-01 ), ( 4.55351802266005e-02 , 3.83384706650591e-02 , 2.07850323953260e-01 ), ( 1.65419654283315e-02 , 2.33508396129858e-02 , 1.56006654147788e-01 ), ( 1.17623071559089e-01 , 5.92732325055574e-02 , 1.97252398101077e-01 ), ( 1.65914171330411e-01 , 6.57358934809209e-02 , 1.25559452111701e-01 ), ( 2.49446866519542e-01 , 9.33476751587075e-02 , 1.41925441933804e-01 ), ( 1.35820530901668e-01 , 4.80070651290457e-02 , 5.31906530259548e-02 ), ( 1.31133350000300e-01 , 3.88711228798389e-02 , -1.25366315702819e-02 ), ( 1.11893800416555e-01 , 4.20443734061019e-02 , 6.51292744036224e-02 ), ( 7.46495670413767e-02 , 2.35829464428652e-02 , 5.29272412948312e-03 ), ( 6.10494845332212e-02 , 2.34105382084128e-02 , 3.95585779705800e-02 ), ( -1.49904702789122e-03 , -3.03320911966064e-03 , -2.19721513373768e-02 ), ( -1.57506866378678e-02 , -1.58034704681422e-02 , -9.36121029512557e-02 ), ( -5.10772738514363e-02 , -1.16022560104394e-02 , 3.51092021854199e-02 ), ( -1.21708473978073e-01 , -3.52530958312200e-02 , 1.86769218150234e-02 ), ( -1.65211821674086e-01 , -3.92421347287457e-02 , 9.89195626694808e-02 ), ( -1.08474076072152e-01 , -3.67888706144353e-02 , -2.92202414212849e-02 ), ( -1.46352990341894e-01 , -5.53767489712473e-02 , -8.84691794821692e-02 ), ( -5.26685027683792e-02 , -1.68706990068804e-02 , -5.71534278842813e-03 ), ( -3.06261870181251e-02 , -1.51043739933480e-02 , -4.85497857183163e-02 ), ( 2.84462460092408e-02 , 8.87557161011229e-03 , 1.06834129297995e-03 ), ( 2.48765332295214e-03 , -1.48835771769152e-02 , -1.33681054412397e-01 ), ( -1.59195681968530e-02 , -2.71470722396890e-02 , -1.90071771994133e-01 ), ( 5.11746940255364e-02 , -1.27618104709343e-03 , -1.45380096964017e-01 ), ( 8.16563048292831e-02 , -1.07608224995226e-03 , -2.23771136294045e-01 ), ( 1.45217880141445e-01 , 1.97963220172846e-02 , -2.12496073319685e-01 ), ( 2.01291864255175e-02 , -2.64510443993880e-02 , -2.78855795220795e-01 ), ( 2.12543849167845e-02 , -3.45190587966575e-02 , -3.50734163088580e-01 ), ( -3.55984867246216e-02 , -3.97132551308617e-02 , -2.45706420571687e-01 ), ( -9.97649977540289e-02 , -6.45817026217195e-02 , -2.89528277972865e-01 ), ( -1.39412977565508e-01 , -7.08068240309979e-02 , -2.38518757703770e-01 ), ( -1.59645044756055e-01 , -8.56256780612288e-02 , -3.11943417990449e-01 ), ( -1.88622827480064e-01 , -1.02308355531449e-01 , -3.78307685579187e-01 ), ( -2.03290614725154e-01 , -9.97037153885587e-02 , -3.17512971009593e-01 ), ( -2.47218961600788e-01 , -1.16493877672746e-01 , -3.45507940216820e-01 ), ( -1.25791019609101e-01 , -7.67039286620122e-02 , -3.24691307323793e-01 ), ( -1.80420898008196e-01 , -8.55064433798007e-02 , -2.56329502163869e-01 ), ( -2.36102526876132e-01 , -1.04360796236778e-01 , -2.71072364016474e-01 ), ( -2.73350213448780e-01 , -1.06320100221581e-01 , -1.89929374319025e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 19, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 19, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 19, atoms_positions[size = 51] = { ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 ), ( 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 ), ( 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 ), ( 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 ), ( 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 ), ( 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 ), ( 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 ), ( 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 ), ( 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 ), ( 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 ), ( 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 ), ( 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 ), ( 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 ), ( 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 ), ( 2.79449313515955e+00 , 4.15799608277627e+00 , 2.49284759025593e+00 ), ( 3.93454759904606e+00 , 3.24104521362461e+00 , 7.31951298720477e-01 ), ( 2.65726401670662e+00 , 3.00924108365266e+00 , -1.05498188100982e-01 ), ( 3.04736003109482e+00 , 2.71004105763005e+00 , -1.51686507513849e+00 ), ( 1.59697894003139e+00 , 2.18796462741218e+00 , 4.53650193681246e-01 ), ( 3.84316586534183e-01 , 2.57242261776813e+00 , 5.13703608345861e-01 ), ( 2.03953806329203e+00 , 1.05551294165828e+00 , 1.07378939657437e+00 ), ( 1.17135282528705e+00 , 1.15035186348851e-01 , 1.69589580000055e+00 ), ( 2.03987486871026e+00 , -1.10729221445392e+00 , 2.00847688085443e+00 ), ( 5.60359091293224e-01 , 6.10390355972048e-01 , 2.93786782504420e+00 ), ( -6.07652617336230e-01 , 3.49468198602874e-01 , 3.16222771402236e+00 ), ( 1.31974871895307e+00 , 1.34554477618616e+00 , 3.78504529634619e+00 ), ( 8.45272575166906e-01 , 1.97598108814588e+00 , 5.02552654623703e+00 ), ( 2.07056674430801e+00 , 2.67820079829358e+00 , 5.67522110011561e+00 ), ( -3.37337329784998e-01 , 2.91531659103695e+00 , 4.96763711296850e+00 ), ( -1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 ), ( -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 ), ( -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 ), ( -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 ), ( -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 ), ( -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 ), ( -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 ), ( -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 ), ( -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 ), ( -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 ), ( -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 ), ( -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 ), ( -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 ), ( -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 ), ( -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 ), ( -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 ), ( -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 ), ( -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 ), ( -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 ), ( -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 ), ( -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 ), ( -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ) } +colvars: Step 19, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 ). +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.05077482584572e-01 , 8.59223702593821e-04 , 9.52327145131592e-01 ). +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 , 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 , 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 , 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 , 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 , 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 , 2.79449313515955e+00 , 4.15799608277627e+00 , 2.49284759025593e+00 , 3.93454759904606e+00 , 3.24104521362461e+00 , 7.31951298720477e-01 , 2.65726401670662e+00 , 3.00924108365266e+00 , -1.05498188100982e-01 , 3.04736003109482e+00 , 2.71004105763005e+00 , -1.51686507513849e+00 , 1.59697894003139e+00 , 2.18796462741218e+00 , 4.53650193681246e-01 , 3.84316586534183e-01 , 2.57242261776813e+00 , 5.13703608345861e-01 , 2.03953806329203e+00 , 1.05551294165828e+00 , 1.07378939657437e+00 , 1.17135282528705e+00 , 1.15035186348851e-01 , 1.69589580000055e+00 , 2.03987486871026e+00 , -1.10729221445392e+00 , 2.00847688085443e+00 , 5.60359091293224e-01 , 6.10390355972048e-01 , 2.93786782504420e+00 , -6.07652617336230e-01 , 3.49468198602874e-01 , 3.16222771402236e+00 , 1.31974871895307e+00 , 1.34554477618616e+00 , 3.78504529634619e+00 , 8.45272575166906e-01 , 1.97598108814588e+00 , 5.02552654623703e+00 , 2.07056674430801e+00 , 2.67820079829358e+00 , 5.67522110011561e+00 , -3.37337329784998e-01 , 2.91531659103695e+00 , 4.96763711296850e+00 , -1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 , -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 , -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 , -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 , -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 , -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 , -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 , -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 , -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 , -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 , -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 , -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 , -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 , -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 , -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 , -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 , -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 , -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 , -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 , -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 , -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 , -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.05077482584572e-01 , 8.59223702593821e-04 , 9.52327145131592e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.28846125690671e+00 , 4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 , 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 , 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 , 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 , 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 , 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 , 2.79449313515955e+00 , 4.15799608277627e+00 , 2.49284759025593e+00 , 3.93454759904606e+00 , 3.24104521362461e+00 , 7.31951298720477e-01 , 2.65726401670662e+00 , 3.00924108365266e+00 , -1.05498188100982e-01 , 3.04736003109482e+00 , 2.71004105763005e+00 , -1.51686507513849e+00 , 1.59697894003139e+00 , 2.18796462741218e+00 , 4.53650193681246e-01 , 3.84316586534183e-01 , 2.57242261776813e+00 , 5.13703608345861e-01 , 2.03953806329203e+00 , 1.05551294165828e+00 , 1.07378939657437e+00 , 1.17135282528705e+00 , 1.15035186348851e-01 , 1.69589580000055e+00 , 2.03987486871026e+00 , -1.10729221445392e+00 , 2.00847688085443e+00 , 5.60359091293224e-01 , 6.10390355972048e-01 , 2.93786782504420e+00 , -6.07652617336230e-01 , 3.49468198602874e-01 , 3.16222771402236e+00 , 1.31974871895307e+00 , 1.34554477618616e+00 , 3.78504529634619e+00 , 8.45272575166906e-01 , 1.97598108814588e+00 , 5.02552654623703e+00 , 2.07056674430801e+00 , 2.67820079829358e+00 , 5.67522110011561e+00 , -3.37337329784998e-01 , 2.91531659103695e+00 , 4.96763711296850e+00 , -1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 , -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 , -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 , -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 , -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 , -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 , -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 , -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 , -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 , -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 , -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 , -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 , -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 , -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 , -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 , -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 , -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 , -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 , -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 , -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 , -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 , -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.1038 , 6.61038 , 13.2208 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.1038 , 6.61038 , 13.2208 ) to colvar "one". +colvars: Adding total bias energy: 56.6361 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.1038 , 6.61038 , 13.2208 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17347 , -0.561901 , -1.53062 ) +colvars: ( -4.43625 , -0.48183 , -1.31251 ) +colvars: ( -4.43625 , -0.48183 , -1.31251 ) +colvars: ( -5.90921 , -0.641811 , -1.7483 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.940097 , 0.205758 , 0.652548 ) +colvars: ( 0.814226 , 0.280198 , 0.678227 ) +colvars: ( 0.797523 , 0.272966 , 0.658881 ) +colvars: ( 0.696458 , 0.281001 , 0.610698 ) +colvars: ( 0.683936 , 0.211014 , 0.510333 ) +colvars: ( 0.605357 , 0.362211 , 0.665633 ) +colvars: ( 0.492452 , 0.376922 , 0.619433 ) +colvars: ( 0.411711 , 0.479167 , 0.708375 ) +colvars: ( 0.40653 , 0.330141 , 0.507174 ) +colvars: ( 0.369889 , 0.286411 , 0.427677 ) +colvars: ( 0.375764 , 0.33575 , 0.496712 ) +colvars: ( 0.300867 , 0.290737 , 0.393226 ) +colvars: ( 0.272449 , 0.321292 , 0.417307 ) +colvars: ( 0.366633 , 0.187889 , 0.29476 ) +colvars: ( 0.304857 , 0.14235 , 0.198216 ) +colvars: ( 0.495889 , 0.148937 , 0.318246 ) +colvars: ( 0.572284 , 0.0528582 , 0.234973 ) +colvars: ( 0.708717 , 0.0307971 , 0.285102 ) +colvars: ( 0.581231 , 0.0193501 , 0.195623 ) +colvars: ( 0.564642 , -0.0490533 , 0.0949931 ) +colvars: ( 0.603162 , 0.0697015 , 0.275358 ) +colvars: ( 0.601476 , 0.0526639 , 0.251717 ) +colvars: ( 0.639884 , 0.120685 , 0.364548 ) +colvars: ( 0.47057 , 0.0573557 , 0.181708 ) +colvars: ( 0.463367 , -0.00146975 , 0.0992828 ) +colvars: ( 0.363256 , 0.126384 , 0.211 ) +colvars: ( 0.232171 , 0.135403 , 0.146641 ) +colvars: ( 0.135887 , 0.225581 , 0.210482 ) +colvars: ( 0.202513 , 0.0579058 , 0.0263043 ) +colvars: ( 0.150633 , 0.0198521 , -0.0545199 ) +colvars: ( 0.237947 , 0.0310775 , 0.0112659 ) +colvars: ( 0.223232 , -0.0451169 , -0.0986334 ) +colvars: ( 0.260464 , -0.0485769 , -0.0815483 ) +colvars: ( 0.302418 , -0.135499 , -0.172705 ) +colvars: ( 0.256118 , -0.19135 , -0.273948 ) +colvars: ( 0.423633 , -0.151294 , -0.123106 ) +colvars: ( 0.505134 , -0.230682 , -0.181209 ) +colvars: ( 0.643205 , -0.233396 , -0.104397 ) +colvars: ( 0.455291 , -0.235458 , -0.216593 ) +colvars: ( 0.4611 , -0.307031 , -0.308392 ) +colvars: ( 0.403931 , -0.15842 , -0.14406 ) +colvars: ( 0.346777 , -0.151901 , -0.16868 ) +colvars: ( 0.329342 , -0.0607935 , -0.0576753 ) +colvars: ( 0.217013 , -0.161154 , -0.256569 ) +colvars: ( 0.191298 , -0.205353 , -0.330326 ) +colvars: ( 0.00526842 , -0.209198 , -0.443796 ) +colvars: ( -0.0904425 , -0.227918 , -0.52444 ) +colvars: ( 0.110934 , -0.261641 , -0.451991 ) +colvars: ( 0.130949 , -0.118429 , -0.249881 ) +colvars: ( 0.00537865 , -0.123038 , -0.329151 ) +colvars: ( -0.0882579 , -0.0382154 , -0.270889 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17347 , 0.561901 , 1.53062 ) +colvars: ( 4.43625 , 0.48183 , 1.31251 ) +colvars: ( 4.43625 , 0.48183 , 1.31251 ) +colvars: ( 5.90921 , 0.641811 , 1.7483 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.648543 , -0.0851979 , -0.390134 ) +colvars: ( -0.583282 , -0.171711 , -0.358239 ) +colvars: ( -0.531413 , -0.148795 , -0.29738 ) +colvars: ( -0.541871 , -0.20043 , -0.327861 ) +colvars: ( -0.531781 , -0.13889 , -0.293912 ) +colvars: ( -0.515655 , -0.296613 , -0.338841 ) +colvars: ( -0.481021 , -0.338751 , -0.320452 ) +colvars: ( -0.458043 , -0.450919 , -0.340869 ) +colvars: ( -0.415078 , -0.301841 , -0.240067 ) +colvars: ( -0.410152 , -0.275368 , -0.224877 ) +colvars: ( -0.363633 , -0.296032 , -0.186259 ) +colvars: ( -0.300371 , -0.257534 , -0.107946 ) +colvars: ( -0.249658 , -0.273221 , -0.0631978 ) +colvars: ( -0.320974 , -0.14968 , -0.0868193 ) +colvars: ( -0.288134 , -0.119088 , -0.042058 ) +colvars: ( -0.378223 , -0.0896943 , -0.12096 ) +colvars: ( -0.406355 , 0.0130035 , -0.109377 ) +colvars: ( -0.459327 , 0.0627639 , -0.143192 ) +colvars: ( -0.445471 , 0.0287905 , -0.142464 ) +colvars: ( -0.433542 , 0.0881434 , -0.107519 ) +colvars: ( -0.491424 , -0.0276187 , -0.210367 ) +colvars: ( -0.527054 , -0.0290611 , -0.246635 ) +colvars: ( -0.579168 , -0.097365 , -0.325319 ) +colvars: ( -0.472218 , -0.0604278 , -0.203827 ) +colvars: ( -0.479277 , -0.0143118 , -0.193039 ) +colvars: ( -0.414397 , -0.138142 , -0.17598 ) +colvars: ( -0.353853 , -0.17087 , -0.127979 ) +colvars: ( -0.300997 , -0.265176 , -0.111534 ) +colvars: ( -0.310871 , -0.0947888 , -0.0554333 ) +colvars: ( -0.296851 , -0.075304 , -0.0338356 ) +colvars: ( -0.290445 , -0.0479556 , -0.0168229 ) +colvars: ( -0.253607 , 0.0301291 , 0.0503411 ) +colvars: ( -0.231711 , 0.0576293 , 0.0829371 ) +colvars: ( -0.299745 , 0.120864 , 0.0392458 ) +colvars: ( -0.271801 , 0.164513 , 0.0841578 ) +colvars: ( -0.372391 , 0.150311 , -0.0221541 ) +colvars: ( -0.423487 , 0.230015 , -0.0424916 ) +colvars: ( -0.498115 , 0.253642 , -0.108132 ) +colvars: ( -0.435207 , 0.209366 , -0.0622356 ) +colvars: ( -0.439892 , 0.272962 , -0.0422984 ) +colvars: ( -0.439606 , 0.11892 , -0.101676 ) +colvars: ( -0.446649 , 0.0874676 , -0.120917 ) +colvars: ( -0.468922 , -0.0100199 , -0.180999 ) +colvars: ( -0.376653 , 0.0756528 , -0.055343 ) +colvars: ( -0.379925 , 0.1032 , -0.0479525 ) +colvars: ( -0.208254 , 0.109681 , 0.126607 ) +colvars: ( -0.156387 , 0.111609 , 0.179335 ) +colvars: ( -0.236446 , 0.185251 , 0.127623 ) +colvars: ( -0.311256 , 0.0329906 , -0.00632615 ) +colvars: ( -0.241254 , 0.0187193 , 0.0583023 ) +colvars: ( -0.184781 , -0.0681894 , 0.0812374 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 19. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 19. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atoms_new_colvar_forces = { ( -4.88191171719184e+00 , -4.41340748118462e-01 , -1.26820824536058e+00 ), ( -4.20530221680057e+00 , -3.73342976770697e-01 , -9.92520433481477e-01 ), ( -4.28165931112879e+00 , -4.01259264608975e-01 , -1.02967036003239e+00 ), ( -5.75705258921491e+00 , -5.69686746119912e-01 , -1.53187762037129e+00 ), ( 2.66110051993996e-01 , 1.24170798212882e-01 , 3.61501230465698e-01 ), ( 5.26316777428457e+00 , 6.27498310071210e-01 , 1.85741369607553e+00 ), ( 4.44767675245246e+00 , 5.20001094476915e-01 , 1.61148885882558e+00 ), ( -4.63322505446268e-02 , 2.82473186619320e-02 , 3.67505260898104e-01 ), ( 4.42769795664276e+00 , 5.10130300487824e-01 , 1.57961461004834e+00 ), ( 5.86894508044445e+00 , 6.52854373367683e-01 , 1.95109862860026e+00 ), ( 1.21315126980281e-02 , 3.97171205298853e-02 , 3.10453126119482e-01 ), ( 4.96304438557249e-04 , 3.32027922309193e-02 , 2.85279954745149e-01 ), ( 2.27906777543655e-02 , 4.80708483874093e-02 , 3.54109275355419e-01 ), ( 4.56597958389400e-02 , 3.82094250766497e-02 , 2.07940850769046e-01 ), ( 1.67233174273261e-02 , 2.32622384094650e-02 , 1.56158425509746e-01 ), ( 1.17666638015727e-01 , 5.92422707318476e-02 , 1.97285509487435e-01 ), ( 1.65929222178092e-01 , 6.58617567097613e-02 , 1.25595978990976e-01 ), ( 2.49389894292330e-01 , 9.35610160162401e-02 , 1.41910759755505e-01 ), ( 1.35760111023169e-01 , 4.81405430433821e-02 , 5.31585978127963e-02 ), ( 1.31100423685580e-01 , 3.90900854400270e-02 , -1.25262494798617e-02 ), ( 1.11738458009229e-01 , 4.20828261715862e-02 , 6.49903348382647e-02 ), ( 7.44215102507678e-02 , 2.36027894382352e-02 , 5.08274108428097e-03 ), ( 6.07162010857553e-02 , 2.33203908347595e-02 , 3.92290332781103e-02 ), ( -1.64796713521265e-03 , -3.07204273987724e-03 , -2.21187490800692e-02 ), ( -1.59100927771452e-02 , -1.57815680205100e-02 , -9.37564347734113e-02 ), ( -5.11413081282260e-02 , -1.17578540735976e-02 , 3.50196613746180e-02 ), ( -1.21682005274002e-01 , -3.54668009988348e-02 , 1.86614180094759e-02 ), ( -1.65110072478926e-01 , -3.95953568229259e-02 , 9.89476231459412e-02 ), ( -1.08358081653477e-01 , -3.68829912496071e-02 , -2.91289612228090e-02 ), ( -1.46217540157399e-01 , -5.54518984572675e-02 , -8.83555420336157e-02 ), ( -5.24980141277098e-02 , -1.68781488453493e-02 , -5.55696233807787e-03 ), ( -3.03751562906074e-02 , -1.49877474249199e-02 , -4.82922428985002e-02 ), ( 2.87528869169160e-02 , 9.05237715686172e-03 , 1.38880574068770e-03 ), ( 2.67290144676630e-03 , -1.46345448100467e-02 , -1.33459465872841e-01 ), ( -1.56826354748457e-02 , -2.68365573891298e-02 , -1.89789678322153e-01 ), ( 5.12424070455644e-02 , -9.82089695742538e-04 , -1.45260050778780e-01 ), ( 8.16474062134026e-02 , -6.66934530635710e-04 , -2.23700511610446e-01 ), ( 1.45090396667341e-01 , 2.02462557789115e-02 , -2.12528996987919e-01 ), ( 2.00833633686362e-02 , -2.60913869136274e-02 , -2.78828527022585e-01 ), ( 2.12077334206092e-02 , -3.40687437189181e-02 , -3.50689961213515e-01 ), ( -3.56748573250362e-02 , -3.95001765829997e-02 , -2.45735608642734e-01 ), ( -9.98716562022168e-02 , -6.44336257370528e-02 , -2.89597625160121e-01 ), ( -1.39579880116700e-01 , -7.08134918227497e-02 , -2.38674087078582e-01 ), ( -1.59639329639736e-01 , -8.55011180542551e-02 , -3.11911686917638e-01 ), ( -1.88626091817599e-01 , -1.02153381409446e-01 , -3.78278020535754e-01 ), ( -2.02985561273833e-01 , -9.95167954380901e-02 , -3.17189040017282e-01 ), ( -2.46829299567918e-01 , -1.16308956872553e-01 , -3.45104849554674e-01 ), ( -1.25511433933694e-01 , -7.63904543746538e-02 , -3.24367407250947e-01 ), ( -1.80306272262975e-01 , -8.54388010075336e-02 , -2.56206956184511e-01 ), ( -2.35874895896961e-01 , -1.04318953534194e-01 , -2.70848650142971e-01 ), ( -2.73038541180380e-01 , -1.06404775091823e-01 , -1.89651456564909e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 20, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 ), ( 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 ), ( 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 ), ( 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ), ( 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 ), ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 ), ( 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 ), ( 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 ), ( 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 ), ( 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ), ( 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 ), ( 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 ), ( 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 ), ( 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 ), ( 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 ), ( 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 ), ( 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 ), ( 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 ), ( 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 ), ( 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 ), ( 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 ), ( 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 ), ( 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 ), ( 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 ), ( -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 ), ( 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 ), ( 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 ), ( 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 ), ( -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 ), ( -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 ), ( -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 ), ( -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 ), ( -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 ), ( -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 ), ( -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 ), ( -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 ), ( -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 ), ( -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 ), ( -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 ), ( -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 ), ( -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 ), ( -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 ), ( -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 ), ( -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 ), ( -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 ), ( -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 ), ( -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 ), ( -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 ), ( -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 ), ( -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 ), ( -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.0363 , 6.60363 , 13.2073 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.0363 , 6.60363 , 13.2073 ) to colvar "one". +colvars: Adding total bias energy: 56.5387 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.0363 , 6.60363 , 13.2073 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17524 , -0.560146 , -1.5236 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -5.91123 , -0.639807 , -1.74028 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.939145 , 0.205822 , 0.650791 ) +colvars: ( 0.813493 , 0.280183 , 0.676344 ) +colvars: ( 0.79671 , 0.272971 , 0.657011 ) +colvars: ( 0.695988 , 0.280925 , 0.60896 ) +colvars: ( 0.683489 , 0.210958 , 0.508858 ) +colvars: ( 0.605096 , 0.362058 , 0.663721 ) +colvars: ( 0.492454 , 0.376702 , 0.617613 ) +colvars: ( 0.411895 , 0.478868 , 0.706292 ) +colvars: ( 0.40664 , 0.329912 , 0.505603 ) +colvars: ( 0.370107 , 0.286173 , 0.426316 ) +colvars: ( 0.375838 , 0.335525 , 0.495129 ) +colvars: ( 0.30102 , 0.290509 , 0.391871 ) +colvars: ( 0.272557 , 0.321061 , 0.415847 ) +colvars: ( 0.366646 , 0.187731 , 0.293691 ) +colvars: ( 0.304985 , 0.14218 , 0.19738 ) +colvars: ( 0.495648 , 0.148851 , 0.317164 ) +colvars: ( 0.571887 , 0.0528434 , 0.234141 ) +colvars: ( 0.70803 , 0.0308578 , 0.284183 ) +colvars: ( 0.580911 , 0.0193309 , 0.194928 ) +colvars: ( 0.564352 , -0.0490553 , 0.0945605 ) +colvars: ( 0.602884 , 0.069656 , 0.274483 ) +colvars: ( 0.601296 , 0.052603 , 0.250934 ) +colvars: ( 0.639709 , 0.120601 , 0.363501 ) +colvars: ( 0.470661 , 0.05723 , 0.181065 ) +colvars: ( 0.463505 , -0.0015853 , 0.098867 ) +colvars: ( 0.363526 , 0.126191 , 0.210227 ) +colvars: ( 0.232697 , 0.135147 , 0.145989 ) +colvars: ( 0.136568 , 0.225255 , 0.209612 ) +colvars: ( 0.203032 , 0.0576775 , 0.0259439 ) +colvars: ( 0.151284 , 0.019607 , -0.0546754 ) +colvars: ( 0.238306 , 0.0308947 , 0.0109328 ) +colvars: ( 0.223552 , -0.0452647 , -0.0986978 ) +colvars: ( 0.260612 , -0.0486848 , -0.0816732 ) +colvars: ( 0.30262 , -0.135586 , -0.17253 ) +colvars: ( 0.256401 , -0.191436 , -0.273522 ) +colvars: ( 0.423642 , -0.151329 , -0.123003 ) +colvars: ( 0.505029 , -0.230661 , -0.180906 ) +colvars: ( 0.642858 , -0.233317 , -0.104237 ) +colvars: ( 0.455372 , -0.235478 , -0.216188 ) +colvars: ( 0.461185 , -0.307026 , -0.307735 ) +colvars: ( 0.404175 , -0.158505 , -0.14385 ) +colvars: ( 0.347218 , -0.152033 , -0.168403 ) +colvars: ( 0.329883 , -0.0609799 , -0.0576822 ) +colvars: ( 0.217684 , -0.161336 , -0.256114 ) +colvars: ( 0.192064 , -0.205541 , -0.32967 ) +colvars: ( 0.00617868 , -0.209423 , -0.442974 ) +colvars: ( -0.0893621 , -0.228177 , -0.523444 ) +colvars: ( 0.111592 , -0.261789 , -0.451119 ) +colvars: ( 0.131717 , -0.118651 , -0.249498 ) +colvars: ( 0.00636188 , -0.12331 , -0.328614 ) +colvars: ( -0.0871363 , -0.0385503 , -0.270558 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17524 , 0.560146 , 1.5236 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 5.91123 , 0.639807 , 1.74028 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.647974 , -0.0852573 , -0.388753 ) +colvars: ( -0.582839 , -0.171838 , -0.35665 ) +colvars: ( -0.530769 , -0.148883 , -0.295681 ) +colvars: ( -0.541646 , -0.200563 , -0.326377 ) +colvars: ( -0.531553 , -0.138947 , -0.29266 ) +colvars: ( -0.515626 , -0.296838 , -0.337183 ) +colvars: ( -0.481227 , -0.338999 , -0.318864 ) +colvars: ( -0.458422 , -0.451281 , -0.339024 ) +colvars: ( -0.415265 , -0.302019 , -0.238601 ) +colvars: ( -0.41045 , -0.275508 , -0.22362 ) +colvars: ( -0.363672 , -0.296189 , -0.184669 ) +colvars: ( -0.300365 , -0.257621 , -0.106457 ) +colvars: ( -0.2495 , -0.273312 , -0.0614974 ) +colvars: ( -0.320837 , -0.149656 , -0.0856129 ) +colvars: ( -0.288058 , -0.119011 , -0.0410273 ) +colvars: ( -0.377907 , -0.0896324 , -0.119807 ) +colvars: ( -0.405907 , 0.0131673 , -0.108485 ) +colvars: ( -0.458652 , 0.0629527 , -0.142267 ) +colvars: ( -0.445189 , 0.028964 , -0.141797 ) +colvars: ( -0.433263 , 0.0883914 , -0.107081 ) +colvars: ( -0.491292 , -0.0275236 , -0.209633 ) +colvars: ( -0.527109 , -0.028974 , -0.246079 ) +colvars: ( -0.579343 , -0.0973742 , -0.324623 ) +colvars: ( -0.472472 , -0.0603448 , -0.203347 ) +colvars: ( -0.479594 , -0.0141749 , -0.192798 ) +colvars: ( -0.414746 , -0.138121 , -0.175297 ) +colvars: ( -0.354373 , -0.170853 , -0.127338 ) +colvars: ( -0.301597 , -0.265244 , -0.110611 ) +colvars: ( -0.311285 , -0.09467 , -0.0549772 ) +colvars: ( -0.297384 , -0.0751509 , -0.0335708 ) +colvars: ( -0.290629 , -0.0477842 , -0.0163181 ) +colvars: ( -0.253661 , 0.0304013 , 0.050676 ) +colvars: ( -0.23152 , 0.0579314 , 0.0834089 ) +colvars: ( -0.299747 , 0.121221 , 0.039285 ) +colvars: ( -0.271833 , 0.164934 , 0.084002 ) +colvars: ( -0.37232 , 0.150668 , -0.022156 ) +colvars: ( -0.42338 , 0.230441 , -0.0427631 ) +colvars: ( -0.497883 , 0.254059 , -0.108372 ) +colvars: ( -0.435341 , 0.209775 , -0.062665 ) +colvars: ( -0.440031 , 0.273443 , -0.0429754 ) +colvars: ( -0.439945 , 0.119231 , -0.101963 ) +colvars: ( -0.447231 , 0.0877498 , -0.121324 ) +colvars: ( -0.469676 , -0.00985306 , -0.181203 ) +colvars: ( -0.377354 , 0.0759564 , -0.0558201 ) +colvars: ( -0.380737 , 0.103539 , -0.0486444 ) +colvars: ( -0.208877 , 0.110092 , 0.126079 ) +colvars: ( -0.157097 , 0.112049 , 0.178715 ) +colvars: ( -0.23683 , 0.185727 , 0.127043 ) +colvars: ( -0.311938 , 0.0332713 , -0.00662132 ) +colvars: ( -0.242039 , 0.0190178 , 0.0579609 ) +colvars: ( -0.185619 , -0.0679661 , 0.0811767 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -4.88406726017846e+00 , -4.39582030019637e-01 , -1.26156546289831e+00 ), ( -4.20711207586693e+00 , -3.71980090924366e-01 , -9.86796367004215e-01 ), ( -4.28342445948863e+00 , -3.99963693514908e-01 , -1.02390709400074e+00 ), ( -5.75929727923110e+00 , -5.67796041518724e-01 , -1.52408480248038e+00 ), ( 2.65941268390902e-01 , 1.24088041235363e-01 , 3.61330101161847e-01 ), ( 5.26470856148017e+00 , 6.25365994053560e-01 , 1.85014148432867e+00 ), ( 4.44899395969789e+00 , 5.18028786716414e-01 , 1.60523898998076e+00 ), ( -4.65272910606424e-02 , 2.75874394655633e-02 , 3.67268098303653e-01 ), ( 4.42914052995064e+00 , 5.08218685700347e-01 , 1.57349215273307e+00 ), ( 5.87089063969169e+00 , 6.50472344458009e-01 , 1.94297816123059e+00 ), ( 1.21655890342579e-02 , 3.93361229409889e-02 , 3.10460529518665e-01 ), ( 6.54352727631202e-04 , 3.28877838588784e-02 , 2.85413778669853e-01 ), ( 2.30575218111934e-02 , 4.77496012635013e-02 , 3.54349709040753e-01 ), ( 4.58084561993378e-02 , 3.80749776841854e-02 , 2.08077917584342e-01 ), ( 1.69271357430614e-02 , 2.31692671284452e-02 , 1.56352523085799e-01 ), ( 1.17740497737709e-01 , 5.92187670987907e-02 , 1.97356769209817e-01 ), ( 1.65979650547149e-01 , 6.60107587124940e-02 , 1.25656124587784e-01 ), ( 2.49378084035319e-01 , 9.38105312411004e-02 , 1.41916759655613e-01 ), ( 1.35721171926268e-01 , 4.82948683031030e-02 , 5.31311614239589e-02 ), ( 1.31089117563867e-01 , 3.93361615661934e-02 , -1.25202269468064e-02 ), ( 1.11591946272047e-01 , 4.21324308431365e-02 , 6.48498773882783e-02 ), ( 7.41875459869102e-02 , 2.36289347234540e-02 , 4.85459631934207e-03 ), ( 6.03658790245055e-02 , 2.32264957257031e-02 , 3.88781977774767e-02 ), ( -1.81078736534573e-03 , -3.11478153248525e-03 , -2.22818060419844e-02 ), ( -1.60885473686671e-02 , -1.57601748864797e-02 , -9.39304968271742e-02 ), ( -5.12199048641456e-02 , -1.19297840935810e-02 , 3.49304717831433e-02 ), ( -1.21675813902335e-01 , -3.57064899870657e-02 , 1.86508224653453e-02 ), ( -1.65028468419942e-01 , -3.99882775272279e-02 , 9.90005933951236e-02 ), ( -1.08252979508245e-01 , -3.69924344963437e-02 , -2.90333247285238e-02 ), ( -1.46099690198963e-01 , -5.55439012742997e-02 , -8.82462486637547e-02 ), ( -5.23225535297807e-02 , -1.68894940154288e-02 , -5.38529268697861e-03 ), ( -3.01087883421307e-02 , -1.48633476968855e-02 , -4.80218171751865e-02 ), ( 2.90920024039188e-02 , 9.24664271438187e-03 , 1.73568422449372e-03 ), ( 2.87212446123969e-03 , -1.43653564917826e-02 , -1.33245075124415e-01 ), ( -1.54318476939863e-02 , -2.65024240836628e-02 , -1.89520159508813e-01 ), ( 5.13226740441255e-02 , -6.61117676194450e-04 , -1.45158995615856e-01 ), ( 8.16483892005009e-02 , -2.20115925109621e-04 , -2.23668733880816e-01 ), ( 1.44974583626733e-01 , 2.07414644297433e-02 , -2.12608633585807e-01 ), ( 2.00313536000674e-02 , -2.57030285264907e-02 , -2.78852997194507e-01 ), ( 2.11535019058627e-02 , -3.35827543487625e-02 , -3.50709917556565e-01 ), ( -3.57699416572513e-02 , -3.92742347993370e-02 , -2.45813691592460e-01 ), ( -1.00012769612954e-01 , -6.42830113991747e-02 , -2.89726269929375e-01 ), ( -1.39792965314805e-01 , -7.08329385419267e-02 , -2.38885255145827e-01 ), ( -1.59669948187276e-01 , -8.53800481419532e-02 , -3.11933814118016e-01 ), ( -1.88673377030574e-01 , -1.02001994075380e-01 , -3.78314516895504e-01 ), ( -2.02698784283931e-01 , -9.93305031383851e-02 , -3.16894644449761e-01 ), ( -2.46459346918119e-01 , -1.16127914776370e-01 , -3.44729104647447e-01 ), ( -1.25237872776220e-01 , -7.60618339454901e-02 , -3.24076090847715e-01 ), ( -1.80221106740230e-01 , -8.53800525072640e-02 , -2.56119533999097e-01 ), ( -2.35677590614575e-01 , -1.04291860665546e-01 , -2.70653229134327e-01 ), ( -2.72755086907763e-01 , -1.06516369333094e-01 , -1.89380901188017e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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..37633c6e6 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,32 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x ( -0.30360404081666 , -7.3012941347679e-05 , 0.95279828981212 ) +} + +colvar { + name group1 + x ( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 ) +} + +colvar { + name group2 + x ( 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 ) +} + +colvar { + name fitting_group1 + x ( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 7.0480762025172 , -2.0513347736704 , -0.93377134820149 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 , 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 7.0809081020816 , -0.35496020632887 , 4.3146586251214 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 , 5.8432995748295 , 2.2535778944039 , 2.9902963417856 , 5.2384055225152 , 3.5783754026257 , 2.9215354050906 , 6.3223993673226 , 4.5011441587991 , 2.3655584831763 , 3.8818312912342 , 3.7064721784147 , 2.0444644100133 , 2.7920736373314 , 4.1608362314759 , 2.4877638737485 , 3.9386798899873 , 3.2395859717867 , 0.73126389979658 , 2.6624894551197 , 3.0062849992536 , -0.10369017207615 , 3.0530237576774 , 2.7050981729996 , -1.515126439405 , 1.5978477264343 , 2.1831908534433 , 0.4458975934194 , 0.37935536668417 , 2.5812137098021 , 0.51015292695301 , 2.0475904030464 , 1.0706502363152 , 1.069723927279 , 1.1690699177228 , 0.11658295312925 , 1.6974226380185 , 2.0431803877623 , -1.1033045581944 , 2.0106005316873 , 0.56210382605836 , 0.61178504571473 , 2.9428051810465 , -0.60199958586972 , 0.34968520789238 , 3.1615301713297 , 1.3167209916681 , 1.3457617287353 , 3.7754423945574 , 0.84267356054463 , 1.9787990415851 , 5.0254234233262 , 2.0796156959584 , 2.6878063101542 , 5.6821293955537 , -0.33739104868865 , 2.9146961524331 , 4.9679941584516 , -1.1371464701093 , 3.062469534534 , 5.8877740932039 , -0.51179726121506 , 3.5352900024754 , 3.8463150986082 , -1.5180503491383 , 4.5391900691402 , 3.4442608843563 , -0.69961559166787 , 5.4143954882994 , 2.4637912416459 , -2.7602287545827 , 3.8895007500064 , 2.8949751960402 , -3.8174896819283 , 4.5099047856922 , 2.8146284855071 , -2.6251714284554 , 2.6732886369457 , 2.4014323234568 , -3.7726963733907 , 1.8037184430191 , 1.9982779981764 , -3.3886595184775 , 0.88672154595831 , 0.87409788378727 , -4.3225504216986 , 1.0700082818202 , 3.2121699488068 , -5.4999729212229 , 0.81876098547252 , 3.3291853384002 , -3.3690633481624 , 0.69157744271515 , 4.2041288719456 , -3.7011250996533 , 0.046206366217123 , 5.434092539774 , -2.3903901778542 , -0.31709933730245 , 6.1701094743001 , -4.4618292827148 , 0.98680918149928 , 6.4395743693712 , -5.3588837067265 , 0.5981100423375 , 7.2179576344598 , -6.2383325096938 , 3.6054824579338 , 6.7336443061013 , -6.9602157879944 , 4.2977470185681 , 7.4756432850253 , -6.741403987979 , 3.1822575304318 , 5.5078493030856 , -4.1287524553974 , 2.2462119095443 , 6.4096637239512 , -4.8089365560512 , 3.2066271871716 , 7.2417022510827 , -4.0950888618816 , 4.5754896432564 , 7.2828123626203 ) +} + +restraint { + 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..0269cb435 --- /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 group1 group2 fitting_group1 E_harmonic1 + 0 ( -3.39806527406457e-01 , 7.75672148823430e-03 , 9.40463373664131e-01 ) ( 6.78285239239432e+01 , 6.78285239239432e+00 , 1.35657047847886e+01 ) ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ) ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ) ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) 5.90741150968082e+01 + 1 ( -3.39355617493064e-01 , 6.97292683121385e-03 , 9.40632310293086e-01 ) ( 6.78086594552381e+01 , 6.78086594552381e+00 , 1.35617318910476e+01 ) ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 ) ( 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 ) ( 8.42020303490900e+00 , 4.21984069360959e-02 , -7.45621958662384e-01 , 7.00355608592927e+00 , -4.79961958151159e-01 , -6.79277613780946e-01 , 7.03907223754463e+00 , -2.00682939080258e+00 , -1.03762081772998e+00 , 6.23767243690126e+00 , -2.51247664976774e-01 , 6.26721383509191e-01 , 5.02836169011813e+00 , -2.08046144316483e-01 , 6.39278154297242e-01 , 6.90866341721336e+00 , -2.67401315526429e-01 , 1.77894611421926e+00 , 6.18213190571957e+00 , -1.31162429050258e-01 , 3.03990730230419e+00 , 7.19806646042565e+00 , -3.16977085957312e-01 , 4.30310573442264e+00 , 5.30277713134754e+00 , 1.14009103853889e+00 , 3.26020667822888e+00 , 4.09169403081403e+00 , 1.07931946025693e+00 , 3.60442085174786e+00 , 5.87383600352927e+00 , 2.34423028519429e+00 , 2.94316695743598e+00 , 5.23330841320636e+00 , 3.60157586558440e+00 , 2.87824114047597e+00 , 6.32195902365124e+00 , 4.64361834811927e+00 , 2.47418873628834e+00 , 3.90567268252602e+00 , 3.68544884197466e+00 , 2.03017241936737e+00 , 2.93268292003271e+00 , 4.11879117672839e+00 , 2.57740419512650e+00 , 3.81729640659816e+00 , 3.24363113269698e+00 , 7.83854480662681e-01 , 2.65736315754659e+00 , 3.20810259530773e+00 , -6.18610499897525e-02 , 3.04748253961770e+00 , 2.73697181600532e+00 , -1.57072847317123e+00 , 1.65396548416683e+00 , 2.17247889412925e+00 , 5.62166342903270e-01 , 4.23522938188373e-01 , 2.41894535575529e+00 , 5.75950497753486e-01 , 1.99311759970864e+00 , 9.90200255894917e-01 , 1.06367253825329e+00 , 1.11563876641110e+00 , 1.72486259471821e-02 , 1.68771528424288e+00 , 2.01680440836458e+00 , -1.21223505194812e+00 , 2.02283232615496e+00 , 4.93808100265990e-01 , 5.72993723252768e-01 , 3.01393252624362e+00 , -6.88662698730657e-01 , 3.95917840203135e-01 , 3.20168907388110e+00 , 1.26635417611879e+00 , 1.30187283605317e+00 , 3.82424717202003e+00 , 8.02055834821374e-01 , 1.87550270986128e+00 , 5.08797243977945e+00 , 2.07403799566278e+00 , 2.57688568440885e+00 , 5.62065013454311e+00 , -3.48560352797116e-01 , 2.92052150124506e+00 , 4.98852920872505e+00 , -1.18494615851311e+00 , 3.01232055610406e+00 , 5.89678755591211e+00 , -3.82031918238650e-01 , 3.70595277200685e+00 , 3.87941563994321e+00 , -1.45082115186687e+00 , 4.62175502345249e+00 , 3.53071327033099e+00 , -7.75724366525815e-01 , 5.37503395323720e+00 , 2.40305640303963e+00 , -2.70209506606141e+00 , 3.89870943264086e+00 , 2.94981369790254e+00 , -3.85031568262129e+00 , 4.39752347927427e+00 , 2.87664281947560e+00 , -2.54961280488281e+00 , 2.62499766456799e+00 , 2.51165327325743e+00 , -3.73779767197526e+00 , 1.87724750035443e+00 , 2.08367023958821e+00 , -3.40254375149229e+00 , 7.87407342268081e-01 , 1.02115002063011e+00 , -4.34988391190048e+00 , 1.12609473436594e+00 , 3.21266554638434e+00 , -5.52818382437095e+00 , 9.52475200207846e-01 , 3.35258462236387e+00 , -3.48967725995040e+00 , 6.30398518804684e-01 , 4.18272105949592e+00 , -3.74839325777039e+00 , 1.02522482050505e-01 , 5.46548318451194e+00 , -2.45559663530938e+00 , -4.43402918780902e-01 , 6.12151729171110e+00 , -4.45577168758924e+00 , 1.02426396186823e+00 , 6.42056223292720e+00 , -5.32862106310225e+00 , 5.86032608861608e-01 , 7.17433844471589e+00 , -6.29033034988321e+00 , 3.54932209171370e+00 , 6.69033955942084e+00 , -6.93486374837418e+00 , 4.31932161889822e+00 , 7.41926514792909e+00 , -6.77302671646158e+00 , 3.20630969504711e+00 , 5.49497848134986e+00 , -4.07615699975561e+00 , 2.28779013613902e+00 , 6.46796959170672e+00 , -4.91096654810336e+00 , 3.24745826093006e+00 , 7.21735228072137e+00 , -4.05359797432833e+00 , 4.48287924773665e+00 , 7.26229835759540e+00 ) 5.90465591981215e+01 + 2 ( -3.38665979440331e-01 , 6.30649599530219e-03 , 9.40885531017447e-01 ) ( 6.77757577292584e+01 , 6.77757577292585e+00 , 1.35551515458517e+01 ) ( 8.41227992013219e+00 , 4.24296095854182e-02 , -7.47576039175839e-01 , 7.00087276435700e+00 , -4.83666411671671e-01 , -6.72810126955104e-01 , 6.24365298395912e+00 , -2.51599818330505e-01 , 6.35896385968118e-01 , 5.02196942434676e+00 , -2.08650124708023e-01 , 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6.77293020124180e+01 , 6.77293020124180e+00 , 1.35458604024836e+01 ) ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 ) ( 6.90604151213354e+00 , -2.69075122022935e-01 , 1.79261520445473e+00 , 6.17825106062569e+00 , -1.26836068277437e-01 , 3.04744941545049e+00 , 5.30622602793432e+00 , 1.12822247822679e+00 , 3.27357027281935e+00 , 4.08713564709557e+00 , 1.07381061693489e+00 , 3.61288828153524e+00 ) ( 8.40427540879187e+00 , 4.26955339190803e-02 , -7.49809617218978e-01 , 6.99822903944800e+00 , -4.88105295326062e-01 , -6.66635933770367e-01 , 7.03895648245530e+00 , -2.01326311992394e+00 , -1.02797838719508e+00 , 6.24911302176878e+00 , -2.53053896745395e-01 , 6.44388904905101e-01 , 5.01522823474419e+00 , -2.08807296451475e-01 , 6.51152357911502e-01 , 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2.94244555060088e+00 , -3.85397053576677e+00 , 4.40886756444619e+00 , 2.86514516774913e+00 , -2.56238506116784e+00 , 2.61704024891841e+00 , 2.50463181837573e+00 , -3.72731643876335e+00 , 1.89477467803205e+00 , 2.07833877584790e+00 , -3.40648156887254e+00 , 7.94791232819169e-01 , 1.00822680892803e+00 , -4.33411882415833e+00 , 1.11540735259212e+00 , 3.21618665289234e+00 , -5.53124166287250e+00 , 9.37678141365137e-01 , 3.34930895407962e+00 , -3.48029094709608e+00 , 6.29573410663773e-01 , 4.17165487361038e+00 , -3.76293275749598e+00 , 1.04889802261908e-01 , 5.47218621190268e+00 , -2.43524588666670e+00 , -4.28569461663175e-01 , 6.12917122951268e+00 , -4.46137649623060e+00 , 1.01289625333700e+00 , 6.41730232819765e+00 , -5.32589115570178e+00 , 5.92468773578644e-01 , 7.17853617485579e+00 , -6.29516769539657e+00 , 3.54677241164914e+00 , 6.69520675760253e+00 , -6.92401331507501e+00 , 4.31155127751032e+00 , 7.41786311270827e+00 , -6.76023169634102e+00 , 3.20798125963454e+00 , 5.50142649101242e+00 , -4.07780957165642e+00 , 2.29340326975858e+00 , 6.47430882879828e+00 , -4.91395903808343e+00 , 3.24497944548098e+00 , 7.21568189570881e+00 , -4.06367067238762e+00 , 4.48963222565441e+00 , 7.26344679813068e+00 ) 5.89363553041026e+01 + 4 ( -3.36535507777281e-01 , 5.34093077602620e-03 , 9.41655630505937e-01 ) ( 6.76691680506708e+01 , 6.76691680506708e+00 , 1.35338336101342e+01 ) ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 ) ( 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 ) ( 8.39621737393096e+00 , 4.29824140035993e-02 , -7.52225103696128e-01 , 6.99584360642709e+00 , -4.93200146641622e-01 , -6.60831582611319e-01 , 7.03961402811947e+00 , -2.01594139169677e+00 , -1.02262515973272e+00 , 6.25325647529797e+00 , -2.55585814979377e-01 , 6.52111956786374e-01 , 5.00854038034081e+00 , -2.08519575229910e-01 , 6.56795766599812e-01 , 6.90495577782123e+00 , -2.69460751739895e-01 , 1.79998969458102e+00 , 6.17730488849261e+00 , -1.24583435557060e-01 , 3.05440472690255e+00 , 7.18263107927866e+00 , -3.19480089396305e-01 , 4.30080092569281e+00 , 5.30648382345244e+00 , 1.12358994478953e+00 , 3.27975628594841e+00 , 4.08709523252034e+00 , 1.07095658701188e+00 , 3.61691225696668e+00 , 5.87480764488488e+00 , 2.32183686533172e+00 , 2.96385254574563e+00 , 5.22401915183515e+00 , 3.59700477415841e+00 , 2.88058327697453e+00 , 6.33313570021503e+00 , 4.61702980999795e+00 , 2.46480956657247e+00 , 3.89738406195389e+00 , 3.71211858828403e+00 , 2.02161720094553e+00 , 2.91712114215221e+00 , 4.11520025647612e+00 , 2.55927386034751e+00 , 3.82085296337469e+00 , 3.24332233066367e+00 , 7.80301686015539e-01 , 2.66609770711206e+00 , 3.18393431987549e+00 , -8.09705050535790e-02 , 3.04894089721518e+00 , 2.72636651203978e+00 , -1.59291354258671e+00 , 1.63335360042310e+00 , 2.15440665420680e+00 , 5.80233789005463e-01 , 4.29821162657453e-01 , 2.44050687154264e+00 , 5.61388262297594e-01 , 1.97583268223827e+00 , 1.00857712075152e+00 , 1.05487950606214e+00 , 1.13634384344120e+00 , 1.23094447637546e-02 , 1.68772205218768e+00 , 2.01544944665330e+00 , -1.19309491346669e+00 , 2.02278136537242e+00 , 5.08048333153570e-01 , 5.94101081614504e-01 , 3.00574642221439e+00 , -6.78413165214166e-01 , 3.80967459534790e-01 , 3.18874502103966e+00 , 1.28890110593016e+00 , 1.31089100241892e+00 , 3.82435214018651e+00 , 8.22531842555876e-01 , 1.89379420588718e+00 , 5.07838514404901e+00 , 2.06388948264212e+00 , 2.58645856620776e+00 , 5.62114756606659e+00 , -3.57123410136767e-01 , 2.92054092805364e+00 , 4.98576466907933e+00 , 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2.92618062941570e+00 , -3.84350979118735e+00 , 4.44311833599332e+00 , 2.83901385111706e+00 , -2.59424078421361e+00 , 2.61756447057102e+00 , 2.47332265275974e+00 , -3.71776428270011e+00 , 1.90472662963754e+00 , 2.04900898232867e+00 , -3.41684883684250e+00 , 8.35005077067841e-01 , 9.60645300188595e-01 , -4.29617863159136e+00 , 1.07717277958882e+00 , 3.24618592561956e+00 , -5.53957557884789e+00 , 8.95479823423629e-01 , 3.33694106164903e+00 , -3.44486641989230e+00 , 6.51469263012818e-01 , 4.13808335413135e+00 , -3.77814080719281e+00 , 7.51467720119500e-02 , 5.48157211684484e+00 , -2.39186254573543e+00 , -3.65567061631359e-01 , 6.15472938358984e+00 , -4.47416091116603e+00 , 9.92504191471163e-01 , 6.42476346159115e+00 , -5.32436805963122e+00 , 6.07382985793919e-01 , 7.19056088071845e+00 , -6.28584768858397e+00 , 3.55966157939073e+00 , 6.70552129588939e+00 , -6.91381653581022e+00 , 4.29555219962006e+00 , 7.42406249450056e+00 , -6.74146889551814e+00 , 3.20810530389003e+00 , 5.51983078309189e+00 , -4.10253652397379e+00 , 2.30200516652139e+00 , 6.48139290802677e+00 , -4.88525999105680e+00 , 3.21491520126340e+00 , 7.21274573397417e+00 , -4.09094721606025e+00 , 4.54235951819630e+00 , 7.28354775104310e+00 ) 5.81832812371270e+01 + 10 ( -3.24830306441272e-01 , 4.56308785799901e-03 , 9.45761307226337e-01 ) ( 6.70705385563117e+01 , 6.70705385563117e+00 , 1.34141077112623e+01 ) ( 8.34775811559923e+00 , 4.39270288750945e-02 , -7.64674527447090e-01 , 6.99015060344983e+00 , -5.28654838136395e-01 , -6.34144555536668e-01 , 6.22743396930196e+00 , -2.89879607184241e-01 , 6.83197187675189e-01 , 4.98332409334377e+00 , -1.98456890727064e-01 , 6.87234950535801e-01 ) ( 6.90131845320265e+00 , -2.67628622636842e-01 , 1.84264357169036e+00 , 6.18261440050233e+00 , -1.17670220777049e-01 , 3.13118660804336e+00 , 5.29253135527729e+00 , 1.11289914537956e+00 , 3.31144920081355e+00 , 4.11341113553082e+00 , 1.05270222696094e+00 , 3.63946188402543e+00 ) ( 8.34775811559923e+00 , 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-4.47491739437376e+00 , 9.93160103503444e-01 , 6.42790245984648e+00 , -5.32587875364056e+00 , 6.08348264432282e-01 , 7.19295012540872e+00 , -6.27935941976524e+00 , 3.56260233814347e+00 , 6.70653063020309e+00 , -6.91604181506208e+00 , 4.29488461026496e+00 , 7.42745578704558e+00 , -6.74194524338962e+00 , 3.20747938706531e+00 , 5.52161705465893e+00 , -4.10781226164041e+00 , 2.29942706847021e+00 , 6.47894013701247e+00 , -4.87668857972487e+00 , 3.20892310894696e+00 , 7.21294517264761e+00 , -4.09422317163253e+00 , 4.55260246966294e+00 , 7.28741798003129e+00 ) 5.80140759953297e+01 + 11 ( -3.22392395713355e-01 , 4.49513088585881e-03 , 9.46595445258703e-01 ) ( 6.69472596157287e+01 , 6.69472596157287e+00 , 1.33894519231457e+01 ) ( 8.33989652596687e+00 , 4.37784895057247e-02 , -7.65588589205091e-01 , 6.98942183552189e+00 , -5.33578963318607e-01 , -6.30345719465742e-01 , 6.21574626624381e+00 , -2.97977564188025e-01 , 6.86730285151580e-01 , 4.98174048287727e+00 , -1.95662624042359e-01 , 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4.31742444534008e-02 , -7.65992702671467e-01 , 6.98579761238656e+00 , -5.41302762154104e-01 , -6.21997153294249e-01 , 7.05340970890828e+00 , -2.03495888751512e+00 , -9.67476492555219e-01 , 6.19145501838282e+00 , -3.15376295438507e-01 , 6.93681465535873e-01 , 4.97889311117172e+00 , -1.89389031405752e-01 , 7.00081615672793e-01 , 6.89679384979129e+00 , -2.65138335651727e-01 , 1.86100053518602e+00 , 6.18683014355840e+00 , -1.23415268786750e-01 , 3.17186764755464e+00 , 7.10309841127393e+00 , -3.45759530453527e-01 , 4.28331168871171e+00 , 5.28913229808589e+00 , 1.11149493017644e+00 , 3.32487934984546e+00 , 4.13324562616224e+00 , 1.04364744373900e+00 , 3.65202775194807e+00 , 5.86815440142525e+00 , 2.25034149365315e+00 , 2.99790333277585e+00 , 5.22090398616814e+00 , 3.59158459704341e+00 , 2.90072616259581e+00 , 6.33290764378279e+00 , 4.52789025408997e+00 , 2.42625959687694e+00 , 3.90925927185836e+00 , 3.73837146560840e+00 , 2.03355325371678e+00 , 2.83214575810826e+00 , 4.13595170834672e+00 , 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4.05502039483995e-02 , -7.57168135415501e-01 , 6.94444631047559e+00 , -5.50848294673966e-01 , -5.84586689082513e-01 , 7.05074224898966e+00 , -2.04924419646287e+00 , -9.38119125911342e-01 , 6.15474269366648e+00 , -3.68707517852149e-01 , 7.22954578598341e-01 , 4.95571081637387e+00 , -1.67057208625230e-01 , 7.19810311796842e-01 , 6.87021723100255e+00 , -2.62665597401684e-01 , 1.90023627044304e+00 , 6.18093140628753e+00 , -1.54333271284537e-01 , 3.19817299288735e+00 , 7.07971683776361e+00 , -3.55414706610481e-01 , 4.30771070148019e+00 , 5.31464679241726e+00 , 1.09854957403808e+00 , 3.34885324905130e+00 , 4.15890935635952e+00 , 1.02756470888611e+00 , 3.68638208858502e+00 , 5.84635123779372e+00 , 2.25159689796611e+00 , 2.99222675162208e+00 , 5.23917797329710e+00 , 3.58015899263768e+00 , 2.92046406983865e+00 , 6.32330542542503e+00 , 4.50267221116147e+00 , 2.37539066105213e+00 , 3.88703075489342e+00 , 3.71259813244409e+00 , 2.04395687204498e+00 , 2.79449313515955e+00 , 4.15799608277627e+00 , 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-1.14066671171434e+00 , 3.06133251025107e+00 , 5.89050816644362e+00 , -5.06584618690582e-01 , 3.54400640737262e+00 , 3.84795853152810e+00 , -1.51674973142102e+00 , 4.54215964326285e+00 , 3.45372113421616e+00 , -7.00823430958750e-01 , 5.41258718813179e+00 , 2.46173889125928e+00 , -2.76400867601426e+00 , 3.88360022843555e+00 , 2.89986003767659e+00 , -3.81857657654143e+00 , 4.50404620190123e+00 , 2.81572188994286e+00 , -2.62031365615965e+00 , 2.67416763261886e+00 , 2.40870237905015e+00 , -3.76873221650147e+00 , 1.80728380628970e+00 , 1.99907792708978e+00 , -3.39298428671144e+00 , 8.86588325768584e-01 , 8.80444026278585e-01 , -4.32512356141035e+00 , 1.06938124085425e+00 , 3.21604911681993e+00 , -5.50267365567089e+00 , 8.25985966172653e-01 , 3.32868072792900e+00 , -3.37284622344555e+00 , 6.87967166719032e-01 , 4.19921402874200e+00 , -3.70814230271072e+00 , 4.17028521175029e-02 , 5.43435839827501e+00 , -2.38895678968084e+00 , -3.15480360664442e-01 , 6.17178165219393e+00 , -4.46319250108227e+00 , 9.93073126987608e-01 , 6.44118607162257e+00 , -5.35590546450845e+00 , 5.99770709641098e-01 , 7.21648720821253e+00 , -6.23464583015447e+00 , 3.59975206887441e+00 , 6.72936331675915e+00 , -6.95633074420952e+00 , 4.29807118150865e+00 , 7.47131215283029e+00 , -6.74631574836826e+00 , 3.18607012100168e+00 , 5.50984733662542e+00 , -4.13002092791531e+00 , 2.24932512531288e+00 , 6.41674299777508e+00 , -4.81160275051361e+00 , 3.20067856672055e+00 , 7.23705621286995e+00 , -4.09954380419939e+00 , 4.58068638458722e+00 , 7.28570495890731e+00 ) 5.66360741304630e+01 + 20 ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ) ( 6.60362557644092e+01 , 6.60362557644092e+00 , 1.32072511528818e+01 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ) ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) 5.65386573831414e+01 diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..d647ffabf --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.out @@ -0,0 +1,10271 @@ +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: - Multiple replicas: enabled (replica number 1 of 1) +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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Initializing a new "distanceDir" component, with configuration: +colvars: +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: 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 value = "off". +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = off +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: 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: 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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: ". +colvars: Done initializing a "distanceDir" component, named "distanceDir0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a 3-dimensional unit vector with 3 individual components. +colvars: DEPS: disabling feature "scalar" in colvar one +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: feature "linear" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar one enabled, ref_count = 1. +colvars: DEPS: colvar one enabling "single_component" +colvars: DEPS: feature "single_component" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword value = "0.5". +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 0.5 +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar one +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar one +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar one +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar one enabling "output_value" +colvars: DEPS: feature "output_value" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar one +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword value = "on". +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = on +colvars: DEPS: colvar one enabling "output_applied_force" +colvars: DEPS: feature "output_applied_force" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar one +colvars: DEPS: colvar one enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar one testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar one testing "linear" +colvars: DEPS: colvar one enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar one enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "one". +colvars: Configuration string for "colvar": " +colvars: +colvars: name one +colvars: outputAppliedForce on +colvars: width 0.5 +colvars: distanceDir { +colvars: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group1 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group1" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group1 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group1 +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group1 enabled, ref_count = 1. +colvars: DEPS: colvar group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group1 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group1 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group1 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group1 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group1 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group1 +colvars: DEPS: colvar group1 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group1 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group1 testing "linear" +colvars: DEPS: colvar group1 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group1 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group1". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "group2" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup group2 +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "group2" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup group2 +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 12 individual components. +colvars: DEPS: disabling feature "scalar" in colvar group2 +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: feature "linear" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar group2 enabled, ref_count = 1. +colvars: DEPS: colvar group2 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar group2 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar group2 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar group2 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar group2 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar group2 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar group2 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar group2 +colvars: DEPS: colvar group2 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar group2 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar group2 testing "linear" +colvars: DEPS: colvar group2 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar group2 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "group2". +colvars: Configuration string for "colvar": " +colvars: +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting_group1" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting_group1 enabled, ref_count = 1. +colvars: DEPS: colvar fitting_group1 enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting_group1 enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting_group1 +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting_group1 +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting_group1 +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar fitting_group1 enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting_group1 enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar fitting_group1 +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting_group1 +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting_group1 +colvars: DEPS: colvar fitting_group1 enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar fitting_group1 testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar fitting_group1 testing "linear" +colvars: DEPS: colvar fitting_group1 enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar fitting_group1 enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "fitting_group1". +colvars: Configuration string for "colvar": " +colvars: +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 4 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: outputEnergy on +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 value = "on". +colvars: Looking for the keyword "outputEnergy" and its value. +colvars: Keyword "outputEnergy" not found. +colvars: # outputEnergy = on +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 +colvars: - scalable_calculation +colvars: - 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: outputEnergy on +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: scalable off +colvars: group1 { +colvars: indexGroup group1 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: group2 { +colvars: indexGroup group2 +colvars: centerToReference yes +colvars: rotateToReference yes +colvars: fittingGroup { +colvars: indexGroup heavy_atoms +colvars: } +colvars: refPositionsFile heavy_atoms_refpos.xyz +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group1 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name group2 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup group2 +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting_group1 +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (1.0, 0.1, 0.2) +colvars: forceConstant 10.0 +colvars: outputEnergy on +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +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: - cartesian colvar component: +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 = "2024-10-11". +colvars: Looking for the keyword "version" and its value. +colvars: Keyword "version" not found. +colvars: Looking for the keyword "units" and its value. +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 = "( -0.30360404081666 , -7.3012941347679e-05 , 0.95279828981212 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "one" from value: ( -0.303604 , -7.30129e-05 , 0.952798 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "group1": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "group1" from value: ( 8.28396 , 0.0403341 , -0.754693 , 6.93309 , -0.55189 , -0.576983 , 6.1554 , -0.375947 , 0.729836 , 4.94923 , -0.163317 , 0.722359 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "group2": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "group2": this colvar is named "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "group2" from value: ( 6.8638 , -0.263219 , 1.90772 , 6.17692 , -0.161108 , 3.19479 , 5.32108 , 1.09516 , 3.35245 , 4.16123 , 1.02516 , 3.69346 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting_group1": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting_group1": this colvar is named "group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting_group1": this colvar is named "group2". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting_group1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 8.2839564797565 , 0.040334089702466 , -0.75469277487022 , 6.9330916258798 , -0.55188978329377 , -0.5769830051483 , 7.0480762025172 , -2.0513347736704 , -0.93377134820149 , 6.1553969711517 , -0.37594665090128 , 0.72983610650554 , 4.9492269022447 , -0.16331739498617 , 0.72235927156532 , 6.8638035298209 , -0.26321917795372 , 1.9077241989278 , 6.1769195352621 , -0.1611081435099 , 3.1947897437904 , 7.0809081020816 , -0.35496020632887 , 4.3146586251214 , 5.3210770751533 , 1.0951579306264 , 3.3524452234051 , 4.1612311509276 , 1.0251600738253 , 3.6934589086536 , 5.8432995748295 , 2.2535778944039 , 2.9902963417856 , 5.2384055225152 , 3.5783754026257 , 2.9215354050906 , 6.3223993673226 , 4.5011441587991 , 2.3655584831763 , 3.8818312912342 , 3.7064721784147 , 2.0444644100133 , 2.7920736373314 , 4.1608362314759 , 2.4877638737485 , 3.9386798899873 , 3.2395859717867 , 0.73126389979658 , 2.6624894551197 , 3.0062849992536 , -0.10369017207615 , 3.0530237576774 , 2.7050981729996 , -1.515126439405 , 1.5978477264343 , 2.1831908534433 , 0.4458975934194 , 0.37935536668417 , 2.5812137098021 , 0.51015292695301 , 2.0475904030464 , 1.0706502363152 , 1.069723927279 , 1.1690699177228 , 0.11658295312925 , 1.6974226380185 , 2.0431803877623 , -1.1033045581944 , 2.0106005316873 , 0.56210382605836 , 0.61178504571473 , 2.9428051810465 , -0.60199958586972 , 0.34968520789238 , 3.1615301713297 , 1.3167209916681 , 1.3457617287353 , 3.7754423945574 , 0.84267356054463 , 1.9787990415851 , 5.0254234233262 , 2.0796156959584 , 2.6878063101542 , 5.6821293955537 , -0.33739104868865 , 2.9146961524331 , 4.9679941584516 , -1.1371464701093 , 3.062469534534 , 5.8877740932039 , -0.51179726121506 , 3.5352900024754 , 3.8463150986082 , -1.5180503491383 , 4.5391900691402 , 3.4442608843563 , -0.69961559166787 , 5.4143954882994 , 2.4637912416459 , -2.7602287545827 , 3.8895007500064 , 2.8949751960402 , -3.8174896819283 , 4.5099047856922 , 2.8146284855071 , -2.6251714284554 , 2.6732886369457 , 2.4014323234568 , -3.7726963733907 , 1.8037184430191 , 1.9982779981764 , -3.3886595184775 , 0.88672154595831 , 0.87409788378727 , -4.3225504216986 , 1.0700082818202 , 3.2121699488068 , -5.4999729212229 , 0.81876098547252 , 3.3291853384002 , -3.3690633481624 , 0.69157744271515 , 4.2041288719456 , -3.7011250996533 , 0.046206366217123 , 5.434092539774 , -2.3903901778542 , -0.31709933730245 , 6.1701094743001 , -4.4618292827148 , 0.98680918149928 , 6.4395743693712 , -5.3588837067265 , 0.5981100423375 , 7.2179576344598 , -6.2383325096938 , 3.6054824579338 , 6.7336443061013 , -6.9602157879944 , 4.2977470185681 , 7.4756432850253 , -6.741403987979 , 3.1822575304318 , 5.5078493030856 , -4.1287524553974 , 2.2462119095443 , 6.4096637239512 , -4.8089365560512 , 3.2066271871716 , 7.2417022510827 , -4.0950888618816 , 4.5754896432564 , 7.2828123626203 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "fitting_group1" from value: ( 8.28396 , 0.0403341 , -0.754693 , 6.93309 , -0.55189 , -0.576983 , 7.04808 , -2.05133 , -0.933771 , 6.1554 , -0.375947 , 0.729836 , 4.94923 , -0.163317 , 0.722359 , 6.8638 , -0.263219 , 1.90772 , 6.17692 , -0.161108 , 3.19479 , 7.08091 , -0.35496 , 4.31466 , 5.32108 , 1.09516 , 3.35245 , 4.16123 , 1.02516 , 3.69346 , 5.8433 , 2.25358 , 2.9903 , 5.23841 , 3.57838 , 2.92154 , 6.3224 , 4.50114 , 2.36556 , 3.88183 , 3.70647 , 2.04446 , 2.79207 , 4.16084 , 2.48776 , 3.93868 , 3.23959 , 0.731264 , 2.66249 , 3.00628 , -0.10369 , 3.05302 , 2.7051 , -1.51513 , 1.59785 , 2.18319 , 0.445898 , 0.379355 , 2.58121 , 0.510153 , 2.04759 , 1.07065 , 1.06972 , 1.16907 , 0.116583 , 1.69742 , 2.04318 , -1.1033 , 2.0106 , 0.562104 , 0.611785 , 2.94281 , -0.602 , 0.349685 , 3.16153 , 1.31672 , 1.34576 , 3.77544 , 0.842674 , 1.9788 , 5.02542 , 2.07962 , 2.68781 , 5.68213 , -0.337391 , 2.9147 , 4.96799 , -1.13715 , 3.06247 , 5.88777 , -0.511797 , 3.53529 , 3.84632 , -1.51805 , 4.53919 , 3.44426 , -0.699616 , 5.4144 , 2.46379 , -2.76023 , 3.8895 , 2.89498 , -3.81749 , 4.5099 , 2.81463 , -2.62517 , 2.67329 , 2.40143 , -3.7727 , 1.80372 , 1.99828 , -3.38866 , 0.886722 , 0.874098 , -4.32255 , 1.07001 , 3.21217 , -5.49997 , 0.818761 , 3.32919 , -3.36906 , 0.691577 , 4.20413 , -3.70113 , 0.0462064 , 5.43409 , -2.39039 , -0.317099 , 6.17011 , -4.46183 , 0.986809 , 6.43957 , -5.35888 , 0.59811 , 7.21796 , -6.23833 , 3.60548 , 6.73364 , -6.96022 , 4.29775 , 7.47564 , -6.7414 , 3.18226 , 5.50785 , -4.12875 , 2.24621 , 6.40966 , -4.80894 , 3.20663 , 7.2417 , -4.09509 , 4.57549 , 7.28281 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "harmonic1". +colvars: Looking for the keyword "name" and its value. +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: Re-initialized atom group for variable "group1":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "group2":0/0. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: Re-initialized atom group for variable "fitting_group1":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 20 +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 20, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 ), ( 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 ), ( 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 ), ( 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ), ( 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 ), ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 ), ( 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 ), ( 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 ), ( 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 ), ( 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ), ( 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 ), ( 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 ), ( 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 ), ( 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 ), ( 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 ), ( 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 ), ( 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 ), ( 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 ), ( 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 ), ( 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 ), ( 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 ), ( 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 ), ( 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 ), ( 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 ), ( -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 ), ( 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 ), ( 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 ), ( 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 ), ( -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 ), ( -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 ), ( -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 ), ( -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 ), ( -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 ), ( -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 ), ( -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 ), ( -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 ), ( -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 ), ( -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 ), ( -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 ), ( -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 ), ( -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 ), ( -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 ), ( -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 ), ( -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 ), ( -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 ), ( -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 ), ( -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 ), ( -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 ), ( -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 ), ( -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 ), ( -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 66.0363 , 6.60363 , 13.2073 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 66.0363 , 6.60363 , 13.2073 ) to colvar "one". +colvars: Adding total bias energy: 56.5387 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 66.0363 , 6.60363 , 13.2073 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17524 , -0.560146 , -1.5236 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -4.43777 , -0.480325 , -1.30649 ) +colvars: ( -5.91123 , -0.639807 , -1.74028 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.939145 , 0.205822 , 0.650791 ) +colvars: ( 0.813493 , 0.280183 , 0.676344 ) +colvars: ( 0.79671 , 0.272971 , 0.657011 ) +colvars: ( 0.695988 , 0.280925 , 0.60896 ) +colvars: ( 0.683489 , 0.210958 , 0.508858 ) +colvars: ( 0.605096 , 0.362058 , 0.663721 ) +colvars: ( 0.492454 , 0.376702 , 0.617613 ) +colvars: ( 0.411895 , 0.478868 , 0.706292 ) +colvars: ( 0.40664 , 0.329912 , 0.505603 ) +colvars: ( 0.370107 , 0.286173 , 0.426316 ) +colvars: ( 0.375838 , 0.335525 , 0.495129 ) +colvars: ( 0.30102 , 0.290509 , 0.391871 ) +colvars: ( 0.272557 , 0.321061 , 0.415847 ) +colvars: ( 0.366646 , 0.187731 , 0.293691 ) +colvars: ( 0.304985 , 0.14218 , 0.19738 ) +colvars: ( 0.495648 , 0.148851 , 0.317164 ) +colvars: ( 0.571887 , 0.0528434 , 0.234141 ) +colvars: ( 0.70803 , 0.0308578 , 0.284183 ) +colvars: ( 0.580911 , 0.0193309 , 0.194928 ) +colvars: ( 0.564352 , -0.0490553 , 0.0945605 ) +colvars: ( 0.602884 , 0.069656 , 0.274483 ) +colvars: ( 0.601296 , 0.052603 , 0.250934 ) +colvars: ( 0.639709 , 0.120601 , 0.363501 ) +colvars: ( 0.470661 , 0.05723 , 0.181065 ) +colvars: ( 0.463505 , -0.0015853 , 0.098867 ) +colvars: ( 0.363526 , 0.126191 , 0.210227 ) +colvars: ( 0.232697 , 0.135147 , 0.145989 ) +colvars: ( 0.136568 , 0.225255 , 0.209612 ) +colvars: ( 0.203032 , 0.0576775 , 0.0259439 ) +colvars: ( 0.151284 , 0.019607 , -0.0546754 ) +colvars: ( 0.238306 , 0.0308947 , 0.0109328 ) +colvars: ( 0.223552 , -0.0452647 , -0.0986978 ) +colvars: ( 0.260612 , -0.0486848 , -0.0816732 ) +colvars: ( 0.30262 , -0.135586 , -0.17253 ) +colvars: ( 0.256401 , -0.191436 , -0.273522 ) +colvars: ( 0.423642 , -0.151329 , -0.123003 ) +colvars: ( 0.505029 , -0.230661 , -0.180906 ) +colvars: ( 0.642858 , -0.233317 , -0.104237 ) +colvars: ( 0.455372 , -0.235478 , -0.216188 ) +colvars: ( 0.461185 , -0.307026 , -0.307735 ) +colvars: ( 0.404175 , -0.158505 , -0.14385 ) +colvars: ( 0.347218 , -0.152033 , -0.168403 ) +colvars: ( 0.329883 , -0.0609799 , -0.0576822 ) +colvars: ( 0.217684 , -0.161336 , -0.256114 ) +colvars: ( 0.192064 , -0.205541 , -0.32967 ) +colvars: ( 0.00617868 , -0.209423 , -0.442974 ) +colvars: ( -0.0893621 , -0.228177 , -0.523444 ) +colvars: ( 0.111592 , -0.261789 , -0.451119 ) +colvars: ( 0.131717 , -0.118651 , -0.249498 ) +colvars: ( 0.00636188 , -0.12331 , -0.328614 ) +colvars: ( -0.0871363 , -0.0385503 , -0.270558 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17524 , 0.560146 , 1.5236 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 4.43777 , 0.480325 , 1.30649 ) +colvars: ( 5.91123 , 0.639807 , 1.74028 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.647974 , -0.0852573 , -0.388753 ) +colvars: ( -0.582839 , -0.171838 , -0.35665 ) +colvars: ( -0.530769 , -0.148883 , -0.295681 ) +colvars: ( -0.541646 , -0.200563 , -0.326377 ) +colvars: ( -0.531553 , -0.138947 , -0.29266 ) +colvars: ( -0.515626 , -0.296838 , -0.337183 ) +colvars: ( -0.481227 , -0.338999 , -0.318864 ) +colvars: ( -0.458422 , -0.451281 , -0.339024 ) +colvars: ( -0.415265 , -0.302019 , -0.238601 ) +colvars: ( -0.41045 , -0.275508 , -0.22362 ) +colvars: ( -0.363672 , -0.296189 , -0.184669 ) +colvars: ( -0.300365 , -0.257621 , -0.106457 ) +colvars: ( -0.2495 , -0.273312 , -0.0614974 ) +colvars: ( -0.320837 , -0.149656 , -0.0856129 ) +colvars: ( -0.288058 , -0.119011 , -0.0410273 ) +colvars: ( -0.377907 , -0.0896324 , -0.119807 ) +colvars: ( -0.405907 , 0.0131673 , -0.108485 ) +colvars: ( -0.458652 , 0.0629527 , -0.142267 ) +colvars: ( -0.445189 , 0.028964 , -0.141797 ) +colvars: ( -0.433263 , 0.0883914 , -0.107081 ) +colvars: ( -0.491292 , -0.0275236 , -0.209633 ) +colvars: ( -0.527109 , -0.028974 , -0.246079 ) +colvars: ( -0.579343 , -0.0973742 , -0.324623 ) +colvars: ( -0.472472 , -0.0603448 , -0.203347 ) +colvars: ( -0.479594 , -0.0141749 , -0.192798 ) +colvars: ( -0.414746 , -0.138121 , -0.175297 ) +colvars: ( -0.354373 , -0.170853 , -0.127338 ) +colvars: ( -0.301597 , -0.265244 , -0.110611 ) +colvars: ( -0.311285 , -0.09467 , -0.0549772 ) +colvars: ( -0.297384 , -0.0751509 , -0.0335708 ) +colvars: ( -0.290629 , -0.0477842 , -0.0163181 ) +colvars: ( -0.253661 , 0.0304013 , 0.050676 ) +colvars: ( -0.23152 , 0.0579314 , 0.0834089 ) +colvars: ( -0.299747 , 0.121221 , 0.039285 ) +colvars: ( -0.271833 , 0.164934 , 0.084002 ) +colvars: ( -0.37232 , 0.150668 , -0.022156 ) +colvars: ( -0.42338 , 0.230441 , -0.0427631 ) +colvars: ( -0.497883 , 0.254059 , -0.108372 ) +colvars: ( -0.435341 , 0.209775 , -0.062665 ) +colvars: ( -0.440031 , 0.273443 , -0.0429754 ) +colvars: ( -0.439945 , 0.119231 , -0.101963 ) +colvars: ( -0.447231 , 0.0877498 , -0.121324 ) +colvars: ( -0.469676 , -0.00985306 , -0.181203 ) +colvars: ( -0.377354 , 0.0759564 , -0.0558201 ) +colvars: ( -0.380737 , 0.103539 , -0.0486444 ) +colvars: ( -0.208877 , 0.110092 , 0.126079 ) +colvars: ( -0.157097 , 0.112049 , 0.178715 ) +colvars: ( -0.23683 , 0.185727 , 0.127043 ) +colvars: ( -0.311938 , 0.0332713 , -0.00662132 ) +colvars: ( -0.242039 , 0.0190178 , 0.0579609 ) +colvars: ( -0.185619 , -0.0679661 , 0.0811767 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 20. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -4.88406726017846e+00 , -4.39582030019637e-01 , -1.26156546289831e+00 ), ( -4.20711207586693e+00 , -3.71980090924366e-01 , -9.86796367004215e-01 ), ( -4.28342445948863e+00 , -3.99963693514908e-01 , -1.02390709400074e+00 ), ( -5.75929727923110e+00 , -5.67796041518724e-01 , -1.52408480248038e+00 ), ( 2.65941268390902e-01 , 1.24088041235363e-01 , 3.61330101161847e-01 ), ( 5.26470856148017e+00 , 6.25365994053560e-01 , 1.85014148432867e+00 ), ( 4.44899395969789e+00 , 5.18028786716414e-01 , 1.60523898998076e+00 ), ( -4.65272910606424e-02 , 2.75874394655633e-02 , 3.67268098303653e-01 ), ( 4.42914052995064e+00 , 5.08218685700347e-01 , 1.57349215273307e+00 ), ( 5.87089063969169e+00 , 6.50472344458009e-01 , 1.94297816123059e+00 ), ( 1.21655890342579e-02 , 3.93361229409889e-02 , 3.10460529518665e-01 ), ( 6.54352727631202e-04 , 3.28877838588784e-02 , 2.85413778669853e-01 ), ( 2.30575218111934e-02 , 4.77496012635013e-02 , 3.54349709040753e-01 ), ( 4.58084561993378e-02 , 3.80749776841854e-02 , 2.08077917584342e-01 ), ( 1.69271357430614e-02 , 2.31692671284452e-02 , 1.56352523085799e-01 ), ( 1.17740497737709e-01 , 5.92187670987907e-02 , 1.97356769209817e-01 ), ( 1.65979650547149e-01 , 6.60107587124940e-02 , 1.25656124587784e-01 ), ( 2.49378084035319e-01 , 9.38105312411004e-02 , 1.41916759655613e-01 ), ( 1.35721171926268e-01 , 4.82948683031030e-02 , 5.31311614239589e-02 ), ( 1.31089117563867e-01 , 3.93361615661934e-02 , -1.25202269468064e-02 ), ( 1.11591946272047e-01 , 4.21324308431365e-02 , 6.48498773882783e-02 ), ( 7.41875459869102e-02 , 2.36289347234540e-02 , 4.85459631934207e-03 ), ( 6.03658790245055e-02 , 2.32264957257031e-02 , 3.88781977774767e-02 ), ( -1.81078736534573e-03 , -3.11478153248525e-03 , -2.22818060419844e-02 ), ( -1.60885473686671e-02 , -1.57601748864797e-02 , -9.39304968271742e-02 ), ( -5.12199048641456e-02 , -1.19297840935810e-02 , 3.49304717831433e-02 ), ( -1.21675813902335e-01 , -3.57064899870657e-02 , 1.86508224653453e-02 ), ( -1.65028468419942e-01 , -3.99882775272279e-02 , 9.90005933951236e-02 ), ( -1.08252979508245e-01 , -3.69924344963437e-02 , -2.90333247285238e-02 ), ( -1.46099690198963e-01 , -5.55439012742997e-02 , -8.82462486637547e-02 ), ( -5.23225535297807e-02 , -1.68894940154288e-02 , -5.38529268697861e-03 ), ( -3.01087883421307e-02 , -1.48633476968855e-02 , -4.80218171751865e-02 ), ( 2.90920024039188e-02 , 9.24664271438187e-03 , 1.73568422449372e-03 ), ( 2.87212446123969e-03 , -1.43653564917826e-02 , -1.33245075124415e-01 ), ( -1.54318476939863e-02 , -2.65024240836628e-02 , -1.89520159508813e-01 ), ( 5.13226740441255e-02 , -6.61117676194450e-04 , -1.45158995615856e-01 ), ( 8.16483892005009e-02 , -2.20115925109621e-04 , -2.23668733880816e-01 ), ( 1.44974583626733e-01 , 2.07414644297433e-02 , -2.12608633585807e-01 ), ( 2.00313536000674e-02 , -2.57030285264907e-02 , -2.78852997194507e-01 ), ( 2.11535019058627e-02 , -3.35827543487625e-02 , -3.50709917556565e-01 ), ( -3.57699416572513e-02 , -3.92742347993370e-02 , -2.45813691592460e-01 ), ( -1.00012769612954e-01 , -6.42830113991747e-02 , -2.89726269929375e-01 ), ( -1.39792965314805e-01 , -7.08329385419267e-02 , -2.38885255145827e-01 ), ( -1.59669948187276e-01 , -8.53800481419532e-02 , -3.11933814118016e-01 ), ( -1.88673377030574e-01 , -1.02001994075380e-01 , -3.78314516895504e-01 ), ( -2.02698784283931e-01 , -9.93305031383851e-02 , -3.16894644449761e-01 ), ( -2.46459346918119e-01 , -1.16127914776370e-01 , -3.44729104647447e-01 ), ( -1.25237872776220e-01 , -7.60618339454901e-02 , -3.24076090847715e-01 ), ( -1.80221106740230e-01 , -8.53800525072640e-02 , -2.56119533999097e-01 ), ( -2.35677590614575e-01 , -1.04291860665546e-01 , -2.70653229134327e-01 ), ( -2.72755086907763e-01 , -1.06516369333094e-01 , -1.89380901188017e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 21, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 21, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 21, atoms_positions[size = 51] = { ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 ), ( 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 ), ( 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 ), ( 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ), ( 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 ), ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 ), ( 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 ), ( 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 ), ( 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 ), ( 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ), ( 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 ), ( 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 ), ( 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 ), ( 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 ), ( 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 ), ( 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 ), ( 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 ), ( 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 ), ( 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 ), ( 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 ), ( 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 ), ( 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 ), ( 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 ), ( 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 ), ( -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 ), ( 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 ), ( 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 ), ( 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 ), ( -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 ), ( -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 ), ( -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 ), ( -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 ), ( -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 ), ( -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 ), ( -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 ), ( -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 ), ( -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 ), ( -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 ), ( -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 ), ( -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 ), ( -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 ), ( -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 ), ( -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 ), ( -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 ), ( -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 ), ( -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 ), ( -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 ), ( -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 ), ( -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 ), ( -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 ), ( -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ) } +colvars: Step 21, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ). +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( -3.02299978352974e-01 , -1.10908187249818e-03 , 9.53212197270467e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ). +colvars: Calculating colvar components. +colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group2". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 , 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 , 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 , 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 , 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 , 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 , 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 , 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 , 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 , 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 , 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 , 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 , 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 , 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 , 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 , 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 , -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 , 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 , 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 , 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 , -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 , -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 , -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 , -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 , -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 , -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 , -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 , -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 , -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 , -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 , -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 , -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 , -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 , -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 , -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 , -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 , -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 , -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 , -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 , -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 , -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 , -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 , -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.02299978352974e-01 , -1.10908187249818e-03 , 9.53212197270467e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 , 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 , 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 , 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 , 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 , 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 , 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 , 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 , 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 , 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 , 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 , 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 , 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 , 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 , 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 , 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 , -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 , 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 , 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 , 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 , -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 , -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 , -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 , -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 , -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 , -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 , -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 , -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 , -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 , -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 , -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 , -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 , -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 , -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 , -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 , -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 , -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 , -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 , -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 , -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 , -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 , -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 , -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.9776 , 6.59776 , 13.1955 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.9776 , 6.59776 , 13.1955 ) to colvar "one". +colvars: Adding total bias energy: 56.454 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.9776 , 6.59776 , 13.1955 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17763 , -0.55873 , -1.51773 ) +colvars: ( -4.43981 , -0.479111 , -1.30145 ) +colvars: ( -4.43981 , -0.479111 , -1.30145 ) +colvars: ( -5.91396 , -0.638189 , -1.73357 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.938409 , 0.205917 , 0.649308 ) +colvars: ( 0.812939 , 0.280222 , 0.674741 ) +colvars: ( 0.796084 , 0.273021 , 0.655411 ) +colvars: ( 0.695659 , 0.280911 , 0.607479 ) +colvars: ( 0.683179 , 0.210948 , 0.507605 ) +colvars: ( 0.604944 , 0.361991 , 0.662085 ) +colvars: ( 0.492527 , 0.376581 , 0.616054 ) +colvars: ( 0.412122 , 0.478697 , 0.704501 ) +colvars: ( 0.4068 , 0.329772 , 0.504253 ) +colvars: ( 0.37036 , 0.286018 , 0.425148 ) +colvars: ( 0.375962 , 0.335386 , 0.49376 ) +colvars: ( 0.301207 , 0.290356 , 0.390692 ) +colvars: ( 0.272701 , 0.320908 , 0.414568 ) +colvars: ( 0.366714 , 0.18762 , 0.292764 ) +colvars: ( 0.305151 , 0.142051 , 0.196652 ) +colvars: ( 0.495502 , 0.148798 , 0.316233 ) +colvars: ( 0.57161 , 0.0528351 , 0.233434 ) +colvars: ( 0.707507 , 0.0309113 , 0.283406 ) +colvars: ( 0.580703 , 0.0193165 , 0.194346 ) +colvars: ( 0.56417 , -0.049067 , 0.0942064 ) +colvars: ( 0.602717 , 0.0696309 , 0.273751 ) +colvars: ( 0.601217 , 0.052565 , 0.250287 ) +colvars: ( 0.639638 , 0.120557 , 0.362631 ) +colvars: ( 0.47081 , 0.0571361 , 0.180534 ) +colvars: ( 0.463698 , -0.0016794 , 0.0985368 ) +colvars: ( 0.363826 , 0.126049 , 0.209575 ) +colvars: ( 0.233212 , 0.134951 , 0.145435 ) +colvars: ( 0.137212 , 0.225013 , 0.20886 ) +colvars: ( 0.203537 , 0.0574894 , 0.0256383 ) +colvars: ( 0.151903 , 0.0193983 , -0.054803 ) +colvars: ( 0.238672 , 0.0307383 , 0.0106473 ) +colvars: ( 0.223882 , -0.0454067 , -0.098754 ) +colvars: ( 0.260791 , -0.0487962 , -0.0817865 ) +colvars: ( 0.302852 , -0.135689 , -0.17237 ) +colvars: ( 0.256701 , -0.191549 , -0.273147 ) +colvars: ( 0.423714 , -0.151388 , -0.122896 ) +colvars: ( 0.505007 , -0.230683 , -0.180616 ) +colvars: ( 0.642633 , -0.233287 , -0.104063 ) +colvars: ( 0.455513 , -0.235533 , -0.215807 ) +colvars: ( 0.461329 , -0.307071 , -0.307132 ) +colvars: ( 0.404456 , -0.158601 , -0.143639 ) +colvars: ( 0.34767 , -0.152165 , -0.168129 ) +colvars: ( 0.330422 , -0.0611416 , -0.0576542 ) +colvars: ( 0.218327 , -0.161517 , -0.255695 ) +colvars: ( 0.19279 , -0.205733 , -0.329075 ) +colvars: ( 0.00701507 , -0.209656 , -0.442258 ) +colvars: ( -0.0883831 , -0.228444 , -0.522584 ) +colvars: ( 0.112213 , -0.261965 , -0.450357 ) +colvars: ( 0.132438 , -0.118861 , -0.249152 ) +colvars: ( 0.00726368 , -0.123565 , -0.328143 ) +colvars: ( -0.0861204 , -0.0388487 , -0.270274 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17763 , 0.55873 , 1.51773 ) +colvars: ( 4.43981 , 0.479111 , 1.30145 ) +colvars: ( 4.43981 , 0.479111 , 1.30145 ) +colvars: ( 5.91396 , 0.638189 , 1.73357 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.647597 , -0.08533 , -0.387635 ) +colvars: ( -0.582553 , -0.172014 , -0.355315 ) +colvars: ( -0.530273 , -0.149005 , -0.294208 ) +colvars: ( -0.54155 , -0.200763 , -0.325126 ) +colvars: ( -0.531451 , -0.139049 , -0.291615 ) +colvars: ( -0.515703 , -0.297172 , -0.335767 ) +colvars: ( -0.481511 , -0.33938 , -0.317504 ) +colvars: ( -0.45886 , -0.451822 , -0.337425 ) +colvars: ( -0.415505 , -0.302316 , -0.237317 ) +colvars: ( -0.410791 , -0.275762 , -0.222529 ) +colvars: ( -0.363752 , -0.296458 , -0.183238 ) +colvars: ( -0.300376 , -0.257805 , -0.105085 ) +colvars: ( -0.249345 , -0.2735 , -0.0598991 ) +colvars: ( -0.320733 , -0.149685 , -0.0845037 ) +colvars: ( -0.287998 , -0.11898 , -0.0400642 ) +colvars: ( -0.377658 , -0.0895964 , -0.118768 ) +colvars: ( -0.405546 , 0.0133467 , -0.107695 ) +colvars: ( -0.458097 , 0.0631835 , -0.141463 ) +colvars: ( -0.445 , 0.0291528 , -0.141238 ) +colvars: ( -0.433071 , 0.0886758 , -0.106725 ) +colvars: ( -0.491263 , -0.0274384 , -0.209044 ) +colvars: ( -0.52727 , -0.0289039 , -0.245679 ) +colvars: ( -0.579639 , -0.0974287 , -0.324126 ) +colvars: ( -0.472798 , -0.0602975 , -0.202995 ) +colvars: ( -0.479984 , -0.0140596 , -0.192671 ) +colvars: ( -0.415139 , -0.138167 , -0.174734 ) +colvars: ( -0.354901 , -0.170922 , -0.12679 ) +colvars: ( -0.302178 , -0.265433 , -0.109782 ) +colvars: ( -0.311696 , -0.0946061 , -0.0545715 ) +colvars: ( -0.297902 , -0.0750502 , -0.0333377 ) +colvars: ( -0.290814 , -0.0476428 , -0.0158476 ) +colvars: ( -0.253709 , 0.0306758 , 0.0510159 ) +colvars: ( -0.231328 , 0.0582544 , 0.0838957 ) +colvars: ( -0.299767 , 0.121614 , 0.0393331 ) +colvars: ( -0.271869 , 0.165405 , 0.0838853 ) +colvars: ( -0.372299 , 0.151075 , -0.0221797 ) +colvars: ( -0.423348 , 0.230947 , -0.0430581 ) +colvars: ( -0.497764 , 0.254569 , -0.108671 ) +colvars: ( -0.43554 , 0.210247 , -0.0631204 ) +colvars: ( -0.440237 , 0.274011 , -0.0436597 ) +colvars: ( -0.44034 , 0.119566 , -0.1023 ) +colvars: ( -0.447858 , 0.0880366 , -0.121783 ) +colvars: ( -0.470473 , -0.0097224 , -0.181497 ) +colvars: ( -0.378063 , 0.0762557 , -0.0563131 ) +colvars: ( -0.381553 , 0.10388 , -0.0493399 ) +colvars: ( -0.209444 , 0.110513 , 0.12563 ) +colvars: ( -0.157725 , 0.112495 , 0.178205 ) +colvars: ( -0.237182 , 0.186248 , 0.126541 ) +colvars: ( -0.312603 , 0.0335326 , -0.0069135 ) +colvars: ( -0.242773 , 0.0192876 , 0.0576581 ) +colvars: ( -0.186378 , -0.0678045 , 0.0811573 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 21. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 21. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atoms_new_colvar_forces = { ( -4.88681301186317e+00 , -4.38142611451578e-01 , -1.25605632275411e+00 ), ( -4.20942626585542e+00 , -3.70902641485592e-01 , -9.82025645932571e-01 ), ( -4.28570386568547e+00 , -3.98963378348128e-01 , -1.01909902049081e+00 ), ( -5.76223057131802e+00 , -5.66289864819247e-01 , -1.51758168776074e+00 ), ( 2.65810606302739e-01 , 1.24016480312968e-01 , 3.61202368754497e-01 ), ( 5.26686559508448e+00 , 6.23549055462795e-01 , 1.84404742943105e+00 ), ( 4.45082867480974e+00 , 5.16312088873669e-01 , 1.60000276006648e+00 ), ( -4.67385379774749e-02 , 2.68758955307641e-02 , 3.67076186758324e-01 ), ( 4.43110671587295e+00 , 5.06566237586873e-01 , 1.56838816363311e+00 ), ( 5.87352774759951e+00 , 6.48445584579502e-01 , 1.93619144039310e+00 ), ( 1.22105484682847e-02 , 3.89284962080426e-02 , 3.10521313852066e-01 ), ( 8.30806279725038e-04 , 3.25506410605702e-02 , 2.85606721608083e-01 ), ( 2.33566070435660e-02 , 4.74077026791327e-02 , 3.54668873907143e-01 ), ( 4.59808096591225e-02 , 3.79344612434137e-02 , 2.08260281796434e-01 ), ( 1.71532152156076e-02 , 2.30715085108427e-02 , 1.56588051806439e-01 ), ( 1.17843888649354e-01 , 5.92017591302691e-02 , 1.97465023267645e-01 ), ( 1.66064399253842e-01 , 6.61818901802171e-02 , 1.25739234136756e-01 ), ( 2.49409891604407e-01 , 9.40948051046991e-02 , 1.41942715167110e-01 ), ( 1.35702889108031e-01 , 4.84693232741650e-02 , 5.31080880870635e-02 ), ( 1.31098615693591e-01 , 3.96088076835292e-02 , -1.25183758706906e-02 ), ( 1.11453651775268e-01 , 4.21925387711198e-02 , 6.47074859023176e-02 ), ( 7.39473382241158e-02 , 2.36610277247961e-02 , 4.60818526619372e-03 ), ( 5.99983354497177e-02 , 2.31284701305178e-02 , 3.85056635527237e-02 ), ( -1.98740889840437e-03 , -3.16138005557178e-03 , -2.24612720389368e-02 ), ( -1.62858593716134e-02 , -1.57390193591765e-02 , -9.41337890726690e-02 ), ( -5.13126973059539e-02 , -1.21179100784611e-02 , 3.48413140346601e-02 ), ( -1.21689139585961e-01 , -3.59716748440565e-02 , 1.86449118538971e-02 ), ( -1.64966012524163e-01 , -4.04203988914852e-02 , 9.90777284254870e-02 ), ( -1.08158151523756e-01 , -3.71166524479201e-02 , -2.89331725816984e-02 ), ( -1.45998597057365e-01 , -5.56519067784839e-02 , -8.81407756172215e-02 ), ( -5.21418898735860e-02 , -1.69044790281512e-02 , -5.20024110085091e-03 ), ( -2.98270445056342e-02 , -1.47309100218884e-02 , -4.77380634500729e-02 ), ( 2.94632244389206e-02 , 9.45826634269505e-03 , 2.10918770612323e-03 ), ( 3.08518437828148e-03 , -1.40757002641254e-02 , -1.33036887430632e-01 ), ( -1.51672610063517e-02 , -2.61441463003034e-02 , -1.89261836390765e-01 ), ( 5.14151178066671e-02 , -3.13146900668526e-04 , -1.45075886124961e-01 ), ( 8.16587237509778e-02 , 2.64533872962491e-04 , -2.23674261611173e-01 ), ( 1.44869579244897e-01 , 2.12817967175752e-02 , -2.12733528087116e-01 ), ( 1.99730376436439e-02 , -2.52854174630152e-02 , -2.78927384985975e-01 ), ( 2.10915592826001e-02 , -3.30603781613270e-02 , -3.50791739134924e-01 ), ( -3.58834833768484e-02 , -3.90347146482197e-02 , -2.45939138853539e-01 ), ( -1.00187657538689e-01 , -6.41287669796099e-02 , -2.89912474780319e-01 ), ( -1.40051259963949e-01 , -7.08640215953256e-02 , -2.39150934755377e-01 ), ( -1.59735908643585e-01 , -8.52610549438823e-02 , -3.12007902837183e-01 ), ( -1.88763505911318e-01 , -1.01852501930192e-01 , -3.78414875914119e-01 ), ( -2.02429196905031e-01 , -9.91431990223937e-02 , -3.16627707005783e-01 ), ( -2.46107790543223e-01 , -1.15948849811382e-01 , -3.44378434217234e-01 ), ( -1.24969727827573e-01 , -7.57167501644633e-02 , -3.23815174894414e-01 ), ( -1.80164339933053e-01 , -8.53288138440845e-02 , -2.56065656112749e-01 ), ( -2.35509264809481e-01 , -1.04277848727155e-01 , -2.70484408150589e-01 ), ( -2.72498312834940e-01 , -1.06653232615234e-01 , -1.89116531449463e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 22, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 22, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 22, atoms_positions[size = 51] = { ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 ), ( 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 ), ( 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 ), ( 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ), ( 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 ), ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 ), ( 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 ), ( 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 ), ( 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 ), ( 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ), ( 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 ), ( 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 ), ( 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 ), ( 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 ), ( 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 ), ( 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 ), ( 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 ), ( 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 ), ( 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 ), ( 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 ), ( 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 ), ( 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 ), ( 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 ), ( 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 ), ( -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 ), ( 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 ), ( 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 ), ( 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 ), ( -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 ), ( -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 ), ( -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 ), ( -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 ), ( -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 ), ( -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 ), ( -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 ), ( -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 ), ( -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 ), ( -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 ), ( -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 ), ( -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 ), ( -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 ), ( -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 ), ( -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 ), ( -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 ), ( -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 ), ( -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 ), ( -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 ), ( -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 ), ( -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 ), ( -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 ), ( -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ) } +colvars: Step 22, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.01144188109486e-01 , -2.24212177402314e-03 , 9.53575980642250e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 , 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 , 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 , 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 , 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 , 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 , 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 , 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 , 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 , 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 , 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 , 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 , 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 , 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 , 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 , 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 , -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 , 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 , 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 , 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 , -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 , -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 , -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 , -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 , -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 , -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 , -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 , -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 , -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 , -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 , -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 , -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 , -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 , -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 , -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 , -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 , -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 , -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 , -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 , -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 , -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 , -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 , -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.01144188109486e-01 , -2.24212177402314e-03 , 9.53575980642250e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 , 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 , 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 , 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 , 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 , 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 , 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 , 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 , 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 , 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 , 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 , 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 , 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 , 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 , 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 , 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 , -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 , 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 , 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 , 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 , -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 , -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 , -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 , -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 , -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 , -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 , -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 , -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 , -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 , -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 , -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 , -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 , -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 , -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 , -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 , -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 , -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 , -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 , -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 , -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 , -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 , -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 , -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.9267 , 6.59267 , 13.1853 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.9267 , 6.59267 , 13.1853 ) to colvar "one". +colvars: Adding total bias energy: 56.3804 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.9267 , 6.59267 , 13.1853 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.18039 , -0.557572 , -1.51281 ) +colvars: ( -4.44219 , -0.478118 , -1.29723 ) +colvars: ( -4.44219 , -0.478118 , -1.29723 ) +colvars: ( -5.91712 , -0.636867 , -1.72795 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.937837 , 0.206033 , 0.648045 ) +colvars: ( 0.812522 , 0.280295 , 0.673367 ) +colvars: ( 0.795602 , 0.2731 , 0.654034 ) +colvars: ( 0.695433 , 0.280937 , 0.606208 ) +colvars: ( 0.68297 , 0.21097 , 0.506535 ) +colvars: ( 0.60487 , 0.361982 , 0.660675 ) +colvars: ( 0.492646 , 0.376527 , 0.614708 ) +colvars: ( 0.412372 , 0.478612 , 0.702948 ) +colvars: ( 0.406991 , 0.329692 , 0.503084 ) +colvars: ( 0.370632 , 0.285921 , 0.42414 ) +colvars: ( 0.376121 , 0.335305 , 0.49257 ) +colvars: ( 0.301419 , 0.290253 , 0.389663 ) +colvars: ( 0.272874 , 0.320806 , 0.413447 ) +colvars: ( 0.366824 , 0.187542 , 0.29196 ) +colvars: ( 0.305344 , 0.141951 , 0.196021 ) +colvars: ( 0.495429 , 0.148768 , 0.315432 ) +colvars: ( 0.571426 , 0.0528323 , 0.232832 ) +colvars: ( 0.707113 , 0.0309606 , 0.282747 ) +colvars: ( 0.58058 , 0.0193069 , 0.193858 ) +colvars: ( 0.564069 , -0.049083 , 0.093918 ) +colvars: ( 0.60263 , 0.0696209 , 0.273135 ) +colvars: ( 0.601208 , 0.0525443 , 0.249749 ) +colvars: ( 0.639636 , 0.120543 , 0.361902 ) +colvars: ( 0.470996 , 0.0570661 , 0.180093 ) +colvars: ( 0.463921 , -0.00175612 , 0.0982735 ) +colvars: ( 0.364139 , 0.125944 , 0.209023 ) +colvars: ( 0.233708 , 0.134797 , 0.144962 ) +colvars: ( 0.137817 , 0.224829 , 0.208208 ) +colvars: ( 0.204024 , 0.0573313 , 0.0253808 ) +colvars: ( 0.152487 , 0.0192176 , -0.0549051 ) +colvars: ( 0.239038 , 0.0306024 , 0.0104057 ) +colvars: ( 0.224216 , -0.0455418 , -0.0987971 ) +colvars: ( 0.260994 , -0.0489072 , -0.0818819 ) +colvars: ( 0.303103 , -0.1358 , -0.172218 ) +colvars: ( 0.25701 , -0.191677 , -0.272809 ) +colvars: ( 0.42383 , -0.151459 , -0.122784 ) +colvars: ( 0.505043 , -0.230729 , -0.180339 ) +colvars: ( 0.642498 , -0.233286 , -0.10388 ) +colvars: ( 0.45569 , -0.235607 , -0.215448 ) +colvars: ( 0.46151 , -0.307145 , -0.306577 ) +colvars: ( 0.404754 , -0.158699 , -0.14343 ) +colvars: ( 0.348115 , -0.152294 , -0.167864 ) +colvars: ( 0.330943 , -0.0612825 , -0.0576031 ) +colvars: ( 0.218936 , -0.16169 , -0.255308 ) +colvars: ( 0.19347 , -0.205921 , -0.328533 ) +colvars: ( 0.00778441 , -0.209889 , -0.441625 ) +colvars: ( -0.0874925 , -0.22871 , -0.521829 ) +colvars: ( 0.112797 , -0.262155 , -0.44968 ) +colvars: ( 0.133112 , -0.119059 , -0.248836 ) +colvars: ( 0.00809018 , -0.123806 , -0.327722 ) +colvars: ( -0.0851976 , -0.0391176 , -0.270024 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.18039 , 0.557572 , 1.51281 ) +colvars: ( 4.44219 , 0.478118 , 1.29723 ) +colvars: ( 4.44219 , 0.478118 , 1.29723 ) +colvars: ( 5.91712 , 0.636867 , 1.72795 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.647364 , -0.0854076 , -0.38673 ) +colvars: ( -0.582385 , -0.172223 , -0.354183 ) +colvars: ( -0.529887 , -0.149147 , -0.29292 ) +colvars: ( -0.541548 , -0.201012 , -0.324061 ) +colvars: ( -0.531439 , -0.139183 , -0.290737 ) +colvars: ( -0.515857 , -0.297587 , -0.334546 ) +colvars: ( -0.48185 , -0.339862 , -0.316327 ) +colvars: ( -0.459337 , -0.452499 , -0.336023 ) +colvars: ( -0.415779 , -0.302705 , -0.236181 ) +colvars: ( -0.41116 , -0.276103 , -0.221573 ) +colvars: ( -0.363856 , -0.296811 , -0.181939 ) +colvars: ( -0.300394 , -0.258063 , -0.103809 ) +colvars: ( -0.249187 , -0.273762 , -0.0583855 ) +colvars: ( -0.320649 , -0.149755 , -0.0834752 ) +colvars: ( -0.287944 , -0.118983 , -0.0391583 ) +colvars: ( -0.377454 , -0.0895778 , -0.117824 ) +colvars: ( -0.405245 , 0.013541 , -0.106988 ) +colvars: ( -0.457631 , 0.0634506 , -0.140759 ) +colvars: ( -0.444876 , 0.0293556 , -0.140769 ) +colvars: ( -0.432942 , 0.0889898 , -0.106438 ) +colvars: ( -0.491307 , -0.0273588 , -0.208572 ) +colvars: ( -0.527507 , -0.0288458 , -0.245405 ) +colvars: ( -0.580022 , -0.097517 , -0.323791 ) +colvars: ( -0.473173 , -0.0602778 , -0.20275 ) +colvars: ( -0.480422 , -0.0139616 , -0.192638 ) +colvars: ( -0.415558 , -0.138265 , -0.174271 ) +colvars: ( -0.355429 , -0.171058 , -0.126319 ) +colvars: ( -0.302738 , -0.265719 , -0.10903 ) +colvars: ( -0.312097 , -0.0945859 , -0.0542093 ) +colvars: ( -0.2984 , -0.0749921 , -0.0331333 ) +colvars: ( -0.290994 , -0.0475251 , -0.0154077 ) +colvars: ( -0.253747 , 0.0309515 , 0.0513563 ) +colvars: ( -0.231129 , 0.0585939 , 0.0843908 ) +colvars: ( -0.299791 , 0.122034 , 0.0393848 ) +colvars: ( -0.271899 , 0.165915 , 0.083796 ) +colvars: ( -0.372311 , 0.15152 , -0.0222244 ) +colvars: ( -0.423366 , 0.231516 , -0.0433753 ) +colvars: ( -0.497724 , 0.255152 , -0.109021 ) +colvars: ( -0.435782 , 0.210769 , -0.0636002 ) +colvars: ( -0.440487 , 0.274644 , -0.0443533 ) +colvars: ( -0.440769 , 0.119918 , -0.102679 ) +colvars: ( -0.448509 , 0.0883243 , -0.122288 ) +colvars: ( -0.471295 , -0.00962246 , -0.181865 ) +colvars: ( -0.37877 , 0.076548 , -0.056822 ) +colvars: ( -0.382363 , 0.104218 , -0.0500419 ) +colvars: ( -0.209959 , 0.110937 , 0.125241 ) +colvars: ( -0.158279 , 0.112941 , 0.177779 ) +colvars: ( -0.237503 , 0.186802 , 0.126099 ) +colvars: ( -0.313245 , 0.0337755 , -0.00720674 ) +colvars: ( -0.243457 , 0.0195311 , 0.0573828 ) +colvars: ( -0.187067 , -0.067695 , 0.0811675 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 22. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 22. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atoms_new_colvar_forces = { ( -4.88991995188348e+00 , -4.36946445275235e-01 , -1.25149461155740e+00 ), ( -4.21204835856932e+00 , -3.70045365021465e-01 , -9.78049932265430e-01 ), ( -4.28830017318750e+00 , -3.98192282580132e-01 , -1.01508752696021e+00 ), ( -5.76558894916333e+00 , -5.65079608774376e-01 , -1.51215513117753e+00 ), ( 2.65714588002630e-01 , 1.23953162992971e-01 , 3.61114033541836e-01 ), ( 5.26940568272368e+00 , 6.21967404854857e-01 , 1.83893911324893e+00 ), ( 4.45298177352149e+00 , 5.14782959611222e-01 , 1.59561479154313e+00 ), ( -4.69653548536075e-02 , 2.61128669902641e-02 , 3.66924827739270e-01 ), ( 4.43339738650594e+00 , 5.05105060382023e-01 , 1.56413748727237e+00 ), ( 5.87659165785773e+00 , 6.46684102044952e-01 , 1.93052040100729e+00 ), ( 1.22657857418941e-02 , 3.84937365477269e-02 , 3.10631368933218e-01 ), ( 1.02494327094066e-03 , 3.21909155756814e-02 , 2.85854826252792e-01 ), ( 2.36865799529954e-02 , 4.70443236203994e-02 , 3.55061815992946e-01 ), ( 4.61756614547097e-02 , 3.77870723926189e-02 , 2.08485111756280e-01 ), ( 1.74006656661443e-02 , 2.29684679904045e-02 , 1.56862733462639e-01 ), ( 1.17974872682656e-01 , 5.91897907116165e-02 , 1.97607824197787e-01 ), ( 1.66181044062799e-01 , 6.63733125927542e-02 , 1.25843935345487e-01 ), ( 2.49481938764797e-01 , 9.44111917516189e-02 , 1.41987290852278e-01 ), ( 1.35703529942543e-01 , 4.86625189401672e-02 , 5.30890090442296e-02 ), ( 1.31127257116666e-01 , 3.99067370549339e-02 , -1.25202432380951e-02 ), ( 1.11322397989908e-01 , 4.22620650541622e-02 , 6.45627197135051e-02 ), ( 7.37004755222272e-02 , 2.36984886005551e-02 , 4.34388828501744e-03 ), ( 5.96135757901188e-02 , 2.30259159161144e-02 , 3.81114773666195e-02 ), ( -2.17739370652986e-03 , -3.21167852637620e-03 , -2.26566557148560e-02 ), ( -1.65012835652354e-02 , -1.57177052995119e-02 , -9.43648859583682e-02 ), ( -5.14188739398183e-02 , -1.23217047604133e-02 , 3.47517177224063e-02 ), ( -1.21720438664443e-01 , -3.62611662717751e-02 , 1.86431783259751e-02 ), ( -1.64920872577396e-01 , -4.08902450237653e-02 , 9.91772771063290e-02 ), ( -1.08072408022284e-01 , -3.72546053487651e-02 , -2.88284781753466e-02 ), ( -1.45912540068657e-01 , -5.57744380285779e-02 , -8.80384104123101e-02 ), ( -5.19557555905013e-02 , -1.69227001208000e-02 , -5.00206290059414e-03 ), ( -2.95301122443954e-02 , -1.45902680960036e-02 , -4.74407408728579e-02 ), ( 2.98653644956911e-02 , 9.68671388074512e-03 , 2.50893473059546e-03 ), ( 3.31172592715373e-03 , -1.37655931017732e-02 , -1.32833386301177e-01 ), ( -1.48890495525763e-02 , -2.57615300512833e-02 , -1.89012552501226e-01 ), ( 5.15190514455810e-02 , 6.14202551529885e-05 , -1.45008800370079e-01 ), ( 8.16776106883810e-02 , 7.86456634676358e-04 , -2.23713976281361e-01 ), ( 1.44774027279720e-01 , 2.18661324134917e-02 , -2.12900431025935e-01 ), ( 1.99086080623049e-02 , -2.48383951721095e-02 , -2.79047907498041e-01 ), ( 2.10221735453149e-02 , -3.25013833690241e-02 , -3.50930690512529e-01 ), ( -3.60145013731311e-02 , -3.87809076824542e-02 , -2.46108666501084e-01 ), ( -1.00394342916154e-01 , -6.39694589856976e-02 , -2.90152454127178e-01 ), ( -1.40352158627249e-01 , -7.09049175416535e-02 , -2.39468004797145e-01 ), ( -1.59834696369235e-01 , -8.51421622671409e-02 , -3.12130135994516e-01 ), ( -1.88893469108966e-01 , -1.01702550693814e-01 , -3.78574445271921e-01 ), ( -2.02174476583266e-01 , -9.89526975671664e-02 , -3.16384827623661e-01 ), ( -2.45771905014202e-01 , -1.15769166566491e-01 , -3.44049265510704e-01 ), ( -1.24705642671454e-01 , -7.53537734390434e-02 , -3.23580986419401e-01 ), ( -1.80133532150737e-01 , -8.52830504276501e-02 , -2.56042427496679e-01 ), ( -2.35367008744962e-01 , -1.04274392403073e-01 , -2.70339355104522e-01 ), ( -2.72265128865591e-01 , -1.06812624413538e-01 , -1.88856770870786e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 23, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 23, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 23, atoms_positions[size = 51] = { ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 ), ( 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 ), ( 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 ), ( 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ), ( 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 ), ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 ), ( 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 ), ( 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 ), ( 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 ), ( 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ), ( 5.83759674592644e+00 , 2.25770089769487e+00 , 2.98449539776859e+00 ), ( 5.22544047027611e+00 , 3.57340227971898e+00 , 2.91910068664912e+00 ), ( 6.31973750751939e+00 , 4.49732575828523e+00 , 2.33613701154318e+00 ), ( 3.86857472003622e+00 , 3.68676300605869e+00 , 2.04327709509885e+00 ), ( 2.79093067267769e+00 , 4.16716972365170e+00 , 2.47196221045982e+00 ), ( 3.94119151819773e+00 , 3.23124212258785e+00 , 7.30595183661825e-01 ), ( 2.68926925665233e+00 , 3.00989334754145e+00 , -9.59122997804579e-02 ), ( 3.07320511801156e+00 , 2.68709232043194e+00 , -1.51899240103286e+00 ), ( 1.58745463578995e+00 , 2.17137449129282e+00 , 4.30768375140066e-01 ), ( 3.74893053327457e-01 , 2.60223269819607e+00 , 4.97582150370188e-01 ), ( 2.06796916608957e+00 , 1.11473680732208e+00 , 1.05552745142886e+00 ), ( 1.16799543789882e+00 , 1.16883822816026e-01 , 1.70093177320460e+00 ), ( 2.05458997515211e+00 , -1.09486128414112e+00 , 2.01968650669132e+00 ), ( 5.67883464785948e-01 , 6.16145271973744e-01 , 2.95739749655181e+00 ), ( -5.88978848799477e-01 , 3.51029880586444e-01 , 3.16194777116286e+00 ), ( 1.30611054901562e+00 , 1.34984121792820e+00 , 3.75187246907796e+00 ), ( 8.39644418143578e-01 , 1.98341133130423e+00 , 5.02625058152132e+00 ), ( 2.10215209936077e+00 , 2.71472163130683e+00 , 5.70145420435647e+00 ), ( -3.41315746205403e-01 , 2.91178403953984e+00 , 4.96991681387973e+00 ), ( -1.12692790956357e+00 , 3.06510460555331e+00 , 5.88054746281053e+00 ), ( -5.26560721980815e-01 , 3.51792887631429e+00 , 3.83522223943442e+00 ), ( -1.51417661879093e+00 , 4.52540121678735e+00 , 3.42279866771453e+00 ), ( -7.01905641915050e-01 , 5.41958098611354e+00 , 2.46832654436502e+00 ), ( -2.74963800407086e+00 , 3.91239748034020e+00 , 2.87388428339751e+00 ), ( -3.81432915765696e+00 , 4.52662820628417e+00 , 2.81274804277420e+00 ), ( -2.64354354981511e+00 , 2.66159372775565e+00 , 2.38103086872300e+00 ), ( -3.78183833193364e+00 , 1.80523478755800e+00 , 1.99994175515576e+00 ), ( -3.37664147509234e+00 , 8.82895505941315e-01 , 8.55338259758225e-01 ), ( -4.30286895448029e+00 , 1.06811651610639e+00 , 3.20934511498940e+00 ), ( -5.49470587750599e+00 , 7.97217291484228e-01 , 3.33144764474570e+00 ), ( -3.36448212751923e+00 , 7.04325113298133e-01 , 4.20622989499706e+00 ), ( -3.68483166538681e+00 , 6.25748844992158e-02 , 5.44360082864042e+00 ), ( -2.39256797298429e+00 , -3.23186883095115e-01 , 6.16148240638997e+00 ), ( -4.46133565763009e+00 , 9.61155447571340e-01 , 6.43253440601395e+00 ), ( -5.36445983873112e+00 , 5.92921715202873e-01 , 7.21880615656639e+00 ), ( -6.25992913038621e+00 , 3.62103269698498e+00 , 6.74487895486376e+00 ), ( -6.97079787066806e+00 , 4.29611545936923e+00 , 7.48729266024479e+00 ), ( -6.71761880599661e+00 , 3.17153101534265e+00 , 5.50641855142913e+00 ), ( -4.12201369887225e+00 , 2.24375136131545e+00 , 6.39437863736119e+00 ), ( -4.80711291753279e+00 , 3.23063933516567e+00 , 7.25347545818975e+00 ), ( -4.07513539547727e+00 , 4.55814099458782e+00 , 7.27526406844747e+00 ) } +colvars: Step 23, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -3.00108439186526e-01 , -3.46138019158803e-03 , 9.53898812021588e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 , 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 , 5.83759674592644e+00 , 2.25770089769487e+00 , 2.98449539776859e+00 , 5.22544047027611e+00 , 3.57340227971898e+00 , 2.91910068664912e+00 , 6.31973750751939e+00 , 4.49732575828523e+00 , 2.33613701154318e+00 , 3.86857472003622e+00 , 3.68676300605869e+00 , 2.04327709509885e+00 , 2.79093067267769e+00 , 4.16716972365170e+00 , 2.47196221045982e+00 , 3.94119151819773e+00 , 3.23124212258785e+00 , 7.30595183661825e-01 , 2.68926925665233e+00 , 3.00989334754145e+00 , -9.59122997804579e-02 , 3.07320511801156e+00 , 2.68709232043194e+00 , -1.51899240103286e+00 , 1.58745463578995e+00 , 2.17137449129282e+00 , 4.30768375140066e-01 , 3.74893053327457e-01 , 2.60223269819607e+00 , 4.97582150370188e-01 , 2.06796916608957e+00 , 1.11473680732208e+00 , 1.05552745142886e+00 , 1.16799543789882e+00 , 1.16883822816026e-01 , 1.70093177320460e+00 , 2.05458997515211e+00 , -1.09486128414112e+00 , 2.01968650669132e+00 , 5.67883464785948e-01 , 6.16145271973744e-01 , 2.95739749655181e+00 , -5.88978848799477e-01 , 3.51029880586444e-01 , 3.16194777116286e+00 , 1.30611054901562e+00 , 1.34984121792820e+00 , 3.75187246907796e+00 , 8.39644418143578e-01 , 1.98341133130423e+00 , 5.02625058152132e+00 , 2.10215209936077e+00 , 2.71472163130683e+00 , 5.70145420435647e+00 , -3.41315746205403e-01 , 2.91178403953984e+00 , 4.96991681387973e+00 , -1.12692790956357e+00 , 3.06510460555331e+00 , 5.88054746281053e+00 , -5.26560721980815e-01 , 3.51792887631429e+00 , 3.83522223943442e+00 , -1.51417661879093e+00 , 4.52540121678735e+00 , 3.42279866771453e+00 , -7.01905641915050e-01 , 5.41958098611354e+00 , 2.46832654436502e+00 , -2.74963800407086e+00 , 3.91239748034020e+00 , 2.87388428339751e+00 , -3.81432915765696e+00 , 4.52662820628417e+00 , 2.81274804277420e+00 , -2.64354354981511e+00 , 2.66159372775565e+00 , 2.38103086872300e+00 , -3.78183833193364e+00 , 1.80523478755800e+00 , 1.99994175515576e+00 , -3.37664147509234e+00 , 8.82895505941315e-01 , 8.55338259758225e-01 , -4.30286895448029e+00 , 1.06811651610639e+00 , 3.20934511498940e+00 , -5.49470587750599e+00 , 7.97217291484228e-01 , 3.33144764474570e+00 , -3.36448212751923e+00 , 7.04325113298133e-01 , 4.20622989499706e+00 , -3.68483166538681e+00 , 6.25748844992158e-02 , 5.44360082864042e+00 , -2.39256797298429e+00 , -3.23186883095115e-01 , 6.16148240638997e+00 , -4.46133565763009e+00 , 9.61155447571340e-01 , 6.43253440601395e+00 , -5.36445983873112e+00 , 5.92921715202873e-01 , 7.21880615656639e+00 , -6.25992913038621e+00 , 3.62103269698498e+00 , 6.74487895486376e+00 , -6.97079787066806e+00 , 4.29611545936923e+00 , 7.48729266024479e+00 , -6.71761880599661e+00 , 3.17153101534265e+00 , 5.50641855142913e+00 , -4.12201369887225e+00 , 2.24375136131545e+00 , 6.39437863736119e+00 , -4.80711291753279e+00 , 3.23063933516567e+00 , 7.25347545818975e+00 , -4.07513539547727e+00 , 4.55814099458782e+00 , 7.27526406844747e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -3.00108439186526e-01 , -3.46138019158803e-03 , 9.53898812021588e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 , 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 , 5.83759674592644e+00 , 2.25770089769487e+00 , 2.98449539776859e+00 , 5.22544047027611e+00 , 3.57340227971898e+00 , 2.91910068664912e+00 , 6.31973750751939e+00 , 4.49732575828523e+00 , 2.33613701154318e+00 , 3.86857472003622e+00 , 3.68676300605869e+00 , 2.04327709509885e+00 , 2.79093067267769e+00 , 4.16716972365170e+00 , 2.47196221045982e+00 , 3.94119151819773e+00 , 3.23124212258785e+00 , 7.30595183661825e-01 , 2.68926925665233e+00 , 3.00989334754145e+00 , -9.59122997804579e-02 , 3.07320511801156e+00 , 2.68709232043194e+00 , -1.51899240103286e+00 , 1.58745463578995e+00 , 2.17137449129282e+00 , 4.30768375140066e-01 , 3.74893053327457e-01 , 2.60223269819607e+00 , 4.97582150370188e-01 , 2.06796916608957e+00 , 1.11473680732208e+00 , 1.05552745142886e+00 , 1.16799543789882e+00 , 1.16883822816026e-01 , 1.70093177320460e+00 , 2.05458997515211e+00 , -1.09486128414112e+00 , 2.01968650669132e+00 , 5.67883464785948e-01 , 6.16145271973744e-01 , 2.95739749655181e+00 , -5.88978848799477e-01 , 3.51029880586444e-01 , 3.16194777116286e+00 , 1.30611054901562e+00 , 1.34984121792820e+00 , 3.75187246907796e+00 , 8.39644418143578e-01 , 1.98341133130423e+00 , 5.02625058152132e+00 , 2.10215209936077e+00 , 2.71472163130683e+00 , 5.70145420435647e+00 , -3.41315746205403e-01 , 2.91178403953984e+00 , 4.96991681387973e+00 , -1.12692790956357e+00 , 3.06510460555331e+00 , 5.88054746281053e+00 , -5.26560721980815e-01 , 3.51792887631429e+00 , 3.83522223943442e+00 , -1.51417661879093e+00 , 4.52540121678735e+00 , 3.42279866771453e+00 , -7.01905641915050e-01 , 5.41958098611354e+00 , 2.46832654436502e+00 , -2.74963800407086e+00 , 3.91239748034020e+00 , 2.87388428339751e+00 , -3.81432915765696e+00 , 4.52662820628417e+00 , 2.81274804277420e+00 , -2.64354354981511e+00 , 2.66159372775565e+00 , 2.38103086872300e+00 , -3.78183833193364e+00 , 1.80523478755800e+00 , 1.99994175515576e+00 , -3.37664147509234e+00 , 8.82895505941315e-01 , 8.55338259758225e-01 , -4.30286895448029e+00 , 1.06811651610639e+00 , 3.20934511498940e+00 , -5.49470587750599e+00 , 7.97217291484228e-01 , 3.33144764474570e+00 , -3.36448212751923e+00 , 7.04325113298133e-01 , 4.20622989499706e+00 , -3.68483166538681e+00 , 6.25748844992158e-02 , 5.44360082864042e+00 , -2.39256797298429e+00 , -3.23186883095115e-01 , 6.16148240638997e+00 , -4.46133565763009e+00 , 9.61155447571340e-01 , 6.43253440601395e+00 , -5.36445983873112e+00 , 5.92921715202873e-01 , 7.21880615656639e+00 , -6.25992913038621e+00 , 3.62103269698498e+00 , 6.74487895486376e+00 , -6.97079787066806e+00 , 4.29611545936923e+00 , 7.48729266024479e+00 , -6.71761880599661e+00 , 3.17153101534265e+00 , 5.50641855142913e+00 , -4.12201369887225e+00 , 2.24375136131545e+00 , 6.39437863736119e+00 , -4.80711291753279e+00 , 3.23063933516567e+00 , 7.25347545818975e+00 , -4.07513539547727e+00 , 4.55814099458782e+00 , 7.27526406844747e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.8822 , 6.58822 , 13.1764 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.8822 , 6.58822 , 13.1764 ) to colvar "one". +colvars: Adding total bias energy: 56.3159 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.8822 , 6.58822 , 13.1764 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.1833 , -0.556583 , -1.50862 ) +colvars: ( -4.44468 , -0.477269 , -1.29364 ) +colvars: ( -4.44468 , -0.477269 , -1.29364 ) +colvars: ( -5.92044 , -0.635737 , -1.72317 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.937369 , 0.206157 , 0.646941 ) +colvars: ( 0.812191 , 0.280383 , 0.672161 ) +colvars: ( 0.795216 , 0.27319 , 0.652825 ) +colvars: ( 0.69527 , 0.280983 , 0.605092 ) +colvars: ( 0.682821 , 0.211007 , 0.505598 ) +colvars: ( 0.604839 , 0.361999 , 0.659432 ) +colvars: ( 0.492784 , 0.376503 , 0.61352 ) +colvars: ( 0.412625 , 0.478565 , 0.701573 ) +colvars: ( 0.407195 , 0.32964 , 0.502054 ) +colvars: ( 0.370905 , 0.285851 , 0.423253 ) +colvars: ( 0.376299 , 0.33525 , 0.49152 ) +colvars: ( 0.301644 , 0.290176 , 0.388756 ) +colvars: ( 0.273067 , 0.320728 , 0.412456 ) +colvars: ( 0.36696 , 0.187481 , 0.291256 ) +colvars: ( 0.305554 , 0.141867 , 0.19547 ) +colvars: ( 0.495405 , 0.148749 , 0.314732 ) +colvars: ( 0.571303 , 0.0528337 , 0.232312 ) +colvars: ( 0.706806 , 0.031009 , 0.282179 ) +colvars: ( 0.580509 , 0.0193019 , 0.193441 ) +colvars: ( 0.564018 , -0.0490979 , 0.0936797 ) +colvars: ( 0.602589 , 0.0696201 , 0.272604 ) +colvars: ( 0.601233 , 0.0525344 , 0.249288 ) +colvars: ( 0.639666 , 0.120544 , 0.361271 ) +colvars: ( 0.471192 , 0.0570108 , 0.179716 ) +colvars: ( 0.464149 , -0.00182034 , 0.0980557 ) +colvars: ( 0.364447 , 0.125858 , 0.208543 ) +colvars: ( 0.234179 , 0.134668 , 0.144552 ) +colvars: ( 0.138384 , 0.224675 , 0.207634 ) +colvars: ( 0.204488 , 0.0571917 , 0.0251625 ) +colvars: ( 0.153036 , 0.0190555 , -0.0549852 ) +colvars: ( 0.239397 , 0.0304802 , 0.0102023 ) +colvars: ( 0.224549 , -0.0456687 , -0.0988228 ) +colvars: ( 0.261214 , -0.049014 , -0.0819538 ) +colvars: ( 0.303362 , -0.135908 , -0.172068 ) +colvars: ( 0.257321 , -0.191804 , -0.272491 ) +colvars: ( 0.42397 , -0.15153 , -0.122667 ) +colvars: ( 0.505112 , -0.230782 , -0.180071 ) +colvars: ( 0.642414 , -0.233293 , -0.103694 ) +colvars: ( 0.455881 , -0.235683 , -0.215108 ) +colvars: ( 0.461703 , -0.307226 , -0.306062 ) +colvars: ( 0.405049 , -0.158793 , -0.143225 ) +colvars: ( 0.348538 , -0.152413 , -0.167611 ) +colvars: ( 0.331431 , -0.0614071 , -0.0575418 ) +colvars: ( 0.219503 , -0.161853 , -0.254948 ) +colvars: ( 0.194098 , -0.206098 , -0.328034 ) +colvars: ( 0.00849678 , -0.210114 , -0.44105 ) +colvars: ( -0.0866731 , -0.228968 , -0.521146 ) +colvars: ( 0.113348 , -0.262344 , -0.449064 ) +colvars: ( 0.133738 , -0.119242 , -0.248541 ) +colvars: ( 0.00885107 , -0.12403 , -0.327337 ) +colvars: ( -0.0843512 , -0.0393653 , -0.269794 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.1833 , 0.556583 , 1.50862 ) +colvars: ( 4.44468 , 0.477269 , 1.29364 ) +colvars: ( 4.44468 , 0.477269 , 1.29364 ) +colvars: ( 5.92044 , 0.635737 , 1.72317 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.64722 , -0.0854819 , -0.385978 ) +colvars: ( -0.582287 , -0.172448 , -0.3532 ) +colvars: ( -0.529568 , -0.149296 , -0.291765 ) +colvars: ( -0.5416 , -0.201288 , -0.323134 ) +colvars: ( -0.531479 , -0.139334 , -0.289981 ) +colvars: ( -0.516053 , -0.298051 , -0.333467 ) +colvars: ( -0.482216 , -0.340407 , -0.315285 ) +colvars: ( -0.459832 , -0.453265 , -0.334766 ) +colvars: ( -0.416068 , -0.303151 , -0.235153 ) +colvars: ( -0.411539 , -0.276501 , -0.220717 ) +colvars: ( -0.363969 , -0.297218 , -0.180735 ) +colvars: ( -0.300408 , -0.258367 , -0.102605 ) +colvars: ( -0.249022 , -0.274069 , -0.056936 ) +colvars: ( -0.32057 , -0.149849 , -0.0825079 ) +colvars: ( -0.287886 , -0.119007 , -0.0382971 ) +colvars: ( -0.377274 , -0.0895675 , -0.11695 ) +colvars: ( -0.404977 , 0.0137486 , -0.106344 ) +colvars: ( -0.457217 , 0.0637466 , -0.140131 ) +colvars: ( -0.444789 , 0.0295703 , -0.140368 ) +colvars: ( -0.432845 , 0.0893255 , -0.106205 ) +colvars: ( -0.491392 , -0.0272806 , -0.208189 ) +colvars: ( -0.527786 , -0.0287939 , -0.245226 ) +colvars: ( -0.580454 , -0.0976259 , -0.323574 ) +colvars: ( -0.473572 , -0.0602761 , -0.202583 ) +colvars: ( -0.480882 , -0.0138754 , -0.192677 ) +colvars: ( -0.415985 , -0.138398 , -0.173882 ) +colvars: ( -0.355946 , -0.171241 , -0.125907 ) +colvars: ( -0.303275 , -0.266069 , -0.108338 ) +colvars: ( -0.312482 , -0.0945964 , -0.053882 ) +colvars: ( -0.298875 , -0.0749649 , -0.0329531 ) +colvars: ( -0.291161 , -0.0474238 , -0.0149939 ) +colvars: ( -0.253768 , 0.0312272 , 0.0516926 ) +colvars: ( -0.230918 , 0.0589448 , 0.0848873 ) +colvars: ( -0.299812 , 0.122472 , 0.0394347 ) +colvars: ( -0.271919 , 0.166448 , 0.0837218 ) +colvars: ( -0.372336 , 0.151992 , -0.0222881 ) +colvars: ( -0.423408 , 0.232125 , -0.0437123 ) +colvars: ( -0.497728 , 0.255785 , -0.10941 ) +colvars: ( -0.436042 , 0.211321 , -0.064101 ) +colvars: ( -0.440757 , 0.275319 , -0.0450575 ) +colvars: ( -0.441211 , 0.120281 , -0.103093 ) +colvars: ( -0.449167 , 0.0886095 , -0.122829 ) +colvars: ( -0.472122 , -0.00954615 , -0.182289 ) +colvars: ( -0.379465 , 0.0768315 , -0.0573463 ) +colvars: ( -0.383157 , 0.104549 , -0.0507523 ) +colvars: ( -0.210428 , 0.111357 , 0.124889 ) +colvars: ( -0.158775 , 0.113382 , 0.177408 ) +colvars: ( -0.237792 , 0.187372 , 0.125695 ) +colvars: ( -0.313863 , 0.034002 , -0.00750483 ) +colvars: ( -0.244098 , 0.0197518 , 0.0571226 ) +colvars: ( -0.1877 , -0.0676254 , 0.0811942 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 23. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 23. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atoms_new_colvar_forces = { ( -4.89314969389035e+00 , -4.35907137065574e-01 , -1.24765646733718e+00 ), ( -4.21477401221486e+00 , -3.69333721068355e-01 , -9.74679364978744e-01 ), ( -4.29100768593370e+00 , -3.97574682406545e-01 , -1.01168245402456e+00 ), ( -5.76909754228417e+00 , -5.64064012876958e-01 , -1.50754931217094e+00 ), ( 2.65647982056842e-01 , 1.23894479901734e-01 , 3.61059540383409e-01 ), ( 5.27208481710348e+00 , 6.20530406439631e-01 , 1.83458495674507e+00 ), ( 4.45524528716730e+00 , 5.13364888628985e-01 , 1.59187595082763e+00 ), ( -4.72066769307715e-02 , 2.53003561132784e-02 , 3.66807496622965e-01 ), ( 4.43580435738879e+00 , 5.03758669118885e-01 , 1.56054100287330e+00 ), ( 5.87980588495882e+00 , 6.45086157379882e-01 , 1.92570262804706e+00 ), ( 1.23300936446108e-02 , 3.80322097438575e-02 , 3.10784463856866e-01 ), ( 1.23516685310776e-03 , 3.18088674650605e-02 , 2.86151774428636e-01 ), ( 2.40446317099675e-02 , 4.66592456226977e-02 , 3.55520449396829e-01 ), ( 4.63907693763088e-02 , 3.76321269229097e-02 , 2.08747794627587e-01 ), ( 1.76676424568742e-02 , 2.28597506509051e-02 , 1.57172642590895e-01 ), ( 1.18130225018854e-01 , 5.91810339714630e-02 , 1.97781322269948e-01 ), ( 1.66325716747012e-01 , 6.65822400602615e-02 , 1.25968044082477e-01 ), ( 2.49589011677952e-01 , 9.47555887836199e-02 , 1.42048514184550e-01 ), ( 1.35720495711020e-01 , 4.88722394536000e-02 , 5.30734688426321e-02 ), ( 1.31172548010176e-01 , 4.02276207050443e-02 , -1.25251264924779e-02 ), ( 1.11196622837668e-01 , 4.23394699460265e-02 , 6.44152907848379e-02 ), ( 7.34467643592223e-02 , 2.37404968034808e-02 , 4.06286851783905e-03 ), ( 5.92122318410697e-02 , 2.29185708403596e-02 , 3.76966007488264e-02 ), ( -2.37975725320438e-03 , -3.26535363717052e-03 , -2.28668074312608e-02 ), ( -1.67332878195299e-02 , -1.56957741515205e-02 , -9.46212012221707e-02 ), ( -5.15370806614827e-02 , -1.25400226966476e-02 , 3.46611814337565e-02 ), ( -1.21767390465137e-01 , -3.65727788305644e-02 , 1.86448501550935e-02 ), ( -1.64890487711056e-01 , -4.13948489082473e-02 , 9.92964181665753e-02 ), ( -1.07994115777278e-01 , -3.74046514749819e-02 , -2.87194668954239e-02 ), ( -1.45839060119007e-01 , -5.59093326149074e-02 , -8.79383847404050e-02 ), ( -5.17640665749411e-02 , -1.69436044010904e-02 , -4.79158573032616e-03 ), ( -2.92187372042236e-02 , -1.44415415137458e-02 , -4.71301677964168e-02 ), ( 3.02959845424302e-02 , 9.93076877737005e-03 , 2.93348973091517e-03 ), ( 3.55093488455888e-03 , -1.34357795361606e-02 , -1.32632812986454e-01 ), ( -1.45978076103804e-02 , -2.53552203687047e-02 , -1.88769723481286e-01 ), ( 5.16333866955254e-02 , 4.61201424862168e-04 , -1.44955071525014e-01 ), ( 8.17039952653785e-02 , 1.34373147957856e-03 , -2.23783221111909e-01 ), ( 1.44686235761542e-01 , 2.24916926317148e-02 , -2.13104193749752e-01 ), ( 1.98386555000443e-02 , -2.43627951147422e-02 , -2.79208778152793e-01 ), ( 2.09461059634538e-02 , -3.19067697320235e-02 , -3.51119555670142e-01 ), ( -3.61611505030088e-02 , -3.85124983394166e-02 , -2.46317122521031e-01 ), ( -1.00629349898272e-01 , -6.38036286111886e-02 , -2.90440187066860e-01 ), ( -1.40691133450162e-01 , -7.09532054445123e-02 , -2.39831253054555e-01 ), ( -1.59962208142437e-01 , -8.50211287502061e-02 , -3.12294725781383e-01 ), ( -1.89058332749189e-01 , -1.01549489241001e-01 , -3.78786145436480e-01 ), ( -2.01931398764172e-01 , -9.87566631838512e-02 , -3.16161649965062e-01 ), ( -2.45447988208696e-01 , -1.15585984090497e-01 , -3.43737194989054e-01 ), ( -1.24443831071177e-01 , -7.49719303565766e-02 , -3.23368729472479e-01 ), ( -1.80124949712414e-01 , -8.52402792912854e-02 , -2.56045733255299e-01 ), ( -2.35246572579257e-01 , -1.04278288000303e-01 , -2.70214333657193e-01 ), ( -2.72051230003134e-01 , -1.06990691158431e-01 , -1.88599978621055e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 24, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 24, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 24, atoms_positions[size = 51] = { ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 ), ( 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 ), ( 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 ), ( 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 ), ( 7.03126813606480e+00 , -2.05847485579762e+00 , -9.14970306289443e-01 ), ( 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 ), ( 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 ), ( 7.09828140808973e+00 , -3.49387967535437e-01 , 4.34546489528286e+00 ), ( 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 ), ( 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 ), ( 5.83708577362795e+00 , 2.25805562238920e+00 , 2.98267974249273e+00 ), ( 5.21773856017340e+00 , 3.57161922298348e+00 , 2.91648092208761e+00 ), ( 6.31853699913758e+00 , 4.49563391089305e+00 , 2.32683719497759e+00 ), ( 3.86542883065045e+00 , 3.68004921258471e+00 , 2.04195217412088e+00 ), ( 2.79235867300471e+00 , 4.16850146661707e+00 , 2.46662324468102e+00 ), ( 3.93901678661429e+00 , 3.22713308244348e+00 , 7.30934829859977e-01 ), ( 2.70074991752688e+00 , 3.01477796821894e+00 , -9.26397229315416e-02 ), ( 3.08032379131617e+00 , 2.68056690895662e+00 , -1.52252992080645e+00 ), ( 1.58047066505810e+00 , 2.17006440922225e+00 , 4.27998664327955e-01 ), ( 3.76967736525154e-01 , 2.60711789557844e+00 , 4.92778015884306e-01 ), ( 2.07258571616031e+00 , 1.12654210139324e+00 , 1.05134192945661e+00 ), ( 1.17056965170568e+00 , 1.16846335574401e-01 , 1.70099692768423e+00 ), ( 2.05876861292423e+00 , -1.09329159651842e+00 , 2.02324596919490e+00 ), ( 5.69776935670213e-01 , 6.17172001264618e-01 , 2.96095152671806e+00 ), ( -5.86240810892193e-01 , 3.51655835381281e-01 , 3.16311391312009e+00 ), ( 1.30244214709959e+00 , 1.35290545677039e+00 , 3.74694619494776e+00 ), ( 8.40806889312496e-01 , 1.98370498943023e+00 , 5.02675267008423e+00 ), ( 2.10672782636876e+00 , 2.72269083586604e+00 , 5.70697757475891e+00 ), ( -3.43581917981181e-01 , 2.91048819849154e+00 , 4.97014961072114e+00 ), ( -1.12395824489167e+00 , 3.06579184791982e+00 , 5.87888757790117e+00 ), ( -5.30970941621663e-01 , 3.51482581213725e+00 , 3.82943937819702e+00 ), ( -1.51011506620662e+00 , 4.51943360596667e+00 , 3.41840963676036e+00 ), ( -7.04729435523050e-01 , 5.42139775431779e+00 , 2.46955331052980e+00 ), ( -2.74711525410010e+00 , 3.92044849944355e+00 , 2.86440245108706e+00 ), ( -3.81315857722728e+00 , 4.53201123870925e+00 , 2.81253836569199e+00 ), ( -2.65053563595890e+00 , 2.65589915977239e+00 , 2.37517162843526e+00 ), ( -3.78436308048801e+00 , 1.80875030731400e+00 , 2.00126773291067e+00 ), ( -3.37318244314476e+00 , 8.80925739265677e-01 , 8.48890367251137e-01 ), ( -4.29365096406740e+00 , 1.06598119459501e+00 , 3.21152967601072e+00 ), ( -5.49323932631666e+00 , 7.90224912843538e-01 , 3.33236985776319e+00 ), ( -3.36483009077098e+00 , 7.08962306720196e-01 , 4.20288051489971e+00 ), ( -3.68104475168581e+00 , 6.77352039955146e-02 , 5.44944272745980e+00 ), ( -2.39228872483380e+00 , -3.24629174087243e-01 , 6.15756470761386e+00 ), ( -4.46264273224480e+00 , 9.51772161204549e-01 , 6.42996170595173e+00 ), ( -5.36509137781691e+00 , 5.90958189414682e-01 , 7.21777131508051e+00 ), ( -6.26912352257721e+00 , 3.62484190850191e+00 , 6.74752042761964e+00 ), ( -6.97441870236570e+00 , 4.29566443046527e+00 , 7.49091504085849e+00 ), ( -6.70727158666970e+00 , 3.16858712993869e+00 , 5.50784391680945e+00 ), ( -4.11917776391675e+00 , 2.24484839689618e+00 , 6.39160224714446e+00 ), ( -4.80813146866083e+00 , 3.23977411463558e+00 , 7.25597976490504e+00 ), ( -4.06701458125265e+00 , 4.55353074713024e+00 , 7.27349002869644e+00 ) } +colvars: Step 24, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.99159391330660e-01 , -4.75166803868142e-03 , 9.54191322654696e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 7.03126813606480e+00 , -2.05847485579762e+00 , -9.14970306289443e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 , 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 7.09828140808973e+00 , -3.49387967535437e-01 , 4.34546489528286e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 , 5.83708577362795e+00 , 2.25805562238920e+00 , 2.98267974249273e+00 , 5.21773856017340e+00 , 3.57161922298348e+00 , 2.91648092208761e+00 , 6.31853699913758e+00 , 4.49563391089305e+00 , 2.32683719497759e+00 , 3.86542883065045e+00 , 3.68004921258471e+00 , 2.04195217412088e+00 , 2.79235867300471e+00 , 4.16850146661707e+00 , 2.46662324468102e+00 , 3.93901678661429e+00 , 3.22713308244348e+00 , 7.30934829859977e-01 , 2.70074991752688e+00 , 3.01477796821894e+00 , -9.26397229315416e-02 , 3.08032379131617e+00 , 2.68056690895662e+00 , -1.52252992080645e+00 , 1.58047066505810e+00 , 2.17006440922225e+00 , 4.27998664327955e-01 , 3.76967736525154e-01 , 2.60711789557844e+00 , 4.92778015884306e-01 , 2.07258571616031e+00 , 1.12654210139324e+00 , 1.05134192945661e+00 , 1.17056965170568e+00 , 1.16846335574401e-01 , 1.70099692768423e+00 , 2.05876861292423e+00 , -1.09329159651842e+00 , 2.02324596919490e+00 , 5.69776935670213e-01 , 6.17172001264618e-01 , 2.96095152671806e+00 , -5.86240810892193e-01 , 3.51655835381281e-01 , 3.16311391312009e+00 , 1.30244214709959e+00 , 1.35290545677039e+00 , 3.74694619494776e+00 , 8.40806889312496e-01 , 1.98370498943023e+00 , 5.02675267008423e+00 , 2.10672782636876e+00 , 2.72269083586604e+00 , 5.70697757475891e+00 , -3.43581917981181e-01 , 2.91048819849154e+00 , 4.97014961072114e+00 , -1.12395824489167e+00 , 3.06579184791982e+00 , 5.87888757790117e+00 , -5.30970941621663e-01 , 3.51482581213725e+00 , 3.82943937819702e+00 , -1.51011506620662e+00 , 4.51943360596667e+00 , 3.41840963676036e+00 , -7.04729435523050e-01 , 5.42139775431779e+00 , 2.46955331052980e+00 , -2.74711525410010e+00 , 3.92044849944355e+00 , 2.86440245108706e+00 , -3.81315857722728e+00 , 4.53201123870925e+00 , 2.81253836569199e+00 , -2.65053563595890e+00 , 2.65589915977239e+00 , 2.37517162843526e+00 , -3.78436308048801e+00 , 1.80875030731400e+00 , 2.00126773291067e+00 , -3.37318244314476e+00 , 8.80925739265677e-01 , 8.48890367251137e-01 , -4.29365096406740e+00 , 1.06598119459501e+00 , 3.21152967601072e+00 , -5.49323932631666e+00 , 7.90224912843538e-01 , 3.33236985776319e+00 , -3.36483009077098e+00 , 7.08962306720196e-01 , 4.20288051489971e+00 , -3.68104475168581e+00 , 6.77352039955146e-02 , 5.44944272745980e+00 , -2.39228872483380e+00 , -3.24629174087243e-01 , 6.15756470761386e+00 , -4.46264273224480e+00 , 9.51772161204549e-01 , 6.42996170595173e+00 , -5.36509137781691e+00 , 5.90958189414682e-01 , 7.21777131508051e+00 , -6.26912352257721e+00 , 3.62484190850191e+00 , 6.74752042761964e+00 , -6.97441870236570e+00 , 4.29566443046527e+00 , 7.49091504085849e+00 , -6.70727158666970e+00 , 3.16858712993869e+00 , 5.50784391680945e+00 , -4.11917776391675e+00 , 2.24484839689618e+00 , 6.39160224714446e+00 , -4.80813146866083e+00 , 3.23977411463558e+00 , 7.25597976490504e+00 , -4.06701458125265e+00 , 4.55353074713024e+00 , 7.27349002869644e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.99159391330660e-01 , -4.75166803868142e-03 , 9.54191322654696e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.26793750846419e+00 , 4.08406812473590e-02 , -7.43462045888475e-01 , 6.88394214522358e+00 , -5.60210594905619e-01 , -5.49100381449560e-01 , 7.03126813606480e+00 , -2.05847485579762e+00 , -9.14970306289443e-01 , 6.15979967199652e+00 , -3.91633584332336e-01 , 7.61922732277114e-01 , 4.92352419920527e+00 , -1.51500136643612e-01 , 7.31407621564915e-01 , 6.83758204400626e+00 , -2.69923112253956e-01 , 1.93780993781114e+00 , 6.15128055840055e+00 , -1.89322426418475e-01 , 3.17349937996150e+00 , 7.09828140808973e+00 , -3.49387967535437e-01 , 4.34546489528286e+00 , 5.33955946282306e+00 , 1.08150589697671e+00 , 3.36436835730329e+00 , 4.16950609305666e+00 , 1.01623881644646e+00 , 3.72513725791437e+00 , 5.83708577362795e+00 , 2.25805562238920e+00 , 2.98267974249273e+00 , 5.21773856017340e+00 , 3.57161922298348e+00 , 2.91648092208761e+00 , 6.31853699913758e+00 , 4.49563391089305e+00 , 2.32683719497759e+00 , 3.86542883065045e+00 , 3.68004921258471e+00 , 2.04195217412088e+00 , 2.79235867300471e+00 , 4.16850146661707e+00 , 2.46662324468102e+00 , 3.93901678661429e+00 , 3.22713308244348e+00 , 7.30934829859977e-01 , 2.70074991752688e+00 , 3.01477796821894e+00 , -9.26397229315416e-02 , 3.08032379131617e+00 , 2.68056690895662e+00 , -1.52252992080645e+00 , 1.58047066505810e+00 , 2.17006440922225e+00 , 4.27998664327955e-01 , 3.76967736525154e-01 , 2.60711789557844e+00 , 4.92778015884306e-01 , 2.07258571616031e+00 , 1.12654210139324e+00 , 1.05134192945661e+00 , 1.17056965170568e+00 , 1.16846335574401e-01 , 1.70099692768423e+00 , 2.05876861292423e+00 , -1.09329159651842e+00 , 2.02324596919490e+00 , 5.69776935670213e-01 , 6.17172001264618e-01 , 2.96095152671806e+00 , -5.86240810892193e-01 , 3.51655835381281e-01 , 3.16311391312009e+00 , 1.30244214709959e+00 , 1.35290545677039e+00 , 3.74694619494776e+00 , 8.40806889312496e-01 , 1.98370498943023e+00 , 5.02675267008423e+00 , 2.10672782636876e+00 , 2.72269083586604e+00 , 5.70697757475891e+00 , -3.43581917981181e-01 , 2.91048819849154e+00 , 4.97014961072114e+00 , -1.12395824489167e+00 , 3.06579184791982e+00 , 5.87888757790117e+00 , -5.30970941621663e-01 , 3.51482581213725e+00 , 3.82943937819702e+00 , -1.51011506620662e+00 , 4.51943360596667e+00 , 3.41840963676036e+00 , -7.04729435523050e-01 , 5.42139775431779e+00 , 2.46955331052980e+00 , -2.74711525410010e+00 , 3.92044849944355e+00 , 2.86440245108706e+00 , -3.81315857722728e+00 , 4.53201123870925e+00 , 2.81253836569199e+00 , -2.65053563595890e+00 , 2.65589915977239e+00 , 2.37517162843526e+00 , -3.78436308048801e+00 , 1.80875030731400e+00 , 2.00126773291067e+00 , -3.37318244314476e+00 , 8.80925739265677e-01 , 8.48890367251137e-01 , -4.29365096406740e+00 , 1.06598119459501e+00 , 3.21152967601072e+00 , -5.49323932631666e+00 , 7.90224912843538e-01 , 3.33236985776319e+00 , -3.36483009077098e+00 , 7.08962306720196e-01 , 4.20288051489971e+00 , -3.68104475168581e+00 , 6.77352039955146e-02 , 5.44944272745980e+00 , -2.39228872483380e+00 , -3.24629174087243e-01 , 6.15756470761386e+00 , -4.46264273224480e+00 , 9.51772161204549e-01 , 6.42996170595173e+00 , -5.36509137781691e+00 , 5.90958189414682e-01 , 7.21777131508051e+00 , -6.26912352257721e+00 , 3.62484190850191e+00 , 6.74752042761964e+00 , -6.97441870236570e+00 , 4.29566443046527e+00 , 7.49091504085849e+00 , -6.70727158666970e+00 , 3.16858712993869e+00 , 5.50784391680945e+00 , -4.11917776391675e+00 , 2.24484839689618e+00 , 6.39160224714446e+00 , -4.80813146866083e+00 , 3.23977411463558e+00 , 7.25597976490504e+00 , -4.06701458125265e+00 , 4.55353074713024e+00 , 7.27349002869644e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.8422 , 6.58422 , 13.1684 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.8422 , 6.58422 , 13.1684 ) to colvar "one". +colvars: Adding total bias energy: 56.2581 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.8422 , 6.58422 , 13.1684 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.18611 , -0.555666 , -1.50491 ) +colvars: ( -4.44708 , -0.476484 , -1.29046 ) +colvars: ( -4.44708 , -0.476484 , -1.29046 ) +colvars: ( -5.92364 , -0.63469 , -1.71893 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.936944 , 0.206277 , 0.645931 ) +colvars: ( 0.811894 , 0.280466 , 0.671058 ) +colvars: ( 0.794877 , 0.273275 , 0.651723 ) +colvars: ( 0.695127 , 0.281024 , 0.604071 ) +colvars: ( 0.682692 , 0.211041 , 0.504743 ) +colvars: ( 0.604817 , 0.36201 , 0.658293 ) +colvars: ( 0.492915 , 0.376474 , 0.612431 ) +colvars: ( 0.412861 , 0.47851 , 0.70031 ) +colvars: ( 0.407391 , 0.329585 , 0.501112 ) +colvars: ( 0.371164 , 0.28578 , 0.422442 ) +colvars: ( 0.376477 , 0.335192 , 0.490564 ) +colvars: ( 0.30187 , 0.290096 , 0.387936 ) +colvars: ( 0.273271 , 0.320647 , 0.411562 ) +colvars: ( 0.367106 , 0.187421 , 0.290623 ) +colvars: ( 0.305768 , 0.141784 , 0.194979 ) +colvars: ( 0.495401 , 0.14873 , 0.314103 ) +colvars: ( 0.571209 , 0.0528377 , 0.23185 ) +colvars: ( 0.706543 , 0.0310594 , 0.281673 ) +colvars: ( 0.580458 , 0.0193011 , 0.193071 ) +colvars: ( 0.563984 , -0.0491063 , 0.0934744 ) +colvars: ( 0.602559 , 0.0696222 , 0.272124 ) +colvars: ( 0.601258 , 0.0525286 , 0.24887 ) +colvars: ( 0.639691 , 0.120548 , 0.360691 ) +colvars: ( 0.471375 , 0.0569605 , 0.179376 ) +colvars: ( 0.46436 , -0.0018774 , 0.0978609 ) +colvars: ( 0.364737 , 0.125777 , 0.208109 ) +colvars: ( 0.234617 , 0.134543 , 0.144183 ) +colvars: ( 0.138914 , 0.224523 , 0.207115 ) +colvars: ( 0.204925 , 0.0570589 , 0.0249731 ) +colvars: ( 0.153549 , 0.018902 , -0.0550477 ) +colvars: ( 0.239743 , 0.0303647 , 0.01003 ) +colvars: ( 0.224876 , -0.0457868 , -0.0988281 ) +colvars: ( 0.261443 , -0.0491127 , -0.0819981 ) +colvars: ( 0.303619 , -0.136006 , -0.171911 ) +colvars: ( 0.257626 , -0.191917 , -0.272181 ) +colvars: ( 0.424112 , -0.151591 , -0.122543 ) +colvars: ( 0.505186 , -0.230821 , -0.17981 ) +colvars: ( 0.642346 , -0.233288 , -0.103511 ) +colvars: ( 0.456062 , -0.235746 , -0.214784 ) +colvars: ( 0.461885 , -0.307289 , -0.305576 ) +colvars: ( 0.405323 , -0.158874 , -0.143027 ) +colvars: ( 0.348924 , -0.152519 , -0.167372 ) +colvars: ( 0.331873 , -0.0615207 , -0.0574831 ) +colvars: ( 0.220024 , -0.162001 , -0.25461 ) +colvars: ( 0.194674 , -0.206259 , -0.327568 ) +colvars: ( 0.0091648 , -0.210322 , -0.440505 ) +colvars: ( -0.0859047 , -0.229207 , -0.520499 ) +colvars: ( 0.11387 , -0.262515 , -0.448479 ) +colvars: ( 0.134318 , -0.119413 , -0.248259 ) +colvars: ( 0.009559 , -0.12424 , -0.32697 ) +colvars: ( -0.0835612 , -0.0396007 , -0.269569 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.18611 , 0.555666 , 1.50491 ) +colvars: ( 4.44708 , 0.476484 , 1.29046 ) +colvars: ( 4.44708 , 0.476484 , 1.29046 ) +colvars: ( 5.92364 , 0.63469 , 1.71893 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.647108 , -0.0855449 , -0.385318 ) +colvars: ( -0.582214 , -0.172671 , -0.352304 ) +colvars: ( -0.529273 , -0.149439 , -0.290691 ) +colvars: ( -0.541668 , -0.20157 , -0.322287 ) +colvars: ( -0.531534 , -0.139487 , -0.289298 ) +colvars: ( -0.516259 , -0.298533 , -0.332472 ) +colvars: ( -0.482583 , -0.340979 , -0.314323 ) +colvars: ( -0.460322 , -0.454068 , -0.333594 ) +colvars: ( -0.416351 , -0.303621 , -0.234192 ) +colvars: ( -0.411909 , -0.276924 , -0.219922 ) +colvars: ( -0.364075 , -0.297646 , -0.179591 ) +colvars: ( -0.300412 , -0.25869 , -0.101447 ) +colvars: ( -0.248844 , -0.274394 , -0.0555288 ) +colvars: ( -0.320483 , -0.149951 , -0.081581 ) +colvars: ( -0.287816 , -0.119039 , -0.037467 ) +colvars: ( -0.377096 , -0.0895564 , -0.116123 ) +colvars: ( -0.404716 , 0.0139673 , -0.105741 ) +colvars: ( -0.456819 , 0.064063 , -0.139549 ) +colvars: ( -0.444707 , 0.0297942 , -0.14001 ) +colvars: ( -0.432753 , 0.0896742 , -0.106007 ) +colvars: ( -0.491484 , -0.0271994 , -0.207859 ) +colvars: ( -0.528072 , -0.0287426 , -0.245103 ) +colvars: ( -0.580895 , -0.0977416 , -0.323428 ) +colvars: ( -0.473968 , -0.0602824 , -0.202466 ) +colvars: ( -0.481339 , -0.0137954 , -0.19276 ) +colvars: ( -0.416402 , -0.138548 , -0.17354 ) +colvars: ( -0.356444 , -0.171446 , -0.125534 ) +colvars: ( -0.303786 , -0.266452 , -0.107684 ) +colvars: ( -0.312847 , -0.0946234 , -0.0535798 ) +colvars: ( -0.299325 , -0.0749557 , -0.0327923 ) +colvars: ( -0.291311 , -0.0473312 , -0.0146004 ) +colvars: ( -0.25377 , 0.0315015 , 0.0520206 ) +colvars: ( -0.230692 , 0.059301 , 0.0853781 ) +colvars: ( -0.299818 , 0.122917 , 0.0394778 ) +colvars: ( -0.27192 , 0.16699 , 0.0836499 ) +colvars: ( -0.372355 , 0.152474 , -0.022368 ) +colvars: ( -0.42345 , 0.232753 , -0.0440656 ) +colvars: ( -0.497741 , 0.256442 , -0.109827 ) +colvars: ( -0.436297 , 0.211885 , -0.0646188 ) +colvars: ( -0.441021 , 0.27601 , -0.0457727 ) +colvars: ( -0.441644 , 0.120644 , -0.10353 ) +colvars: ( -0.449812 , 0.0888893 , -0.123395 ) +colvars: ( -0.472935 , -0.00948528 , -0.18275 ) +colvars: ( -0.380137 , 0.0771049 , -0.0578842 ) +colvars: ( -0.383926 , 0.104869 , -0.0514724 ) +colvars: ( -0.210861 , 0.111769 , 0.124551 ) +colvars: ( -0.159227 , 0.11381 , 0.177062 ) +colvars: ( -0.238052 , 0.187943 , 0.125306 ) +colvars: ( -0.314452 , 0.0342147 , -0.00781104 ) +colvars: ( -0.244702 , 0.0199544 , 0.0568652 ) +colvars: ( -0.18829 , -0.0675819 , 0.0812242 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 24. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 24. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atoms_new_colvar_forces = { ( -4.89626902453616e+00 , -4.34934047979890e-01 , -1.24429415551852e+00 ), ( -4.21740348009850e+00 , -3.68688958737982e-01 , -9.71704355524009e-01 ), ( -4.29362495193560e+00 , -3.97030214100938e-01 , -1.00867393366114e+00 ), ( -5.77248701097877e+00 , -5.63136126905229e-01 , -1.50348167626380e+00 ), ( 2.65604080467865e-01 , 1.23836488345376e-01 , 3.61032061404946e-01 ), ( 5.27466345113280e+00 , 6.19143717272684e-01 , 1.83072879871677e+00 ), ( 4.45741547617010e+00 , 5.11978879374643e-01 , 1.58856588034739e+00 ), ( -4.74608480652595e-02 , 2.44429386696295e-02 , 3.66716235475066e-01 ), ( 4.43812333803963e+00 , 5.02447893550157e-01 , 1.55737802379602e+00 ), ( 5.88289941732060e+00 , 6.43545901115343e-01 , 1.92144777727568e+00 ), ( 1.24016433386963e-02 , 3.75456368131752e-02 , 3.10972373256576e-01 ), ( 1.45886759925512e-03 , 3.14058728257868e-02 , 2.86488883408213e-01 ), ( 2.44262732103448e-02 , 4.62533087339251e-02 , 3.56033477622558e-01 ), ( 4.66227332062297e-02 , 3.74692841203345e-02 , 2.09041889539189e-01 ), ( 1.79511722286483e-02 , 2.27452144363720e-02 , 1.57512086791239e-01 ), ( 1.18305422862440e-01 , 5.91734330988370e-02 , 1.97980266559822e-01 ), ( 1.66493135046941e-01 , 6.68049109244647e-02 , 1.26108538004343e-01 ), ( 2.49724184384160e-01 , 9.51223530091758e-02 , 1.42123796070175e-01 ), ( 1.35750417810693e-01 , 4.90953697137610e-02 , 5.30609553254026e-02 ), ( 1.31231229580206e-01 , 4.05679005501801e-02 , -1.25321033842958e-02 ), ( 1.11074561932630e-01 , 4.24227818820005e-02 , 6.42652101238391e-02 ), ( 7.31864739674444e-02 , 2.37859994089552e-02 , 3.76728123495579e-03 ), ( 5.87959065637369e-02 , 2.28064395855190e-02 , 3.72632532332031e-02 ), ( -2.59282218585777e-03 , -3.32188576626139e-03 , -2.30897730450607e-02 ), ( -1.69794002718247e-02 , -1.56727660768182e-02 , -9.48988603002960e-02 ), ( -5.16653715240636e-02 , -1.27709429823289e-02 , 3.45692803765967e-02 ), ( -1.21826956291034e-01 , -3.69031440306104e-02 , 1.86489272804351e-02 ), ( -1.64871713353343e-01 , -4.19294068108170e-02 , 9.94312761794511e-02 ), ( -1.07921341588612e-01 , -3.75644978733913e-02 , -2.86067046427358e-02 ), ( -1.45775132593793e-01 , -5.60537477220428e-02 , -8.78399963980796e-02 ), ( -5.15671043676920e-02 , -1.69665033073845e-02 , -4.57036833381938e-03 ), ( -2.88944787560477e-02 , -1.42852866288890e-02 , -4.68074965365949e-02 ), ( 3.07511026606865e-02 , 1.01883566235371e-02 , 3.38002850592339e-03 ), ( 3.80135633296647e-03 , -1.30880392102020e-02 , -1.32433429512259e-01 ), ( -1.42947871960597e-02 , -2.49270998374891e-02 , -1.88530674616993e-01 ), ( 5.17565811238943e-02 , 8.83493066172997e-04 , -1.44911454793012e-01 ), ( 8.17365981274858e-02 , 1.93259663316131e-03 , -2.23875940318661e-01 ), ( 1.44604341951858e-01 , 2.31535458410976e-02 , -2.13337805515812e-01 ), ( 1.97642194162512e-02 , -2.38609104471018e-02 , -2.79402307490500e-01 ), ( 2.08646629753179e-02 , -3.12793561260939e-02 , -3.51348774530305e-01 ), ( -3.63206558482552e-02 , -3.82298862228425e-02 , -2.46557514114021e-01 ), ( -1.00887625598192e-01 , -6.36300842019940e-02 , -2.90767406376349e-01 ), ( -1.41061607304820e-01 , -7.10059932715915e-02 , -2.40233258645865e-01 ), ( -1.60112800777942e-01 , -8.48957452663499e-02 , -3.12494005513725e-01 ), ( -1.89251286005236e-01 , -1.01390732569457e-01 , -3.79040572547699e-01 ), ( -2.01696192185051e-01 , -9.85529912690795e-02 , -3.15953251461666e-01 ), ( -2.45131811811532e-01 , -1.15396540618694e-01 , -3.43437461913683e-01 ), ( -1.24182386218190e-01 , -7.45711920909637e-02 , -3.23172886379091e-01 ), ( -1.80133726500473e-01 , -8.51977949817432e-02 , -2.56070407852133e-01 ), ( -2.35142654285279e-01 , -1.04285877684321e-01 , -2.70104973972601e-01 ), ( -2.71851477173310e-01 , -1.07182542873783e-01 , -1.88344751365079e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 25, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 25, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 25, atoms_positions[size = 51] = { ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 ), ( 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 ), ( 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 ), ( 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 ), ( 7.02601780850771e+00 , -2.06015488067759e+00 , -9.09492224700635e-01 ), ( 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 ), ( 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 ), ( 7.10489589023969e+00 , -3.47758956392679e-01 , 4.35321300563372e+00 ), ( 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 ), ( 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 ), ( 5.83732729632828e+00 , 2.25785810405961e+00 , 2.98093128297857e+00 ), ( 5.20869462502566e+00 , 3.56959681912101e+00 , 2.91307028328090e+00 ), ( 6.31702728307081e+00 , 4.49345110958214e+00 , 2.31808179186695e+00 ), ( 3.86300150802905e+00 , 3.67341219998733e+00 , 2.04017422536762e+00 ), ( 2.79457049211183e+00 , 4.16943048780216e+00 , 2.46130448350710e+00 ), ( 3.93567494128755e+00 , 3.22241188154132e+00 , 7.31665097008206e-01 ), ( 2.71267750097800e+00 , 3.02113169189251e+00 , -8.91310614028259e-02 ), ( 3.08732123000904e+00 , 2.67413534581401e+00 , -1.52662014513167e+00 ), ( 1.57269474677811e+00 , 2.17070869266575e+00 , 4.26058642461620e-01 ), ( 3.80555829918894e-01 , 2.61090721785921e+00 , 4.87721454392032e-01 ), ( 2.07565081504512e+00 , 1.13592640012642e+00 , 1.04794811588010e+00 ), ( 1.17497779195547e+00 , 1.17363818366492e-01 , 1.70020616076127e+00 ), ( 2.06302853920080e+00 , -1.09229653109778e+00 , 2.02682408795984e+00 ), ( 5.71499907914238e-01 , 6.17806942729092e-01 , 2.96338906413119e+00 ), ( -5.84375440137461e-01 , 3.52346628945102e-01 , 3.16484827373788e+00 ), ( 1.29890503570500e+00 , 1.35697344446113e+00 , 3.74385161333402e+00 ), ( 8.43209552958302e-01 , 1.98348034433225e+00 , 5.02735651599704e+00 ), ( 2.10930944408490e+00 , 2.73006003201001e+00 , 5.71186839017599e+00 ), ( -3.46113376698924e-01 , 2.90906060189559e+00 , 4.96980143944285e+00 ), ( -1.12136107320199e+00 , 3.06641515542823e+00 , 5.87779237318429e+00 ), ( -5.34941623924234e-01 , 3.51275008627904e+00 , 3.82272372999129e+00 ), ( -1.50479759285668e+00 , 4.51306813747961e+00 , 3.41541854829753e+00 ), ( -7.08550151619272e-01 , 5.42337212444133e+00 , 2.47077640178917e+00 ), ( -2.74531373746629e+00 , 3.92796338514317e+00 , 2.85367775142689e+00 ), ( -3.81189755702219e+00 , 4.53737709243637e+00 , 2.81249160218273e+00 ), ( -2.65769350477280e+00 , 2.65007832275566e+00 , 2.36998223012328e+00 ), ( -3.78683922216990e+00 , 1.81296910506803e+00 , 2.00265894129983e+00 ), ( -3.37002983699502e+00 , 8.79015851476826e-01 , 8.42270333198377e-01 ), ( -4.28408110971430e+00 , 1.06310797908519e+00 , 3.21505584648410e+00 ), ( -5.49148724796687e+00 , 7.83401806260949e-01 , 3.33335876241182e+00 ), ( -3.36577486954441e+00 , 7.13539644075190e-01 , 4.19797163127101e+00 ), ( -3.67799115688145e+00 , 7.22227416989530e-02 , 5.45594885427104e+00 ), ( -2.39141448198009e+00 , -3.25383286486184e-01 , 6.15326448174159e+00 ), ( -4.46471526135512e+00 , 9.42860744303390e-01 , 6.42752883167951e+00 ), ( -5.36514180386212e+00 , 5.88755929827167e-01 , 7.21607462723538e+00 ), ( -6.27839620697427e+00 , 3.62760689447500e+00 , 6.74946980865791e+00 ), ( -6.97833374705994e+00 , 4.29541023538326e+00 , 7.49449652406574e+00 ), ( -6.69616584445880e+00 , 3.16611776307592e+00 , 5.51025229428525e+00 ), ( -4.11627741428843e+00 , 2.24655326574761e+00 , 6.39001782480647e+00 ), ( -4.80965119349014e+00 , 3.24891673341217e+00 , 7.25749358057592e+00 ), ( -4.05860175930149e+00 , 4.55028941202804e+00 , 7.27220105324414e+00 ) } +colvars: Step 25, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.98260726975113e-01 , -6.09344114517502e-03 , 9.54464985591031e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 7.02601780850771e+00 , -2.06015488067759e+00 , -9.09492224700635e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 , 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 7.10489589023969e+00 , -3.47758956392679e-01 , 4.35321300563372e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 , 5.83732729632828e+00 , 2.25785810405961e+00 , 2.98093128297857e+00 , 5.20869462502566e+00 , 3.56959681912101e+00 , 2.91307028328090e+00 , 6.31702728307081e+00 , 4.49345110958214e+00 , 2.31808179186695e+00 , 3.86300150802905e+00 , 3.67341219998733e+00 , 2.04017422536762e+00 , 2.79457049211183e+00 , 4.16943048780216e+00 , 2.46130448350710e+00 , 3.93567494128755e+00 , 3.22241188154132e+00 , 7.31665097008206e-01 , 2.71267750097800e+00 , 3.02113169189251e+00 , -8.91310614028259e-02 , 3.08732123000904e+00 , 2.67413534581401e+00 , -1.52662014513167e+00 , 1.57269474677811e+00 , 2.17070869266575e+00 , 4.26058642461620e-01 , 3.80555829918894e-01 , 2.61090721785921e+00 , 4.87721454392032e-01 , 2.07565081504512e+00 , 1.13592640012642e+00 , 1.04794811588010e+00 , 1.17497779195547e+00 , 1.17363818366492e-01 , 1.70020616076127e+00 , 2.06302853920080e+00 , -1.09229653109778e+00 , 2.02682408795984e+00 , 5.71499907914238e-01 , 6.17806942729092e-01 , 2.96338906413119e+00 , -5.84375440137461e-01 , 3.52346628945102e-01 , 3.16484827373788e+00 , 1.29890503570500e+00 , 1.35697344446113e+00 , 3.74385161333402e+00 , 8.43209552958302e-01 , 1.98348034433225e+00 , 5.02735651599704e+00 , 2.10930944408490e+00 , 2.73006003201001e+00 , 5.71186839017599e+00 , -3.46113376698924e-01 , 2.90906060189559e+00 , 4.96980143944285e+00 , -1.12136107320199e+00 , 3.06641515542823e+00 , 5.87779237318429e+00 , -5.34941623924234e-01 , 3.51275008627904e+00 , 3.82272372999129e+00 , -1.50479759285668e+00 , 4.51306813747961e+00 , 3.41541854829753e+00 , -7.08550151619272e-01 , 5.42337212444133e+00 , 2.47077640178917e+00 , -2.74531373746629e+00 , 3.92796338514317e+00 , 2.85367775142689e+00 , -3.81189755702219e+00 , 4.53737709243637e+00 , 2.81249160218273e+00 , -2.65769350477280e+00 , 2.65007832275566e+00 , 2.36998223012328e+00 , -3.78683922216990e+00 , 1.81296910506803e+00 , 2.00265894129983e+00 , -3.37002983699502e+00 , 8.79015851476826e-01 , 8.42270333198377e-01 , -4.28408110971430e+00 , 1.06310797908519e+00 , 3.21505584648410e+00 , -5.49148724796687e+00 , 7.83401806260949e-01 , 3.33335876241182e+00 , -3.36577486954441e+00 , 7.13539644075190e-01 , 4.19797163127101e+00 , -3.67799115688145e+00 , 7.22227416989530e-02 , 5.45594885427104e+00 , -2.39141448198009e+00 , -3.25383286486184e-01 , 6.15326448174159e+00 , -4.46471526135512e+00 , 9.42860744303390e-01 , 6.42752883167951e+00 , -5.36514180386212e+00 , 5.88755929827167e-01 , 7.21607462723538e+00 , -6.27839620697427e+00 , 3.62760689447500e+00 , 6.74946980865791e+00 , -6.97833374705994e+00 , 4.29541023538326e+00 , 7.49449652406574e+00 , -6.69616584445880e+00 , 3.16611776307592e+00 , 5.51025229428525e+00 , -4.11627741428843e+00 , 2.24655326574761e+00 , 6.39001782480647e+00 , -4.80965119349014e+00 , 3.24891673341217e+00 , 7.25749358057592e+00 , -4.05860175930149e+00 , 4.55028941202804e+00 , 7.27220105324414e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.98260726975113e-01 , -6.09344114517502e-03 , 9.54464985591031e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.26372109631143e+00 , 4.12656060234079e-02 , -7.40403075448119e-01 , 6.87261151453456e+00 , -5.63853645461934e-01 , -5.43635684711059e-01 , 7.02601780850771e+00 , -2.06015488067759e+00 , -9.09492224700635e-01 , 6.15799059248153e+00 , -3.91341503583579e-01 , 7.70404846708157e-01 , 4.91851139751400e+00 , -1.49769910097631e-01 , 7.33616281432402e-01 , 6.83170775717235e+00 , -2.72805529085410e-01 , 1.94451569349181e+00 , 6.14296696728108e+00 , -1.96101189429633e-01 , 3.16926147566366e+00 , 7.10489589023969e+00 , -3.47758956392679e-01 , 4.35321300563372e+00 , 5.34096566769606e+00 , 1.07852542140089e+00 , 3.36643191758465e+00 , 4.17192049033079e+00 , 1.01419976673032e+00 , 3.73382207081438e+00 , 5.83732729632828e+00 , 2.25785810405961e+00 , 2.98093128297857e+00 , 5.20869462502566e+00 , 3.56959681912101e+00 , 2.91307028328090e+00 , 6.31702728307081e+00 , 4.49345110958214e+00 , 2.31808179186695e+00 , 3.86300150802905e+00 , 3.67341219998733e+00 , 2.04017422536762e+00 , 2.79457049211183e+00 , 4.16943048780216e+00 , 2.46130448350710e+00 , 3.93567494128755e+00 , 3.22241188154132e+00 , 7.31665097008206e-01 , 2.71267750097800e+00 , 3.02113169189251e+00 , -8.91310614028259e-02 , 3.08732123000904e+00 , 2.67413534581401e+00 , -1.52662014513167e+00 , 1.57269474677811e+00 , 2.17070869266575e+00 , 4.26058642461620e-01 , 3.80555829918894e-01 , 2.61090721785921e+00 , 4.87721454392032e-01 , 2.07565081504512e+00 , 1.13592640012642e+00 , 1.04794811588010e+00 , 1.17497779195547e+00 , 1.17363818366492e-01 , 1.70020616076127e+00 , 2.06302853920080e+00 , -1.09229653109778e+00 , 2.02682408795984e+00 , 5.71499907914238e-01 , 6.17806942729092e-01 , 2.96338906413119e+00 , -5.84375440137461e-01 , 3.52346628945102e-01 , 3.16484827373788e+00 , 1.29890503570500e+00 , 1.35697344446113e+00 , 3.74385161333402e+00 , 8.43209552958302e-01 , 1.98348034433225e+00 , 5.02735651599704e+00 , 2.10930944408490e+00 , 2.73006003201001e+00 , 5.71186839017599e+00 , -3.46113376698924e-01 , 2.90906060189559e+00 , 4.96980143944285e+00 , -1.12136107320199e+00 , 3.06641515542823e+00 , 5.87779237318429e+00 , -5.34941623924234e-01 , 3.51275008627904e+00 , 3.82272372999129e+00 , -1.50479759285668e+00 , 4.51306813747961e+00 , 3.41541854829753e+00 , -7.08550151619272e-01 , 5.42337212444133e+00 , 2.47077640178917e+00 , -2.74531373746629e+00 , 3.92796338514317e+00 , 2.85367775142689e+00 , -3.81189755702219e+00 , 4.53737709243637e+00 , 2.81249160218273e+00 , -2.65769350477280e+00 , 2.65007832275566e+00 , 2.36998223012328e+00 , -3.78683922216990e+00 , 1.81296910506803e+00 , 2.00265894129983e+00 , -3.37002983699502e+00 , 8.79015851476826e-01 , 8.42270333198377e-01 , -4.28408110971430e+00 , 1.06310797908519e+00 , 3.21505584648410e+00 , -5.49148724796687e+00 , 7.83401806260949e-01 , 3.33335876241182e+00 , -3.36577486954441e+00 , 7.13539644075190e-01 , 4.19797163127101e+00 , -3.67799115688145e+00 , 7.22227416989530e-02 , 5.45594885427104e+00 , -2.39141448198009e+00 , -3.25383286486184e-01 , 6.15326448174159e+00 , -4.46471526135512e+00 , 9.42860744303390e-01 , 6.42752883167951e+00 , -5.36514180386212e+00 , 5.88755929827167e-01 , 7.21607462723538e+00 , -6.27839620697427e+00 , 3.62760689447500e+00 , 6.74946980865791e+00 , -6.97833374705994e+00 , 4.29541023538326e+00 , 7.49449652406574e+00 , -6.69616584445880e+00 , 3.16611776307592e+00 , 5.51025229428525e+00 , -4.11627741428843e+00 , 2.24655326574761e+00 , 6.39001782480647e+00 , -4.80965119349014e+00 , 3.24891673341217e+00 , 7.25749358057592e+00 , -4.05860175930149e+00 , 4.55028941202804e+00 , 7.27220105324414e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.805 , 6.5805 , 13.161 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.805 , 6.5805 , 13.161 ) to colvar "one". +colvars: Adding total bias energy: 56.2041 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.805 , 6.5805 , 13.161 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.18859 , -0.55473 , -1.50141 ) +colvars: ( -4.44922 , -0.475681 , -1.28746 ) +colvars: ( -4.44922 , -0.475681 , -1.28746 ) +colvars: ( -5.92649 , -0.633621 , -1.71494 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.936502 , 0.206381 , 0.644948 ) +colvars: ( 0.811582 , 0.280524 , 0.66999 ) +colvars: ( 0.794534 , 0.273337 , 0.650666 ) +colvars: ( 0.694964 , 0.281038 , 0.603083 ) +colvars: ( 0.682542 , 0.211058 , 0.503917 ) +colvars: ( 0.60477 , 0.361985 , 0.657193 ) +colvars: ( 0.493015 , 0.376405 , 0.611379 ) +colvars: ( 0.413062 , 0.478405 , 0.69909 ) +colvars: ( 0.407561 , 0.329496 , 0.50021 ) +colvars: ( 0.371393 , 0.285679 , 0.421665 ) +colvars: ( 0.376639 , 0.335101 , 0.489655 ) +colvars: ( 0.302088 , 0.289988 , 0.387165 ) +colvars: ( 0.273476 , 0.320536 , 0.410729 ) +colvars: ( 0.367245 , 0.187345 , 0.290032 ) +colvars: ( 0.305975 , 0.141691 , 0.194528 ) +colvars: ( 0.495393 , 0.148701 , 0.313512 ) +colvars: ( 0.571113 , 0.0528428 , 0.231418 ) +colvars: ( 0.706282 , 0.0311145 , 0.281197 ) +colvars: ( 0.580393 , 0.0193038 , 0.19272 ) +colvars: ( 0.563938 , -0.0491038 , 0.0932843 ) +colvars: ( 0.602507 , 0.0696211 , 0.271662 ) +colvars: ( 0.601251 , 0.0525201 , 0.24846 ) +colvars: ( 0.639675 , 0.12054 , 0.360119 ) +colvars: ( 0.471523 , 0.0569059 , 0.179043 ) +colvars: ( 0.464531 , -0.00193279 , 0.0976668 ) +colvars: ( 0.364992 , 0.125683 , 0.207692 ) +colvars: ( 0.235021 , 0.134404 , 0.143831 ) +colvars: ( 0.139412 , 0.224347 , 0.206625 ) +colvars: ( 0.205335 , 0.0569213 , 0.0248015 ) +colvars: ( 0.154031 , 0.0187472 , -0.0550976 ) +colvars: ( 0.240072 , 0.0302491 , 0.00988053 ) +colvars: ( 0.225192 , -0.0458957 , -0.098811 ) +colvars: ( 0.261672 , -0.0492001 , -0.0820124 ) +colvars: ( 0.303862 , -0.136084 , -0.171743 ) +colvars: ( 0.257918 , -0.192006 , -0.271861 ) +colvars: ( 0.424238 , -0.15163 , -0.122414 ) +colvars: ( 0.50524 , -0.23083 , -0.179554 ) +colvars: ( 0.642255 , -0.233253 , -0.103335 ) +colvars: ( 0.456212 , -0.235779 , -0.214471 ) +colvars: ( 0.462036 , -0.307316 , -0.305109 ) +colvars: ( 0.405559 , -0.158937 , -0.142841 ) +colvars: ( 0.349263 , -0.152609 , -0.16715 ) +colvars: ( 0.33226 , -0.061629 , -0.0574391 ) +colvars: ( 0.220499 , -0.162132 , -0.254286 ) +colvars: ( 0.195199 , -0.2064 , -0.327124 ) +colvars: ( 0.00980286 , -0.210506 , -0.439962 ) +colvars: ( -0.0851655 , -0.22942 , -0.519855 ) +colvars: ( 0.114368 , -0.262655 , -0.447897 ) +colvars: ( 0.134859 , -0.11957 , -0.247983 ) +colvars: ( 0.0102288 , -0.124437 , -0.326605 ) +colvars: ( -0.0828059 , -0.0398325 , -0.269335 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.18859 , 0.55473 , 1.50141 ) +colvars: ( 4.44922 , 0.475681 , 1.28746 ) +colvars: ( 4.44922 , 0.475681 , 1.28746 ) +colvars: ( 5.92649 , 0.633621 , 1.71494 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.646973 , -0.0855897 , -0.384683 ) +colvars: ( -0.582119 , -0.172876 , -0.351435 ) +colvars: ( -0.528959 , -0.149562 , -0.289642 ) +colvars: ( -0.541713 , -0.201837 , -0.321465 ) +colvars: ( -0.531566 , -0.139627 , -0.288639 ) +colvars: ( -0.516441 , -0.298999 , -0.331503 ) +colvars: ( -0.482927 , -0.341537 , -0.313386 ) +colvars: ( -0.460788 , -0.454857 , -0.332448 ) +colvars: ( -0.416612 , -0.304081 , -0.233254 ) +colvars: ( -0.412256 , -0.277339 , -0.219149 ) +colvars: ( -0.364161 , -0.298063 , -0.17847 ) +colvars: ( -0.300396 , -0.259004 , -0.10031 ) +colvars: ( -0.24865 , -0.274707 , -0.0541421 ) +colvars: ( -0.320378 , -0.150046 , -0.0806729 ) +colvars: ( -0.287728 , -0.119066 , -0.0366541 ) +colvars: ( -0.376899 , -0.089536 , -0.115314 ) +colvars: ( -0.404436 , 0.0141939 , -0.105157 ) +colvars: ( -0.456403 , 0.0643899 , -0.138987 ) +colvars: ( -0.444604 , 0.0300241 , -0.139669 ) +colvars: ( -0.432639 , 0.0900265 , -0.105824 ) +colvars: ( -0.491553 , -0.0271114 , -0.207549 ) +colvars: ( -0.528331 , -0.0286863 , -0.245 ) +colvars: ( -0.581308 , -0.0978506 , -0.323304 ) +colvars: ( -0.474337 , -0.0602864 , -0.202366 ) +colvars: ( -0.481767 , -0.0137155 , -0.19286 ) +colvars: ( -0.416793 , -0.138695 , -0.173216 ) +colvars: ( -0.356917 , -0.171651 , -0.125177 ) +colvars: ( -0.304273 , -0.266834 , -0.107048 ) +colvars: ( -0.313187 , -0.0946526 , -0.0532926 ) +colvars: ( -0.299749 , -0.0749514 , -0.0326451 ) +colvars: ( -0.291438 , -0.0472397 , -0.0142213 ) +colvars: ( -0.253752 , 0.0317731 , 0.0523361 ) +colvars: ( -0.230447 , 0.0596566 , 0.0858566 ) +colvars: ( -0.299801 , 0.123358 , 0.0395094 ) +colvars: ( -0.2719 , 0.167526 , 0.0835685 ) +colvars: ( -0.372351 , 0.152954 , -0.0224603 ) +colvars: ( -0.423466 , 0.233377 , -0.0444307 ) +colvars: ( -0.497729 , 0.257097 , -0.110258 ) +colvars: ( -0.436525 , 0.212443 , -0.065148 ) +colvars: ( -0.441257 , 0.276692 , -0.0464979 ) +colvars: ( -0.442048 , 0.121002 , -0.10398 ) +colvars: ( -0.450425 , 0.0891608 , -0.123974 ) +colvars: ( -0.473715 , -0.00943105 , -0.183225 ) +colvars: ( -0.380779 , 0.0773675 , -0.0584331 ) +colvars: ( -0.384663 , 0.105175 , -0.0522024 ) +colvars: ( -0.211268 , 0.112166 , 0.124207 ) +colvars: ( -0.159654 , 0.114222 , 0.17671 ) +colvars: ( -0.238287 , 0.188502 , 0.12491 ) +colvars: ( -0.315013 , 0.034417 , -0.00812794 ) +colvars: ( -0.245278 , 0.0201441 , 0.0565986 ) +colvars: ( -0.188854 , -0.06755 , 0.0812445 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 25. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 25. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atoms_new_colvar_forces = { ( -4.89906344512746e+00 , -4.33938364367410e-01 , -1.24115033796379e+00 ), ( -4.21975323856767e+00 , -3.68033246133372e-01 , -9.68907737532198e-01 ), ( -4.29596648242177e+00 , -3.96479038081813e-01 , -1.00584456901772e+00 ), ( -5.77550926213070e+00 , -5.62190338593654e-01 , -1.49965933822439e+00 ), ( 2.65575053488895e-01 , 1.23775230972432e-01 , 3.61023834344683e-01 ), ( 5.27692066837987e+00 , 6.17715929648311e-01 , 1.82710484760370e+00 ), ( 4.45930492273777e+00 , 5.10549164289448e-01 , 1.58545585835120e+00 ), ( -4.77255546796858e-02 , 2.35481056867184e-02 , 3.66642095775605e-01 ), ( 4.44016596401227e+00 , 5.01096548538967e-01 , 1.55441908869634e+00 ), ( 5.88562268790459e+00 , 6.41960795400982e-01 , 1.91745446249927e+00 ), ( 1.24780301557004e-02 , 3.70373505205272e-02 , 3.11185168550698e-01 ), ( 1.69241797134606e-03 , 3.09846409440507e-02 , 2.86855333206734e-01 ), ( 2.48253284184641e-02 , 4.58286694429199e-02 , 3.56586645172988e-01 ), ( 4.68670239076926e-02 , 3.72986979803460e-02 , 2.09359268835667e-01 ), ( 1.82471308431904e-02 , 2.26250706506449e-02 , 1.57873686277293e-01 ), ( 1.18494763765411e-01 , 5.91648545536552e-02 , 1.98198140672188e-01 ), ( 1.66676763625072e-01 , 6.70366787723358e-02 , 1.26261615730529e-01 ), ( 2.49879079930532e-01 , 9.55044108262005e-02 , 1.42210003532049e-01 ), ( 1.35789306078350e-01 , 4.93279399934362e-02 , 5.30509265501526e-02 ), ( 1.31299404400352e-01 , 4.09227746112109e-02 , -1.25400780020407e-02 ), ( 1.10954407540443e-01 , 4.25096693434524e-02 , 6.41128700817514e-02 ), ( 7.29204770810634e-02 , 2.38337472084800e-02 , 3.46033763471382e-03 ), ( 5.83673410714052e-02 , 2.26898767897394e-02 , 3.68150536138672e-02 ), ( -2.81417491461955e-03 , -3.38055311866311e-03 , -2.33227595269628e-02 ), ( -1.72361850855943e-02 , -1.56482716024989e-02 , -9.51927272087079e-02 ), ( -5.18012291731317e-02 , -1.30117255619673e-02 , 3.44757424901483e-02 ), ( -1.21895494406184e-01 , -3.72476900194439e-02 , 1.86542324467333e-02 ), ( -1.64860988387478e-01 , -4.24871995380767e-02 , 9.95770385555629e-02 ), ( -1.07851990658685e-01 , -3.77312358709509e-02 , -2.84911315327581e-02 ), ( -1.45717354015014e-01 , -5.62042458653846e-02 , -8.77426949607180e-02 ), ( -5.13656188036761e-02 , -1.69906013000250e-02 , -4.34075107217456e-03 ), ( -2.85598245708901e-02 , -1.41225759925339e-02 , -4.64748435203859e-02 ), ( 3.12251203305847e-02 , 1.04564940755888e-02 , 3.84421526758397e-03 ), ( 4.06081923678608e-03 , -1.27253296414948e-02 , -1.32233719356317e-01 ), ( -1.39820142505577e-02 , -2.44804858510322e-02 , -1.88292909504336e-01 ), ( 5.18866424281385e-02 , 1.32413341724485e-03 , -1.44874312914186e-01 ), ( 8.17739607959403e-02 , 2.54725668195610e-03 , -2.23984923597530e-01 ), ( 1.44526454345390e-01 , 2.38444392452565e-02 , -2.13592605133995e-01 ), ( 1.96867827703129e-02 , -2.33367225853583e-02 , -2.79619166290604e-01 ), ( 2.07796823395160e-02 , -3.06240695121803e-02 , -3.51606776559521e-01 ), ( -3.64893536398806e-02 , -3.79343777355108e-02 , -2.46821207445439e-01 ), ( -1.01162634768527e-01 , -6.34481201221322e-02 , -2.91123807410638e-01 ), ( -1.41455057710474e-01 , -7.10600811515679e-02 , -2.40664514657477e-01 ), ( -1.60279478554847e-01 , -8.47640865434852e-02 , -3.12718681263706e-01 ), ( -1.89463860663062e-01 , -1.01224065656580e-01 , -3.79326301540552e-01 ), ( -2.01464862171674e-01 , -9.83401100189178e-02 , -3.15754496397993e-01 ), ( -2.44819014924519e-01 , -1.15198529484133e-01 , -3.43145344898522e-01 ), ( -1.23919527404400e-01 , -7.41527837840532e-02 , -3.22987595567234e-01 ), ( -1.80154097344774e-01 , -8.51528906015948e-02 , -2.56110465485514e-01 ), ( -2.35049221177624e-01 , -1.04293297232310e-01 , -2.70006540020722e-01 ), ( -2.71660268006196e-01 , -1.07382443627761e-01 , -1.88090129283337e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 26, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 26, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 26, atoms_positions[size = 51] = { ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 ), ( 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 ), ( 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 ), ( 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 ), ( 7.02064988657512e+00 , -2.06191346538722e+00 , -9.03579109957654e-01 ), ( 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 ), ( 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 ), ( 7.11195793669239e+00 , -3.46325495992327e-01 , 4.36074587971818e+00 ), ( 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 ), ( 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 ), ( 5.83830582474785e+00 , 2.25717890153626e+00 , 2.97922967102051e+00 ), ( 5.19865579018808e+00 , 3.56722170500424e+00 , 2.90896510948759e+00 ), ( 6.31513193976290e+00 , 4.49065881803907e+00 , 2.31006628798853e+00 ), ( 3.86124831398321e+00 , 3.66693664580130e+00 , 2.03796709771885e+00 ), ( 2.79749545867389e+00 , 4.16995519090235e+00 , 2.45603764179593e+00 ), ( 3.93145764425614e+00 , 3.21713147140614e+00 , 7.32876164373928e-01 ), ( 2.72447956284919e+00 , 3.02868839011924e+00 , -8.54879261581896e-02 ), ( 3.09406236284613e+00 , 2.66805755434709e+00 , -1.53085811413060e+00 ), ( 1.56493869037030e+00 , 2.17347451033929e+00 , 4.24768650699866e-01 ), ( 3.85345919387903e-01 , 2.61366235247257e+00 , 4.82461270335294e-01 ), ( 2.07696380666347e+00 , 1.14254884016557e+00 , 1.04553746637080e+00 ), ( 1.18131227060580e+00 , 1.18719671546719e-01 , 1.69847359328974e+00 ), ( 2.06729318897268e+00 , -1.09179940169616e+00 , 2.03025352172266e+00 ), ( 5.72960077339100e-01 , 6.18013592442385e-01 , 2.96456159475629e+00 ), ( -5.83383313581664e-01 , 3.53085945103520e-01 , 3.16715384200455e+00 ), ( 1.29561687036373e+00 , 1.36203853191918e+00 , 3.74264177973402e+00 ), ( 8.46850384517969e-01 , 1.98285156306198e+00 , 5.02809578988427e+00 ), ( 2.10973305988450e+00 , 2.73681089296750e+00 , 5.71605794165702e+00 ), ( -3.48762046412809e-01 , 2.90752551225505e+00 , 4.96867528030200e+00 ), ( -1.11920791756658e+00 , 3.06699078158662e+00 , 5.87734231670672e+00 ), ( -5.38333623730181e-01 , 3.51142269226990e+00 , 3.81520213881713e+00 ), ( -1.49843560791049e+00 , 4.50654707598769e+00 , 3.41371229948753e+00 ), ( -7.13294121656643e-01 , 5.42557666301716e+00 , 2.47206849802352e+00 ), ( -2.74425913887002e+00 , 3.93451898443147e+00 , 2.84179837821152e+00 ), ( -3.81054992169605e+00 , 4.54277935493174e+00 , 2.81256821995773e+00 ), ( -2.66484198682084e+00 , 2.64461123625328e+00 , 2.36553515139455e+00 ), ( -3.78937150597451e+00 , 1.81732553101476e+00 , 2.00393460363141e+00 ), ( -3.36715965222817e+00 , 8.77401627073931e-01 , 8.35477650714998e-01 ), ( -4.27482462124773e+00 , 1.05958388107734e+00 , 3.21962204538203e+00 ), ( -5.48918404843012e+00 , 7.76784618642079e-01 , 3.33442191610955e+00 ), ( -3.36706253375617e+00 , 7.17851868366844e-01 , 4.19196428516940e+00 ), ( -3.67556292758813e+00 , 7.58218748188693e-02 , 5.46260107999588e+00 ), ( -2.38991324934671e+00 , -3.25296840409072e-01 , 6.14870951617098e+00 ), ( -4.46749439379339e+00 , 9.34969453495375e-01 , 6.42536132477543e+00 ), ( -5.36467953327721e+00 , 5.86231116048637e-01 , 7.21375288174230e+00 ), ( -6.28718665126741e+00 , 3.62919036014076e+00 , 6.75076513126300e+00 ), ( -6.98266884576581e+00 , 4.29541408722657e+00 , 7.49806320906888e+00 ), ( -6.68463458476356e+00 , 3.16418550162232e+00 , 5.51356624786938e+00 ), ( -4.11347763262476e+00 , 2.24859562081623e+00 , 6.38957541942517e+00 ), ( -4.81143882202094e+00 , 3.25770940668724e+00 , 7.25789425619000e+00 ), ( -4.05017605728786e+00 , 4.54876606599830e+00 , 7.27143130377330e+00 ) } +colvars: Step 26, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 ). +colvars: Done calculating colvar "group2". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.97375216352616e-01 , -7.46356788846571e-03 , 9.54731520299612e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 7.02064988657512e+00 , -2.06191346538722e+00 , -9.03579109957654e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 , 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 7.11195793669239e+00 , -3.46325495992327e-01 , 4.36074587971818e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 , 5.83830582474785e+00 , 2.25717890153626e+00 , 2.97922967102051e+00 , 5.19865579018808e+00 , 3.56722170500424e+00 , 2.90896510948759e+00 , 6.31513193976290e+00 , 4.49065881803907e+00 , 2.31006628798853e+00 , 3.86124831398321e+00 , 3.66693664580130e+00 , 2.03796709771885e+00 , 2.79749545867389e+00 , 4.16995519090235e+00 , 2.45603764179593e+00 , 3.93145764425614e+00 , 3.21713147140614e+00 , 7.32876164373928e-01 , 2.72447956284919e+00 , 3.02868839011924e+00 , -8.54879261581896e-02 , 3.09406236284613e+00 , 2.66805755434709e+00 , -1.53085811413060e+00 , 1.56493869037030e+00 , 2.17347451033929e+00 , 4.24768650699866e-01 , 3.85345919387903e-01 , 2.61366235247257e+00 , 4.82461270335294e-01 , 2.07696380666347e+00 , 1.14254884016557e+00 , 1.04553746637080e+00 , 1.18131227060580e+00 , 1.18719671546719e-01 , 1.69847359328974e+00 , 2.06729318897268e+00 , -1.09179940169616e+00 , 2.03025352172266e+00 , 5.72960077339100e-01 , 6.18013592442385e-01 , 2.96456159475629e+00 , -5.83383313581664e-01 , 3.53085945103520e-01 , 3.16715384200455e+00 , 1.29561687036373e+00 , 1.36203853191918e+00 , 3.74264177973402e+00 , 8.46850384517969e-01 , 1.98285156306198e+00 , 5.02809578988427e+00 , 2.10973305988450e+00 , 2.73681089296750e+00 , 5.71605794165702e+00 , -3.48762046412809e-01 , 2.90752551225505e+00 , 4.96867528030200e+00 , -1.11920791756658e+00 , 3.06699078158662e+00 , 5.87734231670672e+00 , -5.38333623730181e-01 , 3.51142269226990e+00 , 3.81520213881713e+00 , -1.49843560791049e+00 , 4.50654707598769e+00 , 3.41371229948753e+00 , -7.13294121656643e-01 , 5.42557666301716e+00 , 2.47206849802352e+00 , -2.74425913887002e+00 , 3.93451898443147e+00 , 2.84179837821152e+00 , -3.81054992169605e+00 , 4.54277935493174e+00 , 2.81256821995773e+00 , -2.66484198682084e+00 , 2.64461123625328e+00 , 2.36553515139455e+00 , -3.78937150597451e+00 , 1.81732553101476e+00 , 2.00393460363141e+00 , -3.36715965222817e+00 , 8.77401627073931e-01 , 8.35477650714998e-01 , -4.27482462124773e+00 , 1.05958388107734e+00 , 3.21962204538203e+00 , -5.48918404843012e+00 , 7.76784618642079e-01 , 3.33442191610955e+00 , -3.36706253375617e+00 , 7.17851868366844e-01 , 4.19196428516940e+00 , -3.67556292758813e+00 , 7.58218748188693e-02 , 5.46260107999588e+00 , -2.38991324934671e+00 , -3.25296840409072e-01 , 6.14870951617098e+00 , -4.46749439379339e+00 , 9.34969453495375e-01 , 6.42536132477543e+00 , -5.36467953327721e+00 , 5.86231116048637e-01 , 7.21375288174230e+00 , -6.28718665126741e+00 , 3.62919036014076e+00 , 6.75076513126300e+00 , -6.98266884576581e+00 , 4.29541408722657e+00 , 7.49806320906888e+00 , -6.68463458476356e+00 , 3.16418550162232e+00 , 5.51356624786938e+00 , -4.11347763262476e+00 , 2.24859562081623e+00 , 6.38957541942517e+00 , -4.81143882202094e+00 , 3.25770940668724e+00 , 7.25789425619000e+00 , -4.05017605728786e+00 , 4.54876606599830e+00 , 7.27143130377330e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.97375216352616e-01 , -7.46356788846571e-03 , 9.54731520299612e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.25910067603718e+00 , 4.17570729520058e-02 , -7.37241123865735e-01 , 6.86233310578465e+00 , -5.68204970820706e-01 , -5.38955931947489e-01 , 7.02064988657512e+00 , -2.06191346538722e+00 , -9.03579109957654e-01 , 6.15407623986303e+00 , -3.89256651041783e-01 , 7.78708742192945e-01 , 4.91439978702935e+00 , -1.48623102010218e-01 , 7.35905910616266e-01 , 6.82633107048891e+00 , -2.76132387923813e-01 , 1.95052743858925e+00 , 6.13425997832957e+00 , -2.02550265780395e-01 , 3.16659320598056e+00 , 7.11195793669239e+00 , -3.46325495992327e-01 , 4.36074587971818e+00 , 5.34085762923080e+00 , 1.07583744791912e+00 , 3.36801109733845e+00 , 4.17458676945527e+00 , 1.01225799709654e+00 , 3.74279415810527e+00 , 5.83830582474785e+00 , 2.25717890153626e+00 , 2.97922967102051e+00 , 5.19865579018808e+00 , 3.56722170500424e+00 , 2.90896510948759e+00 , 6.31513193976290e+00 , 4.49065881803907e+00 , 2.31006628798853e+00 , 3.86124831398321e+00 , 3.66693664580130e+00 , 2.03796709771885e+00 , 2.79749545867389e+00 , 4.16995519090235e+00 , 2.45603764179593e+00 , 3.93145764425614e+00 , 3.21713147140614e+00 , 7.32876164373928e-01 , 2.72447956284919e+00 , 3.02868839011924e+00 , -8.54879261581896e-02 , 3.09406236284613e+00 , 2.66805755434709e+00 , -1.53085811413060e+00 , 1.56493869037030e+00 , 2.17347451033929e+00 , 4.24768650699866e-01 , 3.85345919387903e-01 , 2.61366235247257e+00 , 4.82461270335294e-01 , 2.07696380666347e+00 , 1.14254884016557e+00 , 1.04553746637080e+00 , 1.18131227060580e+00 , 1.18719671546719e-01 , 1.69847359328974e+00 , 2.06729318897268e+00 , -1.09179940169616e+00 , 2.03025352172266e+00 , 5.72960077339100e-01 , 6.18013592442385e-01 , 2.96456159475629e+00 , -5.83383313581664e-01 , 3.53085945103520e-01 , 3.16715384200455e+00 , 1.29561687036373e+00 , 1.36203853191918e+00 , 3.74264177973402e+00 , 8.46850384517969e-01 , 1.98285156306198e+00 , 5.02809578988427e+00 , 2.10973305988450e+00 , 2.73681089296750e+00 , 5.71605794165702e+00 , -3.48762046412809e-01 , 2.90752551225505e+00 , 4.96867528030200e+00 , -1.11920791756658e+00 , 3.06699078158662e+00 , 5.87734231670672e+00 , -5.38333623730181e-01 , 3.51142269226990e+00 , 3.81520213881713e+00 , -1.49843560791049e+00 , 4.50654707598769e+00 , 3.41371229948753e+00 , -7.13294121656643e-01 , 5.42557666301716e+00 , 2.47206849802352e+00 , -2.74425913887002e+00 , 3.93451898443147e+00 , 2.84179837821152e+00 , -3.81054992169605e+00 , 4.54277935493174e+00 , 2.81256821995773e+00 , -2.66484198682084e+00 , 2.64461123625328e+00 , 2.36553515139455e+00 , -3.78937150597451e+00 , 1.81732553101476e+00 , 2.00393460363141e+00 , -3.36715965222817e+00 , 8.77401627073931e-01 , 8.35477650714998e-01 , -4.27482462124773e+00 , 1.05958388107734e+00 , 3.21962204538203e+00 , -5.48918404843012e+00 , 7.76784618642079e-01 , 3.33442191610955e+00 , -3.36706253375617e+00 , 7.17851868366844e-01 , 4.19196428516940e+00 , -3.67556292758813e+00 , 7.58218748188693e-02 , 5.46260107999588e+00 , -2.38991324934671e+00 , -3.25296840409072e-01 , 6.14870951617098e+00 , -4.46749439379339e+00 , 9.34969453495375e-01 , 6.42536132477543e+00 , -5.36467953327721e+00 , 5.86231116048637e-01 , 7.21375288174230e+00 , -6.28718665126741e+00 , 3.62919036014076e+00 , 6.75076513126300e+00 , -6.98266884576581e+00 , 4.29541408722657e+00 , 7.49806320906888e+00 , -6.68463458476356e+00 , 3.16418550162232e+00 , 5.51356624786938e+00 , -4.11347763262476e+00 , 2.24859562081623e+00 , 6.38957541942517e+00 , -4.81143882202094e+00 , 3.25770940668724e+00 , 7.25789425619000e+00 , -4.05017605728786e+00 , 4.54876606599830e+00 , 7.27143130377330e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.7687 , 6.57687 , 13.1537 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.7687 , 6.57687 , 13.1537 ) to colvar "one". +colvars: Adding total bias energy: 56.1514 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.7687 , 6.57687 , 13.1537 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.19057 , -0.553687 , -1.49789 ) +colvars: ( -4.45091 , -0.474786 , -1.28444 ) +colvars: ( -4.45091 , -0.474786 , -1.28444 ) +colvars: ( -5.92875 , -0.632429 , -1.71091 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.935987 , 0.206459 , 0.643928 ) +colvars: ( 0.811207 , 0.28054 , 0.668894 ) +colvars: ( 0.794139 , 0.273363 , 0.649593 ) +colvars: ( 0.694742 , 0.281008 , 0.602072 ) +colvars: ( 0.682336 , 0.211041 , 0.503069 ) +colvars: ( 0.604666 , 0.361898 , 0.656068 ) +colvars: ( 0.493062 , 0.376268 , 0.610304 ) +colvars: ( 0.413213 , 0.478209 , 0.697849 ) +colvars: ( 0.407691 , 0.329348 , 0.499297 ) +colvars: ( 0.37158 , 0.285524 , 0.420877 ) +colvars: ( 0.376771 , 0.334951 , 0.488747 ) +colvars: ( 0.302287 , 0.289832 , 0.386407 ) +colvars: ( 0.273672 , 0.320373 , 0.409919 ) +colvars: ( 0.367362 , 0.187239 , 0.289454 ) +colvars: ( 0.306165 , 0.141576 , 0.194094 ) +colvars: ( 0.495355 , 0.148652 , 0.312927 ) +colvars: ( 0.570983 , 0.0528474 , 0.230991 ) +colvars: ( 0.70598 , 0.0311767 , 0.28072 ) +colvars: ( 0.580286 , 0.0193091 , 0.192365 ) +colvars: ( 0.563851 , -0.0490865 , 0.0930919 ) +colvars: ( 0.602403 , 0.0696111 , 0.271184 ) +colvars: ( 0.601183 , 0.0525025 , 0.248025 ) +colvars: ( 0.639588 , 0.12051 , 0.35951 ) +colvars: ( 0.471617 , 0.0568383 , 0.178693 ) +colvars: ( 0.464647 , -0.0019918 , 0.0974527 ) +colvars: ( 0.365203 , 0.125562 , 0.207264 ) +colvars: ( 0.235389 , 0.134234 , 0.143477 ) +colvars: ( 0.139882 , 0.224123 , 0.206139 ) +colvars: ( 0.205716 , 0.0567687 , 0.0246361 ) +colvars: ( 0.154486 , 0.0185821 , -0.0551404 ) +colvars: ( 0.240379 , 0.030127 , 0.00974479 ) +colvars: ( 0.225494 , -0.0459954 , -0.0987711 ) +colvars: ( 0.261894 , -0.0492736 , -0.0819963 ) +colvars: ( 0.304083 , -0.136136 , -0.171558 ) +colvars: ( 0.258192 , -0.192059 , -0.271521 ) +colvars: ( 0.424329 , -0.15164 , -0.122279 ) +colvars: ( 0.505251 , -0.230795 , -0.1793 ) +colvars: ( 0.642111 , -0.233171 , -0.103172 ) +colvars: ( 0.456315 , -0.235772 , -0.214166 ) +colvars: ( 0.462138 , -0.30729 , -0.304649 ) +colvars: ( 0.405744 , -0.158975 , -0.142666 ) +colvars: ( 0.349546 , -0.15268 , -0.166945 ) +colvars: ( 0.332587 , -0.0617376 , -0.0574198 ) +colvars: ( 0.22093 , -0.162244 , -0.253969 ) +colvars: ( 0.195677 , -0.206515 , -0.326689 ) +colvars: ( 0.0104263 , -0.210661 , -0.439396 ) +colvars: ( -0.084433 , -0.229603 , -0.519181 ) +colvars: ( 0.114849 , -0.262753 , -0.447293 ) +colvars: ( 0.135367 , -0.119716 , -0.247702 ) +colvars: ( 0.0108769 , -0.124624 , -0.326226 ) +colvars: ( -0.0820626 , -0.0400688 , -0.269078 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.19057 , 0.553687 , 1.49789 ) +colvars: ( 4.45091 , 0.474786 , 1.28444 ) +colvars: ( 4.45091 , 0.474786 , 1.28444 ) +colvars: ( 5.92875 , 0.632429 , 1.71091 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.646765 , -0.0856109 , -0.384012 ) +colvars: ( -0.58196 , -0.173048 , -0.350532 ) +colvars: ( -0.528587 , -0.149656 , -0.288566 ) +colvars: ( -0.541701 , -0.202069 , -0.320614 ) +colvars: ( -0.531541 , -0.139741 , -0.287955 ) +colvars: ( -0.516571 , -0.29942 , -0.330504 ) +colvars: ( -0.483223 , -0.342046 , -0.312422 ) +colvars: ( -0.461211 , -0.455583 , -0.331273 ) +colvars: ( -0.416834 , -0.304498 , -0.232297 ) +colvars: ( -0.412564 , -0.277715 , -0.218359 ) +colvars: ( -0.364215 , -0.298439 , -0.177336 ) +colvars: ( -0.300355 , -0.259282 , -0.0991682 ) +colvars: ( -0.248438 , -0.274984 , -0.0527552 ) +colvars: ( -0.320244 , -0.150118 , -0.0797632 ) +colvars: ( -0.287614 , -0.119076 , -0.0358451 ) +colvars: ( -0.376664 , -0.0894993 , -0.1145 ) +colvars: ( -0.404113 , 0.0144248 , -0.104568 ) +colvars: ( -0.455936 , 0.0647169 , -0.138416 ) +colvars: ( -0.444453 , 0.0302562 , -0.139322 ) +colvars: ( -0.432479 , 0.0903729 , -0.10564 ) +colvars: ( -0.491569 , -0.0270136 , -0.207225 ) +colvars: ( -0.528533 , -0.0286201 , -0.244879 ) +colvars: ( -0.581658 , -0.0979401 , -0.323153 ) +colvars: ( -0.474658 , -0.0602788 , -0.202255 ) +colvars: ( -0.482146 , -0.0136302 , -0.192949 ) +colvars: ( -0.417145 , -0.138821 , -0.172883 ) +colvars: ( -0.357358 , -0.171835 , -0.124817 ) +colvars: ( -0.304737 , -0.267183 , -0.106411 ) +colvars: ( -0.3135 , -0.0946702 , -0.0530102 ) +colvars: ( -0.300148 , -0.074939 , -0.0325057 ) +colvars: ( -0.29154 , -0.047142 , -0.0138506 ) +colvars: ( -0.253712 , 0.0320404 , 0.0526359 ) +colvars: ( -0.230183 , 0.060005 , 0.0863166 ) +colvars: ( -0.299757 , 0.123784 , 0.0395259 ) +colvars: ( -0.271854 , 0.168039 , 0.0834665 ) +colvars: ( -0.372308 , 0.153418 , -0.022561 ) +colvars: ( -0.423436 , 0.233975 , -0.0448024 ) +colvars: ( -0.49766 , 0.257726 , -0.110687 ) +colvars: ( -0.436707 , 0.212976 , -0.0656826 ) +colvars: ( -0.441445 , 0.277342 , -0.0472312 ) +colvars: ( -0.442407 , 0.121347 , -0.104432 ) +colvars: ( -0.450993 , 0.0894222 , -0.124552 ) +colvars: ( -0.474448 , -0.00937457 , -0.183694 ) +colvars: ( -0.381384 , 0.0776191 , -0.0589894 ) +colvars: ( -0.385363 , 0.105467 , -0.0529413 ) +colvars: ( -0.21166 , 0.112544 , 0.123836 ) +colvars: ( -0.160072 , 0.114613 , 0.176324 ) +colvars: ( -0.238503 , 0.189034 , 0.124486 ) +colvars: ( -0.315547 , 0.0346126 , -0.00845726 ) +colvars: ( -0.245837 , 0.0203268 , 0.0563122 ) +colvars: ( -0.189409 , -0.0675153 , 0.0812428 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 26. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 26. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atoms_new_colvar_forces = { ( -4.90134830340811e+00 , -4.32838534106888e-01 , -1.23797148234851e+00 ), ( -4.22166551672096e+00 , -3.67294361066177e-01 , -9.66076111553409e-01 ), ( -4.29787238386828e+00 , -3.95846618103073e-01 , -1.00298079083088e+00 ), ( -5.77795036103874e+00 , -5.61128776172026e-01 , -1.49579437993151e+00 ), ( 2.65552369057024e-01 , 1.23707017344092e-01 , 3.61026525861699e-01 ), ( 5.27866578934323e+00 , 6.16164346414365e-01 , 1.82345157951742e+00 ), ( 4.46075239357411e+00 , 5.09008069397666e-01 , 1.58232076279526e+00 ), ( -4.79978613650726e-02 , 2.26261342476859e-02 , 3.66575602512266e-01 ), ( 4.44176967124551e+00 , 4.99636295182185e-01 , 1.55143793146276e+00 ), ( 5.88776065054872e+00 , 6.40238071629797e-01 , 1.91342600203500e+00 ), ( 1.25563953201117e-02 , 3.65122831702803e-02 , 3.11411663891079e-01 ), ( 1.93131901570776e-03 , 3.05492085375823e-02 , 2.87238624822341e-01 ), ( 2.52341760514982e-02 , 4.53888331213753e-02 , 3.57163324219363e-01 ), ( 4.71181684901467e-02 , 3.71210769891694e-02 , 2.09690449230305e-01 ), ( 1.85503935244117e-02 , 2.24999200605314e-02 , 1.58248660998203e-01 ), ( 1.18691620709629e-01 , 5.91532301902236e-02 , 1.98427428892123e-01 ), ( 1.66869107853703e-01 , 6.72722223839669e-02 , 1.26422837881091e-01 ), ( 2.50044263602652e-01 , 9.58935654325778e-02 , 1.42303574511977e-01 ), ( 1.35832742955127e-01 , 4.95652907963995e-02 , 5.30428277677530e-02 ), ( 1.31372715595156e-01 , 4.12863670414696e-02 , -1.25478450973073e-02 ), ( 1.10834429394443e-01 , 4.25975568390924e-02 , 6.39590476471605e-02 ), ( 7.26502653425661e-02 , 2.38823552624212e-02 , 3.14620475251415e-03 ), ( 5.79303744930678e-02 , 2.25696084109297e-02 , 3.63569311625431e-02 ), ( -3.04073876000827e-03 , -3.44045630873283e-03 , -2.35622234125922e-02 ), ( -1.74993631339265e-02 , -1.56219694704138e-02 , -9.54965949274292e-02 ), ( -5.19416587071601e-02 , -1.32588934206399e-02 , 3.43804865668219e-02 ), ( -1.21968925985347e-01 , -3.76008008019011e-02 , 1.86594793017237e-02 ), ( -1.64854509848420e-01 , -4.30598051972382e-02 , 9.97281777556352e-02 ), ( -1.07783928431990e-01 , -3.79014628017018e-02 , -2.83740304163566e-02 ), ( -1.45662130286669e-01 , -5.63569575602671e-02 , -8.76461169834020e-02 ), ( -5.11608353418905e-02 , -1.70150367783029e-02 , -4.10578440009852e-03 ), ( -2.82181429484682e-02 , -1.39549920990087e-02 , -4.61352529549631e-02 ), ( 3.17109978720648e-02 , 1.07313777416710e-02 , 4.32031562018576e-03 ), ( 4.32647986589957e-03 , -1.23517381398462e-02 , -1.32032505804376e-01 ), ( -1.36622675730687e-02 , -2.40200925147125e-02 , -1.88054283567087e-01 ), ( 5.20211908117395e-02 , 1.77759685189685e-03 , -1.44839809187743e-01 ), ( 8.18144971946119e-02 , 3.18001275358909e-03 , -2.24102147796891e-01 ), ( 1.44450751982475e-01 , 2.45549924434867e-02 , -2.13858668981877e-01 ), ( 1.96081985059248e-02 , -2.27958532330345e-02 , -2.79848803768936e-01 ), ( 2.06934393004506e-02 , -2.99478881630010e-02 , -3.51880501458444e-01 ), ( -3.66628517639210e-02 , -3.76282206819420e-02 , -2.47098296326837e-01 ), ( -1.01446643061048e-01 , -6.32576371288947e-02 , -2.91497474093415e-01 ), ( -1.41861370342853e-01 , -7.11121497690519e-02 , -2.41113794952804e-01 ), ( -1.60454224762985e-01 , -8.46246900122311e-02 , -3.12958230653173e-01 ), ( -1.89686330106093e-01 , -1.01047855434558e-01 , -3.79630375014570e-01 ), ( -2.01233460291664e-01 , -9.81171667056875e-02 , -3.15560315382003e-01 ), ( -2.44505411686068e-01 , -1.14990326731746e-01 , -3.42856436960405e-01 ), ( -1.23653766302172e-01 , -7.37192713634164e-02 , -3.22806971054668e-01 ), ( -1.80179697047576e-01 , -8.51030518346081e-02 , -2.56159372505237e-01 ), ( -2.34959848327602e-01 , -1.04296723642412e-01 , -2.69914164759479e-01 ), ( -2.71471870539900e-01 , -1.07584103000942e-01 , -1.87835674080815e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 27, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 27, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 27, atoms_positions[size = 51] = { ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 ), ( 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 ), ( 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 ), ( 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 ), ( 7.01535203749725e+00 , -2.06381635889530e+00 , -8.97206548208713e-01 ), ( 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 ), ( 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 ), ( 7.11920452994009e+00 , -3.45209208680255e-01 , 4.36798290506035e+00 ), ( 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 ), ( 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 ), ( 5.83996242946139e+00 , 2.25614165217745e+00 , 2.97754417816735e+00 ), ( 5.18803371200831e+00 , 3.56439300374262e+00 , 2.90427264395260e+00 ), ( 6.31278682030528e+00 , 4.48718193168801e+00 , 2.30297883289902e+00 ), ( 3.86007818050917e+00 , 3.66069984853279e+00 , 2.03536695968349e+00 ), ( 2.80106427502878e+00 , 4.17007867900681e+00 , 2.45085264233098e+00 ), ( 3.92668633537448e+00 , 3.21135139059605e+00 , 7.34662256057969e-01 ), ( 2.73559409674514e+00 , 3.03718396101823e+00 , -8.18396133359087e-02 ), ( 3.10046791929361e+00 , 2.66260233391187e+00 , -1.53484189859099e+00 ), ( 1.55806782248441e+00 , 2.17837165364119e+00 , 4.23990219910245e-01 ), ( 3.90966682471660e-01 , 2.61549156173092e+00 , 4.77048162595421e-01 ), ( 2.07642940287190e+00 , 1.14626556479653e+00 , 1.04418936403971e+00 ), ( 1.18955214262897e+00 , 1.21097540077628e-01 , 1.69579939021184e+00 ), ( 2.07148676383460e+00 , -1.09170139783296e+00 , 2.03336886456757e+00 ), ( 5.74083444381060e-01 , 6.17814367178178e-01 , 2.96441739552478e+00 ), ( -5.83239870189212e-01 , 3.53854569089529e-01 , 3.17001185669136e+00 ), ( 1.29268717567358e+00 , 1.36802499737871e+00 , 3.74325367718469e+00 ), ( 8.51662531290306e-01 , 1.98196151284385e+00 , 5.02902636009038e+00 ), ( 2.10795727843958e+00 , 2.74294345881718e+00 , 5.71950307343801e+00 ), ( -3.51380465494013e-01 , 2.90590727965994e+00 , 4.96662567680565e+00 ), ( -1.11754635934422e+00 , 3.06753233047963e+00 , 5.87758275384854e+00 ), ( -5.41004249476953e-01 , 3.51052928934131e+00 , 3.80702706112940e+00 ), ( -1.49131798447236e+00 , 4.50013366924590e+00 , 3.41310948361751e+00 ), ( -7.18849617362706e-01 , 5.42808066275172e+00 , 2.47348306051379e+00 ), ( -2.74391507090231e+00 , 3.93976116451634e+00 , 2.82892247842410e+00 ), ( -3.80912868669978e+00 , 4.54826517460901e+00 , 2.81272152384039e+00 ), ( -2.67181385610276e+00 , 2.63993240683156e+00 , 2.36185920063368e+00 ), ( -3.79203712233535e+00 , 1.82126172263691e+00 , 2.00493708536667e+00 ), ( -3.36452697779479e+00 , 8.76290545235428e-01 , 8.28533001648633e-01 ), ( -4.26651678313547e+00 , 1.05553751337188e+00 , 3.22484550789925e+00 ), ( -5.48609767217338e+00 , 7.70398431245772e-01 , 3.33557934330755e+00 ), ( -3.36843730934644e+00 , 7.21681435894418e-01 , 4.18538959592939e+00 ), ( -3.67363375907043e+00 , 7.83952627655409e-02 , 5.46885930333576e+00 ), ( -2.38776057883782e+00 , -3.24274265963382e-01 , 6.14405952976137e+00 ), ( -4.47086570247857e+00 , 9.28599829856636e-01 , 6.42355235353585e+00 ), ( -5.36379962330255e+00 , 5.83302207573987e-01 , 7.21086622603019e+00 ), ( -6.29498544377212e+00 , 3.62952728769432e+00 , 6.75153578478002e+00 ), ( -6.98751438372502e+00 , 4.29570395973377e+00 , 7.50160948168672e+00 ), ( -6.67303020010390e+00 , 3.16282932646508e+00 , 5.51765282119227e+00 ), ( -4.11095650389687e+00 , 2.25069892237787e+00 , 6.39019118562185e+00 ), ( -4.81324504379703e+00 , 3.26580560272371e+00 , 7.25708721992280e+00 ), ( -4.04200929478364e+00 , 4.54919603154869e+00 , 7.27119176699306e+00 ) } +colvars: Step 27, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "one", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.96466575557498e-01 , -8.83665802952108e-03 , 9.55002347144801e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 7.01535203749725e+00 , -2.06381635889530e+00 , -8.97206548208713e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 , 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 7.11920452994009e+00 , -3.45209208680255e-01 , 4.36798290506035e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 , 5.83996242946139e+00 , 2.25614165217745e+00 , 2.97754417816735e+00 , 5.18803371200831e+00 , 3.56439300374262e+00 , 2.90427264395260e+00 , 6.31278682030528e+00 , 4.48718193168801e+00 , 2.30297883289902e+00 , 3.86007818050917e+00 , 3.66069984853279e+00 , 2.03536695968349e+00 , 2.80106427502878e+00 , 4.17007867900681e+00 , 2.45085264233098e+00 , 3.92668633537448e+00 , 3.21135139059605e+00 , 7.34662256057969e-01 , 2.73559409674514e+00 , 3.03718396101823e+00 , -8.18396133359087e-02 , 3.10046791929361e+00 , 2.66260233391187e+00 , -1.53484189859099e+00 , 1.55806782248441e+00 , 2.17837165364119e+00 , 4.23990219910245e-01 , 3.90966682471660e-01 , 2.61549156173092e+00 , 4.77048162595421e-01 , 2.07642940287190e+00 , 1.14626556479653e+00 , 1.04418936403971e+00 , 1.18955214262897e+00 , 1.21097540077628e-01 , 1.69579939021184e+00 , 2.07148676383460e+00 , -1.09170139783296e+00 , 2.03336886456757e+00 , 5.74083444381060e-01 , 6.17814367178178e-01 , 2.96441739552478e+00 , -5.83239870189212e-01 , 3.53854569089529e-01 , 3.17001185669136e+00 , 1.29268717567358e+00 , 1.36802499737871e+00 , 3.74325367718469e+00 , 8.51662531290306e-01 , 1.98196151284385e+00 , 5.02902636009038e+00 , 2.10795727843958e+00 , 2.74294345881718e+00 , 5.71950307343801e+00 , -3.51380465494013e-01 , 2.90590727965994e+00 , 4.96662567680565e+00 , -1.11754635934422e+00 , 3.06753233047963e+00 , 5.87758275384854e+00 , -5.41004249476953e-01 , 3.51052928934131e+00 , 3.80702706112940e+00 , -1.49131798447236e+00 , 4.50013366924590e+00 , 3.41310948361751e+00 , -7.18849617362706e-01 , 5.42808066275172e+00 , 2.47348306051379e+00 , -2.74391507090231e+00 , 3.93976116451634e+00 , 2.82892247842410e+00 , -3.80912868669978e+00 , 4.54826517460901e+00 , 2.81272152384039e+00 , -2.67181385610276e+00 , 2.63993240683156e+00 , 2.36185920063368e+00 , -3.79203712233535e+00 , 1.82126172263691e+00 , 2.00493708536667e+00 , -3.36452697779479e+00 , 8.76290545235428e-01 , 8.28533001648633e-01 , -4.26651678313547e+00 , 1.05553751337188e+00 , 3.22484550789925e+00 , -5.48609767217338e+00 , 7.70398431245772e-01 , 3.33557934330755e+00 , -3.36843730934644e+00 , 7.21681435894418e-01 , 4.18538959592939e+00 , -3.67363375907043e+00 , 7.83952627655409e-02 , 5.46885930333576e+00 , -2.38776057883782e+00 , -3.24274265963382e-01 , 6.14405952976137e+00 , -4.47086570247857e+00 , 9.28599829856636e-01 , 6.42355235353585e+00 , -5.36379962330255e+00 , 5.83302207573987e-01 , 7.21086622603019e+00 , -6.29498544377212e+00 , 3.62952728769432e+00 , 6.75153578478002e+00 , -6.98751438372502e+00 , 4.29570395973377e+00 , 7.50160948168672e+00 , -6.67303020010390e+00 , 3.16282932646508e+00 , 5.51765282119227e+00 , -4.11095650389687e+00 , 2.25069892237787e+00 , 6.39019118562185e+00 , -4.81324504379703e+00 , 3.26580560272371e+00 , 7.25708721992280e+00 , -4.04200929478364e+00 , 4.54919603154869e+00 , 7.27119176699306e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.96466575557498e-01 , -8.83665802952108e-03 , 9.55002347144801e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.25392473243704e+00 , 4.22763506717783e-02 , -7.33964811094362e-01 , 6.85330609540617e+00 , -5.73222733414117e-01 , -5.35043039430192e-01 , 7.01535203749725e+00 , -2.06381635889530e+00 , -8.97206548208713e-01 , 6.14793758889599e+00 , -3.85491491024697e-01 , 7.86629259396274e-01 , 4.91119162456391e+00 , -1.48045663681169e-01 , 7.38323375572400e-01 , 6.82147581359024e+00 , -2.79842494096914e-01 , 1.95568616152081e+00 , 6.12541129157456e+00 , -2.08579445372828e-01 , 3.16591907364259e+00 , 7.11920452994009e+00 , -3.45209208680255e-01 , 4.36798290506035e+00 , 5.33931486536376e+00 , 1.07346631358339e+00 , 3.36906770129338e+00 , 4.17748335434935e+00 , 1.01043167885946e+00 , 3.75205049727017e+00 , 5.83996242946139e+00 , 2.25614165217745e+00 , 2.97754417816735e+00 , 5.18803371200831e+00 , 3.56439300374262e+00 , 2.90427264395260e+00 , 6.31278682030528e+00 , 4.48718193168801e+00 , 2.30297883289902e+00 , 3.86007818050917e+00 , 3.66069984853279e+00 , 2.03536695968349e+00 , 2.80106427502878e+00 , 4.17007867900681e+00 , 2.45085264233098e+00 , 3.92668633537448e+00 , 3.21135139059605e+00 , 7.34662256057969e-01 , 2.73559409674514e+00 , 3.03718396101823e+00 , -8.18396133359087e-02 , 3.10046791929361e+00 , 2.66260233391187e+00 , -1.53484189859099e+00 , 1.55806782248441e+00 , 2.17837165364119e+00 , 4.23990219910245e-01 , 3.90966682471660e-01 , 2.61549156173092e+00 , 4.77048162595421e-01 , 2.07642940287190e+00 , 1.14626556479653e+00 , 1.04418936403971e+00 , 1.18955214262897e+00 , 1.21097540077628e-01 , 1.69579939021184e+00 , 2.07148676383460e+00 , -1.09170139783296e+00 , 2.03336886456757e+00 , 5.74083444381060e-01 , 6.17814367178178e-01 , 2.96441739552478e+00 , -5.83239870189212e-01 , 3.53854569089529e-01 , 3.17001185669136e+00 , 1.29268717567358e+00 , 1.36802499737871e+00 , 3.74325367718469e+00 , 8.51662531290306e-01 , 1.98196151284385e+00 , 5.02902636009038e+00 , 2.10795727843958e+00 , 2.74294345881718e+00 , 5.71950307343801e+00 , -3.51380465494013e-01 , 2.90590727965994e+00 , 4.96662567680565e+00 , -1.11754635934422e+00 , 3.06753233047963e+00 , 5.87758275384854e+00 , -5.41004249476953e-01 , 3.51052928934131e+00 , 3.80702706112940e+00 , -1.49131798447236e+00 , 4.50013366924590e+00 , 3.41310948361751e+00 , -7.18849617362706e-01 , 5.42808066275172e+00 , 2.47348306051379e+00 , -2.74391507090231e+00 , 3.93976116451634e+00 , 2.82892247842410e+00 , -3.80912868669978e+00 , 4.54826517460901e+00 , 2.81272152384039e+00 , -2.67181385610276e+00 , 2.63993240683156e+00 , 2.36185920063368e+00 , -3.79203712233535e+00 , 1.82126172263691e+00 , 2.00493708536667e+00 , -3.36452697779479e+00 , 8.76290545235428e-01 , 8.28533001648633e-01 , -4.26651678313547e+00 , 1.05553751337188e+00 , 3.22484550789925e+00 , -5.48609767217338e+00 , 7.70398431245772e-01 , 3.33557934330755e+00 , -3.36843730934644e+00 , 7.21681435894418e-01 , 4.18538959592939e+00 , -3.67363375907043e+00 , 7.83952627655409e-02 , 5.46885930333576e+00 , -2.38776057883782e+00 , -3.24274265963382e-01 , 6.14405952976137e+00 , -4.47086570247857e+00 , 9.28599829856636e-01 , 6.42355235353585e+00 , -5.36379962330255e+00 , 5.83302207573987e-01 , 7.21086622603019e+00 , -6.29498544377212e+00 , 3.62952728769432e+00 , 6.75153578478002e+00 , -6.98751438372502e+00 , 4.29570395973377e+00 , 7.50160948168672e+00 , -6.67303020010390e+00 , 3.16282932646508e+00 , 5.51765282119227e+00 , -4.11095650389687e+00 , 2.25069892237787e+00 , 6.39019118562185e+00 , -4.81324504379703e+00 , 3.26580560272371e+00 , 7.25708721992280e+00 , -4.04200929478364e+00 , 4.54919603154869e+00 , 7.27119176699306e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.7313 , 6.57313 , 13.1463 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.7313 , 6.57313 , 13.1463 ) to colvar "one". +colvars: Adding total bias energy: 56.0971 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.7313 , 6.57313 , 13.1463 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.19189 , -0.552461 , -1.49409 ) +colvars: ( -4.45204 , -0.473736 , -1.28118 ) +colvars: ( -4.45204 , -0.473736 , -1.28118 ) +colvars: ( -5.93025 , -0.63103 , -1.70657 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.93535 , 0.206502 , 0.642814 ) +colvars: ( 0.810728 , 0.280502 , 0.667712 ) +colvars: ( 0.793651 , 0.273341 , 0.648447 ) +colvars: ( 0.694429 , 0.280918 , 0.600981 ) +colvars: ( 0.68204 , 0.210981 , 0.502152 ) +colvars: ( 0.604481 , 0.361727 , 0.654861 ) +colvars: ( 0.493039 , 0.376038 , 0.609153 ) +colvars: ( 0.413302 , 0.477894 , 0.696524 ) +colvars: ( 0.407766 , 0.329118 , 0.498328 ) +colvars: ( 0.371715 , 0.285295 , 0.420037 ) +colvars: ( 0.37686 , 0.334723 , 0.487796 ) +colvars: ( 0.302457 , 0.289608 , 0.385625 ) +colvars: ( 0.273851 , 0.32014 , 0.409095 ) +colvars: ( 0.367443 , 0.187094 , 0.288858 ) +colvars: ( 0.306328 , 0.14143 , 0.193655 ) +colvars: ( 0.495265 , 0.148577 , 0.312317 ) +colvars: ( 0.570791 , 0.0528502 , 0.230542 ) +colvars: ( 0.705601 , 0.0312475 , 0.280212 ) +colvars: ( 0.58011 , 0.0193161 , 0.191981 ) +colvars: ( 0.563698 , -0.0490518 , 0.0928808 ) +colvars: ( 0.602221 , 0.0695874 , 0.27066 ) +colvars: ( 0.60103 , 0.0524704 , 0.247537 ) +colvars: ( 0.639405 , 0.120446 , 0.358828 ) +colvars: ( 0.471642 , 0.0567505 , 0.178299 ) +colvars: ( 0.464693 , -0.00205918 , 0.0972 ) +colvars: ( 0.365361 , 0.125404 , 0.206799 ) +colvars: ( 0.235721 , 0.13402 , 0.143098 ) +colvars: ( 0.140331 , 0.223832 , 0.205631 ) +colvars: ( 0.206071 , 0.0565921 , 0.0244659 ) +colvars: ( 0.15492 , 0.0183989 , -0.0551817 ) +colvars: ( 0.240662 , 0.0299928 , 0.00961332 ) +colvars: ( 0.225779 , -0.0460863 , -0.0987095 ) +colvars: ( 0.262101 , -0.0493315 , -0.0819511 ) +colvars: ( 0.304275 , -0.136157 , -0.171353 ) +colvars: ( 0.258443 , -0.19207 , -0.271148 ) +colvars: ( 0.424373 , -0.151614 , -0.122139 ) +colvars: ( 0.5052 , -0.230706 , -0.179044 ) +colvars: ( 0.641884 , -0.233031 , -0.103024 ) +colvars: ( 0.456356 , -0.235714 , -0.213864 ) +colvars: ( 0.462177 , -0.307198 , -0.304186 ) +colvars: ( 0.405869 , -0.158986 , -0.142505 ) +colvars: ( 0.349771 , -0.152731 , -0.166757 ) +colvars: ( 0.332852 , -0.0618516 , -0.0574335 ) +colvars: ( 0.221321 , -0.162337 , -0.253652 ) +colvars: ( 0.196116 , -0.206604 , -0.326251 ) +colvars: ( 0.0110507 , -0.210784 , -0.438785 ) +colvars: ( -0.0836857 , -0.229751 , -0.518447 ) +colvars: ( 0.115321 , -0.2628 , -0.446644 ) +colvars: ( 0.135851 , -0.119851 , -0.24741 ) +colvars: ( 0.0115201 , -0.124801 , -0.32582 ) +colvars: ( -0.0813092 , -0.0403172 , -0.26879 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.19189 , 0.552461 , 1.49409 ) +colvars: ( 4.45204 , 0.473736 , 1.28118 ) +colvars: ( 4.45204 , 0.473736 , 1.28118 ) +colvars: ( 5.93025 , 0.63103 , 1.70657 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.646438 , -0.0856051 , -0.383247 ) +colvars: ( -0.5817 , -0.173176 , -0.349543 ) +colvars: ( -0.528123 , -0.149712 , -0.287416 ) +colvars: ( -0.541601 , -0.20225 , -0.319685 ) +colvars: ( -0.531429 , -0.139818 , -0.287202 ) +colvars: ( -0.516623 , -0.299769 , -0.329424 ) +colvars: ( -0.483452 , -0.342474 , -0.311382 ) +colvars: ( -0.461577 , -0.456204 , -0.330017 ) +colvars: ( -0.417004 , -0.304843 , -0.231285 ) +colvars: ( -0.412823 , -0.278025 , -0.21752 ) +colvars: ( -0.364227 , -0.298746 , -0.176156 ) +colvars: ( -0.300286 , -0.259503 , -0.0980001 ) +colvars: ( -0.248207 , -0.275201 , -0.0513497 ) +colvars: ( -0.320073 , -0.150156 , -0.0788332 ) +colvars: ( -0.287473 , -0.119059 , -0.0350276 ) +colvars: ( -0.376376 , -0.0894403 , -0.113657 ) +colvars: ( -0.403729 , 0.0146557 , -0.103955 ) +colvars: ( -0.455391 , 0.0650334 , -0.137812 ) +colvars: ( -0.444234 , 0.0304862 , -0.138945 ) +colvars: ( -0.432251 , 0.0907039 , -0.105435 ) +colvars: ( -0.491508 , -0.0269036 , -0.206855 ) +colvars: ( -0.528652 , -0.02854 , -0.244707 ) +colvars: ( -0.581915 , -0.0979989 , -0.322933 ) +colvars: ( -0.474911 , -0.060251 , -0.202103 ) +colvars: ( -0.482457 , -0.0135345 , -0.193003 ) +colvars: ( -0.417445 , -0.138912 , -0.172515 ) +colvars: ( -0.357764 , -0.171976 , -0.124435 ) +colvars: ( -0.30518 , -0.26747 , -0.105752 ) +colvars: ( -0.313786 , -0.0946636 , -0.0527228 ) +colvars: ( -0.300526 , -0.0749067 , -0.0323683 ) +colvars: ( -0.291616 , -0.0470318 , -0.0134824 ) +colvars: ( -0.253652 , 0.0323018 , 0.052917 ) +colvars: ( -0.229901 , 0.0603401 , 0.0867526 ) +colvars: ( -0.29968 , 0.124185 , 0.0395245 ) +colvars: ( -0.271782 , 0.168518 , 0.0833345 ) +colvars: ( -0.372215 , 0.153851 , -0.0226655 ) +colvars: ( -0.423343 , 0.234527 , -0.0451751 ) +colvars: ( -0.497508 , 0.258305 , -0.111101 ) +colvars: ( -0.436825 , 0.213469 , -0.0662159 ) +colvars: ( -0.441568 , 0.277938 , -0.0479697 ) +colvars: ( -0.442705 , 0.121672 , -0.104873 ) +colvars: ( -0.451502 , 0.0896716 , -0.125118 ) +colvars: ( -0.475121 , -0.00930739 , -0.184135 ) +colvars: ( -0.381949 , 0.0778601 , -0.0595491 ) +colvars: ( -0.386024 , 0.105742 , -0.0536875 ) +colvars: ( -0.212049 , 0.112899 , 0.123419 ) +colvars: ( -0.160502 , 0.11498 , 0.17588 ) +colvars: ( -0.238705 , 0.189526 , 0.124018 ) +colvars: ( -0.316055 , 0.0348052 , -0.00879985 ) +colvars: ( -0.246388 , 0.0205083 , 0.0559968 ) +colvars: ( -0.189972 , -0.0674639 , 0.0812087 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 27. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 27. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atoms_new_colvar_forces = { ( -4.90297655930186e+00 , -4.31564598362340e-01 , -1.23451929484002e+00 ), ( -4.22301490947878e+00 , -3.66409523998744e-01 , -9.63009441633488e-01 ), ( -4.29921507948663e+00 , -3.95067683893615e-01 , -9.99882446130243e-01 ), ( -5.77963954597886e+00 , -5.59866521172678e-01 , -1.49161677631946e+00 ), ( 2.65527260322840e-01 , 1.23628653485763e-01 , 3.61031590181063e-01 ), ( 5.27974646954245e+00 , 6.14419419153178e-01 , 1.81952345279918e+00 ), ( 4.46162967145464e+00 , 5.07299643765269e-01 , 1.57894916998740e+00 ), ( -4.82743241495473e-02 , 2.16895511471460e-02 , 3.66507217577568e-01 ), ( 4.44280460194297e+00 , 4.98010304535323e-01 , 1.54822165188190e+00 ), ( 5.88914188343682e+00 , 6.38299694509511e-01 , 1.90908373748824e+00 ), ( 1.26336184694665e-02 , 3.59767195402972e-02 , 3.11639976954039e-01 ), ( 2.17048365549943e-03 , 3.01047401153576e-02 , 2.87625220041250e-01 ), ( 2.56442106990420e-02 , 4.49384889127548e-02 , 3.57745367438639e-01 ), ( 4.73700704272918e-02 , 3.69376612171887e-02 , 2.10025072640884e-01 ), ( 1.88551353404702e-02 , 2.23707320686415e-02 , 1.58627286028723e-01 ), ( 1.18888812289482e-01 , 5.91366857630878e-02 , 1.98659980139205e-01 ), ( 1.67062115254590e-01 , 6.75058472539935e-02 , 1.26587327234455e-01 ), ( 2.50209738909345e-01 , 9.62809572487406e-02 , 1.42400655013567e-01 ), ( 1.35876110676286e-01 , 4.98023324542390e-02 , 5.30360938215380e-02 ), ( 1.31446564035049e-01 , 4.16520495316130e-02 , -1.25541724310451e-02 ), ( 1.10713057823198e-01 , 4.26837708917003e-02 , 6.38048341305867e-02 ), ( 7.23778528572883e-02 , 2.39303788995603e-02 , 2.82976345134767e-03 ), ( 5.74897230395530e-02 , 2.24466943149810e-02 , 3.58948369294677e-02 ), ( -3.26894775493036e-03 , -3.50056963281915e-03 , -2.38040628525799e-02 ), ( -1.77640583668389e-02 , -1.55936516353163e-02 , -9.58035098578173e-02 ), ( -5.20833412153556e-02 , -1.35084208200437e-02 , 3.42836272455017e-02 ), ( -1.22042937854008e-01 , -3.79561229325308e-02 , 1.86633568178097e-02 ), ( -1.64848403067069e-01 , -4.36375536383752e-02 , 9.98787618112569e-02 ), ( -1.07715082816831e-01 , -3.80714707276125e-02 , -2.82569356268102e-02 ), ( -1.45605860021386e-01 , -5.65078001143671e-02 , -8.75500698611540e-02 ), ( -5.09543775943533e-02 , -1.70389294955693e-02 , -3.86905163471307e-03 ), ( -2.78734948133564e-02 , -1.37845437989526e-02 , -4.57925150521701e-02 ), ( 3.22006418712004e-02 , 1.10085934876183e-02 , 4.80151016462491e-03 ), ( 4.59496470661985e-03 , -1.19722673451992e-02 , -1.31828992832570e-01 ), ( -1.33389425313040e-02 , -2.35517859756418e-02 , -1.87813085650682e-01 ), ( 5.21575656499301e-02 , 2.23728617328495e-03 , -1.44804100200169e-01 ), ( 8.18565414688788e-02 , 3.82166798429712e-03 , -2.24219191277604e-01 ), ( 1.44375534846891e-01 , 2.52741958145053e-02 , -2.14125341398563e-01 ), ( 1.95305507393448e-02 , -2.22452771279715e-02 , -2.80079983418342e-01 ), ( 2.06084758356913e-02 , -2.92594854232303e-02 , -3.52156060929541e-01 ), ( -3.68362960553995e-02 , -3.73144996840226e-02 , -2.47378100856292e-01 ), ( -1.01731162781690e-01 , -6.30591699462869e-02 , -2.91875472071768e-01 ), ( -1.42269404346626e-01 , -7.11589608638280e-02 , -2.41568713100870e-01 ), ( -1.60628454636257e-01 , -8.44766596906788e-02 , -3.13201406497748e-01 ), ( -1.89908259778623e-01 , -1.00861169075825e-01 , -3.79938925588426e-01 ), ( -2.00998302938112e-01 , -9.78840980049558e-02 , -3.15365899917112e-01 ), ( -2.44187218124645e-01 , -1.14771105738640e-01 , -3.42566792240620e-01 ), ( -1.23384003562032e-01 , -7.32744448733386e-02 , -3.22625351507596e-01 ), ( -1.80203911027726e-01 , -8.50461141373376e-02 , -2.56210337503168e-01 ), ( -2.34868063876506e-01 , -1.04292605055861e-01 , -2.69823037582932e-01 ), ( -2.71280713736117e-01 , -1.07781035102270e-01 , -1.87581420964736e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 28, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 28, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 28, atoms_positions[size = 51] = { ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 ), ( 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 ), ( 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 ), ( 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 ), ( 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 ), ( 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 ), ( 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 ), ( 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 ), ( 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 ), ( 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ), ( 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 ), ( 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 ), ( 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 ), ( 3.85937142086407e+00 , 3.65476800818372e+00 , 2.03242241887767e+00 ), ( 2.80520731119718e+00 , 4.16980990587374e+00 , 2.44577776086260e+00 ), ( 3.92168837067129e+00 , 3.20513239434971e+00 , 7.37110387602193e-01 ), ( 2.74551095179179e+00 , 3.04637900756662e+00 , -7.83395650577801e-02 ), ( 3.10651351184068e+00 , 2.65802010971575e+00 , -1.53820581896094e+00 ), ( 1.55291908343130e+00 , 2.18526376293626e+00 , 4.23646231165986e-01 ), ( 3.97023085359059e-01 , 2.61653681210940e+00 , 4.71528039126549e-01 ), ( 2.07408053148835e+00 , 1.14713474881058e+00 , 1.04385983224942e+00 ), ( 1.19955193319812e+00 , 1.24564427667697e-01 , 1.69227225709674e+00 ), ( 2.07553838430586e+00 , -1.09189218971752e+00 , 2.03601799284642e+00 ), ( 5.74823989510068e-01 , 6.17290818940561e-01 , 2.96300100013889e+00 ), ( -5.83898258154936e-01 , 3.54630202666306e-01 , 3.17338193171358e+00 ), ( 1.29020966581429e+00 , 1.37479271877028e+00 , 3.74551657544280e+00 ), ( 8.57517755667383e-01 , 1.98097267107643e+00 , 5.03021891991004e+00 ), ( 2.10406883090063e+00 , 2.74847213498538e+00 , 5.72218933392951e+00 ), ( -3.53830914026017e-01 , 2.90422784614850e+00 , 4.96357786386462e+00 ), ( -1.11639515743135e+00 , 3.06805024433165e+00 , 5.87851704282217e+00 ), ( -5.42819948952781e-01 , 3.50974182912348e+00 , 3.79836330023223e+00 ), ( -1.48379373747290e+00 , 4.49409089265994e+00 , 3.41337438050243e+00 ), ( -7.25068428095970e-01 , 5.43094844567604e+00 , 2.47504725896066e+00 ), ( -2.74419589737474e+00 , 3.94343705131208e+00 , 2.81527629901103e+00 ), ( -3.80764989378887e+00 , 4.55386775866711e+00 , 2.81289844042620e+00 ), ( -2.67846005853101e+00 , 2.63639340040332e+00 , 2.35893527799379e+00 ), ( -3.79488408376771e+00 , 1.82427471834219e+00 , 2.00553854828854e+00 ), ( -3.36207299177903e+00 , 8.75851608815310e-01 , 8.21469624610845e-01 ), ( -4.25970519633382e+00 , 1.05112692742183e+00 , 3.23029437542200e+00 ), ( -5.48205487497069e+00 , 7.64253587136305e-01 , 3.33686201327005e+00 ), ( -3.36966131575411e+00 , 7.24816832000888e-01 , 4.17880261487107e+00 ), ( -3.67207461868132e+00 , 7.98819122703938e-02 , 5.47420527196600e+00 ), ( -2.38493540889624e+00 , -3.22269513423801e-01 , 6.13950212616605e+00 ), ( -4.47466027138304e+00 , 9.24168826467613e-01 , 6.42215542008482e+00 ), ( -5.36261681826659e+00 , 5.79896591202222e-01 , 7.20749397034283e+00 ), ( -6.30136810957071e+00 , 3.62863215113119e+00 , 6.75199664585806e+00 ), ( -6.99291556511097e+00 , 4.29626870478854e+00 , 7.50509315120895e+00 ), ( -6.66170596291076e+00 , 3.16206566291018e+00 , 5.52233572516693e+00 ), ( -4.10889386711924e+00 , 2.25260742398120e+00 , 6.39175665473791e+00 ), ( -4.81482104509748e+00 , 3.27289024772811e+00 , 7.25500513526501e+00 ), ( -4.03435454731309e+00 , 4.55168732224255e+00 , 7.27146621538718e+00 ) } +colvars: Step 28, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 , 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 , 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 , 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 , 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 , 3.85937142086407e+00 , 3.65476800818372e+00 , 2.03242241887767e+00 , 2.80520731119718e+00 , 4.16980990587374e+00 , 2.44577776086260e+00 , 3.92168837067129e+00 , 3.20513239434971e+00 , 7.37110387602193e-01 , 2.74551095179179e+00 , 3.04637900756662e+00 , -7.83395650577801e-02 , 3.10651351184068e+00 , 2.65802010971575e+00 , -1.53820581896094e+00 , 1.55291908343130e+00 , 2.18526376293626e+00 , 4.23646231165986e-01 , 3.97023085359059e-01 , 2.61653681210940e+00 , 4.71528039126549e-01 , 2.07408053148835e+00 , 1.14713474881058e+00 , 1.04385983224942e+00 , 1.19955193319812e+00 , 1.24564427667697e-01 , 1.69227225709674e+00 , 2.07553838430586e+00 , -1.09189218971752e+00 , 2.03601799284642e+00 , 5.74823989510068e-01 , 6.17290818940561e-01 , 2.96300100013889e+00 , -5.83898258154936e-01 , 3.54630202666306e-01 , 3.17338193171358e+00 , 1.29020966581429e+00 , 1.37479271877028e+00 , 3.74551657544280e+00 , 8.57517755667383e-01 , 1.98097267107643e+00 , 5.03021891991004e+00 , 2.10406883090063e+00 , 2.74847213498538e+00 , 5.72218933392951e+00 , -3.53830914026017e-01 , 2.90422784614850e+00 , 4.96357786386462e+00 , -1.11639515743135e+00 , 3.06805024433165e+00 , 5.87851704282217e+00 , -5.42819948952781e-01 , 3.50974182912348e+00 , 3.79836330023223e+00 , -1.48379373747290e+00 , 4.49409089265994e+00 , 3.41337438050243e+00 , -7.25068428095970e-01 , 5.43094844567604e+00 , 2.47504725896066e+00 , -2.74419589737474e+00 , 3.94343705131208e+00 , 2.81527629901103e+00 , -3.80764989378887e+00 , 4.55386775866711e+00 , 2.81289844042620e+00 , -2.67846005853101e+00 , 2.63639340040332e+00 , 2.35893527799379e+00 , -3.79488408376771e+00 , 1.82427471834219e+00 , 2.00553854828854e+00 , -3.36207299177903e+00 , 8.75851608815310e-01 , 8.21469624610845e-01 , -4.25970519633382e+00 , 1.05112692742183e+00 , 3.23029437542200e+00 , -5.48205487497069e+00 , 7.64253587136305e-01 , 3.33686201327005e+00 , -3.36966131575411e+00 , 7.24816832000888e-01 , 4.17880261487107e+00 , -3.67207461868132e+00 , 7.98819122703938e-02 , 5.47420527196600e+00 , -2.38493540889624e+00 , -3.22269513423801e-01 , 6.13950212616605e+00 , -4.47466027138304e+00 , 9.24168826467613e-01 , 6.42215542008482e+00 , -5.36261681826659e+00 , 5.79896591202222e-01 , 7.20749397034283e+00 , -6.30136810957071e+00 , 3.62863215113119e+00 , 6.75199664585806e+00 , -6.99291556511097e+00 , 4.29626870478854e+00 , 7.50509315120895e+00 , -6.66170596291076e+00 , 3.16206566291018e+00 , 5.52233572516693e+00 , -4.10889386711924e+00 , 2.25260742398120e+00 , 6.39175665473791e+00 , -4.81482104509748e+00 , 3.27289024772811e+00 , 7.25500513526501e+00 , -4.03435454731309e+00 , 4.55168732224255e+00 , 7.27146621538718e+00 ). +colvars: Done calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.95501027381301e-01 , -1.01866880614680e-02 , 9.55288110573420e-01 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating colvar "group2". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.95501027381301e-01 , -1.01866880614680e-02 , 9.55288110573420e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 , 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 , 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 , 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 , 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 , 3.85937142086407e+00 , 3.65476800818372e+00 , 2.03242241887767e+00 , 2.80520731119718e+00 , 4.16980990587374e+00 , 2.44577776086260e+00 , 3.92168837067129e+00 , 3.20513239434971e+00 , 7.37110387602193e-01 , 2.74551095179179e+00 , 3.04637900756662e+00 , -7.83395650577801e-02 , 3.10651351184068e+00 , 2.65802010971575e+00 , -1.53820581896094e+00 , 1.55291908343130e+00 , 2.18526376293626e+00 , 4.23646231165986e-01 , 3.97023085359059e-01 , 2.61653681210940e+00 , 4.71528039126549e-01 , 2.07408053148835e+00 , 1.14713474881058e+00 , 1.04385983224942e+00 , 1.19955193319812e+00 , 1.24564427667697e-01 , 1.69227225709674e+00 , 2.07553838430586e+00 , -1.09189218971752e+00 , 2.03601799284642e+00 , 5.74823989510068e-01 , 6.17290818940561e-01 , 2.96300100013889e+00 , -5.83898258154936e-01 , 3.54630202666306e-01 , 3.17338193171358e+00 , 1.29020966581429e+00 , 1.37479271877028e+00 , 3.74551657544280e+00 , 8.57517755667383e-01 , 1.98097267107643e+00 , 5.03021891991004e+00 , 2.10406883090063e+00 , 2.74847213498538e+00 , 5.72218933392951e+00 , -3.53830914026017e-01 , 2.90422784614850e+00 , 4.96357786386462e+00 , -1.11639515743135e+00 , 3.06805024433165e+00 , 5.87851704282217e+00 , -5.42819948952781e-01 , 3.50974182912348e+00 , 3.79836330023223e+00 , -1.48379373747290e+00 , 4.49409089265994e+00 , 3.41337438050243e+00 , -7.25068428095970e-01 , 5.43094844567604e+00 , 2.47504725896066e+00 , -2.74419589737474e+00 , 3.94343705131208e+00 , 2.81527629901103e+00 , -3.80764989378887e+00 , 4.55386775866711e+00 , 2.81289844042620e+00 , -2.67846005853101e+00 , 2.63639340040332e+00 , 2.35893527799379e+00 , -3.79488408376771e+00 , 1.82427471834219e+00 , 2.00553854828854e+00 , -3.36207299177903e+00 , 8.75851608815310e-01 , 8.21469624610845e-01 , -4.25970519633382e+00 , 1.05112692742183e+00 , 3.23029437542200e+00 , -5.48205487497069e+00 , 7.64253587136305e-01 , 3.33686201327005e+00 , -3.36966131575411e+00 , 7.24816832000888e-01 , 4.17880261487107e+00 , -3.67207461868132e+00 , 7.98819122703938e-02 , 5.47420527196600e+00 , -2.38493540889624e+00 , -3.22269513423801e-01 , 6.13950212616605e+00 , -4.47466027138304e+00 , 9.24168826467613e-01 , 6.42215542008482e+00 , -5.36261681826659e+00 , 5.79896591202222e-01 , 7.20749397034283e+00 , -6.30136810957071e+00 , 3.62863215113119e+00 , 6.75199664585806e+00 , -6.99291556511097e+00 , 4.29626870478854e+00 , 7.50509315120895e+00 , -6.66170596291076e+00 , 3.16206566291018e+00 , 5.52233572516693e+00 , -4.10889386711924e+00 , 2.25260742398120e+00 , 6.39175665473791e+00 , -4.81482104509748e+00 , 3.27289024772811e+00 , 7.25500513526501e+00 , -4.03435454731309e+00 , 4.55168732224255e+00 , 7.27146621538718e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.6912 , 6.56912 , 13.1382 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.6912 , 6.56912 , 13.1382 ) to colvar "one". +colvars: Adding total bias energy: 56.0388 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.6912 , 6.56912 , 13.1382 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.19244 , -0.550995 , -1.4898 ) +colvars: ( -4.45251 , -0.472478 , -1.2775 ) +colvars: ( -4.45251 , -0.472478 , -1.2775 ) +colvars: ( -5.93088 , -0.629354 , -1.70167 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.934549 , 0.206504 , 0.641555 ) +colvars: ( 0.81011 , 0.280399 , 0.66639 ) +colvars: ( 0.793032 , 0.273262 , 0.647179 ) +colvars: ( 0.693998 , 0.280756 , 0.599764 ) +colvars: ( 0.68163 , 0.210868 , 0.501124 ) +colvars: ( 0.604194 , 0.361456 , 0.653521 ) +colvars: ( 0.492933 , 0.375698 , 0.607876 ) +colvars: ( 0.413321 , 0.477434 , 0.695063 ) +colvars: ( 0.407777 , 0.328791 , 0.497262 ) +colvars: ( 0.371791 , 0.284978 , 0.41911 ) +colvars: ( 0.376895 , 0.3344 , 0.486761 ) +colvars: ( 0.302591 , 0.289303 , 0.384787 ) +colvars: ( 0.274005 , 0.319823 , 0.408224 ) +colvars: ( 0.367478 , 0.1869 , 0.288219 ) +colvars: ( 0.306457 , 0.141245 , 0.19319 ) +colvars: ( 0.495104 , 0.148469 , 0.311653 ) +colvars: ( 0.570515 , 0.0528501 , 0.230048 ) +colvars: ( 0.705113 , 0.0313286 , 0.279648 ) +colvars: ( 0.579844 , 0.019324 , 0.191548 ) +colvars: ( 0.563458 , -0.0489979 , 0.0926362 ) +colvars: ( 0.60194 , 0.0695462 , 0.270064 ) +colvars: ( 0.600775 , 0.0524196 , 0.24697 ) +colvars: ( 0.639108 , 0.120341 , 0.358039 ) +colvars: ( 0.471589 , 0.0566364 , 0.177843 ) +colvars: ( 0.46466 , -0.00213892 , 0.0968931 ) +colvars: ( 0.365462 , 0.125197 , 0.206276 ) +colvars: ( 0.236021 , 0.13375 , 0.142678 ) +colvars: ( 0.140767 , 0.223459 , 0.205081 ) +colvars: ( 0.206402 , 0.0563844 , 0.0242802 ) +colvars: ( 0.155338 , 0.0181912 , -0.0552269 ) +colvars: ( 0.240919 , 0.0298421 , 0.00947681 ) +colvars: ( 0.226045 , -0.0461692 , -0.0986283 ) +colvars: ( 0.262287 , -0.0493725 , -0.08188 ) +colvars: ( 0.304431 , -0.136145 , -0.171126 ) +colvars: ( 0.258669 , -0.192032 , -0.270733 ) +colvars: ( 0.424356 , -0.151547 , -0.121994 ) +colvars: ( 0.505072 , -0.230553 , -0.178785 ) +colvars: ( 0.641553 , -0.232824 , -0.102895 ) +colvars: ( 0.456325 , -0.2356 , -0.21356 ) +colvars: ( 0.462143 , -0.307029 , -0.30371 ) +colvars: ( 0.405929 , -0.158968 , -0.142357 ) +colvars: ( 0.349938 , -0.152762 , -0.166586 ) +colvars: ( 0.333058 , -0.0619757 , -0.0574861 ) +colvars: ( 0.221679 , -0.162411 , -0.253329 ) +colvars: ( 0.196525 , -0.206665 , -0.3258 ) +colvars: ( 0.011691 , -0.210872 , -0.438109 ) +colvars: ( -0.0829034 , -0.229862 , -0.517629 ) +colvars: ( 0.115791 , -0.262792 , -0.445928 ) +colvars: ( 0.136322 , -0.119979 , -0.247101 ) +colvars: ( 0.0121751 , -0.124972 , -0.325374 ) +colvars: ( -0.0805249 , -0.0405837 , -0.268461 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.19244 , 0.550995 , 1.4898 ) +colvars: ( 4.45251 , 0.472478 , 1.2775 ) +colvars: ( 4.45251 , 0.472478 , 1.2775 ) +colvars: ( 5.93088 , 0.629354 , 1.70167 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.645957 , -0.0855706 , -0.382339 ) +colvars: ( -0.58131 , -0.173249 , -0.348419 ) +colvars: ( -0.527541 , -0.149725 , -0.286148 ) +colvars: ( -0.541388 , -0.202367 , -0.318635 ) +colvars: ( -0.531208 , -0.139849 , -0.286341 ) +colvars: ( -0.516576 , -0.300023 , -0.328217 ) +colvars: ( -0.4836 , -0.342794 , -0.310225 ) +colvars: ( -0.461873 , -0.456682 , -0.328635 ) +colvars: ( -0.417112 , -0.305093 , -0.230183 ) +colvars: ( -0.413023 , -0.278246 , -0.2166 ) +colvars: ( -0.364189 , -0.298962 , -0.174903 ) +colvars: ( -0.300187 , -0.259646 , -0.0967859 ) +colvars: ( -0.247958 , -0.27534 , -0.0499097 ) +colvars: ( -0.319862 , -0.15015 , -0.0778664 ) +colvars: ( -0.287301 , -0.119007 , -0.0341909 ) +colvars: ( -0.376025 , -0.089355 , -0.112766 ) +colvars: ( -0.403268 , 0.0148817 , -0.103298 ) +colvars: ( -0.454747 , 0.065329 , -0.137151 ) +colvars: ( -0.443929 , 0.0307098 , -0.138518 ) +colvars: ( -0.431942 , 0.0910107 , -0.105194 ) +colvars: ( -0.491351 , -0.0267805 , -0.206413 ) +colvars: ( -0.528669 , -0.0284432 , -0.244453 ) +colvars: ( -0.582057 , -0.0980181 , -0.322603 ) +colvars: ( -0.475084 , -0.0601962 , -0.201887 ) +colvars: ( -0.482685 , -0.0134243 , -0.192999 ) +colvars: ( -0.417685 , -0.138953 , -0.17209 ) +colvars: ( -0.358134 , -0.172057 , -0.124013 ) +colvars: ( -0.305606 , -0.267669 , -0.105058 ) +colvars: ( -0.314046 , -0.0946219 , -0.0524217 ) +colvars: ( -0.300883 , -0.0748439 , -0.0322276 ) +colvars: ( -0.291667 , -0.0469035 , -0.0131112 ) +colvars: ( -0.253575 , 0.0325556 , 0.0531774 ) +colvars: ( -0.229602 , 0.0606559 , 0.0871603 ) +colvars: ( -0.299569 , 0.124552 , 0.0395031 ) +colvars: ( -0.271685 , 0.168949 , 0.0831651 ) +colvars: ( -0.372063 , 0.154243 , -0.0227692 ) +colvars: ( -0.423174 , 0.235015 , -0.0455429 ) +colvars: ( -0.497253 , 0.258814 , -0.111487 ) +colvars: ( -0.436869 , 0.213908 , -0.0667411 ) +colvars: ( -0.441615 , 0.278461 , -0.0487097 ) +colvars: ( -0.442934 , 0.121971 , -0.105293 ) +colvars: ( -0.451945 , 0.0899081 , -0.125659 ) +colvars: ( -0.475725 , -0.00922189 , -0.18453 ) +colvars: ( -0.382473 , 0.0780912 , -0.0601077 ) +colvars: ( -0.386644 , 0.106001 , -0.0544383 ) +colvars: ( -0.212447 , 0.11323 , 0.122942 ) +colvars: ( -0.160958 , 0.115321 , 0.175356 ) +colvars: ( -0.238901 , 0.189969 , 0.123491 ) +colvars: ( -0.316543 , 0.0349987 , -0.00915565 ) +colvars: ( -0.246943 , 0.0206943 , 0.0556451 ) +colvars: ( -0.190557 , -0.0673832 , 0.0811333 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 28. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 28. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atoms_new_colvar_forces = { ( -4.90384292994753e+00 , -4.30061181581498e-01 , -1.23057952812698e+00 ), ( -4.22371186491589e+00 , -3.65328134592081e-01 , -9.59528374484244e-01 ), ( -4.29990290450085e+00 , -3.94089117624900e-01 , -9.96370093803767e-01 ), ( -5.78045406497317e+00 , -5.58335320147910e-01 , -1.48688424495571e+00 ), ( 2.65491211108552e-01 , 1.23537620122648e-01 , 3.61030596854383e-01 ), ( 5.28005307439269e+00 , 6.12427671368205e-01 , 1.81509982664923e+00 ), ( 4.46184518444030e+00 , 5.05381939262143e-01 , 1.57515106003945e+00 ), ( -4.85511434600487e-02 , 2.07523457083486e-02 , 3.66427779977786e-01 ), ( 4.44317734724211e+00 , 4.96175596962890e-01 , 1.54457853589311e+00 ), ( 5.88964346729490e+00 , 6.36085627200129e-01 , 1.90417721308489e+00 ), ( 1.27065569628440e-02 , 3.54379029990088e-02 , 3.11858139856113e-01 ), ( 2.40460741769399e-03 , 2.96572082798891e-02 , 2.88001274027708e-01 ), ( 2.60464416327941e-02 , 4.44832211558429e-02 , 3.58314100587555e-01 ), ( 4.76164130373470e-02 , 3.67501453875118e-02 , 2.10352464448447e-01 ), ( 1.91552247804718e-02 , 2.22387880855930e-02 , 1.58999439605174e-01 ), ( 1.19079038755758e-01 , 5.91136525176453e-02 , 1.98887416976434e-01 ), ( 1.67247634293701e-01 , 6.77318328512975e-02 , 1.26749993997087e-01 ), ( 2.50365492999829e-01 , 9.66576024456339e-02 , 1.42497236290738e-01 ), ( 1.35914831022483e-01 , 5.00338541708416e-02 , 5.30301367535333e-02 ), ( 1.31516340541352e-01 , 4.20128478226181e-02 , -1.25578957164632e-02 ), ( 1.10588937804259e-01 , 4.27656964481660e-02 , 6.36515136061283e-02 ), ( 7.21056067747657e-02 , 2.39763933217968e-02 , 2.51627788784559e-03 ), ( 5.70506452097048e-02 , 2.23224487984691e-02 , 3.54353290813819e-02 ), ( -3.49498224547207e-03 , -3.55980944662710e-03 , -2.40438716129163e-02 ), ( -1.80251213873387e-02 , -1.55632398454448e-02 , -9.61061720210136e-02 ), ( -5.22228202101327e-02 , -1.37559842833952e-02 , 3.41854584073593e-02 ), ( -1.22113199988620e-01 , -3.83069555546568e-02 , 1.86646247074351e-02 ), ( -1.64838877506732e-01 , -4.42101195798790e-02 , 1.00022815522024e-01 ), ( -1.07643528114771e-01 , -3.82374689828629e-02 , -2.81415013149803e-02 ), ( -1.45545107039339e-01 , -5.66527208265858e-02 , -8.74544759496076e-02 ), ( -5.07481347952446e-02 , -1.70614277419447e-02 , -3.63442572658323e-03 ), ( -2.75303586094378e-02 , -1.36135315070125e-02 , -4.54508915928700e-02 ), ( 3.26854205876072e-02 , 1.12833999575029e-02 , 5.28033027176517e-03 ), ( 4.86257228490999e-03 , -1.15925166900537e-02 , -1.31622750055179e-01 ), ( -1.30158458610466e-02 , -2.30822092133307e-02 , -1.87568050888589e-01 ), ( 5.22929541320235e-02 , 2.69594482492658e-03 , -1.44763519972368e-01 ), ( 8.18983854683275e-02 , 4.46209863263042e-03 , -2.24327679868213e-01 ), ( 1.44299232500828e-01 , 2.59900880514667e-02 , -2.14381841188795e-01 ), ( 1.94559709679941e-02 , -2.16928875058797e-02 , -2.80301373302201e-01 ), ( 2.05273767674185e-02 , -2.85686888289193e-02 , -3.52419464644292e-01 ), ( -3.70047024666399e-02 , -3.69969429078039e-02 , -2.47649729164660e-01 ), ( -1.02007495861232e-01 , -6.28538507615143e-02 , -2.92244523767052e-01 ), ( -1.42667681901288e-01 , -7.11975564555364e-02 , -2.42016381025123e-01 ), ( -1.60793536960711e-01 , -8.43197125593010e-02 , -3.13436781697989e-01 ), ( -1.90119143852607e-01 , -1.00663821186063e-01 , -3.80237852238786e-01 ), ( -2.00756150443214e-01 , -9.76416131339598e-02 , -3.15166820975150e-01 ), ( -2.43861219043207e-01 , -1.14540863153326e-01 , -3.42272967562807e-01 ), ( -1.23109579423653e-01 , -7.28230655412529e-02 , -3.22437483096700e-01 ), ( -1.80220249912241e-01 , -8.49803842830974e-02 , -2.56256592503782e-01 ), ( -2.34767687699287e-01 , -1.04277862695358e-01 , -2.69728540895261e-01 ), ( -2.71081637300971e-01 , -1.07966939745010e-01 , -1.87327736373501e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 29, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 29, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 29, atoms_positions[size = 51] = { ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 ), ( 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 ), ( 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 ), ( 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 ), ( 7.00574000274244e+00 , -2.06829116643861e+00 , -8.83119811461982e-01 ), ( 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 ), ( 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 ), ( 7.13320400449730e+00 , -3.44298734592438e-01 , 4.38138305680023e+00 ), ( 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 ), ( 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 ), ( 5.84483325162435e+00 , 2.25366187654745e+00 , 2.97407896818342e+00 ), ( 5.16683406263612e+00 , 3.55710110763794e+00 , 2.89359751215032e+00 ), ( 6.30656262174781e+00 , 4.47811840330492e+00 , 2.29216448789625e+00 ), ( 3.85900015836979e+00 , 3.64919255486691e+00 , 2.02919404735743e+00 ), ( 2.80985216815857e+00 , 4.16916506605627e+00 , 2.44083999838906e+00 ), ( 3.91677382204270e+00 , 3.19853200587872e+00 , 7.40288243836124e-01 ), ( 2.75380836420530e+00 , 3.05607818870335e+00 , -7.51581894515900e-02 ), ( 3.11221705383647e+00 , 2.65451308061572e+00 , -1.54064705756131e+00 ), ( 1.55022078277182e+00 , 2.19389175197648e+00 , 4.23731258073612e-01 ), ( 4.03133879451812e-01 , 2.61695797841092e+00 , 4.65936542913617e-01 ), ( 2.07008191781880e+00 , 1.14541073584410e+00 , 1.04438132515448e+00 ), ( 1.21104098873384e+00 , 1.29064314915337e-01 , 1.68806278825048e+00 ), ( 2.07938437129022e+00 , -1.09226055507971e+00 , 2.03807229463835e+00 ), ( 5.75169096535490e-01 , 6.16577762840044e-01 , 2.96044663850816e+00 ), ( -5.85292110472713e-01 , 3.55388149199515e-01 , 3.17720325125777e+00 ), ( 1.28825494086657e+00 , 1.38214738369001e+00 , 3.74916833208051e+00 ), ( 8.64233237372221e-01 , 1.98005512142267e+00 , 5.03174948282925e+00 ), ( 2.09827944546896e+00 , 2.75342470994007e+00 , 5.72413575586123e+00 ), ( -3.55992882575887e-01 , 2.90250467361778e+00 , 4.95954123194611e+00 ), ( -1.11574172694153e+00 , 3.06855139255186e+00 , 5.88010232961502e+00 ), ( -5.43668601286061e-01 , 3.50874101319027e+00 , 3.78937424004920e+00 ), ( -1.47624956703860e+00 , 4.48866017004579e+00 , 3.41423298783339e+00 ), ( -7.31770235550961e-01 , 5.43423902569644e+00 , 2.47675782651417e+00 ), ( -2.74498269317940e+00 , 3.94541871314426e+00 , 2.80114869378689e+00 ), ( -3.80612628970205e+00 , 4.55960025539404e+00 , 2.81304026673475e+00 ), ( -2.68465775625360e+00 , 2.63423256162810e+00 , 2.35669571741840e+00 ), ( -3.79793299657600e+00 , 1.82595829823249e+00 , 2.00564398238562e+00 ), ( -3.35973166964488e+00 , 8.76210294949400e-01 , 8.14326802538322e-01 ), ( -4.25479988283804e+00 , 1.04652539212958e+00 , 3.23552373700253e+00 ), ( -5.47696169161307e+00 , 7.58343767602588e-01 , 3.33830903166301e+00 ), ( -3.37052998783529e+00 , 7.27070269086146e-01 , 4.17273383545135e+00 ), ( -3.67076853636612e+00 , 8.02890411004126e-02 , 5.47818496853563e+00 ), ( -2.38141785804304e+00 , -3.19276966689693e-01 , 6.13524375348765e+00 ), ( -4.47866085407106e+00 , 9.21976672545687e-01 , 6.42118098012691e+00 ), ( -5.36125694717558e+00 , 5.75956580523933e-01 , 7.20372858904930e+00 ), ( -6.30602052652239e+00 , 3.62659966444639e+00 , 6.75243212712343e+00 ), ( -6.99886722165190e+00 , 4.29705609045011e+00 , 7.50843520996675e+00 ), ( -6.65099617909420e+00 , 3.16189006812619e+00 , 5.52741041258270e+00 ), ( -4.10745542008092e+00 , 2.25411177669687e+00 , 6.39414571125951e+00 ), ( -4.81593837698548e+00 , 3.27869885909781e+00 , 7.25161049228686e+00 ), ( -4.02743393174070e+00 , 4.55621888094300e+00 , 7.27220719639921e+00 ) } +colvars: Step 29, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.94448500277034e-01 , -1.14886070422289e-02 , 9.55598290388192e-01 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 7.00574000274244e+00 , -2.06829116643861e+00 , -8.83119811461982e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 , 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 7.13320400449730e+00 , -3.44298734592438e-01 , 4.38138305680023e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 , 5.84483325162435e+00 , 2.25366187654745e+00 , 2.97407896818342e+00 , 5.16683406263612e+00 , 3.55710110763794e+00 , 2.89359751215032e+00 , 6.30656262174781e+00 , 4.47811840330492e+00 , 2.29216448789625e+00 , 3.85900015836979e+00 , 3.64919255486691e+00 , 2.02919404735743e+00 , 2.80985216815857e+00 , 4.16916506605627e+00 , 2.44083999838906e+00 , 3.91677382204270e+00 , 3.19853200587872e+00 , 7.40288243836124e-01 , 2.75380836420530e+00 , 3.05607818870335e+00 , -7.51581894515900e-02 , 3.11221705383647e+00 , 2.65451308061572e+00 , -1.54064705756131e+00 , 1.55022078277182e+00 , 2.19389175197648e+00 , 4.23731258073612e-01 , 4.03133879451812e-01 , 2.61695797841092e+00 , 4.65936542913617e-01 , 2.07008191781880e+00 , 1.14541073584410e+00 , 1.04438132515448e+00 , 1.21104098873384e+00 , 1.29064314915337e-01 , 1.68806278825048e+00 , 2.07938437129022e+00 , -1.09226055507971e+00 , 2.03807229463835e+00 , 5.75169096535490e-01 , 6.16577762840044e-01 , 2.96044663850816e+00 , -5.85292110472713e-01 , 3.55388149199515e-01 , 3.17720325125777e+00 , 1.28825494086657e+00 , 1.38214738369001e+00 , 3.74916833208051e+00 , 8.64233237372221e-01 , 1.98005512142267e+00 , 5.03174948282925e+00 , 2.09827944546896e+00 , 2.75342470994007e+00 , 5.72413575586123e+00 , -3.55992882575887e-01 , 2.90250467361778e+00 , 4.95954123194611e+00 , -1.11574172694153e+00 , 3.06855139255186e+00 , 5.88010232961502e+00 , -5.43668601286061e-01 , 3.50874101319027e+00 , 3.78937424004920e+00 , -1.47624956703860e+00 , 4.48866017004579e+00 , 3.41423298783339e+00 , -7.31770235550961e-01 , 5.43423902569644e+00 , 2.47675782651417e+00 , -2.74498269317940e+00 , 3.94541871314426e+00 , 2.80114869378689e+00 , -3.80612628970205e+00 , 4.55960025539404e+00 , 2.81304026673475e+00 , -2.68465775625360e+00 , 2.63423256162810e+00 , 2.35669571741840e+00 , -3.79793299657600e+00 , 1.82595829823249e+00 , 2.00564398238562e+00 , -3.35973166964488e+00 , 8.76210294949400e-01 , 8.14326802538322e-01 , -4.25479988283804e+00 , 1.04652539212958e+00 , 3.23552373700253e+00 , -5.47696169161307e+00 , 7.58343767602588e-01 , 3.33830903166301e+00 , -3.37052998783529e+00 , 7.27070269086146e-01 , 4.17273383545135e+00 , -3.67076853636612e+00 , 8.02890411004126e-02 , 5.47818496853563e+00 , -2.38141785804304e+00 , -3.19276966689693e-01 , 6.13524375348765e+00 , -4.47866085407106e+00 , 9.21976672545687e-01 , 6.42118098012691e+00 , -5.36125694717558e+00 , 5.75956580523933e-01 , 7.20372858904930e+00 , -6.30602052652239e+00 , 3.62659966444639e+00 , 6.75243212712343e+00 , -6.99886722165190e+00 , 4.29705609045011e+00 , 7.50843520996675e+00 , -6.65099617909420e+00 , 3.16189006812619e+00 , 5.52741041258270e+00 , -4.10745542008092e+00 , 2.25411177669687e+00 , 6.39414571125951e+00 , -4.81593837698548e+00 , 3.27869885909781e+00 , 7.25161049228686e+00 , -4.02743393174070e+00 , 4.55621888094300e+00 , 7.27220719639921e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.94448500277034e-01 , -1.14886070422289e-02 , 9.55598290388192e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.24140141499203e+00 , 4.32314614978802e-02 , -7.27033479207094e-01 , 6.83921517105711e+00 , -5.84828897869708e-01 , -5.29149827488078e-01 , 7.00574000274244e+00 , -2.06829116643861e+00 , -8.83119811461982e-01 , 6.12968714615115e+00 , -3.73839051632670e-01 , 8.00514046519711e-01 , 4.90696185576029e+00 , -1.48361309918792e-01 , 7.43688765344616e-01 , 6.81312981263618e+00 , -2.88059413087962e-01 , 1.96299723620461e+00 , 6.10838678760977e+00 , -2.19130954514834e-01 , 3.17157551935181e+00 , 7.13320400449730e+00 , -3.44298734592438e-01 , 4.38138305680023e+00 , 5.33273438978970e+00 , 1.06968759370690e+00 , 3.36957437190884e+00 , 4.18368000776035e+00 , 1.00721839031286e+00 , 3.77141423681502e+00 , 5.84483325162435e+00 , 2.25366187654745e+00 , 2.97407896818342e+00 , 5.16683406263612e+00 , 3.55710110763794e+00 , 2.89359751215032e+00 , 6.30656262174781e+00 , 4.47811840330492e+00 , 2.29216448789625e+00 , 3.85900015836979e+00 , 3.64919255486691e+00 , 2.02919404735743e+00 , 2.80985216815857e+00 , 4.16916506605627e+00 , 2.44083999838906e+00 , 3.91677382204270e+00 , 3.19853200587872e+00 , 7.40288243836124e-01 , 2.75380836420530e+00 , 3.05607818870335e+00 , -7.51581894515900e-02 , 3.11221705383647e+00 , 2.65451308061572e+00 , -1.54064705756131e+00 , 1.55022078277182e+00 , 2.19389175197648e+00 , 4.23731258073612e-01 , 4.03133879451812e-01 , 2.61695797841092e+00 , 4.65936542913617e-01 , 2.07008191781880e+00 , 1.14541073584410e+00 , 1.04438132515448e+00 , 1.21104098873384e+00 , 1.29064314915337e-01 , 1.68806278825048e+00 , 2.07938437129022e+00 , -1.09226055507971e+00 , 2.03807229463835e+00 , 5.75169096535490e-01 , 6.16577762840044e-01 , 2.96044663850816e+00 , -5.85292110472713e-01 , 3.55388149199515e-01 , 3.17720325125777e+00 , 1.28825494086657e+00 , 1.38214738369001e+00 , 3.74916833208051e+00 , 8.64233237372221e-01 , 1.98005512142267e+00 , 5.03174948282925e+00 , 2.09827944546896e+00 , 2.75342470994007e+00 , 5.72413575586123e+00 , -3.55992882575887e-01 , 2.90250467361778e+00 , 4.95954123194611e+00 , -1.11574172694153e+00 , 3.06855139255186e+00 , 5.88010232961502e+00 , -5.43668601286061e-01 , 3.50874101319027e+00 , 3.78937424004920e+00 , -1.47624956703860e+00 , 4.48866017004579e+00 , 3.41423298783339e+00 , -7.31770235550961e-01 , 5.43423902569644e+00 , 2.47675782651417e+00 , -2.74498269317940e+00 , 3.94541871314426e+00 , 2.80114869378689e+00 , -3.80612628970205e+00 , 4.55960025539404e+00 , 2.81304026673475e+00 , -2.68465775625360e+00 , 2.63423256162810e+00 , 2.35669571741840e+00 , -3.79793299657600e+00 , 1.82595829823249e+00 , 2.00564398238562e+00 , -3.35973166964488e+00 , 8.76210294949400e-01 , 8.14326802538322e-01 , -4.25479988283804e+00 , 1.04652539212958e+00 , 3.23552373700253e+00 , -5.47696169161307e+00 , 7.58343767602588e-01 , 3.33830903166301e+00 , -3.37052998783529e+00 , 7.27070269086146e-01 , 4.17273383545135e+00 , -3.67076853636612e+00 , 8.02890411004126e-02 , 5.47818496853563e+00 , -2.38141785804304e+00 , -3.19276966689693e-01 , 6.13524375348765e+00 , -4.47866085407106e+00 , 9.21976672545687e-01 , 6.42118098012691e+00 , -5.36125694717558e+00 , 5.75956580523933e-01 , 7.20372858904930e+00 , -6.30602052652239e+00 , 3.62659966444639e+00 , 6.75243212712343e+00 , -6.99886722165190e+00 , 4.29705609045011e+00 , 7.50843520996675e+00 , -6.65099617909420e+00 , 3.16189006812619e+00 , 5.52741041258270e+00 , -4.10745542008092e+00 , 2.25411177669687e+00 , 6.39414571125951e+00 , -4.81593837698548e+00 , 3.27869885909781e+00 , 7.25161049228686e+00 , -4.02743393174070e+00 , 4.55621888094300e+00 , 7.27220719639921e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.6468 , 6.56468 , 13.1294 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.6468 , 6.56468 , 13.1294 ) to colvar "one". +colvars: Adding total bias energy: 55.9741 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.6468 , 6.56468 , 13.1294 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.19215 , -0.549244 , -1.48483 ) +colvars: ( -4.45226 , -0.470977 , -1.27324 ) +colvars: ( -4.45226 , -0.470977 , -1.27324 ) +colvars: ( -5.93055 , -0.627354 , -1.696 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.933555 , 0.206463 , 0.64011 ) +colvars: ( 0.809328 , 0.280226 , 0.664886 ) +colvars: ( 0.792255 , 0.273123 , 0.645744 ) +colvars: ( 0.69343 , 0.280516 , 0.598381 ) +colvars: ( 0.681086 , 0.210698 , 0.499951 ) +colvars: ( 0.603789 , 0.361076 , 0.652005 ) +colvars: ( 0.492735 , 0.375235 , 0.606434 ) +colvars: ( 0.413267 , 0.476816 , 0.693419 ) +colvars: ( 0.407719 , 0.328356 , 0.496064 ) +colvars: ( 0.371807 , 0.284561 , 0.418066 ) +colvars: ( 0.37687 , 0.333974 , 0.485609 ) +colvars: ( 0.302685 , 0.288909 , 0.383863 ) +colvars: ( 0.274125 , 0.319413 , 0.407274 ) +colvars: ( 0.367457 , 0.186651 , 0.287512 ) +colvars: ( 0.306545 , 0.141018 , 0.192681 ) +colvars: ( 0.494858 , 0.148324 , 0.31091 ) +colvars: ( 0.570137 , 0.0528469 , 0.229489 ) +colvars: ( 0.704491 , 0.0314211 , 0.279004 ) +colvars: ( 0.579471 , 0.0193324 , 0.191047 ) +colvars: ( 0.563117 , -0.0489236 , 0.0923454 ) +colvars: ( 0.601545 , 0.0694852 , 0.269374 ) +colvars: ( 0.600405 , 0.052347 , 0.246303 ) +colvars: ( 0.638685 , 0.120189 , 0.357117 ) +colvars: ( 0.471451 , 0.0564921 , 0.177306 ) +colvars: ( 0.464545 , -0.00223408 , 0.0965196 ) +colvars: ( 0.365504 , 0.124937 , 0.205675 ) +colvars: ( 0.236292 , 0.133418 , 0.1422 ) +colvars: ( 0.141197 , 0.222994 , 0.204467 ) +colvars: ( 0.206715 , 0.0561406 , 0.0240697 ) +colvars: ( 0.15575 , 0.0179541 , -0.0552811 ) +colvars: ( 0.24115 , 0.0296715 , 0.00932647 ) +colvars: ( 0.22629 , -0.0462448 , -0.0985307 ) +colvars: ( 0.262446 , -0.0493964 , -0.0817871 ) +colvars: ( 0.304549 , -0.136097 , -0.170874 ) +colvars: ( 0.258869 , -0.191943 , -0.270271 ) +colvars: ( 0.424271 , -0.151438 , -0.121847 ) +colvars: ( 0.504857 , -0.230333 , -0.17852 ) +colvars: ( 0.641101 , -0.232543 , -0.102785 ) +colvars: ( 0.456217 , -0.235427 , -0.21325 ) +colvars: ( 0.46203 , -0.30678 , -0.30321 ) +colvars: ( 0.405921 , -0.15892 , -0.142222 ) +colvars: ( 0.350049 , -0.152774 , -0.166428 ) +colvars: ( 0.33321 , -0.0621138 , -0.0575816 ) +colvars: ( 0.222013 , -0.162468 , -0.252993 ) +colvars: ( 0.196915 , -0.2067 , -0.325323 ) +colvars: ( 0.012361 , -0.210925 , -0.437352 ) +colvars: ( -0.0820684 , -0.229936 , -0.516708 ) +colvars: ( 0.116268 , -0.262725 , -0.445131 ) +colvars: ( 0.13679 , -0.120101 , -0.246768 ) +colvars: ( 0.0128574 , -0.12514 , -0.324878 ) +colvars: ( -0.079691 , -0.0408737 , -0.268085 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.19215 , 0.549244 , 1.48483 ) +colvars: ( 4.45226 , 0.470977 , 1.27324 ) +colvars: ( 4.45226 , 0.470977 , 1.27324 ) +colvars: ( 5.93055 , 0.627354 , 1.696 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.645293 , -0.0855079 , -0.381244 ) +colvars: ( -0.580767 , -0.173263 , -0.34712 ) +colvars: ( -0.526819 , -0.149691 , -0.284729 ) +colvars: ( -0.541046 , -0.202411 , -0.317426 ) +colvars: ( -0.53086 , -0.139829 , -0.285341 ) +colvars: ( -0.516416 , -0.300167 , -0.326848 ) +colvars: ( -0.483655 , -0.342984 , -0.308916 ) +colvars: ( -0.462091 , -0.456987 , -0.32709 ) +colvars: ( -0.417152 , -0.305228 , -0.228965 ) +colvars: ( -0.413161 , -0.27836 , -0.215573 ) +colvars: ( -0.364098 , -0.29907 , -0.173554 ) +colvars: ( -0.300056 , -0.259696 , -0.0955096 ) +colvars: ( -0.247693 , -0.275384 , -0.0484223 ) +colvars: ( -0.319606 , -0.150091 , -0.0768493 ) +colvars: ( -0.2871 , -0.118912 , -0.033326 ) +colvars: ( -0.375602 , -0.0892412 , -0.111808 ) +colvars: ( -0.402719 , 0.0150979 , -0.102584 ) +colvars: ( -0.453989 , 0.0655939 , -0.136414 ) +colvars: ( -0.443527 , 0.0309225 , -0.138022 ) +colvars: ( -0.43154 , 0.0912854 , -0.104903 ) +colvars: ( -0.491084 , -0.0266443 , -0.205874 ) +colvars: ( -0.528569 , -0.028328 , -0.244092 ) +colvars: ( -0.582066 , -0.0979911 , -0.322132 ) +colvars: ( -0.475166 , -0.0601092 , -0.201583 ) +colvars: ( -0.482822 , -0.0132967 , -0.192917 ) +colvars: ( -0.417861 , -0.138934 , -0.171589 ) +colvars: ( -0.358468 , -0.172064 , -0.123537 ) +colvars: ( -0.306019 , -0.267761 , -0.104313 ) +colvars: ( -0.314282 , -0.0945364 , -0.0520991 ) +colvars: ( -0.301227 , -0.074742 , -0.0320782 ) +colvars: ( -0.291694 , -0.0467533 , -0.0127323 ) +colvars: ( -0.253484 , 0.0328004 , 0.0534159 ) +colvars: ( -0.22929 , 0.0609474 , 0.0875362 ) +colvars: ( -0.299424 , 0.124878 , 0.0394608 ) +colvars: ( -0.271566 , 0.169325 , 0.0829526 ) +colvars: ( -0.371847 , 0.154584 , -0.0228674 ) +colvars: ( -0.422919 , 0.235424 , -0.0459 ) +colvars: ( -0.496881 , 0.259234 , -0.111833 ) +colvars: ( -0.43683 , 0.21428 , -0.0672517 ) +colvars: ( -0.441577 , 0.278895 , -0.0494469 ) +colvars: ( -0.443085 , 0.122241 , -0.105681 ) +colvars: ( -0.452316 , 0.0901308 , -0.126164 ) +colvars: ( -0.476255 , -0.00911166 , -0.184862 ) +colvars: ( -0.382954 , 0.0783136 , -0.0606604 ) +colvars: ( -0.387224 , 0.106244 , -0.0551903 ) +colvars: ( -0.212865 , 0.113534 , 0.122393 ) +colvars: ( -0.161457 , 0.115635 , 0.174736 ) +colvars: ( -0.239098 , 0.190354 , 0.122893 ) +colvars: ( -0.317013 , 0.0351964 , -0.00952375 ) +colvars: ( -0.247511 , 0.0208901 , 0.055252 ) +colvars: ( -0.191179 , -0.0672623 , 0.0810102 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 29. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 29. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atoms_new_colvar_forces = { ( -4.90388470444026e+00 , -4.28289104919460e-01 , -1.22596789453914e+00 ), ( -4.22370330889374e+00 , -3.64013340286007e-01 , -9.55479082116101e-01 ), ( -4.29988082918930e+00 , -3.92871668764587e-01 , -9.92289815064867e-01 ), ( -5.78032017698676e+00 , -5.56485710829078e-01 , -1.48138875975285e+00 ), ( 2.65436412419126e-01 , 1.23432205013646e-01 , 3.61015504658820e-01 ), ( 5.27951965394827e+00 , 6.10153151808775e-01 , 1.80999086904950e+00 ), ( 4.46134472541105e+00 , 5.03228023946892e-01 , 1.57076293939137e+00 ), ( -4.88243202180547e-02 , 1.98291196022474e-02 , 3.66328893876211e-01 ), ( 4.44283179133334e+00 , 4.94104124514341e-01 , 1.54034330697099e+00 ), ( 5.88919200362309e+00 , 6.33555443350639e-01 , 1.89849095076082e+00 ), ( 1.27722939774814e-02 , 3.49036002064003e-02 , 3.12054682102050e-01 ), ( 2.62855837803455e-03 , 2.92130414109863e-02 , 2.88353353101378e-01 ), ( 2.64321191832927e-02 , 4.40291847042301e-02 , 3.58851302354692e-01 ), ( 4.78510755342696e-02 , 3.65605819176930e-02 , 2.10662183138591e-01 ), ( 1.94446358242152e-02 , 2.21056133467002e-02 , 1.59355152750432e-01 ), ( 1.19255318064586e-01 , 5.90829601993783e-02 , 1.99101529679476e-01 ), ( 1.67417865358364e-01 , 6.79447725851201e-02 , 1.26905750536153e-01 ), ( 2.50502022208297e-01 , 9.70149229774446e-02 , 1.42589273410329e-01 ), ( 1.35944591084775e-01 , 5.02548302993018e-02 , 5.30243228988204e-02 ), ( 1.31577645234685e-01 , 4.23618557494827e-02 , -1.25580151752921e-02 ), ( 1.10460962785987e-01 , 4.28409226539961e-02 , 6.35004209083846e-02 ), ( 7.18360525468564e-02 , 2.40190650859722e-02 , 2.21104358600527e-03 ), ( 5.66185743156440e-02 , 2.21983420701025e-02 , 3.49851238161996e-02 ), ( -3.71501795080909e-03 , -3.61710716139713e-03 , -2.42772046554661e-02 ), ( -1.82774681201741e-02 , -1.55307982010578e-02 , -9.63973408755327e-02 ), ( -5.23566890301552e-02 , -1.39972246478159e-02 , 3.40864271931882e-02 ), ( -1.22175571268548e-01 , -3.86466486191643e-02 , 1.86622092763202e-02 ), ( -1.64822359079624e-01 , -4.47671337353124e-02 , 1.00154681170970e-01 ), ( -1.07567551526852e-01 , -3.83958029009566e-02 , -2.80293564394553e-02 ), ( -1.45476752410774e-01 , -5.67879292724929e-02 , -8.73592958614700e-02 ), ( -5.05441106137904e-02 , -1.70817490308973e-02 , -3.40580986306796e-03 ), ( -2.71933321735205e-02 , -1.34443945792793e-02 , -4.51148137209192e-02 ), ( 3.31567041165365e-02 , 1.15510292059906e-02 , 5.74912202390174e-03 ), ( 5.12548771500154e-03 , -1.12183356352275e-02 , -1.31413667649949e-01 ), ( -1.26969732526753e-02 , -2.26183691537531e-02 , -1.87318333347491e-01 ), ( 5.24245184693471e-02 , 3.14609573447067e-03 , -1.44714743694516e-01 ), ( 8.19383039125556e-02 , 5.09086058050195e-03 , -2.24419711810447e-01 ), ( 1.44220385621418e-01 , 2.66904650807004e-02 , -2.14617859029491e-01 ), ( 1.93864419091029e-02 , -2.11470238825605e-02 , -2.80502113489434e-01 ), ( 2.04525315757620e-02 , -2.78858915037756e-02 , -3.52657316455056e-01 ), ( -3.71632993521555e-02 , -3.66797004597271e-02 , -2.47902622416249e-01 ), ( -1.02267285942677e-01 , -6.26433434786494e-02 , -2.92591665316858e-01 ), ( -1.43045087993155e-01 , -7.12254412658033e-02 , -2.42444060097500e-01 ), ( -1.60941311107296e-01 , -8.41541902437907e-02 , -3.13653263595172e-01 ), ( -1.90309037605197e-01 , -1.00456379160913e-01 , -3.80513460538421e-01 ), ( -2.00504352349957e-01 , -9.73911287359829e-02 , -3.14959089005219e-01 ), ( -2.43524891112127e-01 , -1.14300390862316e-01 , -3.41971994990497e-01 ), ( -1.22830298603008e-01 , -7.23705604781537e-02 , -3.22238645318066e-01 ), ( -1.80222707121762e-01 , -8.49047305933428e-02 , -2.56291639019387e-01 ), ( -2.34653139435091e-01 , -1.04250056839972e-01 , -2.69626339802510e-01 ), ( -2.70870098773619e-01 , -1.08136056803538e-01 , -1.87075129014182e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 30, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 30, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 30, atoms_positions[size = 51] = { ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 ), ( 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 ), ( 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 ), ( 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 ), ( 7.00179272944133e+00 , -2.07095885497099e+00 , -8.75491056010624e-01 ), ( 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 ), ( 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 ), ( 7.13947148087372e+00 , -3.44628618609811e-01 , 4.38752600282718e+00 ), ( 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 ), ( 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 ), ( 5.84769593592378e+00 , 2.25258259280822e+00 , 2.97223352646978e+00 ), ( 5.15712897643352e+00 , 3.55259326287517e+00 , 2.88787080381333e+00 ), ( 6.30263481720254e+00 , 4.47262732959847e+00 , 2.28857170764563e+00 ), ( 3.85884878145450e+00 , 3.64400695573177e+00 , 2.02575330229727e+00 ), ( 2.81492116217015e+00 , 4.16816889347436e+00 , 2.43606553713223e+00 ), ( 3.91221506128496e+00 , 3.19160143027793e+00 , 7.44232253440439e-01 ), ( 2.76018260154900e+00 , 3.06614324543301e+00 , -7.24728508156735e-02 ), ( 3.11761872578935e+00 , 2.65220893877964e+00 , -1.54194181951570e+00 ), ( 1.55052096634640e+00 , 2.20390576899866e+00 , 4.24310057950213e-01 ), ( 4.08967072570339e-01 , 2.61691637371786e+00 , 4.60295766316534e-01 ), ( 2.06471405218342e+00 , 1.14152786367528e+00 , 1.04547520577357e+00 ), ( 1.22363440295663e+00 , 1.34422713256255e-01 , 1.68340962837078e+00 ), ( 2.08296960540123e+00 , -1.09270347969594e+00 , 2.03943454632966e+00 ), ( 5.75140118533064e-01 , 6.15852237276473e-01 , 2.95696634425776e+00 ), ( -5.87337993010753e-01 , 3.56102791107019e-01 , 3.18139678367157e+00 ), ( 1.28686553960385e+00 , 1.38985539851835e+00 , 3.75387808173765e+00 ), ( 8.71581213781113e-01 , 1.97937280596719e+00 , 5.03368878532427e+00 ), ( 2.09091280725987e+00 , 2.75784401097805e+00 , 5.72539968524939e+00 ), ( -3.57768212748633e-01 , 2.90074927861900e+00 , 4.95461545553292e+00 ), ( -1.11554222952123e+00 , 3.06903884572973e+00 , 5.88224856520018e+00 ), ( -5.43470468797353e-01 , 3.50723766989847e+00 , 3.78020889899794e+00 ), ( -1.46908402225090e+00 , 4.48404195684652e+00 , 3.41539030314352e+00 ), ( -7.38749726302167e-01 , 5.43800592755974e+00 , 2.47858102155479e+00 ), ( -2.74614024084795e+00 , 3.94571582605938e+00 , 2.78688191587597e+00 ), ( -3.80456188043702e+00 , 4.56545175952191e+00 , 2.81308347109975e+00 ), ( -2.69031627012295e+00 , 2.63355520190254e+00 , 2.35502689986891e+00 ), ( -3.80117961442763e+00 , 1.82603520976220e+00 , 2.00519120200254e+00 ), ( -3.35743595995106e+00 , 8.77447571394055e-01 , 8.07147138799860e-01 ), ( -4.25203598650743e+00 , 1.04190649943011e+00 , 3.24011232459274e+00 ), ( -5.47081705260917e+00 , 7.52645385579587e-01 , 3.33996390727483e+00 ), ( -3.37088261372906e+00 , 7.28293718826388e-01 , 4.16764293445449e+00 ), ( -3.66962243217793e+00 , 7.96804089726750e-02 , 5.48044598803836e+00 ), ( -2.37718892734588e+00 , -3.15323915248872e-01 , 6.13149608054584e+00 ), ( -4.48261437121052e+00 , 9.22182642162836e-01 , 6.42059748851612e+00 ), ( -5.35984713546564e+00 , 5.71444489587300e-01 , 7.19966823538954e+00 ), ( -6.30875455261292e+00 , 3.62359930558049e+00 , 6.75317130616448e+00 ), ( -7.00531321202099e+00 , 4.29797500437580e+00 , 7.51152444314271e+00 ), ( -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 ), ( -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 ), ( -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 ), ( -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ) } +colvars: Step 30, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 ). +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.93283423674133e-01 , -1.27196382432982e-02 , 9.55940920873742e-01 ). +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group1". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 7.00179272944133e+00 , -2.07095885497099e+00 , -8.75491056010624e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 , 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 7.13947148087372e+00 , -3.44628618609811e-01 , 4.38752600282718e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 , 5.84769593592378e+00 , 2.25258259280822e+00 , 2.97223352646978e+00 , 5.15712897643352e+00 , 3.55259326287517e+00 , 2.88787080381333e+00 , 6.30263481720254e+00 , 4.47262732959847e+00 , 2.28857170764563e+00 , 3.85884878145450e+00 , 3.64400695573177e+00 , 2.02575330229727e+00 , 2.81492116217015e+00 , 4.16816889347436e+00 , 2.43606553713223e+00 , 3.91221506128496e+00 , 3.19160143027793e+00 , 7.44232253440439e-01 , 2.76018260154900e+00 , 3.06614324543301e+00 , -7.24728508156735e-02 , 3.11761872578935e+00 , 2.65220893877964e+00 , -1.54194181951570e+00 , 1.55052096634640e+00 , 2.20390576899866e+00 , 4.24310057950213e-01 , 4.08967072570339e-01 , 2.61691637371786e+00 , 4.60295766316534e-01 , 2.06471405218342e+00 , 1.14152786367528e+00 , 1.04547520577357e+00 , 1.22363440295663e+00 , 1.34422713256255e-01 , 1.68340962837078e+00 , 2.08296960540123e+00 , -1.09270347969594e+00 , 2.03943454632966e+00 , 5.75140118533064e-01 , 6.15852237276473e-01 , 2.95696634425776e+00 , -5.87337993010753e-01 , 3.56102791107019e-01 , 3.18139678367157e+00 , 1.28686553960385e+00 , 1.38985539851835e+00 , 3.75387808173765e+00 , 8.71581213781113e-01 , 1.97937280596719e+00 , 5.03368878532427e+00 , 2.09091280725987e+00 , 2.75784401097805e+00 , 5.72539968524939e+00 , -3.57768212748633e-01 , 2.90074927861900e+00 , 4.95461545553292e+00 , -1.11554222952123e+00 , 3.06903884572973e+00 , 5.88224856520018e+00 , -5.43470468797353e-01 , 3.50723766989847e+00 , 3.78020889899794e+00 , -1.46908402225090e+00 , 4.48404195684652e+00 , 3.41539030314352e+00 , -7.38749726302167e-01 , 5.43800592755974e+00 , 2.47858102155479e+00 , -2.74614024084795e+00 , 3.94571582605938e+00 , 2.78688191587597e+00 , -3.80456188043702e+00 , 4.56545175952191e+00 , 2.81308347109975e+00 , -2.69031627012295e+00 , 2.63355520190254e+00 , 2.35502689986891e+00 , -3.80117961442763e+00 , 1.82603520976220e+00 , 2.00519120200254e+00 , -3.35743595995106e+00 , 8.77447571394055e-01 , 8.07147138799860e-01 , -4.25203598650743e+00 , 1.04190649943011e+00 , 3.24011232459274e+00 , -5.47081705260917e+00 , 7.52645385579587e-01 , 3.33996390727483e+00 , -3.37088261372906e+00 , 7.28293718826388e-01 , 4.16764293445449e+00 , -3.66962243217793e+00 , 7.96804089726750e-02 , 5.48044598803836e+00 , -2.37718892734588e+00 , -3.15323915248872e-01 , 6.13149608054584e+00 , -4.48261437121052e+00 , 9.22182642162836e-01 , 6.42059748851612e+00 , -5.35984713546564e+00 , 5.71444489587300e-01 , 7.19966823538954e+00 , -6.30875455261292e+00 , 3.62359930558049e+00 , 6.75317130616448e+00 , -7.00531321202099e+00 , 4.29797500437580e+00 , 7.51152444314271e+00 , -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 , -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 , -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 , -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.93283423674133e-01 , -1.27196382432982e-02 , 9.55940920873742e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.23387051394085e+00 , 4.35866132345685e-02 , -7.23379518931402e-01 , 6.83395764559833e+00 , -5.91089414177458e-01 , -5.26867516248850e-01 , 7.00179272944133e+00 , -2.07095885497099e+00 , -8.75491056010624e-01 , 6.11844619554635e+00 , -3.66594500965152e-01 , 8.06110774178722e-01 , 4.90544760404356e+00 , -1.49063762224549e-01 , 7.46683558459345e-01 , 6.80941031387781e+00 , -2.92349902978454e-01 , 1.96504835762460e+00 , 6.10077003277008e+00 , -2.23592931295068e-01 , 3.17803416944414e+00 , 7.13947148087372e+00 , -3.44628618609811e-01 , 4.38752600282718e+00 , 5.32828031549080e+00 , 1.06825676317885e+00 , 3.36907522328697e+00 , 4.18676490629667e+00 , 1.00588609446256e+00 , 3.78152103880474e+00 , 5.84769593592378e+00 , 2.25258259280822e+00 , 2.97223352646978e+00 , 5.15712897643352e+00 , 3.55259326287517e+00 , 2.88787080381333e+00 , 6.30263481720254e+00 , 4.47262732959847e+00 , 2.28857170764563e+00 , 3.85884878145450e+00 , 3.64400695573177e+00 , 2.02575330229727e+00 , 2.81492116217015e+00 , 4.16816889347436e+00 , 2.43606553713223e+00 , 3.91221506128496e+00 , 3.19160143027793e+00 , 7.44232253440439e-01 , 2.76018260154900e+00 , 3.06614324543301e+00 , -7.24728508156735e-02 , 3.11761872578935e+00 , 2.65220893877964e+00 , -1.54194181951570e+00 , 1.55052096634640e+00 , 2.20390576899866e+00 , 4.24310057950213e-01 , 4.08967072570339e-01 , 2.61691637371786e+00 , 4.60295766316534e-01 , 2.06471405218342e+00 , 1.14152786367528e+00 , 1.04547520577357e+00 , 1.22363440295663e+00 , 1.34422713256255e-01 , 1.68340962837078e+00 , 2.08296960540123e+00 , -1.09270347969594e+00 , 2.03943454632966e+00 , 5.75140118533064e-01 , 6.15852237276473e-01 , 2.95696634425776e+00 , -5.87337993010753e-01 , 3.56102791107019e-01 , 3.18139678367157e+00 , 1.28686553960385e+00 , 1.38985539851835e+00 , 3.75387808173765e+00 , 8.71581213781113e-01 , 1.97937280596719e+00 , 5.03368878532427e+00 , 2.09091280725987e+00 , 2.75784401097805e+00 , 5.72539968524939e+00 , -3.57768212748633e-01 , 2.90074927861900e+00 , 4.95461545553292e+00 , -1.11554222952123e+00 , 3.06903884572973e+00 , 5.88224856520018e+00 , -5.43470468797353e-01 , 3.50723766989847e+00 , 3.78020889899794e+00 , -1.46908402225090e+00 , 4.48404195684652e+00 , 3.41539030314352e+00 , -7.38749726302167e-01 , 5.43800592755974e+00 , 2.47858102155479e+00 , -2.74614024084795e+00 , 3.94571582605938e+00 , 2.78688191587597e+00 , -3.80456188043702e+00 , 4.56545175952191e+00 , 2.81308347109975e+00 , -2.69031627012295e+00 , 2.63355520190254e+00 , 2.35502689986891e+00 , -3.80117961442763e+00 , 1.82603520976220e+00 , 2.00519120200254e+00 , -3.35743595995106e+00 , 8.77447571394055e-01 , 8.07147138799860e-01 , -4.25203598650743e+00 , 1.04190649943011e+00 , 3.24011232459274e+00 , -5.47081705260917e+00 , 7.52645385579587e-01 , 3.33996390727483e+00 , -3.37088261372906e+00 , 7.28293718826388e-01 , 4.16764293445449e+00 , -3.66962243217793e+00 , 7.96804089726750e-02 , 5.48044598803836e+00 , -2.37718892734588e+00 , -3.15323915248872e-01 , 6.13149608054584e+00 , -4.48261437121052e+00 , 9.22182642162836e-01 , 6.42059748851612e+00 , -5.35984713546564e+00 , 5.71444489587300e-01 , 7.19966823538954e+00 , -6.30875455261292e+00 , 3.62359930558049e+00 , 6.75317130616448e+00 , -7.00531321202099e+00 , 4.29797500437580e+00 , 7.51152444314271e+00 , -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 , -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 , -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 , -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.5967 , 6.55967 , 13.1193 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.5967 , 6.55967 , 13.1193 ) to colvar "one". +colvars: Adding total bias energy: 55.9013 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.5967 , 6.55967 , 13.1193 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.191 , -0.547183 , -1.47905 ) +colvars: ( -4.45128 , -0.46921 , -1.26828 ) +colvars: ( -4.45128 , -0.46921 , -1.26828 ) +colvars: ( -5.92923 , -0.625001 , -1.68939 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.932346 , 0.206377 , 0.638445 ) +colvars: ( 0.808364 , 0.279981 , 0.663164 ) +colvars: ( 0.791301 , 0.272923 , 0.64411 ) +colvars: ( 0.692712 , 0.280195 , 0.5968 ) +colvars: ( 0.680396 , 0.210468 , 0.498605 ) +colvars: ( 0.603259 , 0.360583 , 0.650278 ) +colvars: ( 0.492442 , 0.374646 , 0.604794 ) +colvars: ( 0.413138 , 0.476033 , 0.691557 ) +colvars: ( 0.407588 , 0.327808 , 0.494705 ) +colvars: ( 0.371761 , 0.28404 , 0.416878 ) +colvars: ( 0.376781 , 0.333439 , 0.484309 ) +colvars: ( 0.302734 , 0.288423 , 0.382828 ) +colvars: ( 0.274208 , 0.318908 , 0.406218 ) +colvars: ( 0.367376 , 0.186346 , 0.286716 ) +colvars: ( 0.30659 , 0.140745 , 0.192111 ) +colvars: ( 0.494516 , 0.148142 , 0.310066 ) +colvars: ( 0.569644 , 0.0528405 , 0.228848 ) +colvars: ( 0.703717 , 0.0315265 , 0.27826 ) +colvars: ( 0.578982 , 0.0193411 , 0.190463 ) +colvars: ( 0.562665 , -0.0488283 , 0.0919979 ) +colvars: ( 0.601028 , 0.0694035 , 0.268572 ) +colvars: ( 0.599913 , 0.0522514 , 0.245521 ) +colvars: ( 0.63813 , 0.11999 , 0.356042 ) +colvars: ( 0.471228 , 0.0563151 , 0.176676 ) +colvars: ( 0.464346 , -0.00234667 , 0.0960701 ) +colvars: ( 0.365488 , 0.124619 , 0.204982 ) +colvars: ( 0.236541 , 0.133018 , 0.141651 ) +colvars: ( 0.141629 , 0.222432 , 0.203776 ) +colvars: ( 0.207013 , 0.0558573 , 0.0238263 ) +colvars: ( 0.156162 , 0.0176842 , -0.0553488 ) +colvars: ( 0.241358 , 0.0294788 , 0.00915434 ) +colvars: ( 0.226516 , -0.0463143 , -0.0984203 ) +colvars: ( 0.262575 , -0.0494032 , -0.0816775 ) +colvars: ( 0.304627 , -0.136013 , -0.170599 ) +colvars: ( 0.259041 , -0.191803 , -0.269757 ) +colvars: ( 0.424114 , -0.151285 , -0.121699 ) +colvars: ( 0.504548 , -0.230045 , -0.178247 ) +colvars: ( 0.640519 , -0.232189 , -0.102696 ) +colvars: ( 0.456029 , -0.235192 , -0.212931 ) +colvars: ( 0.461837 , -0.30645 , -0.30268 ) +colvars: ( 0.405848 , -0.158843 , -0.142099 ) +colvars: ( 0.35011 , -0.152769 , -0.166282 ) +colvars: ( 0.333317 , -0.0622691 , -0.0577221 ) +colvars: ( 0.222332 , -0.162509 , -0.252638 ) +colvars: ( 0.197298 , -0.206712 , -0.324813 ) +colvars: ( 0.0130725 , -0.210946 , -0.436504 ) +colvars: ( -0.0811659 , -0.229975 , -0.515669 ) +colvars: ( 0.116757 , -0.262599 , -0.444241 ) +colvars: ( 0.137266 , -0.12022 , -0.246407 ) +colvars: ( 0.0135809 , -0.125308 , -0.324327 ) +colvars: ( -0.0787918 , -0.0411915 , -0.267659 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.191 , 0.547183 , 1.47905 ) +colvars: ( 4.45128 , 0.46921 , 1.26828 ) +colvars: ( 4.45128 , 0.46921 , 1.26828 ) +colvars: ( 5.92923 , 0.625001 , 1.68939 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.644429 , -0.0854198 , -0.37993 ) +colvars: ( -0.580056 , -0.173214 , -0.345616 ) +colvars: ( -0.525945 , -0.149611 , -0.283131 ) +colvars: ( -0.540562 , -0.202376 , -0.316032 ) +colvars: ( -0.530375 , -0.139755 , -0.284174 ) +colvars: ( -0.516134 , -0.300189 , -0.325286 ) +colvars: ( -0.483611 , -0.343029 , -0.307427 ) +colvars: ( -0.462228 , -0.457099 , -0.325353 ) +colvars: ( -0.41712 , -0.305235 , -0.227609 ) +colvars: ( -0.413232 , -0.278353 , -0.214421 ) +colvars: ( -0.363952 , -0.299057 , -0.17209 ) +colvars: ( -0.299897 , -0.259644 , -0.0941589 ) +colvars: ( -0.247415 , -0.275325 , -0.046878 ) +colvars: ( -0.319307 , -0.149975 , -0.0757713 ) +colvars: ( -0.286872 , -0.118772 , -0.0324257 ) +colvars: ( -0.375105 , -0.0890983 , -0.110772 ) +colvars: ( -0.402078 , 0.0152993 , -0.101798 ) +colvars: ( -0.453106 , 0.0658187 , -0.135587 ) +colvars: ( -0.44302 , 0.0311195 , -0.137445 ) +colvars: ( -0.431038 , 0.0915208 , -0.104552 ) +colvars: ( -0.4907 , -0.0264961 , -0.20522 ) +colvars: ( -0.528341 , -0.0281942 , -0.243602 ) +colvars: ( -0.581931 , -0.0979139 , -0.321491 ) +colvars: ( -0.475153 , -0.0599866 , -0.201176 ) +colvars: ( -0.482863 , -0.0131499 , -0.19274 ) +colvars: ( -0.41797 , -0.138847 , -0.170995 ) +colvars: ( -0.358767 , -0.171987 , -0.122995 ) +colvars: ( -0.306425 , -0.26773 , -0.103507 ) +colvars: ( -0.314499 , -0.0944004 , -0.0517483 ) +colvars: ( -0.30156 , -0.0745943 , -0.0319157 ) +colvars: ( -0.291702 , -0.0465781 , -0.0123412 ) +colvars: ( -0.253383 , 0.0330348 , 0.0536317 ) +colvars: ( -0.228969 , 0.0612102 , 0.0878779 ) +colvars: ( -0.299247 , 0.125157 , 0.0393974 ) +colvars: ( -0.271427 , 0.169636 , 0.0826935 ) +colvars: ( -0.371565 , 0.154866 , -0.022956 ) +colvars: ( -0.422574 , 0.235743 , -0.046241 ) +colvars: ( -0.496382 , 0.259552 , -0.112128 ) +colvars: ( -0.436706 , 0.214576 , -0.0677412 ) +colvars: ( -0.441452 , 0.279228 , -0.0501769 ) +colvars: ( -0.443156 , 0.122476 , -0.106028 ) +colvars: ( -0.452613 , 0.0903393 , -0.126623 ) +colvars: ( -0.476708 , -0.00897167 , -0.185118 ) +colvars: ( -0.383397 , 0.0785284 , -0.0612022 ) +colvars: ( -0.387767 , 0.106472 , -0.0559396 ) +colvars: ( -0.213313 , 0.113811 , 0.121765 ) +colvars: ( -0.162011 , 0.115924 , 0.174008 ) +colvars: ( -0.239304 , 0.190677 , 0.122216 ) +colvars: ( -0.317472 , 0.0354017 , -0.00990243 ) +colvars: ( -0.248101 , 0.0211007 , 0.0548143 ) +colvars: ( -0.191851 , -0.0670919 , 0.0808348 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 30. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atoms_new_colvar_forces = { ( -4.90307975326005e+00 , -4.26225733543381e-01 , -1.22053308603671e+00 ), ( -4.22297087183505e+00 , -3.62442494199016e-01 , -9.50735661238479e-01 ), ( -4.29912876445352e+00 , -3.91390533005689e-01 , -9.87515580247239e-01 ), ( -5.77921092303390e+00 , -5.54287649069281e-01 , -1.47495977987086e+00 ), ( 2.65356136002934e-01 , 1.23311593976203e-01 , 3.60978862767604e-01 ), ( 5.27812205617514e+00 , 6.07577602247141e-01 , 1.80404050943655e+00 ), ( 4.46010973872665e+00 , 5.00825927650522e-01 , 1.56565042090778e+00 ), ( -4.90897880799366e-02 , 1.89343442395363e-02 , 3.66203231954696e-01 ), ( 4.44174750876430e+00 , 4.91782779902844e-01 , 1.53537982250556e+00 ), ( 5.88776138997431e+00 , 6.30688490985852e-01 , 1.89184786482823e+00 ), ( 1.28283537456188e-02 , 3.43817190501085e-02 , 3.12219109929325e-01 ), ( 2.83771733227506e-03 , 2.87788165107353e-02 , 2.88669034847300e-01 ), ( 2.67932791979905e-02 , 4.35828210810016e-02 , 3.59340026944051e-01 ), ( 4.80684918524901e-02 , 3.63712934235141e-02 , 2.10944480492789e-01 ), ( 1.97178060164150e-02 , 2.19729176863718e-02 , 1.59685074926066e-01 ), ( 1.19411355480934e-01 , 5.90439089539159e-02 , 1.99294600559298e-01 ), ( 1.67565738963702e-01 , 6.81398575978061e-02 , 1.27049685373802e-01 ), ( 2.50610767595632e-01 , 9.73451889769484e-02 , 1.42672772601171e-01 ), ( 1.35961527713089e-01 , 5.04606763981971e-02 , 5.30179462490662e-02 ), ( 1.31626466862644e-01 , 4.26925863778725e-02 , -1.25537800418007e-02 ), ( 1.10328293789497e-01 , 4.29073593685366e-02 , 6.33528096761839e-02 ), ( 7.15716970003757e-02 , 2.40572059566817e-02 , 1.91907793334617e-03 ), ( 5.61987920052449e-02 , 2.20759052549978e-02 , 3.45506974196925e-02 ), ( -3.92544322628813e-03 , -3.67147461751479e-03 , -2.44998085731401e-02 ), ( -1.85163739274176e-02 , -1.54965444868468e-02 , -9.66701812716143e-02 ), ( -5.24817497216751e-02 , -1.42279729139575e-02 , 3.39871081690175e-02 ), ( -1.22226267813040e-01 , -3.89689410312519e-02 , 1.86552866093206e-02 ), ( -1.64795590399548e-01 , -4.52987029464466e-02 , 1.00269326059522e-01 ), ( -1.07485701129673e-01 , -3.85431349333781e-02 , -2.79219738188176e-02 ), ( -1.45398113546843e-01 , -5.69100868662167e-02 , -8.72644510579588e-02 ), ( -5.03442862864434e-02 , -1.70992094567624e-02 , -3.18690917892174e-03 ), ( -2.68668696109236e-02 , -1.32795723850870e-02 , -4.47886120406747e-02 ), ( 3.36063332857089e-02 , 1.18069508173135e-02 , 6.20045228222160e-03 ), ( 5.37996985271089e-03 , -1.08555182075379e-02 , -1.31201903447125e-01 ), ( -1.23863135856905e-02 , -2.21672711799062e-02 , -1.87063462802220e-01 ), ( 5.25495022970470e-02 , 3.58042204385178e-03 , -1.44654917000879e-01 ), ( 8.19745689427886e-02 , 5.69771351052933e-03 , -2.24488208253491e-01 ), ( 1.44137616563263e-01 , 2.73634872833788e-02 , -2.14824060751566e-01 ), ( 1.93236245879557e-02 , -2.06160606388858e-02 , -2.80672285281673e-01 ), ( 2.03859247467640e-02 , -2.72215389072033e-02 , -3.52857389215979e-01 ), ( -3.73078227940338e-02 , -3.63671480543213e-02 , -2.48127007216322e-01 ), ( -1.02502990872602e-01 , -6.24297787506450e-02 , -2.92904792063159e-01 ), ( -1.43391468186843e-01 , -7.12407323732318e-02 , -2.42839706278146e-01 ), ( -1.61064523353043e-01 , -8.39810555831483e-02 , -3.13840511755964e-01 ), ( -1.90469091696610e-01 , -1.00240151837942e-01 , -3.80752983783105e-01 ), ( -2.00240955151833e-01 , -9.71346913169516e-02 , -3.14739172740795e-01 ), ( -2.43176487154285e-01 , -1.14051226274309e-01 , -3.41661320813026e-01 ), ( -1.22546440124743e-01 , -7.19227416119533e-02 , -3.22024727428344e-01 ), ( -1.80206054113815e-01 , -8.48186453910810e-02 , -2.56309436200485e-01 ), ( -2.34519685297022e-01 , -1.04207509689336e-01 , -2.69512431299437e-01 ), ( -2.70642328820642e-01 , -1.08283450022580e-01 , -1.86824062764667e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 31, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 31, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 31, atoms_positions[size = 51] = { ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 ), ( 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 ), ( 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 ), ( 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ), ( 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 ), ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 ), ( 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 ), ( 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 ), ( 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 ), ( 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ), ( 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 ), ( 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 ), ( 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 ), ( 3.85883200520895e+00 , 3.63922436728402e+00 , 2.02218088752858e+00 ), ( 2.82032938923108e+00 , 4.16685554537813e+00 , 2.43148015867431e+00 ), ( 3.90823079911895e+00 , 3.18438414673290e+00 , 7.48937105961854e-01 ), ( 2.76446920336375e+00 , 3.07649753215611e+00 , -7.04562871516674e-02 ), ( 3.12275971679476e+00 , 2.65114321973004e+00 , -1.54195140972224e+00 ), ( 1.55413078649145e+00 , 2.21490189090784e+00 , 4.25503959006978e-01 ), ( 4.14270175753656e-01 , 2.61655984189511e+00 , 4.54613742887889e-01 ), ( 2.05834193471718e+00 , 1.13607220316182e+00 , 1.04677734263664e+00 ), ( 1.23685466879391e+00 , 1.40361714181966e-01 , 1.67860069408059e+00 ), ( 2.08624910163651e+00 , -1.09313299449642e+00 , 2.04004343834517e+00 ), ( 5.74788204227826e-01 , 6.15318561758292e-01 , 2.95283366787829e+00 ), ( -5.89937439010981e-01 , 3.56749652514227e-01 , 3.18586841039378e+00 ), ( 1.28605494288232e+00 , 1.39766210774256e+00 , 3.75927316980631e+00 ), ( 8.79300716591884e-01 , 1.97906955320727e+00 , 5.03609181574402e+00 ), ( 2.08238116459080e+00 , 2.76179089252899e+00 , 5.72607895327535e+00 ), ( -3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 ), ( -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 ), ( -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 ), ( -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 ), ( -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 ), ( -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 ), ( -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 ), ( -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 ), ( -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 ), ( -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 ), ( -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 ), ( -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 ), ( -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 ), ( -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 ), ( -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 ), ( -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 ), ( -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 ), ( -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 ), ( -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 ), ( -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 ), ( -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 ), ( -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 ), ( -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ) } +colvars: Step 31, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.91985130036785e-01 , -1.38601172701375e-02 , 9.56322425224181e-01 ). +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 , 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 , 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 , 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 , 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 , 3.85883200520895e+00 , 3.63922436728402e+00 , 2.02218088752858e+00 , 2.82032938923108e+00 , 4.16685554537813e+00 , 2.43148015867431e+00 , 3.90823079911895e+00 , 3.18438414673290e+00 , 7.48937105961854e-01 , 2.76446920336375e+00 , 3.07649753215611e+00 , -7.04562871516674e-02 , 3.12275971679476e+00 , 2.65114321973004e+00 , -1.54195140972224e+00 , 1.55413078649145e+00 , 2.21490189090784e+00 , 4.25503959006978e-01 , 4.14270175753656e-01 , 2.61655984189511e+00 , 4.54613742887889e-01 , 2.05834193471718e+00 , 1.13607220316182e+00 , 1.04677734263664e+00 , 1.23685466879391e+00 , 1.40361714181966e-01 , 1.67860069408059e+00 , 2.08624910163651e+00 , -1.09313299449642e+00 , 2.04004343834517e+00 , 5.74788204227826e-01 , 6.15318561758292e-01 , 2.95283366787829e+00 , -5.89937439010981e-01 , 3.56749652514227e-01 , 3.18586841039378e+00 , 1.28605494288232e+00 , 1.39766210774256e+00 , 3.75927316980631e+00 , 8.79300716591884e-01 , 1.97906955320727e+00 , 5.03609181574402e+00 , 2.08238116459080e+00 , 2.76179089252899e+00 , 5.72607895327535e+00 , -3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 , -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 , -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 , -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 , -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 , -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 , -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 , -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 , -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 , -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 , -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 , -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 , -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 , -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 , -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 , -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 , -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 , -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 , -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 , -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 , -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 , -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 , -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.91985130036785e-01 , -1.38601172701375e-02 , 9.56322425224181e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 , 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 , 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 , 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 , 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 , 3.85883200520895e+00 , 3.63922436728402e+00 , 2.02218088752858e+00 , 2.82032938923108e+00 , 4.16685554537813e+00 , 2.43148015867431e+00 , 3.90823079911895e+00 , 3.18438414673290e+00 , 7.48937105961854e-01 , 2.76446920336375e+00 , 3.07649753215611e+00 , -7.04562871516674e-02 , 3.12275971679476e+00 , 2.65114321973004e+00 , -1.54195140972224e+00 , 1.55413078649145e+00 , 2.21490189090784e+00 , 4.25503959006978e-01 , 4.14270175753656e-01 , 2.61655984189511e+00 , 4.54613742887889e-01 , 2.05834193471718e+00 , 1.13607220316182e+00 , 1.04677734263664e+00 , 1.23685466879391e+00 , 1.40361714181966e-01 , 1.67860069408059e+00 , 2.08624910163651e+00 , -1.09313299449642e+00 , 2.04004343834517e+00 , 5.74788204227826e-01 , 6.15318561758292e-01 , 2.95283366787829e+00 , -5.89937439010981e-01 , 3.56749652514227e-01 , 3.18586841039378e+00 , 1.28605494288232e+00 , 1.39766210774256e+00 , 3.75927316980631e+00 , 8.79300716591884e-01 , 1.97906955320727e+00 , 5.03609181574402e+00 , 2.08238116459080e+00 , 2.76179089252899e+00 , 5.72607895327535e+00 , -3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 , -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 , -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 , -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 , -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 , -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 , -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 , -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 , -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 , -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 , -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 , -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 , -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 , -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 , -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 , -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 , -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 , -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 , -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 , -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 , -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 , -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 , -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.54 , 6.554 , 13.108 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.54 , 6.554 , 13.108 ) to colvar "one". +colvars: Adding total bias energy: 55.8186 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.54 , 6.554 , 13.108 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.189 , -0.544804 , -1.47232 ) +colvars: ( -4.44957 , -0.467169 , -1.26252 ) +colvars: ( -4.44957 , -0.467169 , -1.26252 ) +colvars: ( -5.92695 , -0.622283 , -1.68171 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.930911 , 0.20625 , 0.636538 ) +colvars: ( 0.80721 , 0.279668 , 0.661201 ) +colvars: ( 0.790157 , 0.272663 , 0.642249 ) +colvars: ( 0.691838 , 0.279795 , 0.594997 ) +colvars: ( 0.679555 , 0.210179 , 0.497067 ) +colvars: ( 0.602599 , 0.359978 , 0.648316 ) +colvars: ( 0.492055 , 0.373929 , 0.602931 ) +colvars: ( 0.412938 , 0.475086 , 0.689449 ) +colvars: ( 0.407387 , 0.327149 , 0.493166 ) +colvars: ( 0.371657 , 0.283416 , 0.41553 ) +colvars: ( 0.376626 , 0.332796 , 0.482841 ) +colvars: ( 0.302739 , 0.287844 , 0.381662 ) +colvars: ( 0.274252 , 0.318307 , 0.405035 ) +colvars: ( 0.367231 , 0.185985 , 0.285815 ) +colvars: ( 0.306589 , 0.140427 , 0.191466 ) +colvars: ( 0.494073 , 0.147924 , 0.309106 ) +colvars: ( 0.569027 , 0.0528321 , 0.22811 ) +colvars: ( 0.70278 , 0.0316464 , 0.277403 ) +colvars: ( 0.578371 , 0.0193509 , 0.189785 ) +colvars: ( 0.562095 , -0.0487117 , 0.0915853 ) +colvars: ( 0.600385 , 0.0693014 , 0.267646 ) +colvars: ( 0.599299 , 0.0521327 , 0.244612 ) +colvars: ( 0.637443 , 0.119742 , 0.3548 ) +colvars: ( 0.47092 , 0.0561049 , 0.175943 ) +colvars: ( 0.464067 , -0.00247766 , 0.0955378 ) +colvars: ( 0.365418 , 0.124243 , 0.204185 ) +colvars: ( 0.236774 , 0.13255 , 0.141022 ) +colvars: ( 0.142071 , 0.22177 , 0.202993 ) +colvars: ( 0.207302 , 0.0555329 , 0.0235434 ) +colvars: ( 0.156581 , 0.0173793 , -0.0554341 ) +colvars: ( 0.241544 , 0.0292629 , 0.0089535 ) +colvars: ( 0.226724 , -0.046379 , -0.0983013 ) +colvars: ( 0.262671 , -0.0493937 , -0.0815566 ) +colvars: ( 0.304665 , -0.135895 , -0.170302 ) +colvars: ( 0.259187 , -0.191614 , -0.269189 ) +colvars: ( 0.423883 , -0.15109 , -0.121551 ) +colvars: ( 0.504145 , -0.229688 , -0.177966 ) +colvars: ( 0.639803 , -0.231759 , -0.102628 ) +colvars: ( 0.455764 , -0.234899 , -0.212599 ) +colvars: ( 0.461566 , -0.306038 , -0.302114 ) +colvars: ( 0.405713 , -0.158739 , -0.141987 ) +colvars: ( 0.350128 , -0.152749 , -0.166146 ) +colvars: ( 0.333387 , -0.0624439 , -0.0579083 ) +colvars: ( 0.222646 , -0.162539 , -0.252261 ) +colvars: ( 0.197685 , -0.206702 , -0.324263 ) +colvars: ( 0.0138353 , -0.210938 , -0.435556 ) +colvars: ( -0.0801846 , -0.229983 , -0.514502 ) +colvars: ( 0.117266 , -0.262419 , -0.443249 ) +colvars: ( 0.137759 , -0.120339 , -0.246015 ) +colvars: ( 0.0143571 , -0.12548 , -0.323714 ) +colvars: ( -0.0778146 , -0.0415406 , -0.26718 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.189 , 0.544804 , 1.47232 ) +colvars: ( 4.44957 , 0.467169 , 1.26252 ) +colvars: ( 4.44957 , 0.467169 , 1.26252 ) +colvars: ( 5.92695 , 0.622283 , 1.68171 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.643354 , -0.0853105 , -0.378373 ) +colvars: ( -0.579171 , -0.173105 , -0.343885 ) +colvars: ( -0.524912 , -0.149487 , -0.281335 ) +colvars: ( -0.539931 , -0.20226 , -0.31443 ) +colvars: ( -0.529746 , -0.139626 , -0.282823 ) +colvars: ( -0.515725 , -0.300083 , -0.323511 ) +colvars: ( -0.483467 , -0.342921 , -0.305739 ) +colvars: ( -0.462281 , -0.457004 , -0.323404 ) +colvars: ( -0.417016 , -0.305106 , -0.2261 ) +colvars: ( -0.413239 , -0.278216 , -0.213128 ) +colvars: ( -0.363753 , -0.298916 , -0.170499 ) +colvars: ( -0.29971 , -0.259483 , -0.0927249 ) +colvars: ( -0.247128 , -0.275156 , -0.0452702 ) +colvars: ( -0.318967 , -0.1498 , -0.0746245 ) +colvars: ( -0.286619 , -0.118584 , -0.0314847 ) +colvars: ( -0.374531 , -0.0889273 , -0.109646 ) +colvars: ( -0.401342 , 0.0154809 , -0.100933 ) +colvars: ( -0.452096 , 0.0659954 , -0.134659 ) +colvars: ( -0.442409 , 0.0312965 , -0.136775 ) +colvars: ( -0.430436 , 0.0917109 , -0.10413 ) +colvars: ( -0.490195 , -0.0263381 , -0.204436 ) +colvars: ( -0.527984 , -0.0280429 , -0.242967 ) +colvars: ( -0.581647 , -0.0977853 , -0.320662 ) +colvars: ( -0.475043 , -0.059827 , -0.200651 ) +colvars: ( -0.482805 , -0.0129832 , -0.192456 ) +colvars: ( -0.418013 , -0.138687 , -0.170296 ) +colvars: ( -0.359036 , -0.171818 , -0.122378 ) +colvars: ( -0.306827 , -0.267566 , -0.102631 ) +colvars: ( -0.314699 , -0.0942094 , -0.0513639 ) +colvars: ( -0.301888 , -0.0743957 , -0.0317357 ) +colvars: ( -0.291694 , -0.0463761 , -0.0119346 ) +colvars: ( -0.253279 , 0.0332576 , 0.053825 ) +colvars: ( -0.228644 , 0.0614407 , 0.088184 ) +colvars: ( -0.299042 , 0.125385 , 0.0393137 ) +colvars: ( -0.271275 , 0.169878 , 0.0823858 ) +colvars: ( -0.371218 , 0.155082 , -0.0230309 ) +colvars: ( -0.422139 , 0.235961 , -0.046561 ) +colvars: ( -0.495753 , 0.259757 , -0.112364 ) +colvars: ( -0.436495 , 0.214791 , -0.068204 ) +colvars: ( -0.441237 , 0.279452 , -0.050895 ) +colvars: ( -0.443148 , 0.122675 , -0.106327 ) +colvars: ( -0.452837 , 0.0905332 , -0.127027 ) +colvars: ( -0.477085 , -0.00879841 , -0.185284 ) +colvars: ( -0.383803 , 0.0787369 , -0.0617281 ) +colvars: ( -0.388277 , 0.106685 , -0.0566816 ) +colvars: ( -0.2138 , 0.114063 , 0.121052 ) +colvars: ( -0.162631 , 0.116188 , 0.173164 ) +colvars: ( -0.239525 , 0.190933 , 0.121456 ) +colvars: ( -0.317925 , 0.0356172 , -0.0102892 ) +colvars: ( -0.248721 , 0.0213301 , 0.054331 ) +colvars: ( -0.192581 , -0.0668646 , 0.0806049 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 31. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 31. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atoms_new_colvar_forces = { ( -4.90144222016788e+00 , -4.23864257099841e-01 , -1.21415720448235e+00 ), ( -4.22152714599171e+00 , -3.60606652926227e-01 , -9.45200369488746e-01 ), ( -4.29765787123894e+00 , -3.89634933189831e-01 , -9.81949458363150e-01 ), ( -5.77714122557610e+00 , -5.51729841418288e-01 , -1.46746457308585e+00 ), ( 2.65244985751738e-01 , 1.23175919990679e-01 , 3.60913931938642e-01 ), ( 5.27587366386101e+00 , 6.04699578189318e-01 , 1.79712677627654e+00 ), ( 4.45815359902672e+00 , 4.98177747468405e-01 , 1.55970854735073e+00 ), ( -4.93435107962240e-02 , 1.80818210618536e-02 , 3.66044731198671e-01 ), ( 4.43993612550304e+00 , 4.89212550815491e-01 , 1.52958148500933e+00 ), ( 5.88536791075441e+00 , 6.27482878378142e-01 , 1.88410969097645e+00 ), ( 1.28728543357713e-02 , 3.38800306994377e-02 , 3.12342235519133e-01 ), ( 3.02822265175950e-03 , 2.83610379603259e-02 , 2.88937327860488e-01 ), ( 2.71231346340420e-02 , 4.31506543398560e-02 , 3.59765182140659e-01 ), ( 4.82639070398871e-02 , 3.61848084920411e-02 , 2.11190624263480e-01 ), ( 1.99698947164141e-02 , 2.18425541911243e-02 , 1.59980804519905e-01 ), ( 1.19541803339789e-01 , 5.89963159669183e-02 , 1.99459627645205e-01 ), ( 1.67685179467105e-01 , 6.83130744210906e-02 , 1.27177181741412e-01 ), ( 2.50684414945042e-01 , 9.76418262240051e-02 , 1.42743844983514e-01 ), ( 1.35962352709605e-01 , 5.06474272574466e-02 , 5.30102049910314e-02 ), ( 1.31659305261756e-01 , 4.29992197584826e-02 , -1.25447496959555e-02 ), ( 1.10190365494213e-01 , 4.29633137144669e-02 , 6.32097506790836e-02 ), ( 7.13148945687689e-02 , 2.40898048632275e-02 , 1.64489252262806e-03 ), ( 5.57961860012975e-02 , 2.19566534196813e-02 , 3.41379911528583e-02 ), ( -4.12301707828355e-03 , -3.72205361655326e-03 , -2.47077891875423e-02 ), ( -1.87376859605212e-02 , -1.54608598283945e-02 , -9.69185106205518e-02 ), ( -5.25951259489728e-02 , -1.44444125662340e-02 , 3.38881817813012e-02 ), ( -1.22261978100019e-01 , -3.92681995555317e-02 , 1.86433422852362e-02 ), ( -1.64755694359793e-01 , -4.57957779646179e-02 , 1.00362561077624e-01 ), ( -1.07396813606457e-01 , -3.86765688817021e-02 , -2.78205718323948e-02 ), ( -1.45307020710455e-01 , -5.70164349484808e-02 , -8.71697605177388e-02 ), ( -5.01505174429595e-02 , -1.71132398292599e-02 , -2.98106270317924e-03 ), ( -2.65550870531150e-02 , -1.31213981811457e-02 , -4.44763148658900e-02 ), ( 3.40269595685157e-02 , 1.20470666639079e-02 , 6.62740678459722e-03 ), ( 5.62248896412298e-03 , -1.05095785421364e-02 , -1.30987834272355e-01 ), ( -1.20877032066805e-02 , -2.17356493494404e-02 , -1.86803299055070e-01 ), ( 5.26653065073497e-02 , 3.99204202264597e-03 , -1.44581740234569e-01 ), ( 8.20054579045542e-02 , 6.27299736081671e-03 , -2.24527154211662e-01 ), ( 1.44049600904254e-01 , 2.79981112550022e-02 , -2.14992441317378e-01 ), ( 1.92687340086861e-02 , -2.01081097732543e-02 , -2.80803235316266e-01 ), ( 2.03289853616425e-02 , -2.65857576566909e-02 , -3.53009021152050e-01 ), ( -3.74347269455836e-02 , -3.60637435431861e-02 , -2.48314209794155e-01 ), ( -1.02708217603532e-01 , -6.22157029994321e-02 , -2.93173037870197e-01 ), ( -1.43698052848084e-01 , -7.12422629468525e-02 , -2.43192352918266e-01 ), ( -1.61157131361194e-01 , -8.38018816078552e-02 , -3.13989221872837e-01 ), ( -1.90591925485021e-01 , -1.00017171316205e-01 , -3.80944937908953e-01 ), ( -1.99964764452263e-01 , -9.68749058109831e-02 , -3.14503989721018e-01 ), ( -2.42815078108033e-01 , -1.13795597600375e-01 , -3.41338735400356e-01 ), ( -1.22258752994438e-01 , -7.14855908353005e-02 , -3.21792260756661e-01 ), ( -1.80166041310635e-01 , -8.47222792156294e-02 , -2.56304520193778e-01 ), ( -2.34363599989835e-01 , -1.04149378931977e-01 , -2.69383160504516e-01 ), ( -2.70395424944746e-01 , -1.08405194378942e-01 , -1.86574805355087e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 32, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 32, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 32, atoms_positions[size = 51] = { ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 ), ( 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 ), ( 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 ), ( 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 ), ( 6.99636965808843e+00 , -2.07731145361172e+00 , -8.59449502083637e-01 ), ( 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 ), ( 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 ), ( 7.14955265421951e+00 , -3.46986465905089e-01 , 4.39885094483582e+00 ), ( 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 ), ( 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 ), ( 5.85317742297030e+00 , 2.25152071574275e+00 , 2.96821115597796e+00 ), ( 5.14128268036406e+00 , 3.54208563801708e+00 , 2.87632129489601e+00 ), ( 6.29318546387223e+00 , 4.46027939653308e+00 , 2.28475137700503e+00 ), ( 3.85890832969753e+00 , 3.63483645880957e+00 , 2.01856465892203e+00 ), ( 2.82598393890567e+00 , 4.16526878663514e+00 , 2.42710952820913e+00 ), ( 3.90497564120259e+00 , 3.17691629066992e+00 , 7.54347976532677e-01 ), ( 2.76665453227033e+00 , 3.08712116761594e+00 , -6.92647638868437e-02 ), ( 3.12766530233767e+00 , 2.65125298941404e+00 , -1.54062208706149e+00 ), ( 1.56108836342069e+00 , 2.22646006317573e+00 , 4.27466820905454e-01 ), ( 4.18892362207154e-01 , 2.61601125231008e+00 , 4.48886833088300e-01 ), ( 2.05137669540285e+00 , 1.12973908190385e+00 , 1.04787473634801e+00 ), ( 1.25016168604201e+00 , 1.46524404541997e-01 , 1.67395149106674e+00 ), ( 2.08919058564287e+00 , -1.09348074895053e+00 , 2.03987423391713e+00 ), ( 5.74186168979523e-01 , 6.15190892667854e-01 , 2.94836413187145e+00 ), ( -5.92978661025754e-01 , 3.57307762930446e-01 , 3.19051283305154e+00 ), ( 1.28581112343911e+00 , 1.40531159189369e+00 , 3.76496783945832e+00 ), ( 8.87110543080602e-01 , 1.97925651490093e+00 , 5.03898868931191e+00 ), ( 2.07315291122048e+00 , 2.76534667037865e+00 , 5.72630877966077e+00 ), ( -3.59890086708776e-01 , 2.89715477683727e+00 , 4.94292409024734e+00 ), ( -1.11619198406425e+00 , 3.06996673284450e+00 , 5.88764729411060e+00 ), ( -5.39828293654177e-01 , 3.50182389775589e+00 , 3.76181263491333e+00 ), ( -1.45737995469276e+00 , 4.47774979548157e+00 , 3.41742259521307e+00 ), ( -7.52656402540314e-01 , 5.44714686176258e+00 , 2.48230963624217e+00 ), ( -2.74903816285443e+00 , 3.94197213054861e+00 , 2.75948540916468e+00 ), ( -3.80126368217889e+00 , 4.57734229189021e+00 , 2.81260271492884e+00 ), ( -2.69983596459315e+00 , 2.63637902047927e+00 , 2.35275320372801e+00 ), ( -3.80812945779466e+00 , 1.82100657589145e+00 , 2.00251302485744e+00 ), ( -3.35273987959584e+00 , 8.82670239652218e-01 , 7.92872005460967e-01 ), ( -4.25289060329676e+00 , 1.03322899973819e+00 , 3.24599742591875e+00 ), ( -5.45585612158692e+00 , 7.41707491159396e-01 , 3.34406841611962e+00 ), ( -3.36965129496242e+00 , 7.27336540574501e-01 , 4.16165346261809e+00 ), ( -3.66759582428271e+00 , 7.58826722683877e-02 , 5.47907665313511e+00 ), ( -2.36653676520567e+00 , -3.04791642260045e-01 , 6.12630281893083e+00 ), ( -4.48930593261884e+00 , 9.29643058404834e-01 , 6.42030281138112e+00 ), ( -5.35733093367902e+00 , 5.60676121557277e-01 , 7.19103315777678e+00 ), ( -6.30836676717657e+00 , 3.61567551810552e+00 , 6.75690769854272e+00 ), ( -7.01923456785992e+00 , 4.29968920159194e+00 , 7.51639637407081e+00 ), ( -6.62521134252802e+00 , 3.16456400975179e+00 , 5.54286904467815e+00 ), ( -4.10800032264489e+00 , 2.25520167794132e+00 , 6.40478878792620e+00 ), ( -4.81497251925987e+00 , 3.28690173612652e+00 , 7.23378205285441e+00 ), ( -4.01261784991035e+00 , 4.58020866242027e+00 , 7.27629588974665e+00 ) } +colvars: Step 32, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 ). +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 ). +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.90537915957777e-01 , -1.48938555217606e-02 , 9.56747559421297e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.99636965808843e+00 , -2.07731145361172e+00 , -8.59449502083637e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 , 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 7.14955265421951e+00 , -3.46986465905089e-01 , 4.39885094483582e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 , 5.85317742297030e+00 , 2.25152071574275e+00 , 2.96821115597796e+00 , 5.14128268036406e+00 , 3.54208563801708e+00 , 2.87632129489601e+00 , 6.29318546387223e+00 , 4.46027939653308e+00 , 2.28475137700503e+00 , 3.85890832969753e+00 , 3.63483645880957e+00 , 2.01856465892203e+00 , 2.82598393890567e+00 , 4.16526878663514e+00 , 2.42710952820913e+00 , 3.90497564120259e+00 , 3.17691629066992e+00 , 7.54347976532677e-01 , 2.76665453227033e+00 , 3.08712116761594e+00 , -6.92647638868437e-02 , 3.12766530233767e+00 , 2.65125298941404e+00 , -1.54062208706149e+00 , 1.56108836342069e+00 , 2.22646006317573e+00 , 4.27466820905454e-01 , 4.18892362207154e-01 , 2.61601125231008e+00 , 4.48886833088300e-01 , 2.05137669540285e+00 , 1.12973908190385e+00 , 1.04787473634801e+00 , 1.25016168604201e+00 , 1.46524404541997e-01 , 1.67395149106674e+00 , 2.08919058564287e+00 , -1.09348074895053e+00 , 2.03987423391713e+00 , 5.74186168979523e-01 , 6.15190892667854e-01 , 2.94836413187145e+00 , -5.92978661025754e-01 , 3.57307762930446e-01 , 3.19051283305154e+00 , 1.28581112343911e+00 , 1.40531159189369e+00 , 3.76496783945832e+00 , 8.87110543080602e-01 , 1.97925651490093e+00 , 5.03898868931191e+00 , 2.07315291122048e+00 , 2.76534667037865e+00 , 5.72630877966077e+00 , -3.59890086708776e-01 , 2.89715477683727e+00 , 4.94292409024734e+00 , -1.11619198406425e+00 , 3.06996673284450e+00 , 5.88764729411060e+00 , -5.39828293654177e-01 , 3.50182389775589e+00 , 3.76181263491333e+00 , -1.45737995469276e+00 , 4.47774979548157e+00 , 3.41742259521307e+00 , -7.52656402540314e-01 , 5.44714686176258e+00 , 2.48230963624217e+00 , -2.74903816285443e+00 , 3.94197213054861e+00 , 2.75948540916468e+00 , -3.80126368217889e+00 , 4.57734229189021e+00 , 2.81260271492884e+00 , -2.69983596459315e+00 , 2.63637902047927e+00 , 2.35275320372801e+00 , -3.80812945779466e+00 , 1.82100657589145e+00 , 2.00251302485744e+00 , -3.35273987959584e+00 , 8.82670239652218e-01 , 7.92872005460967e-01 , -4.25289060329676e+00 , 1.03322899973819e+00 , 3.24599742591875e+00 , -5.45585612158692e+00 , 7.41707491159396e-01 , 3.34406841611962e+00 , -3.36965129496242e+00 , 7.27336540574501e-01 , 4.16165346261809e+00 , -3.66759582428271e+00 , 7.58826722683877e-02 , 5.47907665313511e+00 , -2.36653676520567e+00 , -3.04791642260045e-01 , 6.12630281893083e+00 , -4.48930593261884e+00 , 9.29643058404834e-01 , 6.42030281138112e+00 , -5.35733093367902e+00 , 5.60676121557277e-01 , 7.19103315777678e+00 , -6.30836676717657e+00 , 3.61567551810552e+00 , 6.75690769854272e+00 , -7.01923456785992e+00 , 4.29968920159194e+00 , 7.51639637407081e+00 , -6.62521134252802e+00 , 3.16456400975179e+00 , 5.54286904467815e+00 , -4.10800032264489e+00 , 2.25520167794132e+00 , 6.40478878792620e+00 , -4.81497251925987e+00 , 3.28690173612652e+00 , 7.23378205285441e+00 , -4.01261784991035e+00 , 4.58020866242027e+00 , 7.27629588974665e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.90537915957777e-01 , -1.48938555217606e-02 , 9.56747559421297e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.99636965808843e+00 , -2.07731145361172e+00 , -8.59449502083637e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 8.13892335246470e-01 , 4.90195452297008e+00 , -1.50969954934607e-01 , 7.53327274849284e-01 , 6.80206083914832e+00 , -3.00698036673864e-01 , 1.96609971161351e+00 , 6.08865478282285e+00 , -2.30902226586820e-01 , 3.19738008499610e+00 , 7.14955265421951e+00 , -3.46986465905089e-01 , 4.39885094483582e+00 , 5.31873232170359e+00 , 1.06621271802952e+00 , 3.36693630642323e+00 , 4.19229185739994e+00 , 1.00392190964589e+00 , 3.80256102082976e+00 , 5.85317742297030e+00 , 2.25152071574275e+00 , 2.96821115597796e+00 , 5.14128268036406e+00 , 3.54208563801708e+00 , 2.87632129489601e+00 , 6.29318546387223e+00 , 4.46027939653308e+00 , 2.28475137700503e+00 , 3.85890832969753e+00 , 3.63483645880957e+00 , 2.01856465892203e+00 , 2.82598393890567e+00 , 4.16526878663514e+00 , 2.42710952820913e+00 , 3.90497564120259e+00 , 3.17691629066992e+00 , 7.54347976532677e-01 , 2.76665453227033e+00 , 3.08712116761594e+00 , -6.92647638868437e-02 , 3.12766530233767e+00 , 2.65125298941404e+00 , -1.54062208706149e+00 , 1.56108836342069e+00 , 2.22646006317573e+00 , 4.27466820905454e-01 , 4.18892362207154e-01 , 2.61601125231008e+00 , 4.48886833088300e-01 , 2.05137669540285e+00 , 1.12973908190385e+00 , 1.04787473634801e+00 , 1.25016168604201e+00 , 1.46524404541997e-01 , 1.67395149106674e+00 , 2.08919058564287e+00 , -1.09348074895053e+00 , 2.03987423391713e+00 , 5.74186168979523e-01 , 6.15190892667854e-01 , 2.94836413187145e+00 , -5.92978661025754e-01 , 3.57307762930446e-01 , 3.19051283305154e+00 , 1.28581112343911e+00 , 1.40531159189369e+00 , 3.76496783945832e+00 , 8.87110543080602e-01 , 1.97925651490093e+00 , 5.03898868931191e+00 , 2.07315291122048e+00 , 2.76534667037865e+00 , 5.72630877966077e+00 , -3.59890086708776e-01 , 2.89715477683727e+00 , 4.94292409024734e+00 , -1.11619198406425e+00 , 3.06996673284450e+00 , 5.88764729411060e+00 , -5.39828293654177e-01 , 3.50182389775589e+00 , 3.76181263491333e+00 , -1.45737995469276e+00 , 4.47774979548157e+00 , 3.41742259521307e+00 , -7.52656402540314e-01 , 5.44714686176258e+00 , 2.48230963624217e+00 , -2.74903816285443e+00 , 3.94197213054861e+00 , 2.75948540916468e+00 , -3.80126368217889e+00 , 4.57734229189021e+00 , 2.81260271492884e+00 , -2.69983596459315e+00 , 2.63637902047927e+00 , 2.35275320372801e+00 , -3.80812945779466e+00 , 1.82100657589145e+00 , 2.00251302485744e+00 , -3.35273987959584e+00 , 8.82670239652218e-01 , 7.92872005460967e-01 , -4.25289060329676e+00 , 1.03322899973819e+00 , 3.24599742591875e+00 , -5.45585612158692e+00 , 7.41707491159396e-01 , 3.34406841611962e+00 , -3.36965129496242e+00 , 7.27336540574501e-01 , 4.16165346261809e+00 , -3.66759582428271e+00 , 7.58826722683877e-02 , 5.47907665313511e+00 , -2.36653676520567e+00 , -3.04791642260045e-01 , 6.12630281893083e+00 , -4.48930593261884e+00 , 9.29643058404834e-01 , 6.42030281138112e+00 , -5.35733093367902e+00 , 5.60676121557277e-01 , 7.19103315777678e+00 , -6.30836676717657e+00 , 3.61567551810552e+00 , 6.75690769854272e+00 , -7.01923456785992e+00 , 4.29968920159194e+00 , 7.51639637407081e+00 , -6.62521134252802e+00 , 3.16456400975179e+00 , 5.54286904467815e+00 , -4.10800032264489e+00 , 2.25520167794132e+00 , 6.40478878792620e+00 , -4.81497251925987e+00 , 3.28690173612652e+00 , 7.23378205285441e+00 , -4.01261784991035e+00 , 4.58020866242027e+00 , 7.27629588974665e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.4759 , 6.54759 , 13.0952 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.4759 , 6.54759 , 13.0952 ) to colvar "one". +colvars: Adding total bias energy: 55.725 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.4759 , 6.54759 , 13.0952 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.1862 , -0.542113 , -1.46457 ) +colvars: ( -4.44716 , -0.464862 , -1.25587 ) +colvars: ( -4.44716 , -0.464862 , -1.25587 ) +colvars: ( -5.92375 , -0.61921 , -1.67285 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.929247 , 0.206087 , 0.634371 ) +colvars: ( 0.805863 , 0.27929 , 0.658977 ) +colvars: ( 0.788819 , 0.272351 , 0.640143 ) +colvars: ( 0.69081 , 0.279321 , 0.592956 ) +colvars: ( 0.678563 , 0.209837 , 0.495321 ) +colvars: ( 0.601814 , 0.359267 , 0.6461 ) +colvars: ( 0.491577 , 0.373091 , 0.60083 ) +colvars: ( 0.412672 , 0.473979 , 0.687076 ) +colvars: ( 0.407119 , 0.326381 , 0.491429 ) +colvars: ( 0.371498 , 0.282692 , 0.414008 ) +colvars: ( 0.376408 , 0.332051 , 0.481188 ) +colvars: ( 0.302699 , 0.287176 , 0.380351 ) +colvars: ( 0.274254 , 0.317615 , 0.403709 ) +colvars: ( 0.367022 , 0.18557 , 0.284797 ) +colvars: ( 0.306543 , 0.140065 , 0.190735 ) +colvars: ( 0.493528 , 0.147671 , 0.308016 ) +colvars: ( 0.568286 , 0.0528233 , 0.227266 ) +colvars: ( 0.701676 , 0.0317829 , 0.276421 ) +colvars: ( 0.577637 , 0.0193628 , 0.189005 ) +colvars: ( 0.561409 , -0.0485738 , 0.0911015 ) +colvars: ( 0.599617 , 0.0691808 , 0.266585 ) +colvars: ( 0.598566 , 0.0519924 , 0.243569 ) +colvars: ( 0.636629 , 0.119448 , 0.353382 ) +colvars: ( 0.470534 , 0.0558623 , 0.175101 ) +colvars: ( 0.463714 , -0.00262705 , 0.0949186 ) +colvars: ( 0.365299 , 0.12381 , 0.203276 ) +colvars: ( 0.236997 , 0.132014 , 0.140305 ) +colvars: ( 0.142531 , 0.221011 , 0.20211 ) +colvars: ( 0.207588 , 0.0551672 , 0.0232156 ) +colvars: ( 0.157015 , 0.0170386 , -0.0555402 ) +colvars: ( 0.241711 , 0.0290234 , 0.00871818 ) +colvars: ( 0.226914 , -0.04644 , -0.0981778 ) +colvars: ( 0.262733 , -0.0493688 , -0.08143 ) +colvars: ( 0.304664 , -0.135745 , -0.169983 ) +colvars: ( 0.259308 , -0.191378 , -0.268567 ) +colvars: ( 0.42358 , -0.150854 , -0.121405 ) +colvars: ( 0.503647 , -0.229266 , -0.177676 ) +colvars: ( 0.638952 , -0.231257 , -0.102582 ) +colvars: ( 0.455424 , -0.234549 , -0.212253 ) +colvars: ( 0.461221 , -0.305551 , -0.301507 ) +colvars: ( 0.405522 , -0.15861 , -0.141886 ) +colvars: ( 0.350113 , -0.152716 , -0.166017 ) +colvars: ( 0.333432 , -0.0626397 , -0.0581401 ) +colvars: ( 0.222963 , -0.162559 , -0.251858 ) +colvars: ( 0.198086 , -0.206676 , -0.323668 ) +colvars: ( 0.0146568 , -0.210905 , -0.434504 ) +colvars: ( -0.0791164 , -0.229966 , -0.513202 ) +colvars: ( 0.1178 , -0.262188 , -0.442151 ) +colvars: ( 0.138277 , -0.120462 , -0.245591 ) +colvars: ( 0.0151954 , -0.125658 , -0.323038 ) +colvars: ( -0.0767504 , -0.0419235 , -0.266647 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.1862 , 0.542113 , 1.46457 ) +colvars: ( 4.44716 , 0.464862 , 1.25587 ) +colvars: ( 4.44716 , 0.464862 , 1.25587 ) +colvars: ( 5.92375 , 0.61921 , 1.67285 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.642068 , -0.0851862 , -0.376556 ) +colvars: ( -0.578111 , -0.172937 , -0.341911 ) +colvars: ( -0.52372 , -0.149325 , -0.279328 ) +colvars: ( -0.539153 , -0.202066 , -0.312608 ) +colvars: ( -0.528976 , -0.139445 , -0.281275 ) +colvars: ( -0.51519 , -0.299847 , -0.321509 ) +colvars: ( -0.483222 , -0.342655 , -0.303838 ) +colvars: ( -0.462253 , -0.456695 , -0.321228 ) +colvars: ( -0.416844 , -0.304836 , -0.224427 ) +colvars: ( -0.413183 , -0.277948 , -0.211685 ) +colvars: ( -0.363504 , -0.298645 , -0.168772 ) +colvars: ( -0.299502 , -0.25921 , -0.0912023 ) +colvars: ( -0.246837 , -0.274876 , -0.0435951 ) +colvars: ( -0.318588 , -0.149567 , -0.0734041 ) +colvars: ( -0.286346 , -0.118348 , -0.0304997 ) +colvars: ( -0.373885 , -0.0887306 , -0.108426 ) +colvars: ( -0.400515 , 0.015638 , -0.099982 ) +colvars: ( -0.450959 , 0.0661167 , -0.133622 ) +colvars: ( -0.441693 , 0.0314491 , -0.136005 ) +colvars: ( -0.429736 , 0.0918506 , -0.103632 ) +colvars: ( -0.48957 , -0.0261733 , -0.203513 ) +colvars: ( -0.527498 , -0.0278763 , -0.242176 ) +colvars: ( -0.581214 , -0.0976062 , -0.31963 ) +colvars: ( -0.474839 , -0.0596305 , -0.199999 ) +colvars: ( -0.482652 , -0.0127972 , -0.192056 ) +colvars: ( -0.417993 , -0.138453 , -0.169485 ) +colvars: ( -0.359277 , -0.171554 , -0.121679 ) +colvars: ( -0.307231 , -0.267261 , -0.101679 ) +colvars: ( -0.314888 , -0.0939609 , -0.0509416 ) +colvars: ( -0.302217 , -0.0741435 , -0.0315347 ) +colvars: ( -0.291675 , -0.0461468 , -0.0115093 ) +colvars: ( -0.253175 , 0.033468 , 0.0539963 ) +colvars: ( -0.22832 , 0.0616366 , 0.0884538 ) +colvars: ( -0.298815 , 0.125559 , 0.0392107 ) +colvars: ( -0.271113 , 0.170048 , 0.0820294 ) +colvars: ( -0.37081 , 0.155229 , -0.0230887 ) +colvars: ( -0.421617 , 0.236074 , -0.0468554 ) +colvars: ( -0.494997 , 0.259841 , -0.112534 ) +colvars: ( -0.436202 , 0.214918 , -0.0686346 ) +colvars: ( -0.440938 , 0.279563 , -0.0515964 ) +colvars: ( -0.443064 , 0.122836 , -0.106571 ) +colvars: ( -0.452991 , 0.0907125 , -0.12737 ) +colvars: ( -0.47739 , -0.00858991 , -0.185352 ) +colvars: ( -0.384178 , 0.0789403 , -0.0622331 ) +colvars: ( -0.388758 , 0.106886 , -0.0574115 ) +colvars: ( -0.214332 , 0.11429 , 0.120253 ) +colvars: ( -0.163324 , 0.11643 , 0.1722 ) +colvars: ( -0.239769 , 0.191123 , 0.120612 ) +colvars: ( -0.318376 , 0.0358451 , -0.010681 ) +colvars: ( -0.249378 , 0.0215821 , 0.0538028 ) +colvars: ( -0.193377 , -0.0665749 , 0.0803201 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 32. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 32. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atoms_new_colvar_forces = { ( -4.89901623608828e+00 , -4.21212105439454e-01 , -1.20675405543204e+00 ), ( -4.21941026749058e+00 , -3.58509287615206e-01 , -9.38802091181616e-01 ), ( -4.29550516629087e+00 , -3.87606873394999e-01 , -9.75520065438497e-01 ), ( -5.77416070326823e+00 , -5.48818010972503e-01 , -1.45880616208910e+00 ), ( 2.65099014903990e-01 , 1.23026262617554e-01 , 3.60814731993440e-01 ), ( 5.27281908690535e+00 , 6.01532720199336e-01 , 1.78915998936798e+00 ), ( 4.45551616813221e+00 , 4.95298085272648e-01 , 1.55286025808800e+00 ), ( -4.95815471725800e-02 , 1.72843496173996e-02 , 3.65848675189791e-01 ), ( 4.43743592731942e+00 , 4.86406990199900e-01 , 1.52286976483447e+00 ), ( 5.88206302540194e+00 , 6.23953510095548e-01 , 1.87517495993694e+00 ), ( 1.29045883632012e-02 , 3.34059942768686e-02 , 3.12416348184590e-01 ), ( 3.19710743210999e-03 , 2.79659989125077e-02 , 2.89148900271214e-01 ), ( 2.74162961204530e-02 , 4.27391604120190e-02 , 3.60113848518582e-01 ), ( 4.84335198759082e-02 , 3.60038159593996e-02 , 2.11393076425405e-01 ), ( 2.01969306989698e-02 , 2.17164911558664e-02 , 1.60235075960962e-01 ), ( 1.19642400128311e-01 , 5.89405306509370e-02 , 1.99590445877788e-01 ), ( 1.67771244691595e-01 , 6.84613089428121e-02 , 1.27283983130076e-01 ), ( 2.50717048694493e-01 , 9.78995789947894e-02 , 1.42798733669189e-01 ), ( 1.35944414670681e-01 , 5.08118322422355e-02 , 5.30001864232874e-02 ), ( 1.31673233890351e-01 , 4.32767424108246e-02 , -1.25308255102823e-02 ), ( 1.10046878858193e-01 , 4.30075248940974e-02 , 6.30720670584440e-02 ), ( 7.10677615500781e-02 , 2.41160393221906e-02 , 1.39235609554561e-03 ), ( 5.54150999536903e-02 , 2.18420305923133e-02 , 3.37522292529012e-02 ), ( -4.30496233894195e-03 , -3.76814654740749e-03 , -2.48977117651731e-02 ), ( -1.89379453745768e-02 , -1.54242926734249e-02 , -9.71369411860667e-02 ), ( -5.26943270100179e-02 , -1.46431749814066e-02 , 3.37904161404535e-02 ), ( -1.22279922078893e-01 , -3.95395538730484e-02 , 1.86262020671471e-02 ), ( -1.64700201434934e-01 , -4.62503640619868e-02 , 1.00431159156065e-01 ), ( -1.07300021070443e-01 , -3.87937148986723e-02 , -2.77260550974223e-02 ), ( -1.45201848022389e-01 , -5.71048577355892e-02 , -8.70748982326622e-02 ), ( -4.99644683248194e-02 , -1.71233897329648e-02 , -2.79114193213090e-03 ), ( -2.62616432622688e-02 , -1.29720294014966e-02 , -4.41815213489942e-02 ), ( 3.44122448293593e-02 , 1.22678289936801e-02 , 7.02377292264314e-03 ), ( 5.84981230496784e-03 , -1.01856109948020e-02 , -1.30772013183318e-01 ), ( -1.18047324085575e-02 , -2.13297960364434e-02 , -1.86537986109577e-01 ), ( 5.27695344595943e-02 , 4.37467489199533e-03 , -1.44493504104997e-01 ), ( 8.20292579336356e-02 , 6.80785814848911e-03 , -2.24531721265885e-01 ), ( 1.43955044997743e-01 , 2.85843428374076e-02 , -2.15116515543712e-01 ), ( 1.92224718115093e-02 , -1.96308372910681e-02 , -2.80887745664687e-01 ), ( 2.02825062721775e-02 , -2.59881258034823e-02 , -3.53103323051673e-01 ), ( -3.75412989644534e-02 , -3.57739328582618e-02 , -2.48456825072293e-01 ), ( -1.02877904682546e-01 , -6.20040345771192e-02 , -2.93386981776436e-01 ), ( -1.43957691018780e-01 , -7.12296304161886e-02 , -2.43492325778459e-01 ), ( -1.61214463063843e-01 , -8.36188257382807e-02 , -3.14091273937705e-01 ), ( -1.90671822527993e-01 , -9.97901592326389e-02 , -3.81079307509172e-01 ), ( -1.99675356076596e-01 , -9.66148671802132e-02 , -3.14250876260084e-01 ), ( -2.42440547743016e-01 , -1.13536360807562e-01 , -3.41002304847089e-01 ), ( -1.21968433860914e-01 , -7.10651110429882e-02 , -3.21538410973349e-01 ), ( -1.80099495368551e-01 , -8.46164409888168e-02 , -2.56272057953793e-01 ), ( -2.34182235834206e-01 , -1.04075676068759e-01 , -2.69235211898796e-01 ), ( -2.70127379422657e-01 , -1.08498461276038e-01 , -1.86327326419902e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 33, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 33, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 33, atoms_positions[size = 51] = { ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 ), ( 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 ), ( 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 ), ( 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 ), ( 6.99509325210347e+00 , -2.08102315018244e+00 , -8.51239526379223e-01 ), ( 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 ), ( 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 ), ( 7.15309251672616e+00 , -3.48991057622104e-01 , 4.40415429079846e+00 ), ( 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 ), ( 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 ), ( 5.85534783979395e+00 , 2.25171936216251e+00 , 2.96602427149247e+00 ), ( 5.13558337522206e+00 , 3.53632879253126e+00 , 2.87076331408032e+00 ), ( 6.28774885930353e+00 , 4.45372648078627e+00 , 2.28417976249521e+00 ), ( 3.85908723581206e+00 , 3.63081375049325e+00 , 2.01499724284678e+00 ), ( 2.83178466907853e+00 , 4.16346128405932e+00 , 2.42297929173377e+00 ), ( 3.90253559195207e+00 , 3.16922867849155e+00 , 7.60356539199559e-01 ), ( 2.76687652775309e+00 , 3.09803742331921e+00 , -6.90270019545529e-02 ), ( 3.13233554654883e+00 , 2.65238218952684e+00 , -1.53798330454818e+00 ), ( 1.57114708712370e+00 , 2.23818005953628e+00 , 4.30353855151207e-01 ), ( 4.22796268348754e-01 , 2.61536158033979e+00 , 4.43104669199612e-01 ), ( 2.04423949219399e+00 , 1.12327685472541e+00 , 1.04834816265126e+00 ), ( 1.26298783718215e+00 , 1.52506881281894e-01 , 1.66978214121657e+00 ), ( 2.09177823302583e+00 , -1.09370073248940e+00 , 2.03893578485241e+00 ), ( 5.73417726860450e-01 , 6.15674672417228e-01 , 2.94389370237568e+00 ), ( -5.96338169794170e-01 , 3.57762044608908e-01 , 3.19521810188232e+00 ), ( 1.28610395291346e+00 , 1.41256628505262e+00 , 3.77059120683749e+00 ), ( 8.94722599964565e-01 , 1.98000248398792e+00 , 5.04237791544858e+00 ), ( 2.06371481301180e+00 , 2.76861304176402e+00 , 5.72625229173133e+00 ), ( -3.60161112465007e-01 , 2.89530689759080e+00 , 4.93674531845192e+00 ), ( -1.11683273650727e+00 , 3.07039671856267e+00 , 5.89052569085821e+00 ), ( -5.36455406120775e-01 , 3.49762953162092e+00 , 3.75272953810346e+00 ), ( -1.45345915236555e+00 , 4.47615452090498e+00 , 3.41776036947466e+00 ), ( -7.59147033137468e-01 , 5.45258244167206e+00 , 2.48405525316260e+00 ), ( -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 ), ( -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 ), ( -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 ), ( -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 ), ( -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 ), ( -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 ), ( -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 ), ( -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 ), ( -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 ), ( -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 ), ( -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 ), ( -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 ), ( -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 ), ( -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 ), ( -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 ), ( -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 ), ( -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 ), ( -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ) } +colvars: Step 33, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.99509325210347e+00 , -2.08102315018244e+00 , -8.51239526379223e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 , 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 7.15309251672616e+00 , -3.48991057622104e-01 , 4.40415429079846e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 , 5.85534783979395e+00 , 2.25171936216251e+00 , 2.96602427149247e+00 , 5.13558337522206e+00 , 3.53632879253126e+00 , 2.87076331408032e+00 , 6.28774885930353e+00 , 4.45372648078627e+00 , 2.28417976249521e+00 , 3.85908723581206e+00 , 3.63081375049325e+00 , 2.01499724284678e+00 , 2.83178466907853e+00 , 4.16346128405932e+00 , 2.42297929173377e+00 , 3.90253559195207e+00 , 3.16922867849155e+00 , 7.60356539199559e-01 , 2.76687652775309e+00 , 3.09803742331921e+00 , -6.90270019545529e-02 , 3.13233554654883e+00 , 2.65238218952684e+00 , -1.53798330454818e+00 , 1.57114708712370e+00 , 2.23818005953628e+00 , 4.30353855151207e-01 , 4.22796268348754e-01 , 2.61536158033979e+00 , 4.43104669199612e-01 , 2.04423949219399e+00 , 1.12327685472541e+00 , 1.04834816265126e+00 , 1.26298783718215e+00 , 1.52506881281894e-01 , 1.66978214121657e+00 , 2.09177823302583e+00 , -1.09370073248940e+00 , 2.03893578485241e+00 , 5.73417726860450e-01 , 6.15674672417228e-01 , 2.94389370237568e+00 , -5.96338169794170e-01 , 3.57762044608908e-01 , 3.19521810188232e+00 , 1.28610395291346e+00 , 1.41256628505262e+00 , 3.77059120683749e+00 , 8.94722599964565e-01 , 1.98000248398792e+00 , 5.04237791544858e+00 , 2.06371481301180e+00 , 2.76861304176402e+00 , 5.72625229173133e+00 , -3.60161112465007e-01 , 2.89530689759080e+00 , 4.93674531845192e+00 , -1.11683273650727e+00 , 3.07039671856267e+00 , 5.89052569085821e+00 , -5.36455406120775e-01 , 3.49762953162092e+00 , 3.75272953810346e+00 , -1.45345915236555e+00 , 4.47615452090498e+00 , 3.41776036947466e+00 , -7.59147033137468e-01 , 5.45258244167206e+00 , 2.48405525316260e+00 , -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 , -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 , -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 , -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 , -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 , -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 , -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 , -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 , -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 , -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 , -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 , -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 , -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 , -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 , -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 , -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 , -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 , -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ). +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Done calculating colvar "fitting_group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.88930838111525e-01 , -1.58081418249705e-02 , 9.57219448945859e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.88930838111525e-01 , -1.58081418249705e-02 , 9.57219448945859e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.20576749576985e+00 , 4.37907383306815e-02 , -7.11926493060761e-01 , 6.82229247280645e+00 , -6.09199060466783e-01 , -5.20316649000995e-01 , 6.99509325210347e+00 , -2.08102315018244e+00 , -8.51239526379223e-01 , 6.08408087112893e+00 , -3.43732101086614e-01 , 8.15901028772818e-01 , 4.89927340566222e+00 , -1.51939494855060e-01 , 7.56956095819018e-01 , 6.79808010965941e+00 , -3.04519869477516e-01 , 1.96532016192913e+00 , 6.08462532509194e+00 , -2.33796608683004e-01 , 3.20953490009967e+00 , 7.15309251672616e+00 , -3.48991057622104e-01 , 4.40415429079846e+00 , 5.31427532870300e+00 , 1.06556010643314e+00 , 3.36554040334277e+00 , 4.19451368838683e+00 , 1.00335219720559e+00 , 3.81346543165755e+00 , 5.85534783979395e+00 , 2.25171936216251e+00 , 2.96602427149247e+00 , 5.13558337522206e+00 , 3.53632879253126e+00 , 2.87076331408032e+00 , 6.28774885930353e+00 , 4.45372648078627e+00 , 2.28417976249521e+00 , 3.85908723581206e+00 , 3.63081375049325e+00 , 2.01499724284678e+00 , 2.83178466907853e+00 , 4.16346128405932e+00 , 2.42297929173377e+00 , 3.90253559195207e+00 , 3.16922867849155e+00 , 7.60356539199559e-01 , 2.76687652775309e+00 , 3.09803742331921e+00 , -6.90270019545529e-02 , 3.13233554654883e+00 , 2.65238218952684e+00 , -1.53798330454818e+00 , 1.57114708712370e+00 , 2.23818005953628e+00 , 4.30353855151207e-01 , 4.22796268348754e-01 , 2.61536158033979e+00 , 4.43104669199612e-01 , 2.04423949219399e+00 , 1.12327685472541e+00 , 1.04834816265126e+00 , 1.26298783718215e+00 , 1.52506881281894e-01 , 1.66978214121657e+00 , 2.09177823302583e+00 , -1.09370073248940e+00 , 2.03893578485241e+00 , 5.73417726860450e-01 , 6.15674672417228e-01 , 2.94389370237568e+00 , -5.96338169794170e-01 , 3.57762044608908e-01 , 3.19521810188232e+00 , 1.28610395291346e+00 , 1.41256628505262e+00 , 3.77059120683749e+00 , 8.94722599964565e-01 , 1.98000248398792e+00 , 5.04237791544858e+00 , 2.06371481301180e+00 , 2.76861304176402e+00 , 5.72625229173133e+00 , -3.60161112465007e-01 , 2.89530689759080e+00 , 4.93674531845192e+00 , -1.11683273650727e+00 , 3.07039671856267e+00 , 5.89052569085821e+00 , -5.36455406120775e-01 , 3.49762953162092e+00 , 3.75272953810346e+00 , -1.45345915236555e+00 , 4.47615452090498e+00 , 3.41776036947466e+00 , -7.59147033137468e-01 , 5.45258244167206e+00 , 2.48405525316260e+00 , -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 , -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 , -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 , -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 , -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 , -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 , -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 , -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 , -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 , -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 , -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 , -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 , -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 , -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 , -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 , -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 , -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 , -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.4039 , 6.54039 , 13.0808 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.4039 , 6.54039 , 13.0808 ) to colvar "one". +colvars: Adding total bias energy: 55.6197 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.4039 , 6.54039 , 13.0808 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.18265 , -0.53913 , -1.45573 ) +colvars: ( -4.44412 , -0.462304 , -1.24829 ) +colvars: ( -4.44412 , -0.462304 , -1.24829 ) +colvars: ( -5.9197 , -0.615802 , -1.66276 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.92736 , 0.205895 , 0.631936 ) +colvars: ( 0.804327 , 0.278857 , 0.656483 ) +colvars: ( 0.787291 , 0.271993 , 0.637781 ) +colvars: ( 0.689631 , 0.27878 , 0.590667 ) +colvars: ( 0.677425 , 0.209447 , 0.49336 ) +colvars: ( 0.600907 , 0.358459 , 0.643621 ) +colvars: ( 0.491016 , 0.372142 , 0.598481 ) +colvars: ( 0.412348 , 0.472727 , 0.684429 ) +colvars: ( 0.406788 , 0.325514 , 0.489486 ) +colvars: ( 0.371292 , 0.281874 , 0.412303 ) +colvars: ( 0.376131 , 0.33121 , 0.47934 ) +colvars: ( 0.302618 , 0.286425 , 0.378884 ) +colvars: ( 0.274215 , 0.316838 , 0.402227 ) +colvars: ( 0.366751 , 0.185107 , 0.283653 ) +colvars: ( 0.306454 , 0.139663 , 0.189911 ) +colvars: ( 0.492882 , 0.147389 , 0.306789 ) +colvars: ( 0.567421 , 0.0528162 , 0.226308 ) +colvars: ( 0.700405 , 0.0319381 , 0.275306 ) +colvars: ( 0.576784 , 0.0193783 , 0.188117 ) +colvars: ( 0.560608 , -0.0484147 , 0.0905421 ) +colvars: ( 0.598729 , 0.0690446 , 0.265385 ) +colvars: ( 0.59772 , 0.051833 , 0.242387 ) +colvars: ( 0.635697 , 0.119113 , 0.351784 ) +colvars: ( 0.470076 , 0.0555896 , 0.174146 ) +colvars: ( 0.463294 , -0.00279396 , 0.0942105 ) +colvars: ( 0.365138 , 0.123323 , 0.20225 ) +colvars: ( 0.237218 , 0.131414 , 0.139497 ) +colvars: ( 0.143015 , 0.220159 , 0.201121 ) +colvars: ( 0.207877 , 0.0547615 , 0.022839 ) +colvars: ( 0.157469 , 0.0166622 , -0.05567 ) +colvars: ( 0.241863 , 0.0287611 , 0.00844368 ) +colvars: ( 0.227089 , -0.0464987 , -0.098054 ) +colvars: ( 0.262761 , -0.0493299 , -0.0813031 ) +colvars: ( 0.304628 , -0.135566 , -0.169645 ) +colvars: ( 0.259407 , -0.1911 , -0.267893 ) +colvars: ( 0.423208 , -0.150581 , -0.121263 ) +colvars: ( 0.503059 , -0.228783 , -0.177378 ) +colvars: ( 0.637971 , -0.230687 , -0.102558 ) +colvars: ( 0.455016 , -0.234148 , -0.211891 ) +colvars: ( 0.460806 , -0.304993 , -0.300857 ) +colvars: ( 0.405283 , -0.158459 , -0.141795 ) +colvars: ( 0.350072 , -0.152675 , -0.165894 ) +colvars: ( 0.333461 , -0.0628575 , -0.0584163 ) +colvars: ( 0.223293 , -0.162574 , -0.251427 ) +colvars: ( 0.198511 , -0.206638 , -0.323023 ) +colvars: ( 0.015542 , -0.210853 , -0.433347 ) +colvars: ( -0.0779568 , -0.229931 , -0.511768 ) +colvars: ( 0.118363 , -0.261913 , -0.440945 ) +colvars: ( 0.138828 , -0.12059 , -0.245134 ) +colvars: ( 0.0161022 , -0.125847 , -0.322298 ) +colvars: ( -0.0755929 , -0.0423426 , -0.266063 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.18265 , 0.53913 , 1.45573 ) +colvars: ( 4.44412 , 0.462304 , 1.24829 ) +colvars: ( 4.44412 , 0.462304 , 1.24829 ) +colvars: ( 5.9197 , 0.615802 , 1.66276 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.640575 , -0.0850538 , -0.374471 ) +colvars: ( -0.576881 , -0.172718 , -0.339688 ) +colvars: ( -0.522375 , -0.149129 , -0.277105 ) +colvars: ( -0.538234 , -0.201796 , -0.310558 ) +colvars: ( -0.528068 , -0.139217 , -0.279523 ) +colvars: ( -0.514534 , -0.299485 , -0.319272 ) +colvars: ( -0.482882 , -0.342234 , -0.301717 ) +colvars: ( -0.462149 , -0.456173 , -0.318818 ) +colvars: ( -0.416607 , -0.304428 , -0.222584 ) +colvars: ( -0.413069 , -0.277547 , -0.210084 ) +colvars: ( -0.363208 , -0.298243 , -0.166905 ) +colvars: ( -0.299276 , -0.258826 , -0.0895881 ) +colvars: ( -0.246546 , -0.274484 , -0.0418512 ) +colvars: ( -0.318177 , -0.149275 , -0.0721074 ) +colvars: ( -0.286058 , -0.118066 , -0.0294687 ) +colvars: ( -0.373172 , -0.0885114 , -0.107107 ) +colvars: ( -0.399601 , 0.0157662 , -0.0989418 ) +colvars: ( -0.449701 , 0.0661765 , -0.132472 ) +colvars: ( -0.440879 , 0.0315731 , -0.13513 ) +colvars: ( -0.428942 , 0.0919357 , -0.103054 ) +colvars: ( -0.488831 , -0.0260055 , -0.202445 ) +colvars: ( -0.526888 , -0.0276977 , -0.241222 ) +colvars: ( -0.580638 , -0.0973796 , -0.318386 ) +colvars: ( -0.474545 , -0.0593988 , -0.199213 ) +colvars: ( -0.482409 , -0.0125936 , -0.191531 ) +colvars: ( -0.417915 , -0.138145 , -0.168556 ) +colvars: ( -0.359496 , -0.171193 , -0.120893 ) +colvars: ( -0.307642 , -0.266814 , -0.100648 ) +colvars: ( -0.315072 , -0.0936542 , -0.050478 ) +colvars: ( -0.302551 , -0.0738361 , -0.0313093 ) +colvars: ( -0.291651 , -0.0458904 , -0.0110632 ) +colvars: ( -0.253078 , 0.0336653 , 0.0541467 ) +colvars: ( -0.228004 , 0.0617962 , 0.0886872 ) +colvars: ( -0.298569 , 0.125678 , 0.0390902 ) +colvars: ( -0.270948 , 0.170145 , 0.0816251 ) +colvars: ( -0.370348 , 0.155303 , -0.0231264 ) +colvars: ( -0.421014 , 0.236078 , -0.0471206 ) +colvars: ( -0.494119 , 0.2598 , -0.112633 ) +colvars: ( -0.435831 , 0.214956 , -0.0690286 ) +colvars: ( -0.440559 , 0.279556 , -0.0522767 ) +colvars: ( -0.442908 , 0.122957 , -0.106754 ) +colvars: ( -0.45308 , 0.0908766 , -0.127645 ) +colvars: ( -0.477626 , -0.00834566 , -0.185315 ) +colvars: ( -0.384526 , 0.0791395 , -0.0627124 ) +colvars: ( -0.389216 , 0.107076 , -0.0581242 ) +colvars: ( -0.214915 , 0.114495 , 0.11937 ) +colvars: ( -0.164097 , 0.116654 , 0.171117 ) +colvars: ( -0.24004 , 0.191246 , 0.119684 ) +colvars: ( -0.318832 , 0.0360871 , -0.0110743 ) +colvars: ( -0.250076 , 0.0218595 , 0.053232 ) +colvars: ( -0.194244 , -0.0662189 , 0.079982 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 33. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 33. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atoms_new_colvar_forces = { ( -4.89586815295081e+00 , -4.18288661428291e-01 , -1.19826590804559e+00 ), ( -4.21667724742114e+00 , -3.56164364871705e-01 , -9.31493539162552e-01 ), ( -4.29272685181666e+00 , -3.85319228898944e-01 , -9.68179759181285e-01 ), ( -5.77034476910618e+00 , -5.45572293537170e-01 , -1.44891957464345e+00 ), ( 2.64915722897845e-01 , 1.22864580939093e-01 , 3.60676035934643e-01 ), ( 5.26902630036997e+00 , 5.98103291404388e-01 , 1.78007941301694e+00 ), ( 4.45225704520376e+00 , 4.92211901595681e-01 , 1.54505351836818e+00 ), ( -4.98000970229364e-02 , 1.65535296997307e-02 , 3.65611674083054e-01 ), ( 4.43430513812878e+00 , 4.83390092105504e-01 , 1.51519136124869e+00 ), ( 5.87792441423127e+00 , 6.20129313106024e-01 , 1.86497520701249e+00 ), ( 1.29230396392084e-02 , 3.29666365657545e-02 , 3.12435254808471e-01 ), ( 3.34234509871706e-03 , 2.75996833065102e-02 , 2.89296152444240e-01 ), ( 2.76688487399397e-02 , 4.23546637103761e-02 , 3.60375390154767e-01 ), ( 4.85745297195058e-02 , 3.58311160222937e-02 , 2.11545556675541e-01 ), ( 2.03958682345369e-02 , 2.15967805778263e-02 , 1.60441833025958e-01 ), ( 1.19710006871534e-01 , 5.88774090515197e-02 , 1.99681770123455e-01 ), ( 1.67820160542212e-01 , 6.85823669256171e-02 , 1.27366223768150e-01 ), ( 2.50704181138953e-01 , 9.81145488528216e-02 , 1.42833830221747e-01 ), ( 1.35905706267073e-01 , 5.09513821603064e-02 , 5.29868643664593e-02 ), ( 1.31665912015475e-01 , 4.35210034266095e-02 , -1.25122522047927e-02 ), ( 1.09897779079899e-01 , 4.30391622522975e-02 , 6.29403019603845e-02 ), ( 7.08321266490427e-02 , 2.41352720145787e-02 , 1.16463071399242e-03 ), ( 5.50592541635683e-02 , 2.17333711719896e-02 , 3.33978252823109e-02 ), ( -4.46900686890672e-03 , -3.80922940105193e-03 , -2.50666492114297e-02 ), ( -1.91144356427754e-02 , -1.53875496586136e-02 , -9.73209400723725e-02 ), ( -5.27772725973002e-02 , -1.48213849078601e-02 , 3.36946470716469e-02 ), ( -1.22277863399888e-01 , -3.97789521628804e-02 , 1.86040326368210e-02 ), ( -1.64627046451288e-01 , -4.66556174907358e-02 , 1.00472884175944e-01 ), ( -1.07194738160474e-01 , -3.88927066699034e-02 , -2.76389901901821e-02 ), ( -1.45081503082860e-01 , -5.71738881989172e-02 , -8.69793720398932e-02 ), ( -4.97875743463240e-02 , -1.71293229075876e-02 , -2.61950305523130e-03 ), ( -2.59896779157611e-02 , -1.28334042956098e-02 , -4.39073317195441e-02 ), ( 3.47569491170505e-02 , 1.24662963114502e-02 , 7.38413631730400e-03 ), ( 6.05905111978139e-03 , -9.88820691397341e-03 , -1.30555126271493e-01 ), ( -1.15406889596824e-02 , -2.09554556714439e-02 , -1.86267900379892e-01 ), ( 5.28600147704486e-02 , 4.72273260669220e-03 , -1.44389080105876e-01 ), ( 8.20442708466673e-02 , 7.29437414268397e-03 , -2.24498287373445e-01 ), ( 1.43852669424415e-01 , 2.91133684798466e-02 , -2.15191368310404e-01 ), ( 1.91850096005293e-02 , -1.91913456295390e-02 , -2.80920075470312e-01 ), ( 2.02466254432048e-02 , -2.54375250906080e-02 , -3.53133227572521e-01 ), ( -3.76256921832037e-02 , -3.55020742444178e-02 , -2.48548768519691e-01 ), ( -1.03008375312877e-01 , -6.17980014296811e-02 , -2.93538718662919e-01 ), ( -1.44164924912362e-01 , -7.12031808104580e-02 , -2.43731329943684e-01 ), ( -1.61233249667508e-01 , -8.34345673503705e-02 , -3.14139775300582e-01 ), ( -1.90704772557553e-01 , -9.95624504003784e-02 , -3.81147600804688e-01 ), ( -1.99373035235729e-01 , -9.63580709974224e-02 , -3.13977542407785e-01 ), ( -2.42053536834788e-01 , -1.13276905026004e-01 , -3.40650306216223e-01 ), ( -1.21677080599663e-01 , -7.06672045203527e-02 , -3.21260935674461e-01 ), ( -1.80004324558336e-01 , -8.45025517452499e-02 , -2.56207852610082e-01 ), ( -2.33974007025502e-01 , -1.03987221353875e-01 , -2.69065585766027e-01 ), ( -2.69837044682870e-01 , -1.08561510816550e-01 , -1.86081242494781e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 34, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 34, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 34, atoms_positions[size = 51] = { ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 ), ( 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 ), ( 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 ), ( 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ), ( 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 ), ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 ), ( 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 ), ( 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 ), ( 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 ), ( 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ), ( 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 ), ( 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 ), ( 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 ), ( 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 ), ( 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 ), ( 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 ), ( 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 ), ( 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 ), ( 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 ), ( 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 ), ( 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 ), ( 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 ), ( 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 ), ( 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 ), ( -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 ), ( 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 ), ( 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 ), ( 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 ), ( -3.59887877851289e-01 , 2.89341210824563e+00 , 4.93080537448977e+00 ), ( -1.11752535128005e+00 , 3.07079403948851e+00 , 5.89323910393435e+00 ), ( -5.32183156670204e-01 , 3.49237702712859e+00 , 3.74376491377976e+00 ), ( -1.45110993394368e+00 , 4.47552471132078e+00 , 3.41735254418937e+00 ), ( -7.65070322521645e-01 , 5.45860851201285e+00 , 2.48561592211971e+00 ), ( -2.75200839518506e+00 , 3.93473792506609e+00 , 2.73631425357401e+00 ), ( -3.79753915657748e+00 , 4.58898675042232e+00 , 2.81090688733797e+00 ), ( -2.70703679486343e+00 , 2.64312058255035e+00 , 2.35056268991001e+00 ), ( -3.81520007124380e+00 , 1.80992449237204e+00 , 1.99756322640363e+00 ), ( -3.34760852615227e+00 , 8.91368221115539e-01 , 7.79124805166928e-01 ), ( -4.26031034996816e+00 , 1.02599952098258e+00 , 3.24616744685834e+00 ), ( -5.43899565340654e+00 , 7.30961009524662e-01 , 3.34945957410753e+00 ), ( -3.36573818489708e+00 , 7.21994493966916e-01 , 4.16188646216874e+00 ), ( -3.66587207559550e+00 , 6.97286392999179e-02 , 5.47015820635550e+00 ), ( -2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 ), ( -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 ), ( -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 ), ( -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 ), ( -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 ), ( -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 ), ( -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 ), ( -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 ), ( -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ) } +colvars: Step 34, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.87157334453261e-01 , -1.65935395079231e-02 , 9.57739693088000e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 , 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 , 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 , 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 , 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 , 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 , 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 , 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 , 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 , 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 , 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 , 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 , 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 , 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 , 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 , 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 , -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 , 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 , 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 , 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 , -3.59887877851289e-01 , 2.89341210824563e+00 , 4.93080537448977e+00 , -1.11752535128005e+00 , 3.07079403948851e+00 , 5.89323910393435e+00 , -5.32183156670204e-01 , 3.49237702712859e+00 , 3.74376491377976e+00 , -1.45110993394368e+00 , 4.47552471132078e+00 , 3.41735254418937e+00 , -7.65070322521645e-01 , 5.45860851201285e+00 , 2.48561592211971e+00 , -2.75200839518506e+00 , 3.93473792506609e+00 , 2.73631425357401e+00 , -3.79753915657748e+00 , 4.58898675042232e+00 , 2.81090688733797e+00 , -2.70703679486343e+00 , 2.64312058255035e+00 , 2.35056268991001e+00 , -3.81520007124380e+00 , 1.80992449237204e+00 , 1.99756322640363e+00 , -3.34760852615227e+00 , 8.91368221115539e-01 , 7.79124805166928e-01 , -4.26031034996816e+00 , 1.02599952098258e+00 , 3.24616744685834e+00 , -5.43899565340654e+00 , 7.30961009524662e-01 , 3.34945957410753e+00 , -3.36573818489708e+00 , 7.21994493966916e-01 , 4.16188646216874e+00 , -3.66587207559550e+00 , 6.97286392999179e-02 , 5.47015820635550e+00 , -2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 , -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 , -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 , -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 , -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 , -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 , -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 , -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 , -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.87157334453261e-01 , -1.65935395079231e-02 , 9.57739693088000e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 , 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 , 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 , 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 , 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 , 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 , 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 , 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 , 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 , 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 , 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 , 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 , 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 , 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 , 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 , 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 , -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 , 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 , 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 , 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 , -3.59887877851289e-01 , 2.89341210824563e+00 , 4.93080537448977e+00 , -1.11752535128005e+00 , 3.07079403948851e+00 , 5.89323910393435e+00 , -5.32183156670204e-01 , 3.49237702712859e+00 , 3.74376491377976e+00 , -1.45110993394368e+00 , 4.47552471132078e+00 , 3.41735254418937e+00 , -7.65070322521645e-01 , 5.45860851201285e+00 , 2.48561592211971e+00 , -2.75200839518506e+00 , 3.93473792506609e+00 , 2.73631425357401e+00 , -3.79753915657748e+00 , 4.58898675042232e+00 , 2.81090688733797e+00 , -2.70703679486343e+00 , 2.64312058255035e+00 , 2.35056268991001e+00 , -3.81520007124380e+00 , 1.80992449237204e+00 , 1.99756322640363e+00 , -3.34760852615227e+00 , 8.91368221115539e-01 , 7.79124805166928e-01 , -4.26031034996816e+00 , 1.02599952098258e+00 , 3.24616744685834e+00 , -5.43899565340654e+00 , 7.30961009524662e-01 , 3.34945957410753e+00 , -3.36573818489708e+00 , 7.21994493966916e-01 , 4.16188646216874e+00 , -3.66587207559550e+00 , 6.97286392999179e-02 , 5.47015820635550e+00 , -2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 , -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 , -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 , -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 , -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 , -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 , -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 , -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 , -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.3236 , 6.53236 , 13.0647 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.3236 , 6.53236 , 13.0647 ) to colvar "one". +colvars: Adding total bias energy: 55.5021 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.3236 , 6.53236 , 13.0647 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17845 , -0.535884 , -1.44577 ) +colvars: ( -4.44052 , -0.45952 , -1.23975 ) +colvars: ( -4.44052 , -0.45952 , -1.23975 ) +colvars: ( -5.9149 , -0.612094 , -1.65138 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.92526 , 0.205682 , 0.629229 ) +colvars: ( 0.802614 , 0.278379 , 0.653714 ) +colvars: ( 0.785579 , 0.2716 , 0.635157 ) +colvars: ( 0.688312 , 0.278184 , 0.588128 ) +colvars: ( 0.67615 , 0.209017 , 0.491181 ) +colvars: ( 0.599889 , 0.357566 , 0.640873 ) +colvars: ( 0.49038 , 0.371093 , 0.59588 ) +colvars: ( 0.411977 , 0.471342 , 0.681502 ) +colvars: ( 0.406404 , 0.324558 , 0.487333 ) +colvars: ( 0.371045 , 0.280972 , 0.410412 ) +colvars: ( 0.3758 , 0.330284 , 0.47729 ) +colvars: ( 0.3025 , 0.285601 , 0.377255 ) +colvars: ( 0.274139 , 0.315987 , 0.40058 ) +colvars: ( 0.366423 , 0.1846 , 0.282377 ) +colvars: ( 0.306325 , 0.139224 , 0.188987 ) +colvars: ( 0.492139 , 0.147082 , 0.305419 ) +colvars: ( 0.566438 , 0.0528135 , 0.225232 ) +colvars: ( 0.698973 , 0.0321143 , 0.274054 ) +colvars: ( 0.575818 , 0.0193994 , 0.187117 ) +colvars: ( 0.559699 , -0.0482344 , 0.0899044 ) +colvars: ( 0.597729 , 0.0688965 , 0.264043 ) +colvars: ( 0.596771 , 0.051658 , 0.241066 ) +colvars: ( 0.634657 , 0.118742 , 0.350005 ) +colvars: ( 0.469554 , 0.0552899 , 0.173077 ) +colvars: ( 0.462816 , -0.0029768 , 0.0934132 ) +colvars: ( 0.364943 , 0.122788 , 0.201106 ) +colvars: ( 0.237444 , 0.130754 , 0.138594 ) +colvars: ( 0.143528 , 0.219221 , 0.200021 ) +colvars: ( 0.208173 , 0.0543178 , 0.022411 ) +colvars: ( 0.157949 , 0.016251 , -0.0558256 ) +colvars: ( 0.242004 , 0.028477 , 0.00812639 ) +colvars: ( 0.227251 , -0.0465563 , -0.0979338 ) +colvars: ( 0.262757 , -0.0492784 , -0.0811809 ) +colvars: ( 0.304559 , -0.135361 , -0.169292 ) +colvars: ( 0.259487 , -0.190785 , -0.267168 ) +colvars: ( 0.42277 , -0.150273 , -0.121126 ) +colvars: ( 0.502386 , -0.228245 , -0.177071 ) +colvars: ( 0.636868 , -0.230053 , -0.102556 ) +colvars: ( 0.454546 , -0.233701 , -0.211514 ) +colvars: ( 0.460329 , -0.304373 , -0.300162 ) +colvars: ( 0.405002 , -0.158289 , -0.141712 ) +colvars: ( 0.350014 , -0.152626 , -0.165775 ) +colvars: ( 0.333484 , -0.0630974 , -0.0587352 ) +colvars: ( 0.223642 , -0.162587 , -0.250968 ) +colvars: ( 0.198967 , -0.206593 , -0.322328 ) +colvars: ( 0.0164937 , -0.210789 , -0.432086 ) +colvars: ( -0.0767039 , -0.229883 , -0.510199 ) +colvars: ( 0.118957 , -0.261601 , -0.439633 ) +colvars: ( 0.139417 , -0.120727 , -0.244643 ) +colvars: ( 0.0170817 , -0.12605 , -0.321494 ) +colvars: ( -0.074339 , -0.0427993 , -0.265429 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17845 , 0.535884 , 1.44577 ) +colvars: ( 4.44052 , 0.45952 , 1.23975 ) +colvars: ( 4.44052 , 0.45952 , 1.23975 ) +colvars: ( 5.9149 , 0.612094 , 1.65138 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.638885 , -0.0849213 , -0.372115 ) +colvars: ( -0.575488 , -0.172453 , -0.337212 ) +colvars: ( -0.520885 , -0.148907 , -0.274664 ) +colvars: ( -0.537181 , -0.201457 , -0.308278 ) +colvars: ( -0.527032 , -0.138947 , -0.277564 ) +colvars: ( -0.513763 , -0.299003 , -0.316798 ) +colvars: ( -0.482454 , -0.341662 , -0.299373 ) +colvars: ( -0.461972 , -0.455443 , -0.316171 ) +colvars: ( -0.416311 , -0.303885 , -0.220569 ) +colvars: ( -0.412903 , -0.277017 , -0.208325 ) +colvars: ( -0.362872 , -0.297716 , -0.164896 ) +colvars: ( -0.299037 , -0.258333 , -0.0878816 ) +colvars: ( -0.246261 , -0.273984 , -0.0400389 ) +colvars: ( -0.317738 , -0.14893 , -0.0707336 ) +colvars: ( -0.285761 , -0.117739 , -0.0283908 ) +colvars: ( -0.372397 , -0.0882735 , -0.10569 ) +colvars: ( -0.398608 , 0.0158614 , -0.0978112 ) +colvars: ( -0.448331 , 0.0661698 , -0.131209 ) +colvars: ( -0.439973 , 0.0316649 , -0.134148 ) +colvars: ( -0.428064 , 0.0919631 , -0.102394 ) +colvars: ( -0.487986 , -0.0258387 , -0.201228 ) +colvars: ( -0.526162 , -0.027511 , -0.240102 ) +colvars: ( -0.579925 , -0.09711 , -0.316927 ) +colvars: ( -0.474168 , -0.0591348 , -0.198289 ) +colvars: ( -0.482081 , -0.0123747 , -0.19088 ) +colvars: ( -0.417785 , -0.137765 , -0.167504 ) +colvars: ( -0.359698 , -0.170737 , -0.120017 ) +colvars: ( -0.308063 , -0.266227 , -0.0995345 ) +colvars: ( -0.315253 , -0.0932899 , -0.0499706 ) +colvars: ( -0.302894 , -0.0734736 , -0.0310569 ) +colvars: ( -0.291625 , -0.0456078 , -0.0105944 ) +colvars: ( -0.252993 , 0.0338491 , 0.0542775 ) +colvars: ( -0.2277 , 0.0619185 , 0.0888848 ) +colvars: ( -0.298311 , 0.12574 , 0.0389541 ) +colvars: ( -0.270785 , 0.170168 , 0.0811748 ) +colvars: ( -0.369836 , 0.155304 , -0.0231416 ) +colvars: ( -0.420337 , 0.235971 , -0.0473534 ) +colvars: ( -0.493127 , 0.25963 , -0.112658 ) +colvars: ( -0.43539 , 0.214905 , -0.0693822 ) +colvars: ( -0.440108 , 0.279431 , -0.0529318 ) +colvars: ( -0.442689 , 0.123036 , -0.106873 ) +colvars: ( -0.453112 , 0.0910253 , -0.127847 ) +colvars: ( -0.4778 , -0.0080665 , -0.185167 ) +colvars: ( -0.384853 , 0.0793352 , -0.0631615 ) +colvars: ( -0.389655 , 0.107255 , -0.0588148 ) +colvars: ( -0.215552 , 0.114681 , 0.118404 ) +colvars: ( -0.164951 , 0.116862 , 0.169918 ) +colvars: ( -0.240343 , 0.191304 , 0.118675 ) +colvars: ( -0.319297 , 0.0363442 , -0.0114655 ) +colvars: ( -0.25082 , 0.0221642 , 0.0526219 ) +colvars: ( -0.195185 , -0.0657943 , 0.0795931 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 34. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 34. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atoms_new_colvar_forces = { ( -4.89207790183618e+00 , -4.15122393422152e-01 , -1.18865944944393e+00 ), ( -4.21339656599004e+00 , -3.53593925479209e-01 , -9.23247799910002e-01 ), ( -4.28939089016549e+00 , -3.82793309350308e-01 , -9.59901188084321e-01 ), ( -5.76578470637730e+00 , -5.42023922197129e-01 , -1.43776721768089e+00 ), ( 2.64693961548336e-01 , 1.22693563549609e-01 , 3.60493344381193e-01 ), ( 5.26457783516552e+00 , 5.94447048429273e-01 , 1.76984911150636e+00 ), ( 4.44844802111224e+00 , 4.88951823046885e-01 , 1.53625774796560e+00 ), ( -4.99955465911185e-02 , 1.58996003715131e-02 , 3.65331568545859e-01 ), ( 4.43061438957446e+00 , 4.80193617553499e-01 , 1.50651464907953e+00 ), ( 5.87304597055867e+00 , 6.16049737988205e-01 , 1.85347026095904e+00 ), ( 1.29283499682310e-02 , 3.25684264792283e-02 , 3.12394236530586e-01 ), ( 3.46282923948704e-03 , 2.72676561698180e-02 , 2.89373192147298e-01 ), ( 2.78783281890533e-02 , 4.20032047720394e-02 , 3.60541438087145e-01 ), ( 4.86851167124881e-02 , 3.56695428925346e-02 , 2.11643038440695e-01 ), ( 2.05645813430333e-02 , 2.14855039556672e-02 , 1.60596234655948e-01 ), ( 1.19742571689663e-01 , 5.88082390684821e-02 , 1.99729197953058e-01 ), ( 1.67829283865154e-01 , 6.86749286807425e-02 , 1.27420450066263e-01 ), ( 2.50642695719310e-01 , 9.82841416736648e-02 , 1.42845702609494e-01 ), ( 1.35844833766718e-01 , 5.10642887969307e-02 , 5.29691138827324e-02 ), ( 1.31635563968384e-01 , 4.37287221381917e-02 , -1.24895896717630e-02 ), ( 1.09743220442345e-01 , 4.30577943864882e-02 , 6.28147116457306e-02 ), ( 7.06095024240929e-02 , 2.41470395377948e-02 , 9.64154857561572e-04 ), ( 5.47317076653039e-02 , 2.16318689297221e-02 , 3.30783409709317e-02 ), ( -4.61339196130928e-03 , -3.84495031494735e-03 , -2.52122009401218e-02 ), ( -1.92651819617661e-02 , -1.53514658164406e-02 , -9.74668415745923e-02 ), ( -5.28422936009517e-02 , -1.49766796886275e-02 , 3.36017509450781e-02 ), ( -1.22254091212308e-01 , -3.99831713070345e-02 , 1.85773137146949e-02 ), ( -1.64534546870824e-01 , -4.70058861347695e-02 , 1.00486451106187e-01 ), ( -1.07080634123299e-01 , -3.89721870900899e-02 , -2.75596095017998e-02 ), ( -1.44945385628667e-01 , -5.72226697247052e-02 , -8.68825241028128e-02 ), ( -4.96210210320117e-02 , -1.71308080191692e-02 , -2.46797329567554e-03 ), ( -2.57417833491587e-02 , -1.27072104130814e-02 , -4.36563096528796e-02 ), ( 3.50569488762591e-02 , 1.26401492722969e-02 , 7.70393273253328e-03 ), ( 6.24768816248500e-03 , -9.62139053241703e-03 , -1.30337943322201e-01 ), ( -1.12985180071072e-02 , -2.06177355430267e-02 , -1.85993589056636e-01 ), ( 5.29348141254694e-02 , 5.03138439773476e-03 , -1.44267875163925e-01 ), ( 8.20488240947292e-02 , 7.72564961274524e-03 , -2.24424383109399e-01 ), ( 1.43741200481599e-01 , 2.95776404414769e-02 , -2.15213605094362e-01 ), ( 1.91560122699135e-02 , -1.87960611889979e-02 , -2.80895918416516e-01 ), ( 2.02208567094964e-02 , -2.49419990716658e-02 , -3.53093435084104e-01 ), ( -3.76869002135258e-02 , -3.52523426763374e-02 , -2.48585256624855e-01 ), ( -1.03097299401374e-01 , -6.16010311536067e-02 , -2.93621852395483e-01 ), ( -1.44315955892824e-01 , -7.11639239898008e-02 , -2.43902469408960e-01 ), ( -1.61211568058450e-01 , -8.32521849218474e-02 , -3.14129047786798e-01 ), ( -1.90688403130903e-01 , -9.93378441717621e-02 , -3.81142834348199e-01 ), ( -1.99058749744944e-01 , -9.61082746547262e-02 , -3.13682024238514e-01 ), ( -2.41655340583087e-01 , -1.13020999449668e-01 , -3.40281173242029e-01 ), ( -1.21386618258863e-01 , -7.02975300165448e-02 , -3.20958120944753e-01 ), ( -1.79879455960514e-01 , -8.43825397273040e-02 , -2.56108328278949e-01 ), ( -2.33738308587350e-01 , -1.03885528953455e-01 , -2.68871577117677e-01 ), ( -2.69524049133083e-01 , -1.08593607135721e-01 , -1.85835805291378e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 35, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 35, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 35, atoms_positions[size = 51] = { ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 ), ( 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 ), ( 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 ), ( 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 ), ( 6.99557007941534e+00 , -2.08949019947414e+00 , -8.34982348421562e-01 ), ( 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 ), ( 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 ), ( 7.15684013418872e+00 , -3.54390863773740e-01 , 4.41439619442458e+00 ), ( 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 ), ( 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 ), ( 5.85765441330763e+00 , 2.25357632863418e+00 , 2.96135309177717e+00 ), ( 5.12892956232295e+00 , 3.52475977030786e+00 , 2.86058621031244e+00 ), ( 6.27581259529792e+00 , 4.44068649408999e+00 , 2.28442867565879e+00 ), ( 3.86003778030757e+00 , 3.62365514967571e+00 , 2.00838763634469e+00 ), ( 2.84340461899748e+00 , 4.15942819785390e+00 , 2.41554148010378e+00 ), ( 3.90011501266677e+00 , 3.15331106552999e+00 , 7.73473736426513e-01 ), ( 2.76266377314302e+00 , 3.12093202274932e+00 , -7.17337222929322e-02 ), ( 3.14084718885558e+00 , 2.65670750570764e+00 , -1.52930446548570e+00 ), ( 1.59827200508141e+00 , 2.26078244998539e+00 , 4.39327007224038e-01 ), ( 4.28855127489450e-01 , 2.61395650836417e+00 , 4.31340874109629e-01 ), ( 2.03103823246046e+00 , 1.11283247621894e+00 , 1.04595998456927e+00 ), ( 1.28500694013577e+00 , 1.62305442570039e-01 , 1.66404889101030e+00 ), ( 2.09593707495244e+00 , -1.09369235287619e+00 , 2.03492022443080e+00 ), ( 5.71701501672222e-01 , 6.19146366947443e-01 , 2.93626404368821e+00 ), ( -6.03471256680418e-01 , 3.58340641749683e-01 , 3.20436015880103e+00 ), ( 1.28814514769357e+00 , 1.42513706084500e+00 , 3.78036167098267e+00 ), ( 9.08243457151620e-01 , 1.98320481057185e+00 , 5.05045130621804e+00 ), ( 2.04602747974294e+00 , 2.77475796806591e+00 , 5.72598118253736e+00 ), ( -3.59074828003976e-01 , 2.89145859638115e+00 , 4.92545793713795e+00 ), ( -1.11814862986205e+00 , 3.07115079927318e+00 , 5.89556865291653e+00 ), ( -5.27177213900735e-01 , 3.48610820723234e+00 , 3.73491500917195e+00 ), ( -1.45042715435018e+00 , 4.47572552119355e+00 , 3.41604513508138e+00 ), ( -7.70276122056878e-01 , 5.46520805609154e+00 , 2.48692710701402e+00 ), ( -2.75335044085151e+00 , 3.93091767583567e+00 , 2.72726254319426e+00 ), ( -3.79541596068014e+00 , 4.59448204069508e+00 , 2.80944426413156e+00 ), ( -2.70992237328715e+00 , 2.64703925881070e+00 , 2.34896722069397e+00 ), ( -3.81849439416217e+00 , 1.80287939976997e+00 , 1.99434655132483e+00 ), ( -3.34481882479411e+00 , 8.96831071549861e-01 , 7.72648337869764e-01 ), ( -4.26520399062543e+00 , 1.02303275116830e+00 , 3.24402621763846e+00 ), ( -5.43069766365938e+00 , 7.25474343111396e-01 , 3.35268627716778e+00 ), ( -3.36294899981467e+00 , 7.18002344988279e-01 , 4.16401048308498e+00 ), ( -3.66518114880938e+00 , 6.62673025110593e-02 , 5.46353759127663e+00 ), ( -2.34513938023854e+00 , -2.84218864339135e-01 , 6.12603983596036e+00 ), ( -4.49291987378211e+00 , 9.53913863017457e-01 , 6.42042535520696e+00 ), ( -5.35534261947300e+00 , 5.40785600506347e-01 , 7.17774433235047e+00 ), ( -6.29576538853292e+00 , 3.60348415987392e+00 , 6.77192099230956e+00 ), ( -7.04018281524354e+00 , 4.29966523735166e+00 , 7.51840899176246e+00 ), ( -6.61161190256765e+00 , 3.17067013371524e+00 , 5.55527971765492e+00 ), ( -4.11611022697671e+00 , 2.25256146811143e+00 , 6.41707374462336e+00 ), ( -4.80719704397028e+00 , 3.28162916048152e+00 , 7.20738265589035e+00 ), ( -4.00765081229166e+00 , 4.61319375564242e+00 , 7.28057771414888e+00 ) } +colvars: Step 35, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.85214732151540e-01 , -1.72436288368453e-02 , 9.58308517038361e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Calculating fit gradients. +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.99557007941534e+00 , -2.08949019947414e+00 , -8.34982348421562e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 , 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 7.15684013418872e+00 , -3.54390863773740e-01 , 4.41439619442458e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 , 5.85765441330763e+00 , 2.25357632863418e+00 , 2.96135309177717e+00 , 5.12892956232295e+00 , 3.52475977030786e+00 , 2.86058621031244e+00 , 6.27581259529792e+00 , 4.44068649408999e+00 , 2.28442867565879e+00 , 3.86003778030757e+00 , 3.62365514967571e+00 , 2.00838763634469e+00 , 2.84340461899748e+00 , 4.15942819785390e+00 , 2.41554148010378e+00 , 3.90011501266677e+00 , 3.15331106552999e+00 , 7.73473736426513e-01 , 2.76266377314302e+00 , 3.12093202274932e+00 , -7.17337222929322e-02 , 3.14084718885558e+00 , 2.65670750570764e+00 , -1.52930446548570e+00 , 1.59827200508141e+00 , 2.26078244998539e+00 , 4.39327007224038e-01 , 4.28855127489450e-01 , 2.61395650836417e+00 , 4.31340874109629e-01 , 2.03103823246046e+00 , 1.11283247621894e+00 , 1.04595998456927e+00 , 1.28500694013577e+00 , 1.62305442570039e-01 , 1.66404889101030e+00 , 2.09593707495244e+00 , -1.09369235287619e+00 , 2.03492022443080e+00 , 5.71701501672222e-01 , 6.19146366947443e-01 , 2.93626404368821e+00 , -6.03471256680418e-01 , 3.58340641749683e-01 , 3.20436015880103e+00 , 1.28814514769357e+00 , 1.42513706084500e+00 , 3.78036167098267e+00 , 9.08243457151620e-01 , 1.98320481057185e+00 , 5.05045130621804e+00 , 2.04602747974294e+00 , 2.77475796806591e+00 , 5.72598118253736e+00 , -3.59074828003976e-01 , 2.89145859638115e+00 , 4.92545793713795e+00 , -1.11814862986205e+00 , 3.07115079927318e+00 , 5.89556865291653e+00 , -5.27177213900735e-01 , 3.48610820723234e+00 , 3.73491500917195e+00 , -1.45042715435018e+00 , 4.47572552119355e+00 , 3.41604513508138e+00 , -7.70276122056878e-01 , 5.46520805609154e+00 , 2.48692710701402e+00 , -2.75335044085151e+00 , 3.93091767583567e+00 , 2.72726254319426e+00 , -3.79541596068014e+00 , 4.59448204069508e+00 , 2.80944426413156e+00 , -2.70992237328715e+00 , 2.64703925881070e+00 , 2.34896722069397e+00 , -3.81849439416217e+00 , 1.80287939976997e+00 , 1.99434655132483e+00 , -3.34481882479411e+00 , 8.96831071549861e-01 , 7.72648337869764e-01 , -4.26520399062543e+00 , 1.02303275116830e+00 , 3.24402621763846e+00 , -5.43069766365938e+00 , 7.25474343111396e-01 , 3.35268627716778e+00 , -3.36294899981467e+00 , 7.18002344988279e-01 , 4.16401048308498e+00 , -3.66518114880938e+00 , 6.62673025110593e-02 , 5.46353759127663e+00 , -2.34513938023854e+00 , -2.84218864339135e-01 , 6.12603983596036e+00 , -4.49291987378211e+00 , 9.53913863017457e-01 , 6.42042535520696e+00 , -5.35534261947300e+00 , 5.40785600506347e-01 , 7.17774433235047e+00 , -6.29576538853292e+00 , 3.60348415987392e+00 , 6.77192099230956e+00 , -7.04018281524354e+00 , 4.29966523735166e+00 , 7.51840899176246e+00 , -6.61161190256765e+00 , 3.17067013371524e+00 , 5.55527971765492e+00 , -4.11611022697671e+00 , 2.25256146811143e+00 , 6.41707374462336e+00 , -4.80719704397028e+00 , 3.28162916048152e+00 , 7.20738265589035e+00 , -4.00765081229166e+00 , 4.61319375564242e+00 , 7.28057771414888e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.85214732151540e-01 , -1.72436288368453e-02 , 9.58308517038361e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.99557007941534e+00 , -2.08949019947414e+00 , -8.34982348421562e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 8.16073584119568e-01 , 4.89061357933961e+00 , -1.53433980457300e-01 , 7.64716481026893e-01 , 6.78879241700704e+00 , -3.10940758589153e-01 , 1.96199902827316e+00 , 6.08153568481550e+00 , -2.38215373575986e-01 , 3.23631741569087e+00 , 7.15684013418872e+00 , -3.54390863773740e-01 , 4.41439619442458e+00 , 5.30718500289043e+00 , 1.06492678201416e+00 , 3.36293473937713e+00 , 4.19752524266610e+00 , 1.00318233369175e+00 , 3.83589391843376e+00 , 5.85765441330763e+00 , 2.25357632863418e+00 , 2.96135309177717e+00 , 5.12892956232295e+00 , 3.52475977030786e+00 , 2.86058621031244e+00 , 6.27581259529792e+00 , 4.44068649408999e+00 , 2.28442867565879e+00 , 3.86003778030757e+00 , 3.62365514967571e+00 , 2.00838763634469e+00 , 2.84340461899748e+00 , 4.15942819785390e+00 , 2.41554148010378e+00 , 3.90011501266677e+00 , 3.15331106552999e+00 , 7.73473736426513e-01 , 2.76266377314302e+00 , 3.12093202274932e+00 , -7.17337222929322e-02 , 3.14084718885558e+00 , 2.65670750570764e+00 , -1.52930446548570e+00 , 1.59827200508141e+00 , 2.26078244998539e+00 , 4.39327007224038e-01 , 4.28855127489450e-01 , 2.61395650836417e+00 , 4.31340874109629e-01 , 2.03103823246046e+00 , 1.11283247621894e+00 , 1.04595998456927e+00 , 1.28500694013577e+00 , 1.62305442570039e-01 , 1.66404889101030e+00 , 2.09593707495244e+00 , -1.09369235287619e+00 , 2.03492022443080e+00 , 5.71701501672222e-01 , 6.19146366947443e-01 , 2.93626404368821e+00 , -6.03471256680418e-01 , 3.58340641749683e-01 , 3.20436015880103e+00 , 1.28814514769357e+00 , 1.42513706084500e+00 , 3.78036167098267e+00 , 9.08243457151620e-01 , 1.98320481057185e+00 , 5.05045130621804e+00 , 2.04602747974294e+00 , 2.77475796806591e+00 , 5.72598118253736e+00 , -3.59074828003976e-01 , 2.89145859638115e+00 , 4.92545793713795e+00 , -1.11814862986205e+00 , 3.07115079927318e+00 , 5.89556865291653e+00 , -5.27177213900735e-01 , 3.48610820723234e+00 , 3.73491500917195e+00 , -1.45042715435018e+00 , 4.47572552119355e+00 , 3.41604513508138e+00 , -7.70276122056878e-01 , 5.46520805609154e+00 , 2.48692710701402e+00 , -2.75335044085151e+00 , 3.93091767583567e+00 , 2.72726254319426e+00 , -3.79541596068014e+00 , 4.59448204069508e+00 , 2.80944426413156e+00 , -2.70992237328715e+00 , 2.64703925881070e+00 , 2.34896722069397e+00 , -3.81849439416217e+00 , 1.80287939976997e+00 , 1.99434655132483e+00 , -3.34481882479411e+00 , 8.96831071549861e-01 , 7.72648337869764e-01 , -4.26520399062543e+00 , 1.02303275116830e+00 , 3.24402621763846e+00 , -5.43069766365938e+00 , 7.25474343111396e-01 , 3.35268627716778e+00 , -3.36294899981467e+00 , 7.18002344988279e-01 , 4.16401048308498e+00 , -3.66518114880938e+00 , 6.62673025110593e-02 , 5.46353759127663e+00 , -2.34513938023854e+00 , -2.84218864339135e-01 , 6.12603983596036e+00 , -4.49291987378211e+00 , 9.53913863017457e-01 , 6.42042535520696e+00 , -5.35534261947300e+00 , 5.40785600506347e-01 , 7.17774433235047e+00 , -6.29576538853292e+00 , 3.60348415987392e+00 , 6.77192099230956e+00 , -7.04018281524354e+00 , 4.29966523735166e+00 , 7.51840899176246e+00 , -6.61161190256765e+00 , 3.17067013371524e+00 , 5.55527971765492e+00 , -4.11611022697671e+00 , 2.25256146811143e+00 , 6.41707374462336e+00 , -4.80719704397028e+00 , 3.28162916048152e+00 , 7.20738265589035e+00 , -4.00765081229166e+00 , 4.61319375564242e+00 , 7.28057771414888e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.2351 , 6.52351 , 13.047 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.2351 , 6.52351 , 13.047 ) to colvar "one". +colvars: Adding total bias energy: 55.3721 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.2351 , 6.52351 , 13.047 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.17368 , -0.53241 , -1.43468 ) +colvars: ( -4.43643 , -0.456542 , -1.23024 ) +colvars: ( -4.43643 , -0.456542 , -1.23024 ) +colvars: ( -5.90945 , -0.608127 , -1.63872 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.92296 , 0.205459 , 0.626253 ) +colvars: ( 0.800734 , 0.277868 , 0.650672 ) +colvars: ( 0.783694 , 0.271182 , 0.63227 ) +colvars: ( 0.686863 , 0.277543 , 0.585337 ) +colvars: ( 0.674749 , 0.208556 , 0.488783 ) +colvars: ( 0.598771 , 0.356603 , 0.637858 ) +colvars: ( 0.48968 , 0.369959 , 0.593026 ) +colvars: ( 0.411566 , 0.469844 , 0.678296 ) +colvars: ( 0.405973 , 0.323526 , 0.484968 ) +colvars: ( 0.370767 , 0.279998 , 0.408334 ) +colvars: ( 0.375422 , 0.329285 , 0.475037 ) +colvars: ( 0.302348 , 0.284713 , 0.37546 ) +colvars: ( 0.274028 , 0.315071 , 0.398765 ) +colvars: ( 0.366041 , 0.184056 , 0.280965 ) +colvars: ( 0.30616 , 0.138755 , 0.187961 ) +colvars: ( 0.491308 , 0.146756 , 0.303902 ) +colvars: ( 0.565342 , 0.052818 , 0.224034 ) +colvars: ( 0.697388 , 0.0323139 , 0.272663 ) +colvars: ( 0.574747 , 0.0194281 , 0.186006 ) +colvars: ( 0.558689 , -0.048033 , 0.089187 ) +colvars: ( 0.596626 , 0.0687406 , 0.262559 ) +colvars: ( 0.59573 , 0.0514715 , 0.239607 ) +colvars: ( 0.633521 , 0.118342 , 0.348048 ) +colvars: ( 0.468978 , 0.0549671 , 0.171895 ) +colvars: ( 0.462289 , -0.00317348 , 0.0925278 ) +colvars: ( 0.36472 , 0.12221 , 0.199843 ) +colvars: ( 0.237679 , 0.130039 , 0.137597 ) +colvars: ( 0.144076 , 0.218206 , 0.198809 ) +colvars: ( 0.20848 , 0.0538389 , 0.0219299 ) +colvars: ( 0.158458 , 0.0158065 , -0.0560085 ) +colvars: ( 0.242138 , 0.0281728 , 0.00776365 ) +colvars: ( 0.227403 , -0.0466139 , -0.0978208 ) +colvars: ( 0.262722 , -0.049216 , -0.0810681 ) +colvars: ( 0.30446 , -0.135134 , -0.168925 ) +colvars: ( 0.259549 , -0.19044 , -0.266397 ) +colvars: ( 0.422274 , -0.149934 , -0.120997 ) +colvars: ( 0.501635 , -0.227657 , -0.176757 ) +colvars: ( 0.63565 , -0.229361 , -0.102575 ) +colvars: ( 0.454022 , -0.233213 , -0.21112 ) +colvars: ( 0.459797 , -0.303698 , -0.299422 ) +colvars: ( 0.404687 , -0.158103 , -0.141638 ) +colvars: ( 0.349947 , -0.152574 , -0.165658 ) +colvars: ( 0.333509 , -0.063359 , -0.0590944 ) +colvars: ( 0.224016 , -0.162602 , -0.250478 ) +colvars: ( 0.199459 , -0.206546 , -0.32158 ) +colvars: ( 0.0175125 , -0.210718 , -0.430723 ) +colvars: ( -0.0753586 , -0.22983 , -0.5085 ) +colvars: ( 0.119583 , -0.261262 , -0.438217 ) +colvars: ( 0.140049 , -0.120875 , -0.24412 ) +colvars: ( 0.0181361 , -0.12627 , -0.320627 ) +colvars: ( -0.0729883 , -0.0432945 , -0.264747 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.17368 , 0.53241 , 1.43468 ) +colvars: ( 4.43643 , 0.456542 , 1.23024 ) +colvars: ( 4.43643 , 0.456542 , 1.23024 ) +colvars: ( 5.90945 , 0.608127 , 1.63872 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.637012 , -0.0847962 , -0.36949 ) +colvars: ( -0.573946 , -0.172151 , -0.334485 ) +colvars: ( -0.51926 , -0.148666 , -0.272008 ) +colvars: ( -0.536004 , -0.201058 , -0.30577 ) +colvars: ( -0.525875 , -0.138641 , -0.2754 ) +colvars: ( -0.512888 , -0.298408 , -0.314088 ) +colvars: ( -0.481943 , -0.340946 , -0.296807 ) +colvars: ( -0.46173 , -0.454512 , -0.313288 ) +colvars: ( -0.415963 , -0.303213 , -0.218383 ) +colvars: ( -0.41269 , -0.276364 , -0.206408 ) +colvars: ( -0.362501 , -0.297068 , -0.162747 ) +colvars: ( -0.29879 , -0.257738 , -0.0860838 ) +colvars: ( -0.245984 , -0.273381 , -0.0381594 ) +colvars: ( -0.317277 , -0.148534 , -0.0692831 ) +colvars: ( -0.285459 , -0.11737 , -0.0272661 ) +colvars: ( -0.371569 , -0.0880211 , -0.104173 ) +colvars: ( -0.397545 , 0.0159205 , -0.0965907 ) +colvars: ( -0.446858 , 0.0660931 , -0.129832 ) +colvars: ( -0.438986 , 0.0317213 , -0.13306 ) +colvars: ( -0.427108 , 0.0919305 , -0.101651 ) +colvars: ( -0.487042 , -0.0256772 , -0.199864 ) +colvars: ( -0.525328 , -0.0273204 , -0.238815 ) +colvars: ( -0.579086 , -0.0968031 , -0.315252 ) +colvars: ( -0.473715 , -0.0588422 , -0.197227 ) +colvars: ( -0.481678 , -0.0121435 , -0.1901 ) +colvars: ( -0.417609 , -0.137317 , -0.16633 ) +colvars: ( -0.359886 , -0.170189 , -0.11905 ) +colvars: ( -0.308497 , -0.265502 , -0.0983378 ) +colvars: ( -0.315438 , -0.0928701 , -0.0494177 ) +colvars: ( -0.303251 , -0.0730574 , -0.0307751 ) +colvars: ( -0.291603 , -0.0453005 , -0.0101015 ) +colvars: ( -0.252923 , 0.034019 , 0.0543903 ) +colvars: ( -0.227413 , 0.0620037 , 0.0890476 ) +colvars: ( -0.298047 , 0.125746 , 0.0388042 ) +colvars: ( -0.270629 , 0.170119 , 0.080681 ) +colvars: ( -0.369282 , 0.155231 , -0.0231324 ) +colvars: ( -0.419594 , 0.235753 , -0.0475517 ) +colvars: ( -0.492031 , 0.259332 , -0.112606 ) +colvars: ( -0.434887 , 0.214763 , -0.0696926 ) +colvars: ( -0.439593 , 0.279189 , -0.0535585 ) +colvars: ( -0.442412 , 0.123074 , -0.106925 ) +colvars: ( -0.453091 , 0.0911576 , -0.127973 ) +colvars: ( -0.477918 , -0.0077544 , -0.184906 ) +colvars: ( -0.385164 , 0.0795275 , -0.0635765 ) +colvars: ( -0.390081 , 0.107425 , -0.059479 ) +colvars: ( -0.216246 , 0.114849 , 0.11736 ) +colvars: ( -0.165889 , 0.117058 , 0.168607 ) +colvars: ( -0.240682 , 0.1913 , 0.117589 ) +colvars: ( -0.319774 , 0.0366167 , -0.0118509 ) +colvars: ( -0.251611 , 0.0224974 , 0.0519764 ) +colvars: ( -0.1962 , -0.0653004 , 0.0791571 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 35. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 35. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atoms_new_colvar_forces = { ( -4.88773041589092e+00 , -4.11747518843095e-01 , -1.17792165613234e+00 ), ( -4.20964083320243e+00 , -3.50825276103993e-01 , -9.14054824244604e-01 ), ( -4.28556963406229e+00 , -3.80056019703401e-01 , -9.50673798522474e-01 ), ( -5.76057780104335e+00 , -5.38211345555065e-01 , -1.42533419000840e+00 ), ( 2.64433777671576e-01 , 1.22516386488947e-01 , 3.60262875102062e-01 ), ( 5.25956196086280e+00 , 5.90605514472119e-01 , 1.75845374595699e+00 ), ( 4.44416553275086e+00 , 4.85554943208970e-01 , 1.52646018403272e+00 ), ( -5.01645356454149e-02 , 1.53312307515041e-02 , 3.65007285136006e-01 ), ( 4.42643918786033e+00 , 4.76853917049569e-01 , 1.49682605555635e+00 ), ( 5.86752780851986e+00 , 6.11760618797509e-01 , 1.84064345203498e+00 ), ( 1.29212468468592e-02 , 3.22170935596684e-02 , 3.12289968770812e-01 ), ( 3.55830990268030e-03 , 2.69748988590546e-02 , 2.89375769967817e-01 ), ( 2.80436349964942e-02 , 4.16903335922004e-02 , 3.60605826785305e-01 ), ( 4.87643819756062e-02 , 3.55218396178170e-02 , 2.11681724122980e-01 ), ( 2.07018237491816e-02 , 2.13846809025174e-02 , 1.60694638770488e-01 ), ( 1.19739051482598e-01 , 5.87346125919219e-02 , 1.99729209947583e-01 ), ( 1.67797025916064e-01 , 6.87384570544897e-02 , 1.27443658948740e-01 ), ( 2.50530742622340e-01 , 9.84069560231624e-02 , 1.42831156975679e-01 ), ( 1.35760965628326e-01 , 5.11494379433253e-02 , 5.29457483579534e-02 ), ( 1.31580943542922e-01 , 4.38974800073435e-02 , -1.24636561763200e-02 ), ( 1.09583519653664e-01 , 4.30633374482006e-02 , 6.26952779110617e-02 ), ( 7.04010630709179e-02 , 2.41510393194242e-02 , 7.92648254228812e-04 ), ( 5.44348328275769e-02 , 2.15385449770796e-02 , 3.27964633753685e-02 ), ( -4.73686647494842e-03 , -3.87511753734138e-03 , -2.53325043703360e-02 ), ( -1.93889253197023e-02 , -1.53169493665381e-02 , -9.75718457958037e-02 ), ( -5.28881246319936e-02 , -1.51072241077729e-02 , 3.35126051890826e-02 ), ( -1.22207388663047e-01 , -4.01498134739777e-02 , 1.85467828808255e-02 ), ( -1.64421376548035e-01 , -4.72967471810293e-02 , 1.00471437819341e-01 ), ( -1.06957594948178e-01 , -3.90312780405301e-02 , -2.74878368456391e-02 ), ( -1.44793325520095e-01 , -5.72508869947707e-02 , -8.67835539894558e-02 ), ( -4.94657279405175e-02 , -1.71277082198067e-02 , -2.33785265957891e-03 ), ( -2.55199857872662e-02 , -1.25948513702735e-02 , -4.34304530799997e-02 ), ( 3.53092271896965e-02 , 1.27876886030257e-02 , 7.97949528036909e-03 ), ( 6.41360581866401e-03 , -9.38854054791916e-03 , -1.30121257665082e-01 ), ( -1.10807762782602e-02 , -2.03209922034441e-02 , -1.85715696077113e-01 ), ( 5.29922541427579e-02 , 5.29663563833063e-03 , -1.44129760474241e-01 ), ( 8.20412963040485e-02 , 8.09593520773705e-03 , -2.24308593836000e-01 ), ( 1.43619375022329e-01 , 2.99709825523847e-02 , -2.15181243279100e-01 ), ( 1.91346939294886e-02 , -1.84505750720338e-02 , -2.80812320289916e-01 ), ( 2.02041612678813e-02 , -2.45085522620857e-02 , -3.52980310490388e-01 ), ( -3.77246918730068e-02 , -3.50285835670905e-02 , -2.48562761576247e-01 ), ( -1.03143599841225e-01 , -6.14165720153193e-02 , -2.93631469474359e-01 ), ( -1.44408550166542e-01 , -7.11133800420470e-02 , -2.44000259312310e-01 ), ( -1.61148724977604e-01 , -8.30749564303604e-02 , -3.14054608163947e-01 ), ( -1.90621840589093e-01 , -9.91203630109317e-02 , -3.81059508335726e-01 ), ( -1.98733961295644e-01 , -9.58692876794523e-02 , -3.13362647420307e-01 ), ( -2.41247761119296e-01 , -1.12772561806286e-01 , -3.39893461381864e-01 ), ( -1.21099191399720e-01 , -6.99612980240896e-02 , -3.20628712112169e-01 ), ( -1.79724726253634e-01 , -8.42586700062325e-02 , -2.55970522827265e-01 ), ( -2.33475387983648e-01 , -1.03772620881512e-01 , -2.68650775547765e-01 ), ( -2.69188676099671e-01 , -1.08594874619903e-01 , -1.85589931087990e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 36, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 36, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 36, atoms_positions[size = 51] = { ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 ), ( 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 ), ( 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 ), ( 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 ), ( 6.99723356848930e+00 , -2.09419525812471e+00 , -8.27129300320567e-01 ), ( 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 ), ( 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 ), ( 7.15706021666618e+00 , -3.57597425855947e-01 , 4.41945794203117e+00 ), ( 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 ), ( 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 ), ( 5.85758832793169e+00 , 2.25504488524377e+00 , 2.95891408447770e+00 ), ( 5.12779342097314e+00 , 3.51941981343439e+00 , 2.85605341409322e+00 ), ( 6.26948731267596e+00 , 4.43451101750161e+00 , 2.28466092075193e+00 ), ( 3.86104658422879e+00 , 3.62038375789240e+00 , 2.00553047766542e+00 ), ( 2.84901780336858e+00 , 4.15733284514224e+00 , 2.41228272300415e+00 ), ( 3.90000070771336e+00 , 3.14514793484549e+00 , 7.80126214616235e-01 ), ( 2.75910867030025e+00 , 3.13297851157940e+00 , -7.47200298448949e-02 ), ( 3.14459302428540e+00 , 2.65929421023285e+00 , -1.52372351883350e+00 ), ( 1.61368031524600e+00 , 2.27120350503521e+00 , 4.45440350384779e-01 ), ( 4.31443198308536e-01 , 2.61322851488362e+00 , 4.25368395503651e-01 ), ( 2.02568946456082e+00 , 1.11003293167251e+00 , 1.04256934791582e+00 ), ( 1.29324408837554e+00 , 1.65418978524617e-01 , 1.66294534831571e+00 ), ( 2.09759579563072e+00 , -1.09349147718460e+00 , 2.03197610368111e+00 ), ( 5.70875932381883e-01 , 6.22345595517025e-01 , 2.93368466438564e+00 ), ( -6.06959227306262e-01 , 3.58481065283510e-01 , 3.20858547514740e+00 ), ( 1.28982439599295e+00 , 1.43021466496170e+00 , 3.78404569606397e+00 ), ( 9.13653392685198e-01 , 1.98555734869590e+00 , 5.05495946536194e+00 ), ( 2.03853629348129e+00 , 2.77788525774637e+00 , 5.72608999678792e+00 ), ( -3.57734959834092e-01 , 2.88943674699778e+00 , 4.92102384123755e+00 ), ( -1.11858976612841e+00 , 3.07146048554314e+00 , 5.89730870348002e+00 ), ( -5.21648760875345e-01 , 3.47893075978990e+00 , 3.72615940149803e+00 ), ( -1.45140237321515e+00 , 4.47656846776950e+00 , 3.41374554257939e+00 ), ( -7.74661600225245e-01 , 5.47233806133262e+00 , 2.48794318145854e+00 ), ( -2.75455552906930e+00 , 3.92756827594720e+00 , 2.72030917715245e+00 ), ( -3.79306921941895e+00 , 4.59963166833403e+00 , 2.80750434481269e+00 ), ( -2.71245945596158e+00 , 2.65077731215350e+00 , 2.34677756924521e+00 ), ( -3.82142967663025e+00 , 1.79538957524820e+00 , 1.99072186156305e+00 ), ( -3.34187444427744e+00 , 9.02887036972023e-01 , 7.66561654111795e-01 ), ( -4.27004532929729e+00 , 1.02046130461287e+00 , 3.24056835145711e+00 ), ( -5.42297998545340e+00 , 7.19813061559532e-01 , 3.35626899032413e+00 ), ( -3.35980353726781e+00 , 7.13425912407024e-01 , 4.16704508215239e+00 ), ( -3.66464323877533e+00 , 6.28586029648061e-02 , 5.45607066683593e+00 ), ( -2.33674333981043e+00 , -2.76805072869965e-01 , 6.12800241170569e+00 ), ( -4.49189756436332e+00 , 9.63422943902330e-01 , 6.42018477707952e+00 ), ( -5.35518376619704e+00 , 5.33516535464145e-01 , 7.17330430327523e+00 ), ( -6.28962935081183e+00 , 3.60051004574782e+00 , 6.77976422121130e+00 ), ( -7.04644687483213e+00 , 4.29840961125306e+00 , 7.51729040384008e+00 ), ( -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 ), ( -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 ), ( -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 ), ( -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ) } +colvars: Step 36, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.83103690637276e-01 , -1.77547915732536e-02 , 9.58924954166771e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.99723356848930e+00 , -2.09419525812471e+00 , -8.27129300320567e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 , 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 7.15706021666618e+00 , -3.57597425855947e-01 , 4.41945794203117e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 , 5.85758832793169e+00 , 2.25504488524377e+00 , 2.95891408447770e+00 , 5.12779342097314e+00 , 3.51941981343439e+00 , 2.85605341409322e+00 , 6.26948731267596e+00 , 4.43451101750161e+00 , 2.28466092075193e+00 , 3.86104658422879e+00 , 3.62038375789240e+00 , 2.00553047766542e+00 , 2.84901780336858e+00 , 4.15733284514224e+00 , 2.41228272300415e+00 , 3.90000070771336e+00 , 3.14514793484549e+00 , 7.80126214616235e-01 , 2.75910867030025e+00 , 3.13297851157940e+00 , -7.47200298448949e-02 , 3.14459302428540e+00 , 2.65929421023285e+00 , -1.52372351883350e+00 , 1.61368031524600e+00 , 2.27120350503521e+00 , 4.45440350384779e-01 , 4.31443198308536e-01 , 2.61322851488362e+00 , 4.25368395503651e-01 , 2.02568946456082e+00 , 1.11003293167251e+00 , 1.04256934791582e+00 , 1.29324408837554e+00 , 1.65418978524617e-01 , 1.66294534831571e+00 , 2.09759579563072e+00 , -1.09349147718460e+00 , 2.03197610368111e+00 , 5.70875932381883e-01 , 6.22345595517025e-01 , 2.93368466438564e+00 , -6.06959227306262e-01 , 3.58481065283510e-01 , 3.20858547514740e+00 , 1.28982439599295e+00 , 1.43021466496170e+00 , 3.78404569606397e+00 , 9.13653392685198e-01 , 1.98555734869590e+00 , 5.05495946536194e+00 , 2.03853629348129e+00 , 2.77788525774637e+00 , 5.72608999678792e+00 , -3.57734959834092e-01 , 2.88943674699778e+00 , 4.92102384123755e+00 , -1.11858976612841e+00 , 3.07146048554314e+00 , 5.89730870348002e+00 , -5.21648760875345e-01 , 3.47893075978990e+00 , 3.72615940149803e+00 , -1.45140237321515e+00 , 4.47656846776950e+00 , 3.41374554257939e+00 , -7.74661600225245e-01 , 5.47233806133262e+00 , 2.48794318145854e+00 , -2.75455552906930e+00 , 3.92756827594720e+00 , 2.72030917715245e+00 , -3.79306921941895e+00 , 4.59963166833403e+00 , 2.80750434481269e+00 , -2.71245945596158e+00 , 2.65077731215350e+00 , 2.34677756924521e+00 , -3.82142967663025e+00 , 1.79538957524820e+00 , 1.99072186156305e+00 , -3.34187444427744e+00 , 9.02887036972023e-01 , 7.66561654111795e-01 , -4.27004532929729e+00 , 1.02046130461287e+00 , 3.24056835145711e+00 , -5.42297998545340e+00 , 7.19813061559532e-01 , 3.35626899032413e+00 , -3.35980353726781e+00 , 7.13425912407024e-01 , 4.16704508215239e+00 , -3.66464323877533e+00 , 6.28586029648061e-02 , 5.45607066683593e+00 , -2.33674333981043e+00 , -2.76805072869965e-01 , 6.12800241170569e+00 , -4.49189756436332e+00 , 9.63422943902330e-01 , 6.42018477707952e+00 , -5.35518376619704e+00 , 5.33516535464145e-01 , 7.17330430327523e+00 , -6.28962935081183e+00 , 3.60051004574782e+00 , 6.77976422121130e+00 , -7.04644687483213e+00 , 4.29840961125306e+00 , 7.51729040384008e+00 , -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 , -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 , -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 , -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.83103690637276e-01 , -1.77547915732536e-02 , 9.58924954166771e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.17006384340085e+00 , 4.24710322258860e-02 , -7.00715579679792e-01 , 6.81026330758797e+00 , -6.22179339788135e-01 , -5.10350105286701e-01 , 6.99723356848930e+00 , -2.09419525812471e+00 , -8.27129300320567e-01 , 6.06158812502298e+00 , -3.26337766808664e-01 , 8.14370134089737e-01 , 4.88431700397011e+00 , -1.53831898439526e-01 , 7.68785954084019e-01 , 6.78332987899884e+00 , -3.13380341422373e-01 , 1.95986439798575e+00 , 6.08269094083567e+00 , -2.39797532318015e-01 , 3.24983551267153e+00 , 7.15706021666618e+00 , -3.57597425855947e-01 , 4.41945794203117e+00 , 5.30480311254545e+00 , 1.06493452304878e+00 , 3.36213579803043e+00 , 4.19828435191294e+00 , 1.00363069846155e+00 , 3.84732138572337e+00 , 5.85758832793169e+00 , 2.25504488524377e+00 , 2.95891408447770e+00 , 5.12779342097314e+00 , 3.51941981343439e+00 , 2.85605341409322e+00 , 6.26948731267596e+00 , 4.43451101750161e+00 , 2.28466092075193e+00 , 3.86104658422879e+00 , 3.62038375789240e+00 , 2.00553047766542e+00 , 2.84901780336858e+00 , 4.15733284514224e+00 , 2.41228272300415e+00 , 3.90000070771336e+00 , 3.14514793484549e+00 , 7.80126214616235e-01 , 2.75910867030025e+00 , 3.13297851157940e+00 , -7.47200298448949e-02 , 3.14459302428540e+00 , 2.65929421023285e+00 , -1.52372351883350e+00 , 1.61368031524600e+00 , 2.27120350503521e+00 , 4.45440350384779e-01 , 4.31443198308536e-01 , 2.61322851488362e+00 , 4.25368395503651e-01 , 2.02568946456082e+00 , 1.11003293167251e+00 , 1.04256934791582e+00 , 1.29324408837554e+00 , 1.65418978524617e-01 , 1.66294534831571e+00 , 2.09759579563072e+00 , -1.09349147718460e+00 , 2.03197610368111e+00 , 5.70875932381883e-01 , 6.22345595517025e-01 , 2.93368466438564e+00 , -6.06959227306262e-01 , 3.58481065283510e-01 , 3.20858547514740e+00 , 1.28982439599295e+00 , 1.43021466496170e+00 , 3.78404569606397e+00 , 9.13653392685198e-01 , 1.98555734869590e+00 , 5.05495946536194e+00 , 2.03853629348129e+00 , 2.77788525774637e+00 , 5.72608999678792e+00 , -3.57734959834092e-01 , 2.88943674699778e+00 , 4.92102384123755e+00 , -1.11858976612841e+00 , 3.07146048554314e+00 , 5.89730870348002e+00 , -5.21648760875345e-01 , 3.47893075978990e+00 , 3.72615940149803e+00 , -1.45140237321515e+00 , 4.47656846776950e+00 , 3.41374554257939e+00 , -7.74661600225245e-01 , 5.47233806133262e+00 , 2.48794318145854e+00 , -2.75455552906930e+00 , 3.92756827594720e+00 , 2.72030917715245e+00 , -3.79306921941895e+00 , 4.59963166833403e+00 , 2.80750434481269e+00 , -2.71245945596158e+00 , 2.65077731215350e+00 , 2.34677756924521e+00 , -3.82142967663025e+00 , 1.79538957524820e+00 , 1.99072186156305e+00 , -3.34187444427744e+00 , 9.02887036972023e-01 , 7.66561654111795e-01 , -4.27004532929729e+00 , 1.02046130461287e+00 , 3.24056835145711e+00 , -5.42297998545340e+00 , 7.19813061559532e-01 , 3.35626899032413e+00 , -3.35980353726781e+00 , 7.13425912407024e-01 , 4.16704508215239e+00 , -3.66464323877533e+00 , 6.28586029648061e-02 , 5.45607066683593e+00 , -2.33674333981043e+00 , -2.76805072869965e-01 , 6.12800241170569e+00 , -4.49189756436332e+00 , 9.63422943902330e-01 , 6.42018477707952e+00 , -5.35518376619704e+00 , 5.33516535464145e-01 , 7.17330430327523e+00 , -6.28962935081183e+00 , 3.60051004574782e+00 , 6.77976422121130e+00 , -7.04644687483213e+00 , 4.29840961125306e+00 , 7.51729040384008e+00 , -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 , -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 , -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 , -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.1383 , 6.51383 , 13.0277 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.1383 , 6.51383 , 13.0277 ) to colvar "one". +colvars: Adding total bias energy: 55.2297 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.1383 , 6.51383 , 13.0277 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.16842 , -0.528748 , -1.42246 ) +colvars: ( -4.43192 , -0.453401 , -1.21976 ) +colvars: ( -4.43192 , -0.453401 , -1.21976 ) +colvars: ( -5.90344 , -0.603944 , -1.62476 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.920477 , 0.205233 , 0.62301 ) +colvars: ( 0.798702 , 0.277334 , 0.647358 ) +colvars: ( 0.781649 , 0.27075 , 0.629123 ) +colvars: ( 0.685297 , 0.276868 , 0.582298 ) +colvars: ( 0.673233 , 0.208073 , 0.486169 ) +colvars: ( 0.597564 , 0.355583 , 0.634578 ) +colvars: ( 0.488927 , 0.368755 , 0.589924 ) +colvars: ( 0.411126 , 0.468248 , 0.674813 ) +colvars: ( 0.405505 , 0.322428 , 0.482394 ) +colvars: ( 0.370463 , 0.278961 , 0.406072 ) +colvars: ( 0.375004 , 0.328226 , 0.472581 ) +colvars: ( 0.302169 , 0.283772 , 0.373497 ) +colvars: ( 0.273886 , 0.314101 , 0.396779 ) +colvars: ( 0.365612 , 0.183482 , 0.279416 ) +colvars: ( 0.305963 , 0.138259 , 0.18683 ) +colvars: ( 0.490393 , 0.146416 , 0.302239 ) +colvars: ( 0.564141 , 0.0528321 , 0.222715 ) +colvars: ( 0.69566 , 0.0325386 , 0.271133 ) +colvars: ( 0.573578 , 0.0194665 , 0.184782 ) +colvars: ( 0.557586 , -0.047811 , 0.0883896 ) +colvars: ( 0.59543 , 0.0685809 , 0.260935 ) +colvars: ( 0.594606 , 0.0512773 , 0.238013 ) +colvars: ( 0.632302 , 0.117919 , 0.345916 ) +colvars: ( 0.468356 , 0.0546254 , 0.170601 ) +colvars: ( 0.461721 , -0.00338162 , 0.0915566 ) +colvars: ( 0.364478 , 0.121595 , 0.198463 ) +colvars: ( 0.237929 , 0.129277 , 0.136505 ) +colvars: ( 0.144661 , 0.217122 , 0.197486 ) +colvars: ( 0.208803 , 0.053328 , 0.0213949 ) +colvars: ( 0.158999 , 0.0153309 , -0.0562194 ) +colvars: ( 0.242267 , 0.0278504 , 0.0073537 ) +colvars: ( 0.227546 , -0.0466726 , -0.097718 ) +colvars: ( 0.262658 , -0.0491442 , -0.0809689 ) +colvars: ( 0.304336 , -0.13489 , -0.168548 ) +colvars: ( 0.259595 , -0.190069 , -0.265581 ) +colvars: ( 0.421724 , -0.149569 , -0.120877 ) +colvars: ( 0.500813 , -0.227025 , -0.176436 ) +colvars: ( 0.634327 , -0.228616 , -0.102616 ) +colvars: ( 0.453449 , -0.232691 , -0.21071 ) +colvars: ( 0.459216 , -0.302976 , -0.298637 ) +colvars: ( 0.404345 , -0.157904 , -0.141571 ) +colvars: ( 0.349878 , -0.152521 , -0.165543 ) +colvars: ( 0.333544 , -0.0636412 , -0.0594912 ) +colvars: ( 0.224419 , -0.162622 , -0.249958 ) +colvars: ( 0.199992 , -0.2065 , -0.32078 ) +colvars: ( 0.0185975 , -0.210647 , -0.429261 ) +colvars: ( -0.0739237 , -0.229779 , -0.506674 ) +colvars: ( 0.120242 , -0.260901 , -0.436701 ) +colvars: ( 0.140725 , -0.121037 , -0.243565 ) +colvars: ( 0.0192652 , -0.12651 , -0.319701 ) +colvars: ( -0.071542 , -0.0438282 , -0.26402 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.16842 , 0.528748 , 1.42246 ) +colvars: ( 4.43192 , 0.453401 , 1.21976 ) +colvars: ( 4.43192 , 0.453401 , 1.21976 ) +colvars: ( 5.90344 , 0.603944 , 1.62476 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.634968 , -0.0846854 , -0.366603 ) +colvars: ( -0.572265 , -0.17182 , -0.331514 ) +colvars: ( -0.517513 , -0.148414 , -0.269141 ) +colvars: ( -0.534714 , -0.200604 , -0.303037 ) +colvars: ( -0.52461 , -0.138305 , -0.273034 ) +colvars: ( -0.511916 , -0.297709 , -0.311147 ) +colvars: ( -0.48136 , -0.340097 , -0.294024 ) +colvars: ( -0.46143 , -0.453393 , -0.310174 ) +colvars: ( -0.415568 , -0.302421 , -0.216029 ) +colvars: ( -0.412437 , -0.275595 , -0.204333 ) +colvars: ( -0.362101 , -0.296308 , -0.16046 ) +colvars: ( -0.298539 , -0.257046 , -0.0841962 ) +colvars: ( -0.245721 , -0.27268 , -0.0362146 ) +colvars: ( -0.3168 , -0.148092 , -0.0677573 ) +colvars: ( -0.285156 , -0.116963 , -0.0260951 ) +colvars: ( -0.370694 , -0.087758 , -0.10256 ) +colvars: ( -0.396418 , 0.015941 , -0.0952819 ) +colvars: ( -0.445292 , 0.065944 , -0.128345 ) +colvars: ( -0.437925 , 0.0317398 , -0.131866 ) +colvars: ( -0.426085 , 0.0918367 , -0.100825 ) +colvars: ( -0.48601 , -0.0255249 , -0.198353 ) +colvars: ( -0.524398 , -0.0271302 , -0.237362 ) +colvars: ( -0.578132 , -0.0964649 , -0.313362 ) +colvars: ( -0.473195 , -0.0585251 , -0.196027 ) +colvars: ( -0.481206 , -0.0119033 , -0.189191 ) +colvars: ( -0.417392 , -0.136806 , -0.165035 ) +colvars: ( -0.360066 , -0.169554 , -0.117991 ) +colvars: ( -0.308947 , -0.264647 , -0.0970579 ) +colvars: ( -0.315628 , -0.0923976 , -0.0488182 ) +colvars: ( -0.303624 , -0.0725896 , -0.0304621 ) +colvars: ( -0.291589 , -0.0449704 , -0.00958362 ) +colvars: ( -0.252872 , 0.0341752 , 0.0544869 ) +colvars: ( -0.227146 , 0.0620521 , 0.089177 ) +colvars: ( -0.297781 , 0.125697 , 0.0386426 ) +colvars: ( -0.270485 , 0.17 , 0.0801465 ) +colvars: ( -0.368693 , 0.155085 , -0.0230977 ) +colvars: ( -0.418793 , 0.235426 , -0.0477142 ) +colvars: ( -0.490842 , 0.258905 , -0.112478 ) +colvars: ( -0.434329 , 0.214532 , -0.069958 ) +colvars: ( -0.439021 , 0.278833 , -0.0541544 ) +colvars: ( -0.442084 , 0.12307 , -0.106908 ) +colvars: ( -0.453025 , 0.0912728 , -0.128021 ) +colvars: ( -0.477986 , -0.00741222 , -0.184529 ) +colvars: ( -0.385464 , 0.0797162 , -0.0639548 ) +colvars: ( -0.390497 , 0.107586 , -0.0601134 ) +colvars: ( -0.216998 , 0.115002 , 0.116243 ) +colvars: ( -0.166909 , 0.117244 , 0.167188 ) +colvars: ( -0.241059 , 0.191238 , 0.116429 ) +colvars: ( -0.320266 , 0.0369042 , -0.0122275 ) +colvars: ( -0.252451 , 0.0228594 , 0.0512996 ) +colvars: ( -0.19729 , -0.0647379 , 0.0786778 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 36. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 36. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atoms_new_colvar_forces = { ( -4.88290787959985e+00 , -4.08200374054955e-01 , -1.16605619629334e+00 ), ( -4.20548016891334e+00 , -3.47887950651219e-01 , -9.03918376523148e-01 ), ( -4.28133317148205e+00 , -3.77136784235968e-01 , -9.40500813690554e-01 ), ( -5.75481840725893e+00 , -5.34175996949823e-01 , -1.41162422839094e+00 ), ( 2.64136212576255e-01 , 1.22336397428614e-01 , 3.59981596157192e-01 ), ( 5.25406462462492e+00 , 5.86621840634209e-01 , 1.74589494816703e+00 ), ( 4.43948376393649e+00 , 4.82059265347452e-01 , 1.51566272495863e+00 ), ( -5.03040666377811e-02 , 1.48552310530294e-02 , 3.64638670236814e-01 ), ( 4.42185303103199e+00 , 4.73408400497671e-01 , 1.48612691965680e+00 ), ( 5.86146715504996e+00 , 6.07309596204211e-01 , 1.82649745944155e+00 ), ( 1.29029354738554e-02 , 3.19173781716707e-02 , 3.12120441955794e-01 ), ( 3.62929724733180e-03 , 2.67255802536898e-02 , 2.89301218510092e-01 ), ( 2.81649081397981e-02 , 4.14208231868997e-02 , 3.60564542809657e-01 ), ( 4.88122637735174e-02 , 3.53904866371355e-02 , 2.11659033765666e-01 ), ( 2.08071709543126e-02 , 2.12961419299805e-02 , 1.60734596431752e-01 ), ( 1.19699310346034e-01 , 5.86582555019768e-02 , 1.99679195122940e-01 ), ( 1.67722760500288e-01 , 6.87730799911296e-02 , 1.27433370930817e-01 ), ( 2.50367616662423e-01 , 9.84826443864759e-02 , 1.42787348443313e-01 ), ( 1.35653774193513e-01 , 5.12063332237386e-02 , 5.29155821628234e-02 ), ( 1.31501299079290e-01 , 4.40257174262198e-02 , -1.24354450944110e-02 ), ( 1.09419100990292e-01 , 4.30559922102335e-02 , 6.25817365461039e-02 ), ( 7.02076210386009e-02 , 2.41471186372095e-02 , 6.51122069988325e-04 ), ( 5.41702848644654e-02 , 2.14542111453117e-02 , 3.25539793654729e-02 ), ( -4.83867853065029e-03 , -3.89968113014447e-03 , -2.54262533561946e-02 ), ( -1.94850858323686e-02 , -1.52849045958067e-02 , -9.76340270289430e-02 ), ( -5.29139003296956e-02 , -1.52117330442295e-02 , 3.34280346901958e-02 ), ( -1.22137002841928e-01 , -4.02773087691312e-02 , 1.85133555813677e-02 ), ( -1.64286549852698e-01 , -4.75250698389417e-02 , 1.00428165544681e-01 ), ( -1.06825681469098e-01 , -3.90695463935979e-02 , -2.74233305156697e-02 ), ( -1.44625509671643e-01 , -5.72586807907720e-02 , -8.66815657975791e-02 ), ( -4.93223315313861e-02 , -1.71199718514299e-02 , -2.22991900840161e-03 ), ( -2.53257206748039e-02 , -1.24974058228974e-02 , -4.32311595456356e-02 ), ( 3.55118639307809e-02 , 1.29078301955494e-02 , 8.20812170434740e-03 ), ( 6.55512967237215e-03 , -9.19228409226058e-03 , -1.29905815750122e-01 ), ( -1.08895642309799e-02 , -2.00686786292528e-02 , -1.85434878831553e-01 ), ( 5.30309446781353e-02 , 5.51543872117077e-03 , -1.43974984993789e-01 ), ( 8.20201680367365e-02 , 8.40079875213690e-03 , -2.24150442826249e-01 ), ( 1.43485968790938e-01 , 3.02887459588873e-02 , -2.15093576456319e-01 ), ( 1.91199056930694e-02 , -1.81594217993694e-02 , -2.80667591738177e-01 ), ( 2.01950592746803e-02 , -2.41428714439166e-02 , -3.52791774368278e-01 ), ( -3.77395177613851e-02 , -3.48341122218770e-02 , -2.48478974685638e-01 ), ( -1.03147325075184e-01 , -6.12478506860099e-02 , -2.93564136029933e-01 ), ( -1.44441916425068e-01 , -7.10533735743670e-02 , -2.44020673175622e-01 ), ( -1.61045104498478e-01 , -8.29060934743623e-02 , -3.13913179314616e-01 ), ( -1.90505526545789e-01 , -9.89139305197881e-02 , -3.80893618564478e-01 ), ( -1.98400478959442e-01 , -9.56446980795320e-02 , -3.13018016995541e-01 ), ( -2.40832918734827e-01 , -1.12535358143519e-01 , -3.39485844270407e-01 ), ( -1.20817018294349e-01 , -6.96629991769804e-02 , -3.20271855352053e-01 ), ( -1.79540742003913e-01 , -8.41333214035848e-02 , -2.55792111290274e-01 ), ( -2.33186184157980e-01 , -1.03650786877325e-01 , -2.68401102252966e-01 ), ( -2.68831719246441e-01 , -1.08566119243542e-01 , -1.85342272112195e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 37, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 37, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 37, atoms_positions[size = 51] = { ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 ), ( 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 ), ( 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 ), ( 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ), ( 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 ), ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 ), ( 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 ), ( 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 ), ( 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 ), ( 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ), ( 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 ), ( 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 ), ( 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 ), ( 3.86259944889717e+00 , 3.61722008681940e+00 , 2.00308558020086e+00 ), ( 2.85437670154951e+00 , 4.15527002052534e+00 , 2.40936050794665e+00 ), ( 3.90045897397993e+00 , 3.13690575985605e+00 , 7.86487238395873e-01 ), ( 2.75527536482980e+00 , 3.14541374278433e+00 , -7.87345083063442e-02 ), ( 3.14794216985481e+00 , 2.66173230769858e+00 , -1.51772966163117e+00 ), ( 1.62901901629547e+00 , 2.28088215339071e+00 , 4.52491085121546e-01 ), ( 4.34123539261918e-01 , 2.61246940369668e+00 , 4.19371180847241e-01 ), ( 2.02159602369996e+00 , 1.10937081770796e+00 , 1.03753735465995e+00 ), ( 1.29914298840967e+00 , 1.67015904134200e-01 , 1.66320354438444e+00 ), ( 2.09907830495032e+00 , -1.09321620076143e+00 , 2.02852009135147e+00 ), ( 5.70115136929533e-01 , 6.26554860319424e-01 , 2.93222884904075e+00 ), ( -6.10201928231757e-01 , 3.58551350526315e-01 , 3.21245892405136e+00 ), ( 1.29191109307057e+00 , 1.43443741132798e+00 , 3.78675801241357e+00 ), ( 9.17888105407320e-01 , 1.98827097712886e+00 , 5.05961780707725e+00 ), ( 2.03231605133370e+00 , 2.78119558738282e+00 , 5.72652950117283e+00 ), ( -3.55886113385222e-01 , 2.88734283041279e+00 , 4.91775934200459e+00 ), ( -1.11875187300532e+00 , 3.07171926132761e+00 , 5.89828094798470e+00 ), ( -5.15845484680853e-01 , 3.47100691662013e+00 , 3.71747317327984e+00 ), ( -1.45392488246232e+00 , 4.47782737121568e+00 , 3.41042470589553e+00 ), ( -7.78176466290134e-01 , 5.47992820638078e+00 , 2.48863904731468e+00 ), ( -2.75561566311572e+00 , 3.92507785420583e+00 , 2.71566470414495e+00 ), ( -3.79047766038997e+00 , 4.60435453120212e+00 , 2.80505411222305e+00 ), ( -2.71475155579475e+00 , 2.65396188733802e+00 , 2.34383594524730e+00 ), ( -3.82384628855180e+00 , 1.78790482718998e+00 , 1.98676202535117e+00 ), ( -3.33878680658610e+00 , 9.09404778041523e-01 , 7.60961224505685e-01 ), ( -4.27420503934880e+00 , 1.01820161920294e+00 , 3.23602529439721e+00 ), ( -5.41618360572693e+00 , 7.13913354085080e-01 , 3.36019291686581e+00 ), ( -3.35650294249584e+00 , 7.08539067358897e-01 , 4.17056744070843e+00 ), ( -3.66427165233763e+00 , 5.97526421563971e-02 , 5.44828972260972e+00 ), ( -2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 ), ( -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 ), ( -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 ), ( -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 ), ( -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 ), ( -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 ), ( -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 ), ( -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 ), ( -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ) } +colvars: Step 37, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ). +colvars: Done calculating colvar "group1". +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.80827613502008e-01 , -1.81261010387522e-02 , 9.59587044491483e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 , 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 , 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 , 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 , 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 , 3.86259944889717e+00 , 3.61722008681940e+00 , 2.00308558020086e+00 , 2.85437670154951e+00 , 4.15527002052534e+00 , 2.40936050794665e+00 , 3.90045897397993e+00 , 3.13690575985605e+00 , 7.86487238395873e-01 , 2.75527536482980e+00 , 3.14541374278433e+00 , -7.87345083063442e-02 , 3.14794216985481e+00 , 2.66173230769858e+00 , -1.51772966163117e+00 , 1.62901901629547e+00 , 2.28088215339071e+00 , 4.52491085121546e-01 , 4.34123539261918e-01 , 2.61246940369668e+00 , 4.19371180847241e-01 , 2.02159602369996e+00 , 1.10937081770796e+00 , 1.03753735465995e+00 , 1.29914298840967e+00 , 1.67015904134200e-01 , 1.66320354438444e+00 , 2.09907830495032e+00 , -1.09321620076143e+00 , 2.02852009135147e+00 , 5.70115136929533e-01 , 6.26554860319424e-01 , 2.93222884904075e+00 , -6.10201928231757e-01 , 3.58551350526315e-01 , 3.21245892405136e+00 , 1.29191109307057e+00 , 1.43443741132798e+00 , 3.78675801241357e+00 , 9.17888105407320e-01 , 1.98827097712886e+00 , 5.05961780707725e+00 , 2.03231605133370e+00 , 2.78119558738282e+00 , 5.72652950117283e+00 , -3.55886113385222e-01 , 2.88734283041279e+00 , 4.91775934200459e+00 , -1.11875187300532e+00 , 3.07171926132761e+00 , 5.89828094798470e+00 , -5.15845484680853e-01 , 3.47100691662013e+00 , 3.71747317327984e+00 , -1.45392488246232e+00 , 4.47782737121568e+00 , 3.41042470589553e+00 , -7.78176466290134e-01 , 5.47992820638078e+00 , 2.48863904731468e+00 , -2.75561566311572e+00 , 3.92507785420583e+00 , 2.71566470414495e+00 , -3.79047766038997e+00 , 4.60435453120212e+00 , 2.80505411222305e+00 , -2.71475155579475e+00 , 2.65396188733802e+00 , 2.34383594524730e+00 , -3.82384628855180e+00 , 1.78790482718998e+00 , 1.98676202535117e+00 , -3.33878680658610e+00 , 9.09404778041523e-01 , 7.60961224505685e-01 , -4.27420503934880e+00 , 1.01820161920294e+00 , 3.23602529439721e+00 , -5.41618360572693e+00 , 7.13913354085080e-01 , 3.36019291686581e+00 , -3.35650294249584e+00 , 7.08539067358897e-01 , 4.17056744070843e+00 , -3.66427165233763e+00 , 5.97526421563971e-02 , 5.44828972260972e+00 , -2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 , -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 , -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 , -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 , -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 , -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 , -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 , -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 , -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.80827613502008e-01 , -1.81261010387522e-02 , 9.59587044491483e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 , 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 , 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 , 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 , 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 , 3.86259944889717e+00 , 3.61722008681940e+00 , 2.00308558020086e+00 , 2.85437670154951e+00 , 4.15527002052534e+00 , 2.40936050794665e+00 , 3.90045897397993e+00 , 3.13690575985605e+00 , 7.86487238395873e-01 , 2.75527536482980e+00 , 3.14541374278433e+00 , -7.87345083063442e-02 , 3.14794216985481e+00 , 2.66173230769858e+00 , -1.51772966163117e+00 , 1.62901901629547e+00 , 2.28088215339071e+00 , 4.52491085121546e-01 , 4.34123539261918e-01 , 2.61246940369668e+00 , 4.19371180847241e-01 , 2.02159602369996e+00 , 1.10937081770796e+00 , 1.03753735465995e+00 , 1.29914298840967e+00 , 1.67015904134200e-01 , 1.66320354438444e+00 , 2.09907830495032e+00 , -1.09321620076143e+00 , 2.02852009135147e+00 , 5.70115136929533e-01 , 6.26554860319424e-01 , 2.93222884904075e+00 , -6.10201928231757e-01 , 3.58551350526315e-01 , 3.21245892405136e+00 , 1.29191109307057e+00 , 1.43443741132798e+00 , 3.78675801241357e+00 , 9.17888105407320e-01 , 1.98827097712886e+00 , 5.05961780707725e+00 , 2.03231605133370e+00 , 2.78119558738282e+00 , 5.72652950117283e+00 , -3.55886113385222e-01 , 2.88734283041279e+00 , 4.91775934200459e+00 , -1.11875187300532e+00 , 3.07171926132761e+00 , 5.89828094798470e+00 , -5.15845484680853e-01 , 3.47100691662013e+00 , 3.71747317327984e+00 , -1.45392488246232e+00 , 4.47782737121568e+00 , 3.41042470589553e+00 , -7.78176466290134e-01 , 5.47992820638078e+00 , 2.48863904731468e+00 , -2.75561566311572e+00 , 3.92507785420583e+00 , 2.71566470414495e+00 , -3.79047766038997e+00 , 4.60435453120212e+00 , 2.80505411222305e+00 , -2.71475155579475e+00 , 2.65396188733802e+00 , 2.34383594524730e+00 , -3.82384628855180e+00 , 1.78790482718998e+00 , 1.98676202535117e+00 , -3.33878680658610e+00 , 9.09404778041523e-01 , 7.60961224505685e-01 , -4.27420503934880e+00 , 1.01820161920294e+00 , 3.23602529439721e+00 , -5.41618360572693e+00 , 7.13913354085080e-01 , 3.36019291686581e+00 , -3.35650294249584e+00 , 7.08539067358897e-01 , 4.17056744070843e+00 , -3.66427165233763e+00 , 5.97526421563971e-02 , 5.44828972260972e+00 , -2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 , -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 , -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 , -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 , -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 , -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 , -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 , -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 , -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 65.0336 , 6.50336 , 13.0067 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 65.0336 , 6.50336 , 13.0067 ) to colvar "one". +colvars: Adding total bias energy: 55.0754 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 65.0336 , 6.50336 , 13.0067 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.16274 , -0.524934 , -1.40913 ) +colvars: ( -4.42705 , -0.450131 , -1.20833 ) +colvars: ( -4.42705 , -0.450131 , -1.20833 ) +colvars: ( -5.89696 , -0.599587 , -1.60953 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.917827 , 0.205013 , 0.619508 ) +colvars: ( 0.796532 , 0.276787 , 0.64378 ) +colvars: ( 0.779458 , 0.270312 , 0.625718 ) +colvars: ( 0.683626 , 0.27617 , 0.579018 ) +colvars: ( 0.671614 , 0.207576 , 0.483344 ) +colvars: ( 0.596279 , 0.354519 , 0.631041 ) +colvars: ( 0.488129 , 0.367493 , 0.586579 ) +colvars: ( 0.410666 , 0.466574 , 0.671062 ) +colvars: ( 0.405005 , 0.321278 , 0.479614 ) +colvars: ( 0.370142 , 0.277873 , 0.403628 ) +colvars: ( 0.374551 , 0.327116 , 0.469925 ) +colvars: ( 0.301965 , 0.282785 , 0.37137 ) +colvars: ( 0.273716 , 0.313086 , 0.394622 ) +colvars: ( 0.365141 , 0.182885 , 0.277732 ) +colvars: ( 0.305738 , 0.137743 , 0.185593 ) +colvars: ( 0.489403 , 0.146068 , 0.30043 ) +colvars: ( 0.562844 , 0.0528577 , 0.221275 ) +colvars: ( 0.693798 , 0.0327896 , 0.269463 ) +colvars: ( 0.572322 , 0.019516 , 0.183448 ) +colvars: ( 0.556398 , -0.047569 , 0.0875128 ) +colvars: ( 0.59415 , 0.0684211 , 0.259174 ) +colvars: ( 0.593409 , 0.0510794 , 0.236287 ) +colvars: ( 0.631011 , 0.11748 , 0.343617 ) +colvars: ( 0.467697 , 0.0542687 , 0.1692 ) +colvars: ( 0.46112 , -0.00359885 , 0.0905024 ) +colvars: ( 0.364222 , 0.120948 , 0.196968 ) +colvars: ( 0.238198 , 0.128472 , 0.13532 ) +colvars: ( 0.145286 , 0.215978 , 0.196053 ) +colvars: ( 0.209143 , 0.0527886 , 0.0208062 ) +colvars: ( 0.159573 , 0.0148266 , -0.0564587 ) +colvars: ( 0.242394 , 0.0275118 , 0.00689564 ) +colvars: ( 0.227683 , -0.0467331 , -0.097628 ) +colvars: ( 0.262566 , -0.0490648 , -0.0808868 ) +colvars: ( 0.304187 , -0.13463 , -0.168163 ) +colvars: ( 0.259628 , -0.189678 , -0.264726 ) +colvars: ( 0.421125 , -0.149181 , -0.120767 ) +colvars: ( 0.499926 , -0.226355 , -0.17611 ) +colvars: ( 0.632908 , -0.227825 , -0.102677 ) +colvars: ( 0.452833 , -0.23214 , -0.210283 ) +colvars: ( 0.458592 , -0.302215 , -0.297809 ) +colvars: ( 0.403981 , -0.157695 , -0.141511 ) +colvars: ( 0.34981 , -0.152467 , -0.165427 ) +colvars: ( 0.333595 , -0.0639425 , -0.0599225 ) +colvars: ( 0.224853 , -0.162649 , -0.249408 ) +colvars: ( 0.200567 , -0.20646 , -0.319927 ) +colvars: ( 0.0197462 , -0.21058 , -0.427704 ) +colvars: ( -0.0724034 , -0.229736 , -0.504727 ) +colvars: ( 0.120932 , -0.260526 , -0.435089 ) +colvars: ( 0.141447 , -0.121215 , -0.242979 ) +colvars: ( 0.0204675 , -0.126772 , -0.318716 ) +colvars: ( -0.0700032 , -0.0443999 , -0.263251 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.16274 , 0.524934 , 1.40913 ) +colvars: ( 4.42705 , 0.450131 , 1.20833 ) +colvars: ( 4.42705 , 0.450131 , 1.20833 ) +colvars: ( 5.89696 , 0.599587 , 1.60953 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.632769 , -0.0845946 , -0.36346 ) +colvars: ( -0.570459 , -0.171467 , -0.328306 ) +colvars: ( -0.515654 , -0.148155 , -0.266071 ) +colvars: ( -0.53332 , -0.200104 , -0.300086 ) +colvars: ( -0.523246 , -0.137947 , -0.270472 ) +colvars: ( -0.510857 , -0.296917 , -0.307982 ) +colvars: ( -0.48071 , -0.339123 , -0.291028 ) +colvars: ( -0.461078 , -0.452097 , -0.306835 ) +colvars: ( -0.415133 , -0.301517 , -0.213511 ) +colvars: ( -0.412149 , -0.274719 , -0.202105 ) +colvars: ( -0.361676 , -0.295443 , -0.15804 ) +colvars: ( -0.298289 , -0.256263 , -0.0822212 ) +colvars: ( -0.245472 , -0.271888 , -0.0342064 ) +colvars: ( -0.316311 , -0.147608 , -0.0661579 ) +colvars: ( -0.284857 , -0.116521 , -0.0248784 ) +colvars: ( -0.369779 , -0.0874875 , -0.100853 ) +colvars: ( -0.395238 , 0.0159218 , -0.0938873 ) +colvars: ( -0.443644 , 0.0657222 , -0.126751 ) +colvars: ( -0.436798 , 0.0317191 , -0.13057 ) +colvars: ( -0.425001 , 0.0916817 , -0.0999188 ) +colvars: ( -0.4849 , -0.025385 , -0.1967 ) +colvars: ( -0.52338 , -0.0269441 , -0.235747 ) +colvars: ( -0.577073 , -0.096101 , -0.311265 ) +colvars: ( -0.472615 , -0.0581874 , -0.194693 ) +colvars: ( -0.480674 , -0.0116573 , -0.188155 ) +colvars: ( -0.417142 , -0.136238 , -0.163619 ) +colvars: ( -0.360241 , -0.168837 , -0.116842 ) +colvars: ( -0.309415 , -0.263667 , -0.0956953 ) +colvars: ( -0.315828 , -0.0918756 , -0.0481717 ) +colvars: ( -0.304015 , -0.0720731 , -0.0301169 ) +colvars: ( -0.291585 , -0.0446194 , -0.00904007 ) +colvars: ( -0.252843 , 0.0343175 , 0.0545689 ) +colvars: ( -0.226902 , 0.0620649 , 0.0892749 ) +colvars: ( -0.297516 , 0.125595 , 0.0384711 ) +colvars: ( -0.270354 , 0.169814 , 0.0795739 ) +colvars: ( -0.368075 , 0.154867 , -0.0230368 ) +colvars: ( -0.417942 , 0.234993 , -0.0478405 ) +colvars: ( -0.489569 , 0.258353 , -0.112274 ) +colvars: ( -0.433723 , 0.214214 , -0.0701779 ) +colvars: ( -0.4384 , 0.278366 , -0.0547183 ) +colvars: ( -0.441713 , 0.123024 , -0.106822 ) +colvars: ( -0.45292 , 0.0913699 , -0.127991 ) +colvars: ( -0.478012 , -0.00704334 , -0.184039 ) +colvars: ( -0.385755 , 0.0799005 , -0.0642944 ) +colvars: ( -0.390908 , 0.107738 , -0.0607156 ) +colvars: ( -0.217806 , 0.115143 , 0.115057 ) +colvars: ( -0.16801 , 0.117424 , 0.16567 ) +colvars: ( -0.241474 , 0.19112 , 0.115202 ) +colvars: ( -0.320776 , 0.0372058 , -0.0125929 ) +colvars: ( -0.25334 , 0.0232496 , 0.0505951 ) +colvars: ( -0.198451 , -0.0641088 , 0.0781593 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 37. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 37. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atoms_new_colvar_forces = { ( -4.87768340091064e+00 , -4.04515767829389e-01 , -1.15308077989926e+00 ), ( -4.20097681355703e+00 , -3.44810675996169e-01 , -8.92853789587307e-01 ), ( -4.27674390111940e+00 , -3.74064477872092e-01 , -9.29397030160039e-01 ), ( -5.74859063228890e+00 , -5.29958050663217e-01 , -1.39665675402575e+00 ), ( 2.63803073591474e-01 , 1.22156769296109e-01 , 3.59647315946333e-01 ), ( 5.24816274406836e+00 , 5.82536587822630e-01 , 1.73218869553827e+00 ), ( 4.43446889915649e+00 , 4.78500064884967e-01 , 1.50387962233720e+00 ), ( -5.04116713926906e-02 , 1.44761896627373e-02 , 3.64226325004024e-01 ), ( 4.41692168797072e+00 , 4.69891932048396e-01 , 1.47443120504272e+00 ), ( 5.85495080586629e+00 , 6.02741463937726e-01 , 1.81105128190514e+00 ), ( 1.28749576319738e-02 , 3.16727297019153e-02 , 3.11884909766902e-01 ), ( 3.67694080954450e-03 , 2.65227810484956e-02 , 2.89148426393064e-01 ), ( 2.82433742396482e-02 , 4.11983291947543e-02 , 3.60415726827408e-01 ), ( 4.88294417275390e-02 , 3.52775028285380e-02 , 2.11573629907615e-01 ), ( 2.08809568767205e-02 , 2.12213798958254e-02 , 1.60714878406654e-01 ), ( 1.19624009465562e-01 , 5.85808403129090e-02 , 1.99577517515682e-01 ), ( 1.67606734863712e-01 , 6.87794743067848e-02 , 1.27387745429499e-01 ), ( 2.50153639908545e-01 , 9.85117828115238e-02 , 1.42711944173507e-01 ), ( 1.35523380967889e-01 , 5.12350481214440e-02 , 5.28775171111929e-02 ), ( 1.31396350884718e-01 , 4.41127500705837e-02 , -1.24060209174162e-02 ), ( 1.09250435610859e-01 , 4.30361820912343e-02 , 6.24736166561782e-02 ), ( 7.00295966772967e-02 , 2.41352684722350e-02 , 5.39881366658557e-04 ), ( 5.39389527876329e-02 , 2.13794282805596e-02 , 3.23517320504840e-02 ), ( -4.91857376580790e-03 , -3.91871398765551e-03 , -2.54927330783864e-02 ), ( -1.95537264278258e-02 , -1.52561437342837e-02 , -9.76523676273865e-02 ), ( -5.29191645627358e-02 , -1.52895085259884e-02 , 3.33487448423313e-02 ), ( -1.22042627232472e-01 , -4.03649373402419e-02 , 1.84780260128458e-02 ), ( -1.64129427277217e-01 , -4.76891159906219e-02 , 1.00357565236874e-01 ), ( -1.06685087792716e-01 , -3.90869775394688e-02 , -2.73655377503504e-02 ), ( -1.44442405045796e-01 , -5.72465648154617e-02 , -8.65756363523023e-02 ), ( -4.91911623122935e-02 , -1.71076260251905e-02 , -2.14442688614674e-03 ), ( -2.51597903645701e-02 , -1.24155772310293e-02 , -4.30591764368354e-02 ), ( 3.56640469890183e-02 , 1.30001099744317e-02 , 8.38817710329237e-03 ), ( 6.67109880696493e-03 , -9.03436340479885e-03 , -1.29692238036441e-01 ), ( -1.07264236900141e-02 , -1.98631557679952e-02 , -1.85151718794343e-01 ), ( 5.30498429345028e-02 , 5.68583763969494e-03 , -1.43804083361619e-01 ), ( 8.19841057638790e-02 , 8.63734608329719e-03 , -2.23950276315525e-01 ), ( 1.43339855796387e-01 , 3.05280193383436e-02 , -2.14951039351014e-01 ), ( 1.91102547580405e-02 , -1.79258075663515e-02 , -2.80461242310813e-01 ), ( 2.01917810604034e-02 , -2.38489838462535e-02 , -3.52527220572662e-01 ), ( -3.77323966607108e-02 , -3.46714768692280e-02 , -2.48332802200249e-01 ), ( -1.03109504559677e-01 , -6.10975953308200e-02 , -2.93417945581451e-01 ), ( -1.44416579761663e-01 , -7.09858088855299e-02 , -2.43961250544664e-01 ), ( -1.60901994961709e-01 , -8.27484428513748e-02 , -3.13702754209035e-01 ), ( -1.90341009584740e-01 , -9.87220095142527e-02 , -3.80642732473909e-01 ), ( -1.98060257827384e-01 , -9.54375652645738e-02 , -3.12647039402676e-01 ), ( -2.40413024259414e-01 , -1.12312668677671e-01 , -3.39057144551452e-01 ), ( -1.20542203354837e-01 , -6.94060878279039e-02 , -3.19887059849072e-01 ), ( -1.79328721309453e-01 , -8.40087412672682e-02 , -2.55571471275001e-01 ), ( -2.32872144915632e-01 , -1.03522324988299e-01 , -2.68120889649633e-01 ), ( -2.68454324278848e-01 , -1.08508648212007e-01 , -1.85091323373151e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 38, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 38, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 38, atoms_positions[size = 51] = { ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 ), ( 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 ), ( 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 ), ( 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ), ( 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 ), ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 ), ( 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 ), ( 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 ), ( 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 ), ( 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ), ( 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 ), ( 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 ), ( 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 ), ( 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 ), ( 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 ), ( 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 ), ( 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 ), ( 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 ), ( 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 ), ( 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 ), ( 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 ), ( 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 ), ( 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 ), ( 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 ), ( -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 ), ( 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 ), ( 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 ), ( 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 ), ( -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 ), ( -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 ), ( -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 ), ( -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 ), ( -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 ), ( -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 ), ( -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 ), ( -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 ), ( -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 ), ( -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 ), ( -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 ), ( -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 ), ( -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 ), ( -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 ), ( -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 ), ( -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 ), ( -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 ), ( -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 ), ( -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 ), ( -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 ), ( -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 ), ( -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 ), ( -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ) } +colvars: Step 38, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ). +colvars: Colvar component no. 1 within colvar "one" has value ( -2.78392072118256e-01 , -1.83593331534544e-02 , 9.60292033221074e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 , 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 , 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 , 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 , 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 , 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 , 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 , 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 , 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 , 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 , 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 , 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 , 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 , 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 , 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 , 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 , -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 , 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 , 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 , 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 , -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 , -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 , -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 , -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 , -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 , -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 , -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 , -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 , -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 , -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 , -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 , -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 , -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 , -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 , -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 , -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 , -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 , -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 , -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 , -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 , -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 , -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 , -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ). +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.78392072118256e-01 , -1.83593331534544e-02 , 9.60292033221074e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 , 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 , 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 , 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 , 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 , 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 , 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 , 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 , 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 , 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 , 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 , 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 , 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 , 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 , 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 , 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 , -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 , 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 , 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 , 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 , -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 , -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 , -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 , -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 , -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 , -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 , -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 , -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 , -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 , -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 , -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 , -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 , -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 , -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 , -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 , -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 , -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 , -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 , -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 , -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 , -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 , -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 , -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 64.9214 , 6.49214 , 12.9843 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 64.9214 , 6.49214 , 12.9843 ) to colvar "one". +colvars: Adding total bias energy: 54.9095 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 64.9214 , 6.49214 , 12.9843 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.15671 , -0.521 , -1.39471 ) +colvars: ( -4.42188 , -0.446758 , -1.19596 ) +colvars: ( -4.42188 , -0.446758 , -1.19596 ) +colvars: ( -5.89007 , -0.595094 , -1.59306 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.915026 , 0.204804 , 0.615756 ) +colvars: ( 0.794237 , 0.276235 , 0.639946 ) +colvars: ( 0.777132 , 0.269875 , 0.622065 ) +colvars: ( 0.681862 , 0.275456 , 0.575502 ) +colvars: ( 0.669903 , 0.207071 , 0.480315 ) +colvars: ( 0.594926 , 0.353422 , 0.627253 ) +colvars: ( 0.487295 , 0.366185 , 0.583 ) +colvars: ( 0.410193 , 0.464833 , 0.66705 ) +colvars: ( 0.404481 , 0.320085 , 0.476634 ) +colvars: ( 0.369808 , 0.276742 , 0.40101 ) +colvars: ( 0.37407 , 0.325966 , 0.467073 ) +colvars: ( 0.301743 , 0.281763 , 0.369079 ) +colvars: ( 0.273521 , 0.312035 , 0.392296 ) +colvars: ( 0.364631 , 0.182269 , 0.275913 ) +colvars: ( 0.305487 , 0.137209 , 0.184252 ) +colvars: ( 0.488345 , 0.145716 , 0.298478 ) +colvars: ( 0.561458 , 0.0528961 , 0.219716 ) +colvars: ( 0.691812 , 0.033067 , 0.267658 ) +colvars: ( 0.570984 , 0.0195775 , 0.182005 ) +colvars: ( 0.555131 , -0.0473077 , 0.0865582 ) +colvars: ( 0.592796 , 0.0682641 , 0.25728 ) +colvars: ( 0.59215 , 0.0508806 , 0.234434 ) +colvars: ( 0.629659 , 0.117031 , 0.341156 ) +colvars: ( 0.467005 , 0.0539005 , 0.167695 ) +colvars: ( 0.460492 , -0.003823 , 0.0893691 ) +colvars: ( 0.363957 , 0.120276 , 0.195362 ) +colvars: ( 0.238489 , 0.127632 , 0.134046 ) +colvars: ( 0.145952 , 0.214781 , 0.194513 ) +colvars: ( 0.209502 , 0.0522239 , 0.0201649 ) +colvars: ( 0.160181 , 0.0142961 , -0.056726 ) +colvars: ( 0.242521 , 0.0271589 , 0.00638947 ) +colvars: ( 0.227813 , -0.046796 , -0.0975526 ) +colvars: ( 0.262448 , -0.0489789 , -0.0808242 ) +colvars: ( 0.304017 , -0.134358 , -0.167772 ) +colvars: ( 0.259647 , -0.18927 , -0.263833 ) +colvars: ( 0.420481 , -0.148772 , -0.120668 ) +colvars: ( 0.498979 , -0.225653 , -0.175778 ) +colvars: ( 0.631401 , -0.226993 , -0.102759 ) +colvars: ( 0.452179 , -0.231564 , -0.209841 ) +colvars: ( 0.457929 , -0.301422 , -0.296937 ) +colvars: ( 0.4036 , -0.157478 , -0.141456 ) +colvars: ( 0.349749 , -0.152416 , -0.165308 ) +colvars: ( 0.333665 , -0.0642611 , -0.0603849 ) +colvars: ( 0.225321 , -0.162684 , -0.248828 ) +colvars: ( 0.201186 , -0.206427 , -0.319021 ) +colvars: ( 0.0209552 , -0.210521 , -0.426057 ) +colvars: ( -0.0708031 , -0.229704 , -0.502663 ) +colvars: ( 0.121652 , -0.260143 , -0.433385 ) +colvars: ( 0.142214 , -0.121407 , -0.242362 ) +colvars: ( 0.0217403 , -0.127056 , -0.317675 ) +colvars: ( -0.068376 , -0.045008 , -0.262441 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.15671 , 0.521 , 1.39471 ) +colvars: ( 4.42188 , 0.446758 , 1.19596 ) +colvars: ( 4.42188 , 0.446758 , 1.19596 ) +colvars: ( 5.89007 , 0.595094 , 1.59306 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.630429 , -0.0845273 , -0.360072 ) +colvars: ( -0.568538 , -0.171096 , -0.324869 ) +colvars: ( -0.513695 , -0.147894 , -0.262806 ) +colvars: ( -0.531834 , -0.199563 , -0.296926 ) +colvars: ( -0.521793 , -0.137569 , -0.267722 ) +colvars: ( -0.50972 , -0.296038 , -0.3046 ) +colvars: ( -0.48 , -0.338036 , -0.287827 ) +colvars: ( -0.460679 , -0.450637 , -0.303278 ) +colvars: ( -0.414663 , -0.300509 , -0.210834 ) +colvars: ( -0.411831 , -0.273742 , -0.199729 ) +colvars: ( -0.361231 , -0.294481 , -0.155489 ) +colvars: ( -0.29804 , -0.255395 , -0.0801613 ) +colvars: ( -0.24524 , -0.27101 , -0.0321365 ) +colvars: ( -0.315813 , -0.147085 , -0.0644872 ) +colvars: ( -0.284563 , -0.116047 , -0.023617 ) +colvars: ( -0.36883 , -0.087212 , -0.0990548 ) +colvars: ( -0.394008 , 0.0158627 , -0.0924098 ) +colvars: ( -0.441922 , 0.0654288 , -0.125055 ) +colvars: ( -0.435614 , 0.0316587 , -0.129174 ) +colvars: ( -0.423864 , 0.0914666 , -0.0989346 ) +colvars: ( -0.483718 , -0.0252596 , -0.19491 ) +colvars: ( -0.522283 , -0.026765 , -0.233976 ) +colvars: ( -0.575918 , -0.0957166 , -0.308966 ) +colvars: ( -0.471982 , -0.0578329 , -0.193227 ) +colvars: ( -0.480087 , -0.0114083 , -0.186996 ) +colvars: ( -0.416861 , -0.135617 , -0.162087 ) +colvars: ( -0.360413 , -0.168045 , -0.115605 ) +colvars: ( -0.309902 , -0.26257 , -0.0942516 ) +colvars: ( -0.316038 , -0.0913079 , -0.0474786 ) +colvars: ( -0.304426 , -0.0715114 , -0.0297389 ) +colvars: ( -0.291593 , -0.0442496 , -0.00847057 ) +colvars: ( -0.252836 , 0.0344464 , 0.0546381 ) +colvars: ( -0.226682 , 0.0620436 , 0.0893434 ) +colvars: ( -0.297256 , 0.125443 , 0.0382911 ) +colvars: ( -0.270239 , 0.169565 , 0.0789661 ) +colvars: ( -0.367433 , 0.154579 , -0.0229498 ) +colvars: ( -0.417047 , 0.234457 , -0.047931 ) +colvars: ( -0.488221 , 0.257681 , -0.111996 ) +colvars: ( -0.433075 , 0.213812 , -0.0703527 ) +colvars: ( -0.437736 , 0.277793 , -0.0552503 ) +colvars: ( -0.441305 , 0.122936 , -0.106668 ) +colvars: ( -0.452781 , 0.0914478 , -0.127884 ) +colvars: ( -0.477999 , -0.00665133 , -0.183436 ) +colvars: ( -0.386042 , 0.0800796 , -0.0645949 ) +colvars: ( -0.391316 , 0.10788 , -0.0612847 ) +colvars: ( -0.21867 , 0.115271 , 0.113808 ) +colvars: ( -0.169187 , 0.117597 , 0.164057 ) +colvars: ( -0.241929 , 0.19095 , 0.113911 ) +colvars: ( -0.321304 , 0.0375202 , -0.0129455 ) +colvars: ( -0.254275 , 0.0236664 , 0.0498664 ) +colvars: ( -0.199682 , -0.0634162 , 0.0776055 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 38. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 38. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atoms_new_colvar_forces = { ( -4.87211628471813e+00 , -4.00723696435930e-01 , -1.13902559685542e+00 ), ( -4.19618112062730e+00 , -3.41618652775116e-01 , -8.80886640494536e-01 ), ( -4.27185249304519e+00 , -3.70864683261145e-01 , -9.17387542307019e-01 ), ( -5.74196285124811e+00 , -5.25592613345036e-01 , -1.38046516841937e+00 ), ( 2.63436695172010e-01 , 1.21980183873108e-01 , 3.59258822687694e-01 ), ( 5.24191905370620e+00 , 5.78383900025139e-01 , 1.71736382057580e+00 ), ( 4.42917469889649e+00 , 4.74906575536316e-01 , 1.49113614173051e+00 ), ( -5.04856316323478e-02 , 1.41960855031390e-02 , 3.63771460263893e-01 ), ( 4.41169880812001e+00 , 4.66333549843916e-01 , 1.46176418728760e+00 ), ( 5.84804936609122e+00 , 5.98093948311445e-01 , 1.79433848850076e+00 ), ( 1.28390258135648e-02 , 3.14849985990572e-02 , 3.11583875992712e-01 ), ( 3.70289354056513e-03 , 2.63682143155367e-02 , 2.88917857719304e-01 ), ( 2.82811857352332e-02 , 4.10250507590758e-02 , 3.60159740153088e-01 ), ( 4.88172382287936e-02 , 3.51842526209211e-02 , 2.11425482513839e-01 ), ( 2.09242125707623e-02 , 2.11614057207995e-02 , 1.60635538220059e-01 ), ( 1.19514499385215e-01 , 5.85038153619524e-02 , 1.99423621621964e-01 ), ( 1.67449994282037e-01 , 6.87587757502283e-02 , 1.27305729225293e-01 ), ( 2.49890063073903e-01 , 9.84957788584253e-02 , 1.42603323462884e-01 ), ( 1.35370312059017e-01 , 5.12361986108216e-02 , 5.28306435895485e-02 ), ( 1.31266286226148e-01 , 4.41588078367218e-02 , -1.23764059304486e-02 ), ( 1.09077979208189e-01 , 4.30045041094490e-02 , 6.23702845380885e-02 ), ( 6.98669807188264e-02 , 2.41156230644165e-02 , 4.58514556624962e-04 ), ( 5.37408900422847e-02 , 2.13144634124023e-02 , 3.21895567314332e-02 ), ( -4.97680321526328e-03 , -3.93239731200813e-03 , -2.55318716107590e-02 ), ( -1.95955224962919e-02 , -1.52313040682568e-02 , -9.76268191527637e-02 ), ( -5.29038951167375e-02 , -1.53404889564458e-02 , 3.32752471439421e-02 ), ( -1.21924401426481e-01 , -4.04128727814948e-02 , 1.84417597620489e-02 ), ( -1.63949746135120e-01 , -4.77886697639920e-02 , 1.00261047281662e-01 ), ( -1.06536103855439e-01 , -3.90839635592086e-02 , -2.73137530310096e-02 ), ( -1.44244684364032e-01 , -5.72153615265834e-02 , -8.64648961120009e-02 ), ( -4.90722160147482e-02 , -1.70907738552945e-02 , -2.08109649362115e-03 ), ( -2.50223025757974e-02 , -1.23496395013128e-02 , -4.29145362918981e-02 ), ( 3.57661110053366e-02 , 1.30647037335049e-02 , 8.51922866820989e-03 ), ( 6.76096283443661e-03 , -8.91549215319049e-03 , -1.29480937298523e-01 ), ( -1.05922023196020e-02 , -1.97054936783417e-02 , -1.84866633030489e-01 ), ( 5.30483383961673e-02 , 5.80712809585909e-03 , -1.43617788492431e-01 ), ( 8.19320773382444e-02 , 8.80446263001067e-03 , -2.23709166098813e-01 ), ( 1.43180098258807e-01 , 3.06878669656324e-02 , -2.14755093475696e-01 ), ( 1.91042482792362e-02 , -1.77513282747287e-02 , -2.80193948256684e-01 ), ( 2.01924497840280e-02 , -2.36289028306198e-02 , -3.52187475693729e-01 ), ( -3.77047905553755e-02 , -3.45422233218000e-02 , -2.48124399881779e-01 ), ( -1.03032000452791e-01 , -6.09677714260224e-02 , -2.93192620152274e-01 ), ( -1.44334266803832e-01 , -7.09124683497476e-02 , -2.43821262073845e-01 ), ( -1.60721410136378e-01 , -8.26042071975248e-02 , -3.13422711508172e-01 ), ( -1.90130730016332e-01 , -9.85472626624001e-02 , -3.80306128235332e-01 ), ( -1.97715174740678e-01 , -9.52501299041566e-02 , -3.12248973167422e-01 ), ( -2.39990125847505e-01 , -1.12106974818264e-01 , -3.38606393215890e-01 ), ( -1.20276516750188e-01 , -6.91926694174377e-02 , -3.19474183656651e-01 ), ( -1.79090329393824e-01 , -8.38868210874086e-02 , -2.55307785632367e-01 ), ( -2.32535036301363e-01 , -1.03389308783731e-01 , -2.67808995162089e-01 ), ( -2.68057828977866e-01 , -1.08424122490680e-01 , -1.84835550495924e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 39, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 39, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 39, atoms_positions[size = 51] = { ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 ), ( 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 ), ( 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 ), ( 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ), ( 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 ), ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 ), ( 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 ), ( 7.15209468106941e+00 , -3.67624117504530e-01 , 4.43478070280023e+00 ), ( 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 ), ( 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ), ( 5.85248794713263e+00 , 2.25938076251533e+00 , 2.95153690628167e+00 ), ( 5.13075591770814e+00 , 3.50792385890992e+00 , 2.84425719233370e+00 ), ( 6.24995676938641e+00 , 4.41880966581118e+00 , 2.28256973292094e+00 ), ( 3.86783704089829e+00 , 3.61096286566776e+00 , 1.99970444568263e+00 ), ( 2.86406518132278e+00 , 4.15145858317519e+00 , 2.40459705297965e+00 ), ( 3.90250111205385e+00 , 3.12041888120911e+00 , 7.97223726672285e-01 ), ( 2.74882732907450e+00 , 3.17112421441466e+00 , -8.93440550655717e-02 ), ( 3.15343423214524e+00 , 2.66497450487673e+00 , -1.50593128968213e+00 ), ( 1.65563470587165e+00 , 2.29806247818938e+00 , 4.68317536017901e-01 ), ( 4.40964171499351e-01 , 2.61077705421038e+00 , 4.07537300936663e-01 ), ( 2.01821656468275e+00 , 1.11484345357438e+00 , 1.02272875349485e+00 ), ( 1.30314111019426e+00 , 1.65390561871593e-01 , 1.66780700656013e+00 ), ( 2.10196684283618e+00 , -1.09273041986010e+00 , 2.02048684397801e+00 ), ( 5.68768745235939e-01 , 6.37675112563199e-01 , 2.93317291449566e+00 ), ( -6.15407244554440e-01 , 3.58633018326628e-01 , 3.21889462115816e+00 ), ( 1.29725121846989e+00 , 1.44057397906235e+00 , 3.78929213200849e+00 ), ( 9.22284891708561e-01 , 1.99418215931574e+00 , 5.06879541844135e+00 ), ( 2.02425336785241e+00 , 2.78863082044487e+00 , 5.72865046142383e+00 ), ( -3.50745637122294e-01 , 2.88297630164963e+00 , 4.91528578031121e+00 ), ( -1.11796558039258e+00 , 3.07208771619379e+00 , 5.89741374769812e+00 ), ( -5.04511543035556e-01 , 3.45375176842667e+00 , 3.70025979089654e+00 ), ( -1.46271168084986e+00 , 4.48061232010830e+00 , 3.40090560148433e+00 ), ( -7.82655702934262e-01 , 5.49608057962156e+00 , 2.48906287015350e+00 ), ( -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 ), ( -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 ), ( -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 ), ( -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 ), ( -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 ), ( -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 ), ( -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 ), ( -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 ), ( -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 ), ( -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 ), ( -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 ), ( -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 ), ( -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 ), ( -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 ), ( -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 ), ( -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 ), ( -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 ), ( -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ) } +colvars: Step 39, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Done calculating gradients of colvar "group1". +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Done calculating colvar "group1". +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( -2.75804320334978e-01 , -1.84590719592386e-02 , 9.61036544334795e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 , 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 7.15209468106941e+00 , -3.67624117504530e-01 , 4.43478070280023e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 , 5.85248794713263e+00 , 2.25938076251533e+00 , 2.95153690628167e+00 , 5.13075591770814e+00 , 3.50792385890992e+00 , 2.84425719233370e+00 , 6.24995676938641e+00 , 4.41880966581118e+00 , 2.28256973292094e+00 , 3.86783704089829e+00 , 3.61096286566776e+00 , 1.99970444568263e+00 , 2.86406518132278e+00 , 4.15145858317519e+00 , 2.40459705297965e+00 , 3.90250111205385e+00 , 3.12041888120911e+00 , 7.97223726672285e-01 , 2.74882732907450e+00 , 3.17112421441466e+00 , -8.93440550655717e-02 , 3.15343423214524e+00 , 2.66497450487673e+00 , -1.50593128968213e+00 , 1.65563470587165e+00 , 2.29806247818938e+00 , 4.68317536017901e-01 , 4.40964171499351e-01 , 2.61077705421038e+00 , 4.07537300936663e-01 , 2.01821656468275e+00 , 1.11484345357438e+00 , 1.02272875349485e+00 , 1.30314111019426e+00 , 1.65390561871593e-01 , 1.66780700656013e+00 , 2.10196684283618e+00 , -1.09273041986010e+00 , 2.02048684397801e+00 , 5.68768745235939e-01 , 6.37675112563199e-01 , 2.93317291449566e+00 , -6.15407244554440e-01 , 3.58633018326628e-01 , 3.21889462115816e+00 , 1.29725121846989e+00 , 1.44057397906235e+00 , 3.78929213200849e+00 , 9.22284891708561e-01 , 1.99418215931574e+00 , 5.06879541844135e+00 , 2.02425336785241e+00 , 2.78863082044487e+00 , 5.72865046142383e+00 , -3.50745637122294e-01 , 2.88297630164963e+00 , 4.91528578031121e+00 , -1.11796558039258e+00 , 3.07208771619379e+00 , 5.89741374769812e+00 , -5.04511543035556e-01 , 3.45375176842667e+00 , 3.70025979089654e+00 , -1.46271168084986e+00 , 4.48061232010830e+00 , 3.40090560148433e+00 , -7.82655702934262e-01 , 5.49608057962156e+00 , 2.48906287015350e+00 , -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 , -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 , -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 , -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 , -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 , -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 , -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 , -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 , -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 , -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 , -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 , -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 , -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 , -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 , -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 , -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 , -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 , -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ). +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.75804320334978e-01 , -1.84590719592386e-02 , 9.61036544334795e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 , 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 7.15209468106941e+00 , -3.67624117504530e-01 , 4.43478070280023e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 , 5.85248794713263e+00 , 2.25938076251533e+00 , 2.95153690628167e+00 , 5.13075591770814e+00 , 3.50792385890992e+00 , 2.84425719233370e+00 , 6.24995676938641e+00 , 4.41880966581118e+00 , 2.28256973292094e+00 , 3.86783704089829e+00 , 3.61096286566776e+00 , 1.99970444568263e+00 , 2.86406518132278e+00 , 4.15145858317519e+00 , 2.40459705297965e+00 , 3.90250111205385e+00 , 3.12041888120911e+00 , 7.97223726672285e-01 , 2.74882732907450e+00 , 3.17112421441466e+00 , -8.93440550655717e-02 , 3.15343423214524e+00 , 2.66497450487673e+00 , -1.50593128968213e+00 , 1.65563470587165e+00 , 2.29806247818938e+00 , 4.68317536017901e-01 , 4.40964171499351e-01 , 2.61077705421038e+00 , 4.07537300936663e-01 , 2.01821656468275e+00 , 1.11484345357438e+00 , 1.02272875349485e+00 , 1.30314111019426e+00 , 1.65390561871593e-01 , 1.66780700656013e+00 , 2.10196684283618e+00 , -1.09273041986010e+00 , 2.02048684397801e+00 , 5.68768745235939e-01 , 6.37675112563199e-01 , 2.93317291449566e+00 , -6.15407244554440e-01 , 3.58633018326628e-01 , 3.21889462115816e+00 , 1.29725121846989e+00 , 1.44057397906235e+00 , 3.78929213200849e+00 , 9.22284891708561e-01 , 1.99418215931574e+00 , 5.06879541844135e+00 , 2.02425336785241e+00 , 2.78863082044487e+00 , 5.72865046142383e+00 , -3.50745637122294e-01 , 2.88297630164963e+00 , 4.91528578031121e+00 , -1.11796558039258e+00 , 3.07208771619379e+00 , 5.89741374769812e+00 , -5.04511543035556e-01 , 3.45375176842667e+00 , 3.70025979089654e+00 , -1.46271168084986e+00 , 4.48061232010830e+00 , 3.40090560148433e+00 , -7.82655702934262e-01 , 5.49608057962156e+00 , 2.48906287015350e+00 , -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 , -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 , -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 , -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 , -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 , -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 , -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 , -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 , -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 , -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 , -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 , -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 , -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 , -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 , -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 , -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 , -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 , -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 64.802 , 6.4802 , 12.9604 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 64.802 , 6.4802 , 12.9604 ) to colvar "one". +colvars: Adding total bias energy: 54.7326 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 64.802 , 6.4802 , 12.9604 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.15038 , -0.516971 , -1.37925 ) +colvars: ( -4.41645 , -0.443303 , -1.1827 ) +colvars: ( -4.41645 , -0.443303 , -1.1827 ) +colvars: ( -5.88283 , -0.590492 , -1.5754 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.912086 , 0.204609 , 0.611764 ) +colvars: ( 0.791829 , 0.275683 , 0.635866 ) +colvars: ( 0.774684 , 0.269442 , 0.618171 ) +colvars: ( 0.680013 , 0.274732 , 0.571762 ) +colvars: ( 0.668109 , 0.206562 , 0.477089 ) +colvars: ( 0.593515 , 0.352298 , 0.623226 ) +colvars: ( 0.48643 , 0.36484 , 0.579196 ) +colvars: ( 0.409713 , 0.463039 , 0.662789 ) +colvars: ( 0.403938 , 0.318856 , 0.473463 ) +colvars: ( 0.369466 , 0.275577 , 0.398223 ) +colvars: ( 0.373566 , 0.324784 , 0.464034 ) +colvars: ( 0.301503 , 0.28071 , 0.366631 ) +colvars: ( 0.273306 , 0.310954 , 0.389806 ) +colvars: ( 0.364087 , 0.181638 , 0.273963 ) +colvars: ( 0.305213 , 0.13666 , 0.18281 ) +colvars: ( 0.487223 , 0.145361 , 0.296388 ) +colvars: ( 0.55999 , 0.0529475 , 0.21804 ) +colvars: ( 0.689712 , 0.0333701 , 0.265721 ) +colvars: ( 0.569573 , 0.0196513 , 0.180458 ) +colvars: ( 0.553791 , -0.0470284 , 0.0855282 ) +colvars: ( 0.591373 , 0.0681115 , 0.255258 ) +colvars: ( 0.590833 , 0.0506831 , 0.232462 ) +colvars: ( 0.628251 , 0.116575 , 0.338541 ) +colvars: ( 0.466286 , 0.0535234 , 0.166091 ) +colvars: ( 0.459841 , -0.00405233 , 0.0881609 ) +colvars: ( 0.363686 , 0.119583 , 0.193651 ) +colvars: ( 0.238801 , 0.12676 , 0.132687 ) +colvars: ( 0.146659 , 0.21354 , 0.19287 ) +colvars: ( 0.209881 , 0.0516369 , 0.0194726 ) +colvars: ( 0.160823 , 0.0137419 , -0.0570202 ) +colvars: ( 0.242648 , 0.0267932 , 0.00583616 ) +colvars: ( 0.227938 , -0.0468617 , -0.0974928 ) +colvars: ( 0.262305 , -0.048888 , -0.0807827 ) +colvars: ( 0.303826 , -0.134076 , -0.167376 ) +colvars: ( 0.259653 , -0.18885 , -0.262905 ) +colvars: ( 0.419796 , -0.148346 , -0.12058 ) +colvars: ( 0.497976 , -0.224921 , -0.175442 ) +colvars: ( 0.629811 , -0.226123 , -0.102859 ) +colvars: ( 0.451491 , -0.230966 , -0.209384 ) +colvars: ( 0.457229 , -0.300599 , -0.296024 ) +colvars: ( 0.403203 , -0.157254 , -0.141406 ) +colvars: ( 0.349694 , -0.152366 , -0.165187 ) +colvars: ( 0.333755 , -0.0645952 , -0.0608753 ) +colvars: ( 0.22582 , -0.162727 , -0.248217 ) +colvars: ( 0.201846 , -0.206402 , -0.318064 ) +colvars: ( 0.0222204 , -0.210471 , -0.424323 ) +colvars: ( -0.0691285 , -0.229685 , -0.500489 ) +colvars: ( 0.122399 , -0.259753 , -0.431593 ) +colvars: ( 0.143024 , -0.121615 , -0.241717 ) +colvars: ( 0.0230795 , -0.127361 , -0.316581 ) +colvars: ( -0.0666655 , -0.0456504 , -0.261593 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.15038 , 0.516971 , 1.37925 ) +colvars: ( 4.41645 , 0.443303 , 1.1827 ) +colvars: ( 4.41645 , 0.443303 , 1.1827 ) +colvars: ( 5.88283 , 0.590492 , 1.5754 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.627959 , -0.0844848 , -0.35645 ) +colvars: ( -0.566512 , -0.170711 , -0.321215 ) +colvars: ( -0.511644 , -0.147634 , -0.259355 ) +colvars: ( -0.530263 , -0.198987 , -0.293566 ) +colvars: ( -0.520259 , -0.137177 , -0.264791 ) +colvars: ( -0.508512 , -0.295081 , -0.301011 ) +colvars: ( -0.479237 , -0.336843 , -0.284431 ) +colvars: ( -0.460238 , -0.449025 , -0.299513 ) +colvars: ( -0.414161 , -0.299405 , -0.208005 ) +colvars: ( -0.411487 , -0.272674 , -0.197211 ) +colvars: ( -0.360769 , -0.293429 , -0.152814 ) +colvars: ( -0.297794 , -0.254448 , -0.0780193 ) +colvars: ( -0.245025 , -0.270052 , -0.0300066 ) +colvars: ( -0.315309 , -0.146527 , -0.0627475 ) +colvars: ( -0.284275 , -0.115544 , -0.0223119 ) +colvars: ( -0.36785 , -0.0869328 , -0.0971696 ) +colvars: ( -0.392736 , 0.0157651 , -0.0908531 ) +colvars: ( -0.440133 , 0.0650667 , -0.12326 ) +colvars: ( -0.434377 , 0.0315596 , -0.127683 ) +colvars: ( -0.42268 , 0.0911935 , -0.0978757 ) +colvars: ( -0.482471 , -0.0251498 , -0.192987 ) +colvars: ( -0.521113 , -0.0265947 , -0.232056 ) +colvars: ( -0.574676 , -0.0953155 , -0.306475 ) +colvars: ( -0.471301 , -0.0574644 , -0.191636 ) +colvars: ( -0.479452 , -0.0111585 , -0.185719 ) +colvars: ( -0.416555 , -0.134948 , -0.160443 ) +colvars: ( -0.360584 , -0.167182 , -0.114281 ) +colvars: ( -0.310407 , -0.261365 , -0.0927293 ) +colvars: ( -0.31626 , -0.0906982 , -0.0467398 ) +colvars: ( -0.304856 , -0.0709081 , -0.0293284 ) +colvars: ( -0.291613 , -0.0438628 , -0.00787526 ) +colvars: ( -0.252851 , 0.0345623 , 0.0546963 ) +colvars: ( -0.226485 , 0.0619904 , 0.0893849 ) +colvars: ( -0.297001 , 0.125241 , 0.0381039 ) +colvars: ( -0.27014 , 0.169255 , 0.0783257 ) +colvars: ( -0.366769 , 0.154226 , -0.0228374 ) +colvars: ( -0.416113 , 0.233824 , -0.047987 ) +colvars: ( -0.486805 , 0.256893 , -0.111649 ) +colvars: ( -0.43239 , 0.21333 , -0.070484 ) +colvars: ( -0.437034 , 0.277117 , -0.0557512 ) +colvars: ( -0.440862 , 0.122807 , -0.106449 ) +colvars: ( -0.452612 , 0.0915062 , -0.127703 ) +colvars: ( -0.477953 , -0.00623967 , -0.182727 ) +colvars: ( -0.386326 , 0.0802523 , -0.0648572 ) +colvars: ( -0.391723 , 0.10801 , -0.0618212 ) +colvars: ( -0.219587 , 0.115387 , 0.1125 ) +colvars: ( -0.170437 , 0.117766 , 0.162356 ) +colvars: ( -0.24242 , 0.19073 , 0.112559 ) +colvars: ( -0.321851 , 0.0378456 , -0.0132846 ) +colvars: ( -0.255256 , 0.0241077 , 0.049116 ) +colvars: ( -0.200978 , -0.0626641 , 0.0770197 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 39. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 39. +colvars: End of step for colvar "one". +colvars: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atoms_new_colvar_forces = { ( -4.86624888188174e+00 , -3.96846870810409e-01 , -1.12393283910536e+00 ), ( -4.19112890348070e+00 , -3.38331517233914e-01 , -8.68052342709592e-01 ), ( -4.26669521102572e+00 , -3.67557643479787e-01 , -9.04507382720872e-01 ), ( -5.73498403444011e+00 , -5.21106874330410e-01 , -1.36309638276026e+00 ), ( 2.63039719328412e-01 , 1.21808606746486e-01 , 3.58816049029923e-01 ), ( 5.23537853780408e+00 , 5.74188625236823e-01 , 1.70146163887394e+00 ), ( 4.42363942606241e+00 , 4.71299483584489e-01 , 1.47746818775184e+00 ), ( -5.05252225535211e-02 , 1.40139555680489e-02 , 3.63275791484696e-01 ), ( 4.40622288551885e+00 , 4.62753988587406e-01 , 1.44816210595151e+00 ), ( 5.84081329579396e+00 , 5.93394527303759e-01 , 1.77640673879265e+00 ), ( 1.27968526509231e-02 , 3.13541852328310e-02 , 3.11219118021952e-01 ), ( 3.70917523991948e-03 , 2.62619996992839e-02 , 2.88611609060987e-01 ), ( 2.82812640814406e-02 , 4.09014620763242e-02 , 3.59799278659715e-01 ), ( 4.87775267289722e-02 , 3.51112982228473e-02 , 2.11215959969178e-01 ), ( 2.09386115151937e-02 , 2.11166378679873e-02 , 1.60497998048344e-01 ), ( 1.19372725886971e-01 , 5.84282841160213e-02 , 1.99218157241819e-01 ), ( 1.67254327445789e-01 , 6.87125317282526e-02 , 1.27187213018348e-01 ), ( 2.49578995784398e-01 , 9.84368335739027e-02 , 1.42460782216679e-01 ), ( 1.35195468618677e-01 , 5.12109402703477e-02 , 5.27743403932174e-02 ), ( 1.31111771450573e-01 , 4.41650867263977e-02 , -1.23474749183609e-02 ), ( 1.08902116868153e-01 , 4.29617013130471e-02 , 6.22709859610579e-02 ), ( 6.97192969986092e-02 , 2.40884641687701e-02 , 4.05873732892692e-04 ), ( 5.35752380407125e-02 , 2.12592535748896e-02 , 3.20662093135859e-02 ), ( -5.01413743191209e-03 , -3.94101361003935e-03 , -2.55442982851857e-02 ), ( -1.96117385202164e-02 , -1.52107871956150e-02 , -9.75583784328992e-02 ), ( -5.28685391564081e-02 , -1.53652998345423e-02 , 3.32077892656157e-02 ), ( -1.21782927083157e-01 , -4.04222364071606e-02 , 1.84053946066618e-02 ), ( -1.63747672167038e-01 , -4.78251673446656e-02 , 1.00140392817315e-01 ), ( -1.06379087298422e-01 , -3.90613070346572e-02 , -2.72671718419319e-02 ), ( -1.44033164146982e-01 , -5.71661682147888e-02 , -8.63486103204718e-02 ), ( -4.89651244709921e-02 , -1.70695951364150e-02 , -2.03909618221090e-03 ), ( -2.49126009154574e-02 , -1.22993890853467e-02 , -4.27964892910963e-02 ), ( 3.58195935432474e-02 , 1.31024577418579e-02 , 8.60218814107983e-03 ), ( 6.82489061115937e-03 , -8.83523074512255e-03 , -1.29272047426560e-01 ), ( -1.04869053564732e-02 , -1.95953026501091e-02 , -1.84579800551297e-01 ), ( 5.30263513415448e-02 , 5.87999973341891e-03 , -1.43416961499342e-01 ), ( 8.18634837905476e-02 , 8.90302520024833e-03 , -2.23428842175944e-01 ), ( 1.43006056251065e-01 , 3.07695439429659e-02 , -2.14508147633802e-01 ), ( 1.91004446781697e-02 , -1.76357354096791e-02 , -2.79867555273676e-01 ), ( 2.01952733562084e-02 , -2.34823339925463e-02 , -3.51774801986377e-01 ), ( -3.76584821190159e-02 , -3.44467091087731e-02 , -2.47855237136219e-01 ), ( -1.02917371001586e-01 , -6.08593832803947e-02 , -2.92889644212754e-01 ), ( -1.44197811938873e-01 , -7.08348737155169e-02 , -2.43601901479221e-01 ), ( -1.60505924946831e-01 , -8.24747399491582e-02 , -3.13073960838549e-01 ), ( -1.89877822052170e-01 , -9.83913028876804e-02 , -3.79884970331958e-01 ), ( -1.97366811362835e-01 , -9.50835974358932e-02 , -3.11823499450721e-01 ), ( -2.39565864837849e-01 , -1.11919728153128e-01 , -3.38132907776551e-01 ), ( -1.20021171512207e-01 , -6.90232539396338e-02 , -3.19033444303139e-01 ), ( -1.78827528193025e-01 , -8.37689366093193e-02 , -2.55001164246048e-01 ), ( -2.32176768406599e-01 , -1.03253425804644e-01 , -2.67464930231412e-01 ), ( -2.67643623090158e-01 , -1.08314468817058e-01 , -1.84573519231204e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 5, 5, 5, 5, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3 } +colvars: Step 40, atoms_masses[size = 51] = { 14.007, 12.011, 12.011, 15.999, 12.011, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011, 12.011 } +colvars: Step 40, atoms_charges[size = 51] = { -0.62, -0.1, 0.51, -0.51, -0.27, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, -0.47, 0.07, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, 0.07, -0.27 } +colvars: Step 40, atoms_positions[size = 51] = { ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 ), ( 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 ), ( 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 ), ( 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ), ( 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 ), ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 ), ( 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 ), ( 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 ), ( 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 ), ( 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ), ( 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 ), ( 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 ), ( 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 ), ( 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 ), ( 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 ), ( 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 ), ( 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 ), ( 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 ), ( 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 ), ( 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 ), ( 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 ), ( 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 ), ( 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 ), ( 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 ), ( -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 ), ( 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 ), ( 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 ), ( 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 ), ( -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 ), ( -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 ), ( -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 ), ( -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 ), ( -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 ), ( -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 ), ( -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 ), ( -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 ), ( -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 ), ( -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 ), ( -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 ), ( -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 ), ( -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 ), ( -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 ), ( -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 ), ( -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 ), ( -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 ), ( -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 ), ( -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 ), ( -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 ), ( -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 ), ( -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 ), ( -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ) } +colvars: Step 40, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = group2, cvc = 0 +colvars: Calculating colvar "group2", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 3, last = 3, cv = fitting_group1, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = group1, cvc = 0 +colvars: Calculating colvar "fitting_group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "group1", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "group2" has value ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ). +colvars: Calculating gradients of colvar "group2". +colvars: Done calculating gradients of colvar "group2". +colvars: Done calculating colvar "group2". +colvars: Colvar component no. 1 within colvar "one" has value ( -2.73073003055543e-01 , -1.84328428660908e-02 , 9.61816700471613e-01 ). +colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ). +colvars: Calculating gradients of colvar "group1". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "group1". +colvars: Done calculating colvar "group1". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting_group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 , 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 , 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 , 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 , 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 , 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 , 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 , 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 , 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 , 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 , 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 , 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 , 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 , 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 , 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 , 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 , -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 , 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 , 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 , 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 , -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 , -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 , -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 , -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 , -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 , -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 , -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 , -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 , -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 , -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 , -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 , -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 , -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 , -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 , -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 , -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 , -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 , -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 , -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 , -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 , -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 , -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 , -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting_group1". +colvars: Done calculating gradients of colvar "fitting_group1". +colvars: Done calculating colvar "fitting_group1". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( -2.73073003055543e-01 , -1.84328428660908e-02 , 9.61816700471613e-01 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "group1"'s properties. +colvars: Colvar "group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ). +colvars: Done calculating colvar "group1"'s properties. +colvars: Calculating colvar "group2"'s properties. +colvars: Colvar "group2" has value ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ). +colvars: Done calculating colvar "group2"'s properties. +colvars: Calculating colvar "fitting_group1"'s properties. +colvars: Colvar "fitting_group1" has value ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 , 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 , 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 , 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 , 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 , 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 , 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 , 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 , 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 , 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 , 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 , 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 , 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 , 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 , 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 , 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 , -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 , 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 , 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 , 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 , -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 , -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 , -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 , -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 , -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 , -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 , -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 , -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 , -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 , -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 , -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 , -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 , -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 , -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 , -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 , -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 , -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 , -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 , -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 , -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 , -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 , -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 , -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ). +colvars: Done calculating colvar "fitting_group1"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +colvars: Done updating the restraint bias "harmonic1". +colvars: Current forces for the restraint bias "harmonic1": { ( 64.6761 , 6.46761 , 12.9352 ) }. +colvars: Collecting forces from all biases. +colvars: Communicating a force to colvar "one". +colvars: Adding biasing force ( 64.6761 , 6.46761 , 12.9352 ) to colvar "one". +colvars: Adding total bias energy: 54.5456 +colvars: Updating the internal degrees of freedom of colvars (if they have any). +colvars: Updating colvar "one". +colvars: Done updating colvar "one". +colvars: Updating colvar "group1". +colvars: Done updating colvar "group1". +colvars: Updating colvar "group2". +colvars: Done updating colvar "group2". +colvars: Updating colvar "fitting_group1". +colvars: Done updating colvar "fitting_group1". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +colvars: Force to be applied: ( 64.6761 , 6.46761 , 12.9352 ) +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( -5.14375 , -0.512863 , -1.36279 ) +colvars: ( -4.41077 , -0.43978 , -1.16859 ) +colvars: ( -4.41077 , -0.43978 , -1.16859 ) +colvars: ( -5.87527 , -0.5858 , -1.5566 ) +colvars: Applying force on the fitting group of main group: +colvars: ( 0.909017 , 0.20443 , 0.607544 ) +colvars: ( 0.789318 , 0.275132 , 0.631553 ) +colvars: ( 0.772123 , 0.269017 , 0.614048 ) +colvars: ( 0.678088 , 0.274001 , 0.567808 ) +colvars: ( 0.666238 , 0.206052 , 0.473678 ) +colvars: ( 0.59205 , 0.351153 , 0.618972 ) +colvars: ( 0.48554 , 0.363463 , 0.575179 ) +colvars: ( 0.409228 , 0.461198 , 0.658292 ) +colvars: ( 0.403378 , 0.317597 , 0.470111 ) +colvars: ( 0.369117 , 0.27438 , 0.395276 ) +colvars: ( 0.373041 , 0.323572 , 0.460815 ) +colvars: ( 0.301249 , 0.279631 , 0.364032 ) +colvars: ( 0.273071 , 0.309845 , 0.387158 ) +colvars: ( 0.363511 , 0.180995 , 0.27189 ) +colvars: ( 0.304919 , 0.136099 , 0.18127 ) +colvars: ( 0.486043 , 0.145005 , 0.294165 ) +colvars: ( 0.558446 , 0.0530113 , 0.216254 ) +colvars: ( 0.687506 , 0.0336974 , 0.263657 ) +colvars: ( 0.568092 , 0.0197369 , 0.178811 ) +colvars: ( 0.552385 , -0.0467322 , 0.0844263 ) +colvars: ( 0.589888 , 0.0679639 , 0.253115 ) +colvars: ( 0.589463 , 0.0504879 , 0.230375 ) +colvars: ( 0.626794 , 0.116114 , 0.335782 ) +colvars: ( 0.465543 , 0.0531392 , 0.164394 ) +colvars: ( 0.459168 , -0.0042856 , 0.0868822 ) +colvars: ( 0.36341 , 0.11887 , 0.191839 ) +colvars: ( 0.239134 , 0.12586 , 0.131246 ) +colvars: ( 0.147406 , 0.212258 , 0.191129 ) +colvars: ( 0.210277 , 0.0510297 , 0.0187322 ) +colvars: ( 0.161495 , 0.0131664 , -0.0573398 ) +colvars: ( 0.242776 , 0.026416 , 0.00523774 ) +colvars: ( 0.228057 , -0.0469302 , -0.0974483 ) +colvars: ( 0.262137 , -0.0487927 , -0.0807623 ) +colvars: ( 0.303616 , -0.133786 , -0.166976 ) +colvars: ( 0.259646 , -0.188419 , -0.261946 ) +colvars: ( 0.419071 , -0.147905 , -0.120502 ) +colvars: ( 0.496921 , -0.224164 , -0.175101 ) +colvars: ( 0.628144 , -0.22522 , -0.102978 ) +colvars: ( 0.450769 , -0.230349 , -0.20891 ) +colvars: ( 0.456495 , -0.299752 , -0.29507 ) +colvars: ( 0.402793 , -0.157023 , -0.141359 ) +colvars: ( 0.349646 , -0.152317 , -0.16506 ) +colvars: ( 0.333865 , -0.0649427 , -0.061391 ) +colvars: ( 0.226349 , -0.162778 , -0.247576 ) +colvars: ( 0.202543 , -0.206384 , -0.317056 ) +colvars: ( 0.0235368 , -0.21043 , -0.422507 ) +colvars: ( -0.0673859 , -0.22968 , -0.498209 ) +colvars: ( 0.12317 , -0.25936 , -0.429718 ) +colvars: ( 0.143874 , -0.121836 , -0.241042 ) +colvars: ( 0.0244801 , -0.127687 , -0.315435 ) +colvars: ( -0.0648778 , -0.0463245 , -0.260709 ) +colvars: Done applying force on the fitting group of main group: +colvars: Communicating a colvar force from atom group to the MD engine. +colvars: Applying force on main group : +colvars: ( 5.14375 , 0.512863 , 1.36279 ) +colvars: ( 4.41077 , 0.43978 , 1.16859 ) +colvars: ( 4.41077 , 0.43978 , 1.16859 ) +colvars: ( 5.87527 , 0.5858 , 1.5566 ) +colvars: Applying force on the fitting group of main group: +colvars: ( -0.625368 , -0.0844664 , -0.35261 ) +colvars: ( -0.564389 , -0.170315 , -0.317356 ) +colvars: ( -0.509508 , -0.147373 , -0.255728 ) +colvars: ( -0.528612 , -0.198378 , -0.290017 ) +colvars: ( -0.518649 , -0.136771 , -0.26169 ) +colvars: ( -0.507237 , -0.294051 , -0.297227 ) +colvars: ( -0.478424 , -0.335553 , -0.280849 ) +colvars: ( -0.459758 , -0.447272 , -0.295551 ) +colvars: ( -0.413631 , -0.298213 , -0.205031 ) +colvars: ( -0.411117 , -0.271521 , -0.194558 ) +colvars: ( -0.360291 , -0.292294 , -0.150021 ) +colvars: ( -0.297551 , -0.253428 , -0.0757988 ) +colvars: ( -0.244824 , -0.269019 , -0.0278188 ) +colvars: ( -0.314798 , -0.145936 , -0.0609419 ) +colvars: ( -0.283992 , -0.115013 , -0.0209648 ) +colvars: ( -0.366841 , -0.0866503 , -0.0952017 ) +colvars: ( -0.391423 , 0.0156314 , -0.0892212 ) +colvars: ( -0.438282 , 0.0646406 , -0.121372 ) +colvars: ( -0.433092 , 0.031424 , -0.126102 ) +colvars: ( -0.421451 , 0.090866 , -0.0967462 ) +colvars: ( -0.481165 , -0.0250553 , -0.190941 ) +colvars: ( -0.519878 , -0.0264336 , -0.229995 ) +colvars: ( -0.573354 , -0.0949003 , -0.303803 ) +colvars: ( -0.470575 , -0.0570841 , -0.189926 ) +colvars: ( -0.478772 , -0.0109091 , -0.184331 ) +colvars: ( -0.416224 , -0.134236 , -0.158693 ) +colvars: ( -0.360754 , -0.166255 , -0.112877 ) +colvars: ( -0.31093 , -0.26006 , -0.0911316 ) +colvars: ( -0.316492 , -0.0900499 , -0.0459571 ) +colvars: ( -0.305303 , -0.0702667 , -0.0288864 ) +colvars: ( -0.291645 , -0.0434603 , -0.00725477 ) +colvars: ( -0.252887 , 0.0346661 , 0.0547448 ) +colvars: ( -0.22631 , 0.0619076 , 0.0894017 ) +colvars: ( -0.296752 , 0.124994 , 0.0379104 ) +colvars: ( -0.270056 , 0.168889 , 0.0776549 ) +colvars: ( -0.366086 , 0.153811 , -0.0227007 ) +colvars: ( -0.415142 , 0.2331 , -0.0480107 ) +colvars: ( -0.485326 , 0.255996 , -0.111236 ) +colvars: ( -0.431671 , 0.212772 , -0.0705746 ) +colvars: ( -0.436297 , 0.276346 , -0.0562233 ) +colvars: ( -0.440388 , 0.122639 , -0.106169 ) +colvars: ( -0.452415 , 0.0915445 , -0.127452 ) +colvars: ( -0.477876 , -0.00581152 , -0.181915 ) +colvars: ( -0.386607 , 0.0804178 , -0.065083 ) +colvars: ( -0.392129 , 0.10813 , -0.0623269 ) +colvars: ( -0.220553 , 0.115492 , 0.111136 ) +colvars: ( -0.171755 , 0.117928 , 0.160573 ) +colvars: ( -0.242947 , 0.190464 , 0.111153 ) +colvars: ( -0.322416 , 0.0381802 , -0.0136105 ) +colvars: ( -0.256279 , 0.024571 , 0.0483461 ) +colvars: ( -0.202335 , -0.0618573 , 0.0764049 ) +colvars: Done applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 40. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "group1". +colvars: End of step for colvar "group2". +colvars: End of step for colvar "fitting_group1". +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atoms_new_colvar_forces = { ( -4.86010500487513e+00 , -3.92899476781565e-01 , -1.10785721873104e+00 ), ( -4.18584012135942e+00 , -3.34962322561261e-01 , -8.54396583409615e-01 ), ( -4.26129258537055e+00 , -3.64157246411969e-01 , -8.90801999102965e-01 ), ( -5.72768189464099e+00 , -5.16518692575566e-01 , -1.34461147393970e+00 ), ( 2.62614933737386e-01 , 1.21643196582163e-01 , 3.58320228267059e-01 ), ( 5.22856653164363e+00 , 5.69964893972689e-01 , 1.68453660030878e+00 ), ( 4.41788419879669e+00 , 4.67689682026466e-01 , 1.46292282216087e+00 ), ( -5.05309252132559e-02 , 1.39257115269364e-02 , 3.62741493084848e-01 ), ( 4.40051564040493e+00 , 4.59164448844135e-01 , 1.43367269992625e+00 ), ( 5.83327082858468e+00 , 5.88658850729039e-01 , 1.75731846986772e+00 ), ( 1.27500039872741e-02 , 3.12783106080479e-02 , 3.10793732251512e-01 ), ( 3.69805211512170e-03 , 2.62025486681574e-02 , 2.88233477601792e-01 ), ( 2.82471623542027e-02 , 4.08261801951898e-02 , 3.59339489691045e-01 ), ( 4.87126546060106e-02 , 3.50583306953602e-02 , 2.10947915841365e-01 ), ( 2.09264208987602e-02 , 2.10868507446829e-02 , 1.60305126941948e-01 ), ( 1.19201158802730e-01 , 5.83549571087401e-02 , 1.98963090804411e-01 ), ( 1.67022234450991e-01 , 6.86426967088851e-02 , 1.27033160175296e-01 ), ( 2.49223370441218e-01 , 9.83379500123318e-02 , 1.42284699220159e-01 ), ( 1.35000114916889e-01 , 5.11609815544152e-02 , 5.27083545084148e-02 ), ( 1.30933975271148e-01 , 4.41337908242187e-02 , -1.23198772055619e-02 ), ( 1.08723128264765e-01 , 4.29086581040898e-02 , 6.21748839294782e-02 ), ( 6.95855807919954e-02 , 2.40542268943943e-02 , 3.80060658965092e-04 ), ( 5.34401709694688e-02 , 2.12133864559464e-02 , 3.19793165209076e-02 ), ( -5.03187648228520e-03 , -3.94494665803143e-03 , -2.55313892881111e-02 ), ( -1.96042067736224e-02 , -1.51947328419243e-02 , -9.74491528415509e-02 ), ( -5.28140476899892e-02 , -1.53652878309355e-02 , 3.31463057759504e-02 ), ( -1.21619293554667e-01 , -4.03951395042048e-02 , 1.83695676879411e-02 ), ( -1.63523861300645e-01 , -4.78017821499703e-02 , 9.99976808830524e-02 ), ( -1.06214451109011e-01 , -3.90202332767928e-02 , -2.72249337865024e-02 ), ( -1.43808766912087e-01 , -5.71003535725851e-02 , -8.62262480146662e-02 ), ( -4.88691380386168e-02 , -1.70443490260226e-02 , -2.01703003472374e-03 ), ( -2.48292115802329e-02 , -1.22641177815657e-02 , -4.27034572360182e-02 ), ( 3.58272815045241e-02 , 1.31149152258394e-02 , 8.63941847240535e-03 ), ( 6.86386165582842e-03 , -8.79191657407025e-03 , -1.29065382176512e-01 ), ( -1.04095724900709e-02 , -1.95306413489265e-02 , -1.84291124342117e-01 ), ( 5.29844218525999e-02 , 5.90661814191340e-03 , -1.43202552188758e-01 ), ( 8.17782812299959e-02 , 8.93602219704753e-03 , -2.23111662214294e-01 ), ( 1.42817498250238e-01 , 3.07766230419280e-02 , -2.14213517111727e-01 ), ( 1.90975872719274e-02 , -1.75768123337172e-02 , -2.79485105483733e-01 ), ( 2.01987133536012e-02 , -2.34065200978483e-02 , -3.51292930914822e-01 ), ( -3.75954707463619e-02 , -3.43840123366401e-02 , -2.47528167059879e-01 ), ( -1.02768759885532e-01 , -6.07723846491564e-02 , -2.92512391019645e-01 ), ( -1.44011086499806e-01 , -7.07542340805300e-02 , -2.43306450783254e-01 ), ( -1.60258548256346e-01 , -8.23604570604809e-02 , -3.12659079784094e-01 ), ( -1.89585960104167e-01 , -9.82545854569550e-02 , -3.79382475231133e-01 ), ( -1.97016290220132e-01 , -9.49380420681069e-02 , -3.11370803813321e-01 ), ( -2.39141293687696e-01 , -1.11751250135048e-01 , -3.37636382369183e-01 ), ( -1.19776646754559e-01 , -6.88966356000031e-02 , -3.18565456170577e-01 ), ( -1.78542464818243e-01 , -8.36558831046468e-02 , -2.54652758549066e-01 ), ( -2.31799270250000e-01 , -1.03115915983205e-01 , -2.67088981711532e-01 ), ( -2.67213057543186e-01 , -1.08181859060886e-01 , -1.84304010066073e-01 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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..946d37af4 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,32 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x ( -0.27307300305554 , -0.018432842866091 , 0.96181670047161 ) +} + +colvar { + name group1 + x ( 8.1149547406244 , 0.039025973728438 , -0.6883939751094 , 6.7853094963308 , -0.62690773735816 , -0.48927248081367 , 6.0570819222823 , -0.3204984026977 , 0.79983438945443 , 4.8474758357047 , -0.15265005661356 , 0.78539193495272 ) +} + +colvar { + name group2 + x ( 6.7569195116675 , -0.31726772022198 , 1.9526785556885 , 6.1045094882016 , -0.24248172346477 , 3.2933184881202 , 5.3025069575603 , 1.0670731950028 , 3.3674918263121 , 4.1976525207215 , 1.0093055490164 , 3.8928528477676 ) +} + +colvar { + name fitting_group1 + x ( 8.1149547406244 , 0.039025973728438 , -0.6883939751094 , 6.7853094963308 , -0.62690773735816 , -0.48927248081367 , 7.010066781814 , -2.1149340872622 , -0.79871868234416 , 6.0570819222823 , -0.3204984026977 , 0.79983438945443 , 4.8474758357047 , -0.15265005661356 , 0.78539193495272 , 6.7569195116675 , -0.31726772022198 , 1.9526785556885 , 6.1045094882016 , -0.24248172346477 , 3.2933184881202 , 7.1490449752629 , -0.37058757233971 , 4.4399196197799 , 5.3025069575603 , 1.0670731950028 , 3.3674918263121 , 4.1976525207215 , 1.0093055490164 , 3.8928528477676 , 5.8493891412547 , 2.259999877851 , 2.9491637404497 , 5.1330973450144 , 3.5061330235678 , 2.8406622822242 , 6.2433790945366 , 4.4147409098211 , 2.2802690895513 , 3.8716714078007 , 3.6077840924352 , 1.9988572259436 , 2.8683227898067 , 4.1497902846583 , 2.4027808174741 , 3.9037961131111 , 3.1123185616756 , 0.8010841726464 , 2.7470790455553 , 3.1841148212122 , -0.09556990656272 , 3.1556634001638 , 2.6652943276712 , -1.5007967041156 , 1.6653262429665 , 2.3057555454737 , 0.47631763100361 , 0.44560810177051 , 2.6098182262123 , 0.40186304979305 , 2.0193190829342 , 1.1206659142018 , 1.0133417993941 , 1.3011677521639 , 0.1623577837318 , 1.6718961286692 , 2.103628243052 , -1.0926954426178 , 2.0161544932039 , 0.56812713179284 , 0.64424808838615 , 2.935622587854 , -0.61713346155249 , 0.3587424368388 , 3.2213863603549 , 1.3004699607377 , 1.4427613668925 , 3.7893374633666 , 0.92231170569283 , 1.9970437445982 , 5.0730168340908 , 2.022467523431 , 2.7927865699648 , 5.7303382474983 , -0.34750321982683 , 2.8807589865422 , 4.916061499821 , -1.1169478598693 , 3.072210023565 , 5.8954444765507 , -0.49953629598684 , 3.4448766860833 , 3.6917631985707 , -1.4683449913708 , 4.4816678223792 , 3.3949326423562 , -0.78376920558253 , 5.504389713531 , 2.4888239527826 , -2.7579909921335 , 3.9249525693942 , 2.7161928948191 , -3.7813569682913 , 4.6155151357506 , 2.794589224195 , -2.7209505257799 , 2.6577136814415 , 2.3296106064383 , -3.8266527670617 , 1.7696270105557 , 1.9735601737672 , -3.3289525461208 , 0.93034839318414 , 0.74788408689063 , -4.277696268604 , 1.0119162061298 , 3.2188841996731 , -5.4037207127892 , 0.69441249408377 , 3.3736636976958 , -3.3478383186157 , 0.69487591672332 , 4.1796284021595 , -3.6639337506895 , 0.054701081155268 , 5.4283456514115 , -2.3006455799535 , -0.25065988383128 , 6.1423365190653 , -4.4779626075131 , 0.99178687455206 , 6.416269786801 , -5.3549594957076 , 0.50489047118977 , 7.1544211891747 , -6.2654163308751 , 3.5984702819319 , 6.8193217922678 , -7.0644511389725 , 4.2856069056051 , 7.5042704740056 , -6.6100994654206 , 3.1823589471874 , 5.5688401074549 , -4.1392877914223 , 2.2555968316084 , 6.4286170126916 , -4.7922326877167 , 3.2624257062394 , 7.1680690755413 , -4.012470999143 , 4.6600285619364 , 7.2826034153248 ) +} + +restraint { + 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..b1cdf8add --- /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 group1 group2 fitting_group1 E_harmonic1 + 20 ( -3.03604040816661e-01 , -7.30129413476793e-05 , 9.52798289812123e-01 ) ( 6.60362557644092e+01 , 6.60362557644092e+00 , 1.32072511528818e+01 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 ) ( 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 ) ( 8.28395647975654e+00 , 4.03340897024664e-02 , -7.54692774870218e-01 , 6.93309162587977e+00 , -5.51889783293773e-01 , -5.76983005148295e-01 , 7.04807620251723e+00 , -2.05133477367044e+00 , -9.33771348201489e-01 , 6.15539697115169e+00 , -3.75946650901275e-01 , 7.29836106505539e-01 , 4.94922690224466e+00 , -1.63317394986167e-01 , 7.22359271565317e-01 , 6.86380352982087e+00 , -2.63219177953716e-01 , 1.90772419892779e+00 , 6.17691953526213e+00 , -1.61108143509896e-01 , 3.19478974379045e+00 , 7.08090810208157e+00 , -3.54960206328871e-01 , 4.31465862512141e+00 , 5.32107707515329e+00 , 1.09515793062643e+00 , 3.35244522340509e+00 , 4.16123115092757e+00 , 1.02516007382529e+00 , 3.69345890865362e+00 , 5.84329957482954e+00 , 2.25357789440387e+00 , 2.99029634178557e+00 , 5.23840552251523e+00 , 3.57837540262567e+00 , 2.92153540509063e+00 , 6.32239936732264e+00 , 4.50114415879910e+00 , 2.36555848317626e+00 , 3.88183129123417e+00 , 3.70647217841465e+00 , 2.04446441001327e+00 , 2.79207363733137e+00 , 4.16083623147590e+00 , 2.48776387374853e+00 , 3.93867988998728e+00 , 3.23958597178669e+00 , 7.31263899796578e-01 , 2.66248945511966e+00 , 3.00628499925364e+00 , -1.03690172076150e-01 , 3.05302375767742e+00 , 2.70509817299964e+00 , -1.51512643940498e+00 , 1.59784772643429e+00 , 2.18319085344327e+00 , 4.45897593419401e-01 , 3.79355366684171e-01 , 2.58121370980211e+00 , 5.10152926953013e-01 , 2.04759040304637e+00 , 1.07065023631519e+00 , 1.06972392727901e+00 , 1.16906991772277e+00 , 1.16582953129249e-01 , 1.69742263801853e+00 , 2.04318038776227e+00 , -1.10330455819436e+00 , 2.01060053168732e+00 , 5.62103826058360e-01 , 6.11785045714727e-01 , 2.94280518104649e+00 , -6.01999585869718e-01 , 3.49685207892384e-01 , 3.16153017132967e+00 , 1.31672099166815e+00 , 1.34576172873528e+00 , 3.77544239455742e+00 , 8.42673560544634e-01 , 1.97879904158510e+00 , 5.02542342332618e+00 , 2.07961569595841e+00 , 2.68780631015424e+00 , 5.68212939555367e+00 , -3.37391048688651e-01 , 2.91469615243309e+00 , 4.96799415845159e+00 , -1.13714647010933e+00 , 3.06246953453401e+00 , 5.88777409320388e+00 , -5.11797261215062e-01 , 3.53529000247540e+00 , 3.84631509860824e+00 , -1.51805034913830e+00 , 4.53919006914023e+00 , 3.44426088435633e+00 , -6.99615591667867e-01 , 5.41439548829936e+00 , 2.46379124164586e+00 , -2.76022875458268e+00 , 3.88950075000640e+00 , 2.89497519604018e+00 , -3.81748968192835e+00 , 4.50990478569222e+00 , 2.81462848550707e+00 , -2.62517142845536e+00 , 2.67328863694572e+00 , 2.40143232345677e+00 , -3.77269637339072e+00 , 1.80371844301910e+00 , 1.99827799817643e+00 , -3.38865951847747e+00 , 8.86721545958307e-01 , 8.74097883787267e-01 , -4.32255042169857e+00 , 1.07000828182024e+00 , 3.21216994880678e+00 , -5.49997292122287e+00 , 8.18760985472524e-01 , 3.32918533840020e+00 , -3.36906334816240e+00 , 6.91577442715154e-01 , 4.20412887194558e+00 , -3.70112509965331e+00 , 4.62063662171233e-02 , 5.43409253977396e+00 , -2.39039017785424e+00 , -3.17099337302450e-01 , 6.17010947430015e+00 , -4.46182928271480e+00 , 9.86809181499275e-01 , 6.43957436937118e+00 , -5.35888370672653e+00 , 5.98110042337499e-01 , 7.21795763445978e+00 , -6.23833250969378e+00 , 3.60548245793384e+00 , 6.73364430610127e+00 , -6.96021578799442e+00 , 4.29774701856807e+00 , 7.47564328502527e+00 , -6.74140398797900e+00 , 3.18225753043178e+00 , 5.50784930308555e+00 , -4.12875245539737e+00 , 2.24621190954430e+00 , 6.40966372395121e+00 , -4.80893655605122e+00 , 3.20662718717156e+00 , 7.24170225108268e+00 , -4.09508886188165e+00 , 4.57548964325637e+00 , 7.28281236262029e+00 ) 5.65386573831414e+01 + 21 ( -3.02299978352974e-01 , -1.10908187249818e-03 , 9.53212197270467e-01 ) ( 6.59775965870217e+01 , 6.59775965870217e+00 , 1.31955193174043e+01 ) ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 ) ( 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 ) ( 8.27977574068469e+00 , 4.02528291673913e-02 , -7.52057108166630e-01 , 6.92099506493311e+00 , -5.53213682491376e-01 , -5.69426147303285e-01 , 7.04473198105960e+00 , -2.05327920797844e+00 , -9.29375006637541e-01 , 6.15694677141603e+00 , -3.82089095587422e-01 , 7.37277734299099e-01 , 4.94246607501893e+00 , -1.59790516152810e-01 , 7.24752036501007e-01 , 6.85715505294327e+00 , -2.64188295117223e-01 , 1.91537420101822e+00 , 6.17190026416596e+00 , -1.68100574783552e-01 , 3.19004474570480e+00 , 7.08349974932374e+00 , -3.54003860502016e-01 , 4.32205906386207e+00 , 5.32714081832865e+00 , 1.09165312730471e+00 , 3.35584946545827e+00 , 4.16330605896384e+00 , 1.02282521639228e+00 , 3.70089104134379e+00 , 5.84076474641052e+00 , 2.25536979270325e+00 , 2.98832898375822e+00 , 5.23587857093527e+00 , 3.57669110122797e+00 , 2.92166897452928e+00 , 6.32156958072965e+00 , 4.49988622761485e+00 , 2.35565128281177e+00 , 3.87689241246030e+00 , 3.70006461122386e+00 , 2.04452990951658e+00 , 2.79071649208267e+00 , 4.16332485499335e+00 , 2.48256664176617e+00 , 3.94115111212568e+00 , 3.23747951589492e+00 , 7.30802489699480e-01 , 2.66973082330689e+00 , 3.00547149084645e+00 , -1.01477303070280e-01 , 3.05934866991274e+00 , 2.69953472563322e+00 , -1.51501433052804e+00 , 1.59651250234961e+00 , 2.17844111925864e+00 , 4.39559175880339e-01 , 3.76047644814525e-01 , 2.58920379782601e+00 , 5.06286618437136e-01 , 2.05518303906289e+00 , 1.08608294356329e+00 , 1.06507897580422e+00 , 1.16752914107841e+00 , 1.17153377091661e-01 , 1.69892244776945e+00 , 2.04674784123738e+00 , -1.09987382702508e+00 , 2.01323738316812e+00 , 5.63968280702454e-01 , 6.13311674880878e-01 , 2.94797623919976e+00 , -5.96930658286561e-01 , 3.50029768580982e-01 , 3.16120628953547e+00 , 1.31336537228541e+00 , 1.34641721755719e+00 , 3.76643935962485e+00 , 8.40728449927844e-01 , 1.98098520536555e+00 , 5.02555184853601e+00 , 2.08820061944047e+00 , 2.69718674093485e+00 , 5.68890384646120e+00 , -3.38114968555006e-01 , 2.91390005959590e+00 , 4.96861695275058e+00 , -1.13362055740874e+00 , 3.06346357994511e+00 , 5.88511738748569e+00 , -5.16891315828975e-01 , 3.52804588261768e+00 , 3.84367741672581e+00 , -1.51813147003523e+00 , 4.53539145184990e+00 , 3.43581998125376e+00 , -6.99361331071878e-01 , 5.41613871574232e+00 , 2.46552726451282e+00 , -2.75639385539036e+00 , 3.89649838479966e+00 , 2.88910160993987e+00 , -3.81645795712067e+00 , 4.51561102856821e+00 , 2.81377417640470e+00 , -2.63072320794555e+00 , 2.67070099638364e+00 , 2.39430060280448e+00 , -3.77613361942622e+00 , 1.80233455186507e+00 , 1.99826039719624e+00 , -3.38443261847325e+00 , 8.86024620907593e-01 , 8.67866695010067e-01 , -4.31779735421500e+00 , 1.07008299629866e+00 , 3.20965805787089e+00 , -5.49784639932540e+00 , 8.11531039486521e-01 , 3.32983458708000e+00 , -3.36644838334232e+00 , 6.95528858554952e-01 , 4.20698539052351e+00 , -3.69486418291344e+00 , 5.14459899190286e-02 , 5.43563090521232e+00 , -2.39154195444351e+00 , -3.19136836845920e-01 , 6.16781250330953e+00 , -4.46099237623323e+00 , 9.79156472164992e-01 , 6.43749791116706e+00 , -5.36134076822315e+00 , 5.96438183369795e-01 , 7.21887189473186e+00 , -6.24403048306993e+00 , 3.61110702709758e+00 , 6.73779050651341e+00 , -6.96384309159946e+00 , 4.29725442143745e+00 , 7.47971710345799e+00 , -6.73489973132291e+00 , 3.17847947242598e+00 , 5.50650590430004e+00 , -4.12692317265498e+00 , 2.24428240880414e+00 , 6.40348191725874e+00 , -4.80736530051318e+00 , 3.21376399330973e+00 , 7.24613849765850e+00 , -4.08941478160782e+00 , 4.56964182139912e+00 , 7.28001954395008e+00 ) 5.64539548629295e+01 + 22 ( -3.01144188109486e-01 , -2.24212177402314e-03 , 9.53575980642250e-01 ) ( 6.59267215416616e+01 , 6.59267215416616e+00 , 1.31853443083323e+01 ) ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 ) ( 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 ) ( 8.27580645279437e+00 , 4.03144292974492e-02 , -7.49294164501566e-01 , 6.90851133792285e+00 , -5.54964907881422e-01 , -5.62132589412726e-01 , 7.04075609092289e+00 , -2.05509216928041e+00 , -9.24835802711356e-01 , 6.15867488488193e+00 , -3.86886131588075e-01 , 7.45192783240674e-01 , 4.93573332343163e+00 , -1.56581380597025e-01 , 7.27026766523629e-01 , 6.85045157939743e+00 , -2.65613298957738e-01 , 1.92305183937779e+00 , 6.16589697736237e+00 , -1.75207808542855e-01 , 3.18450270663626e+00 , 7.08737182354233e+00 , -3.52661466736525e-01 , 4.32975748594848e+00 , 5.33244977682571e+00 , 1.08814504982147e+00 , 3.35901300377007e+00 , 4.16528888746438e+00 , 1.02055858637831e+00 , 3.70865931656678e+00 , 5.83883956346146e+00 , 2.25678595257415e+00 , 2.98638325946264e+00 , 5.23154005964565e+00 , 3.57505928759151e+00 , 2.92084908898945e+00 , 6.32071620380121e+00 , 4.49868179694454e+00 , 2.34579647353445e+00 , 3.87242354430216e+00 , 3.69346486449938e+00 , 2.04413682862027e+00 , 2.79035895271567e+00 , 4.16544092253518e+00 , 2.47728808408468e+00 , 3.94195944148036e+00 , 3.23469843265051e+00 , 7.30569602600790e-01 , 2.67877485305899e+00 , 3.00672314624182e+00 , -9.88747085463408e-02 , 3.06614504628802e+00 , 2.69347985600063e+00 , -1.51638199336772e+00 , 1.59296471549361e+00 , 2.17431817427231e+00 , 4.34561985410307e-01 , 3.74551635270970e-01 , 2.59624464254731e+00 , 5.02093669381059e-01 , 2.06207008647046e+00 , 1.10102967553633e+00 , 1.06022179406861e+00 , 1.16706822216552e+00 , 1.17119035768345e-01 , 1.70017001805172e+00 , 2.05056370047854e+00 , -1.09705167374273e+00 , 2.01630386041430e+00 , 5.65917406689346e-01 , 6.14815594529273e-01 , 2.95296639810210e+00 , -5.92561323286166e-01 , 3.50483170844519e-01 , 3.16132607319908e+00 , 1.30979074653958e+00 , 1.34771939589797e+00 , 3.75846177691960e+00 , 8.39659487050740e-01 , 1.98251940370906e+00 , 5.02584329054212e+00 , 2.09585542742799e+00 , 2.70619542623450e+00 , 5.69539103348607e+00 , -3.39453600119534e-01 , 2.91292665634030e+00 , 4.96932895106535e+00 , -1.13018134977445e+00 , 3.06433510367654e+00 , 5.88266519513549e+00 , -5.21834683647455e-01 , 3.52228388457848e+00 , 3.83998269916387e+00 , -1.51685915605967e+00 , 4.53076906079569e+00 , 3.42861948744449e+00 , -7.00115417114287e-01 , 5.41784981777582e+00 , 2.46701284158963e+00 , -2.75278642927085e+00 , 3.90426502047422e+00 , 2.88210318273694e+00 , -3.81541970104260e+00 , 4.52117590121498e+00 , 2.81315225258630e+00 , -2.63688822752028e+00 , 2.66667730940391e+00 , 2.38745162720783e+00 , -3.77913960669741e+00 , 1.80294849170096e+00 , 1.99887473612028e+00 , -3.38040345666998e+00 , 8.84676270302760e-01 , 8.61643303633521e-01 , -4.31110016330817e+00 , 1.06947745632192e+00 , 3.20869723370402e+00 , -5.49615834085791e+00 , 8.04334903040934e-01 , 3.33059712155689e+00 , -3.36496056397399e+00 , 6.99803595818000e-01 , 4.20766853358105e+00 , -3.68942737295836e+00 , 5.70297556228080e-02 , 5.43887800846685e+00 , -2.39229749416928e+00 , -3.21267765742309e-01 , 6.16492124395660e+00 , -4.46079973975974e+00 , 9.70456537680205e-01 , 6.43509918517061e+00 , -5.36321040423276e+00 , 5.94725719692260e-01 , 7.21916802127185e+00 , -6.25138476692940e+00 , 3.61637550011506e+00 , 6.74159454926052e+00 , -6.96732363287335e+00 , 4.29667805101419e+00 , 7.48358027211582e+00 , -6.72691038071533e+00 , 3.17486375320610e+00 , 5.50599009064887e+00 , -4.12463851109464e+00 , 2.24350087117162e+00 , 6.39835345590596e+00 , -4.80680087346617e+00 , 3.22186169538980e+00 , 7.25013364008186e+00 , -4.08268858913279e+00 , 4.56367958244269e+00 , 7.27746724089791e+00 ) 5.63804021930095e+01 + 23 ( -3.00108439186526e-01 , -3.46138019158803e-03 , 9.53898812021588e-01 ) ( 6.58821694759094e+01 , 6.58821694759094e+00 , 1.31764338951819e+01 ) ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 ) ( 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 5.33667217947578e+00 , 1.08473429392310e+00 , 3.36187438660770e+00 , 4.16731893938856e+00 , 1.01836147462050e+00 , 3.71674618604507e+00 ) ( 8.27191173552656e+00 , 4.05153252786273e-02 , -7.46425723809631e-01 , 6.89602939038122e+00 , -5.57266153578187e-01 , -5.55302788936733e-01 , 7.03622967820893e+00 , -2.05680748997666e+00 , -9.20061965768672e-01 , 6.15984908159940e+00 , -3.90121076674033e-01 , 7.53459019467111e-01 , 4.92933089237804e+00 , -1.53789910861105e-01 , 7.29228581722215e-01 , 6.84387296758845e+00 , -2.67521658967245e-01 , 1.93059190133915e+00 , 6.15898219979111e+00 , -1.82319965102567e-01 , 3.17877877298373e+00 , 7.09236442152371e+00 , -3.51072436584830e-01 , 4.33760539310293e+00 , 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4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 ) ( 8.24806061998922e+00 , 4.27817338562571e-02 , -7.30563764400409e-01 , 6.84561335002554e+00 , -5.78812053257388e-01 , -5.31817982543653e-01 , 7.01031857100853e+00 , -2.06592459884321e+00 , -8.90376877361532e-01 , 6.13969365199301e+00 , -3.80255146195349e-01 , 7.93962234555889e-01 , 4.90878093983634e+00 , -1.47986248793553e-01 , 7.40907930091750e-01 , 6.81710596773214e+00 , -2.83852141625931e-01 , 1.95986849722660e+00 , 6.11669331010497e+00 , -2.14120585377203e-01 , 3.16753216458447e+00 , 7.12637116076117e+00 , -3.44508860897163e-01 , 4.37487022681369e+00 , 5.33651908518604e+00 , 1.07141871179348e+00 , 3.36958535708554e+00 , 4.18054672132406e+00 , 1.00874316253316e+00 , 3.76159044724664e+00 , 5.84218996743558e+00 , 2.25490858291028e+00 , 2.97583907708979e+00 , 5.17727606260770e+00 , 3.56103383921320e+00 , 2.89910876229602e+00 , 6.30994169685273e+00 , 4.48299385729493e+00 , 2.29697704996517e+00 , 3.85937142086407e+00 , 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7.51152444314271e+00 , -6.64119633275520e+00 , 3.16227875394137e+00 , 5.53266077125256e+00 , -4.10677583560449e+00 , 2.25507037452862e+00 , 6.39721827362956e+00 , -4.81640955795581e+00 , 3.28303404577876e+00 , 7.24690223413902e+00 , -4.02142734029468e+00 , 4.56265150640650e+00 , 7.27333485760413e+00 ) 5.59012647095673e+01 + 31 ( -2.91985130036785e-01 , -1.38601172701375e-02 , 9.56322425224181e-01 ) ( 6.55400487407042e+01 , 6.55400487407042e+00 , 1.31080097481408e+01 ) ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 ) ( 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 ) ( 8.22542381934642e+00 , 4.38137743473108e-02 , -7.19620291054511e-01 , 6.82959416910687e+00 , -5.97383580286563e-01 , -5.24773325225644e-01 , 6.99862931541371e+00 , -2.07395910964527e+00 , -8.67568974643385e-01 , 6.10662655445034e+00 , -3.58905624261097e-01 , 8.10606745220287e-01 , 4.90389828945101e+00 , -1.49973767096478e-01 , 7.49898149764478e-01 , 6.80578033569276e+00 , -2.96603002645971e-01 , 1.96605381019871e+00 , 6.09411003864182e+00 , -2.27510296408335e-01 , 3.18673867921045e+00 , 7.14497419758621e+00 , -3.45524141899361e-01 , 4.39333076564163e+00 , 5.32350076846520e+00 , 1.06710550505983e+00 , 3.36816062954644e+00 , 4.18967541401037e+00 , 1.00477683341492e+00 , 3.79190667020650e+00 , 5.85055443956478e+00 , 2.25182954443016e+00 , 2.97028115425135e+00 , 5.14852083348922e+00 , 3.54755602330275e+00 , 2.88206623226889e+00 , 6.29816547197643e+00 , 4.46663332802275e+00 , 2.28614594699954e+00 , 3.85883200520895e+00 , 3.63922436728402e+00 , 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-3.59083544239309e-01 , 2.89896652613168e+00 , 4.94898820404714e+00 , -1.11572428551058e+00 , 3.06951194796054e+00 , 5.88482115690961e+00 , -5.42187169180604e-01 , 3.50499123381347e+00 , 3.77099118695669e+00 , -1.46268031975569e+00 , 4.48037988434406e+00 , 3.41654813098619e+00 , -7.45786335642670e-01 , 5.44229603299638e+00 , 2.48045722963077e+00 , -2.74753298530087e+00 , 3.94447594376211e+00 , 2.77285864687686e+00 , -3.80294829977424e+00 , 4.57138591255157e+00 , 2.81296076604628e+00 , -2.69538109697117e+00 , 2.63432663216405e+00 , 2.35377479386011e+00 , -3.80459599624279e+00 , 1.82437654980050e+00 , 2.00414879694824e+00 , -3.35512325585638e+00 , 8.79601502060006e-01 , 7.99977482450302e-01 , -4.25145271767769e+00 , 1.03742992909174e+00 , 3.24369637790920e+00 , -5.46371805461782e+00 , 7.47118259786219e-01 , 3.34187039072449e+00 , -3.37060866584118e+00 , 7.28392606558757e-01 , 4.16387932480070e+00 , -3.66857442981740e+00 , 7.81641484127516e-02 , 5.48076695237109e+00 , -2.37223207155897e+00 , -3.10466811258121e-01 , 6.12845908105643e+00 , -4.48625071769480e+00 , 9.24790283713843e-01 , 6.42033675272418e+00 , -5.35850547061473e+00 , 5.66346626307901e-01 , 7.19540834605961e+00 , -6.30951335127693e+00 , 3.61986424323407e+00 , 6.75455640363207e+00 , -7.01215009480842e+00 , 4.29890165641281e+00 , 7.51422649189039e+00 , -6.63254527016206e+00 , 3.16318975044108e+00 , 5.53787631786702e+00 , -4.10694496489526e+00 , 2.25542395604395e+00 , 6.40082128292832e+00 , -4.81610628218901e+00 , 3.28577818682328e+00 , 7.24092545777286e+00 , -4.01646404561254e+00 , 4.57074955201275e+00 , 7.27474056067541e+00 ) 5.58186127140044e+01 + 32 ( -2.90537915957777e-01 , -1.48938555217606e-02 , 9.56747559421297e-01 ) ( 6.54759494932359e+01 , 6.54759494932359e+00 , 1.30951898986472e+01 ) ( 8.21604973865016e+00 , 4.38872629266947e-02 , -7.15787848422008e-01 , 6.82581675660456e+00 , -6.03491327362550e-01 , -5.22657841556667e-01 , 6.09494065528993e+00 , -3.51161704595987e-01 , 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2.48405525316260e+00 , -2.75055485164224e+00 , 3.93857883605007e+00 , 2.74717290226130e+00 , -3.79947434743322e+00 , 4.58324051602894e+00 , 2.81194006988307e+00 , -2.70370249645647e+00 , 2.63943140723273e+00 , 2.35175453708781e+00 , -3.81170023052065e+00 , 1.81609297876280e+00 , 2.00030427278206e+00 , -3.35024424937264e+00 , 8.86615762420448e-01 , 7.85895448329279e-01 , -4.25600728982660e+00 , 1.02940081946531e+00 , 3.24684139436670e+00 , -5.44750415310821e+00 , 7.36346477912971e-01 , 3.34659059763180e+00 , -3.36800931852192e+00 , 7.25166121602237e-01 , 4.16102175120312e+00 , -3.66668759745866e+00 , 7.30060485395939e-02 , 5.47546121430661e+00 , -2.36010423974749e+00 , -2.98416861465315e-01 , 6.12515037800238e+00 , -4.49154627052291e+00 , 9.36430734260290e-01 , 6.42038312667324e+00 , -5.35639452263458e+00 , 5.54474511149445e-01 , 7.18660811004136e+00 , -6.30549791791672e+00 , 3.61134238103496e+00 , 6.76048835821352e+00 , -7.02639410132082e+00 , 4.30017985271576e+00 , 7.51789300492319e+00 , -6.61928419648995e+00 , 3.16632727106042e+00 , 5.54748910403362e+00 , -4.10992686580126e+00 , 2.25451768982159e+00 , 6.40894333161392e+00 , -4.81303089237992e+00 , 3.28646717434411e+00 , 7.22563971345172e+00 , -4.00990493721068e+00 , 4.59068289810483e+00 , 7.27786625272608e+00 ) 5.56196504735476e+01 + 34 ( -2.87157334453261e-01 , -1.65935395079231e-02 , 9.57739693088000e-01 ) ( 6.53236447432373e+01 , 6.53236447432373e+00 , 1.30647289486475e+01 ) ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 ) ( 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 ) ( 8.19462435601307e+00 , 4.35180719634744e-02 , -7.08089415597664e-01 , 6.81869985092047e+00 , -6.14314720278650e-01 , -5.17568466321731e-01 , 6.99483285784450e+00 , -2.08508886015886e+00 , -8.43049023566560e-01 , 6.07464485669273e+00 , -3.36945960424488e-01 , 8.16615660533306e-01 , 4.89556326832947e+00 , -1.52785904261389e-01 , 7.60762035996543e-01 , 6.79369213100074e+00 , -3.07963925506575e-01 , 1.96388735717601e+00 , 6.08220647663526e+00 , -2.36224297242654e-01 , 3.22269762551378e+00 , 7.15552751647424e+00 , -3.51485998226716e-01 , 4.40931338722213e+00 , 5.31037078448124e+00 , 1.06513416259727e+00 , 3.36414149586749e+00 , 4.19626977535556e+00 , 1.00309690542341e+00 , 3.82459037791640e+00 , 5.85688378227482e+00 , 2.25242598094240e+00 , 2.96373170187796e+00 , 5.13148123045509e+00 , 3.53047778736394e+00 , 2.86549608617996e+00 , 6.28192924564344e+00 , 4.44714141082224e+00 , 2.28416937087293e+00 , 3.85942910541793e+00 , 3.62710776152751e+00 , 2.01157346904339e+00 , 2.83762671134946e+00 , 4.16149292315767e+00 , 2.41911494843471e+00 , 3.90092937760287e+00 , 3.16135007055786e+00 , 7.66801479043737e-01 , 2.76541390511661e+00 , 3.10929249722064e+00 , -6.98345192382389e-02 , 3.13674448343201e+00 , 2.65429689296057e+00 , -1.53414667102645e+00 , 1.58379031740219e+00 , 2.24971251416356e+00 , 4.34287769502383e-01 , 4.26058017508510e-01 , 2.61466798132072e+00 , 4.37256927932297e-01 , 2.03733513416962e+00 , 1.11742178412332e+00 , 1.04781411079880e+00 , 1.27477454077088e+00 , 1.57895397740626e-01 , 1.66639430569332e+00 , 2.09401707005528e+00 , -1.09377065068389e+00 , 2.03726496504889e+00 , 5.72565775214997e-01 , 6.16948305501507e-01 , 2.93975662921241e+00 , -5.99882620699964e-01 , 3.58105451210291e-01 , 3.19987058173645e+00 , 1.28689468249891e+00 , 1.41922485100528e+00 , 3.77581244201658e+00 , 9.01854870242432e-01 , 1.98132815362818e+00 , 5.04622279494481e+00 , 2.05453431427715e+00 , 2.77170808364941e+00 , 5.72608573525488e+00 , 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-2.35295529902296e+00 , -2.91496214171908e-01 , 6.12506447934450e+00 , -4.49278938704928e+00 , 9.44706462021771e-01 , 6.42046061637585e+00 , -5.35573250591647e+00 , 5.47811919178203e-01 , 7.18217409536394e+00 , -6.30118284703126e+00 , 3.60717975726917e+00 , 6.76547267477656e+00 , -7.03344009382229e+00 , 4.30021830812776e+00 , 7.51859397744713e+00 , -6.61477310737558e+00 , 3.16839347849365e+00 , 5.55163827381939e+00 , -4.11266297569249e+00 , 2.25355834928994e+00 , 6.41310008967249e+00 , -4.81038197243659e+00 , 3.28462888958214e+00 , 7.21673698926397e+00 , -4.00828295303965e+00 , 4.60180466069819e+00 , 7.27932685734565e+00 ) 5.55020602440511e+01 + 35 ( -2.85214732151540e-01 , -1.72436288368453e-02 , 9.58308517038361e-01 ) ( 6.52350826417709e+01 , 6.52350826417709e+00 , 1.30470165283542e+01 ) ( 8.18269220341527e+00 , 4.30734997067870e-02 , -7.04333862529214e-01 , 6.81476061808635e+00 , -6.18680042644568e-01 , -5.14273526959778e-01 , 6.06707062277475e+00 , -3.31077644962110e-01 , 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7.51729040384008e+00 , -6.60966967566509e+00 , 3.17306518565685e+00 , 5.55844233973410e+00 , -4.12014434625173e+00 , 2.25179015334399e+00 , 6.42068671713882e+00 , -4.80370532371153e+00 , 3.27779009600733e+00 , 7.19794836160135e+00 , -4.00785084851779e+00 , 4.62445719391590e+00 , 7.28155397986291e+00 ) 5.52297493225922e+01 + 37 ( -2.80827613502008e-01 , -1.81261010387522e-02 , 9.59587044491483e-01 ) ( 6.50336393323266e+01 , 6.50336393323266e+00 , 1.30067278664653e+01 ) ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 ) ( 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 ) ( 8.15684913476551e+00 , 4.17332468926048e-02 , -6.97283312354115e-01 , 6.80507705380192e+00 , -6.24744776630280e-01 , -5.05786787773760e-01 , 6.99970058262444e+00 , -2.09915825278410e+00 , -8.19556716328211e-01 , 6.05819250285732e+00 , -3.22868943948837e-01 , 8.11659603303800e-01 , 4.87668134921795e+00 , -1.53950962576301e-01 , 7.72932622053599e-01 , 6.77731363834010e+00 , -3.15236176432316e-01 , 1.95768987205017e+00 , 6.08567942889092e+00 , -2.40995787023137e-01 , 3.26272076327158e+00 , 7.15626171005683e+00 , -3.60973160591484e-01 , 4.42453550626092e+00 , 5.30323134296638e+00 , 1.06515657983261e+00 , 3.36197211586406e+00 , 4.19858937008628e+00 , 1.00445912444389e+00 , 3.85880668941060e+00 , 5.85667328325878e+00 , 2.25665290010868e+00 , 2.95644404289031e+00 , 5.12787474322313e+00 , 3.51469925394693e+00 , 2.85186916114883e+00 , 6.26303311891066e+00 , 4.42874399272984e+00 , 2.28458594287792e+00 , 3.86259944889717e+00 , 3.61722008681940e+00 , 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-2.32789802423290e+00 , -2.69496964968616e-01 , 6.13081564224639e+00 , -4.48975823213902e+00 , 9.72572887944186e-01 , 6.41967144798889e+00 , -5.35517941164353e+00 , 5.26143832632194e-01 , 7.16881479260779e+00 , -6.28316991275009e+00 , 3.59844924398044e+00 , 6.78880014694712e+00 , -7.05208578306713e+00 , 4.29637881354837e+00 , 7.51523987787603e+00 , -6.60876581954708e+00 , 3.17549426557786e+00 , 5.56121828157859e+00 , -4.12462545171249e+00 , 2.25150462900518e+00 , 6.42377680883530e+00 , -4.80017670147808e+00 , 3.27350105220607e+00 , 7.18885421021920e+00 , -4.00867644294528e+00 , 4.63518651810601e+00 , 7.28222891899726e+00 ) 5.50754068284698e+01 + 38 ( -2.78392072118256e-01 , -1.83593331534544e-02 , 9.60292033221074e-01 ) ( 6.49213858693483e+01 , 6.49213858693483e+00 , 1.29842771738697e+01 ) ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 ) ( 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 ) ( 8.14317093894644e+00 , 4.08896312044839e-02 , -6.94074034673630e-01 , 6.79915554953232e+00 , -6.26358591425215e-01 , -5.00648482024885e-01 , 7.00280245128076e+00 , -2.10431955166301e+00 , -8.12301560120350e-01 , 6.05664189019526e+00 , -3.20745134100653e-01 , 8.08152838814866e-01 , 4.86783008030533e+00 , -1.53783739404710e-01 , 7.77114291223269e-01 , 6.77081413356385e+00 , -3.16489191537951e-01 , 1.95566554928851e+00 , 6.09042903255942e+00 , -2.41832191283301e-01 , 3.27450150043844e+00 , 7.15455777268900e+00 , -3.64368009262130e-01 , 4.42964476260485e+00 , 5.30240708686752e+00 , 1.06559176049868e+00 , 3.36267156876022e+00 , 4.19851578554890e+00 , 1.00567887632417e+00 , 3.87027538926459e+00 , 5.85494795574971e+00 , 2.25818027878328e+00 , 2.95397429466817e+00 , 5.12894151219028e+00 , 3.51081222301051e+00 , 2.84796602318766e+00 , 6.25651104172497e+00 , 4.42348737770058e+00 , 2.28395674279983e+00 , 3.86482940974540e+00 , 3.61409733006715e+00 , 2.00112505416949e+00 , 2.85940899684290e+00 , 4.15329639509451e+00 , 2.40679366461416e+00 , 3.90134260652991e+00 , 3.12864037947994e+00 , 7.92276715459309e-01 , 2.75168903476846e+00 , 3.15816900531727e+00 , -8.36637783985127e-02 , 3.15088134644206e+00 , 2.66371529910241e+00 , -1.51168072525205e+00 , 1.64329947872382e+00 , 2.28981240646360e+00 , 4.60232743048537e-01 , 4.37205012745545e-01 , 2.61165826536389e+00 , 4.13402854761311e-01 , 2.01902956426518e+00 , 1.11099376671263e+00 , 1.03087851648227e+00 , 1.30247589721074e+00 , 1.66996236220522e-01 , 1.66484954043529e+00 , 2.10049357804753e+00 , -1.09293465860674e+00 , 2.02465224144721e+00 , 5.69419737456688e-01 , 6.31710122136895e-01 , 2.93203698981679e+00 , -6.13060359718318e-01 , 3.58586951716438e-01 , 3.21591113164397e+00 , 1.29439114475718e+00 , 1.43785349181185e+00 , 3.78848274061292e+00 , 9.20797541898652e-01 , 1.99120065569285e+00 , 5.06428037584568e+00 , 2.02753078233163e+00 , 2.78476507419461e+00 , 5.72737402297864e+00 , -3.53548762271608e-01 , 2.88518286663840e+00 , 4.91582895443542e+00 , -1.11856005523393e+00 , 3.07192696712867e+00 , 5.89834634168051e+00 , -5.10039314731810e-01 , 3.46253882301967e+00 , 3.70883934610700e+00 , -1.45778968098559e+00 , 4.47925694034357e+00 , 3.40611516463201e+00 , -7.80823600930033e-01 , 5.48788197934297e+00 , 2.48900883811119e+00 , -2.75653442102174e+00 , 3.92373326272683e+00 , 2.71344352115087e+00 , -3.78764081932449e+00 , 4.60859146768582e+00 , 2.80207843552365e+00 , -2.71689106242136e+00 , 2.65629275720039e+00 , 2.34002776499601e+00 , -3.82559520576644e+00 , 1.78086130735621e+00 , 1.98253926344502e+00 , -3.33557880736609e+00 , 9.16245860472653e-01 , 7.55936284692066e-01 , -4.27712667888646e+00 , 1.01613085668107e+00 , 3.23068488381043e+00 , -5.41059133652115e+00 , 7.07727173253667e-01 , 3.36442996647586e+00 , -3.35326897579306e+00 , 7.03632051594981e-01 , 4.17412371401115e+00 , -3.66405677339002e+00 , 5.72022654159407e-02 , 5.44074247495913e+00 , -2.31878068856242e+00 , -2.62545144025280e-01 , 6.13429257677787e+00 , -4.48660725424403e+00 , 9.80719072148375e-01 , 6.41884769219465e+00 , -5.35522444998312e+00 , 5.18816914467423e-01 , 7.16421765555230e+00 , -6.27676603331432e+00 , 3.59741614456411e+00 , 6.79870257878442e+00 , -7.05699416041304e+00 , 4.29354567185494e+00 , 7.51231065273461e+00 , -6.60868744415733e+00 , 3.17788655378310e+00 , 5.56375294870633e+00 , -4.12940671412453e+00 , 2.25193559988155e+00 , 6.42620273683433e+00 , -4.79690111728020e+00 , 3.26920090813837e+00 , 7.18054781522804e+00 , -4.00988745505869e+00 , 4.64496165010535e+00 , 7.28260882698680e+00 ) 5.49095053111686e+01 + 39 ( -2.75804320334978e-01 , -1.84590719592386e-02 , 9.61036544334795e-01 ) ( 6.48020344197421e+01 , 6.48020344197421e+00 , 1.29604068839484e+01 ) ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 4.85799124682764e+00 , -1.53341294884784e-01 , 7.81284309442242e-01 ) ( 6.76395834944810e+00 , -3.17151223564478e-01 , 1.95395349460530e+00 , 6.09678450766290e+00 , -2.42324307098027e-01 , 3.28479282127207e+00 , 5.30221500875152e+00 , 1.06623489201134e+00 , 3.36444902266742e+00 , 4.19816458364542e+00 , 1.00729488136564e+00 , 3.88164939576731e+00 ) ( 8.12916085201023e+00 , 3.99746824480268e-02 , -6.91109433383504e-01 , 6.79253237316532e+00 , -6.27052911201560e-01 , -4.95075049659964e-01 , 7.00633405239422e+00 , -2.10960632604147e+00 , -8.05366496954219e-01 , 6.05648010968517e+00 , -3.19973529610401e-01 , 8.04110865515096e-01 , 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2.48906287015350e+00 , -2.75732186737653e+00 , 3.92368967871629e+00 , 2.71365369477263e+00 , -3.78458343707577e+00 , 4.61231149268170e+00 , 2.79858191461417e+00 , -2.71894607481113e+00 , 2.65757022140094e+00 , 2.33528904277398e+00 , -3.82655594542095e+00 , 1.77465596273868e+00 , 1.97811982989606e+00 , -3.33228499826833e+00 , 9.23271479562673e-01 , 7.51560398602594e-01 , -4.27837901996573e+00 , 1.01409445679621e+00 , 3.22486448462943e+00 , -5.40640346925876e+00 , 7.01227576936707e-01 , 3.36893858932527e+00 , -3.35031899401458e+00 , 6.98990237021571e-01 , 4.17727305723755e+00 , -3.66396349938553e+00 , 5.54480758973155e-02 , 5.43394610861833e+00 , -2.30961179465269e+00 , -2.56192852805586e-01 , 6.13821204626671e+00 , -4.48260742619145e+00 , 9.87280925201492e-01 , 6.41770665300712e+00 , -5.35519490384767e+00 , 5.11685830996736e-01 , 7.15944361716923e+00 , -6.27075576476656e+00 , 3.59744071828715e+00 , 6.80904286805965e+00 , -7.06111641476086e+00 , 4.28993179367045e+00 , 7.50860544772823e+00 , -6.60920715895394e+00 , 3.18018769892193e+00 , 5.56622814477778e+00 , -4.13434129069484e+00 , 2.25326223610649e+00 , 6.42784705590425e+00 , -4.79416589340515e+00 , 3.26535481052450e+00 , 7.17347846350296e+00 , -4.01123229986279e+00 , 4.65336809852236e+00 , 7.28272173761062e+00 ) 5.47326482987988e+01 + 40 ( -2.73073003055543e-01 , -1.84328428660908e-02 , 9.61816700471613e-01 ) ( 6.46761268758138e+01 , 6.46761268758138e+00 , 1.29352253751628e+01 ) ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 ) ( 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 ) ( 8.11495474062438e+00 , 3.90259737284379e-02 , -6.88393975109401e-01 , 6.78530949633075e+00 , -6.26907737358158e-01 , -4.89272480813665e-01 , 7.01006678181398e+00 , -2.11493408726218e+00 , -7.98718682344158e-01 , 6.05708192228230e+00 , -3.20498402697696e-01 , 7.99834389454430e-01 , 4.84747583570465e+00 , -1.52650056613561e-01 , 7.85391934952724e-01 , 6.75691951166751e+00 , -3.17267720221977e-01 , 1.95267855568845e+00 , 6.10450948820159e+00 , -2.42481723464772e-01 , 3.29331848812019e+00 , 7.14904497526293e+00 , -3.70587572339713e-01 , 4.43991961977992e+00 , 5.30250695756027e+00 , 1.06707319500285e+00 , 3.36749182631206e+00 , 4.19765252072150e+00 , 1.00930554901639e+00 , 3.89285284776761e+00 , 5.84938914125474e+00 , 2.25999987785099e+00 , 2.94916374044967e+00 , 5.13309734501436e+00 , 3.50613302356783e+00 , 2.84066228222419e+00 , 6.24337909453664e+00 , 4.41474090982113e+00 , 2.28026908955126e+00 , 3.87167140780073e+00 , 3.60778409243525e+00 , 1.99885722594360e+00 , 2.86832278980672e+00 , 4.14979028465830e+00 , 2.40278081747413e+00 , 3.90379611311113e+00 , 3.11231856167557e+00 , 8.01084172646395e-01 , 2.74707904555533e+00 , 3.18411482121218e+00 , -9.55699065627204e-02 , 3.15566340016384e+00 , 2.66529432767118e+00 , -1.50079670411565e+00 , 1.66532624296654e+00 , 2.30575554547368e+00 , 4.76317631003612e-01 , 4.45608101770511e-01 , 2.60981822621226e+00 , 4.01863049793049e-01 , 2.01931908293421e+00 , 1.12066591420180e+00 , 1.01334179939411e+00 , 1.30116775216391e+00 , 1.62357783731801e-01 , 1.67189612866917e+00 , 2.10362824305197e+00 , -1.09269544261782e+00 , 2.01615449320386e+00 , 5.68127131792841e-01 , 6.44248088386151e-01 , 2.93562258785401e+00 , -6.17133461552485e-01 , 3.58742436838797e-01 , 3.22138636035490e+00 , 1.30046996073769e+00 , 1.44276136689252e+00 , 3.78933746336662e+00 , 9.22311705692830e-01 , 1.99704374459824e+00 , 5.07301683409079e+00 , 2.02246752343104e+00 , 2.79278656996483e+00 , 5.73033824749834e+00 , -3.47503219826831e-01 , 2.88075898654219e+00 , 4.91606149982095e+00 , -1.11694785986929e+00 , 3.07221002356498e+00 , 5.89544447655073e+00 , -4.99536295986837e-01 , 3.44487668608325e+00 , 3.69176319857068e+00 , -1.46834499137075e+00 , 4.48166782237923e+00 , 3.39493264235618e+00 , -7.83769205582526e-01 , 5.50438971353099e+00 , 2.48882395278260e+00 , -2.75799099213347e+00 , 3.92495256939421e+00 , 2.71619289481911e+00 , -3.78135696829132e+00 , 4.61551513575064e+00 , 2.79458922419504e+00 , -2.72095052577993e+00 , 2.65771368144152e+00 , 2.32961060643832e+00 , -3.82665276706169e+00 , 1.76962701055572e+00 , 1.97356017376723e+00 , -3.32895254612084e+00 , 9.30348393184138e-01 , 7.47884086890626e-01 , -4.27769626860396e+00 , 1.01191620612976e+00 , 3.21888419967310e+00 , -5.40372071278918e+00 , 6.94412494083765e-01 , 3.37366369769584e+00 , -3.34783831861565e+00 , 6.94875916723317e-01 , 4.17962840215950e+00 , -3.66393375068949e+00 , 5.47010811552680e-02 , 5.42834565141154e+00 , -2.30064557995352e+00 , -2.50659883831275e-01 , 6.14233651906525e+00 , -4.47796260751307e+00 , 9.91786874552058e-01 , 6.41626978680100e+00 , -5.35495949570760e+00 , 5.04890471189771e-01 , 7.15442118917469e+00 , -6.26541633087511e+00 , 3.59847028193186e+00 , 6.81932179226784e+00 , -7.06445113897255e+00 , 4.28560690560506e+00 , 7.50427047400559e+00 , -6.61009946542058e+00 , 3.18235894718735e+00 , 5.56884010745485e+00 , -4.13928779142226e+00 , 2.25559683160842e+00 , 6.42861701269159e+00 , -4.79223268771666e+00 , 3.26242570623937e+00 , 7.16806907554133e+00 , -4.01247099914300e+00 , 4.66002856193637e+00 , 7.28260341532478e+00 ) 5.45455543522492e+01 diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py new file mode 100644 index 000000000..86b7620e4 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/compare_with_pytorch.py @@ -0,0 +1,262 @@ +#!/usr/bin/env python3 +import torch +import re +import numpy as np + +torch.set_printoptions(precision=10) + + +# function to extract grad +def set_grad(var): + def hook(grad): + var.grad = grad + return hook + +mass1 = torch.tensor([14.0070, 12.0110, 12.0110, 15.999], dtype=torch.float64) + +mass2 = torch.tensor([14.0070, 12.0110, 12.0110, 15.999], dtype=torch.float64) + +ref_fitting_group = torch.tensor( + [[ 5.69469 , -1.80418 , -5.22382 ], + [ 6.37169 , -1.08118 , -4.10382 ], + [ 6.61169 , 0.365824 , -4.58082 ], + [ 5.62269 , -1.09518 , -2.77982 ], + [ 4.39969 , -0.986176 , -2.72882 ], + [ 6.36569 , -1.21018 , -1.66282 ], + [ 5.83469 , -1.37018 , -0.318824 ], + [ 7.00969 , -1.45018 , 0.678176 ], + [ 4.84269 , -0.296176 , 0.126176 ], + [ 3.77369 , -0.596176 , 0.648176 ], + [ 5.15669 , 0.991824 , -0.113824 ], + [ 4.27869 , 2.10682 , 0.190176 ], + [ 5.03669 , 3.42282 , -0.0748235 ], + [ 2.96669 , 2.09282 , -0.596824 ], + [ 1.89969 , 2.39182 , -0.0678235 ], + [ 3.01469 , 1.69682 , -1.88382 ], + [ 1.84869 , 1.57082 , -2.73482 ], + [ 2.30269 , 1.40782 , -4.19882 ], + [ 0.962686 , 0.399824 , -2.31982 ], + [-0.255314 , 0.522824 , -2.22882 ], + [ 1.57569 , -0.758176 , -2.00882 ], + [ 0.900686 , -1.92218 , -1.46882 ], + [ 1.91969 , -3.07218 , -1.33582 ], + [ 0.223686 , -1.65518 , -0.123824 ], + [-0.930314 , -2.01818 , 0.0891765 ], + [ 0.918686 , -0.964176 , 0.800176 ], + [ 0.372686 , -0.514176 , 2.06618 ], + [ 1.49069 , 0.164824 , 2.88418 ], + [-0.814314 , 0.435824 , 1.92118 ], + [-1.84631 , 0.257824 , 2.56118 ], + [-0.707314 , 1.45482 , 1.04518 ], + [-1.78431 , 2.37982 , 0.745176 ], + [-1.24331 , 3.48882 , -0.178824 ], + [-3.00931 , 1.72082 , 0.109176 ], + [-4.14731 , 2.02882 , 0.455176 ], + [-2.80331 , 0.769824 , -0.821824 ], + [-3.86731 , -0.00917647, -1.42282 ], + [-3.28731 , -0.820176 , -2.59882 ], + [-4.57231 , -0.946176 , -0.440824 ], + [-5.78931 , -1.10018 , -0.475824 ], + [-3.81431 , -1.58718 , 0.469176 ], + [-4.35131 , -2.44718 , 1.50418 ], + [-3.19331 , -3.25818 , 2.12018 ], + [-5.10031 , -1.70118 , 2.61018 ], + [-6.15131 , -2.13818 , 3.07218 ], + [-6.33131 , 1.19882 , 3.62918 ], + [-7.08531 , 1.74482 , 4.44018 ], + [-6.45431 , 1.44382 , 2.30618 ], + [-4.56431 , -0.557176 , 3.07518 ], + [-5.19131 , 0.240824 , 4.11318 ], + [-4.10131 , 1.05882 , 4.83518 ]], dtype=torch.float64) + +# fitting_group = atom_positions +# main_group = atom_positions[[0, 1, 2, 3]] + + +def get_optimal_rotation(fitting_atoms: torch.tensor, reference_atoms: torch.tensor): + fitting_atoms_centered = fitting_atoms - fitting_atoms.mean(dim=0) + reference_atoms_centered = reference_atoms - reference_atoms.mean(dim=0) + mat_R = torch.linalg.matmul(fitting_atoms_centered.T, reference_atoms_centered) + F00 = mat_R[0][0] + mat_R[1][1] + mat_R[2][2] + F01 = mat_R[1][2] - mat_R[2][1] + F02 = mat_R[2][0] - mat_R[0][2] + F03 = mat_R[0][1] - mat_R[1][0] + F10 = F01 + F11 = mat_R[0][0] - mat_R[1][1] - mat_R[2][2] + F12 = mat_R[0][1] + mat_R[1][0] + F13 = mat_R[0][2] + mat_R[2][0] + F20 = F02 + F21 = F12 + F22 = -mat_R[0][0] + mat_R[1][1] - mat_R[2][2] + F23 = mat_R[1][2] + mat_R[2][1] + F30 = F03 + F31 = F13 + F32 = F23 + F33 = -mat_R[0][0] - mat_R[1][1] + mat_R[2][2] + row0 = torch.stack((F00, F01, F02, F03)) + row1 = torch.stack((F10, F11, F12, F13)) + row2 = torch.stack((F20, F21, F22, F23)) + row3 = torch.stack((F30, F31, F32, F33)) + F = torch.stack((row0, row1, row2, row3)) + w, v = torch.linalg.eigh(F) + q = v[:, -1] + q.register_hook(set_grad(q)) + R00 = q[0] * q[0] + q[1] * q[1] - q[2] * q[2] - q[3] * q[3] + R01 = 2.0 * (q[1] * q[2] - q[0] * q[3]) + R02 = 2.0 * (q[1] * q[3] + q[0] * q[2]) + R10 = 2.0 * (q[1] * q[2] + q[0] * q[3]) + R11 = q[0] * q[0] - q[1] * q[1] + q[2] * q[2] - q[3] * q[3] + R12 = 2.0 * (q[2] * q[3] - q[0] * q[1]) + R20 = 2.0 * (q[1] * q[3] - q[0] * q[2]) + R21 = 2.0 * (q[2] * q[3] + q[0] * q[1]) + R22 = q[0] * q[0] - q[1] * q[1] - q[2] * q[2] + q[3] * q[3] + row0 = torch.stack((R00, R01, R02)) + row1 = torch.stack((R10, R11, R12)) + row2 = torch.stack((R20, R21, R22)) + R = torch.stack((row0, row1, row2)) + return w, v, R, q + + +def center_of_mass(pos, mass): + return torch.sum(pos * mass[:, None], dim=0) / torch.sum(mass) + + +def read_data_from_traj(filename): + group1_positions = [] + group2_positions = [] + fitting_group1_positions = [] + fitting_group2_positions = [] + forces = [] + with open(filename, 'r') as f_input: + for line in f_input: + s = line.strip() + if s.startswith('#'): + # skip comment lines + continue + if len(s) > 0: + # skip empty lines + # match the data in parentheses + result = re.findall(r'\(([^)]+)\)', s) + # get the force applied on the orientation + forces.append(torch.tensor(list(map(float, result[1].split(','))), dtype=torch.float64)) + # get the group1 position + tmp = np.array(list(map(float, result[2].split(',')))).reshape(-1, 3) + group1_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + # get the group2 position + tmp = np.array(list(map(float, result[3].split(',')))).reshape(-1, 3) + group2_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + # get the fitting group1 position + tmp = np.array(list(map(float, result[4].split(',')))).reshape(-1, 3) + fitting_group1_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + fitting_group2_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + return forces, group1_positions, group2_positions, fitting_group1_positions, fitting_group2_positions + + +# Use Colvars definition: the distance between two unit vectors is angle between them +def dist2_distance_dir(v1, v2): + v1_normalized = v1 / torch.linalg.norm(v1) + v2_normalized = v2 / torch.linalg.norm(v2) + dist = torch.acos(torch.sum(v1_normalized * v2_normalized)) + return dist * dist + + +def scan_force_from_log(filename): + main_group_forces = [] + fitting_group_forces = [] + with open(filename, 'r') as f_input: + new_main_group_started = False + main_group_force = [] + new_fitting_group_started = False + fitting_group_force = [] + for line in f_input: + if new_main_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + main_group_force.append(list(map(float, result[0].split(',')))) + else: + new_main_group_started = False + main_group_forces.append(np.array(main_group_force)) + main_group_force = [] + if new_fitting_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + fitting_group_force.append(list(map(float, result[0].split(',')))) + else: + new_fitting_group_started = False + fitting_group_forces.append(np.array(fitting_group_force)) + fitting_group_force = [] + if line.startswith('colvars: Applying force on the fitting group of main group:'): + new_fitting_group_started = True + continue + if line.startswith('colvars: Applying force on main group'): + new_main_group_started = True + continue + return main_group_forces, fitting_group_forces + + +def test(group1, group2, fitting_group_1, fitting_group_2): + # Fit group 1 + w1, v1, R1, q1 = get_optimal_rotation(fitting_group_1, ref_fitting_group) + rpg_cog1 = fitting_group_1.mean(dim=0) + # group1_c = group1.mean(dim=0) + group1_centered = group1 - rpg_cog1 + group1_rotated = (R1 @ group1_centered.T).T + # Fit group 2 + w2, v2, R2, q2 = get_optimal_rotation(fitting_group_2, ref_fitting_group) + rpg_cog2 = fitting_group_2.mean(dim=0) + # group2_c = group2.mean(dim=0) + group2_centered = group2 - rpg_cog2 + group2_rotated = (R2 @ group2_centered.T).T + # distanceDir + c2 = center_of_mass(group2_rotated, mass2) + c1 = center_of_mass(group1_rotated, mass1) + d = c2 - c1 + d_dir = d / torch.linalg.norm(d) + ref = torch.tensor([1.0, 0.1, 0.2], dtype=torch.float64) + energy = 0.5 * 10.0 * dist2_distance_dir(d_dir, ref) / 0.25 + energy.backward(retain_graph=True) + return -group1.grad.cpu().detach().numpy(), -group2.grad.cpu().detach().numpy(), \ + -fitting_group_1.grad.cpu().detach().numpy(), -fitting_group_2.grad.cpu().detach().numpy() + + +if __name__ == '__main__': + print('Compare AutoDiff/test.colvars.traj and AutoDiff/test.colvars.out') + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.colvars.out') + group1_forces_colvars = main_group_forces_colvars[::2] + group2_forces_colvars = main_group_forces_colvars[1::2] + fitting_group1_forces_colvars = fitting_group_forces_colvars[::2] + fitting_group2_forces_colvars = fitting_group_forces_colvars[1::2] + # read the positions from .colvars.traj + _, group1_positions, group2_positions, fitting_group1_positions, fitting_group2_positions = read_data_from_traj('AutoDiff/test.colvars.traj') + for i in range(len(group1_positions)): + # calculate forces from pytorch + gf1_pytorch, gf2_pytorch, fgf1_pytorch, fgf2_pytorch = test( + group1_positions[i], group2_positions[i], fitting_group1_positions[i], fitting_group2_positions[i]) + # error with respect to colvars + error_group1 = np.mean(np.abs(group1_forces_colvars[i] - gf1_pytorch) / np.abs(gf1_pytorch)) + error_group2 = np.mean(np.abs(group2_forces_colvars[i] - gf2_pytorch) / np.abs(gf2_pytorch)) + error_fitting_group1 = np.mean(np.abs(fitting_group1_forces_colvars[i] - fgf1_pytorch) / np.abs(fgf1_pytorch)) + error_fitting_group2 = np.mean(np.abs(fitting_group2_forces_colvars[i] - fgf2_pytorch) / np.abs(fgf2_pytorch)) + print(f'Error of forces: group1 = {error_group1:12.5e}, group2 = {error_group2:12.5e}, fitting_group1 = {error_fitting_group1:12.5e}, fitting_group2 = {error_fitting_group2:12.5e}') + + # Do the same thing with the restart file + print('Compare AutoDiff/test.restart.colvars.traj and AutoDiff/test.restart.colvars.out') + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.restart.colvars.out') + group1_forces_colvars = main_group_forces_colvars[::2] + group2_forces_colvars = main_group_forces_colvars[1::2] + fitting_group1_forces_colvars = fitting_group_forces_colvars[::2] + fitting_group2_forces_colvars = fitting_group_forces_colvars[1::2] + # read the positions from .colvars.traj + _, group1_positions, group2_positions, fitting_group1_positions, fitting_group2_positions = read_data_from_traj('AutoDiff/test.restart.colvars.traj') + for i in range(len(group1_positions)): + # calculate forces from pytorch + gf1_pytorch, gf2_pytorch, fgf1_pytorch, fgf2_pytorch = test( + group1_positions[i], group2_positions[i], fitting_group1_positions[i], fitting_group2_positions[i]) + # error with respect to colvars + error_group1 = np.mean(np.abs(group1_forces_colvars[i] - gf1_pytorch) / np.abs(gf1_pytorch)) + error_group2 = np.mean(np.abs(group2_forces_colvars[i] - gf2_pytorch) / np.abs(gf2_pytorch)) + error_fitting_group1 = np.mean(np.abs(fitting_group1_forces_colvars[i] - fgf1_pytorch) / np.abs(fgf1_pytorch)) + error_fitting_group2 = np.mean(np.abs(fitting_group2_forces_colvars[i] - fgf2_pytorch) / np.abs(fgf2_pytorch)) + print(f'Error of forces: group1 = {error_group1:12.5e}, group2 = {error_group2:12.5e}, fitting_group1 = {error_fitting_group1:12.5e}, fitting_group2 = {error_fitting_group2:12.5e}') diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/namd-version.txt new file mode 100644 index 000000000..73471c571 --- /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 2024-10-11. +colvars: Using NAMD interface, version "2024-10-05". diff --git a/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in new file mode 100644 index 000000000..59aca6398 --- /dev/null +++ b/namd/tests/library/000_distancedir-fitgroup_harmonic-ddir-fixed-fit-forces/test.in @@ -0,0 +1,67 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + width 0.5 + + distanceDir { + group1 { + indexGroup group1 + centerToReference yes + rotateToReference yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + group2 { + indexGroup group2 + centerToReference yes + rotateToReference yes + fittingGroup { + indexGroup heavy_atoms + } + refPositionsFile heavy_atoms_refpos.xyz + } + } +} + +colvar { + name group1 + cartesian { + atoms { + indexGroup group1 + } + } +} + +colvar { + name group2 + cartesian { + atoms { + indexGroup group2 + } + } +} + +colvar { + name fitting_group1 + cartesian { + atoms { + indexGroup heavy_atoms + } + } +} + +harmonic { + colvars one + centers (1.0, 0.1, 0.2) + forceConstant 10.0 + outputEnergy on +} 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..9b22d5849 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.out @@ -0,0 +1,7074 @@ +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 value = " +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "main" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "RMSD_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "RMSD_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 30 individual components. +colvars: DEPS: disabling feature "scalar" in colvar main +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: feature "linear" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "single_component" +colvars: DEPS: feature "single_component" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar main +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar main +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar main +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar main enabling "output_value" +colvars: DEPS: feature "output_value" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar main +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar main +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar main +colvars: DEPS: colvar main enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar main testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar main testing "linear" +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "main". +colvars: Configuration string for "colvar": " +colvars: +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar fitting enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar fitting +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting +colvars: DEPS: colvar fitting enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar fitting testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar fitting testing "linear" +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "fitting". +colvars: Configuration string for "colvar": " +colvars: +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 3 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: colvar { +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +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: - cartesian colvar component: +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: Re-initialized atom group for variable "main":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "fitting":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 0 +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 0, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 0, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 0, atoms_positions[size = 51] = { ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 ), ( 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 ), ( 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 ), ( 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 ), ( 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 ), ( 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 ), ( -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 ), ( -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 ), ( -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 ), ( -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ), ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 ), ( 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 ), ( 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 ), ( 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 ), ( 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 ), ( 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 ), ( 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 ), ( 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 ), ( 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 ), ( 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 ), ( 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 ), ( 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 ), ( 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 ), ( 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 ), ( 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 ), ( 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 ), ( 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 ), ( 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 ), ( 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 ), ( -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 ), ( 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 ), ( 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 ), ( -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 ), ( -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 ), ( -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 ), ( -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 ), ( -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 ), ( -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 ), ( -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 ), ( -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 ), ( -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 ), ( -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 ), ( -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 ), ( -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 ), ( -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 ), ( -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 ), ( -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 ), ( -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 ), ( -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 ), ( -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 ), ( -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) } +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating fit gradients. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "main" has value ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 0. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 0. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 0, atoms_new_colvar_forces = { ( -7.17112331393693e-02 , 3.05098327565957e-01 , -3.87711644832293e-01 ), ( 1.19555459248557e-02 , 3.65941097357604e-02 , -2.36512628285003e-01 ), ( -4.16513128784966e-02 , 9.10770464245731e-02 , 8.22518324392786e-02 ), ( -9.62168257886831e-02 , 2.41917479955852e-01 , 6.78847980688516e-02 ), ( -1.89845157517858e-02 , 9.98710219002420e-02 , -1.64599111102358e-01 ), ( 7.03301603774896e-02 , -1.79535932890023e-01 , -4.14067432161946e-02 ), ( 1.07471104828031e-02 , -1.02577848089066e-01 , 2.47364312690905e-01 ), ( -4.02256833871764e-02 , 5.38601721942073e-02 , 1.93139708020977e-01 ), ( 6.58704306067279e-02 , -1.87291492706406e-01 , 3.23878619810793e-02 ), ( 1.14720183887631e-01 , -3.88281468777201e-01 , 2.63754453050035e-01 ), ( 2.42618507983615e-02 , -9.95090220875313e-02 , 9.41691127788629e-02 ), ( 2.64140528573990e-02 , -9.72948413283316e-02 , 5.83337189788877e-02 ), ( 1.22660085012390e-02 , -5.62309126513698e-02 , 7.13109049758973e-02 ), ( 1.24027961622539e-02 , -5.39033622796542e-02 , 6.02813703425287e-02 ), ( 5.50365180277709e-03 , -3.58654134074757e-02 , 7.45595484006017e-02 ), ( -8.56869612739025e-03 , 8.15418354809084e-03 , 7.47590614158032e-02 ), ( -2.04345135727017e-03 , -3.57842067967311e-03 , 3.99322594237481e-02 ), ( -5.72407370686545e-03 , 8.98773129963851e-03 , 3.57708956627444e-02 ), ( 2.80344276950839e-03 , -1.36159740030154e-02 , 1.93567445096325e-02 ), ( 9.22210196636199e-03 , -2.22622813867358e-02 , -2.64859467986244e-02 ), ( 8.79316761791039e-03 , -2.38089040285720e-02 , -1.49202518973436e-02 ), ( 6.70562195329319e-03 , -1.34686650666172e-02 , -3.01395709833031e-02 ), ( 1.50473126186007e-02 , -4.65247806418302e-02 , -2.39287487045654e-03 ), ( 2.75363017231425e-02 , -8.78760894143468e-02 , 6.57333075023515e-03 ), ( 1.42160293860021e-02 , -4.66103438169562e-02 , 8.36819326569623e-03 ), ( 1.41623599363496e-02 , -4.35929741103034e-02 , -3.03504901951588e-03 ), ( 9.21986652441758e-03 , -3.71107050197726e-02 , 3.29673234888841e-02 ), ( -9.63775655681931e-04 , -1.58643052576496e-02 , 7.55701254462465e-02 ), ( -3.83069289063363e-03 , 3.84917215687278e-03 , 3.26059455401106e-02 ), ( -5.91198486374499e-03 , 1.09771288603378e-02 , 3.01642040800903e-02 ), ( -7.28976560942452e-03 , 1.74875351287834e-02 , 2.13767345680998e-02 ), ( -1.61562664646153e-02 , 5.13986449348097e-02 , -3.21420801068685e-03 ), ( -9.68017103615191e-03 , 3.56109507442153e-02 , -2.11960333401958e-02 ), ( -1.37049814773182e-02 , 4.98621539927025e-02 , -2.77874076093298e-02 ), ( -1.91792500276001e-03 , 1.49750007080970e-02 , -3.58941052675410e-02 ), ( 1.06647740597758e-02 , -1.52501737314967e-02 , -7.26305692651966e-02 ), ( 4.39025313827158e-03 , -2.89712934588417e-04 , -5.38644244704754e-02 ), ( 3.37835546017515e-03 , 6.67816083650675e-03 , -6.90684195578746e-02 ), ( 7.08425965807474e-03 , -1.43615244078311e-02 , -3.13117755624624e-02 ), ( 1.29337999684502e-02 , -4.08166651615065e-02 , 1.25159424194878e-03 ), ( 4.21517000834667e-04 , 2.14779898690001e-03 , -1.38787149564562e-02 ), ( 3.30986545488312e-04 , 3.88313347866908e-03 , -1.96891054554931e-02 ), ( -6.59621209084941e-03 , 2.06662848702344e-02 , -3.74608751278817e-05 ), ( -2.06331572427302e-02 , 5.73693700933228e-02 , 2.89999395613771e-02 ), ( -1.89787290812637e-02 , 6.32653631722135e-02 , -1.53318322023093e-02 ), ( -2.26926653990437e-02 , 7.52153031654799e-02 , -1.66095079265972e-02 ), ( -1.67511882905597e-02 , 7.28367292485312e-02 , -8.15558389781937e-02 ), ( -1.98067264091487e-02 , 8.70491413541379e-02 , -1.00140043772665e-01 ), ( -8.52580045706230e-03 , 4.71754189750805e-02 , -8.19464349448593e-02 ), ( -1.85683188859792e-02 , 6.67251710260006e-02 , -3.43221673997345e-02 ), ( -2.42477887341905e-02 , 9.27892795207383e-02 , -6.74521030822303e-02 ) } +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 1, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 1, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 1, atoms_positions[size = 51] = { ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 ), ( 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 ), ( 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 ), ( 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 ), ( 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 ), ( 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 ), ( -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 ), ( -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 ), ( -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 ), ( -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ), ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 ), ( 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 ), ( 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 ), ( 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 ), ( 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 ), ( 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 ), ( 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 ), ( 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 ), ( 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 ), ( 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 ), ( 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 ), ( 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 ), ( 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 ), ( 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 ), ( 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 ), ( 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 ), ( 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 ), ( 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 ), ( 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 ), ( -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 ), ( 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 ), ( 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 ), ( -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 ), ( -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 ), ( -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 ), ( -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 ), ( -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 ), ( -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 ), ( -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 ), ( -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 ), ( -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 ), ( -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 ), ( -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 ), ( -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 ), ( -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 ), ( -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 ), ( -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 ), ( -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 ), ( -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 ), ( -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 ), ( -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ) } +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 , 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 , 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 , 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 , 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 , 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 , 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 , 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 , 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 , 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 , 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 , 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 , 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 , 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 , 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 , -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 , 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 , -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 , -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 , -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 , -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 , -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 , -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 , -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 , -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 , -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 , -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 , -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 , -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 , -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 , -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 , -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 , -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 , 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 , 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 , 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 , 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 , 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 , 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 , 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 , 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 , 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 , 3.81729481803385e+00 , 3.24362956757695e+00 , 7.83851504333612e-01 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 3.04747903331039e+00 , 2.73696896534939e+00 , -1.57073080007172e+00 , 1.65396333263660e+00 , 2.17247726397858e+00 , 5.62165548513518e-01 , 4.23521388528606e-01 , 2.41894430151896e+00 , 5.75950625971697e-01 , 1.99311608582322e+00 , 9.90199051696574e-01 , 1.06367201984294e+00 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 2.01680338046171e+00 , -1.21223568884505e+00 , 2.02283283252712e+00 , 4.93808034160097e-01 , 5.72993835971817e-01 , 3.01393345288970e+00 , -6.88662587998284e-01 , 3.95918192665841e-01 , 3.20169068362452e+00 , 1.26635477965548e+00 , 1.30187324469163e+00 , 3.82424695383716e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , 2.07404053461264e+00 , 2.57688712080968e+00 , 5.62064859626823e+00 , -3.48558593657292e-01 , 2.92052275044325e+00 , 4.98852936958222e+00 , -1.18494438730352e+00 , 3.01232192646286e+00 , 5.89678837558287e+00 , -3.82031156858473e-01 , 3.70595325652449e+00 , 3.87941525332713e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -7.75724578277943e-01 , 5.37503362331272e+00 , 2.40305527265532e+00 , -2.70209499872166e+00 , 3.89870972838548e+00 , 2.94981515235484e+00 , -3.85031539488578e+00 , 4.39752396086661e+00 , 2.87664446547849e+00 , -2.54961340194866e+00 , 2.62499747935017e+00 , 2.51165499898903e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.40254592892452e+00 , 7.87406560318845e-01 , 1.02115353786208e+00 , -4.34988426197066e+00 , 1.12609529023666e+00 , 3.21267021376405e+00 , -5.52818410245595e+00 , 9.52475756759381e-01 , 3.35258900168917e+00 , -3.48967682710215e+00 , 6.30399451503332e-01 , 4.18272475841816e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -2.45559456164414e+00 , -4.43400967147330e-01 , 6.12152159674384e+00 , -4.45576920560752e+00 , 1.02426657962806e+00 , 6.42056745600434e+00 , -5.32861886629457e+00 , 5.86034952743163e-01 , 7.17434322479267e+00 , -6.29032700928911e+00 , 3.54932513442409e+00 , 6.69034378166972e+00 , -6.93486068920707e+00 , 4.31932430953635e+00 , 7.41926845519418e+00 , -6.77302490714592e+00 , 3.20631151044426e+00 , 5.49498208896643e+00 , -4.07615456438687e+00 , 2.28779240614049e+00 , 6.46797298710144e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 , -4.05359381249230e+00 , 4.48288263090664e+00 , 7.26230030181591e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 1. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 1. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 1, atoms_new_colvar_forces = { ( -7.15151729651260e-02 , 3.04899243481533e-01 , -3.87916030963302e-01 ), ( 1.20368649362899e-02 , 3.64235792090596e-02 , -2.36533693202075e-01 ), ( -4.16415878718478e-02 , 9.11022438626934e-02 , 8.22174068287411e-02 ), ( -9.61659395369152e-02 , 2.41989972764637e-01 , 6.77382993270643e-02 ), ( -1.89170945988754e-02 , 9.97945490695020e-02 , -1.64675032270572e-01 ), ( 7.02945076928405e-02 , -1.79595291976670e-01 , -4.12934261331383e-02 ), ( 1.06593636141036e-02 , -1.02444767354498e-01 , 2.47440239914315e-01 ), ( -4.02691431255613e-02 , 5.40107887471147e-02 , 1.93099494398337e-01 ), ( 6.58001964113642e-02 , -1.87274572435745e-01 , 3.24910083791860e-02 ), ( 1.14541196581312e-01 , -3.88171056981776e-01 , 2.64003649424930e-01 ), ( 2.42477192528996e-02 , -9.94947081114131e-02 , 9.42201611607529e-02 ), ( 2.64136166976736e-02 , -9.72996799526701e-02 , 5.83863996262244e-02 ), ( 1.22548721116594e-02 , -5.62266396301048e-02 , 7.13435168350051e-02 ), ( 1.23936399651521e-02 , -5.38979530864836e-02 , 6.03110988177678e-02 ), ( 5.49001413551297e-03 , -3.58637287706379e-02 , 7.45844785550286e-02 ), ( -8.58662775485298e-03 , 8.15197217862955e-03 , 7.47658701006714e-02 ), ( -2.05061868858449e-03 , -3.58458690191429e-03 , 3.99413123521106e-02 ), ( -5.73267269837427e-03 , 8.98459258558919e-03 , 3.57726717890164e-02 ), ( 2.80515992656613e-03 , -1.36318939949399e-02 , 1.93713053854992e-02 ), ( 9.24091216374164e-03 , -2.22963827594714e-02 , -2.64665663613212e-02 ), ( 8.80524457636114e-03 , -2.38284772346292e-02 , -1.49041760335850e-02 ), ( 6.72044863046050e-03 , -1.34897386302215e-02 , -3.01294931954585e-02 ), ( 1.50576435827247e-02 , -4.65389127767602e-02 , -2.36711837470063e-03 ), ( 2.75472753380666e-02 , -8.78822788846253e-02 , 6.61567117283608e-03 ), ( 1.42197676549019e-02 , -4.66103962861243e-02 , 8.39005985454352e-03 ), ( 1.41681378086040e-02 , -4.35920831820608e-02 , -3.01634853592154e-03 ), ( 9.21461496103597e-03 , -3.71036824034249e-02 , 3.29854494207997e-02 ), ( -9.86126451234636e-04 , -1.58417642622825e-02 , 7.55784048787670e-02 ), ( -3.84239612560993e-03 , 3.86150425286693e-03 , 3.26037689714234e-02 ), ( -5.92521514581768e-03 , 1.09937156748894e-02 , 3.01569322569409e-02 ), ( -7.29812275527947e-03 , 1.74916709978540e-02 , 2.13701287787168e-02 ), ( -1.61590546113848e-02 , 5.13892040394262e-02 , -3.23396497301815e-03 ), ( -9.67788551506929e-03 , 3.56052475625837e-02 , -2.12124757482175e-02 ), ( -1.37034108862765e-02 , 4.98582644999593e-02 , -2.78117321811795e-02 ), ( -1.90789273977489e-03 , 1.49631727913749e-02 , -3.59009302348894e-02 ), ( 1.06906045511525e-02 , -1.52740011368780e-02 , -7.26241198821211e-02 ), ( 4.40529849774725e-03 , -2.97823815696022e-04 , -5.38681586639291e-02 ), ( 3.39643922578235e-03 , 6.66896241573230e-03 , -6.90768027297062e-02 ), ( 7.09321783492851e-03 , -1.43609832339387e-02 , -3.13096039888957e-02 ), ( 1.29336183664370e-02 , -4.07998296242983e-02 , 1.26359385658362e-03 ), ( 4.19979277285392e-04 , 2.16348662453615e-03 , -1.38873734861057e-02 ), ( 3.29655166819156e-04 , 3.90209739378588e-03 , -1.97005199557689e-02 ), ( -6.60377269842420e-03 , 2.06837283573336e-02 , -5.32553285992549e-05 ), ( -2.06544209370330e-02 , 5.73950938853213e-02 , 2.89683973885608e-02 ), ( -1.89875466809821e-02 , 6.32816036261560e-02 , -1.53681222592533e-02 ), ( -2.27038413337324e-02 , 7.52356909090834e-02 , -1.66528519569391e-02 ), ( -1.67393048554064e-02 , 7.28311918128840e-02 , -8.15966907597996e-02 ), ( -1.97909234720973e-02 , 8.70391604498609e-02 , -1.00187941489201e-01 ), ( -8.51097375894001e-03 , 4.71708543895567e-02 , -8.19762682790733e-02 ), ( -1.85700756693449e-02 , 6.67309773118485e-02 , -3.43585040385876e-02 ), ( -2.42401880848779e-02 , 9.27786645334536e-02 , -6.74981184484641e-02 ) } +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 2, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 2, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 2, atoms_positions[size = 51] = { ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 ), ( 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 ), ( 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 ), ( 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 ), ( 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 ), ( 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 ), ( -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 ), ( -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 ), ( -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 ), ( -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ), ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 ), ( 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 ), ( 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 ), ( 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 ), ( 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 ), ( 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 ), ( 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 ), ( 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 ), ( 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 ), ( 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 ), ( 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 ), ( 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 ), ( 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 ), ( 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 ), ( 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 ), ( 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 ), ( 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 ), ( 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 ), ( 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 ), ( -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 ), ( 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 ), ( 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 ), ( -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 ), ( -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 ), ( -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 ), ( -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 ), ( -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 ), ( -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 ), ( -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 ), ( -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 ), ( -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 ), ( -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 ), ( -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 ), ( -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 ), ( -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 ), ( -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 ), ( -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 ), ( -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 ), ( -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 ), ( -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 ), ( -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ) } +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Colvar component no. 1 within colvar "main" has value ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Calculating colvar components. +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 , 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 , 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 , 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 , 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 , 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 , 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 , 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 , 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 , 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 , 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 , 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 , 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 , 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 , 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 , -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 , 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 , -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 , -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 , -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 , -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 , -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 , -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 , -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 , -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 , -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 , -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 , -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 , -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 , -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 , -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 , -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 , -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99576075986331e-01 , 2.04849722863537e-02 , 1.41405761102838e-02 , -1.51022625280223e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.41256788777108e+00 , 4.24635905079927e-02 , -7.47486558445232e-01 , 7.00115718441668e+00 , -4.83611297336880e-01 , -6.72765244765201e-01 , 7.03874068577826e+00 , -2.01025510317951e+00 , -1.03299547241448e+00 , 6.24395343138056e+00 , -2.51572533939029e-01 , 6.35983258347552e-01 , 5.02227513144912e+00 , -2.08619613960314e-01 , 6.45415745056365e-01 , 6.90700754434829e+00 , -2.68453533493654e-01 , 1.78542427350977e+00 , 6.17957103044951e+00 , -1.29090027720781e-01 , 3.04251066705877e+00 , 7.19403180126243e+00 , -3.17369471334157e-01 , 4.30319011139727e+00 , 5.30462827218538e+00 , 1.13372558370830e+00 , 3.26693952393414e+00 , 4.08838090315027e+00 , 1.07655770981003e+00 , 3.60860964154594e+00 , 5.87394056151019e+00 , 2.33800390467119e+00 , 2.95024243297848e+00 , 5.23075409103038e+00 , 3.59958849486193e+00 , 2.87914763756514e+00 , 6.32630859443884e+00 , 4.63548709472908e+00 , 2.47114223872092e+00 , 3.90152849281553e+00 , 3.69480957847571e+00 , 2.02630386391081e+00 , 2.92849831508795e+00 , 4.11702349788774e+00 , 2.57103427137554e+00 , 3.81752464560741e+00 , 3.24383975556125e+00 , 7.83680313043258e-01 , 2.66011006332662e+00 , 3.20112702327162e+00 , -6.86039679839120e-02 , 3.04891804402846e+00 , 2.73308389574671e+00 , -1.57998249483723e+00 , 1.64933174748350e+00 , 2.16481814015785e+00 , 5.69609797184805e-01 , 4.24916313956642e-01 , 2.42604965586234e+00 , 5.70944813949882e-01 , 1.98622597538689e+00 , 9.97641377339547e-01 , 1.06028217395022e+00 , 1.12203654296500e+00 , 1.47198392696820e-02 , 1.68716962020504e+00 , 2.01639426111517e+00 , -1.20568532299634e+00 , 2.02326919524489e+00 , 4.98102959782204e-01 , 5.80680270274871e-01 , 3.01309200849258e+00 , -6.84829291497321e-01 , 3.90834420438205e-01 , 3.19686552659774e+00 , 1.27432231396954e+00 , 1.30473171683050e+00 , 3.82336625650493e+00 , 8.08614168094073e-01 , 1.88136200402660e+00 , 5.08537908504189e+00 , 2.07183047547458e+00 , 2.58032349804030e+00 , 5.62056855348324e+00 , -3.51850133553694e-01 , 2.92077539005237e+00 , 4.98737441346762e+00 , -1.18279533646316e+00 , 3.01571408162175e+00 , 5.89917351325073e+00 , -3.87791450499550e-01 , 3.70427931084891e+00 , 3.87473956269402e+00 , -1.45631333070178e+00 , 4.61458666831528e+00 , 3.53260722454383e+00 , -7.71526002767185e-01 , 5.37658752659327e+00 , 2.40420137399517e+00 , -2.70490400268646e+00 , 3.89833545881460e+00 , 2.94597232234461e+00 , -3.85265546184646e+00 , 4.40316903063526e+00 , 2.87070388665419e+00 , -2.55585427163053e+00 , 2.62089124918333e+00 , 2.50850455644648e+00 , -3.73244703150236e+00 , 1.88635799703336e+00 , 2.08120743477195e+00 , -3.40440943481119e+00 , 7.90658441447400e-01 , 1.01491048903463e+00 , -4.34244354382288e+00 , 1.12118204300755e+00 , 3.21350099407044e+00 , -5.52935900934581e+00 , 9.45033098508531e-01 , 3.35104292672649e+00 , -3.48508585009221e+00 , 6.29276686111415e-01 , 4.17783435928156e+00 , -3.75585713524412e+00 , 1.04512093113194e-01 , 5.46866656362123e+00 , -2.44524700543161e+00 , -4.36558136521221e-01 , 6.12526250140405e+00 , -4.45856864052754e+00 , 1.01875249344832e+00 , 6.41864175829419e+00 , -5.32721502990005e+00 , 5.89231521263039e-01 , 7.17652520662030e+00 , -6.29284729365068e+00 , 3.54732601205136e+00 , 6.69279341387888e+00 , -6.92912797439636e+00 , 4.31546587219537e+00 , 7.41851718685831e+00 , -6.76637822708340e+00 , 3.20729201072888e+00 , 5.49814050154377e+00 , -4.07642575952408e+00 , 2.29037016877803e+00 , 6.47114962291977e+00 , -4.91328756573380e+00 , 3.24679031579868e+00 , 7.21657284208710e+00 , -4.05851409025195e+00 , 4.48540809625428e+00 , 7.26245000999439e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 2. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 2. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 2, atoms_new_colvar_forces = { ( -7.13662406347475e-02 , 3.04690881238521e-01 , -3.88189014550433e-01 ), ( 1.21024777996464e-02 , 3.62012543772250e-02 , -2.36560385329191e-01 ), ( -4.16270344260805e-02 , 9.11317483620320e-02 , 8.22453445505728e-02 ), ( -9.61258643475432e-02 , 2.42118549983633e-01 , 6.75964639859510e-02 ), ( -1.88692093361642e-02 , 9.97197189297282e-02 , -1.64805343769547e-01 ), ( 7.02674381185762e-02 , -1.79697300167168e-01 , -4.11729051286209e-02 ), ( 1.05951211671063e-02 , -1.02292489843847e-01 , 2.47571722543744e-01 ), ( -4.03059854417923e-02 , 5.42236285493406e-02 , 1.93046549392435e-01 ), ( 6.57408551090289e-02 , -1.87266309856294e-01 , 3.25601520815156e-02 ), ( 1.14404466188646e-01 , -3.88084904837303e-01 , 2.64302707504789e-01 ), ( 2.42403744165811e-02 , -9.94785187554915e-02 , 9.42791291950214e-02 ), ( 2.64150718872813e-02 , -9.73002134525345e-02 , 5.84427219892992e-02 ), ( 1.22480322060636e-02 , -5.62157918593996e-02 , 7.13815477024520e-02 ), ( 1.23883380687533e-02 , -5.38885112017688e-02 , 6.03455655484888e-02 ), ( 5.48062002843824e-03 , -3.58514915394607e-02 , 7.46148407252745e-02 ), ( -8.60056519272734e-03 , 8.16670443437686e-03 , 7.47778066468873e-02 ), ( -2.05645685993396e-03 , -3.58005212530679e-03 , 3.99526483103971e-02 ), ( -5.73963473120446e-03 , 8.99109627006217e-03 , 3.57767175444479e-02 ), ( 2.80549872017285e-03 , -1.36374684939331e-02 , 1.93857966829495e-02 ), ( 9.25294348776421e-03 , -2.23212932966850e-02 , -2.64521663051807e-02 ), ( 8.81336594162522e-03 , -2.38438300993918e-02 , -1.48909470506634e-02 ), ( 6.73030250851154e-03 , -1.35078732001586e-02 , -3.01234731955913e-02 ), ( 1.50653818005725e-02 , -4.65512686167406e-02 , -2.34284311242762e-03 ), ( 2.75570538265062e-02 , -8.78929598017612e-02 , 6.65785423175934e-03 ), ( 1.42236341148245e-02 , -4.66134370995714e-02 , 8.41248205826075e-03 ), ( 1.41735565627240e-02 , -4.35966335485880e-02 , -2.99781666970647e-03 ), ( 9.21202377418917e-03 , -3.70972210496742e-02 , 3.30065277669219e-02 ), ( -1.00090754604269e-03 , -1.58167028261417e-02 , 7.55940860707059e-02 ), ( -3.85036480540487e-03 , 3.87472044758625e-03 , 3.26050293851104e-02 ), ( -5.93416109216629e-03 , 1.10093226221347e-02 , 3.01533130775972e-02 ), ( -7.30451303321866e-03 , 1.74998354864693e-02 , 2.13654311507231e-02 ), ( -1.61630628639610e-02 , 5.13889365763393e-02 , -3.25476401672865e-03 ), ( -9.67740222362291e-03 , 3.56016733585189e-02 , -2.12309147297704e-02 ), ( -1.37036427268514e-02 , 4.98557230830785e-02 , -2.78383479874705e-02 ), ( -1.90156928795647e-03 , 1.49514486553429e-02 , -3.59113664694244e-02 ), ( 1.07086125914830e-02 , -1.53022610381287e-02 , -7.26250027034179e-02 ), ( 4.41605431417831e-03 , -3.12810190896927e-04 , -5.38764592683203e-02 ), ( 3.40925420915234e-03 , 6.65106748886611e-03 , -6.90909274179423e-02 ), ( 7.10036528785388e-03 , -1.43684525078162e-02 , -3.13096231913525e-02 ), ( 1.29357293014539e-02 , -4.07951303363235e-02 , 1.27717136871923e-03 ), ( 4.20013690039623e-04 , 2.16888898682387e-03 , -1.38956021720835e-02 ), ( 3.30067539764028e-04 , 3.90817206331382e-03 , -1.97116211345700e-02 ), ( -6.60857296101589e-03 , 2.06946733874849e-02 , -6.74622074879811e-05 ), ( -2.06697591996960e-02 , 5.74197879098366e-02 , 2.89412848935110e-02 ), ( -1.89943446265396e-02 , 6.32931538792098e-02 , -1.54039897267542e-02 ), ( -2.27123621770474e-02 , 7.52502973237281e-02 , -1.66954809253169e-02 ), ( -1.67323700772781e-02 , 7.28193141294979e-02 , -8.16437923409835e-02 ), ( -1.97816905755823e-02 , 8.70227179902238e-02 , -1.00243802160594e-01 ), ( -8.50116034360863e-03 , 4.71568068651273e-02 , -8.20123108275631e-02 ), ( -1.85724328597233e-02 , 6.67337512843182e-02 , -3.43967090628983e-02 ), ( -2.42373452910282e-02 , 9.27690520615654e-02 , -6.75498229534928e-02 ) } +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 3, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 3, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 3, atoms_positions[size = 51] = { ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 ), ( 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 ), ( 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 ), ( 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 ), ( 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 ), ( 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 ), ( -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 ), ( -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 ), ( -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 ), ( -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ), ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 ), ( 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 ), ( 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 ), ( 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 ), ( 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 ), ( 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 ), ( 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 ), ( 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 ), ( 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 ), ( 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 ), ( 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 ), ( 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 ), ( 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 ), ( 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 ), ( 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 ), ( 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 ), ( 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 ), ( 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 ), ( 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 ), ( -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 ), ( 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 ), ( 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 ), ( -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 ), ( -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 ), ( -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 ), ( -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 ), ( -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 ), ( -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 ), ( -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 ), ( -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 ), ( -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 ), ( -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 ), ( -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 ), ( -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 ), ( -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 ), ( -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 ), ( -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 ), ( -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 ), ( -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 ), ( -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 ), ( -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ) } +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 , 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 , 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 , 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 , 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 , 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 , 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 , 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 , 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 , 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 , 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 , 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 , 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 , 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 , 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 , -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 , 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 , -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 , -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 , -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 , -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 , -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 , -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 , -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 , -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 , -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 , -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 , -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 , -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 , -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 , -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 , -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 , -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99580256392652e-01 , 2.03417668466031e-02 , 1.40469687457128e-02 , -1.51064959740650e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.40492237253135e+00 , 4.27712319253067e-02 , -7.49608803824418e-01 , 6.99886728276969e+00 , -4.87982987061699e-01 , -6.66532683547335e-01 , 7.03892468060191e+00 , -2.01329531121742e+00 , -1.02802195891611e+00 , 6.24977958935082e+00 , -2.52993125690519e-01 , 6.44576573549340e-01 , 5.01591595320429e+00 , -2.08738491322465e-01 , 6.51365661517494e-01 , 6.90538109559906e+00 , -2.69181811829325e-01 , 1.79236023089400e+00 , 6.17758108066146e+00 , -1.26893480921234e-01 , 3.04713605434734e+00 , 7.18887325451962e+00 , -3.18193200106808e-01 , 4.30235579124897e+00 , 5.30552869846807e+00 , 1.12813617822133e+00 , 3.27330004538718e+00 , 4.08643507339333e+00 , 1.07372712927902e+00 , 3.61263351469221e+00 , 5.87428219672233e+00 , 2.33045858639836e+00 , 2.95714950203985e+00 , 5.22755714450830e+00 , 3.59807438420110e+00 , 2.87986798884218e+00 , 6.33004183083580e+00 , 4.62659869385277e+00 , 2.46797164806167e+00 , 3.89874709213175e+00 , 3.70378155047446e+00 , 2.02343876738978e+00 , 2.92333072881415e+00 , 4.11579963781292e+00 , 2.56496367086225e+00 , 3.81868969017614e+00 , 3.24370355222989e+00 , 7.82467843373265e-01 , 2.66307180439271e+00 , 3.19308859627458e+00 , -7.50302924332762e-02 , 3.04935775245423e+00 , 2.72948534129055e+00 , -1.58745596964098e+00 , 1.64231107847575e+00 , 2.15863124120131e+00 , 5.75786473915195e-01 , 4.27076585293291e-01 , 2.43324534734030e+00 , 5.66067315369760e-01 , 1.98042856856752e+00 , 1.00387469872848e+00 , 1.05723266610113e+00 , 1.12900600387164e+00 , 1.29286829059784e-02 , 1.68721635387416e+00 , 2.01589328160856e+00 , -1.19932175120520e+00 , 2.02325568775390e+00 , 5.02872695207554e-01 , 5.87790193489470e-01 , 3.01036205034407e+00 , -6.81443806334731e-01 , 3.85827450014166e-01 , 3.19255649018736e+00 , 1.28185950442151e+00 , 1.30771005083557e+00 , 3.82341210218636e+00 , 8.15515828381665e-01 , 1.88747703370855e+00 , 5.08217983711373e+00 , 2.06841248664032e+00 , 2.58347881889303e+00 , 5.62072595302360e+00 , -3.54737229514580e-01 , 2.92077622367870e+00 , 4.98648132547925e+00 , -1.18058258832769e+00 , 3.01915840075578e+00 , 5.90116487271335e+00 , -3.94236183041075e-01 , 3.70184286895944e+00 , 3.87004727732393e+00 , -1.46136070066471e+00 , 4.60677763489060e+00 , 3.53450674389551e+00 , -7.67377414366297e-01 , 5.37852278071140e+00 , 2.40556782958059e+00 , -2.70861215987738e+00 , 3.89781833954453e+00 , 2.94245881841917e+00 , -3.85396798482233e+00 , 4.40887189959543e+00 , 2.86515994346482e+00 , -2.56239040753395e+00 , 2.61703873126379e+00 , 2.50464747702208e+00 , -3.72733555981267e+00 , 1.89478359774488e+00 , 2.07840355670072e+00 , -3.40650119143540e+00 , 7.94784295107294e-01 , 1.00825858177204e+00 , -4.33412211420060e+00 , 1.11541235179303e+00 , 3.21622883408896e+00 , -5.53124417248555e+00 , 9.37683090999765e-01 , 3.34934840914128e+00 , -3.48028712597954e+00 , 6.29581589471032e-01 , 4.17168842719766e+00 , -3.76290717175077e+00 , 1.04871473901500e-01 , 5.47223651723740e+00 , -2.43522718314973e+00 , -4.28552224949121e-01 , 6.12921002549244e+00 , -4.46135408520385e+00 , 1.01291932684115e+00 , 6.41734916974178e+00 , -5.32587136941757e+00 , 5.92489930735439e-01 , 7.17857924763829e+00 , -6.29513735734330e+00 , 3.54679917537859e+00 , 6.69524463354136e+00 , -6.92398573905670e+00 , 4.31157558405335e+00 , 7.41789290277433e+00 , -6.76021521001507e+00 , 3.20799759117973e+00 , 5.50145895048684e+00 , -4.07778736811767e+00 , 2.29342320802231e+00 , 6.47433933868301e+00 , -4.91390314463876e+00 , 3.24493818534199e+00 , 7.21576000684478e+00 , -4.06363344055185e+00 , 4.48966173936619e+00 , 7.26346455036435e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 3. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 3. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 3, atoms_new_colvar_forces = { ( -7.12644910002888e-02 , 3.04480391919715e-01 , -3.88530416773670e-01 ), ( 1.21543402350703e-02 , 3.59283757073496e-02 , -2.36592346550597e-01 ), ( -4.16092138833091e-02 , 9.11640888447168e-02 , 8.23416306242972e-02 ), ( -9.61000764313615e-02 , 2.42305695294195e-01 , 6.74632194161953e-02 ), ( -1.88405647185787e-02 , 9.96498172188486e-02 , -1.64992595806876e-01 ), ( 7.02514835169250e-02 , -1.79844182937403e-01 , -4.10469774921604e-02 ), ( 1.05532653731170e-02 , -1.02124362545298e-01 , 2.47761381423188e-01 ), ( -4.03387808327078e-02 , 5.44992483058144e-02 , 1.92980165253870e-01 ), ( 6.56942024572184e-02 , -1.87268005160499e-01 , 3.25895903711645e-02 ), ( 1.14312103245404e-01 , -3.88029814824987e-01 , 2.64649278438540e-01 ), ( 2.42399874948257e-02 , -9.94601615884302e-02 , 9.43450526358905e-02 ), ( 2.64187832067172e-02 , -9.72959614091883e-02 , 5.85026645399138e-02 ), ( 1.22455016217257e-02 , -5.61985927602022e-02 , 7.14248035735868e-02 ), ( 1.23869408467411e-02 , -5.38750852851352e-02 , 6.03844516287721e-02 ), ( 5.47533482913114e-03 , -3.58293646823109e-02 , 7.46507658907643e-02 ), ( -8.61093066863975e-03 , 8.19691911326328e-03 , 7.47955564010663e-02 ), ( -2.06113077404795e-03 , -3.56556978390652e-03 , 3.99668789943306e-02 ), ( -5.74519237302200e-03 , 9.00641804914424e-03 , 3.57835237496780e-02 ), ( 2.80447863484305e-03 , -1.36331338607282e-02 , 1.94012145925844e-02 ), ( 9.25852941616702e-03 , -2.23368932576550e-02 , -2.64410106981663e-02 ), ( 8.81779507607160e-03 , -2.38547195085519e-02 , -1.48796460307627e-02 ), ( 6.73545618225761e-03 , -1.35227630184473e-02 , -3.01205268766796e-02 ), ( 1.50708708581964e-02 , -4.65613398889311e-02 , -2.31954133071604e-03 ), ( 2.75661986728460e-02 , -8.79069437037276e-02 , 6.69966718119029e-03 ), ( 1.42278972265037e-02 , -4.66188536979522e-02 , 8.43518305129557e-03 ), ( 1.41789197697816e-02 , -4.36058466193783e-02 , -2.97984094516618e-03 ), ( 9.21216484792188e-03 , -3.70911405406308e-02 , 3.30300824801763e-02 ), ( -1.00842453813973e-03 , -1.57897001341701e-02 , 7.56161841724666e-02 ), ( -3.85480601482357e-03 , 3.88845033974037e-03 , 3.26092204945920e-02 ), ( -5.93907177018090e-03 , 1.10235923365747e-02 , 3.01526170963657e-02 ), ( -7.30916548846552e-03 , 1.75114619452427e-02 , 2.13626571248804e-02 ), ( -1.61686021542056e-02 , 5.13968697461965e-02 , -3.27568354660324e-03 ), ( -9.67884364851469e-03 , 3.55998969369253e-02 , -2.12508875909159e-02 ), ( -1.37058643655233e-02 , 4.98541172211488e-02 , -2.78668434034106e-02 ), ( -1.89885720037668e-03 , 1.49399596092170e-02 , -3.59248246074874e-02 ), ( 1.07192981146069e-02 , -1.53339454667564e-02 , -7.26323591285075e-02 ), ( 4.42280297726436e-03 , -3.33908263890920e-04 , -5.38891907297017e-02 ), ( 3.41711373116267e-03 , 6.62536545954213e-03 , -6.91106420905072e-02 ), ( 7.10595226173296e-03 , -1.43831502417926e-02 , -3.13121755456011e-02 ), ( 1.29403714170504e-02 , -4.08015816582177e-02 , 1.29101937417115e-03 ), ( 4.21650163844445e-04 , 2.16452996514270e-03 , -1.39044294702790e-02 ), ( 3.32265751315244e-04 , 3.90201987778178e-03 , -1.97236621643520e-02 ), ( -6.61077765359962e-03 , 2.06991412040919e-02 , -8.09922488427135e-05 ), ( -2.06797382433100e-02 , 5.74425477014770e-02 , 2.89176437746283e-02 ), ( -1.89994930796128e-02 , 6.32995810538052e-02 , -1.54400667540050e-02 ), ( -2.27186777545924e-02 , 7.52586020414951e-02 , -1.67382012788684e-02 ), ( -1.67304543184278e-02 , 7.28011998778589e-02 , -8.16968210356079e-02 ), ( -1.97790932339822e-02 , 8.69999150277857e-02 , -1.00307053543935e-01 ), ( -8.49625951876390e-03 , 4.71338235969838e-02 , -8.20544860518998e-02 ), ( -1.85756727929090e-02 , 6.67331167231479e-02 , -3.44368813268715e-02 ), ( -2.42395254710581e-02 , 9.27598757209877e-02 , -6.76063492614180e-02 ) } +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 4, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 4, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 4, atoms_positions[size = 51] = { ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 ), ( 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 ), ( 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 ), ( 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 ), ( 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 ), ( 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 ), ( -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 ), ( -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 ), ( -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 ), ( -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ), ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 ), ( 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 ), ( 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 ), ( 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 ), ( 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 ), ( 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 ), ( 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 ), ( 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 ), ( 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 ), ( 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 ), ( 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 ), ( 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 ), ( 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 ), ( 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 ), ( 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 ), ( 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 ), ( 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 ), ( 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 ), ( 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 ), ( -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 ), ( 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 ), ( 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 ), ( -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 ), ( -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 ), ( -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 ), ( -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 ), ( -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 ), ( -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 ), ( -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 ), ( -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 ), ( -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 ), ( -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 ), ( -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 ), ( -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 ), ( -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 ), ( -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 ), ( -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 ), ( -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 ), ( -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 ), ( -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 ), ( -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ) } +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 , 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 , 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 , 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 , 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 , 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 , 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 , 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 , 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 , 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 , 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 , 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 , 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 , 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 , 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 , -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 , 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 , -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 , -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 , -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 , -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 , -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 , -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 , -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 , -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 , -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 , -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 , -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 , -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 , -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 , -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 , -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 , -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99586711667267e-01 , 2.01491176905466e-02 , 1.39360494757458e-02 , -1.50401276431458e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.39736512961776e+00 , 4.31151522461295e-02 , -7.51869499941589e-01 , 6.99697349910249e+00 , -4.92986486773470e-01 , -6.60643058720068e-01 , 7.03956131966061e+00 , -2.01599562043161e+00 , -1.02270138887994e+00 , 6.25441862955798e+00 , -2.55479348668687e-01 , 6.52426733745676e-01 , 5.00976229685634e+00 , -2.08396861630040e-01 , 6.57171707900711e-01 , 6.90379893683661e+00 , -2.69650012378046e-01 , 1.79955180827841e+00 , 6.17612056205818e+00 , -1.24689664713357e-01 , 3.05385717458533e+00 , 7.18262153014659e+00 , -3.19483628176432e-01 , 4.30070788794908e+00 , 5.30525411387688e+00 , 1.12344081057400e+00 , 3.27927653751791e+00 , 4.08585041723905e+00 , 1.07080931566762e+00 , 3.61645869443431e+00 , 5.87478723191782e+00 , 2.32181552083492e+00 , 2.96378504733080e+00 , 5.22400886213973e+00 , 3.59702009468078e+00 , 2.88052887660961e+00 , 6.33313317499486e+00 , 4.61701240970823e+00 , 2.46471442526432e+00 , 3.89737340161281e+00 , 3.71210223408483e+00 , 2.02155544561370e+00 , 2.91711955411185e+00 , 4.11519228287932e+00 , 2.55923462895946e+00 , 3.82082739636300e+00 , 3.24329753291857e+00 , 7.80254000051566e-01 , 2.66602781390261e+00 , 3.18397646387178e+00 , -8.09881540892243e-02 , 3.04888520993354e+00 , 2.72632169155264e+00 , -1.59295007156850e+00 , 1.63331932263642e+00 , 2.15438182003279e+00 , 5.80221200622135e-01 , 4.29796020042417e-01 , 2.44048974225011e+00 , 5.61390282102803e-01 , 1.97580894630859e+00 , 1.00855861677995e+00 , 1.05487032680445e+00 , 1.13631942708259e+00 , 1.23297613840852e-02 , 1.68767856638169e+00 , 2.01543278820312e+00 , -1.19310442452448e+00 , 2.02278872186808e+00 , 5.08047377115700e-01 , 5.94103068750160e-01 , 3.00576024477810e+00 , -6.78411418648937e-01 , 3.80973018167940e-01 , 3.18877091550769e+00 , 1.28890981808355e+00 , 1.31089714917864e+00 , 3.82434829130699e+00 , 8.22584042707296e-01 , 1.89375649165369e+00 , 5.07836903012886e+00 , 2.06392968081906e+00 , 2.58648078693201e+00 , 5.62112319681612e+00 , -3.57094752235283e-01 , 2.92055985013060e+00 , 4.98576720252227e+00 , -1.17833697476329e+00 , 3.02263303059485e+00 , 5.90278131108803e+00 , -4.01289682782926e-01 , 3.69850595235756e+00 , 3.86544814416985e+00 , -1.46589637591304e+00 , 4.59863268927604e+00 , 3.53623502574094e+00 , -7.63237517396049e-01 , 5.38072242092085e+00 , 2.40729817036620e+00 , -2.71330930194677e+00 , 3.89707935741016e+00 , 2.93924692577485e+00 , -3.85425099114441e+00 , 4.41458827492696e+00 , 2.85999315690556e+00 , -2.56892188992922e+00 , 2.61382460963443e+00 , 2.50020874150206e+00 , -3.72284186458065e+00 , 1.90197536108939e+00 , 2.07510646844260e+00 , -3.40871211071732e+00 , 7.99790478292761e-01 , 1.00121225163475e+00 , -4.32545886380702e+00 , 1.10900427868007e+00 , 3.22047025442722e+00 , -5.53351625119123e+00 , 9.30432473555726e-01 , 3.34750831201884e+00 , -3.47525557551475e+00 , 6.31200448929543e-01 , 4.16476361560800e+00 , -3.76911747551295e+00 , 1.03529100531213e-01 , 5.47583733652486e+00 , -2.42576274564526e+00 , -4.19480715080738e-01 , 6.13334206799632e+00 , -4.46406823529463e+00 , 1.00722961600443e+00 , 6.41678815845579e+00 , -5.32468023760679e+00 , 5.95703195156438e-01 , 7.18054979827921e+00 , -6.29678349518607e+00 , 3.54748598832876e+00 , 6.69759414184486e+00 , -6.91961311166484e+00 , 4.30781800108811e+00 , 7.41754894929098e+00 , -6.75470331208230e+00 , 3.20847206840985e+00 , 5.50487816019186e+00 , -4.08016206509908e+00 , 2.29659504362369e+00 , 6.47732157613758e+00 , -4.91278704904784e+00 , 3.24190859075059e+00 , 7.21499860704305e+00 , -4.06879027853620e+00 , 4.49560441647509e+00 , 7.26533547359881e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 4. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 4. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 4, atoms_new_colvar_forces = { ( -7.12080210552797e-02 , 3.04274726531718e-01 , -3.88940587640774e-01 ), ( 1.21950269985741e-02 , 3.56064499150579e-02 , -2.36629571966559e-01 ), ( -4.15896800926495e-02 , 9.11984131701159e-02 , 8.25110748151548e-02 ), ( -9.60913610694842e-02 , 2.42553891617927e-01 , 6.73416799725295e-02 ), ( -1.88301065662091e-02 , 9.95877660607348e-02 , -1.65239019876376e-01 ), ( 7.02486546083075e-02 , -1.80038089572669e-01 , -4.09170337765094e-02 ), ( 1.05318019430700e-02 , -1.01943502700610e-01 , 2.48011589427611e-01 ), ( -4.03702441420600e-02 , 5.48377999542595e-02 , 1.92899941686077e-01 ), ( 6.56614060203969e-02 , -1.87281426243981e-01 , 3.25748774948746e-02 ), ( 1.14264326869696e-01 , -3.88012490794451e-01 , 2.65041892347769e-01 ), ( 2.42467051015945e-02 , -9.94396336710934e-02 , 9.44171391294592e-02 ), ( 2.64251678200815e-02 , -9.72867887154741e-02 , 5.85662658018812e-02 ), ( 1.22472752364769e-02 , -5.61754900662332e-02 , 7.14731700813468e-02 ), ( 1.23894843053070e-02 , -5.38579145569750e-02 , 6.04275201891246e-02 ), ( 5.47399239743080e-03 , -3.57982173847452e-02 , 7.46924353005460e-02 ), ( -8.61820629816763e-03 , 8.24101256205583e-03 , 7.48197995077387e-02 ), ( -2.06481714081862e-03 , -3.54201942450395e-03 , 3.99845925012198e-02 ), ( -5.74960578369700e-03 , 9.02966184445511e-03 , 3.57935634859857e-02 ), ( 2.80215815799665e-03 , -1.36194994617910e-02 , 1.94184830640624e-02 ), ( 9.25813419184906e-03 , -2.23432881756588e-02 , -2.64315357010282e-02 ), ( 8.81887984484594e-03 , -2.38610548708190e-02 , -1.48694441646478e-02 ), ( 6.73627359909724e-03 , -1.35342143700938e-02 , -3.01197791283318e-02 ), ( 1.50745344951528e-02 , -4.65688049220078e-02 , -2.29674594399060e-03 ), ( 2.75753596529584e-02 , -8.79232773311727e-02 , 6.74093354014295e-03 ), ( 1.42328598821259e-02 , -4.66261458490982e-02 , 8.45792361108824e-03 ), ( 1.41845692241518e-02 , -4.36190215434519e-02 , -2.96277053426434e-03 ), ( 9.21509811267395e-03 , -3.70853528776646e-02 , 3.30557103690731e-02 ), ( -1.00908817873593e-03 , -1.57613613752127e-02 , 7.56438621946769e-02 ), ( -3.85598849795090e-03 , 3.90235192006697e-03 , 3.26159055815450e-02 ), ( -5.94027352971036e-03 , 1.10362439836852e-02 , 3.01542014974282e-02 ), ( -7.31235222693024e-03 , 1.75260063960574e-02 , 2.13618346567090e-02 ), ( -1.61760008919845e-02 , 5.14120787753115e-02 , -3.29589385739106e-03 ), ( -9.68233173784903e-03 , 3.55996626468111e-02 , -2.12719940992636e-02 ), ( -1.37102747661633e-02 , 4.98531642203748e-02 , -2.78968717294853e-02 ), ( -1.89961262970978e-03 , 1.49288570247522e-02 , -3.59407974062863e-02 ), ( 1.07232945874884e-02 , -1.53680987893684e-02 , -7.26454605633824e-02 ), ( 4.42589088117630e-03 , -3.60305744266164e-04 , -5.39062707052113e-02 ), ( 3.42040381532136e-03 , 6.59283053457814e-03 , -6.91358624396322e-02 ), ( 7.11026470043291e-03 , -1.44042598923488e-02 , -3.13175947834697e-02 ), ( 1.29477734767760e-02 , -4.08181704267577e-02 , 1.30395382414031e-03 ), ( 4.24885994011587e-04 , 2.15107073748631e-03 , -1.39148029314400e-02 ), ( 3.36253599568686e-04 , 3.88447745033494e-03 , -1.97377999334930e-02 ), ( -6.61061592184173e-03 , 2.06973135737414e-02 , -9.46778005412389e-05 ), ( -2.06850655568149e-02 , 5.74627047385668e-02 , 2.88966154320564e-02 ), ( -1.90034487268360e-02 , 6.33007217508657e-02 , -1.54769495934924e-02 ), ( -2.27233448939688e-02 , 7.52604092524772e-02 , -1.67817706510836e-02 ), ( -1.67336131493115e-02 , 7.27772224080956e-02 , -8.17555554242184e-02 ), ( -1.97831682663396e-02 , 8.69711573163882e-02 , -1.00377263119591e-01 ), ( -8.49613558415377e-03 , 4.71026760275649e-02 , -8.21027934280728e-02 ), ( -1.85801247869260e-02 , 6.67289400821420e-02 , -3.44791463843032e-02 ), ( -2.42469940229704e-02 , 9.27508182648225e-02 , -6.76669719294010e-02 ) } +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 5, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 5, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 5, atoms_positions[size = 51] = { ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 ), ( 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 ), ( 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 ), ( 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 ), ( 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 ), ( 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 ), ( -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 ), ( -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 ), ( -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 ), ( -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ), ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 ), ( 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 ), ( 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 ), ( 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 ), ( 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 ), ( 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 ), ( 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 ), ( 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 ), ( 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 ), ( 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 ), ( 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 ), ( 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 ), ( 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 ), ( 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 ), ( 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 ), ( 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 ), ( 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 ), ( 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 ), ( 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 ), ( -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 ), ( 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 ), ( 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 ), ( -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 ), ( -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 ), ( -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 ), ( -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 ), ( -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 ), ( -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 ), ( -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 ), ( -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 ), ( -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 ), ( -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 ), ( -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 ), ( -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 ), ( -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 ), ( -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 ), ( -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 ), ( -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 ), ( -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 ), ( -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 ), ( -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ) } +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 , 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 , 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 , 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 , 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 , 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 , 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 , 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 , 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 , 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 , 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 , 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 , 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 , 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 , 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 , -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 , 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 , -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 , -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 , -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 , -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 , -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 , -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 , -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 , -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 , -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 , -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 , -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 , -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 , -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 , -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 , -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 , -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99595445042046e-01 , 1.99079588911540e-02 , 1.38036322974998e-02 , -1.49023206037944e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.38991416946031e+00 , 4.34744283801044e-02 , -7.54163337428754e-01 , 6.99563610161170e+00 , -4.98503892706968e-01 , -6.55144260776711e-01 , 7.04058385339468e+00 , -2.01841181213503e+00 , -1.01705397294164e+00 , 6.25717478560494e+00 , -2.58987924142412e-01 , 6.59483395844771e-01 , 5.00417327828658e+00 , -2.07603759314844e-01 , 6.62847998269442e-01 , 6.90231392507291e+00 , -2.69900534616565e-01 , 1.80683414788354e+00 , 6.17518454000746e+00 , -1.22599941856973e-01 , 3.06265661630405e+00 , 7.17535046708298e+00 , -3.21245899628467e-01 , 4.29839323444256e+00 , 5.30378299336962e+00 , 1.11968965139921e+00 , 3.28489244358638e+00 , 4.08662232263213e+00 , 1.06780278031954e+00 , 3.62009299652820e+00 , 5.87535076136378e+00 , 2.31236954087246e+00 , 2.97004540671202e+00 , 5.22044136575024e+00 , 3.59636347002717e+00 , 2.88126440825592e+00 , 6.33556455915016e+00 , 4.60684453637470e+00 , 2.46139494196801e+00 , 3.89732266249652e+00 , 3.71955925026888e+00 , 2.02059535617916e+00 , 2.90986615327995e+00 , 4.11524441189183e+00 , 2.55386708194059e+00 , 3.82398273094590e+00 , 3.24270864770465e+00 , 7.77144401084123e-01 , 2.66872516175658e+00 , 3.17380267993491e+00 , -8.63696039640049e-02 , 3.04763628296157e+00 , 2.72372130407814e+00 , -1.59634805337209e+00 , 1.62295199883903e+00 , 2.15235649040217e+00 , 5.82544903358095e-01 , 4.32785933256953e-01 , 2.44777319480663e+00 , 5.56967165146106e-01 , 1.97242553380123e+00 , 1.01150485189189e+00 , 1.05346125179603e+00 , 1.14374551670247e+00 , 1.32834336786492e-02 , 1.68839829853984e+00 , 2.01513019534791e+00 , -1.18698818787427e+00 , 2.02188658528241e+00 , 5.13508681003715e-01 , 5.99457309942489e-01 , 2.99943529503834e+00 , -6.75606530375219e-01 , 3.76341588023421e-01 , 3.18549204920889e+00 , 1.29543363002580e+00 , 1.31433244180415e+00 , 3.82604179198285e+00 , 8.29610470417314e-01 , 1.90012297295150e+00 , 5.07399500921444e+00 , 2.05862067334984e+00 , 2.58945890510769e+00 , 5.62175929581512e+00 , -3.58818415893731e-01 , 2.92017368887383e+00 , 4.98513015455206e+00 , -1.17608652400434e+00 , 3.02611302167691e+00 , 5.90404717741884e+00 , -4.08842716607003e-01 , 3.69413638103649e+00 , 3.86106843551950e+00 , -1.46991291847253e+00 , 4.59046689134105e+00 , 3.53759696207979e+00 , -7.59066696067204e-01 , 5.38307641646853e+00 , 2.40949753261055e+00 , -2.71897569349727e+00 , 3.89603493340364e+00 , 2.93629882356590e+00 , -3.85355415447074e+00 , 4.42029486846224e+00 , 2.85518408075113e+00 , -2.57518229108618e+00 , 2.61161322572639e+00 , 2.49531965090499e+00 , -3.71928382675516e+00 , 1.90741187103812e+00 , 2.07120736941770e+00 , -3.41091446326512e+00 , 8.05634864431185e-01 , 9.93790600929584e-01 , -4.31703973178664e+00 , 1.10222496869058e+00 , 3.22574946686357e+00 , -5.53583422746099e+00 , 9.23282583266972e-01 , 3.34554218366208e+00 , -3.46994111270676e+00 , 6.33956032883665e-01 , 4.15762259059358e+00 , -3.77412760398606e+00 , 1.00500392768093e-01 , 5.47908217445313e+00 , -2.41703724067338e+00 , -4.09501773354755e-01 , 6.13762485954616e+00 , -4.46664233397935e+00 , 1.00210820754888e+00 , 6.41701701798230e+00 , -5.32373797182862e+00 , 5.98763218038510e-01 , 7.18248858862412e+00 , -6.29741564777949e+00 , 3.54910216134629e+00 , 6.69975370467402e+00 , -6.91617019997971e+00 , 4.30435513329031e+00 , 7.41763267006639e+00 , -6.74999730566890e+00 , 3.20875273708202e+00 , 5.50831792549043e+00 , -4.08343576274177e+00 , 2.29950907626712e+00 , 6.47986891589456e+00 , -4.90998446734960e+00 , 3.23779213227859e+00 , 7.21434460879026e+00 , -4.07382566901237e+00 , 4.50309368156246e+00 , 7.26801347384081e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 5. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 5. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 5, atoms_new_colvar_forces = { ( -7.11930917715262e-02 , 3.04080402889663e-01 , -3.89420117659556e-01 ), ( 1.22274699460667e-02 , 3.52378104756379e-02 , -2.36672496748529e-01 ), ( -4.15700140483639e-02 , 9.12349296696296e-02 , 8.27563970021866e-02 ), ( -9.61016217912612e-02 , 2.42865160914319e-01 , 6.72337999946861e-02 ), ( -1.88360121209974e-02 , 9.95358134491225e-02 , -1.65545997411328e-01 ), ( 7.02602719142824e-02 , -1.80280636028130e-01 , -4.07839832834661e-02 ), ( 1.05279361141261e-02 , -1.01752713338897e-01 , 2.48323952446562e-01 ), ( -4.04029387005403e-02 , 5.52382955877266e-02 , 1.92806022433958e-01 ), ( 6.56430458681339e-02 , -1.87308994968492e-01 , 3.25135719017205e-02 ), ( 1.14259433857731e-01 , -3.88039115593396e-01 , 2.65479921768059e-01 ), ( 2.42605798564394e-02 , -9.94172883871254e-02 , 9.44948179787660e-02 ), ( 2.64346007973788e-02 , -9.72729724027510e-02 , 5.86335564201711e-02 ), ( 1.22532987785135e-02 , -5.61471444227930e-02 , 7.15265885148806e-02 ), ( 1.23959564254596e-02 , -5.38374384588434e-02 , 6.04746134511424e-02 ), ( 5.47639039529515e-03 , -3.57590564742181e-02 , 7.47400233883485e-02 ), ( -8.62288446849312e-03 , 8.29741139291352e-03 , 7.48511040577863e-02 ), ( -2.06769030098720e-03 , -3.51031338390929e-03 , 4.00062583395601e-02 ), ( -5.75313344233234e-03 , 9.05996009845718e-03 , 3.58072218150797e-02 ), ( 2.79862073872496e-03 , -1.35972818387436e-02 , 1.94383059596313e-02 ), ( 9.25229494769087e-03 , -2.23407885089335e-02 , -2.64225913728223e-02 ), ( 8.81700552361751e-03 , -2.38629084835913e-02 , -1.48597374907990e-02 ), ( 6.73316724776024e-03 , -1.35421597401508e-02 , -3.01205976460819e-02 ), ( 1.50768098167967e-02 , -4.65735796171252e-02 , -2.27412576343031e-03 ), ( 2.75851638634807e-02 , -8.79413881509297e-02 , 6.78148943275173e-03 ), ( 1.42388046236963e-02 , -4.66350043773231e-02 , 8.48051060091069e-03 ), ( 1.41908282837240e-02 , -4.36356336581280e-02 , -2.94688817210362e-03 ), ( 9.22084526028328e-03 , -3.70798975284593e-02 , 3.30831159893830e-02 ), ( -1.00338374270740e-03 , -1.57322786602175e-02 , 7.56765366312058e-02 ), ( -3.85421467521831e-03 , 3.91614128972128e-03 , 3.26247802985022e-02 ), ( -5.93813236113047e-03 , 1.10470979535649e-02 , 3.01576079069810e-02 ), ( -7.31435281678647e-03 , 1.75430114049752e-02 , 2.13630069306248e-02 ), ( -1.61855455840492e-02 , 5.14338186761766e-02 , -3.31475159770605e-03 ), ( -9.68795659419696e-03 , 3.56008411236023e-02 , -2.12939333607702e-02 ), ( -1.37170377970814e-02 , 4.98527717794188e-02 , -2.79281712479423e-02 ), ( -1.90365092081225e-03 , 1.49183129164942e-02 , -3.59589220985608e-02 ), ( 1.07212998249860e-02 , -1.54039102464941e-02 , -7.26638156649286e-02 ), ( 4.42569541964384e-03 , -3.91221119058605e-04 , -5.39276752213949e-02 ), ( 3.41955036969028e-03 , 6.55443034604825e-03 , -6.91665708908388e-02 ), ( 7.11358937522634e-03 , -1.44310237929892e-02 , -3.13261600722330e-02 ), ( 1.29581107015235e-02 , -4.08439956241160e-02 , 1.31506744524187e-03 ), ( 4.29688150890716e-04 , 2.12923211316452e-03 , -1.39274449810552e-02 ), ( 3.41999448111169e-04 , 3.85645860323836e-03 , -1.97549178900757e-02 ), ( -6.60834719336973e-03 , 2.06895144376888e-02 , -1.09137290942866e-04 ), ( -2.06864898021626e-02 , 5.74799121391366e-02 , 2.88775969811894e-02 ), ( -1.90066753015798e-02 , 6.32967248326141e-02 , -1.55150723924351e-02 ), ( -2.27269315783031e-02 , 7.52558980269329e-02 , -1.68267407696857e-02 ), ( -1.67418411274645e-02 , 7.27480314369913e-02 , -8.18198566656224e-02 ), ( -1.97938715038249e-02 , 8.69371697033174e-02 , -1.00454140405606e-01 ), ( -8.50060401083803e-03 , 4.70643098012962e-02 , -8.21572711273281e-02 ), ( -1.85860961724292e-02 , 6.67213789483478e-02 , -3.45235959012453e-02 ), ( -2.42599397228173e-02 , 9.27419047946174e-02 , -6.77311545628400e-02 ) } +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 6, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 6, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 6, atoms_positions[size = 51] = { ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 ), ( 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 ), ( 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 ), ( 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 ), ( 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 ), ( 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 ), ( -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 ), ( -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 ), ( -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 ), ( -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ), ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 ), ( 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 ), ( 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 ), ( 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 ), ( 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 ), ( 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 ), ( 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 ), ( 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 ), ( 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 ), ( 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 ), ( 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 ), ( 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 ), ( 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 ), ( 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 ), ( 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 ), ( 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 ), ( 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 ), ( 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 ), ( 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 ), ( -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 ), ( 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 ), ( 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 ), ( -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 ), ( -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 ), ( -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 ), ( -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 ), ( -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 ), ( -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 ), ( -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 ), ( -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 ), ( -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 ), ( -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 ), ( -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 ), ( -2.40918974321355e+00 , -3.98829720444863e-01 , 6.14201010890720e+00 ), ( -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 ), ( -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 ), ( -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 ), ( -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 ), ( -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 ), ( -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 ), ( -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ) } +colvars: Step 6, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 , 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 , 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 , 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 , 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 , 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 , 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 , 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 , 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 , 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 , 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 , 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 , 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 , 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 , 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 , -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 , 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 , -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 , -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 , -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 , -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 , -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 , -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 , -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 , -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 , -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -2.40918974321355e+00 , -3.98829720444863e-01 , 6.14201010890720e+00 , -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 , -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 , -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 , -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 , -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 , -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 , -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99606346319256e-01 , 1.96195846631294e-02 , 1.36473412977861e-02 , -1.46960665286908e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.38258265696262e+00 , 4.38243100129149e-02 , -7.56382104222420e-01 , 6.99493480018597e+00 , -5.04379297901734e-01 , -6.50052162350710e-01 , 7.04192045219270e+00 , -2.02060914336868e+00 , -1.01112290577717e+00 , 6.25753590554966e+00 , -2.63457771557847e-01 , 6.65741443922238e-01 , 4.99943109381142e+00 , -2.06375899064417e-01 , 6.68402217385168e-01 , 6.90093561963359e+00 , -2.69965301856802e-01 , 1.81406531407379e+00 , 6.17472807340147e+00 , -1.20756132596372e-01 , 3.07338425721277e+00 , 7.16717712165691e+00 , -3.23458146754260e-01 , 4.29559376832831e+00 , 5.30121783117646e+00 , 1.11685822545891e+00 , 3.29017447218684e+00 , 4.08866909362767e+00 , 1.06471375415143e+00 , 3.62355786680440e+00 , 5.87584158988332e+00 , 2.30246881392760e+00 , 2.97582888298279e+00 , 5.21719659130833e+00 , 3.59600299230110e+00 , 2.88220182233402e+00 , 6.33732307001950e+00 , 4.59625731267736e+00 , 2.45800600680124e+00 , 3.89839358867627e+00 , 3.72599175789973e+00 , 2.02046961436480e+00 , 2.90163540534503e+00 , 4.11596876949475e+00 , 2.54885550333542e+00 , 3.82819600568103e+00 , 3.24202965650929e+00 , 7.73299000208280e-01 , 2.67090204118526e+00 , 3.16260823283791e+00 , -9.11147529362313e-02 , 3.04578559538098e+00 , 2.72177914885088e+00 , -1.59761039065790e+00 , 1.61192967513041e+00 , 2.15264238962059e+00 , 5.82516535282582e-01 , 4.35699172716917e-01 , 2.45511719345588e+00 , 5.52829531001574e-01 , 1.97032030969334e+00 , 1.01269595755177e+00 , 1.05317099128788e+00 , 1.15105085074227e+00 , 1.60268312697028e-02 , 1.68923779048385e+00 , 2.01508154651517e+00 , -1.18093050219450e+00 , 2.02059001174608e+00 , 5.19103423671912e-01 , 6.03756666017072e-01 , 2.99165961952302e+00 , -6.72883032654414e-01 , 3.71996156105769e-01 , 3.18268109245736e+00 , 1.30140542526947e+00 , 1.31800411947884e+00 , 3.82826976117474e+00 , 8.36368928747995e-01 , 1.90651209247895e+00 , 5.06915594697595e+00 , 2.05280922814607e+00 , 2.59253779797391e+00 , 5.62263770016876e+00 , -3.59832686823414e-01 , 2.91967309951782e+00 , 4.98446195944640e+00 , -1.17385281199993e+00 , 3.02957112786579e+00 , 5.90498806934502e+00 , -4.16761854132303e-01 , 3.68862004966679e+00 , 3.85704173976496e+00 , -1.47346129361931e+00 , 4.58258347619747e+00 , 3.53839177729346e+00 , -7.54830303469802e-01 , 5.38548901830445e+00 , 2.41222293495336e+00 , -2.72548053241780e+00 , 3.89461342424708e+00 , 2.93357180714467e+00 , -3.85197581996961e+00 , 4.42598811644207e+00 , 2.85071362759558e+00 , -2.58095942386458e+00 , 2.61071432045923e+00 , 2.49010599798433e+00 , -3.71690208956073e+00 , 1.91064971639681e+00 , 2.06665837063368e+00 , -3.41297284282220e+00 , 8.12226602873634e-01 , 9.86016881846042e-01 , -4.30944464817421e+00 , 1.09536946285025e+00 , 3.23153342065134e+00 , -5.53786626974458e+00 , 9.16228900280573e-01 , 3.34348533623050e+00 , -3.46428473921671e+00 , 6.37623099911245e-01 , 4.15086559946625e+00 , -3.77765611267382e+00 , 9.58922869679191e-02 , 5.48159808807106e+00 , -2.40918974321355e+00 , -3.98829720444863e-01 , 6.14201010890720e+00 , -4.46899904079206e+00 , 9.97906639586094e-01 , 6.41804406230523e+00 , -5.32313898017923e+00 , 6.01566474951886e-01 , 7.18445002183292e+00 , -6.29673905995442e+00 , 3.55136787590008e+00 , 6.70166252586319e+00 , -6.91378496041778e+00 , 4.30133048619226e+00 , 7.41827299697696e+00 , -6.74623083860888e+00 , 3.20886665458916e+00 , 5.51167990428870e+00 , -4.08746458299264e+00 , 2.30180170026646e+00 , 6.48176168239612e+00 , -4.90560218822515e+00 , 3.23275480884981e+00 , 7.21383483807126e+00 , -4.07860289237029e+00 , 4.51188822781000e+00 , 7.27139331822636e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 6. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 6. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atoms_new_colvar_forces = { ( -7.12142262303992e-02 , 3.03903301715951e-01 , -3.89969129550351e-01 ), ( 1.22547356452154e-02 , 3.48262951672449e-02 , -2.36721963920782e-01 ), ( -4.15518674361304e-02 , 9.12751560648350e-02 , 8.30772582640576e-02 ), ( -9.61317320933757e-02 , 2.43240346979410e-01 , 6.71401363520435e-02 ), ( -1.88556777097379e-02 , 9.94952870708496e-02 , -1.65913347874103e-01 ), ( 7.02868318338666e-02 , -1.80572282391047e-01 , -4.06482640014998e-02 ), ( 1.05381289914209e-02 , -1.01554511095457e-01 , 2.48698582925828e-01 ), ( -4.04390358015067e-02 , 5.56977300193672e-02 , 1.92699294429561e-01 ), ( 6.56391566883627e-02 , -1.87353793800463e-01 , 3.24058940221479e-02 ), ( 1.14293775414791e-01 , -3.88114795924072e-01 , 2.65963163735460e-01 ), ( 2.42814729749294e-02 , -9.93938454081909e-02 , 9.45777245589051e-02 ), ( 2.64473139563615e-02 , -9.72552236470947e-02 , 5.87044852956407e-02 ), ( 1.22634185313900e-02 , -5.61144142202651e-02 , 7.15849993395887e-02 ), ( 1.24062468740887e-02 , -5.38142909992529e-02 , 6.05256176470266e-02 ), ( 5.48226526174388e-03 , -3.57129885325300e-02 , 7.47936140876123e-02 ), ( -8.62544006295660e-03 , 8.36465137573996e-03 , 7.48898030521818e-02 ), ( -2.06991625388785e-03 , -3.47135619509690e-03 , 4.00321364199732e-02 ), ( -5.75601257738078e-03 , 9.09651790518486e-03 , 3.58247231259840e-02 ), ( 2.79396502781401e-03 , -1.35672817619064e-02 , 1.94610539947598e-02 ), ( 9.24159279432052e-03 , -2.23299181608012e-02 , -2.64135889483069e-02 ), ( 8.81256516211873e-03 , -2.38605293913080e-02 , -1.48502275938890e-02 ), ( 6.72657734904847e-03 , -1.35466756974881e-02 , -3.01226642825190e-02 ), ( 1.50780930352461e-02 , -4.65758441774542e-02 , -2.25154451988603e-03 ), ( 2.75961135614895e-02 , -8.79611454331461e-02 , 6.82117273635849e-03 ), ( 1.42459402548999e-02 , -4.66453423016032e-02 , 8.50280256995158e-03 ), ( 1.41979492402755e-02 , -4.36553747142220e-02 , -2.93238398181345e-03 ), ( 9.22935271210501e-03 , -3.70749488738609e-02 , 3.31121184968349e-02 ), ( -9.91874405938806e-04 , -1.57029967626075e-02 , 7.57139032005495e-02 ), ( -3.84980968726093e-03 , 3.92961372844109e-03 , 3.26356944825281e-02 ), ( -5.93303553292432e-03 , 1.10560962669028e-02 , 3.01626091603370e-02 ), ( -7.31542887547996e-03 , 1.75621364522944e-02 , 2.13662184603644e-02 ), ( -1.61974194508721e-02 , 5.14615739051056e-02 , -3.33186857750588e-03 ), ( -9.69573856621547e-03 , 3.56034451247036e-02 , -2.13165194953996e-02 ), ( -1.37262291647893e-02 , 4.98530577430511e-02 , -2.79605666016103e-02 ), ( -1.91073603828273e-03 , 1.49085110410628e-02 , -3.59790018535196e-02 ), ( 1.07140432385856e-02 , -1.54407701911095e-02 , -7.26871956581507e-02 ), ( 4.42261271019295e-03 , -4.25945906022867e-04 , -5.39534073383785e-02 ), ( 3.41501168760073e-03 , 6.51107644294849e-03 , -6.92027722989708e-02 ), ( 7.11618928681650e-03 , -1.44627849641823e-02 , -3.13380424647115e-02 ), ( 1.29714546559885e-02 , -4.08783185679446e-02 , 1.32383933489513e-03 ), ( 4.35990744562140e-04 , 2.09976734191279e-03 , -1.39427446383950e-02 ), ( 3.49433995726934e-04 , 3.81891985606549e-03 , -1.97754914609517e-02 ), ( -6.60423860307248e-03 , 2.06762093489713e-02 , -1.24683954910883e-04 ), ( -2.06847286332335e-02 , 5.74941934675936e-02 , 2.88603238042472e-02 ), ( -1.90095738981270e-02 , 6.32880734562383e-02 , -1.55546171706953e-02 ), ( -2.27299338339649e-02 , 7.52456489187880e-02 , -1.68733466161828e-02 ), ( -1.67550040694721e-02 , 7.27145435033735e-02 , -8.18896108779006e-02 ), ( -1.98109971023338e-02 , 8.68989856646780e-02 , -1.00537483379429e-01 ), ( -8.50939441170508e-03 , 4.70198123865680e-02 , -8.22179224442125e-02 ), ( -1.85938018440016e-02 , 6.67108998990059e-02 , -3.45702310150741e-02 ), ( -2.42783793459124e-02 , 9.27335282708393e-02 , -6.77985489776879e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 6, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 7, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 7, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 7, atoms_positions[size = 51] = { ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 ), ( 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 ), ( 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 ), ( 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 ), ( 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 ), ( 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 ), ( -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 ), ( -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 ), ( -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 ), ( -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ), ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 ), ( 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 ), ( 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 ), ( 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 ), ( 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 ), ( 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 ), ( 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 ), ( 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 ), ( 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 ), ( 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 ), ( 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 ), ( 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 ), ( 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 ), ( 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 ), ( 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 ), ( 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 ), ( 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 ), ( 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 ), ( 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 ), ( -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 ), ( 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 ), ( 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 ), ( -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 ), ( -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 ), ( -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 ), ( -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 ), ( -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 ), ( -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 ), ( -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 ), ( -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 ), ( -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 ), ( -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 ), ( -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 ), ( -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 ), ( -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 ), ( -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 ), ( -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 ), ( -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 ), ( -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 ), ( -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 ), ( -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ) } +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851381e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 , 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 , 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 , 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 , 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 , 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 , 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 , 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 , 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 , 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 , 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 , 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 , 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 , 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 , 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 , -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 , 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 , -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 , -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 , -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 , -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 , -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 , -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 , -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 , -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 , -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 , -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 , -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 , -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 , -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 , -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 , -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 , -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99619179084481e-01 , 1.92861231851381e-02 , 1.34671547412836e-02 , -1.44283748956907e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.37538305304503e+00 , 4.41388436366373e-02 , -7.58420370628889e-01 , 6.99485530719490e+00 , -5.10425985680666e-01 , -6.45346168659808e-01 , 7.04349604580040e+00 , -2.02265726988749e+00 , -1.00497131072062e+00 , 6.25522460774788e+00 , -2.68813372616657e-01 , 6.71237658909363e-01 , 4.99571529768386e+00 , -2.04737167339236e-01 , 6.73835332828750e-01 , 6.89963042567825e+00 , -2.69867518111498e-01 , 1.82113732962654e+00 , 6.17466971546913e+00 , -1.19297096640687e-01 , 3.08576139157299e+00 , 7.15825925972110e+00 , -3.26075038973168e-01 , 4.29252129664713e+00 , 5.29777291642669e+00 , 1.11485581894465e+00 , 3.29515090867905e+00 , 4.09183764793830e+00 , 1.06155560037481e+00 , 3.62688777360407e+00 , 5.87611223212261e+00 , 2.29249108802361e+00 , 2.98104274689862e+00 , 5.21459381623287e+00 , 3.59581082032017e+00 , 2.88345243075439e+00 , 6.33840321355751e+00 , 4.58544579972154e+00 , 2.45450258134005e+00 , 3.90029205305377e+00 , 3.73128961479417e+00 , 2.02106872693413e+00 , 2.89255241484695e+00 , 4.11734958415672e+00 , 2.54417065034282e+00 , 3.83348919628243e+00 , 3.24135332817381e+00 , 7.68916235173976e-01 , 2.67231964082559e+00 , 3.15046671427065e+00 , -9.52081712249815e-02 , 3.04353071203136e+00 , 2.72054289076060e+00 , -1.59676640747671e+00 , 1.60103214584909e+00 , 2.15512270489383e+00 , 5.80033636968762e-01 , 4.38160809087045e-01 , 2.46256963508408e+00 , 5.48987035092467e-01 , 1.96952395415686e+00 , 1.01229183432547e+00 , 1.05405385971704e+00 , 1.15800463290380e+00 , 2.06543690640532e-02 , 1.69008018419135e+00 , 2.01535588789458e+00 , -1.17489723375251e+00 , 2.01896155143762e+00 , 5.24660209509410e-01 , 6.06972818651625e-01 , 2.98281107089649e+00 , -6.70086561769286e-01 , 3.67990179325548e-01 , 3.18028082114786e+00 , 1.30680792442861e+00 , 1.32185223798271e+00 , 3.83073543750918e+00 , 8.42629006530245e-01 , 1.91287265307273e+00 , 5.06399075875505e+00 , 2.04688543780461e+00 , 2.59583496043008e+00 , 5.62377552701592e+00 , -3.60097270530168e-01 , 2.91911566991022e+00 , 4.98366188587041e+00 , -1.17164793907748e+00 , 3.03297868408468e+00 , 5.90562677004631e+00 , -4.24900494521065e-01 , 3.68187352552472e+00 , 3.85349760041473e+00 , -1.47664328422220e+00 , 4.57525379165694e+00 , 3.53842027243101e+00 , -7.50500597797001e-01 , 5.38788478224042e+00 , 2.41547893958021e+00 , -2.73259299953855e+00 , 3.89277108698877e+00 , 2.93102326520036e+00 , -3.84965571878599e+00 , 4.43168040463526e+00 , 2.84656291791354e+00 , -2.58610776493422e+00 , 2.61135177328885e+00 , 2.48467675279635e+00 , -3.71585096120835e+00 , 1.91136898780560e+00 , 2.06147382208497e+00 , -3.41475456757105e+00 , 8.19430115626694e-01 , 9.77920904002122e-01 , -4.30319369163759e+00 , 1.08873703887392e+00 , 3.23727183327302e+00 , -5.53931615248954e+00 , 9.09261305140244e-01 , 3.34138637797004e+00 , -3.45823338391811e+00 , 6.41947152323478e-01 , 4.14507904545802e+00 , -3.77951295574175e+00 , 8.99051557558785e-02 , 5.48306332241890e+00 , -2.40231699169017e+00 , -3.87726330554989e-01 , 6.14643384948275e+00 , -4.47105640184983e+00 , 9.94873487392650e-01 , 6.41982204235366e+00 , -5.32296965964834e+00 , 6.04019223620338e-01 , 7.18648618529336e+00 , -6.29456138380652e+00 , 3.55403516950463e+00 , 6.70329666258755e+00 , -6.91254218250988e+00 , 4.29885508871224e+00 , 7.41956938479278e+00 , -6.74350405756560e+00 , 3.20882705802776e+00 , 5.51485123864818e+00 , -4.09208110184442e+00 , 2.30315441057814e+00 , 6.48279979579388e+00 , -4.89980266641929e+00 , 3.22702788570402e+00 , 7.21349381644343e+00 , -4.08302349660942e+00 , 4.52166291620917e+00 , 7.27530386008066e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 7. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 7. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atoms_new_colvar_forces = { ( -7.12643629297239e-02 , 3.03748456819681e-01 , -3.90586407900473e-01 ), ( 1.22798357354463e-02 , 3.43778085240195e-02 , -2.36779111668179e-01 ), ( -4.15369806328073e-02 , 9.13219268139160e-02 , 8.34694649792220e-02 ), ( -9.61814499206716e-02 , 2.43678342667974e-01 , 6.70597490320277e-02 ), ( -1.88857517066456e-02 , 9.94664433603135e-02 , -1.66338638098737e-01 ), ( 7.03279301363652e-02 , -1.80911714089215e-01 , -4.05099162241549e-02 ), ( 1.05581846145115e-02 , -1.01351207901457e-01 , 2.49133378748630e-01 ), ( -4.04801416450276e-02 , 5.62103343343931e-02 , 1.92581516655002e-01 ), ( 6.56492670474172e-02 , -1.87419378224912e-01 , 3.22551691858707e-02 ), ( 1.14361816218885e-01 , -3.88242959643882e-01 , 2.66491224123914e-01 ), ( 2.43089604741000e-02 , -9.93703389638662e-02 , 9.46656398079235e-02 ), ( 2.64633115886798e-02 , -9.72346559646698e-02 , 5.87788599655936e-02 ), ( 1.22773304643787e-02 , -5.60783277865503e-02 , 7.16482732771626e-02 ), ( 1.24200974597789e-02 , -5.37892737835383e-02 , 6.05804114728067e-02 ), ( 5.49126095479498e-03 , -3.56612002445240e-02 , 7.48531138676496e-02 ), ( -8.62632024734144e-03 , 8.44138021182977e-03 , 7.49358821822966e-02 ), ( -2.07165217509811e-03 , -3.42604475726390e-03 , 4.00622073248809e-02 ), ( -5.75844877153946e-03 , 9.13861103854014e-03 , 3.58460704568341e-02 ), ( 2.78830006708309e-03 , -1.35303913001015e-02 , 1.94867025441895e-02 ), ( 9.22664704378498e-03 , -2.23114382528987e-02 , -2.64045420530178e-02 ), ( 8.80594631376906e-03 , -2.38543535758261e-02 , -1.48409418464280e-02 ), ( 6.71696820112536e-03 , -1.35479989898134e-02 , -3.01259814853926e-02 ), ( 1.50787036067345e-02 , -4.65760405505027e-02 , -2.22907699732124e-03 ), ( 2.76085096907280e-02 , -8.79828374284034e-02 , 6.85982871925105e-03 ), ( 1.42543599808695e-02 , -4.66572795962589e-02 , 8.52471407991169e-03 ), ( 1.42060734830385e-02 , -4.36781388833885e-02 , -2.91933397806573e-03 ), ( 9.24045584481543e-03 , -3.70707957299862e-02 , 3.31426363027339e-02 ), ( -9.75223585295899e-04 , -1.56739823609265e-02 , 7.57558939840137e-02 ), ( -3.84312252210567e-03 , 3.94265579472862e-03 , 3.26486365211450e-02 ), ( -5.92538821370363e-03 , 1.10633157410566e-02 , 3.01692052913536e-02 ), ( -7.31580955849081e-03 , 1.75831579539413e-02 , 2.13714897525162e-02 ), ( -1.62116519386518e-02 , 5.14950342863534e-02 , -3.34714876103200e-03 ), ( -9.70559411338393e-03 , 3.56076117306303e-02 , -2.13396788115714e-02 ), ( -1.37377903715564e-02 , 4.98543287436506e-02 , -2.79939571721177e-02 ), ( -1.92056274355792e-03 , 1.48996290499974e-02 , -3.60009908034978e-02 ), ( 1.07022807165507e-02 , -1.54782919591166e-02 , -7.27155880541698e-02 ), ( 4.41705954600045e-03 , -4.63856402268646e-04 , -5.39834426064317e-02 ), ( 3.40728678849276e-03 , 6.46360802827689e-03 , -6.92444234215556e-02 ), ( 7.11828967127039e-03 , -1.44989851915113e-02 , -3.13532550881224e-02 ), ( 1.29877290166139e-02 , -4.09205362039969e-02 , 1.33018961029169e-03 ), ( 4.43689718407328e-04 , 2.06347307826285e-03 , -1.39606995589763e-02 ), ( 3.58444950702430e-04 , 3.77287300218497e-03 , -1.97995143891151e-02 ), ( -6.59855400003897e-03 , 2.06580134531091e-02 , -1.41289081215124e-04 ), ( -2.06804274679637e-02 , 5.75059489194441e-02 , 2.88448741084997e-02 ), ( -1.90124333628416e-02 , 6.32755773639386e-02 , -1.55954735441749e-02 ), ( -2.27327171854041e-02 , 7.52306358455108e-02 , -1.69214580765575e-02 ), ( -1.67727728860836e-02 , 7.26779069784233e-02 , -8.19646548939965e-02 ), ( -1.98340970554791e-02 , 8.68579024560199e-02 , -1.00627094487174e-01 ), ( -8.52210798867692e-03 , 4.69703868264598e-02 , -8.22846297106070e-02 ), ( -1.86033074160002e-02 , 6.66982592868968e-02 , -3.46189230904566e-02 ), ( -2.43020708962544e-02 , 9.27264054753276e-02 , -6.78689601911793e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 7, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 8, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 8, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 8, atoms_positions[size = 51] = { ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 ), ( 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 ), ( 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 ), ( 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 ), ( 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 ), ( 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 ), ( -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 ), ( -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 ), ( -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 ), ( -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ), ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 ), ( 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 ), ( 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 ), ( 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 ), ( 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 ), ( 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 ), ( 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 ), ( 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 ), ( 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 ), ( 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 ), ( 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 ), ( 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 ), ( 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 ), ( 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 ), ( 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 ), ( 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 ), ( 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 ), ( 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 ), ( 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 ), ( -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 ), ( 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 ), ( 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 ), ( -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 ), ( -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 ), ( -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 ), ( -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 ), ( -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 ), ( -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 ), ( -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 ), ( -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 ), ( -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 ), ( -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 ), ( -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 ), ( -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 ), ( -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 ), ( -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 ), ( -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 ), ( -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 ), ( -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 ), ( -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 ), ( -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ) } +colvars: Step 8, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 , 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 , 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 , 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 , 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 , 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 , 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 , 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 , 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 , 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 , 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 , 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 , 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 , 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 , 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 , -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 , 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 , -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 , -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 , -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 , -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 , -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 , -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 , -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 , -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 , -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 , -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 , -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 , -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 , -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 , -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 , -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 , -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99633583391618e-01 , 1.89110094148737e-02 , 1.32656390000757e-02 , -1.41101204978577e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.36833132438859e+00 , 4.43934708926255e-02 , -7.60180963998387e-01 , 6.99528850313611e+00 , -5.16438610719195e-01 , -6.40966413848880e-01 , 7.04523348286040e+00 , -2.02462487180273e+00 , -9.98677426967164e-01 , 6.25022423682295e+00 , -2.74968928395411e-01 , 6.76045720412779e-01 , 4.99308819284837e+00 , -2.02717140795631e-01 , 6.79141755377523e-01 , 6.89832748021001e+00 , -2.69625394056677e-01 , 1.82798239422403e+00 , 6.17489944055247e+00 , -1.18361589924746e-01 , 3.09939461551429e+00 , 7.14879067968497e+00 , -3.29031189602602e-01 , 4.28940839358242e+00 , 5.29375182165746e+00 , 1.11353824435599e+00 , 3.29985013313384e+00 , 4.09591506796936e+00 , 1.05834752950614e+00 , 3.63012867305904e+00 , 5.87601294876082e+00 , 2.28281758429074e+00 , 2.98560927408790e+00 , 5.21289853885864e+00 , 3.59564890954588e+00 , 2.88510421373726e+00 , 6.33881316429537e+00 , 4.57462414520981e+00 , 2.45080278305836e+00 , 3.90266200531784e+00 , 3.73538997718276e+00 , 2.02227093168697e+00 , 2.88279467514816e+00 , 4.11934561189460e+00 , 2.53976341924127e+00 , 3.83985288096449e+00 , 3.24076542891638e+00 , 7.64214295365312e-01 , 2.67279415759465e+00 , 3.13748892432531e+00 , -9.86697906806874e-02 , 3.04107502222025e+00 , 2.71999914916309e+00 , -1.59390972622565e+00 , 1.59102549258524e+00 , 2.15948958885121e+00 , 5.75131118152071e-01 , 4.39802901033422e-01 , 2.47019663554406e+00 , 5.45430074283381e-01 , 1.97005423601714e+00 , 1.01062281086216e+00 , 1.05605099074660e+00 , 1.16438507832880e+00 , 2.71102955066354e-02 , 1.69083013227601e+00 , 2.01599142897862e+00 , -1.16886635938915e+00 , 2.01708333913158e+00 , 5.30007578794117e-01 , 6.09144252240873e-01 , 2.97334591035292e+00 , -6.67067511924273e-01 , 3.64365718095462e-01 , 3.17822067827332e+00 , 1.31162492621363e+00 , 1.32577633806777e+00 , 3.83309165692328e+00 , 8.48171792185957e-01 , 1.91916556590780e+00 , 5.05866565319295e+00 , 2.04127814111075e+00 , 2.59946132988578e+00 , 5.62521048061959e+00 , -3.59611515076617e-01 , 2.91855540194787e+00 , 4.98265007360569e+00 , -1.16947246677972e+00 , 3.03630655326188e+00 , 5.90597990513468e+00 , -4.33110426330848e-01 , 3.67385585545878e+00 , 3.85054868135281e+00 , -1.47959692439097e+00 , 4.56869894194193e+00 , 3.53749299338068e+00 , -7.46058291703574e-01 , 5.39021246635441e+00 , 2.41921983239877e+00 , -2.74000410101420e+00 , 3.89050611309367e+00 , 2.92861465823649e+00 , -3.84676397633676e+00 , 4.43739472495013e+00 , 2.84271307643886e+00 , -2.59055260580353e+00 , 2.61363871408077e+00 , 2.47911480590441e+00 , -3.71619673143357e+00 , 1.90940802261531e+00 , 2.05572449969956e+00 , -3.41613863608816e+00 , 8.27072951793372e-01 , 9.69543447463883e-01 , -4.29869744321649e+00 , 1.08260730729523e+00 , 3.24243920560572e+00 , -5.53994692026642e+00 , 9.02364976712207e-01 , 3.33930332204511e+00 , -3.45175186425807e+00 , 6.46665636937359e-01 , 4.14078553668613e+00 , -3.77960603765112e+00 , 8.28285620991696e-02 , 5.48323895924115e+00 , -2.39647693359131e+00 , -3.76488347267693e-01 , 6.15081762532764e+00 , -4.47273303485509e+00 , 9.93133388916921e-01 , 6.42224814579644e+00 , -5.32330233976799e+00 , 6.06042472909534e-01 , 7.18864198442596e+00 , -6.29081304575991e+00 , 3.55690960234099e+00 , 6.70467446334067e+00 , -6.91247544807783e+00 , 4.29699704653349e+00 , 7.42158312906331e+00 , -6.74186871217538e+00 , 3.20863060180779e+00 , 5.51770917127955e+00 , -4.09709990880684e+00 , 2.30332167181807e+00 , 6.48281250046281e+00 , -4.89279578950952e+00 , 3.22089159910616e+00 , 7.21334427335935e+00 , -4.08703593420871e+00 , 4.53203131723470e+00 , 7.27950879050770e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 8. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 8. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atoms_new_colvar_forces = { ( -7.13351423072814e-02 , 3.03619825792168e-01 , -3.91268617939964e-01 ), ( 1.23055499660459e-02 , 3.39005917766654e-02 , -2.36845225742551e-01 ), ( -4.15271491397816e-02 , 9.13791618604163e-02 , 8.39245305411535e-02 ), ( -9.62494045652913e-02 , 2.44175455092806e-01 , 6.69902520302190e-02 ), ( -1.89222535399380e-02 , 9.94484271845721e-02 , -1.66816690819095e-01 ), ( 7.03822543304743e-02 , -1.81295378894829e-01 , -4.03686971085317e-02 ), ( 1.05834154712841e-02 , -1.01144992174696e-01 , 2.49623497290294e-01 ), ( -4.05271851974779e-02 , 5.67671746608100e-02 , 1.92455361027341e-01 ), ( 6.56724380837020e-02 , -1.87509424162519e-01 , 3.20679681604366e-02 ), ( 1.14456342649259e-01 , -3.88424805112911e-01 , 2.67062889902466e-01 ), ( 2.43422720664008e-02 , -9.93480134779911e-02 , 9.47584074895654e-02 ), ( 2.64823207884572e-02 , -9.72127013570268e-02 , 5.88563122381287e-02 ), ( 1.22945465945720e-02 , -5.60400376600130e-02 , 7.17161479237924e-02 ), ( 1.24370696655175e-02 , -5.37633069113443e-02 , 6.06388129855506e-02 ), ( 5.50290662739558e-03 , -3.56049421041009e-02 , 7.49181815458750e-02 ), ( -8.62594279342890e-03 , 8.52631563305040e-03 , 7.49889010438597e-02 ), ( -2.07304727561448e-03 , -3.37528964129997e-03 , 4.00961351411889e-02 ), ( -5.76061164789089e-03 , 9.18555649372060e-03 , 3.58710078036011e-02 ), ( 2.78174471784882e-03 , -1.34876115706386e-02 , 1.95148242584832e-02 ), ( 9.20812060560968e-03 , -2.22863671904896e-02 , -2.63960131935174e-02 ), ( 8.79752854486906e-03 , -2.38450026309957e-02 , -1.48322003035765e-02 ), ( 6.70483229466327e-03 , -1.35465340002202e-02 , -3.01308249087184e-02 ), ( 1.50788672216310e-02 , -4.65748402463062e-02 , -2.20698674250556e-03 ), ( 2.76224099666520e-02 , -8.80070809511392e-02 , 6.89732827922292e-03 ), ( 1.42640174897213e-02 , -4.66710917663395e-02 , 8.54621834415306e-03 ), ( 1.42152092039004e-02 , -4.37039689431695e-02 , -2.90768681103621e-03 ), ( 9.25385553881756e-03 , -3.70677988178844e-02 , 3.31746574587554e-02 ), ( -9.54216635819487e-04 , -1.56455971443210e-02 , 7.58025888278880e-02 ), ( -3.83453115114317e-03 , 3.95524868266385e-03 , 3.26636909607623e-02 ), ( -5.91561681798440e-03 , 1.10689709469262e-02 , 3.01775794099485e-02 ), ( -7.31568557729521e-03 , 1.76059473675832e-02 , 2.13787882331402e-02 ), ( -1.62280883237696e-02 , 5.15340202994481e-02 , -3.36079177638940e-03 ), ( -9.71731425170029e-03 , 3.56135592412924e-02 , -2.13634329163894e-02 ), ( -1.37515004753704e-02 , 4.98570258920335e-02 , -2.80282978586587e-02 ), ( -1.93274202187645e-03 , 1.48918151276390e-02 , -3.60249531028628e-02 ), ( 1.06868010425364e-02 , -1.55163054887531e-02 , -7.27491027760079e-02 ), ( 4.40947940082496e-03 , -5.04406089998534e-04 , -5.40176678525476e-02 ), ( 3.39692613696996e-03 , 6.41279540689518e-03 , -6.92913568633797e-02 ), ( 7.12007193986919e-03 , -1.45391352614655e-02 , -3.13716172491232e-02 ), ( 1.30066812693670e-02 , -4.09701058428207e-02 , 1.33447796586508e-03 ), ( 4.52637477376299e-04 , 2.02121811019218e-03 , -1.39809114433900e-02 ), ( 3.68871321751043e-04 , 3.71941944337000e-03 , -1.98264904541570e-02 ), ( -6.59155139229773e-03 , 2.06356960691847e-02 , -1.58597446801268e-04 ), ( -2.06741434674982e-02 , 5.75159193607011e-02 , 2.88316092525700e-02 ), ( -1.90154049605807e-02 , 6.32603313301187e-02 , -1.56372478319434e-02 ), ( -2.27354870994093e-02 , 7.52121778503086e-02 , -1.69705931059206e-02 ), ( -1.67945805077401e-02 , 7.26394386828972e-02 , -8.20447054617394e-02 ), ( -1.98624280707300e-02 , 8.68154008280787e-02 , -1.00722691225296e-01 ), ( -8.53818784940370e-03 , 4.69173202401635e-02 , -8.23570774196874e-02 ), ( -1.86144965450949e-02 , 6.66844476645427e-02 , -3.46693975793695e-02 ), ( -2.43304588010985e-02 , 9.27214764030262e-02 , -6.79422921811020e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 8, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 9, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 9, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 9, atoms_positions[size = 51] = { ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 ), ( 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 ), ( 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 ), ( 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 ), ( 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 ), ( 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 ), ( -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 ), ( -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 ), ( -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 ), ( -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ), ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 ), ( 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 ), ( 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 ), ( 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 ), ( 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 ), ( 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 ), ( 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 ), ( 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 ), ( 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 ), ( 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 ), ( 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 ), ( 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 ), ( 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 ), ( 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 ), ( 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 ), ( 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 ), ( 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 ), ( 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 ), ( 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 ), ( -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 ), ( 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 ), ( 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 ), ( -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 ), ( -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 ), ( -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 ), ( -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 ), ( -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 ), ( -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 ), ( -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 ), ( -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 ), ( -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 ), ( -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 ), ( -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 ), ( -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 ), ( -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 ), ( -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 ), ( -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 ), ( -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 ), ( -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 ), ( -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 ), ( -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ) } +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 , 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 , 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 , 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 , 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 , 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 , 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 , 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 , 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 , 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 , 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 , 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 , 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 , 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 , 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 , -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 , 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 , -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 , -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 , -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 , -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 , -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 , -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 , -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 , -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 , -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 , -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 , -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 , -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 , -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 , -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 , -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 , -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99649095329186e-01 , 1.84993129310618e-02 , 1.30478775114131e-02 , -1.37555269279325e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.36145075364823e+00 , 4.45673478283171e-02 , -7.61579829689750e-01 , 6.99604136943189e+00 , -5.22210029829872e-01 , -6.36813930225694e-01 , 7.04705412400806e+00 , -2.02657433420527e+00 , -9.92328433861711e-01 , 6.24277750477489e+00 , -2.81832722071801e-01 , 6.80270010272083e-01 , 4.99149263691403e+00 , -2.00348785252590e-01 , 6.84309976585855e-01 , 6.89692847538012e+00 , -2.69256718701896e-01 , 1.83457449207068e+00 , 6.17528903888770e+00 , -1.18078238391021e-01 , 3.11379838275944e+00 , 7.13899448370598e+00 , -3.32243969454574e-01 , 4.28649579451921e+00 , 5.28951700950140e+00 , 1.11272371692947e+00 , 3.30429948201705e+00 , 4.10064483705416e+00 , 1.05511277440733e+00 , 3.63333556451041e+00 , 5.87540800816707e+00 , 2.27380668663418e+00 , 2.98947006194145e+00 , 5.21229610143475e+00 , 3.59538603514599e+00 , 2.88721543535589e+00 , 6.33858295523802e+00 , 4.56401302496245e+00 , 2.44679597912864e+00 , 3.90512041196910e+00 , 3.73827201132192e+00 , 2.02394895334967e+00 , 2.87258047870294e+00 , 4.12189410892633e+00 , 2.53557019974883e+00 , 3.84723562431753e+00 , 3.24033692494038e+00 , 7.59411592473856e-01 , 2.67222487877334e+00 , 3.12382798563393e+00 , -1.01542594027123e-01 , 3.03861425188410e+00 , 2.72006297496799e+00 , -1.58919983219425e+00 , 1.58258940960968e+00 , 2.16527437086414e+00 , 5.67970202348528e-01 , 4.40300252054749e-01 , 2.47807179810672e+00 , 5.42134092013262e-01 , 1.97190822649951e+00 , 1.00816777213968e+00 , 1.05899653496919e+00 , 1.16998741006824e+00 , 3.51934907576078e-02 , 1.69141678601589e+00 , 2.01699455968664e+00 , -1.16282948687959e+00 , 2.01505316439218e+00 , 5.34991863186303e-01 , 6.10371297946844e-01 , 2.96376519450520e+00 , -6.63693698828810e-01 , 3.61151989769718e-01 , 3.17642302876694e+00 , 1.31583519692667e+00 , 1.32964699417878e+00 , 3.83496983865264e+00 , 8.52806149428176e-01 , 1.92536167438748e+00 , 5.05335845985683e+00 , 2.03642019466534e+00 , 2.60352231095478e+00 , 5.62700223797633e+00 , -3.58416257523471e-01 , 2.91803751681466e+00 , 4.98137878962374e+00 , -1.16731458344385e+00 , 3.03952614661121e+00 , 5.90605580610089e+00 , -4.41252775351204e-01 , 3.66457849200493e+00 , 3.84827767287246e+00 , -1.48247649205562e+00 , 4.56307453395484e+00 , 3.53544060277815e+00 , -7.41494856267345e-01 , 5.39244616151430e+00 , 2.42335798603898e+00 , -2.74735638382253e+00 , 3.88786934907987e+00 , 2.92631370831390e+00 , -3.84348752401645e+00 , 4.44315861156885e+00 , 2.83914528098142e+00 , -2.59428734470466e+00 , 2.61756159551567e+00 , 2.47347127439062e+00 , -3.71792098567530e+00 , 1.90478284574262e+00 , 2.04952767988583e+00 , -3.41702260113198e+00 , 8.34956600851077e-01 , 9.60940980855217e-01 , -4.29621631979332e+00 , 1.07721841750517e+00 , 3.24657544287079e+00 , -5.53959957396026e+00 , 8.95521734053795e-01 , 3.33729868492281e+00 , -3.44483130650705e+00 , 6.51529850552197e-01 , 4.13839946637360e+00 , -3.77794048245888e+00 , 7.50299005262543e-02 , 5.48199228253982e+00 , -2.39169273154641e+00 , -3.65432098738083e-01 , 6.15507203477771e+00 , -4.47395459710911e+00 , 9.92677075624979e-01 , 6.42517037038473e+00 , -5.32418942859539e+00 , 6.07577020497688e-01 , 7.19095096164881e+00 , -6.28555898805946e+00 , 3.55986394292245e+00 , 6.70585729059817e+00 , -6.91356276773258e+00 , 4.29577575673444e+00 , 7.42433194638229e+00 , -6.74131314486554e+00 , 3.20825629440854e+00 , 5.52012743236282e+00 , -4.10232305344530e+00 , 2.30215197267053e+00 , 6.48166730861349e+00 , -4.88482867810761e+00 , 3.21465407558299e+00 , 7.21341846220008e+00 , -4.09063379459981e+00 , 4.54257145508993e+00 , 7.28372178997338e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 9. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 9. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atoms_new_colvar_forces = { ( -7.14173720653988e-02 , 3.03520052049551e-01 , -3.92009785651569e-01 ), ( 1.23342420189076e-02 , 3.34051155343946e-02 , -2.36921588255221e-01 ), ( -4.15241266423430e-02 , 9.14514427042299e-02 , 8.44297030591049e-02 ), ( -9.63331533612292e-02 , 2.44725046427125e-01 , 6.69280120891988e-02 ), ( -1.89607984864654e-02 , 9.94393414177423e-02 , -1.67339404363429e-01 ), ( 7.04476436573704e-02 , -1.81717278785775e-01 , -4.02242178643844e-02 ), ( 1.06089134397880e-02 , -1.00937973904036e-01 , 2.50161143716076e-01 ), ( -4.05803503902119e-02 , 5.73562046068344e-02 , 1.92324357692035e-01 ), ( 6.57073059950226e-02 , -1.87627270111012e-01 , 3.18539040038509e-02 ), ( 1.14568853707169e-01 , -3.88658891277374e-01 , 2.67675620853643e-01 ), ( 2.43802816273955e-02 , -9.93281874098511e-02 , 9.48558475196411e-02 ), ( 2.65037845454748e-02 , -9.71909867682365e-02 , 5.89362890305023e-02 ), ( 1.23143907242286e-02 , -5.60007579469612e-02 , 7.17881814673141e-02 ), ( 1.24565401286085e-02 , -5.37373630896944e-02 , 6.07005352450290e-02 ), ( 5.51661482992865e-03 , -3.55455043228473e-02 , 7.49881872869175e-02 ), ( -8.62469301701959e-03 , 8.61819191963212e-03 , 7.50479617281995e-02 ), ( -2.07424105302506e-03 , -3.32003763727390e-03 , 4.01332666040666e-02 ), ( -5.76263256060389e-03 , 9.23667566792744e-03 , 3.58990112766273e-02 ), ( 2.77442962802959e-03 , -1.34400622886135e-02 , 1.95446294702857e-02 ), ( 9.18672312511947e-03 , -2.22559787396961e-02 , -2.63889931974540e-02 ), ( 8.78768419625598e-03 , -2.38332647478741e-02 , -1.48245460439309e-02 ), ( 6.69069192888831e-03 , -1.35428452060799e-02 , -3.01376619569618e-02 ), ( 1.50787137839697e-02 , -4.65730867592132e-02 , -2.18567840461609e-03 ), ( 2.76376217799769e-02 , -8.80346894842446e-02 , 6.93358865624684e-03 ), ( 1.42747227515129e-02 , -4.66871377959406e-02 , 8.56734570785393e-03 ), ( 1.42252270283724e-02 , -4.37329821937682e-02 , -2.89726261151908e-03 ), ( 9.26911427579751e-03 , -3.70663365654843e-02 , 3.32082031893864e-02 ), ( -9.29764348433053e-04 , -1.56180778191128e-02 , 7.58541079446727e-02 ), ( -3.82444347630877e-03 , 3.96746298948433e-03 , 3.26809834852590e-02 ), ( -5.90417007842336e-03 , 1.10734044656187e-02 , 3.01880303085623e-02 ), ( -7.31520771406639e-03 , 1.76304377592534e-02 , 2.13880036242598e-02 ), ( -1.62463832765020e-02 , 5.15783873773706e-02 , -3.37326477439168e-03 ), ( -9.73056072304786e-03 , 3.56215314413404e-02 , -2.13878722217663e-02 ), ( -1.37669713898938e-02 , 4.98616515224361e-02 , -2.80635756631084e-02 ), ( -1.94679852005065e-03 , 1.48851647538968e-02 , -3.60510088394936e-02 ), ( 1.06684267389560e-02 , -1.55548296526290e-02 , -7.27878605475705e-02 ), ( 4.40034243909777e-03 , -5.47109796954631e-04 , -5.40558287094212e-02 ), ( 3.38453211590400e-03 , 6.35935043890289e-03 , -6.93432179144250e-02 ), ( 7.12167142475610e-03 , -1.45827751867512e-02 , -3.13927394832841e-02 ), ( 1.30278759427845e-02 , -4.10264554725313e-02 , 1.33745297410013e-03 ), ( 4.62640012449613e-04 , 1.97396863527872e-03 , -1.40026278660333e-02 ), ( 3.80499989890731e-04 , 3.65978008219713e-03 , -1.98554826335769e-02 ), ( -6.58348401757126e-03 , 2.06101712556980e-02 , -1.75982618459972e-04 ), ( -2.06663438231585e-02 , 5.75251140088467e-02 , 2.88210760175877e-02 ), ( -1.90184995833039e-02 , 6.32436419183767e-02 , -1.56793092131453e-02 ), ( -2.27382858128587e-02 , 7.51918527306527e-02 , -1.70199767768858e-02 ), ( -1.68196160872486e-02 , 7.26005373823680e-02 , -8.21293047577027e-02 ), ( -1.98949441245263e-02 , 8.67730382686525e-02 , -1.00823829224095e-01 ), ( -8.55691582416120e-03 , 4.68619408623113e-02 , -8.24346991593813e-02 ), ( -1.86270664811170e-02 , 6.66706057166006e-02 , -3.47212383429930e-02 ), ( -2.43626649786876e-02 , 9.27197710252339e-02 , -6.80184858556002e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 9, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 10, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 10, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 10, atoms_positions[size = 51] = { ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 ), ( 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 ), ( 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 ), ( 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 ), ( 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 ), ( 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 ), ( -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 ), ( -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 ), ( -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 ), ( -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ), ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 ), ( 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 ), ( 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 ), ( 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 ), ( 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 ), ( 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 ), ( 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 ), ( 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 ), ( 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 ), ( 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 ), ( 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 ), ( 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 ), ( 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 ), ( 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 ), ( 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 ), ( 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 ), ( 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 ), ( 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 ), ( 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 ), ( -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 ), ( 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 ), ( 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 ), ( -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 ), ( -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 ), ( -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 ), ( -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 ), ( -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 ), ( -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 ), ( -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 ), ( -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 ), ( -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 ), ( -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 ), ( -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 ), ( -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 ), ( -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 ), ( -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 ), ( -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 ), ( -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 ), ( -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 ), ( -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 ), ( -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ) } +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ). +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 , 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 , 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 , 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 , 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 , 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 , 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 , 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 , 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 , 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 , 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 , 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 , 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 , 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 , 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 , -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 , 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 , -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 , -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 , -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 , -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 , -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 , -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 , -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 , -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 , -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 , -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 , -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 , -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 , -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 , -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 , -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 , -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99665180783326e-01 , 1.80578221627132e-02 , 1.28211421276123e-02 , -1.33813191698144e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.35477480411234e+00 , 4.46452263478150e-02 , -7.62549920991796e-01 , 6.99685729581585e+00 , -5.27550773628815e-01 , -6.32755459852362e-01 , 7.04887809505237e+00 , -2.02855689794704e+00 , -9.86013471634436e-01 , 6.23335865279305e+00 , -2.89310935566490e-01 , 6.84038685634360e-01 , 4.99076223603795e+00 , -1.97665737562761e-01 , 6.89323641141128e-01 , 6.89531949305107e+00 , -2.68783075747803e-01 , 1.84092728736346e+00 , 6.17570248575583e+00 , -1.18554504717775e-01 , 3.12842467153601e+00 , 7.12911451274543e+00 , -3.35615802382476e-01 , 4.28401738527316e+00 , 5.28545466263458e+00 , 1.11221039883597e+00 , 3.30852459277801e+00 , 4.10574619865898e+00 , 1.05187646500509e+00 , 3.63656924399137e+00 , 5.87419167605169e+00 , 2.26576952450680e+00 , 2.99258842324373e+00 , 5.21287275499848e+00 , 3.59491326869358e+00 , 2.88980876817943e+00 , 6.33777159996139e+00 , 4.55382872169931e+00 , 2.44235667425442e+00 , 3.90729289001123e+00 , 3.73995045180771e+00 , 2.02597536644746e+00 , 2.86215468569898e+00 , 4.12491539720393e+00 , 2.53151900530142e+00 , 3.85553701789686e+00 , 3.24011620958211e+00 , 7.54708692293085e-01 , 2.67061475873242e+00 , 3.10968354326322e+00 , -1.03879800011152e-01 , 3.03632973551881e+00 , 2.72057541856768e+00 , -1.58286838988123e+00 , 1.57625221316487e+00 , 2.17189322730777e+00 , 5.58819998005006e-01 , 4.39403821284586e-01 , 2.48626423532292e+00 , 5.39064272715199e-01 , 1.97505140182751e+00 , 1.00551669003055e+00 , 1.06263166413761e+00 , 1.17463368630194e+00 , 4.45741342092704e-02 , 1.69179979088251e+00 , 2.01834260822414e+00 , -1.15679143108512e+00 , 2.01297912838100e+00 , 5.39492773006123e-01 , 6.10807165406729e-01 , 2.95457758137249e+00 , -6.59861594760723e-01 , 3.58364539388519e-01 , 3.17481009330639e+00 , 1.31940942862955e+00 , 1.33332040858045e+00 , 3.83601159257540e+00 , 8.56383787488820e-01 , 1.93143861846319e+00 , 5.04824293038868e+00 , 2.03271069000520e+00 , 2.60811693359759e+00 , 5.62922696256203e+00 , -3.56592830717266e-01 , 2.91759444609820e+00 , 4.97984005160742e+00 , -1.16515067761032e+00 , 3.04261050195828e+00 , 5.90585393921245e+00 , -4.49207347619985e-01 , 3.65411235349798e+00 , 3.84672553975421e+00 , -1.48542977715116e+00 , 4.55846003971702e+00 , 3.53212702372989e+00 , -7.36816181838931e-01 , 5.39458342493432e+00 , 2.42777660497367e+00 , -2.75427791601535e+00 , 3.88497035990242e+00 , 2.92409422976728e+00 , -3.84001536642960e+00 , 4.44899809009598e+00 , 2.83584120784881e+00 , -2.59736608126414e+00 , 2.62297492137127e+00 , 2.46776435292465e+00 , -3.72092739165117e+00 , 1.89768935999766e+00 , 2.04303601045692e+00 , -3.41732711640451e+00 , 8.42868939225701e-01 , 9.52188691723741e-01 , -4.29583296165753e+00 , 1.07274949616062e+00 , 3.24932158331341e+00 , -5.53820488962033e+00 , 8.88711557879661e-01 , 3.33543419387210e+00 , -3.43749430849264e+00 , 6.56325195426439e-01 , 4.13819153204507e+00 , -3.77461025071102e+00 , 6.69354478076759e-02 , 5.47931021025865e+00 , -2.38795654873457e+00 , -3.54876292088308e-01 , 6.15910202957390e+00 , -4.47466143517465e+00 , 9.93363801816784e-01 , 6.42840016686351e+00 , -5.32565803211370e+00 , 6.08588468417515e-01 , 7.19343220275153e+00 , -6.27900028229557e+00 , 3.56284258559166e+00 , 6.70694513379705e+00 , -6.91572640939554e+00 , 4.29516136402317e+00 , 7.42778842609735e+00 , -6.74175012067999e+00 , 3.20766691457969e+00 , 5.52198528500281e+00 , -4.10754620839186e+00 , 2.29960049445239e+00 , 6.47927928044027e+00 , -4.87617405262811e+00 , 3.20862813420942e+00 , 7.21376710962358e+00 , -4.09384256540903e+00 , 4.55285072092665e+00 , 7.28763584806825e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 10. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atoms_new_colvar_forces = { ( -7.15016607715429e-02 , 3.03450248290296e-01 , -3.92801115143173e-01 ), ( 1.23676636514961e-02 , 3.29036024770241e-02 , -2.37009333522469e-01 ), ( -4.15294698469745e-02 , 9.15434694739861e-02 , 8.49684851875917e-02 ), ( -9.64292968119024e-02 , 2.45317517705941e-01 , 6.68684776651641e-02 ), ( -1.89969183888788e-02 , 9.94364123729833e-02 , -1.67895921441165e-01 ), ( 7.05212056674244e-02 , -1.82169054972534e-01 , -4.00760890945773e-02 ), ( 1.06299188456399e-02 , -1.00732179998986e-01 , 2.50735712205887e-01 ), ( -4.06390391411500e-02 , 5.79627727319513e-02 , 1.92192742745201e-01 ), ( 6.57521305972952e-02 , -1.87775429438928e-01 , 3.16250898809561e-02 ), ( 1.14690118965508e-01 , -3.88940933598096e-01 , 2.68325226130177e-01 ), ( 2.44215543618544e-02 , -9.93121128890011e-02 , 9.49576777085680e-02 ), ( 2.65268959319662e-02 , -9.71711911284568e-02 , 5.90180610098199e-02 ), ( 1.23360273326501e-02 , -5.59616922094030e-02 , 7.18637286173737e-02 ), ( 1.24777272206467e-02 , -5.37123954054054e-02 , 6.07651560900780e-02 ), ( 5.53170505664087e-03 , -3.54841808979951e-02 , 7.50622055553943e-02 ), ( -8.62291255185738e-03 , 8.71572042334938e-03 , 7.51117297407181e-02 ), ( -2.07535676767600e-03 , -3.26128095343407e-03 , 4.01726641337359e-02 ), ( -5.76460113859216e-03 , 9.29126628119513e-03 , 3.59293100500467e-02 ), ( 2.76649955079081e-03 , -1.33889700503236e-02 , 1.95750408014193e-02 ), ( 9.16320150588288e-03 , -2.22217657715011e-02 , -2.63847478136887e-02 ), ( 8.77677580102877e-03 , -2.38200554097055e-02 , -1.48186594740397e-02 ), ( 6.67509070954949e-03 , -1.35376306408063e-02 , -3.01470585284635e-02 ), ( 1.50782845708932e-02 , -4.65717205649902e-02 , -2.16564122789622e-03 ), ( 2.76537239190706e-02 , -8.80665291346260e-02 , 6.96858447717808e-03 ), ( 1.42861554171493e-02 , -4.67057844220242e-02 , 8.58817479450385e-03 ), ( 1.42358707997841e-02 , -4.37652957110214e-02 , -2.88776698081043e-03 ), ( 9.28567383034640e-03 , -3.70667515371096e-02 , 3.32432904895662e-02 ), ( -9.02878066972215e-04 , -1.55915280171617e-02 , 7.59105106601410e-02 ), ( -3.81328853416053e-03 , 3.97944496036693e-03 , 3.27006272124911e-02 ), ( -5.89151124666768e-03 , 1.10770632059042e-02 , 3.02008998913624e-02 ), ( -7.31448604032661e-03 , 1.76565883927560e-02 , 2.13989346487279e-02 ), ( -1.62660173524484e-02 , 5.16279375578137e-02 , -3.38524703866288e-03 ), ( -9.74488071294648e-03 , 3.56317430010617e-02 , -2.14131237375987e-02 ), ( -1.37836669147457e-02 , 4.98686933275604e-02 , -2.80997837478720e-02 ), ( -1.96218459227142e-03 , 1.48797039895180e-02 , -3.60792790294987e-02 ), ( 1.06479972601358e-02 , -1.55940292832885e-02 , -7.28318919398761e-02 ), ( 4.39013310678057e-03 , -5.91527552862377e-04 , -5.40974975810518e-02 ), ( 3.37074168129652e-03 , 6.30393571727346e-03 , -6.93994276341061e-02 ), ( 7.12317534535211e-03 , -1.46294393396425e-02 , -3.14160328614953e-02 ), ( 1.30507102522968e-02 , -4.10889103847666e-02 , 1.34016377943251e-03 ), ( 4.73458451596487e-04 , 1.92279396386438e-03 , -1.40248176248883e-02 ), ( 3.93066712348846e-04 , 3.59530102454659e-03 , -1.98852042495396e-02 ), ( -6.57460039163597e-03 , 2.05824681853940e-02 , -1.92624994433700e-04 ), ( -2.06574072402663e-02 , 5.75347116778676e-02 , 2.88139007127607e-02 ), ( -1.90216018460062e-02 , 6.32269308398371e-02 , -1.57208546495785e-02 ), ( -2.27410084662747e-02 , 7.51713819207301e-02 , -1.70686233836183e-02 ), ( -1.68468604051727e-02 , 7.25625867508809e-02 , -8.22177879392403e-02 ), ( -1.99303402800334e-02 , 8.67323329271237e-02 , -1.00929847872743e-01 ), ( -8.57744112834064e-03 , 4.68055646721169e-02 , -8.25166553580956e-02 ), ( -1.86405497075895e-02 , 6.66579250535560e-02 , -3.47739046838852e-02 ), ( -2.43975282009917e-02 , 9.27222723871716e-02 , -6.80974566358273e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 10, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 11, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 11, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 11, atoms_positions[size = 51] = { ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 ), ( 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 ), ( 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 ), ( 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 ), ( 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 ), ( 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 ), ( -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 ), ( -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 ), ( -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 ), ( -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ), ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 ), ( 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 ), ( 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 ), ( 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 ), ( 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 ), ( 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 ), ( 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 ), ( 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 ), ( 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 ), ( 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 ), ( 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 ), ( 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 ), ( 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 ), ( 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 ), ( 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 ), ( 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 ), ( 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 ), ( 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 ), ( 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 ), ( -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 ), ( 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 ), ( 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 ), ( -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 ), ( -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 ), ( -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 ), ( -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 ), ( -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 ), ( -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 ), ( -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 ), ( -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 ), ( -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 ), ( -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 ), ( -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 ), ( -2.38523274426801e+00 , -3.45124047741375e-01 , 6.16281301316000e+00 ), ( -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 ), ( -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 ), ( -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 ), ( -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 ), ( -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 ), ( -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 ), ( -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ) } +colvars: Step 11, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 , 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 , 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 , 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 , 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 , 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 , 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 , 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 , 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 , 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 , 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 , 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 , 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 , 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 , 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 , -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 , 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 , -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 , -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 , -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 , -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 , -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 , -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 , -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 , -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 , -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -2.38523274426801e+00 , -3.45124047741375e-01 , 6.16281301316000e+00 , -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 , -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 , -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 , -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 , -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 , -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 , -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99681277561034e-01 , 1.75948472438382e-02 , 1.25943706821570e-02 , -1.30056323000774e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.34834848366664e+00 , 4.46188008242361e-02 , -7.63043787616505e-01 , 6.99744235445820e+00 , -5.32307908543297e-01 , -6.28633923643096e-01 , 7.05062445826066e+00 , -2.03060871750107e+00 , -9.79816521182622e-01 , 6.22262264173815e+00 , -2.97310116726025e-01 , 6.87496438430098e-01 , 4.99064261229795e+00 , -1.94699744063865e-01 , 6.94162954988490e-01 , 6.89338315086737e+00 , -2.68232750014463e-01 , 1.84708936551995e+00 , 6.17600411795125e+00 , -1.19867052913378e-01 , 3.14269768468219e+00 , 7.11940530720541e+00 , -3.39036437515264e-01 , 4.28218450827047e+00 , 5.28193814298392e+00 , 1.11179409809971e+00 , 3.31254927079100e+00 , 4.11093487287345e+00 , 1.04866349648595e+00 , 3.63989245737134e+00 , 5.87230129061570e+00 , 2.25894924945293e+00 , 2.99495017962971e+00 , 5.21460592048269e+00 , 3.59415565644891e+00 , 2.89286602621248e+00 , 6.33647025826830e+00 , 4.54427314311706e+00 , 2.43736196557291e+00 , 3.90884671168934e+00 , 3.74046861793149e+00 , 2.02822681634682e+00 , 2.85177317416038e+00 , 4.12831773551428e+00 , 2.52753566768619e+00 , 3.86460490867190e+00 , 3.24012243605601e+00 , 7.50273725118491e-01 , 2.66808098041192e+00 , 3.09530303290627e+00 , -1.05733909298262e-01 , 3.03438824028088e+00 , 2.72131377276621e+00 , -1.57522506108074e+00 , 1.57234000702318e+00 , 2.17870417742848e+00 , 5.48034391349972e-01 , 4.36968480777708e-01 , 2.49482675576059e+00 , 5.36179486047533e-01 , 1.97940835714024e+00 , 1.00331926227253e+00 , 1.06662623240972e+00 , 1.17818450296468e+00 , 5.48214125119605e-02 , 1.69197658179989e+00 , 2.01999063139476e+00 , -1.15076833955646e+00 , 2.01097350351278e+00 , 5.43434949940235e-01 , 6.10645067589934e-01 , 2.94626177836360e+00 , -6.55505207604621e-01 , 3.56005212412589e-01 , 3.17331094595996e+00 , 1.32231132461098e+00 , 1.33665481260799e+00 , 3.83589978604366e+00 , 8.58811474311505e-01 , 1.93737695671854e+00 , 5.04347487531459e+00 , 2.03047994347406e+00 , 2.61333374621237e+00 , 5.63196608685044e+00 , -3.54259151433208e-01 , 2.91724334977185e+00 , 4.97806851365945e+00 , -1.16294733493550e+00 , 3.04553538328627e+00 , 5.90536605535984e+00 , -4.56879664376415e-01 , 3.64259117777091e+00 , 3.84588280091643e+00 , -1.48857584621877e+00 , 4.55485406914166e+00 , 3.52746461826982e+00 , -7.32047213986828e-01 , 5.39664038234788e+00 , 2.43234423311210e+00 , -2.76041675699967e+00 , 3.88197765890975e+00 , 2.92193340809934e+00 , -3.83652422169110e+00 , 4.45493227727480e+00 , 2.83278384730017e+00 , -2.59989367222107e+00 , 2.62960747293448e+00 , 2.46198290704097e+00 , -3.72505157732567e+00 , 1.88848863910969e+00 , 2.03642694676304e+00 , -3.41699835571450e+00 , 8.50596758336586e-01 , 9.43380129855806e-01 , -4.29744061047398e+00 , 1.06930888022537e+00 , 3.25044735157309e+00 , -5.53578705028646e+00 , 8.81914030084522e-01 , 3.33376580674255e+00 , -3.42979771138309e+00 , 6.60887381218130e-01 , 4.14026480929848e+00 , -3.76978320280503e+00 , 5.90040335534210e-02 , 5.47530212205500e+00 , -2.38523274426801e+00 , -3.45124047741375e-01 , 6.16281301316000e+00 , -4.47481664158478e+00 , 9.94936038658081e-01 , 6.43172980700564e+00 , -5.32770555986823e+00 , 6.09071280786047e-01 , 7.19608836904477e+00 , -6.27146467185910e+00 , 3.56585656890232e+00 , 6.70806714680862e+00 , -6.91883719799925e+00 , 4.29507940659948e+00 , 7.43188260163705e+00 , -6.74301068526221e+00 , 3.20681331943173e+00 , 5.52317951299923e+00 , -4.11256626281446e+00 , 2.29573272170620e+00 , 6.47562070931801e+00 , -4.86711787558259e+00 , 3.20310981073614e+00 , 7.21446286923602e+00 , -4.09669648835136e+00 , 4.56244730379719e+00 , 7.29096166806618e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 11. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 11. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atoms_new_colvar_forces = { ( -7.15791435066877e-02 , 3.03409844462010e-01 , -3.93631147743522e-01 ), ( 1.24067694561056e-02 , 3.24092617088106e-02 , -2.37109313249408e-01 ), ( -4.15443493045436e-02 , 9.16594876814856e-02 , 8.55215908680847e-02 ), ( -9.65336402837814e-02 , 2.45940639162059e-01 , 6.68066014202904e-02 ), ( -1.90264360132423e-02 , 9.94362277505718e-02 , -1.68473121692907e-01 ), ( 7.05994752262470e-02 , -1.82640351786385e-01 , -3.99240593208832e-02 ), ( 1.06422393313364e-02 , -1.00529505736157e-01 , 2.51334253191404e-01 ), ( -4.07018668681346e-02 , 5.85704993383106e-02 , 1.92065217655378e-01 ), ( 6.58048500158185e-02 , -1.87955153690664e-01 , 3.13953139770057e-02 ), ( 1.14810836548122e-01 , -3.89263845763161e-01 , 2.69005747608971e-01 ), ( 2.44644420365523e-02 , -9.93008604362819e-02 , 9.50634540303170e-02 ), ( 2.65506639926814e-02 , -9.71549085398046e-02 , 5.91007414354448e-02 ), ( 1.23585185415142e-02 , -5.59239645083762e-02 , 7.19419408988772e-02 ), ( 1.24997439276150e-02 , -5.36892724561222e-02 , 6.08321053385152e-02 ), ( 5.54744932916617e-03 , -3.54222256237558e-02 , 7.51390424022061e-02 ), ( -8.62087934123941e-03 , 8.81757783726286e-03 , 7.51785053849693e-02 ), ( -2.07649081258038e-03 , -3.20004659983505e-03 , 4.02131668863943e-02 ), ( -5.76656001638263e-03 , 9.34859228802995e-03 , 3.59609344382249e-02 ), ( 2.75811391441254e-03 , -1.33356313310754e-02 , 1.96047867239134e-02 ), ( 9.13831399376692e-03 , -2.21853675629404e-02 , -2.63846638597659e-02 ), ( 8.76514693055518e-03 , -2.38063605419795e-02 , -1.48152755324360e-02 ), ( 6.65857259966535e-03 , -1.35316767744980e-02 , -3.01595939520679e-02 ), ( 1.50775434890925e-02 , -4.65716981852416e-02 , -2.14739829676824e-03 ), ( 2.76701085567005e-02 , -8.81033908999233e-02 , 7.00234061373576e-03 ), ( 1.42978914433128e-02 , -4.67273424783863e-02 , 8.60881480028640e-03 ), ( 1.42467794788397e-02 , -4.38009674766436e-02 , -2.87882066252855e-03 ), ( 9.30289142383668e-03 , -3.70693093754740e-02 , 3.32798991260648e-02 ), ( -8.74616788559086e-04 , -1.55659268803168e-02 , 7.59717207069584e-02 ), ( -3.80149697823639e-03 , 3.99139497661139e-03 , 3.27226818702287e-02 ), ( -5.87809955712979e-03 , 1.10804620992656e-02 , 3.02165111697874e-02 ), ( -7.31358799819382e-03 , 1.76843548454293e-02 , 2.14112914406596e-02 ), ( -1.62863320779151e-02 , 5.16823604558912e-02 , -3.39755451020750e-03 ), ( -9.75973706289892e-03 , 3.56443383847642e-02 , -2.14393173203162e-02 ), ( -1.38009410110882e-02 , 4.98785618144178e-02 , -2.81368949956214e-02 ), ( -1.97831014138354e-03 , 1.48753846947269e-02 , -3.61098401943824e-02 ), ( 1.06263319165018e-02 , -1.56341624769058e-02 , -7.28810696503613e-02 ), ( 4.37932488352575e-03 , -6.37252128288097e-04 , -5.41420695521195e-02 ), ( 3.35619138322245e-03 , 6.24716942821834e-03 , -6.94591804691144e-02 ), ( 7.12461969116057e-03 , -1.46786360570569e-02 , -3.14407424751560e-02 ), ( 1.30744491935402e-02 , -4.11566574770348e-02 , 1.34384855831248e-03 ), ( 4.84816048636927e-04 , 1.86884529652323e-03 , -1.40462649459062e-02 ), ( 4.06262902972097e-04 , 3.52742628407923e-03 , -1.99141343288618e-02 ), ( -6.56514050363636e-03 , 2.05536818096240e-02 , -2.07595716940282e-04 ), ( -2.06476219371302e-02 , 5.75459498804657e-02 , 2.88107008122013e-02 ), ( -1.90244943026149e-02 , 6.32116292719994e-02 , -1.57609754741589e-02 ), ( -2.27434304429232e-02 , 7.51525034805505e-02 , -1.71154202691943e-02 ), ( -1.68751559011819e-02 , 7.25268655901675e-02 , -8.23092755311854e-02 ), ( -1.99671400786953e-02 , 8.66946604746157e-02 , -1.01039844952936e-01 ), ( -8.59883664831506e-03 , 4.67494396675215e-02 , -8.26018445395924e-02 ), ( -1.86543551069504e-02 , 6.66475511479637e-02 , -3.48267535670694e-02 ), ( -2.44336835714561e-02 , 9.27298049549328e-02 , -6.81790385548220e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 11, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 12, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 12, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 12, atoms_positions[size = 51] = { ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 ), ( 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 ), ( 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 ), ( 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 ), ( 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 ), ( 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 ), ( -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 ), ( -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 ), ( -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 ), ( -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ), ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 ), ( 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 ), ( 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 ), ( 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 ), ( 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 ), ( 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 ), ( 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 ), ( 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 ), ( 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 ), ( 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 ), ( 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 ), ( 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 ), ( 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 ), ( 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 ), ( 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 ), ( 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 ), ( 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 ), ( 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 ), ( 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 ), ( -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 ), ( 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 ), ( 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 ), ( -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 ), ( -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 ), ( -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 ), ( -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 ), ( -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 ), ( -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 ), ( -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 ), ( -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 ), ( -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 ), ( -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 ), ( -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 ), ( -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 ), ( -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 ), ( -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 ), ( -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 ), ( -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 ), ( -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 ), ( -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 ), ( -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ) } +colvars: Step 12, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 , 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 , 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 , 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 , 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 , 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 , 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 , 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 , 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 , 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 , 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 , 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 , 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 , 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 , 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 , -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 , 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 , -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 , -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 , -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 , -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 , -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 , -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 , -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 , -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 , -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 , -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 , -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 , -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 , -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 , -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 , -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 , -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99696838417146e-01 , 1.71197735484166e-02 , 1.23775133182677e-02 , -1.26468089441603e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.34222778257989e+00 , 4.44874988870301e-02 , -7.63034702608645e-01 , 6.99749380474751e+00 , -5.36379861145277e-01 , -6.24284003491755e-01 , 7.05221151175786e+00 , -2.03274821824152e+00 , -9.73809834627880e-01 , 6.21133704571409e+00 , -3.05737598848811e-01 , 6.90797279608376e-01 , 4.99082131166338e+00 , -1.91478896184692e-01 , 6.98806288473288e-01 , 6.89100979494244e+00 , -2.67641873118976e-01 , 1.85313756694068e+00 , 6.17606345160256e+00 , -1.22055721564965e-01 , 3.15605100020287e+00 , 7.11012109415763e+00 , -3.42385927881686e-01 , 4.28117164360406e+00 , 5.27929338871939e+00 , 1.11128467320838e+00 , 3.31639573889102e+00 , 4.11594332660492e+00 , 1.04549666514900e+00 , 3.64336579290387e+00 , 5.86972520325219e+00 , 2.25350550342879e+00 , 2.99656347706784e+00 , 5.21736437819957e+00 , 3.59307852135098e+00 , 2.89632441452221e+00 , 6.33479950199719e+00 , 4.53552377269689e+00 , 2.43170956661405e+00 , 3.90951833162592e+00 , 3.73989148131436e+00 , 2.03058732569043e+00 , 2.84168737214037e+00 , 4.13200224782366e+00 , 2.52354948924682e+00 , 3.87423681061359e+00 , 3.24034111394242e+00 , 7.46232672687410e-01 , 2.66485421649349e+00 , 3.08097810729631e+00 , -1.07149070659058e-01 , 3.03294487570176e+00 , 2.72201569737429e+00 , -1.56665536091977e+00 , 1.57094492662089e+00 , 2.18506939648817e+00 , 5.36026471994885e-01 , 4.32972147860576e-01 , 2.50378548615709e+00 , 5.33434772833755e-01 , 1.98485973325827e+00 , 1.00222445176447e+00 , 1.07060750689829e+00 , 1.18055180206768e+00 , 6.54407285594198e-02 , 1.69198737352241e+00 , 2.02188164505496e+00 , -1.14478511169910e+00 , 2.00914658980997e+00 , 5.46794109560724e-01 , 6.10101893018412e-01 , 2.93923188922391e+00 , -6.50601879403903e-01 , 3.54063028365143e-01 , 3.17186791474769e+00 , 1.32450258658276e+00 , 1.33952714702160e+00 , 3.83438616022535e+00 , 8.60059122313831e-01 , 1.94315591816399e+00 , 5.03918142044198e+00 , 2.02996287234471e+00 , 2.61924344340473e+00 , 5.63529229492491e+00 , -3.51563089774493e-01 , 2.91698531397528e+00 , 4.97613904653083e+00 , -1.16066464919524e+00 , 3.04828032956497e+00 , 5.90457900985643e+00 , -4.64205322001683e-01 , 3.63021045399021e+00 , 3.84568525926716e+00 , -1.49198638528812e+00 , 4.55217629047898e+00 , 3.52142935122960e+00 , -7.27236292069814e-01 , 5.39864422315214e+00 , 2.43692845126780e+00 , -2.76547238994928e+00 , 3.87911226954702e+00 , 2.91980680060914e+00 , -3.83316614930786e+00 , 4.46096925837630e+00 , 2.82995861143047e+00 , -2.60201479010881e+00 , 2.63708009012683e+00 , 2.45609415777650e+00 , -3.73007444068942e+00 , 1.87767759725282e+00 , 2.02989305813899e+00 , -3.41600890451202e+00 , 8.57936888578888e-01 , 9.34622543160770e-01 , -4.30074897279047e+00 , 1.06692893473275e+00 , 3.24986782938829e+00 , -5.53245853212733e+00 , 8.75109500332792e-01 , 3.33233966466508e+00 , -3.42183385312169e+00 , 6.65112706329833e-01 , 4.14454424495742e+00 , -3.76368207226494e+00 , 5.16946302547614e-02 , 5.47019231775250e+00 , -2.38346038389862e+00 , -3.36445137381541e-01 , 6.16611673751907e+00 , -4.47441316259085e+00 , 9.97044277319292e-01 , 6.43495138655299e+00 , -5.33029709156529e+00 , 6.09050214327532e-01 , 7.19890454031354e+00 , -6.26338589736226e+00 , 3.56897022897231e+00 , 6.70936767567691e+00 , -6.92272323391118e+00 , 4.29541996788424e+00 , 7.43650845123546e+00 , -6.74484668960185e+00 , 3.20564142889081e+00 , 5.52363849979777e+00 , -4.11719070432211e+00 , 2.29071876958393e+00 , 6.47072967612998e+00 , -4.85794708160293e+00 , 3.19836263244526e+00 , 7.21559583707487e+00 , -4.09921024458639e+00 , 4.57096755227742e+00 , 7.29346621009461e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 12. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 12. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atoms_new_colvar_forces = { ( -7.16421680750278e-02 , 3.03396548751539e-01 , -3.94486220717945e-01 ), ( 1.24515909749766e-02 , 3.19353701028634e-02 , -2.37221977925211e-01 ), ( -4.15693683146455e-02 , 9.18027746722945e-02 , 8.60682081256656e-02 ), ( -9.66413963586872e-02 , 2.46580175116835e-01 , 6.67373004675043e-02 ), ( -1.90458239292532e-02 , 9.94350184313190e-02 , -1.69056362419433e-01 ), ( 7.06786042823088e-02 , -1.83119401980232e-01 , -3.97681292658151e-02 ), ( 1.06426346587686e-02 , -1.00331643510678e-01 , 2.51942191228477e-01 ), ( -4.07667108107428e-02 , 5.91623733313461e-02 , 1.91946646728410e-01 ), ( 6.58631416517817e-02 , -1.88166122049303e-01 , 3.11790396547625e-02 ), ( 1.14922285106495e-01 , -3.89618039834855e-01 , 2.69709548896305e-01 ), ( 2.45072064690875e-02 , -9.92952513398520e-02 , 9.51725380397601e-02 ), ( 2.65739974674320e-02 , -9.71435419165180e-02 , 5.91833122237861e-02 ), ( 1.23808965877677e-02 , -5.58885675058319e-02 , 7.20217919193645e-02 ), ( 1.25216656406114e-02 , -5.36687337202716e-02 , 6.09006716071647e-02 ), ( 5.56312902213688e-03 , -3.53608099000057e-02 , 7.52172944233854e-02 ), ( -8.61878532719259e-03 , 8.92242158732663e-03 , 7.52463376805510e-02 ), ( -2.07770157462097e-03 , -3.13736891666861e-03 , 4.02534722876005e-02 ), ( -5.76850016691932e-03 , 9.40789227218320e-03 , 3.59927854806369e-02 ), ( 2.74944431517631e-03 , -1.32813564898526e-02 , 1.96325014128746e-02 ), ( 9.11279236113813e-03 , -2.21484706889497e-02 , -2.63901170934249e-02 ), ( 8.75310807004707e-03 , -2.37931703636637e-02 , -1.48151159553400e-02 ), ( 6.64165272602964e-03 , -1.35258005651303e-02 , -3.01757967596976e-02 ), ( 1.50763901547272e-02 , -4.65739180996560e-02 , -2.13146940458401e-03 ), ( 2.76860357759323e-02 , -8.81459002274344e-02 , 7.03490641253195e-03 ), ( 1.43094379929380e-02 , -4.67520260279631e-02 , 8.62938073013699e-03 ), ( 1.42575165045805e-02 , -4.38399629483993e-02 , -2.87000166804047e-03 ), ( 9.32008697586987e-03 , -3.70741783280618e-02 , 3.33179476827687e-02 ), ( -8.46017739415180e-04 , -1.55411561800036e-02 , 7.60374898142787e-02 ), ( -3.78947514792484e-03 , 4.00354032955483e-03 , 3.27471322944331e-02 ), ( -5.86436487064504e-03 , 1.10841396046405e-02 , 3.02351262515297e-02 ), ( -7.31253639742772e-03 , 1.77136686845677e-02 , 2.14247141411940e-02 ), ( -1.63065776924027e-02 , 5.17412136033583e-02 , -3.41105376001136e-03 ), ( -9.77454806826517e-03 , 3.56593718965959e-02 , -2.14665548734431e-02 ), ( -1.38180877017203e-02 , 4.98915524044661e-02 , -2.81748384597231e-02 ), ( -1.99458201197298e-03 , 1.48720940467247e-02 , -3.61426953349021e-02 ), ( 1.06041811229486e-02 , -1.56755236088371e-02 , -7.29350852936609e-02 ), ( 4.36834845946131e-03 , -6.83900191805431e-04 , -5.41887880626871e-02 ), ( 3.34147327126994e-03 , 6.18962776423782e-03 , -6.95214782203114e-02 ), ( 7.12598681052463e-03 , -1.47298439811097e-02 , -3.14660014810572e-02 ), ( 1.30982744407057e-02 , -4.12287535926886e-02 , 1.34981438346009e-03 ), ( 4.96410404255614e-04 , 1.81331109876104e-03 , -1.40656698696598e-02 ), ( 4.19748344476729e-04 , 3.45764211772423e-03 , -1.99406416982656e-02 ), ( -6.55532830509409e-03 , 2.05249114086253e-02 , -2.19934544421135e-04 ), ( -2.06371808932977e-02 , 5.75600182245067e-02 , 2.88120279806772e-02 ), ( -1.90268865001024e-02 , 6.31990805317706e-02 , -1.57987157085621e-02 ), ( -2.27452399178175e-02 , 7.51368540083220e-02 , -1.71592008838816e-02 ), ( -1.69032961322243e-02 , 7.24944830113589e-02 , -8.24026922858791e-02 ), ( -2.00038076931115e-02 , 8.66611845674294e-02 , -1.01152684539195e-01 ), ( -8.62016999247501e-03 , 4.66946998990970e-02 , -8.26889476000254e-02 ), ( -1.86678199864865e-02 , 6.66405053489124e-02 , -3.48790635755432e-02 ), ( -2.44696659839757e-02 , 9.27429691514109e-02 , -6.82629424665393e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 12, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 13, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 13, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 13, atoms_positions[size = 51] = { ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 ), ( 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 ), ( 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 ), ( 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 ), ( 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 ), ( 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 ), ( -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 ), ( -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 ), ( -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 ), ( -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ), ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 ), ( 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 ), ( 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 ), ( 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 ), ( 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 ), ( 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 ), ( 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 ), ( 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 ), ( 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 ), ( 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 ), ( 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 ), ( 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 ), ( 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 ), ( 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 ), ( 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 ), ( 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 ), ( 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 ), ( 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 ), ( 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 ), ( -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 ), ( 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 ), ( 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 ), ( -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 ), ( -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 ), ( -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 ), ( -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 ), ( -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 ), ( -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 ), ( -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 ), ( -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 ), ( -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 ), ( -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 ), ( -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 ), ( -2.38255516970055e+00 , -3.29059335914521e-01 , 6.16893615475952e+00 ), ( -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 ), ( -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 ), ( -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 ), ( -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 ), ( -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 ), ( -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 ), ( -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ) } +colvars: Step 13, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610561e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 , 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 , 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 , 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 , 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 , 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 , 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 , 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 , 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 , 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 , 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 , 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 , 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 , 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 , 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 , -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 , 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 , -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 , -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 , -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 , -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 , -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 , -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 , -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 , -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 , -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -2.38255516970055e+00 , -3.29059335914521e-01 , 6.16893615475952e+00 , -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 , -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 , -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 , -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 , -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 , -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 , -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99711367452522e-01 , 1.66424815610561e-02 , 1.21808078005814e-02 , -1.23222366080573e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.33647690639270e+00 , 4.42587433440356e-02 , -7.62516304789198e-01 , 6.99672735017658e+00 , -5.39724592764943e-01 , -6.19550806154641e-01 , 7.05355738963816e+00 , -2.03497508073079e+00 , -9.68048536293684e-01 , 6.20030382680948e+00 , -3.14499429024642e-01 , 6.94097588787109e-01 , 4.99096308005905e+00 , -1.88027241273686e-01 , 7.03231814643281e-01 , 6.88810696083044e+00 , -2.67053886429773e-01 , 1.85916873773515e+00 , 6.17575671749166e+00 , -1.25122411538304e-01 , 3.16796429269759e+00 , 7.10150444136351e+00 , -3.45538943396029e-01 , 4.28110541996346e+00 , 5.27776918408887e+00 , 1.11051986747539e+00 , 3.32008498124480e+00 , 4.12053893935890e+00 , 1.04239529195251e+00 , 3.64704372960890e+00 , 5.86650427685309e+00 , 2.24950524666156e+00 , 2.99745817184922e+00 , 5.22091808650637e+00 , 3.59168781024863e+00 , 2.90007579701471e+00 , 6.33290029191181e+00 , 4.52772303594069e+00 , 2.42533301106139e+00 , 3.90913316426970e+00 , 3.73829921884896e+00 , 2.03295075119769e+00 , 2.83213020465279e+00 , 4.13586768127461e+00 , 2.51949790135129e+00 , 3.88418521420865e+00 , 3.24072294788353e+00 , 7.42665125135546e-01 , 2.66126638287338e+00 , 3.06703512964004e+00 , -1.08157147298366e-01 , 3.03214439112014e+00 , 2.72241304941243e+00 , -1.55760473907453e+00 , 1.57191572263900e+00 , 2.19041612052319e+00 , 5.23242312543151e-01 , 4.27523997228466e-01 , 2.51313189136459e+00 , 5.30782259613166e-01 , 1.99124782509869e+00 , 1.00281814091270e+00 , 1.07419422466668e+00 , 1.18171091138252e+00 , 7.59176562550391e-02 , 1.69191379980884e+00 , 2.02395876531724e+00 , -1.13887307198220e+00 , 2.00760135971114e+00 , 5.49597059243926e-01 , 6.09399478651684e-01 , 2.93380849836894e+00 , -6.45174555601722e-01 , 3.52515920242022e-01 , 3.17044176018925e+00 , 1.32595042743777e+00 , 1.34184836042843e+00 , 3.83131325063095e+00 , 8.60163057364275e-01 , 1.94874931500651e+00 , 5.03545402040029e+00 , 2.03128394242981e+00 , 2.62588950580498e+00 , 5.63925603887910e+00 , -3.48673541488037e-01 , 2.91680619415150e+00 , 4.97415906744613e+00 , -1.15826055453709e+00 , 3.05082954845457e+00 , 5.90347894546100e+00 , -4.71151568019427e-01 , 3.61722145347632e+00 , 3.84601498497469e+00 , -1.49567289364478e+00 , 4.55027590745828e+00 , 3.51407305980763e+00 , -7.22457612788106e-01 , 5.40062416668333e+00 , 2.44140692994560e+00 , -2.76922120984203e+00 , 3.87663436644978e+00 , 2.91768175874935e+00 , -3.83005921276003e+00 , 4.46710364772418e+00 , 2.82735446547651e+00 , -2.60390264060501e+00 , 2.64493409131422e+00 , 2.45005412892661e+00 , -3.73573913701054e+00 , 1.86584883566659e+00 , 2.02363246037117e+00 , -3.41435784284335e+00 , 8.64704883329246e-01 , 9.26028053148352e-01 , -4.30530748426517e+00 , 1.06556739591713e+00 , 3.24764750025895e+00 , -5.52840656340682e+00 , 8.68279915241568e-01 , 3.33118938864240e+00 , -3.41373069819139e+00 , 6.68961529239267e-01 , 4.15078074525819e+00 , -3.75656449248184e+00 , 4.54305739009396e-02 , 5.46430316905750e+00 , -2.38255516970055e+00 , -3.29059335914521e-01 , 6.16893615475952e+00 , -4.47347844239722e+00 , 9.99278474008528e-01 , 6.43787379316999e+00 , -5.33336527932189e+00 , 6.08577675490398e-01 , 7.20184753921569e+00 , -6.25527269741847e+00 , 3.57228151664655e+00 , 6.71098897232734e+00 , -6.92718269135069e+00 , 4.29605019543175e+00 , 7.44153376080846e+00 , -6.74694331773750e+00 , 3.20410100515264e+00 , 5.52333629677533e+00 , -4.12124855834049e+00 , 2.28481835255087e+00 , 6.46471466844129e+00 , -4.84893812150756e+00 , 3.19460995222533e+00 , 7.21726047171137e+00 , -4.10135288124348e+00 , 4.57806099671453e+00 , 7.29500177042922e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 13. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 13. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atoms_new_colvar_forces = { ( -7.16848023051113e-02 , 3.03406467638824e-01 , -3.95351133644467e-01 ), ( 1.25012248682017e-02 , 3.14943727627139e-02 , -2.37347290328934e-01 ), ( -4.16044411846218e-02 , 9.19752550270075e-02 , 8.65873739393492e-02 ), ( -9.67474317693076e-02 , 2.47220693613752e-01 , 6.66558943569052e-02 ), ( -1.90524738522307e-02 , 9.94289567745098e-02 , -1.69630346467483e-01 ), ( 7.07545776624681e-02 , -1.83593734852738e-01 , -3.96086306355424e-02 ), ( 1.06290758170036e-02 , -1.00140025421509e-01 , 2.52544176616428e-01 ), ( -4.08308398476371e-02 , 5.97218751038243e-02 , 1.91841739524069e-01 ), ( 6.59244950506004e-02 , -1.88406306432059e-01 , 3.09903758344904e-02 ), ( 1.15016863749083e-01 , -3.89991960993715e-01 , 2.70427575233416e-01 ), ( 2.45481445884070e-02 , -9.92958410899460e-02 , 9.52840930616265e-02 ), ( 2.65957911792211e-02 , -9.71382388271649e-02 , 5.92646586708679e-02 ), ( 1.24022347475679e-02 , -5.58563360999198e-02 , 7.21021236988898e-02 ), ( 1.25425974982060e-02 , -5.36513706759085e-02 , 6.09700270201490e-02 ), ( 5.57808745511937e-03 , -3.53009942223408e-02 , 7.52954309343477e-02 ), ( -8.61672322330427e-03 , 9.02891576978659e-03 , 7.53131644443017e-02 ), ( -2.07900302590006e-03 , -3.07425778523136e-03 , 4.02922287168525e-02 ), ( -5.77036135321706e-03 , 9.46839655898241e-03 , 3.60237167170881e-02 ), ( 2.74066918054249e-03 , -1.32274107216640e-02 , 1.96568235606399e-02 ), ( 9.08730461783740e-03 , -2.21127046888010e-02 , -2.64023654543353e-02 ), ( 8.74092384788639e-03 , -2.37814157636701e-02 , -1.48188371221037e-02 ), ( 6.62478995543604e-03 , -1.35207891048719e-02 , -3.01961009405069e-02 ), ( 1.50746759309285e-02 , -4.65791626355137e-02 , -2.11834520072256e-03 ), ( 2.77006951945339e-02 , -8.81944669602844e-02 , 7.06632082557573e-03 ), ( 1.43202720040025e-02 , -4.67799343049266e-02 , 8.64996682972771e-03 ), ( 1.42676038711970e-02 , -4.38821442318173e-02 , -2.86089251963270e-03 ), ( 9.33659139362305e-03 , -3.70814288695834e-02 , 3.33572802635675e-02 ), ( -8.18030508691844e-04 , -1.55170421736455e-02 , 7.61073953459294e-02 ), ( -3.77758137799797e-03 , 4.01610561392807e-03 , 3.27738837575518e-02 ), ( -5.85068443666083e-03 , 1.10886119627274e-02 , 3.02569227489172e-02 ), ( -7.31131086834053e-03 , 1.77444252210332e-02 , 2.14388024426093e-02 ), ( -1.63259668292790e-02 , 5.18039334556752e-02 , -3.42657571196878e-03 ), ( -9.78872925192462e-03 , 3.56768071899492e-02 , -2.14948856921123e-02 ), ( -1.38343934007992e-02 , 4.99078327240418e-02 , -2.82134820935630e-02 ), ( -2.01044257050173e-03 , 1.48696753973150e-02 , -3.61777607784963e-02 ), ( 1.05821837722758e-02 , -1.57183863544096e-02 , -7.29934628812077e-02 ), ( 4.35756463209935e-03 , -7.31103056545404e-04 , -5.42367928014887e-02 ), ( 3.32709631940648e-03 , 6.13185076270507e-03 , -6.95851912988013e-02 ), ( 7.12720782650704e-03 , -1.47825181119657e-02 , -3.14908973687674e-02 ), ( 1.31213393285447e-02 , -4.13041633119196e-02 , 1.35932021834391e-03 ), ( 5.07929024846422e-04 , 1.75736416947850e-03 , -1.40817469322971e-02 ), ( 4.33168120790726e-04 , 3.38741176200941e-03 , -1.99631079092444e-02 ), ( -6.54536392556077e-03 , 2.04972001762583e-02 , -2.28718574320056e-04 ), ( -2.06261824379717e-02 , 5.75779688968008e-02 , 2.88183375108143e-02 ), ( -1.90284464589579e-02 , 6.31904647620932e-02 , -1.58331227728328e-02 ), ( -2.27460733223221e-02 , 7.51258762596511e-02 , -1.71988077928391e-02 ), ( -1.69301143808959e-02 , 7.24663474530252e-02 , -8.24968095319391e-02 ), ( -2.00388592213415e-02 , 8.66328293638355e-02 , -1.01267035271360e-01 ), ( -8.64057100669298e-03 , 4.66423398936291e-02 , -8.27764979146890e-02 ), ( -1.86802642125722e-02 , 6.66376349052638e-02 , -3.49300618005685e-02 ), ( -2.45040168644952e-02 , 9.27621234713303e-02 , -6.83487328322347e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 13, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 14, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 14, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 14, atoms_positions[size = 51] = { ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 ), ( 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 ), ( 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 ), ( 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 ), ( 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 ), ( 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 ), ( -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 ), ( -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 ), ( -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 ), ( -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ), ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 ), ( 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 ), ( 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 ), ( 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 ), ( 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 ), ( 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 ), ( 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 ), ( 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 ), ( 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 ), ( 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 ), ( 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 ), ( 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 ), ( 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 ), ( 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 ), ( 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 ), ( 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 ), ( 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 ), ( 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 ), ( 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 ), ( -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 ), ( 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 ), ( 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 ), ( -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 ), ( -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 ), ( -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 ), ( -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 ), ( -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 ), ( -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 ), ( -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 ), ( -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 ), ( -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 ), ( -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 ), ( -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 ), ( -2.38241107657785e+00 , -3.23121881461259e-01 , 6.17120868209903e+00 ), ( -4.47207562252774e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 ), ( -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 ), ( -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 ), ( -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 ), ( -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 ), ( -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 ), ( -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ) } +colvars: Step 14, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 , 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 , 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 , 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 , 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 , 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 , 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 , 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 , 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 , 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 , 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 , 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 , 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 , 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 , 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 , -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 , 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 , -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 , -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 , -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 , -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 , -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 , -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 , -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 , -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 , -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -2.38241107657785e+00 , -3.23121881461259e-01 , 6.17120868209903e+00 , -4.47207562252774e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 , -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 , -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 , -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 , -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 , -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 , -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99724444151772e-01 , 1.61728123725341e-02 , 1.20140419196446e-02 , -1.20473524952834e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.33116334360793e+00 , 4.39477087037661e-02 , -7.61500918421403e-01 , 6.99490061581011e+00 , -5.42360157630610e-01 , -6.14308588468945e-01 , 7.05458114005209e+00 , -2.03727106976173e+00 , -9.62566843483470e-01 , 6.19027894305835e+00 , -3.23495777589509e-01 , 6.97549554696518e-01 , 4.99074674203511e+00 , -1.84366145867377e-01 , 7.07419037196865e-01 , 6.88460681773507e+00 , -2.66517858372762e-01 , 1.86528994999245e+00 , 6.17496620147102e+00 , -1.29034863275191e-01 , 3.17799683741784e+00 , 7.09377540868788e+00 , -3.48370835039685e-01 , 4.28205839060069e+00 , 5.27751466237441e+00 , 1.10937558064914e+00 , 3.32363680754420e+00 , 4.12453864467047e+00 , 1.03937442782306e+00 , 3.65097128324980e+00 , 5.86272690044328e+00 , 2.24692083190040e+00 , 2.99768492213417e+00 , 5.22495632009146e+00 , 3.59002495574057e+00 , 2.90397050373807e+00 , 6.33091978237007e+00 , 4.52096768040212e+00 , 2.41821103901963e+00 , 3.90761621876802e+00 , 3.73578159682565e+00 , 2.03522239497112e+00 , 2.82330457546162e+00 , 4.13981477813848e+00 , 2.51532985958354e+00 , 3.89416647381658e+00 , 3.24118648160104e+00 , 7.39605332339851e-01 , 2.65772755729676e+00 , 3.05381993126023e+00 , -1.08776995624143e-01 , 3.03211776564529e+00 , 2.72226697682203e+00 , -1.54854853850668e+00 , 1.57487207218836e+00 , 2.19428998139883e+00 , 5.10135411521915e-01 , 4.20860454576299e-01 , 2.52281782410172e+00 , 5.28170965223165e-01 , 1.99838997932447e+00 , 1.00556662091938e+00 , 1.07703287425697e+00 , 1.18170920956455e+00 , 8.57643922704360e-02 , 1.69186856017838e+00 , 2.02617697461607e+00 , -1.13306885731637e+00 , 2.00642939765765e+00 , 5.51915626011207e-01 , 6.08745096623944e-01 , 2.93019769913529e+00 , -6.39290370058285e-01 , 3.51333164160600e-01 , 3.16901512968674e+00 , 1.32663559315063e+00 , 1.34357574942865e+00 , 3.82662921993073e+00 , 8.59224422123319e-01 , 1.95412223839728e+00 , 5.03234530392163e+00 , 2.03445340169394e+00 , 2.63327884666313e+00 , 5.64387509497762e+00 , -3.45769822309295e-01 , 2.91667891796598e+00 , 4.97225631884736e+00 , -1.15569576811500e+00 , 3.05317255996454e+00 , 5.90205636181501e+00 , -4.77716129078488e-01 , 3.60392023334417e+00 , 3.84670657033782e+00 , -1.49958086505261e+00 , 4.54894576871857e+00 , 3.50552992490835e+00 , -7.17810547523736e-01 , 5.40260261678702e+00 , 2.44567503399824e+00 , -2.77153403087914e+00 , 3.87482349853510e+00 , 2.91551027582010e+00 , -3.82728195984711e+00 , 4.47331610809974e+00 , 2.82496481780449e+00 , -2.60574731041817e+00 , 2.65266821153607e+00 , 2.44381920940532e+00 , -3.74177122190060e+00 , 1.85364444976336e+00 , 2.01783839439979e+00 , -3.41207064731492e+00 , 8.70740942561903e-01 , 9.17701848250672e-01 , -4.31054425368226e+00 , 1.06511444750761e+00 , 3.24399122095485e+00 , -5.52387237628445e+00 , 8.61409412304628e-01 , 3.33033486127710e+00 , -3.40565034588127e+00 , 6.72455056412069e-01 , 4.15857012002288e+00 , -3.74870489789953e+00 , 4.05644189334814e-02 , 5.45803072342270e+00 , -2.38241107657785e+00 , -3.23121881461259e-01 , 6.17120868209903e+00 , -4.47207562252774e+00 , 1.00120276040718e+00 , 6.44033511033762e+00 , -5.33681313389437e+00 , 6.07726941027010e-01 , 7.20486579772620e+00 , -6.24766957296722e+00 , 3.57589869924785e+00 , 6.71305245105322e+00 , -6.93199973588589e+00 , 4.29682862468306e+00 , 7.44681231433096e+00 , -6.74894105220994e+00 , 3.20215487144196e+00 , 5.52230375929670e+00 , -4.12460169523711e+00 , 2.27835697982533e+00 , 6.45775251038685e+00 , -4.84034674795820e+00 , 3.19203420614078e+00 , 7.21953610971923e+00 , -4.10303199435416e+00 , 4.58343649989354e+00 , 7.29551904344732e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 14. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 14. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atoms_new_colvar_forces = { ( -7.17030729248560e-02 , 3.03434412847935e-01 , -3.96209881834245e-01 ), ( 1.25539674912846e-02 , 3.10971748466752e-02 , -2.37484688240301e-01 ), ( -4.16487740410050e-02 , 9.21772717626605e-02 , 8.70592462212863e-02 ), ( -9.68465681352754e-02 , 2.47846407485462e-01 , 6.65584771335486e-02 ), ( -1.90448258776952e-02 , 9.94144511414791e-02 , -1.70179970081159e-01 ), ( 7.08234560023367e-02 , -1.84050882202746e-01 , -3.94462726906446e-02 ), ( 1.06008164335397e-02 , -9.99558236220789e-02 , 2.53124929639883e-01 ), ( -4.08911448281357e-02 , 6.02339263019856e-02 , 1.91754774692143e-01 ), ( 6.59863081703112e-02 , -1.88672016902237e-01 , 3.08421610939229e-02 ), ( 1.15088456013817e-01 , -3.90372791027753e-01 , 2.71149704495937e-01 ), ( 2.45856886529822e-02 , -9.93029314643077e-02 , 9.53970980947032e-02 ), ( 2.66150021200131e-02 , -9.71398604141635e-02 , 5.93436150137355e-02 ), ( 1.24217001709229e-02 , -5.58279443000605e-02 , 7.21817026324729e-02 ), ( 1.25617262932672e-02 , -5.36376273244229e-02 , 6.10392612117306e-02 ), ( 5.59176317587432e-03 , -3.52437222501083e-02 , 7.53718830903424e-02 ), ( -8.61469376918818e-03 , 9.13573878138332e-03 , 7.53769537257818e-02 ), ( -2.08036764354214e-03 , -3.01168138675438e-03 , 4.03281283495174e-02 ), ( -5.77204210497506e-03 , 9.52933492292573e-03 , 3.60526155123662e-02 ), ( 2.73196767940916e-03 , -1.31749730390552e-02 , 1.96764929056506e-02 ), ( 9.06243454595903e-03 , -2.20795588291178e-02 , -2.64224504586307e-02 ), ( 8.72881036570473e-03 , -2.37719186216426e-02 , -1.48269814368021e-02 ), ( 6.60837365683509e-03 , -1.35173489297917e-02 , -3.02208077794285e-02 ), ( 1.50722263329384e-02 , -4.65880566497031e-02 , -2.10846056423043e-03 ), ( 2.77132714691932e-02 , -8.82492552943065e-02 , 7.09658509678953e-03 ), ( 1.43298786671376e-02 , -4.68110431832540e-02 , 8.67062510312127e-03 ), ( 1.42765588857720e-02 , -4.39272648779111e-02 , -2.85112288428024e-03 ), ( 9.35178577309465e-03 , -3.70910423075215e-02 , 3.33976601877557e-02 ), ( -7.91476888628810e-04 , -1.54934024438347e-02 , 7.61808486456305e-02 ), ( -3.76611455213548e-03 , 4.02928451363874e-03 , 3.28027615403106e-02 ), ( -5.83737261763688e-03 , 1.10943335602030e-02 , 3.02819747857202e-02 ), ( -7.30985707112403e-03 , 1.77764718021673e-02 , 2.14531452840506e-02 ), ( -1.63437274011271e-02 , 5.18698487860540e-02 , -3.44483737933499e-03 ), ( -9.80172955653648e-03 , 3.56965236015377e-02 , -2.15242878391028e-02 ), ( -1.38491829664301e-02 , 4.99274418679334e-02 , -2.82526227196997e-02 ), ( -2.02539614964378e-03 , 1.48679519023049e-02 , -3.62148591869112e-02 ), ( 1.05608512952179e-02 , -1.57629483249763e-02 , -7.30555800588351e-02 ), ( 4.34725410231149e-03 , -7.78490150777871e-04 , -5.42851718364163e-02 ), ( 3.31346888814621e-03 , 6.07435944700226e-03 , -6.96491258062289e-02 ), ( 7.12817424489928e-03 , -1.48360902169562e-02 , -3.15145377778368e-02 ), ( 1.31428212464034e-02 , -4.13817917713363e-02 , 1.37346881309776e-03 ), ( 5.19064722109667e-04 , 1.70212341462858e-03 , -1.40933202424561e-02 ), ( 4.46170100063452e-04 , 3.31812885537241e-03 , -1.99800460475654e-02 ), ( -6.53542118172565e-03 , 2.04714903649538e-02 , -2.33128257942889e-04 ), ( -2.06146479410913e-02 , 5.76006473823990e-02 , 2.88299600818957e-02 ), ( -1.90288349421176e-02 , 6.31867488549733e-02 , -1.58633007683796e-02 ), ( -2.27455548385216e-02 , 7.51207571365791e-02 , -1.72331583835215e-02 ), ( -1.69545518180850e-02 , 7.24431631875390e-02 , -8.25902995953081e-02 ), ( -2.00709479746416e-02 , 8.66102831783137e-02 , -1.01381424086626e-01 ), ( -8.65927776259550e-03 , 4.65932132315996e-02 , -8.28629606271324e-02 ), ( -1.86910394658317e-02 , 6.66395860461118e-02 , -3.49789572629907e-02 ), ( -2.45353740469984e-02 , 9.27873903110001e-02 , -6.84358195053828e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 14, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 15, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 15, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 15, atoms_positions[size = 51] = { ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 ), ( 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 ), ( 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 ), ( 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 ), ( 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 ), ( 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 ), ( -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 ), ( -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 ), ( -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 ), ( -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ), ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 ), ( 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 ), ( 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 ), ( 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 ), ( 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 ), ( 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 ), ( 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 ), ( 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 ), ( 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 ), ( 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 ), ( 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 ), ( 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 ), ( 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 ), ( 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 ), ( 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 ), ( 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 ), ( 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 ), ( 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 ), ( 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 ), ( -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 ), ( 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 ), ( 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 ), ( -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 ), ( -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 ), ( -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 ), ( -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 ), ( -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 ), ( -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 ), ( -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 ), ( -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 ), ( -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 ), ( -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 ), ( -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 ), ( -2.38290213212964e+00 , -3.18712087726498e-01 , 6.17288759969147e+00 ), ( -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 ), ( -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 ), ( -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 ), ( -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 ), ( -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 ), ( -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 ), ( -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ) } +colvars: Step 15, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155577e-02 , 1.18858573400358e-02 , -1.18348863683821e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 , 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 , 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 , 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 , 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 , 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 , 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 , 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 , 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 , 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 , 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 , 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 , 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 , 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 , 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 , -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 , 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 , -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 , -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 , -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 , -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 , -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 , -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 , -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 , -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 , -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -2.38290213212964e+00 , -3.18712087726498e-01 , 6.17288759969147e+00 , -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 , -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 , -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 , -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 , -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 , -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 , -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99735732840256e-01 , 1.57202526155577e-02 , 1.18858573400358e-02 , -1.18348863683821e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.32635127361166e+00 , 4.35764790714774e-02 , -7.60016835324669e-01 , 6.99183154385133e+00 , -5.44358407275899e-01 , -6.08476599276329e-01 , 7.05520442317257e+00 , -2.03960278492555e+00 , -9.57376117184421e-01 , 6.18189775809451e+00 , -3.32614315339561e-01 , 7.01295030192732e-01 , 4.98989980581151e+00 , -1.80517456442876e-01 , 7.11350124858682e-01 , 6.88047170064052e+00 , -2.66086412954660e-01 , 1.87160732594854e+00 , 6.17357895837486e+00 , -1.33734006382249e-01 , 3.18581550860587e+00 , 7.08712204382820e+00 , -3.50765374436027e-01 , 4.28404816268163e+00 , 5.27856572545349e+00 , 1.10777196018606e+00 , 3.32706930408318e+00 , 4.12781897396638e+00 , 1.03644463364765e+00 , 3.65518164368494e+00 , 5.85851860231635e+00 , 2.24563577313053e+00 , 2.99731369772199e+00 , 5.22911193926279e+00 , 3.58815752903411e+00 , 2.90782650579299e+00 , 6.32899434808593e+00 , 4.51529975473887e+00 , 2.41036930647296e+00 , 3.90499306271619e+00 , 3.73243338127268e+00 , 2.03731973177092e+00 , 2.81537517253318e+00 , 4.14375005695599e+00 , 2.51100787848660e+00 , 3.90387299938054e+00 , 3.24162450037440e+00 , 7.37047797774404e-01 , 2.65469358211235e+00 , 3.04167836103619e+00 , -1.09016024960709e-01 , 3.03297416461474e+00 , 2.72139515579073e+00 , -1.53995362825764e+00 , 1.57924198261769e+00 , 2.19639600593675e+00 , 4.97142746576540e-01 , 4.13328935689060e-01 , 2.53275396870261e+00 , 5.25546331992242e-01 , 2.00609575590436e+00 , 1.01077201344322e+00 , 1.07883222207232e+00 , 1.18066903580826e+00 , 9.45633720039159e-02 , 1.69197619136043e+00 , 2.02851196991083e+00 , -1.12741504982865e+00 , 2.00570822345668e+00 , 5.53855305847925e-01 , 6.08313137958777e-01 , 2.92847949220044e+00 , -6.33055755981356e-01 , 3.50478236385176e-01 , 3.16759396183161e+00 , 1.32655887871883e+00 , 1.34472105957234e+00 , 3.82039491740261e+00 , 8.57403213759460e-01 , 1.95922914070898e+00 , 5.02986943009881e+00 , 2.03937187759238e+00 , 2.64137454646899e+00 , 5.64912840301240e+00 , -3.43030173361580e-01 , 2.91656694364547e+00 , 4.97056334403495e+00 , -1.15293900897184e+00 , 3.05530454759201e+00 , 5.90031156072606e+00 , -4.83923377588040e-01 , 3.59063202931153e+00 , 3.84755793023603e+00 , -1.50359103735193e+00 , 4.54794059322705e+00 , 3.49601502631612e+00 , -7.13415321805456e-01 , 5.40458857719122e+00 , 2.44965009217448e+00 , -2.77238450147497e+00 , 3.87395374886038e+00 , 2.91322248133724e+00 , -3.82487201597931e+00 , 4.47957488512988e+00 , 2.82278791909791e+00 , -2.60774318615234e+00 , 2.65978057028373e+00 , 2.43735720568213e+00 , -3.74790047958566e+00 , 1.84170874811414e+00 , 2.01268749950401e+00 , -3.40919906111614e+00 , 8.75913690721619e-01 , 9.09729350034710e-01 , -4.31581737347933e+00 , 1.06540428755406e+00 , 3.23922314940398e+00 , -5.51912528036329e+00 , 8.54484913137518e-01 , 3.32978236722534e+00 , -3.39778456102664e+00 , 6.75666337977415e-01 , 4.16738585358625e+00 , -3.74037993756623e+00 , 3.73480401968944e-02 , 5.45181495688655e+00 , -2.38290213212964e+00 , -3.18712087726498e-01 , 6.17288759969147e+00 , -4.47030125848173e+00 , 1.00239125344919e+00 , 6.44221024485433e+00 , -5.34051941543057e+00 , 6.06582726361717e-01 , 7.20789024840508e+00 , -6.24111254824546e+00 , 3.57991647287209e+00 , 6.71564086599947e+00 , -6.93696224601118e+00 , 4.29761968503124e+00 , 7.45219714608187e+00 , -6.75046447637097e+00 , 3.19978708919086e+00 , 5.52063391740069e+00 , -4.12715435016055e+00 , 2.27169564273842e+00 , 6.45007850949607e+00 , -4.83239914292510e+00 , 3.19077902790410e+00 , 7.22246575850802e+00 , -4.10409412111135e+00 , 4.58688253264141e+00 , 7.29506315485613e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 15. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 15. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atoms_new_colvar_forces = { ( -7.16949290049834e-02 , 3.03474386830269e-01 , -3.97046304863662e-01 ), ( 1.26075871768279e-02 , 3.07527449828284e-02 , -2.37633102868567e-01 ), ( -4.17009663573045e-02 , 9.24074981387010e-02 , 8.74661003276692e-02 ), ( -9.69339385370995e-02 , 2.48441896040349e-01 , 6.64422051068895e-02 ), ( -1.90223480977663e-02 , 9.93884227003577e-02 , -1.70691018987116e-01 ), ( 7.08816450632660e-02 , -1.84478966273026e-01 , -3.92821711082244e-02 ), ( 1.05582685074796e-02 , -9.97800400249164e-02 , 2.53669949381410e-01 ), ( -4.09444626684395e-02 , 6.06855197421951e-02 , 1.91689409105388e-01 ), ( 6.60460181362832e-02 , -1.88958089484125e-01 , 3.07452614062881e-02 ), ( 1.15132613755772e-01 , -3.90747225325214e-01 , 2.71865086326974e-01 ), ( 2.46184640764127e-02 , -9.93165721706982e-02 , 9.55103597383862e-02 ), ( 2.66307072466724e-02 , -9.71489574950985e-02 , 5.94190206706605e-02 ), ( 1.24385783576097e-02 , -5.58039125261095e-02 , 7.22592691180316e-02 ), ( 1.25783473850690e-02 , -5.36278041390523e-02 , 6.11074116288130e-02 ), ( 5.60369514890443e-03 , -3.51898383705384e-02 , 7.54451200188047e-02 ), ( -8.61263899903098e-03 , 9.24154583271544e-03 , 7.54358198108119e-02 ), ( -2.08174033617832e-03 , -2.95057966487033e-03 , 4.03599892786103e-02 ), ( -5.77342095425320e-03 , 9.58991721603904e-03 , 3.60784709629169e-02 ), ( 2.72351577197190e-03 , -1.31251301023362e-02 , 1.96904464620740e-02 ), ( 9.03869059047243e-03 , -2.20503408746778e-02 , -2.64510800630671e-02 ), ( 8.71694929791340e-03 , -2.37653627920194e-02 , -1.48399149504546e-02 ), ( 6.59273362777682e-03 , -1.35160743118100e-02 , -3.02500320355194e-02 ), ( 1.50688725450407e-02 , -4.66010358784319e-02 , -2.10215211531110e-03 ), ( 2.77230111502822e-02 , -8.83101398980123e-02 , 7.12565967045663e-03 ), ( 1.43377869775359e-02 , -4.68451858579056e-02 , 8.69135479693351e-03 ), ( 1.42839316102877e-02 , -4.39749472823456e-02 , -2.84039866961499e-03 ), ( 9.36512460506414e-03 , -3.71029112834419e-02 , 3.34387634313426e-02 ), ( -7.67051236185160e-04 , -1.54700848230630e-02 , 7.62570819365013e-02 ), ( -3.75532166399210e-03 , 4.04321632367066e-03 , 3.28334978472288e-02 ), ( -5.82469119645842e-03 , 1.11016688047768e-02 , 3.03102195604810e-02 ), ( -7.30810612237383e-03 , 1.78095870567290e-02 , 2.14673383326389e-02 ), ( -1.63591489797325e-02 , 5.19381615875536e-02 , -3.46637651232032e-03 ), ( -9.81305659264498e-03 , 3.57183112578092e-02 , -2.15546526463102e-02 ), ( -1.38618534791799e-02 , 4.99502805211779e-02 , -2.82919814203272e-02 ), ( -2.03901561513156e-03 , 1.48667419014925e-02 , -3.62537044187399e-02 ), ( 1.05405919753518e-02 , -1.58092773650867e-02 , -7.31206596138427e-02 ), ( 4.33763159321967e-03 , -8.25659687975371e-04 , -5.43329959677468e-02 ), ( 3.30091166802390e-03 , 6.01768930062788e-03 , -6.97120700059172e-02 ), ( 7.12876070240522e-03 , -1.48899474877114e-02 , -3.15361024336851e-02 ), ( 1.31619639603794e-02 , -4.14604738001422e-02 , 1.39310822023036e-03 ), ( 5.29527032387889e-04 , 1.64865096373702e-03 , -1.40994166020852e-02 ), ( 4.58418665716035e-04 , 3.25111466051152e-03 , -1.99902166450619e-02 ), ( -6.52565516598718e-03 , 2.04486038718644e-02 , -2.32521360264095e-04 ), ( -2.06025650233246e-02 , 5.76286370246274e-02 , 2.88470449160681e-02 ), ( -1.90277436193707e-02 , 6.31886535767905e-02 , -1.58884792059689e-02 ), ( -2.27433417372783e-02 , 7.51223872874197e-02 , -1.72613295599796e-02 ), ( -1.69756928755969e-02 , 7.24254347727082e-02 , -8.26817853858621e-02 ), ( -2.00989076652020e-02 , 8.65940068037253e-02 , -1.01494282967316e-01 ), ( -8.67565012061669e-03 , 4.65480494214555e-02 , -8.29467996197520e-02 ), ( -1.86995694597294e-02 , 6.66467836543689e-02 , -3.50249837064717e-02 ), ( -2.45625311202662e-02 , 9.28186466441078e-02 , -6.85234543224205e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 15, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 16, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 16, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 16, atoms_positions[size = 51] = { ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 ), ( 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 ), ( 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 ), ( 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 ), ( 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 ), ( 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 ), ( -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 ), ( -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 ), ( -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 ), ( -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ), ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 ), ( 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 ), ( 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 ), ( 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 ), ( 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 ), ( 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 ), ( 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 ), ( 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 ), ( 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 ), ( 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 ), ( 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 ), ( 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 ), ( 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 ), ( 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 ), ( 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 ), ( 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 ), ( 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 ), ( 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 ), ( 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 ), ( -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 ), ( 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 ), ( 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 ), ( -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 ), ( -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 ), ( -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 ), ( -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 ), ( -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 ), ( -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 ), ( -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 ), ( -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 ), ( -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 ), ( -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 ), ( -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 ), ( -2.38388494433046e+00 , -3.15826223986610e-01 , 6.17394163944166e+00 ), ( -4.46828024629853e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 ), ( -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 ), ( -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 ), ( -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 ), ( -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 ), ( -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 ), ( -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ) } +colvars: Step 16, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147334e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 , 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 , 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 , 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 , 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 , 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 , 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 , 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 , 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 , 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 , 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 , 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 , 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 , 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 , 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 , -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 , 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 , -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 , -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 , -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 , -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 , -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 , -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 , -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 , -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 , -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -2.38388494433046e+00 , -3.15826223986610e-01 , 6.17394163944166e+00 , -4.46828024629853e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 , -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 , -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 , -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 , -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 , -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 , -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99744979701586e-01 , 1.52939094147334e-02 , 1.18031399824045e-02 , -1.16943483291964e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.32209400940918e+00 , 4.31725522729266e-02 , -7.58104828563602e-01 , 6.98741152203883e+00 , -5.45833879447372e-01 , -6.02029979426592e-01 , 7.05535394609302e+00 , -2.04192620412505e+00 , -9.52464649974561e-01 , 6.17561350314181e+00 , -3.41722621815623e-01 , 7.05459739059189e-01 , 4.98822718269962e+00 , -1.76508070915148e-01 , 7.15011045909160e-01 , 6.87569802063465e+00 , -2.65813949706184e-01 , 1.87821401596050e+00 , 6.17148639000042e+00 , -1.39142746020155e-01 , 3.19121571527346e+00 , 7.08169297943734e+00 , -3.52623633643266e-01 , 4.28704150333513e+00 , 5.28084131279023e+00 , 1.10567513914669e+00 , 3.33039748220851e+00 , 4.13032082504737e+00 , 1.03361222932880e+00 , 3.65969506056016e+00 , 5.85402845567876e+00 , 2.24545795979266e+00 , 2.99643108511176e+00 , 5.23298906247265e+00 , 3.58616735010571e+00 , 2.91144354317934e+00 , 6.32723298986784e+00 , 4.51070123329190e+00 , 2.40187458082017e+00 , 3.90138154569027e+00 , 3.72835089186044e+00 , 2.03917229358074e+00 , 2.80846398921116e+00 , 4.14758882143530e+00 , 2.50650876295307e+00 , 3.91298844453545e+00 , 3.24191347230775e+00 , 7.34956310876872e-01 , 2.65262683065697e+00 , 3.03093510230568e+00 , -1.08873067632021e-01 , 3.03479075777373e+00 , 2.71968523126834e+00 , -1.53224067036013e+00 , 1.58431933835869e+00 , 2.19662404627226e+00 , 4.84663033011919e-01 , 4.05360654207426e-01 , 2.54281184654100e+00 , 5.22850387885939e-01 , 2.01418222269637e+00 , 1.01854292646923e+00 , 1.07939207284197e+00 , 1.17878373774636e+00 , 1.02002748422149e-01 , 1.69234806189309e+00 , 2.03096394954476e+00 , -1.12196220288857e+00 , 2.00549956258534e+00 , 5.55540127155334e-01 , 6.08230045696014e-01 , 2.92860616802909e+00 , -6.26608613313456e-01 , 3.49911773798373e-01 , 3.16620675590186e+00 , 1.32574469678829e+00 , 1.34535349196886e+00 , 3.81278293561571e+00 , 8.54908805848377e-01 , 1.96401376998257e+00 , 5.02800542768529e+00 , 2.04583973173547e+00 , 2.65009259290902e+00 , 5.65495448529935e+00 , -3.40620249792508e-01 , 2.91642846838716e+00 , 4.96920032530497e+00 , -1.14997197174513e+00 , 3.05722636775602e+00 , 5.89825979919628e+00 , -4.89817965387989e-01 , 3.57769207472447e+00 , 3.84834437342657e+00 , -1.50752708699716e+00 , 4.54699755046542e+00 , 3.48581418810543e+00 , -7.09405549671007e-01 , 5.40657519380610e+00 , 2.45327301607447e+00 , -2.77184817538420e+00 , 3.87426603648019e+00 , 2.91072210268933e+00 , -3.82282861561061e+00 , 4.48583915434735e+00 , 2.82082657632572e+00 , -2.61007533976154e+00 , 2.66581130977978e+00 , 2.43065666196677e+00 , -3.75388232151684e+00 , 1.83064412611471e+00 , 2.00832727071707e+00 , -3.40582052109809e+00 , 8.80123144237023e-01 , 9.02164653183659e-01 , -4.32047384372355e+00 , 1.06622976437023e+00 , 3.23375599776574e+00 , -5.51443419479539e+00 , 8.47496994767350e-01 , 3.32952578476988e+00 , -3.39034568868058e+00 , 6.78706690315382e-01 , 4.17662301781137e+00 , -3.73185754983894e+00 , 3.59121509335084e-02 , 5.44610695064150e+00 , -2.38388494433046e+00 , -3.15826223986610e-01 , 6.17394163944166e+00 , -4.46828024629853e+00 , 1.00246358211908e+00 , 6.44341520689779e+00 , -5.34434591956838e+00 , 6.05231165538184e-01 , 7.21083675273719e+00 , -6.23608399311769e+00 , 3.58439441165737e+00 , 6.71878398660110e+00 , -6.94187963738071e+00 , 4.29830685918498e+00 , 7.45755343459951e+00 , -6.75115377378520e+00 , 3.19700882140964e+00 , 5.51847976538154e+00 , -4.12885813149755e+00 , 2.26519822423989e+00 , 6.44197001454573e+00 , -4.82528442276646e+00 , 3.19094975560253e+00 , 7.22603873033022e+00 , -4.10434314544566e+00 , 4.58829124181495e+00 , 7.29375655534760e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 16. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 16. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atoms_new_colvar_forces = { ( -7.16599920626333e-02 , 3.03520189493113e-01 , -3.97844554110196e-01 ), ( 1.26596866495085e-02 , 3.04680490772271e-02 , -2.37791019205751e-01 ), ( -4.17592178733622e-02 , 9.26629575009944e-02 , 8.77929809589356e-02 ), ( -9.70053794347984e-02 , 2.48992623070873e-01 , 6.63054983454752e-02 ), ( -1.89853945294203e-02 , 9.93485496391635e-02 , -1.71150647534301e-01 ), ( 7.09261775017845e-02 , -1.84867108646044e-01 , -3.91178688867081e-02 ), ( 1.05027258080738e-02 , -9.96136798939432e-02 , 2.54166018544938e-01 ), ( -4.09879563722719e-02 , 6.10659904102842e-02 , 1.91648579072607e-01 ), ( 6.61012658667264e-02 , -1.89258161381491e-01 , 3.07081105841716e-02 ), ( 1.15146596997166e-01 , -3.91102227968993e-01 , 2.72562397837632e-01 ), ( 2.46453030855937e-02 , -9.93365220421225e-02 , 9.56225083588144e-02 ), ( 2.66421414788933e-02 , -9.71657300342827e-02 , 5.94897841061073e-02 ), ( 1.24522694746926e-02 , -5.57846102591163e-02 , 7.23335698331391e-02 ), ( 1.25918663087693e-02 , -5.36220502851586e-02 , 6.11734810795629e-02 ), ( 5.61350142569206e-03 , -3.51401203977188e-02 , 7.55136988866750e-02 ), ( -8.61049745184722e-03 , 9.34488100012719e-03 , 7.54880974356862e-02 ), ( -2.08306110857868e-03 , -2.89191085757777e-03 , 4.03868197279044e-02 ), ( -5.77438653909533e-03 , 9.64928220907088e-03 , 3.61004204614304e-02 ), ( 2.71548615893904e-03 , -1.30789072162389e-02 , 1.96979142124408e-02 ), ( 9.01654505317240e-03 , -2.20261826877445e-02 , -2.64884795675305e-02 ), ( 8.70551878740283e-03 , -2.37622854338400e-02 , -1.48577425980512e-02 ), ( 6.57817314530784e-03 , -1.35174371713845e-02 , -3.02836212361381e-02 ), ( 1.50644910475842e-02 , -4.66183167563982e-02 , -2.09959283310228e-03 ), ( 2.77292875578808e-02 , -8.83766259112437e-02 , 7.15349274759623e-03 ), ( 1.43436005142690e-02 , -4.68820099433303e-02 , 8.71210519613895e-03 ), ( 1.42893406669391e-02 , -4.40246300593357e-02 , -2.82851322219024e-03 ), ( 9.37614206359767e-03 , -3.71168203279471e-02 , 3.34801668491546e-02 ), ( -7.45360757258783e-04 , -1.54469884200433e-02 , 7.63350951705038e-02 ), ( -3.74542386156819e-03 , 4.05796942472545e-03 , 3.28656966491896e-02 ), ( -5.81287991845206e-03 , 1.11108772852015e-02 , 3.03413992192289e-02 ), ( -7.30600279987893e-03 , 1.78434469740859e-02 , 2.14809824211243e-02 ), ( -1.63716194505806e-02 , 5.20078778820190e-02 , -3.49150141876509e-03 ), ( -9.82228967181316e-03 , 3.57418436312302e-02 , -2.15857699885616e-02 ), ( -1.38718942693465e-02 , 4.99760774537983e-02 , -2.83312021543967e-02 ), ( -2.05092887520622e-03 , 1.48658588304507e-02 , -3.62938698788685e-02 ), ( 1.05217736834276e-02 , -1.58572613080413e-02 , -7.31877103025308e-02 ), ( 4.32888255023710e-03 , -8.72137630605546e-04 , -5.43793223663522e-02 ), ( 3.28969909537636e-03 , 5.96243711290140e-03 , -6.97728044235884e-02 ), ( 7.12885665987956e-03 , -1.49433842714813e-02 , -3.15548733162422e-02 ), ( 1.31781063569408e-02 , -4.15389021041050e-02 , 1.41874342019563e-03 ), ( 5.39047621159515e-04 , 1.59798991413939e-03 , -1.40993565514254e-02 ), ( 4.69602162734545e-04 , 3.18766520365181e-03 , -1.99927400393244e-02 ), ( -6.51622058373524e-03 , 2.04292485461563e-02 , -2.26519647382133e-04 ), ( -2.05899546307361e-02 , 5.76622094085089e-02 , 2.88694586745090e-02 ), ( -1.90249363443350e-02 , 6.31966262801517e-02 , -1.59081022548893e-02 ), ( -2.27391746568829e-02 , 7.51313288340186e-02 , -1.72826679888529e-02 ), ( -1.69927675860640e-02 , 7.24134595931749e-02 , -8.27698731950902e-02 ), ( -2.01217530075865e-02 , 8.65842216823478e-02 , -1.01603973274608e-01 ), ( -8.68915196928372e-03 , 4.65074767613662e-02 , -8.30265180199556e-02 ), ( -1.87053800613670e-02 , 6.66594018957553e-02 , -3.50674513075242e-02 ), ( -2.45844639056470e-02 , 9.28554718936520e-02 , -6.86107244708341e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 16, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 17, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 17, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 17, atoms_positions[size = 51] = { ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 ), ( 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 ), ( 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 ), ( 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 ), ( 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 ), ( 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 ), ( -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 ), ( -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 ), ( -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 ), ( -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ), ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 ), ( 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 ), ( 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 ), ( 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 ), ( 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 ), ( 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 ), ( 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 ), ( 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 ), ( 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 ), ( 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 ), ( 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 ), ( 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 ), ( 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 ), ( 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 ), ( 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 ), ( 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 ), ( 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 ), ( 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 ), ( 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 ), ( -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 ), ( 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 ), ( 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 ), ( -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 ), ( -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 ), ( -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 ), ( -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 ), ( -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 ), ( -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 ), ( -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 ), ( -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 ), ( -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 ), ( -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 ), ( -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 ), ( -2.38520263482903e+00 , -3.14375701461253e-01 , 6.17435317935263e+00 ), ( -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 ), ( -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 ), ( -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 ), ( -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 ), ( -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 ), ( -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 ), ( -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ) } +colvars: Step 17, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652892e-02 , -1.16317231514313e-02 ). +colvars: Done calculating gradients of colvar "main". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 , 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 , 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 , 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 , 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 , 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 , 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 , 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 , 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 , 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 , 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 , 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 , 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 , 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 , 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 , -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 , 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 , -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 , -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 , -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 , -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 , -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 , -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 , -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 , -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 , -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -2.38520263482903e+00 , -3.14375701461253e-01 , 6.17435317935263e+00 , -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 , -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 , -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 , -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 , -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 , -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 , -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99752003051336e-01 , 1.49026874155466e-02 , 1.17705275652892e-02 , -1.16317231514313e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31842640890124e+00 , 4.27666563991377e-02 , -7.55814165289470e-01 , 6.98161373431958e+00 , -5.46930447914904e-01 , -5.95004790465557e-01 , 7.05496473779038e+00 , -2.04419265515020e+00 , -9.47798924092956e-01 , 6.17165466731570e+00 , -3.50661228272422e-01 , 7.10147761082447e-01 , 4.98563105360030e+00 , -1.72375088847105e-01 , 7.18392575573988e-01 , 6.87031875639091e+00 , -2.65755508115362e-01 , 1.88517838842659e+00 , 6.16858574027749e+00 , -1.45173936390902e-01 , 3.19413443347359e+00 , 7.07759256602283e+00 , -3.53873038906572e-01 , 4.29096223182200e+00 , 5.28414969071837e+00 , 1.10309488348566e+00 , 3.33363115440586e+00 , 4.13204874507385e+00 , 1.03087987802521e+00 , 3.66451906155028e+00 , 5.84941495190331e+00 , 2.24613913620191e+00 , 2.99513585924582e+00 , 5.23619141464350e+00 , 3.58413771183494e+00 , 2.91462044195537e+00 , 6.32570445219753e+00 , 4.50709396482175e+00 , 2.39282349326215e+00 , 3.89697554112079e+00 , 3.72362972100010e+00 , 2.04072087393042e+00 , 2.80264953840457e+00 , 4.15125725402617e+00 , 2.50182320814122e+00 , 3.92120535314590e+00 , 3.24192473108118e+00 , 7.33275138710238e-01 , 2.65195362896672e+00 , 3.02187350952943e+00 , -1.08341772824846e-01 , 3.03760346030567e+00 , 2.71709372170948e+00 , -1.52575473615491e+00 , 1.58933626987086e+00 , 2.19505672846082e+00 , 4.73037859038400e-01 , 3.97435079025353e-01 , 2.55282941625953e+00 , 5.20023192026839e-01 , 2.02248215076224e+00 , 1.02878118609567e+00 , 1.07862299238941e+00 , 1.17630755791138e+00 , 1.07899791709735e-01 , 1.69305670761448e+00 , 2.03355528944045e+00 , -1.11677096479422e+00 , 2.00584780317634e+00 , 5.57095803785503e-01 , 6.08564289550157e-01 , 2.93041033253442e+00 , -6.20108375355126e-01 , 3.49594334029527e-01 , 3.16490186018110e+00 , 1.32424116087050e+00 , 1.34559724726418e+00 , 3.80406867682204e+00 , 8.51987930043542e-01 , 1.96841119501618e+00 , 5.02670292741534e+00 , 2.05356881044579e+00 , 2.65930414003065e+00 , 5.66125416784870e+00 , -3.38682478026601e-01 , 2.91622090530135e+00 , 4.96825819395479e+00 , -1.14679353516258e+00 , 3.05894421428331e+00 , 5.89593549427650e+00 , -4.95456247157830e-01 , 3.56542447261429e+00 , 3.84883442061416e+00 , -1.51116882016278e+00 , 4.54585747453814e+00 , 3.47526581238745e+00 , -7.05918947191323e-01 , 5.40854235899091e+00 , 2.45650820567437e+00 , -2.77009272878594e+00 , 3.87594044478412e+00 , 2.90788516185326e+00 , -3.82111847761655e+00 , 4.49206379501208e+00 , 2.81908711983506e+00 , -2.61290545334059e+00 , 2.67038135355322e+00 , 2.42373366718188e+00 , -3.75951649017049e+00 , 1.82097294856739e+00 , 2.00486410156684e+00 , -3.40203620539403e+00 , 8.83304370040022e-01 , 8.95022442095609e-01 , -4.32391034156290e+00 , 1.06735870803655e+00 , 3.22805398229467e+00 , -5.51003958205363e+00 , 8.40441207147368e-01 , 3.32954846397289e+00 , -3.38355198439083e+00 , 6.81708889563793e-01 , 4.18564906167931e+00 , -3.72338871222330e+00 , 3.62579539864896e-02 , 5.44133506196972e+00 , -2.38520263482903e+00 , -3.14375701461253e-01 , 6.17435317935263e+00 , -4.46615882900850e+00 , 1.00111836711645e+00 , 6.44390942057885e+00 , -5.34814587140257e+00 , 6.03750779228814e-01 , 7.21361020375718e+00 , -6.23297091659691e+00 , 3.58934024001857e+00 , 6.72245008981203e+00 , -6.94659889839222e+00 , 4.29880323258107e+00 , 7.46276963493827e+00 , -6.75069434733693e+00 , 3.19386110455520e+00 , 5.51604433829556e+00 , -4.12971091235709e+00 , 2.25920129969455e+00 , 6.43372631881558e+00 , -4.81914875580783e+00 , 3.19261004279224e+00 , 7.23018145226995e+00 , -4.10357371665396e+00 , 4.58768136737181e+00 , 7.29177501268788e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 17. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 17. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atoms_new_colvar_forces = { ( -7.15991844821387e-02 , 3.03566046493554e-01 , -3.98589394335568e-01 ), ( 1.27080880761104e-02 , 3.02482168390730e-02 , -2.37956547495990e-01 ), ( -4.18215965128955e-02 , 9.29391300559080e-02 , 8.80280661517742e-02 ), ( -9.70578106655439e-02 , 2.49485275638335e-01 , 6.61481548320793e-02 ), ( -1.89349892460272e-02 , 9.92934578601701e-02 , -1.71547671981010e-01 ), ( 7.09549756938869e-02 , -1.85205681928521e-01 , -3.89553397840212e-02 ), ( 1.04360069804477e-02 , -9.94579562621154e-02 , 2.54601524564221e-01 ), ( -4.10194911993123e-02 , 6.13670159681508e-02 , 1.91634456228622e-01 ), ( 6.61500758622970e-02 , -1.89564992241884e-01 , 3.07364530191407e-02 ), ( 1.15129312716163e-01 , -3.91425701068371e-01 , 2.73230025879347e-01 ), ( 2.46652291494805e-02 , -9.93621704587276e-02 , 9.57319835750408e-02 ), ( 2.66487201515362e-02 , -9.71899657435524e-02 , 5.95549496710853e-02 ), ( 1.24622672888664e-02 , -5.57702453559136e-02 , 7.24033746190143e-02 ), ( 1.26017842784006e-02 , -5.36203395040831e-02 , 6.12364446426536e-02 ), ( 5.62084309259652e-03 , -3.50953115725840e-02 , 7.55762909057078e-02 ), ( -8.60826813568425e-03 , 9.44406645854299e-03 , 7.55323767690547e-02 ), ( -2.08429098101708e-03 , -2.83671367062416e-03 , 4.04078631431500e-02 ), ( -5.77487048564609e-03 , 9.70643059913453e-03 , 3.61177754946845e-02 ), ( 2.70805118577230e-03 , -1.30373194634879e-02 , 1.96985074289443e-02 ), ( 8.99648984984501e-03 , -2.20080768587484e-02 , -2.65342276660742e-02 ), ( 8.69473273520900e-03 , -2.37630816502961e-02 , -1.48802114220181e-02 ), ( 6.56501421850287e-03 , -1.35217932541125e-02 , -3.03210592179037e-02 ), ( 1.50590452715200e-02 , -4.66398655552029e-02 , -2.10071241619051e-03 ), ( 2.77316589065011e-02 , -8.84477423995500e-02 , 7.18007358178622e-03 ), ( 1.43470225305447e-02 , -4.69209172028335e-02 , 8.73278967907639e-03 ), ( 1.42925048375785e-02 , -4.40754955097007e-02 , -2.81534258881912e-03 ), ( 9.38444695561449e-03 , -3.71324088332392e-02 , 3.35213337177348e-02 ), ( -7.26987884782428e-04 , -1.54240642662770e-02 , 7.64135749901224e-02 ), ( -3.73665213056788e-03 , 4.07353264834062e-03 , 3.28987833829794e-02 ), ( -5.80219750707640e-03 , 1.11221101587789e-02 , 3.03749870854370e-02 ), ( -7.30353687369275e-03 , 1.78775846305822e-02 , 2.14936665260160e-02 ), ( -1.63806520613838e-02 , 5.20777052185658e-02 , -3.52025758798729e-03 ), ( -9.82908388362489e-03 , 3.57666323257724e-02 , -2.16173158817409e-02 ), ( -1.38788964719874e-02 , 5.00043362505760e-02 , -2.83698539092529e-02 ), ( -2.06079367882705e-03 , 1.48650968594908e-02 , -3.63347462413643e-02 ), ( 1.05048058308129e-02 , -1.59065676245395e-02 , -7.32554311863814e-02 ), ( 4.32121096086671e-03 , -9.17335633906933e-04 , -5.44231732871726e-02 ), ( 3.28011518369857e-03 , 5.90930783998450e-03 , -6.98300821185564e-02 ), ( 7.12840086648953e-03 , -1.49955402368339e-02 , -3.15702448585199e-02 ), ( 1.31906996331723e-02 , -4.16155160943026e-02 , 1.45046337050662e-03 ), ( 5.47380948155791e-04 , 1.55122543651116e-03 , -1.40928369624718e-02 ), ( 4.79435149741411e-04 , 3.12912676270521e-03 , -1.99871975294202e-02 ), ( -6.50729574857995e-03 , 2.04140395217321e-02 , -2.15099640596014e-04 ), ( -2.05769479255007e-02 , 5.77012793802570e-02 , 2.88966554445180e-02 ), ( -1.90202892635905e-02 , 6.32108127600351e-02 , -1.59219288397588e-02 ), ( -2.27329271959792e-02 , 7.51477831841043e-02 , -1.72969138581540e-02 ), ( -1.70051329242468e-02 , 7.24073007431202e-02 , -8.28531707934525e-02 ), ( -2.01386533689387e-02 , 8.65808706267130e-02 , -1.01708791742204e-01 ), ( -8.69931533541390e-03 , 4.64720375584738e-02 , -8.31006752311498e-02 ), ( -1.87081206453085e-02 , 6.66773226446364e-02 , -3.51058027924910e-02 ), ( -2.46003337460445e-02 , 9.28970579261591e-02 , -6.86965453344270e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 17, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 18, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 18, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 18, atoms_positions[size = 51] = { ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 ), ( 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 ), ( 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 ), ( 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 ), ( 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 ), ( 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 ), ( -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 ), ( -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 ), ( -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 ), ( -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ), ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 ), ( 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 ), ( 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 ), ( 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 ), ( 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 ), ( 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 ), ( 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 ), ( 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 ), ( 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 ), ( 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 ), ( 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 ), ( 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 ), ( 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 ), ( 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 ), ( 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 ), ( 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 ), ( 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 ), ( 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 ), ( 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 ), ( -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 ), ( 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 ), ( 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 ), ( -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 ), ( -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 ), ( -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 ), ( -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 ), ( -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 ), ( -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 ), ( -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 ), ( -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 ), ( -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 ), ( -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 ), ( -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 ), ( -2.38669067542350e+00 , -3.14191400105746e-01 , 6.17411576908559e+00 ), ( -4.46409638252639e+00 , 9.98162053848095e-01 , 6.44369645585639e+00 ), ( -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 ), ( -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 ), ( -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 ), ( -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 ), ( -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 ), ( -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ) } +colvars: Step 18, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 , 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 , 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 , 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 , 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 , 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 , 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 , 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 , 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 , 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 , 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 , 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 , 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 , 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 , 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 , -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 , 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 , -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 , -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 , -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 , -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 , -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 , -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 , -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 , -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 , -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -2.38669067542350e+00 , -3.14191400105746e-01 , 6.17411576908559e+00 , -4.46409638252639e+00 , 9.98162053848095e-01 , 6.44369645585639e+00 , -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 , -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 , -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 , -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 , -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 , -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99756683838998e-01 , 1.45554555894403e-02 , 1.17900504611689e-02 , -1.16493150853541e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31535822708584e+00 , 4.23899561569954e-02 , -7.53198369093050e-01 , 6.97449734947607e+00 , -5.47808134007371e-01 , -5.87497076291308e-01 , 7.05398429189009e+00 , -2.04635560099962e+00 , -9.43326011657834e-01 , 6.17000529439014e+00 , -3.59239249647058e-01 , 7.15436283254258e-01 , 4.98211987427564e+00 , -1.68170371318526e-01 , 7.21491276921323e-01 , 6.86440440050774e+00 , -2.65966163452302e-01 , 1.89253384277864e+00 , 6.16478400768929e+00 , -1.51735840278890e-01 , 3.19465498451155e+00 , 7.07487854317113e+00 , -3.54475329872067e-01 , 4.29570124560701e+00 , 5.28820412886918e+00 , 1.10007880079344e+00 , 3.33677229097238e+00 , 4.13306495168684e+00 , 1.02824738403551e+00 , 3.66964990115015e+00 , 5.84483383956595e+00 , 2.24739850348299e+00 , 2.99353276041589e+00 , 5.23834916979140e+00 , 3.58214113341282e+00 , 2.91717290465518e+00 , 6.32443072536376e+00 , 4.50434557107580e+00 , 2.38332939436494e+00 , 3.89202267489871e+00 , 3.71836356806518e+00 , 2.04191633243679e+00 , 2.79796936148934e+00 , 4.15469351337485e+00 , 2.49695450789214e+00 , 3.92824431965090e+00 , 3.24153579662803e+00 , 7.31941044240104e-01 , 2.65302261952828e+00 , 3.01471878706075e+00 , -1.07413989120535e-01 , 3.04140057121614e+00 , 2.71363435554484e+00 , -1.52074762964215e+00 , 1.59354319294042e+00 , 2.19195942595647e+00 , 4.62536292452320e-01 , 3.90039579386762e-01 , 2.56262010816780e+00 , 5.17005798292244e-01 , 2.03084199078053e+00 , 1.04118440229783e+00 , 1.07655490015984e+00 , 1.17354153936579e+00 , 1.12210486533412e-01 , 1.69411502449577e+00 , 2.03632259588894e+00 , -1.11191250387906e+00 , 2.00677787334977e+00 , 5.58633446427328e-01 , 6.09322528559613e-01 , 2.93362153845632e+00 , -6.13725016099643e-01 , 3.49488708595183e-01 , 3.16374316425058e+00 , 1.32211716477699e+00 , 1.34562375115966e+00 , 3.79461370712043e+00 , 8.48911046259015e-01 , 1.97235189136395e+00 , 5.02588970652357e+00 , 2.06219607051153e+00 , 2.66884415060109e+00 , 5.66789708239521e+00 , -3.37327095880418e-01 , 2.91590512321671e+00 , 4.96778395762448e+00 , -1.14342272086556e+00 , 3.06046897875778e+00 , 5.89339489296298e+00 , -5.00896111169956e-01 , 3.55412105077497e+00 , 3.84880583680172e+00 , -1.51426979697403e+00 , 4.54428518509684e+00 , 3.46473670533679e+00 , -7.03087979035711e-01 , 5.41046392100789e+00 , 2.45934266065583e+00 , -2.76736041350539e+00 , 3.87907185310421e+00 , 2.90456290699963e+00 , -3.81968411527737e+00 , 4.49820503748094e+00 , 2.81757769434002e+00 , -2.61635862042227e+00 , 2.67322342085141e+00 , 2.41663570658713e+00 , -3.76466103489309e+00 , 1.81310678920097e+00 , 2.00235378599809e+00 , -3.39796660949251e+00 , 8.85432670571214e-01 , 8.88275178171236e-01 , -4.32562972228946e+00 , 1.06855072699218e+00 , 3.22259320067218e+00 , -5.50612867151365e+00 , 8.33319770544087e-01 , 3.32982548696592e+00 , -3.37760795896898e+00 , 6.84808536882627e-01 , 4.19385619164959e+00 , -3.71520050105914e+00 , 3.82616194620365e-02 , 5.43787192954506e+00 , -2.38669067542350e+00 , -3.14191400105746e-01 , 6.17411576908559e+00 , -4.46409638252639e+00 , 9.98162053848095e-01 , 6.44369645585639e+00 , -5.35177276573183e+00 , 6.02205161912385e-01 , 7.21610996903272e+00 , -6.23203089944233e+00 , 3.59469976291079e+00 , 6.72654487926828e+00 , -6.95101700425259e+00 , 4.29905851021590e+00 , 7.46776563036093e+00 , -6.74884065894173e+00 , 3.19041425990672e+00 , 5.51356451889491e+00 , -4.12975000385446e+00 , 2.25398964321332e+00 , 6.42564815211718e+00 , -4.81409148715139e+00 , 3.19577513268307e+00 , 7.23475835678264e+00 , -4.10161213506057e+00 , 4.58521207379435e+00 , 7.28932245334770e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 18. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 18. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atoms_new_colvar_forces = { ( -7.15143246749638e-02 , 3.03607143562019e-01 , -3.99266458606129e-01 ), ( 1.27511738446594e-02 , 3.00967629854831e-02 , -2.38127471469929e-01 ), ( -4.18863071949037e-02 , 9.32301455194097e-02 , 8.81628918987510e-02 ), ( -9.70895404804677e-02 , 2.49908041041692e-01 , 6.59713718888419e-02 ), ( -1.88725880515165e-02 , 9.92228346931219e-02 , -1.71872787066905e-01 ), ( 7.09670536741436e-02 , -1.85486495457679e-01 , -3.87969474637418e-02 ), ( 1.03600953886065e-02 , -9.93144409185911e-02 , 2.54966692370490e-01 ), ( -4.10379422641935e-02 , 6.15825267191375e-02 , 1.91648394424666e-01 ), ( 6.61910179362998e-02 , -1.89870815465685e-01 , 3.08332055522194e-02 ), ( 1.15081183601858e-01 , -3.91707048313628e-01 , 2.73856265793050e-01 ), ( 2.46774375424239e-02 , -9.93924532683559e-02 , 9.58370334057540e-02 ), ( 2.66500535243150e-02 , -9.72209778665420e-02 , 5.96137627610270e-02 ), ( 1.24681376732403e-02 , -5.57608422003375e-02 , 7.24674929744034e-02 ), ( 1.26076824836146e-02 , -5.36224387337503e-02 , 6.12952593688761e-02 ), ( 5.62539094638127e-03 , -3.50561345523897e-02 , 7.56316999753237e-02 ), ( -8.60606560277205e-03 , 9.53712138345241e-03 , 7.55675193204442e-02 ), ( -2.08543446117501e-03 , -2.78615340021712e-03 , 4.04226285887230e-02 ), ( -5.77487538308468e-03 , 9.76017420918321e-03 , 3.61300350716817e-02 ), ( 2.70138528408105e-03 , -1.30014125518309e-02 , 1.96922867703026e-02 ), ( 8.97908516827587e-03 , -2.19969142018477e-02 , -2.65871231424575e-02 ), ( 8.68487447282497e-03 , -2.37680120333839e-02 , -1.49066296522007e-02 ), ( 6.55363705774326e-03 , -1.35293937357806e-02 , -3.03613858553427e-02 ), ( 1.50526198911460e-02 , -4.66653732768597e-02 , -2.10512603376900e-03 ), ( 2.77299143813737e-02 , -8.85219509446862e-02 , 7.20549150444689e-03 ), ( 1.43478752729337e-02 , -4.69610108498508e-02 , 8.75330557484605e-03 ), ( 1.42932681641806e-02 , -4.41264084608804e-02 , -2.80083205314169e-03 ), ( 9.38971606170556e-03 , -3.71491334276232e-02 , 3.35616067674381e-02 ), ( -7.12546262469610e-04 , -1.54013014397138e-02 , 7.64908271177000e-02 ), ( -3.72927860592954e-03 , 4.08981429157061e-03 , 3.29319617386191e-02 ), ( -5.79295740178263e-03 , 1.11354132169146e-02 , 3.04101252621499e-02 ), ( -7.30076957302218e-03 , 1.79113599273376e-02 , 2.15049483746605e-02 ), ( -1.63859058028266e-02 , 5.21459645145339e-02 , -3.55241297422586e-03 ), ( -9.83317150417714e-03 , 3.57919846305960e-02 , -2.16488481834581e-02 ), ( -1.38825585085550e-02 , 5.00342849475707e-02 , -2.84074398206996e-02 ), ( -2.06827442900072e-03 , 1.48642117794079e-02 , -3.63755080607341e-02 ), ( 1.04902107573028e-02 , -1.59566230977413e-02 , -7.33221264395743e-02 ), ( 4.31488123513660e-03 , -9.60525185674127e-04 , -5.44635132252315e-02 ), ( 3.27250278479951e-03 , 5.85914181832614e-03 , -6.98826067047734e-02 ), ( 7.12741052770944e-03 , -1.50453533016600e-02 , -3.15817248280361e-02 ), ( 1.31993193745071e-02 , -4.16884063363824e-02 , 1.48789399052296e-03 ), ( 5.54304324758442e-04 , 1.50953505055299e-03 , -1.40799929296691e-02 ), ( 4.87659795907501e-04 , 3.07695750800322e-03 , -1.99737071226952e-02 ), ( -6.49910304176036e-03 , 2.04035182113293e-02 , -1.98666442130922e-04 ), ( -2.05638510973712e-02 , 5.77453732012774e-02 , 2.89275614275457e-02 ), ( -1.90138229562706e-02 , 6.32310314419597e-02 , -1.59301210133700e-02 ), ( -2.27246458259210e-02 , 7.51715617639337e-02 , -1.73043097713145e-02 ), ( -1.70122524685426e-02 , 7.24067493443881e-02 , -8.29303072212396e-02 ), ( -2.01489048049457e-02 , 8.65835663076626e-02 , -1.01806981860336e-01 ), ( -8.70570647921074e-03 , 4.64421864114534e-02 , -8.31679002836407e-02 ), ( -1.87075793223643e-02 , 6.67000943942084e-02 , -3.51396666630672e-02 ), ( -2.46094849727014e-02 , 9.29421201465667e-02 , -6.87796670346709e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 18, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 19, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 19, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 19, atoms_positions[size = 51] = { ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 ), ( 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 ), ( 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 ), ( 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 ), ( 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 ), ( 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 ), ( -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 ), ( -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 ), ( -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 ), ( -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ), ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 ), ( 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 ), ( 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 ), ( 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 ), ( 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 ), ( 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 ), ( 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 ), ( 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 ), ( 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 ), ( 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 ), ( 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 ), ( 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 ), ( 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 ), ( 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 ), ( 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 ), ( 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 ), ( 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 ), ( 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 ), ( 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 ), ( -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 ), ( 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 ), ( 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 ), ( -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 ), ( -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 ), ( -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 ), ( -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 ), ( -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 ), ( -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 ), ( -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 ), ( -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 ), ( -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 ), ( -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 ), ( -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 ), ( -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 ), ( -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 ), ( -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 ), ( -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 ), ( -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 ), ( -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 ), ( -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 ), ( -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ) } +colvars: Step 19, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687068e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 , 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 , 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 , 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 , 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 , 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 , 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 , 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 , 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 , 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 , 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 , 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 , 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 , 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 , 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 , -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 , 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 , -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 , -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 , -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 , -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 , -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 , -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 , -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 , -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 , -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 , -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 , -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 , -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 , -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 , -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 , -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 , -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99758962093459e-01 , 1.42609660687068e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31286924612146e+00 , 4.20709002657016e-02 , -7.50310973601562e-01 , 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 7.05237741202441e+00 , -2.04837739898547e+00 , -9.38976786506497e-01 , 6.17040992269014e+00 , -3.67234567539433e-01 , 7.21370746960566e-01 , 4.97780567708284e+00 , -1.63963227224770e-01 , 7.24310519513121e-01 , 6.85806181218367e+00 , -2.66500438549505e-01 , 1.90027164378462e+00 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 7.07356178480316e+00 , -3.54432133671661e-01 , 4.30112700679283e+00 , 5.29264658067149e+00 , 1.09670404349914e+00 , 3.33981231252106e+00 , 4.13347874889194e+00 , 1.02571260918724e+00 , 3.67507497094714e+00 , 5.84042955734697e+00 , 2.24894766555370e+00 , 2.99172505249207e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 6.32338816326332e+00 , 4.50228050795295e+00 , 2.37351131661641e+00 , 3.88679853006935e+00 , 3.71264405079361e+00 , 2.04271834521290e+00 , 2.79442513540384e+00 , 4.15784784342757e+00 , 2.49191664592584e+00 , 3.93387323007324e+00 , 3.24064027559825e+00 , 7.30894843872545e-01 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 3.04612003658755e+00 , 2.70936239615274e+00 , -1.51737057436414e+00 , 1.59628821127277e+00 , 2.18775314428965e+00 , 4.53343844198391e-01 , 3.83628305926527e-01 , 2.57198487118335e+00 , 5.13744483714906e-01 , 2.03910977928000e+00 , 1.05526433579986e+00 , 1.07333375386716e+00 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 2.03930517641700e+00 , -1.10746568756944e+00 , 2.00829225995639e+00 , 5.60235993768988e-01 , 6.10452440481700e-01 , 2.93788971767506e+00 , -6.07628084827977e-01 , 3.49561605795979e-01 , 3.16280472594167e+00 , 1.31945770427387e+00 , 1.34563923457020e+00 , 3.78484211239001e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , 2.07129981280793e+00 , 2.67852596629928e+00 , 5.67473104185375e+00 , -3.36625555807058e-01 , 2.91544898921130e+00 , 4.96777002454663e+00 , -1.13989999148141e+00 , 3.06181539111291e+00 , 5.89071675225471e+00 , -5.06186165567059e-01 , 3.54402209387388e+00 , 3.84806051603871e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -7.01032040432242e-01 , 5.41231754661095e+00 , 2.46178494948919e+00 , -2.76394446429398e+00 , 3.88365202901328e+00 , 2.90058940268421e+00 , -3.81845347014550e+00 , 4.50422633455713e+00 , 2.81630608663991e+00 , -2.62051278777713e+00 , 2.67420271816074e+00 , 2.40944226964525e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.39374392284059e+00 , 8.86529838998036e-01 , 8.81856576539482e-01 , -4.32528758548522e+00 , 1.06957343542032e+00 , 3.21782288623358e+00 , -5.50281645260406e+00 , 8.26143315255739e-01 , 3.33032614574722e+00 , -3.37268213490958e+00 , 6.88125155379590e-01 , 4.20071001070670e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -2.38818462389785e+00 , -3.15034590810124e-01 , 6.17323190730087e+00 , -4.46225640677927e+00 , 9.93530104985184e-01 , 6.44282281367477e+00 , -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 , -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 , -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 , -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 , -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 , -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 19. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 19. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atoms_new_colvar_forces = { ( -7.14077590702326e-02 , 3.03639970618158e-01 , -3.99862623514067e-01 ), ( 1.27881311797386e-02 , 3.00156744122846e-02 , -2.38301254790407e-01 ), ( -4.19519028873146e-02 , 9.35290707918833e-02 , 8.81926041657877e-02 ), ( -9.71004375206781e-02 , 2.50250971830372e-01 , 6.57776690911294e-02 ), ( -1.87998622166412e-02 , 9.91374485926363e-02 , -1.72118839430279e-01 ), ( 7.09626200046807e-02 , -1.85703030420808e-01 , -3.86453310144054e-02 ), ( 1.02768410340876e-02 , -9.91850800704239e-02 , 2.55253853212102e-01 ), ( -4.10433812807934e-02 , 6.17087230475970e-02 , 1.91690812071477e-01 ), ( 6.62233150611981e-02 , -1.90167721803567e-01 , 3.09983544618496e-02 ), ( 1.15003966443554e-01 , -3.91937648056864e-01 , 2.74429662774009e-01 ), ( 2.46812974419315e-02 , -9.94258146412512e-02 , 9.59357593321758e-02 ), ( 2.66459609072608e-02 , -9.72575765949007e-02 , 5.96657296750887e-02 ), ( 1.24695131914519e-02 , -5.57562195730971e-02 , 7.25248107254090e-02 ), ( 1.26092198409545e-02 , -5.36278872660035e-02 , 6.13488949830409e-02 ), ( 5.62681147971932e-03 , -3.50232748733177e-02 , 7.56788968781099e-02 ), ( -8.60415005884939e-03 , 9.62176625969063e-03 , 7.55926821951814e-02 ), ( -2.08655279010192e-03 , -2.74151909885105e-03 , 4.04309135482712e-02 ), ( -5.77449105629113e-03 , 9.80913615447252e-03 , 3.61368984787320e-02 ), ( 2.69566274999494e-03 , -1.29722622520676e-02 , 1.96797958058926e-02 ), ( 8.96497685882790e-03 , -2.19934906690525e-02 , -2.66451373083052e-02 ), ( 8.67631064794138e-03 , -2.37772038243613e-02 , -1.49358354286275e-02 ), ( 6.54449571419080e-03 , -1.35403908603913e-02 , -3.04031721925374e-02 ), ( 1.50454384630021e-02 , -4.66942483082076e-02 , -2.11209871448278e-03 ), ( 2.77241036133913e-02 , -8.85971246913935e-02 , 7.22997775690740e-03 ), ( 1.43461138727377e-02 , -4.70010830247043e-02 , 8.77355335079920e-03 ), ( 1.42916168907113e-02 , -4.41759052969429e-02 , -2.78498300656853e-03 ), ( 9.39169571445058e-03 , -3.71662534556159e-02 , 3.36002219154809e-02 ), ( -7.02702203154160e-04 , -1.53787093342839e-02 , 7.65647743355094e-02 ), ( -3.72362969097916e-03 , 4.10664783797948e-03 , 3.29642053334803e-02 ), ( -5.78554254176953e-03 , 1.11507318324770e-02 , 3.04456069939036e-02 ), ( -7.29784765745150e-03 , 1.79439584046955e-02 , 2.15143492971677e-02 ), ( -1.63872029943874e-02 , 5.22105740129330e-02 , -3.58746379327102e-03 ), ( -9.83436728933798e-03 , 3.58169908716224e-02 , -2.16798178840036e-02 ), ( -1.38826941479590e-02 , 5.00648597055764e-02 , -2.84434181671928e-02 ), ( -2.07303470268060e-03 , 1.48629103736301e-02 , -3.64151138487412e-02 ), ( 1.04786554117137e-02 , -1.60066238108003e-02 , -7.33856896007904e-02 ), ( 4.31023778396208e-03 , -1.00084497686633e-03 , -5.44992546381539e-02 ), ( 3.26728614384987e-03 , 5.81290388986927e-03 , -6.99290438725339e-02 ), ( 7.12599788830756e-03 , -1.50915587910003e-02 , -3.15889400834817e-02 ), ( 1.32036800757807e-02 , -4.17552991830072e-02 , 1.53018914256153e-03 ), ( 5.59622310848572e-04 , 1.47419140054326e-03 , -1.40614251650752e-02 ), ( 4.94051785359337e-04 , 3.03273025975037e-03 , -1.99529580396408e-02 ), ( -6.49191624788353e-03 , 2.03981522284860e-02 , -1.78085695653598e-04 ), ( -2.05511764922100e-02 , 5.77936243785590e-02 , 2.89605276578091e-02 ), ( -1.90057197022633e-02 , 6.32567607724533e-02 , -1.59332941394232e-02 ), ( -2.27145709982415e-02 , 7.52020714968191e-02 , -1.73056614158674e-02 ), ( -1.70136933099124e-02 , 7.24112968951755e-02 , -8.29999768120055e-02 ), ( -2.01519254267428e-02 , 8.65915569665776e-02 , -1.01896782591472e-01 ), ( -8.70791333279080e-03 , 4.64182692798261e-02 , -8.32269283153985e-02 ), ( -1.87036946668894e-02 , 6.67269139196539e-02 , -3.51688999413350e-02 ), ( -2.46114542240917e-02 , 9.29888646440581e-02 , -6.88587137781561e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 19, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 20, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800977e-02 , 3.00052379356399e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500017e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827238e-02 , 1.91760996033175e-01 ), ( 6.62468727487265e-02 , -1.90448081926945e-01 , 3.12288455216890e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807517e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489683e-02 ), ( 1.24661136135099e-02 , -5.57559811144078e-02 , 7.25743621949596e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332647e-03 , -3.49973301865402e-02 , 7.57170861826678e-02 ), ( -8.60292310050453e-03 , 9.69554753037324e-03 , 7.56073713177290e-02 ), ( -2.08776469672694e-03 , -2.70415172113731e-03 , 4.04328246755312e-02 ), ( -5.77389521453809e-03 , 9.85182430390029e-03 , 3.61382862311481e-02 ), ( 2.69104804092523e-03 , -1.29509138532637e-02 , 1.96620498003800e-02 ), ( 8.95486758503647e-03 , -2.19984645975749e-02 , -2.67054922301013e-02 ), ( 8.66947656368633e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541543e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516849e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879236e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703577e-03 , -3.71828583991163e-02 , 3.36363523912981e-02 ), ( -6.98144545634549e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600071e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540629e-03 , 1.11679149109106e-02 , 3.04799282045032e-02 ), ( -7.29500058088395e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040444e-02 , -3.62466193947451e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308240e-02 ), ( -2.07475381329402e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505724e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288625e-03 , -1.03735135095860e-03 , -5.45293145217132e-02 ), ( 3.26495468493792e-03 , 5.77162454807398e-03 , -6.99680928834496e-02 ), ( 7.12436996401246e-03 , -1.51327555336419e-02 , -3.15916578475220e-02 ), ( 1.32036569636365e-02 , -4.18136663470711e-02 , 1.57606808925122e-03 ), ( 5.63178713376306e-04 , 1.44649438052730e-03 , -1.40381831264554e-02 ), ( 4.98434308056249e-04 , 2.99804808326463e-03 , -1.99261927958005e-02 ), ( -6.48604874882730e-03 , 2.03983070643250e-02 , -1.54655641113389e-04 ), ( -2.05396268108373e-02 , 5.78448103620468e-02 , 2.89933897342496e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654820e-03 , 4.64004872660571e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278478e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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..f60bc06ed --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,27 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x ( 0.99975884202595 , 0.01402736950034 , 0.011979408737928 , -0.011915723314925 ) +} + +colvar { + name main + x ( 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 ) +} + +colvar { + name fitting + x ( 8.3109067593225 , 0.041832105536949 , -0.74720152184922 , 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 7.0501314089404 , -2.0502351229669 , -0.93466980629676 , 6.1724025468072 , -0.37440006998022 , 0.72796068970041 , 4.9728901219597 , -0.15984013302521 , 0.72686147800692 , 6.8514301642465 , -0.26741105895838 , 1.9083377792785 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 7.073607414672 , -0.35378704127878 , 4.3070951913435 , 5.2970773270167 , 1.0930675777403 , 3.3427298943302 , 4.1334323731907 , 1.0232724624507 , 3.6807757981069 , 5.8363306008465 , 2.2505141275817 , 2.9898069553745 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 6.3225154324575 , 4.5006943210992 , 2.3634882582325 , 3.8815799727105 , 3.7065612462023 , 2.0430944440883 , 2.7919894870931 , 4.1606818038692 , 2.4867320360913 , 3.9379247666863 , 3.2391551773311 , 0.73009137441107 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 3.0516504481894 , 2.7043614871659 , -1.5156733303712 , 1.5970874871384 , 2.1829728692071 , 0.44555677054977 , 0.37858437885899 , 2.5807264635357 , 0.51019557090508 , 2.04711677578 , 1.0703813637383 , 1.069206754706 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 2.0425329047304 , -1.1035104960071 , 2.0103674846849 , 0.56194901870408 , 0.61185187522511 , 2.9428132426689 , -0.60197676959252 , 0.34978459930961 , 3.1621649077962 , 1.3163590181237 , 1.3458687673819 , 3.7752112850979 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , 2.0804193492853 , 2.6881595598658 , 5.6815929959461 , -0.33660676483589 , 2.9148298650463 , 4.9681489667417 , -1.1362865907604 , 3.063001046068 , 5.8880007578731 , -0.51135551219128 , 3.535300553984 , 3.8464371088115 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -0.69985197514866 , 5.4140943569769 , 2.4638642323208 , -2.7601618038614 , 3.8895607334677 , 2.895793363421 , -3.8173497124104 , 4.5101036996167 , 2.8152773748772 , -2.6253924219612 , 2.6733261276654 , 2.4022619953018 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.3895014416165 , 0.8866696376631 , 0.87567133268272 , -4.322724391988 , 1.0702172791569 , 3.2141303643402 , -5.5001342374076 , 0.81893213505031 , 3.3310166100638 , -3.3688860558692 , 0.69174478744455 , 4.2057900990597 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -2.3895289778026 , -0.31661424092553 , 6.1717119733279 , -4.4607970213475 , 0.98729806770613 , 6.4413742570766 , -5.3579745601884 , 0.599067686148 , 7.2198955321113 , -6.2369282614895 , 3.6061273507614 , 6.7353796872239 , -6.9588258659327 , 4.2988412219219 , 7.4769553986534 , -6.7403993718841 , 3.1830257218785 , 5.5094675051539 , -4.1276723189508 , 2.2467034673003 , 6.4110909930055 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 , -4.0937877414092 , 4.5760013650879 , 7.2838298499369 ) +} + +restraint { + configuration { + step 20 + 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..bbd980fe3 --- /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 main fitting + 0 ( 9.99574098859265e-01 , 2.06195455610082e-02 , 1.42967532305180e-02 , -1.49016132553111e-02 ) ( -3.25898609205420e-01 , 1.69798809632672e+01 , 1.71828081280911e+01 , 1.81199165160869e+01 ) ( 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 ) ( 8.42800577274180e+00 , 4.20078975080390e-02 , -7.44030813065838e-01 , 7.00603893758568e+00 , -4.77027509506929e-01 , -6.85943612353956e-01 , 7.03995610666207e+00 , -2.00300543189696e+00 , -1.04193958373184e+00 , 6.23200000000000e+00 , -2.52000000000000e-01 , 6.17000000000000e-01 , 5.03400000000000e+00 , -2.07000000000000e-01 , 6.33000000000000e-01 , 6.91001275925403e+00 , -2.66002475871675e-01 , 1.77300130998501e+00 , 6.18497319580413e+00 , -1.33026455636757e-01 , 3.03899989543227e+00 , 7.20098993928912e+00 , -3.16951366942949e-01 , 4.30201369345002e+00 , 5.30000000000000e+00 , 1.14700000000000e+00 , 3.25300000000000e+00 , 4.09600000000000e+00 , 1.08200000000000e+00 , 3.60000000000000e+00 , 5.87400947185545e+00 , 2.34899962073679e+00 , 2.93599795781351e+00 , 5.23499049803933e+00 , 3.60400329104367e+00 , 2.87702476943395e+00 , 6.31703080792449e+00 , 4.65098893716123e+00 , 2.47704670452048e+00 , 3.91100000000000e+00 , 3.67600000000000e+00 , 2.03500000000000e+00 , 2.93600000000000e+00 , 4.12100000000000e+00 , 2.58400000000000e+00 , 3.81797897004672e+00 , 3.24301039349424e+00 , 7.83013174091403e-01 , 2.65497580340953e+00 , 3.21405894953658e+00 , -5.49930612718508e-02 , 3.04500477204551e+00 , 2.74098548721449e+00 , -1.55998622716211e+00 , 1.65600000000000e+00 , 2.18100000000000e+00 , 5.54000000000000e-01 , 4.23000000000000e-01 , 2.41200000000000e+00 , 5.81000000000000e-01 , 2.00097515551602e+00 , 9.82010067699391e-01 , 1.06700297700788e+00 , 1.11002766304188e+00 , 2.00120148972546e-02 , 1.68902446146746e+00 , 2.01697997628800e+00 , -1.21900133911666e+00 , 2.02197084030096e+00 , 4.90000000000000e-01 , 5.65000000000000e-01 , 3.01300000000000e+00 , -6.93000000000000e-01 , 4.01000000000000e-01 , 3.20700000000000e+00 , 1.25802926297224e+00 , 1.29900303953480e+00 , 3.82599576849078e+00 , 7.95996417270253e-01 , 1.86998840091244e+00 , 5.09001061383688e+00 , 2.07499799500588e+00 , 2.57305516052311e+00 , 5.62095663795779e+00 , -3.45000000000000e-01 , 2.92000000000000e+00 , 4.99000000000000e+00 , -1.18700000000000e+00 , 3.00900000000000e+00 , 5.89400000000000e+00 , -3.76990681241235e-01 , 3.70699751602622e+00 , 3.88398801212656e+00 , -1.44499986122152e+00 , 4.62799966287603e+00 , 3.52899942080582e+00 , -7.80011451255797e-01 , 5.37397741217150e+00 , 2.40196060783149e+00 , -2.70000000000000e+00 , 3.89900000000000e+00 , 2.95400000000000e+00 , -3.84700000000000e+00 , 4.39200000000000e+00 , 2.88300000000000e+00 , -2.54397387917553e+00 , 2.62898608950176e+00 , 2.51399134457887e+00 , -3.74298744047542e+00 , 1.86798794555014e+00 , 2.08600523594121e+00 , -3.40099075517477e+00 , 7.84978066500381e-01 , 1.02698122542909e+00 , -4.35600000000000e+00 , 1.13000000000000e+00 , 3.21400000000000e+00 , -5.52800000000000e+00 , 9.60000000000000e-01 , 3.35400000000000e+00 , -3.49404539245506e+00 , 6.32987892129414e-01 , 4.18601013009093e+00 , -3.74097343983803e+00 , 9.90409488016784e-02 , 5.46300171939720e+00 , -2.46600201936297e+00 , -4.49044526334245e-01 , 6.11800127257463e+00 , -4.45300000000000e+00 , 1.02900000000000e+00 , 6.42300000000000e+00 , -5.33000000000000e+00 , 5.83000000000000e-01 , 7.17200000000000e+00 , -6.28800000000000e+00 , 3.55300000000000e+00 , 6.68800000000000e+00 , -6.94100000000000e+00 , 4.32300000000000e+00 , 7.42000000000000e+00 , -6.77997933677039e+00 , 3.20500922354056e+00 , 5.49202066742435e+00 , -4.07700722498099e+00 , 2.28599541101650e+00 , 6.46500631785635e+00 , -4.90700712078004e+00 , 3.24699297811969e+00 , 7.21803418633749e+00 , -4.04901756201105e+00 , 4.48202805957957e+00 , 7.26299741869277e+00 ) + 1 ( 9.99574076610406e-01 , 2.05778482923715e-02 , 1.42220726691057e-02 , -1.50316392022050e-02 ) ( -3.21564188520062e-01 , 1.69819486822241e+01 , 1.71859144849276e+01 , 1.81247073526383e+01 ) ( 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 2.65735869663073e+00 , 3.20810536092089e+00 , -6.18621047542894e-02 , 1.11563723650084e+00 , 1.72500211377211e-02 , 1.68771242079374e+00 , 8.02059211840067e-01 , 1.87550019161783e+00 , 5.08797136205726e+00 , -1.45082032550996e+00 , 4.62175338509398e+00 , 3.53071824705358e+00 , -3.73779980905316e+00 , 1.87724852449342e+00 , 2.08367755150697e+00 , -3.74839036888653e+00 , 1.02520373592432e-01 , 5.46548882618505e+00 , -4.91096021771450e+00 , 3.24745346555996e+00 , 7.21736102186941e+00 ) ( 8.42027508747908e+00 , 4.22069524484729e-02 , -7.45599564775393e-01 , 7.00362726026759e+00 , -4.79948043077682e-01 , -6.79266563863866e-01 , 7.03906842315129e+00 , -2.00683318530416e+00 , -1.03762574157557e+00 , 6.23774818242220e+00 , -2.51240804935942e-01 , 6.26743630924782e-01 , 5.02843811157766e+00 , -2.08038526718274e-01 , 6.39302084935193e-01 , 6.90858888049629e+00 , -2.67413160210852e-01 , 1.77891673502364e+00 , 6.18205698414471e+00 , -1.31168448775211e-01 , 3.03987184776319e+00 , 7.19806687572291e+00 , -3.16977465868230e-01 , 4.30310082014670e+00 , 5.30269892357687e+00 , 1.14008112991251e+00 , 3.26017661095153e+00 , 4.09161617109911e+00 , 1.07931010163127e+00 , 3.60439258538271e+00 , 5.87383580089830e+00 , 2.34422943606168e+00 , 2.94316256987946e+00 , 5.23330761990903e+00 , 3.60157684972257e+00 , 2.87823778366063e+00 , 6.32195885725394e+00 , 4.64361720415354e+00 , 2.47418272460023e+00 , 3.90567205367299e+00 , 3.68544773806702e+00 , 2.03016852186817e+00 , 2.93268281136820e+00 , 4.11879068492859e+00 , 2.57740176303482e+00 , 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4.58521207379435e+00 , 7.28932245334770e+00 ) + 19 ( 9.99758962093459e-01 , 1.42609660687068e-02 , 1.18609117143873e-02 , -1.17456942706996e-02 ) ( -2.38445587445623e-01 , 1.71992487761229e+01 , 1.72761151637582e+01 , 1.80321624270782e+01 ) ( 6.96620781261039e+00 , -5.48631780155980e-01 , -5.79656213349537e-01 , 6.16000426480305e+00 , -1.58734349202500e-01 , 3.19300345166991e+00 , 5.23914294061406e+00 , 3.58022879077665e+00 , 2.91894885823784e+00 , 2.65606862017344e+00 , 3.00962592911220e+00 , -1.06082863161120e-01 , 1.17081805657548e+00 , 1.15025822194893e-01 , 1.69546470434007e+00 , 8.45957893909033e-01 , 1.97576759299258e+00 , 5.02548047778812e+00 , -1.51657819769730e+00 , 4.54208760943432e+00 , 3.45459476634434e+00 , -3.76923998160398e+00 , 1.80732330485264e+00 , 2.00079618505186e+00 , -3.70748943344948e+00 , 4.16903006825175e-02 , 5.43600413888779e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 ) ( 8.31286924612146e+00 , 4.20709002657016e-02 , 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9.93530104985184e-01 , 6.44282281367477e+00 , -5.35508910847790e+00 , 6.00637599513754e-01 , 7.21823607746516e+00 , -6.23336906224988e+00 , 3.60035451730022e+00 , 6.73091843216218e+00 , -6.95508828206415e+00 , 4.29906197536089e+00 , 7.47249705861818e+00 , -6.74543195379567e+00 , 3.18676413708356e+00 , 5.51129105455307e+00 , -4.12904196619339e+00 , 2.24977866391455e+00 , 6.41801921283164e+00 , -4.81016350287603e+00 , 3.20040418268042e+00 , 7.23958220754022e+00 , -4.09835397324189e+00 , 4.58118059213459e+00 , 7.28660838870272e+00 ) + 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ) ( -2.33415112386265e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , 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1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..3a0585f3a --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.out @@ -0,0 +1,7157 @@ +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 value = " +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "main" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "RMSD_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "RMSD_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 10 atoms requested: total mass = 120.11, total charge = 0.53. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup RMSD_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 30 individual components. +colvars: DEPS: disabling feature "scalar" in colvar main +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: feature "linear" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar main enabled, ref_count = 1. +colvars: DEPS: colvar main enabling "single_component" +colvars: DEPS: feature "single_component" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar main +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar main +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar main +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar main enabling "output_value" +colvars: DEPS: feature "output_value" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar main +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar main +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar main +colvars: DEPS: colvar main enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar main testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar main testing "linear" +colvars: DEPS: colvar main enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar main enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "main". +colvars: Configuration string for "colvar": " +colvars: +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword value = " +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "fitting" +colvars: Looking for the keyword "alchFLambda" and its value. +colvars: Keyword "alchFLambda" not found. +colvars: Looking for the keyword "alchLambda" and its value. +colvars: Keyword "alchLambda" not found. +colvars: Looking for the keyword "alpha" and its value. +colvars: Keyword "alpha" not found. +colvars: Looking for the keyword "angle" and its value. +colvars: Keyword "angle" not found. +colvars: Looking for the keyword "aspath" and its value. +colvars: Keyword "aspath" not found. +colvars: Looking for the keyword "aspathCV" and its value. +colvars: Keyword "aspathCV" not found. +colvars: Looking for the keyword "azpath" and its value. +colvars: Keyword "azpath" not found. +colvars: Looking for the keyword "azpathCV" and its value. +colvars: Keyword "azpathCV" not found. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword value = " +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Initializing a new "cartesian" component, with configuration: +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: DEPS: uninitialized colvar component enabling "active" +colvars: DEPS: feature "active" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "explicit_gradient" +colvars: explicit_gradient requires exclude scalable_calculation +colvars: explicit_gradient requires exclude scalable_calculation_of_centers_of_mass +colvars: DEPS: feature "explicit_gradient" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: uninitialized colvar component enabling "use_minimum-image_with_PBCs" +colvars: DEPS: feature "use_minimum-image_with_PBCs" in uninitialized colvar component enabled, ref_count = 1. +colvars: DEPS: disabling feature "explicit_gradient" in unnamed cvc of type "cartesian" +colvars: Initializing cvc base object. +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "componentCoeff" and its value. +colvars: Keyword "componentCoeff" not found. +colvars: # componentCoeff = 1 [default] +colvars: Looking for the keyword "componentExp" and its value. +colvars: Keyword "componentExp" not found. +colvars: # componentExp = 1 [default] +colvars: Looking for the keyword "period" and its value. +colvars: Keyword "period" not found. +colvars: # period = 0 [default] +colvars: Looking for the keyword "wrapAround" and its value. +colvars: Keyword "wrapAround" not found. +colvars: # wrapAround = 0 [default] +colvars: Looking for the keyword "debugGradients" and its value. +colvars: Keyword "debugGradients" not found. +colvars: DEPS: disabling feature "debug_gradient" in unnamed cvc of type "cartesian" +colvars: Looking for the keyword "forceNoPBC" and its value. +colvars: Keyword "forceNoPBC" not found. +colvars: # forceNoPBC = off [default] +colvars: DEPS: unnamed cvc of type "cartesian" enabling "use_minimum-image_with_PBCs" +colvars: Looking for the keyword "scalable" and its value. +colvars: Keyword "scalable" not found. +colvars: # scalable = on [default] +colvars: Done initializing cvc base object. +colvars: Looking for the keyword "atoms" and its value. +colvars: Keyword value = " +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Initializing atom group "atoms". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: # name = "" [default] +colvars: Looking for the keyword "centerToOrigin" and its value. +colvars: Keyword "centerToOrigin" not found. +colvars: # centerToOrigin = off [default] +colvars: DEPS: disabling feature "center_to_origin" in atom group atoms +colvars: Looking for the keyword "centerReference" and its value. +colvars: Keyword "centerReference" not found. +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "centerToReference" and its value. +colvars: Keyword "centerToReference" not found. +colvars: # centerToReference = off [default] +colvars: DEPS: disabling feature "center_to_reference" in atom group atoms +colvars: Looking for the keyword "rotateReference" and its value. +colvars: Keyword "rotateReference" not found. +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "rotateToReference" and its value. +colvars: Keyword "rotateToReference" not found. +colvars: # rotateToReference = off [default] +colvars: DEPS: disabling feature "rotate_to_origin" in atom group atoms +colvars: Looking for the keyword "atomsOfGroup" and its value. +colvars: Keyword "atomsOfGroup" not found. +colvars: # atomsOfGroup = "" [default] +colvars: Looking for the keyword "atomNumbers" and its value. +colvars: Keyword "atomNumbers" not found. +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword value = "heavy_atoms". +colvars: Looking for the keyword "indexGroup" and its value. +colvars: Keyword "indexGroup" not found. +colvars: # indexGroup = "heavy_atoms" +colvars: Looking for the keyword "atomNumbersRange" and its value. +colvars: Keyword "atomNumbersRange" not found. +colvars: Looking for the keyword "psfSegID" and its value. +colvars: Keyword "psfSegID" not found. +colvars: # psfSegID = [default] +colvars: Looking for the keyword "atomNameResidueRange" and its value. +colvars: Keyword "atomNameResidueRange" not found. +colvars: Looking for the keyword "atomsFile" and its value. +colvars: Keyword "atomsFile" not found. +colvars: # atomsFile = "" [default] +colvars: Looking for the keyword "dummyAtom" and its value. +colvars: Keyword "dummyAtom" not found. +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: Looking for the keyword "enableForces" and its value. +colvars: Keyword "enableForces" not found. +colvars: Looking for the keyword "enableFitGradients" and its value. +colvars: Keyword "enableFitGradients" not found. +colvars: # enableFitGradients = on [default] +colvars: Looking for the keyword "printAtomIDs" and its value. +colvars: Keyword "printAtomIDs" not found. +colvars: # printAtomIDs = off [default] +colvars: Done initializing atom group "atoms". +colvars: Atom group "atoms" defined with 51 atoms requested: total mass = 674.397, total charge = -7.64. +colvars: DEPS: unnamed cvc of type "cartesian" enabling "explicit_atom_groups" +colvars: DEPS: feature "explicit_atom_groups" in unnamed cvc of type "cartesian" enabled, ref_count = 1. +colvars: Configuration string for "atoms": " +colvars: +colvars: indexGroup heavy_atoms +colvars: ". +colvars: Looking for the keyword "useX" and its value. +colvars: Keyword "useX" not found. +colvars: # useX = on [default] +colvars: Looking for the keyword "useY" and its value. +colvars: Keyword "useY" not found. +colvars: # useY = on [default] +colvars: Looking for the keyword "useZ" and its value. +colvars: Keyword "useZ" not found. +colvars: # useZ = on [default] +colvars: Configuration string for "cartesian": " +colvars: +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: ". +colvars: Done initializing a "cartesian" component, named "cartesian0001". +colvars: Parsed 1 components at this time. +colvars: Looking for the keyword "cartesian" and its value. +colvars: Keyword "cartesian" not found. +colvars: Looking for the keyword "coordNum" and its value. +colvars: Keyword "coordNum" not found. +colvars: Looking for the keyword "customColvar" and its value. +colvars: Keyword "customColvar" not found. +colvars: Looking for the keyword "dihedral" and its value. +colvars: Keyword "dihedral" not found. +colvars: Looking for the keyword "dihedralPC" and its value. +colvars: Keyword "dihedralPC" not found. +colvars: Looking for the keyword "dipoleAngle" and its value. +colvars: Keyword "dipoleAngle" not found. +colvars: Looking for the keyword "dipoleMagnitude" and its value. +colvars: Keyword "dipoleMagnitude" not found. +colvars: Looking for the keyword "distance" and its value. +colvars: Keyword "distance" not found. +colvars: Looking for the keyword "distanceDir" and its value. +colvars: Keyword "distanceDir" not found. +colvars: Looking for the keyword "distanceInv" and its value. +colvars: Keyword "distanceInv" not found. +colvars: Looking for the keyword "distancePairs" and its value. +colvars: Keyword "distancePairs" not found. +colvars: Looking for the keyword "distanceVec" and its value. +colvars: Keyword "distanceVec" not found. +colvars: Looking for the keyword "distanceXY" and its value. +colvars: Keyword "distanceXY" not found. +colvars: Looking for the keyword "distanceZ" and its value. +colvars: Keyword "distanceZ" not found. +colvars: Looking for the keyword "eigenvector" and its value. +colvars: Keyword "eigenvector" not found. +colvars: Looking for the keyword "eulerPhi" and its value. +colvars: Keyword "eulerPhi" not found. +colvars: Looking for the keyword "eulerPsi" and its value. +colvars: Keyword "eulerPsi" not found. +colvars: Looking for the keyword "eulerTheta" and its value. +colvars: Keyword "eulerTheta" not found. +colvars: Looking for the keyword "groupCoord" and its value. +colvars: Keyword "groupCoord" not found. +colvars: Looking for the keyword "gspath" and its value. +colvars: Keyword "gspath" not found. +colvars: Looking for the keyword "gspathCV" and its value. +colvars: Keyword "gspathCV" not found. +colvars: Looking for the keyword "gyration" and its value. +colvars: Keyword "gyration" not found. +colvars: Looking for the keyword "gzpath" and its value. +colvars: Keyword "gzpath" not found. +colvars: Looking for the keyword "gzpathCV" and its value. +colvars: Keyword "gzpathCV" not found. +colvars: Looking for the keyword "hBond" and its value. +colvars: Keyword "hBond" not found. +colvars: Looking for the keyword "inertia" and its value. +colvars: Keyword "inertia" not found. +colvars: Looking for the keyword "inertiaZ" and its value. +colvars: Keyword "inertiaZ" not found. +colvars: Looking for the keyword "linearCombination" and its value. +colvars: Keyword "linearCombination" not found. +colvars: Looking for the keyword "mapTotal" and its value. +colvars: Keyword "mapTotal" not found. +colvars: Looking for the keyword "neuralNetwork" and its value. +colvars: Keyword "neuralNetwork" not found. +colvars: Looking for the keyword "orientation" and its value. +colvars: Keyword "orientation" not found. +colvars: Looking for the keyword "orientationAngle" and its value. +colvars: Keyword "orientationAngle" not found. +colvars: Looking for the keyword "orientationProj" and its value. +colvars: Keyword "orientationProj" not found. +colvars: Looking for the keyword "polarPhi" and its value. +colvars: Keyword "polarPhi" not found. +colvars: Looking for the keyword "polarTheta" and its value. +colvars: Keyword "polarTheta" not found. +colvars: Looking for the keyword "rmsd" and its value. +colvars: Keyword "rmsd" not found. +colvars: Looking for the keyword "selfCoordNum" and its value. +colvars: Keyword "selfCoordNum" not found. +colvars: Looking for the keyword "spinAngle" and its value. +colvars: Keyword "spinAngle" not found. +colvars: Looking for the keyword "tilt" and its value. +colvars: Keyword "tilt" not found. +colvars: All components initialized. +colvars: Looking for the keyword "customFunction" and its value. +colvars: Keyword "customFunction" not found. +colvars: Looking for the keyword "scriptedFunction" and its value. +colvars: Keyword "scriptedFunction" not found. +colvars: This collective variable is a n-dimensional vector with 153 individual components. +colvars: DEPS: disabling feature "scalar" in colvar fitting +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: feature "linear" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "homogeneous" +colvars: DEPS: feature "homogeneous" in colvar fitting enabled, ref_count = 1. +colvars: DEPS: colvar fitting enabling "single_component" +colvars: DEPS: feature "single_component" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "timeStepFactor" and its value. +colvars: Keyword "timeStepFactor" not found. +colvars: # timeStepFactor = 1 [default] +colvars: Looking for the keyword "width" and its value. +colvars: Keyword "width" not found. +colvars: # width = 1 [default] +colvars: Looking for the keyword "hardLowerBoundary" and its value. +colvars: Keyword "hardLowerBoundary" not found. +colvars: # hardLowerBoundary = off [default] +colvars: DEPS: disabling feature "hard_lower_boundary" in colvar fitting +colvars: Looking for the keyword "hardUpperBoundary" and its value. +colvars: Keyword "hardUpperBoundary" not found. +colvars: # hardUpperBoundary = off [default] +colvars: DEPS: disabling feature "hard_upper_boundary" in colvar fitting +colvars: Looking for the keyword "expandBoundaries" and its value. +colvars: Keyword "expandBoundaries" not found. +colvars: # expandBoundaries = off [default] +colvars: Looking for the keyword "extendedLagrangian" and its value. +colvars: Keyword "extendedLagrangian" not found. +colvars: # extendedLagrangian = off [default] +colvars: DEPS: disabling feature "extended_Lagrangian" in colvar fitting +colvars: Looking for the keyword "outputValue" and its value. +colvars: Keyword "outputValue" not found. +colvars: # outputValue = on [default] +colvars: DEPS: colvar fitting enabling "output_value" +colvars: DEPS: feature "output_value" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "outputVelocity" and its value. +colvars: Keyword "outputVelocity" not found. +colvars: # outputVelocity = off [default] +colvars: Looking for the keyword "outputSystemForce" and its value. +colvars: Keyword "outputSystemForce" not found. +colvars: Looking for the keyword "outputTotalForce" and its value. +colvars: Keyword "outputTotalForce" not found. +colvars: # outputTotalForce = off [default] +colvars: DEPS: disabling feature "output_total_force" in colvar fitting +colvars: Looking for the keyword "outputAppliedForce" and its value. +colvars: Keyword "outputAppliedForce" not found. +colvars: # outputAppliedForce = off [default] +colvars: DEPS: disabling feature "output_applied_force" in colvar fitting +colvars: Looking for the keyword "subtractAppliedForce" and its value. +colvars: Keyword "subtractAppliedForce" not found. +colvars: # subtractAppliedForce = off [default] +colvars: DEPS: disabling feature "subtract_applied_force_from_total_force" in colvar fitting +colvars: DEPS: colvar fitting enabling "active" +colvars: active requires alt scalar +colvars: DEPS: colvar fitting testing "scalar" +colvars: active requires alt linear +colvars: DEPS: colvar fitting testing "linear" +colvars: DEPS: colvar fitting enabling "linear" +colvars: DEPS: bumping ref_count to 1 +colvars: DEPS: feature "active" in colvar fitting enabled, ref_count = 1. +colvars: Looking for the keyword "runAve" and its value. +colvars: Keyword "runAve" not found. +colvars: # runAve = off [default] +colvars: Looking for the keyword "corrFunc" and its value. +colvars: Keyword "corrFunc" not found. +colvars: # corrFunc = off [default] +colvars: Done initializing collective variable "fitting". +colvars: Configuration string for "colvar": " +colvars: +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: ". +colvars: Looking for the keyword "colvar" and its value. +colvars: Keyword "colvar" not found. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 3 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: colvar { +colvars: name main +colvars: cartesian { +colvars: atoms { +colvars: indexGroup RMSD_atoms +colvars: } +colvars: } +colvars: } +colvars: colvar { +colvars: name fitting +colvars: cartesian { +colvars: atoms { +colvars: indexGroup heavy_atoms +colvars: } +colvars: } +colvars: } +colvars: harmonic { +colvars: colvars one +colvars: centers (0.9, 0.5, 0.5, 0.5) +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: - cartesian colvar component: +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 = "2024-09-17". +colvars: Looking for the keyword "version" and its value. +colvars: Keyword "version" not found. +colvars: Looking for the keyword "units" and its value. +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 = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "main": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "main" from value: ( 6.95697 , -0.549562 , -0.571673 , 6.15419 , -0.166072 , 3.18954 , 5.23832 , 3.57842 , 2.91984 , 2.66119 , 3.00667 , -0.104346 , 1.16849 , 0.116557 , 1.69698 , 0.843403 , 1.9786 , 5.02539 , -1.51786 , 4.53913 , 3.44518 , -3.77324 , 1.80375 , 2.00014 , -3.70041 , 0.046227 , 5.43591 , -4.80737 , 3.20639 , 7.24443 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting": this colvar is named "one". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Ignoring state of colvar "fitting": this colvar is named "main". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "fitting". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +colvars: Looking for the keyword "x" and its value. +colvars: Keyword value = "( 8.3109067593225 , 0.041832105536949 , -0.74720152184922 , 6.9569728535207 , -0.54956229684946 , -0.57167287570071 , 7.0501314089404 , -2.0502351229669 , -0.93466980629676 , 6.1724025468072 , -0.37440006998022 , 0.72796068970041 , 4.9728901219597 , -0.15984013302521 , 0.72686147800692 , 6.8514301642465 , -0.26741105895838 , 1.9083377792785 , 6.1541939183655 , -0.16607233271972 , 3.1895367417087 , 7.073607414672 , -0.35378704127878 , 4.3070951913435 , 5.2970773270167 , 1.0930675777403 , 3.3427298943302 , 4.1334323731907 , 1.0232724624507 , 3.6807757981069 , 5.8363306008465 , 2.2505141275817 , 2.9898069553745 , 5.2383242861525 , 3.5784225843899 , 2.9198390382089 , 6.3225154324575 , 4.5006943210992 , 2.3634882582325 , 3.8815799727105 , 3.7065612462023 , 2.0430944440883 , 2.7919894870931 , 4.1606818038692 , 2.4867320360913 , 3.9379247666863 , 3.2391551773311 , 0.73009137441107 , 2.6611861090265 , 3.0066728573286 , -0.10434567805803 , 3.0516504481894 , 2.7043614871659 , -1.5156733303712 , 1.5970874871384 , 2.1829728692071 , 0.44555677054977 , 0.37858437885899 , 2.5807264635357 , 0.51019557090508 , 2.04711677578 , 1.0703813637383 , 1.069206754706 , 1.1684857904105 , 0.11655674742988 , 1.6969763020422 , 2.0425329047304 , -1.1035104960071 , 2.0103674846849 , 0.56194901870408 , 0.61185187522511 , 2.9428132426689 , -0.60197676959252 , 0.34978459930961 , 3.1621649077962 , 1.3163590181237 , 1.3458687673819 , 3.7752112850979 , 0.84340288185055 , 1.9785983971823 , 5.02538632117 , 2.0804193492853 , 2.6881595598658 , 5.6815929959461 , -0.33660676483589 , 2.9148298650463 , 4.9681489667417 , -1.1362865907604 , 3.063001046068 , 5.8880007578731 , -0.51135551219128 , 3.535300553984 , 3.8464371088115 , -1.5178594862197 , 4.5391286011173 , 3.4451817190799 , -0.69985197514866 , 5.4140943569769 , 2.4638642323208 , -2.7601618038614 , 3.8895607334677 , 2.895793363421 , -3.8173497124104 , 4.5101036996167 , 2.8152773748772 , -2.6253924219612 , 2.6733261276654 , 2.4022619953018 , -3.7732437350442 , 1.8037507663113 , 2.0001350505188 , -3.3895014416165 , 0.8866696376631 , 0.87567133268272 , -4.322724391988 , 1.0702172791569 , 3.2141303643402 , -5.5001342374076 , 0.81893213505031 , 3.3310166100638 , -3.3688860558692 , 0.69174478744455 , 4.2057900990597 , -3.7004147832166 , 0.046226964335401 , 5.4359065979691 , -2.3895289778026 , -0.31661424092553 , 6.1717119733279 , -4.4607970213475 , 0.98729806770613 , 6.4413742570766 , -5.3579745601884 , 0.599067686148 , 7.2198955321113 , -6.2369282614895 , 3.6061273507614 , 6.7353796872239 , -6.9588258659327 , 4.2988412219219 , 7.4769553986534 , -6.7403993718841 , 3.1830257218785 , 5.5094675051539 , -4.1276723189508 , 2.2467034673003 , 6.4110909930055 , -4.8073676016966 , 3.2063943768391 , 7.2444311964794 , -4.0937877414092 , 4.5760013650879 , 7.2838298499369 )". +colvars: Looking for the keyword "x" and its value. +colvars: Keyword "x" not found. +colvars: Restarting collective variable "fitting" from value: ( 8.31091 , 0.0418321 , -0.747202 , 6.95697 , -0.549562 , -0.571673 , 7.05013 , -2.05024 , -0.93467 , 6.1724 , -0.3744 , 0.727961 , 4.97289 , -0.15984 , 0.726861 , 6.85143 , -0.267411 , 1.90834 , 6.15419 , -0.166072 , 3.18954 , 7.07361 , -0.353787 , 4.3071 , 5.29708 , 1.09307 , 3.34273 , 4.13343 , 1.02327 , 3.68078 , 5.83633 , 2.25051 , 2.98981 , 5.23832 , 3.57842 , 2.91984 , 6.32252 , 4.50069 , 2.36349 , 3.88158 , 3.70656 , 2.04309 , 2.79199 , 4.16068 , 2.48673 , 3.93792 , 3.23916 , 0.730091 , 2.66119 , 3.00667 , -0.104346 , 3.05165 , 2.70436 , -1.51567 , 1.59709 , 2.18297 , 0.445557 , 0.378584 , 2.58073 , 0.510196 , 2.04712 , 1.07038 , 1.06921 , 1.16849 , 0.116557 , 1.69698 , 2.04253 , -1.10351 , 2.01037 , 0.561949 , 0.611852 , 2.94281 , -0.601977 , 0.349785 , 3.16216 , 1.31636 , 1.34587 , 3.77521 , 0.843403 , 1.9786 , 5.02539 , 2.08042 , 2.68816 , 5.68159 , -0.336607 , 2.91483 , 4.96815 , -1.13629 , 3.063 , 5.888 , -0.511356 , 3.5353 , 3.84644 , -1.51786 , 4.53913 , 3.44518 , -0.699852 , 5.41409 , 2.46386 , -2.76016 , 3.88956 , 2.89579 , -3.81735 , 4.5101 , 2.81528 , -2.62539 , 2.67333 , 2.40226 , -3.77324 , 1.80375 , 2.00014 , -3.3895 , 0.88667 , 0.875671 , -4.32272 , 1.07022 , 3.21413 , -5.50013 , 0.818932 , 3.33102 , -3.36889 , 0.691745 , 4.20579 , -3.70041 , 0.046227 , 5.43591 , -2.38953 , -0.316614 , 6.17171 , -4.4608 , 0.987298 , 6.44137 , -5.35797 , 0.599068 , 7.2199 , -6.23693 , 3.60613 , 6.73538 , -6.95883 , 4.29884 , 7.47696 , -6.7404 , 3.18303 , 5.50947 , -4.12767 , 2.2467 , 6.41109 , -4.80737 , 3.20639 , 7.24443 , -4.09379 , 4.576 , 7.28383 ) +colvars: Looking for the keyword "name" and its value. +colvars: Keyword value = "harmonic1". +colvars: Looking for the keyword "name" and its value. +colvars: Keyword "name" not found. +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: Re-initialized atom group for variable "main":0/0. 10 atoms: total mass = 120.11, total charge = 0.53. +colvars: Re-initialized atom group for variable "fitting":0/0. 51 atoms: total mass = 674.397, total charge = -7.64. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: colvarproxy_namd, step no. 20 +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 20, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 20, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 20, atoms_positions[size = 51] = { ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 ), ( 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 ), ( 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 ), ( 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 ), ( 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 ), ( 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 ), ( -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 ), ( -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 ), ( -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 ), ( -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ), ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 ), ( 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 ), ( 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 ), ( 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 ), ( 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 ), ( 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 ), ( 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 ), ( 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 ), ( 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 ), ( 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 ), ( 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 ), ( 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 ), ( 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 ), ( 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 ), ( 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 ), ( 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 ), ( 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 ), ( 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 ), ( 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 ), ( -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 ), ( 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 ), ( 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 ), ( -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 ), ( -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 ), ( -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 ), ( -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 ), ( -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 ), ( -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 ), ( -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 ), ( -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 ), ( -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 ), ( -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 ), ( -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 ), ( -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 ), ( -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 ), ( -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 ), ( -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 ), ( -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 ), ( -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 ), ( -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 ), ( -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) } +colvars: Step 20, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 20. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: colvarmodule::end_of_step(), step = 20. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atoms_new_colvar_forces = { ( -7.12820780726454e-02 , 3.03662428488388e-01 , -4.00366647072688e-01 ), ( 1.28190711800977e-02 , 3.00052379356399e-02 , -2.38475019553667e-01 ), ( -4.20173971519038e-02 , 9.38282975458011e-02 , 8.81163420469985e-02 ), ( -9.70919363500017e-02 , 2.50506548950009e-01 , 6.55707114253731e-02 ), ( -1.87185357319919e-02 , 9.90390714998469e-02 , -1.72281253781500e-01 ), ( 7.09430607985375e-02 , -1.85850810099678e-01 , -3.85032013909570e-02 ), ( 1.01877677081773e-02 , -9.90720282641528e-02 , 2.55457847603390e-01 ), ( -4.10371148092370e-02 , 6.17443364827238e-02 , 1.91760996033175e-01 ), ( 6.62468727487265e-02 , -1.90448081926945e-01 , 3.12288455216890e-02 ), ( 1.14900536644499e-01 , -3.92111266050618e-01 , 2.74939602306107e-01 ), ( 2.46763909120624e-02 , -9.94602576807517e-02 , 9.60262310496414e-02 ), ( 2.66364888203580e-02 , -9.72981050690524e-02 , 5.97106697489683e-02 ), ( 1.24661136135099e-02 , -5.57559811144078e-02 , 7.25743621949596e-02 ), ( 1.26061529934573e-02 , -5.36360033548245e-02 , 6.13963990989623e-02 ), ( 5.62478200332647e-03 , -3.49973301865402e-02 , 7.57170861826678e-02 ), ( -8.60292310050453e-03 , 9.69554753037324e-03 , 7.56073713177290e-02 ), ( -2.08776469672694e-03 , -2.70415172113731e-03 , 4.04328246755312e-02 ), ( -5.77389521453809e-03 , 9.85182430390029e-03 , 3.61382862311481e-02 ), ( 2.69104804092523e-03 , -1.29509138532637e-02 , 1.96620498003800e-02 ), ( 8.95486758503647e-03 , -2.19984645975749e-02 , -2.67054922301013e-02 ), ( 8.66947656368633e-03 , -2.37906412361185e-02 , -1.49662397602341e-02 ), ( 6.53809880541543e-03 , -1.35548306775218e-02 , -3.04445795977130e-02 ), ( 1.50378586620113e-02 , -4.67256381185873e-02 , -2.12056523516849e-03 ), ( 2.77145468047782e-02 , -8.86706404142584e-02 , 7.25391326879236e-03 ), ( 1.43418350478352e-02 , -4.70396672264757e-02 , 8.79345033286907e-03 ), ( 1.42876873246940e-02 , -4.42222614839394e-02 , -2.76784692702148e-03 ), ( 9.39021759703577e-03 , -3.71828583991163e-02 , 3.36363523912981e-02 ), ( -6.98144545634549e-04 , -1.53563057764578e-02 , 7.66330583610253e-02 ), ( -3.72007257600071e-03 , 4.12380338393483e-03 , 3.29943046613802e-02 ), ( -5.78038960540629e-03 , 1.11679149109106e-02 , 3.04799282045032e-02 ), ( -7.29500058088395e-03 , 1.79744323096259e-02 , 2.15213756089124e-02 ), ( -1.63845466080518e-02 , 5.22691466040444e-02 , -3.62466193947451e-03 ), ( -9.83258166658177e-03 , 3.58405621721076e-02 , -2.17096014344480e-02 ), ( -1.38792471902123e-02 , 5.00947470152904e-02 , -2.84772388308240e-02 ), ( -2.07475381329402e-03 , 1.48608587226011e-02 , -3.64523576292855e-02 ), ( 1.04709256505724e-02 , -1.60555817098572e-02 , -7.34437005969538e-02 ), ( 4.30769248288625e-03 , -1.03735135095860e-03 , -5.45293145217132e-02 ), ( 3.26495468493792e-03 , 5.77162454807398e-03 , -6.99680928834496e-02 ), ( 7.12436996401246e-03 , -1.51327555336419e-02 , -3.15916578475220e-02 ), ( 1.32036569636365e-02 , -4.18136663470711e-02 , 1.57606808925122e-03 ), ( 5.63178713376306e-04 , 1.44649438052730e-03 , -1.40381831264554e-02 ), ( 4.98434308056249e-04 , 2.99804808326463e-03 , -1.99261927958005e-02 ), ( -6.48604874882730e-03 , 2.03983070643250e-02 , -1.54655641113389e-04 ), ( -2.05396268108373e-02 , 5.78448103620468e-02 , 2.89933897342496e-02 ), ( -1.89963215030731e-02 , 6.32871520354796e-02 , -1.59325097026948e-02 ), ( -2.27031336797099e-02 , 7.52383288188215e-02 , -1.73023258192027e-02 ), ( -1.70091515312721e-02 , 7.24201382807392e-02 , -8.30610242241338e-02 ), ( -2.01472890750390e-02 , 8.66037371840124e-02 , -1.01976538096566e-01 ), ( -8.70556581654820e-03 , 4.64004872660571e-02 , -8.32766801657128e-02 ), ( -1.86965654101119e-02 , 6.67566509278478e-02 , -3.51936150293328e-02 ), ( -2.46060023326147e-02 , 9.30350553865569e-02 , -6.89322700552692e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 20, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 21, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 21, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 21, atoms_positions[size = 51] = { ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 ), ( 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 ), ( 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 ), ( 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 ), ( 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 ), ( 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 ), ( -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 ), ( -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 ), ( -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 ), ( -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ), ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 ), ( 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 ), ( 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 ), ( 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 ), ( 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 ), ( 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 ), ( 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 ), ( 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 ), ( 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 ), ( 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 ), ( 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 ), ( 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 ), ( 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 ), ( 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 ), ( 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 ), ( 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 ), ( 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 ), ( 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 ), ( 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 ), ( -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 ), ( 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 ), ( 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 ), ( -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 ), ( -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 ), ( -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 ), ( -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 ), ( -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 ), ( -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 ), ( -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 ), ( -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 ), ( -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 ), ( -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 ), ( -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 ), ( -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 ), ( -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 ), ( -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 ), ( -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 ), ( -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 ), ( -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 ), ( -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 ), ( -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ) } +colvars: Step 21, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating colvar components. +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 , 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 , 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 , 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 , 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 , 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 , 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 , 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 , 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 , 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 , 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 , 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 , 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 , 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 , 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 , -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 , 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 , -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 , -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 , -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 , -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 , -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 , -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 , -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 , -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 , -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 , -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 , -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 , -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 , -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 , -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 , -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 , -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 , 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 , 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 , 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 , 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 , 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 , 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 , 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 , 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 , 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 , 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 , 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 , 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 , 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 , 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 , -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 , 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 , -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 , -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 , -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 , -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 , -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 , -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 , -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 , -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 , -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 , -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 , -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 , -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 , -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 , -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 , -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 , -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 21. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 21. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atoms_new_colvar_forces = { ( -7.11399384318308e-02 , 3.03673714596804e-01 , -4.00770119886634e-01 ), ( 1.28450168410534e-02 , 3.00636017805382e-02 , -2.38645544534818e-01 ), ( -4.20822670353576e-02 , 9.41200209059075e-02 , 8.79377349508917e-02 ), ( -9.70668784584834e-02 , 2.50670455049784e-01 , 6.53550388999108e-02 ), ( -1.86302899611748e-02 , 9.89303159690966e-02 , -1.72358620278118e-01 ), ( 7.09108063101489e-02 , -1.85927916967423e-01 , -3.83730584164822e-02 ), ( 1.00940002734312e-02 , -9.89773108191160e-02 , 2.55576585814222e-01 ), ( -4.10215749964445e-02 , 6.16911466781241e-02 , 1.91856870875936e-01 ), ( 6.62622265583337e-02 , -1.90705006891368e-01 , 3.15184935556135e-02 ), ( 1.14774657066217e-01 , -3.92224428801080e-01 , 2.75377184594162e-01 ), ( 2.46625873851911e-02 , -9.94934972823232e-02 , 9.61066727823309e-02 ), ( 2.66219319601747e-02 , -9.73405519568489e-02 , 5.97487570195681e-02 ), ( 1.24577915943817e-02 , -5.57595264132078e-02 , 7.26154388026604e-02 ), ( 1.25983778171294e-02 , -5.36459257873875e-02 , 6.14369978247319e-02 ), ( 5.61903440744207e-03 , -3.49787311352312e-02 , 7.57458071852306e-02 ), ( -8.60288899774205e-03 , 9.75608155101238e-03 , 7.56115259176666e-02 ), ( -2.08923468684040e-03 , -2.67530457899128e-03 , 4.04287964932555e-02 ), ( -5.77333835969326e-03 , 9.88677812731994e-03 , 3.61343701273132e-02 ), ( 2.68767850620090e-03 , -1.29382633507290e-02 , 1.96404769055550e-02 ), ( 8.94944167110720e-03 , -2.20122654388583e-02 , -2.67648727689498e-02 ), ( 8.66483279553809e-03 , -2.38081467999426e-02 , -1.49959487368344e-02 ), ( 6.53495529803234e-03 , -1.35726331970709e-02 , -3.04835083292054e-02 ), ( 1.50303446132429e-02 , -4.67584847450611e-02 , -2.12920998279256e-03 ), ( 2.77018244289008e-02 , -8.87395931998711e-02 , 7.27779809261200e-03 ), ( 1.43352800222162e-02 , -4.70751609713203e-02 , 8.81293743885319e-03 ), ( 1.42817640632689e-02 , -4.42636422522604e-02 , -2.74952806030974e-03 ), ( 9.38522823558224e-03 , -3.71979422433983e-02 , 3.36691841968735e-02 ), ( -6.99503281119043e-04 , -1.53341150642310e-02 , 7.66932516135838e-02 ), ( -3.71897519690295e-03 , 4.14100412747779e-03 , 3.30209727953179e-02 ), ( -5.77794268053234e-03 , 1.11867179676655e-02 , 3.05114126724248e-02 ), ( -7.29252056176348e-03 , 1.80017851832735e-02 , 2.15255686424142e-02 ), ( -1.63781366214478e-02 , 5.23192063260293e-02 , -3.66306391685651e-03 ), ( -9.82784133106718e-03 , 3.58615231332486e-02 , -2.17375544901125e-02 ), ( -1.38723121061425e-02 , 5.01224906323065e-02 , -2.85083949342105e-02 ), ( -2.07316713877925e-03 , 1.48577122015172e-02 , -3.64859747436524e-02 ), ( 1.04678431390519e-02 , -1.61024070956970e-02 , -7.34936428665872e-02 ), ( 4.30768009091328e-03 , -1.06911031799011e-03 , -5.45527250787330e-02 ), ( 3.26600819838431e-03 , 5.73629579028584e-03 , -6.99986217017486e-02 ), ( 7.12281125111274e-03 , -1.51675396442751e-02 , -3.15898239456440e-02 ), ( 1.31993145017299e-02 , -4.18609641559936e-02 , 1.62390103359611e-03 ), ( 5.64876125100676e-04 , 1.42763294196250e-03 , -1.40117013302236e-02 ), ( 5.00700080314872e-04 , 2.97437334002887e-03 , -1.98951338246221e-02 ), ( -6.48182242008078e-03 , 2.04041914680348e-02 , -1.30015240503271e-04 ), ( -2.05300318216164e-02 , 5.78974351383434e-02 , 2.90236424552305e-02 ), ( -1.89861081468300e-02 , 6.33210745824364e-02 , -1.59292058110389e-02 ), ( -2.26909264798947e-02 , 7.52790104786260e-02 , -1.72961210714089e-02 ), ( -1.69985052661349e-02 , 7.24322155695334e-02 , -8.31125713403870e-02 ), ( -2.01347960952781e-02 , 8.66187159297856e-02 , -1.02044870208897e-01 ), ( -8.69838837231290e-03 , 4.63888524456889e-02 , -8.33163867525162e-02 ), ( -1.86864572755115e-02 , 6.67879237282488e-02 , -3.52141881593768e-02 ), ( -2.45931675112202e-02 , 9.30781934665973e-02 , -6.89990142792918e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 21, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 22, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 22, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 22, atoms_positions[size = 51] = { ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 ), ( 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 ), ( 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 ), ( 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 ), ( 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 ), ( 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 ), ( -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 ), ( -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 ), ( -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 ), ( -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ), ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 ), ( 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 ), ( 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 ), ( 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 ), ( 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 ), ( 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 ), ( 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 ), ( 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 ), ( 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 ), ( 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 ), ( 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 ), ( 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 ), ( 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 ), ( 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 ), ( 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 ), ( 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 ), ( 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 ), ( 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 ), ( 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 ), ( -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 ), ( 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 ), ( 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 ), ( -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 ), ( -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 ), ( -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 ), ( -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 ), ( -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 ), ( -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 ), ( -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 ), ( -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 ), ( -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 ), ( -5.49635790878409e+00 , 8.04534957780669e-01 , 3.33283357586958e+00 ), ( -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 ), ( -2.39123986166852e+00 , -3.20694772050748e-01 , 6.16685140323704e+00 ), ( -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 ), ( -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 ), ( -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 ), ( -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 ), ( -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 ), ( -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 ), ( -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ) } +colvars: Step 22, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072404e-02 , -1.24385326679425e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 , 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 , 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 , 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 , 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 , 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 , 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 , 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 , 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 , 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 , 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 , 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 , 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 , 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 , 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 , -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 , 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 , -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 , -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 , -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 , -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 , -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 , -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 , -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 , -5.49635790878409e+00 , 8.04534957780669e-01 , 3.33283357586958e+00 , -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -2.39123986166852e+00 , -3.20694772050748e-01 , 6.16685140323704e+00 , -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 , -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 , -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 , -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 , -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 , -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 , -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072404e-02 , -1.24385326679425e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 , 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 , 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 , 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 , 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 7.07742880287553e+00 , -3.51058662138113e-01 , 4.32006460998428e+00 , 5.30429558296127e+00 , 1.08543648644419e+00 , 3.34804397820439e+00 , 4.13259359087653e+00 , 1.01866506872685e+00 , 3.69292021345864e+00 , 5.82947456739328e+00 , 2.25280302237787e+00 , 2.98593459062089e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 6.32091925024164e+00 , 4.49808491286909e+00 , 2.34331394212678e+00 , 3.87212705376473e+00 , 3.69366379467365e+00 , 2.04247662914385e+00 , 2.79023441587978e+00 , 4.16528254429990e+00 , 2.47604028230032e+00 , 3.94102776351030e+00 , 3.23422299703997e+00 , 7.29144223316100e-01 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 3.06448772972209e+00 , 2.69261872389132e+00 , -1.51702258353943e+00 , 1.59205403978163e+00 , 2.17408329137029e+00 , 4.34149280329738e-01 , 3.73600478021092e-01 , 2.59565179044381e+00 , 5.02136347735474e-01 , 2.06149255708891e+00 , 1.10072283123108e+00 , 1.05957419904392e+00 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 2.04974209711811e+00 , -1.09734190374326e+00 , 2.01595914666695e+00 , 5.65684489811316e-01 , 6.14892523154908e-01 , 2.95294328642499e+00 , -5.92549085027869e-01 , 3.50591672801086e-01 , 3.16208145393380e+00 , 1.30926440979346e+00 , 1.34785555992719e+00 , 3.75817224091062e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , 2.09681047389937e+00 , 2.70660962151185e+00 , 5.69475856953233e+00 , -3.38519310164484e-01 , 2.91306593652128e+00 , 4.96953005433034e+00 , -1.12911811533403e+00 , 3.06496889461249e+00 , 5.88293282539498e+00 , -5.21303970598241e-01 , 3.52228286885226e+00 , 3.84014795018007e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -7.00410655205485e-01 , 5.41748422807318e+00 , 2.46714445580589e+00 , -2.75271620467150e+00 , 3.90434349251085e+00 , 2.88311172436244e+00 , -3.81524327800776e+00 , 4.52141547274619e+00 , 2.81394250631913e+00 , -2.63715667416963e+00 , 2.66671660514651e+00 , 2.38847967937619e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.38142398126157e+00 , 8.84638843987716e-01 , 8.63564356085663e-01 , -4.31129133571147e+00 , 1.06971825867019e+00 , 3.21105050824305e+00 , -5.49635790878409e+00 , 8.04534957780669e-01 , 3.33283357586958e+00 , -3.36475912649722e+00 , 6.99991140331617e-01 , 4.20968388028405e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -2.39123986166852e+00 , -3.20694772050748e-01 , 6.16685140323704e+00 , -4.45956731599258e+00 , 9.71021547276181e-01 , 6.43725168233538e+00 , -5.36209813390401e+00 , 5.95874824941600e-01 , 7.22151213537313e+00 , -6.24970872547558e+00 , 3.61710818046310e+00 , 6.74372282955839e+00 , -6.96561308753076e+00 , 4.29799368486494e+00 , 7.48516949688798e+00 , -6.72563772065704e+00 , 3.17578918285063e+00 , 5.50799299498004e+00 , -4.12334440481016e+00 , 2.24407363656506e+00 , 6.40011597125614e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 , -4.08115358507919e+00 , 4.56422643834613e+00 , 7.27873556455361e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 22. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 22. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atoms_new_colvar_forces = { ( -7.09839898778747e-02 , 3.03674063527600e-01 , -4.01068648115013e-01 ), ( 1.28677757638464e-02 , 3.01861976186925e-02 , -2.38809348309205e-01 ), ( -4.21463674859759e-02 , 9.43967829010162e-02 , 8.76653672693451e-02 ), ( -9.70292248461031e-02 , 2.50742449438027e-01 , 6.51357190727135e-02 ), ( -1.85367305319293e-02 , 9.88144120703525e-02 , -1.72353345630284e-01 ), ( 7.08691073007723e-02 , -1.85935576884941e-01 , -3.82568663452623e-02 ), ( 9.99629817433111e-03 , -9.89023847961850e-02 , 2.55611691378657e-01 ), ( -4.10000890482683e-02 , 6.15546231916445e-02 , 1.91974826016933e-01 ), ( 6.62704276258435e-02 , -1.90932830035544e-01 , 3.18580020079369e-02 ), ( 1.14630750534917e-01 , -3.92276752466799e-01 , 2.75736313750346e-01 ), ( 2.46401348458040e-02 , -9.95231922332751e-02 , 9.61756954601184e-02 ), ( 2.66028495666390e-02 , -9.73827270437477e-02 , 5.97805459313105e-02 ), ( 1.24445918472298e-02 , -5.57660823956985e-02 , 7.26477167044874e-02 ), ( 1.25859818519026e-02 , -5.36566849366139e-02 , 6.14702165822491e-02 ), ( 5.60941666979545e-03 , -3.49676476401050e-02 , 7.57650503878028e-02 ), ( -8.60459043493705e-03 , 9.80137872000444e-03 , 7.56056143106272e-02 ), ( -2.09115201198730e-03 , -2.65595958743230e-03 , 4.04196007616605e-02 ), ( -5.77311642017531e-03 , 9.91276524030938e-03 , 3.61256035860894e-02 ), ( 2.68564234612566e-03 , -1.29349024719858e-02 , 1.96168163142232e-02 ), ( 8.94925864416898e-03 , -2.20349749067143e-02 , -2.68197445771304e-02 ), ( 8.66280149401487e-03 , -2.38293607684870e-02 , -1.50229481919147e-02 ), ( 6.53549642564500e-03 , -1.35935670322821e-02 , -3.05178145405584e-02 ), ( 1.50234208571289e-02 , -4.67916092089626e-02 , -2.13659458865097e-03 ), ( 2.76867464932989e-02 , -8.88011036791123e-02 , 7.30219119954995e-03 ), ( 1.43268298943310e-02 , -4.71060008041501e-02 , 8.83198042196748e-03 ), ( 1.42742680267957e-02 , -4.42983138073421e-02 , -2.73019093925148e-03 ), ( 9.37682487194691e-03 , -3.72105131562461e-02 , 3.36980129801635e-02 ), ( -7.07234928782566e-04 , -1.53121732294138e-02 , 7.67431469878513e-02 ), ( -3.72064813930677e-03 , 4.15794740228742e-03 , 3.30429937869084e-02 ), ( -5.77858592433564e-03 , 1.12068079161518e-02 , 3.05383925376817e-02 ), ( -7.29072954144173e-03 , 1.80250877442325e-02 , 2.15265738678377e-02 ), ( -1.63683809363363e-02 , 5.23584897961350e-02 , -3.70159935424319e-03 ), ( -9.82031195706152e-03 , 3.58787450236741e-02 , -2.17630809852663e-02 ), ( -1.38621548995544e-02 , 5.01466473790396e-02 , -2.85364839098933e-02 ), ( -2.06812117531274e-03 , 1.48531610368221e-02 , -3.65147867450562e-02 ), ( 1.04701424349007e-02 , -1.61460182290016e-02 , -7.35332062826640e-02 ), ( 4.31059150250448e-03 , -1.09531770379864e-03 , -5.45687792002220e-02 ), ( 3.27087578265066e-03 , 5.70773713995559e-03 , -7.00198422700665e-02 ), ( 7.12165311897482e-03 , -1.51946850165027e-02 , -3.15836085513172e-02 ), ( 1.31909349580735e-02 , -4.18949630055120e-02 , 1.67183642219021e-03 ), ( 5.64699401698964e-04 , 1.41850132131443e-03 , -1.39836938535898e-02 ), ( 5.00837441822996e-04 , 2.96280077134346e-03 , -1.98618599951807e-02 ), ( -6.47952298250981e-03 , 2.04157888640752e-02 , -1.05999642867301e-04 ), ( -2.05232494824155e-02 , 5.79498507924876e-02 , 2.90487025878773e-02 ), ( -1.89756580163051e-02 , 6.33571912361919e-02 , -1.59250752374072e-02 ), ( -2.26786531673934e-02 , 7.53225391086036e-02 , -1.72891702626615e-02 ), ( -1.69818816397503e-02 , 7.24462974551711e-02 , -8.31541664771447e-02 ), ( -2.01145633252694e-02 , 8.66349326960424e-02 , -1.02100887695110e-01 ), ( -8.68627168332183e-03 , 4.63831438807107e-02 , -8.33457370302980e-02 ), ( -1.86738034866789e-02 , 6.68192172662539e-02 , -3.52312486009206e-02 ), ( -2.45733259321368e-02 , 9.31157815017150e-02 , -6.90578829953477e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 22, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 23, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 23, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 23, atoms_positions[size = 51] = { ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 ), ( 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 ), ( 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 ), ( 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 ), ( 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 ), ( 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 ), ( -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 ), ( -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 ), ( -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 ), ( -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ), ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 ), ( 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 ), ( 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 ), ( 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 ), ( 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 ), ( 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 ), ( 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 ), ( 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 ), ( 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 ), ( 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 ), ( 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 ), ( 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 ), ( 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 ), ( 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 ), ( 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 ), ( 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 ), ( 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 ), ( 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 ), ( 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 ), ( -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 ), ( 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 ), ( 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 ), ( -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 ), ( -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 ), ( -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 ), ( -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 ), ( -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 ), ( -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 ), ( -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 ), ( -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 ), ( -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 ), ( -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 ), ( -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 ), ( -2.39140303069694e+00 , -3.22564541882353e-01 , 6.16358793333041e+00 ), ( -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 ), ( -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 ), ( -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 ), ( -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 ), ( -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 ), ( -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 ), ( -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ) } +colvars: Step 23, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 , 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 , 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 , 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 , 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 , 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 , 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 , 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 , 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 , 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 , 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 , 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 , 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 , 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 , 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 , -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 , 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 , -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 , -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 , -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 , -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 , -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 , -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 , -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 , -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 , -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -2.39140303069694e+00 , -3.22564541882353e-01 , 6.16358793333041e+00 , -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 , -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 , -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 , -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 , -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 , -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 , -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99745388099365e-01 , 1.37442866979632e-02 , 1.25428583509018e-02 , -1.27644138762383e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30718417264284e+00 , 4.16871718453483e-02 , -7.36909671849631e-01 , 6.92686289199743e+00 , -5.54415438918252e-01 , -5.49014882438513e-01 , 7.03986615725344e+00 , -2.05488332731408e+00 , -9.21102657855442e-01 , 6.18124903477374e+00 , -3.88383970664949e-01 , 7.51168826297644e-01 , 4.95735596178915e+00 , -1.48993083319897e-01 , 7.33145442690221e-01 , 6.83148904580529e+00 , -2.72841715052572e-01 , 1.93334265972718e+00 , 6.13060921896608e+00 , -1.89062232715222e-01 , 3.17330313438412e+00 , 7.08092425916463e+00 , -3.49233368017395e-01 , 4.32677839592918e+00 , 5.30637332582840e+00 , 1.08164781898213e+00 , 3.35033311370486e+00 , 4.13210066506290e+00 , 1.01649605106676e+00 , 3.69932441678733e+00 , 5.82688480149976e+00 , 2.25321473068541e+00 , 2.98407632497523e+00 , 5.22509289021225e+00 , 3.57335515036696e+00 , 2.91680227337450e+00 , 6.31999448897833e+00 , 4.49663584938670e+00 , 2.33343247619153e+00 , 3.86824967879405e+00 , 3.68702907349141e+00 , 2.04145655226949e+00 , 2.79078148468506e+00 , 4.16701485782358e+00 , 2.47059950031024e+00 , 3.94016415239703e+00 , 3.23074891589654e+00 , 7.29032916424395e-01 , 2.68761705478146e+00 , 3.01026776527402e+00 , -9.67979046711578e-02 , 3.07139729260048e+00 , 2.68616440164051e+00 , -1.51968634013069e+00 , 1.58646260739470e+00 , 2.17112803857450e+00 , 4.30318724403275e-01 , 3.73844471878330e-01 , 2.60158403745825e+00 , 4.97622603005500e-01 , 2.06733243661802e+00 , 1.11441383714785e+00 , 1.05481238848455e+00 , 1.16726272428891e+00 , 1.16807904656177e-01 , 1.70043882774388e+00 , 2.05367154256738e+00 , -1.09520468379986e+00 , 2.01927868883702e+00 , 5.67604086192743e-01 , 6.16227997677166e-01 , 2.95735789157109e+00 , -5.88976821904031e-01 , 3.51140926652656e-01 , 3.16276574530848e+00 , 1.30549157939399e+00 , 1.34999365183146e+00 , 3.75155290052027e+00 , 8.40499861109137e-01 , 1.98326680504138e+00 , 5.02624171448680e+00 , 2.10318795658565e+00 , 2.71516876902028e+00 , 5.70077200183844e+00 , -3.40304593402406e-01 , 2.91192872010019e+00 , 4.97014133609066e+00 , -1.12575479275189e+00 , 3.06579196236028e+00 , 5.88083881477434e+00 , -5.25984704448459e-01 , 3.51792153243344e+00 , 3.83541049993022e+00 , -1.51391477483970e+00 , 4.52536203704104e+00 , 3.42386890523466e+00 , -7.02231447313351e-01 , 5.41918282382161e+00 , 2.46848873178974e+00 , -2.74956688054334e+00 , 3.91248552352833e+00 , 2.87499367666642e+00 , -3.81413366211555e+00 , 4.52688991371594e+00 , 2.81361520701592e+00 , -2.64383741247041e+00 , 2.66163241306205e+00 , 2.38216775483745e+00 , -3.78251425352264e+00 , 1.80525412062537e+00 , 2.00226186579199e+00 , -3.37775868153243e+00 , 8.82865051937304e-01 , 8.57445534910989e-01 , -4.30306801891743e+00 , 1.06837176799812e+00 , 3.21190357529774e+00 , -5.49492444448199e+00 , 7.97432599055719e-01 , 3.33390372725479e+00 , -3.36426952968806e+00 , 7.04523716016644e-01 , 4.20843379224977e+00 , -3.68392264400780e+00 , 6.26974696338538e-02 , 5.44598583975169e+00 , -2.39140303069694e+00 , -3.22564541882353e-01 , 6.16358793333041e+00 , -4.45999983078115e+00 , 9.61766391199147e-01 , 6.43487752303019e+00 , -5.36323713526065e+00 , 5.94170976831314e-01 , 7.22136731745224e+00 , -6.25810757127878e+00 , 3.62181093943853e+00 , 6.74721925546691e+00 , -6.96891477435023e+00 , 4.29754951577123e+00 , 7.48903265085458e+00 , -6.71619957270996e+00 , 3.17253905665998e+00 , 5.50863152034551e+00 , -4.12060645379579e+00 , 2.24436729935346e+00 , 6.39632555906020e+00 , -4.80511720428680e+00 , 3.23056482649072e+00 , 7.25680313213883e+00 , -4.07347802051587e+00 , 4.55870682595936e+00 , 7.27666822909375e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 23. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 23. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atoms_new_colvar_forces = { ( -7.08168814937949e-02 , 3.03664452472894e-01 , -4.01263051701775e-01 ), ( 1.28897282159372e-02 , 3.03652461049390e-02 , -2.38962907009597e-01 ), ( -4.22098006472154e-02 , 9.46520341380242e-02 , 8.73129850632794e-02 ), ( -9.69836961545912e-02 , 2.50727137133401e-01 , 6.49179539830783e-02 ), ( -1.84393958034465e-02 , 9.86949573833386e-02 , -1.72272185409952e-01 ), ( 7.08217601806615e-02 , -1.85878656231814e-01 , -3.81557494152707e-02 ), ( 9.89515936319975e-03 , -9.88477114743486e-02 , 2.55569065601461e-01 ), ( -4.09765694460841e-02 , 6.13444540424881e-02 , 1.92109707586132e-01 ), ( 6.62729002147716e-02 , -1.91127572587650e-01 , 3.22352067094028e-02 ), ( 1.14473689844909e-01 , -3.92271189494705e-01 , 2.76014821802483e-01 ), ( 2.46097378880774e-02 , -9.95472081172002e-02 , 9.62325265867954e-02 ), ( 2.65800661415530e-02 , -9.74224674168165e-02 , 5.98069715723355e-02 ), ( 1.24268052531842e-02 , -5.57747491404972e-02 , 7.26713718002168e-02 ), ( 1.25692908517025e-02 , -5.36672888971867e-02 , 6.14959932071031e-02 ), ( 5.59595460705682e-03 , -3.49639005947200e-02 , 7.57753564150521e-02 ), ( -8.60853344063534e-03 , 9.83018051445572e-03 , 7.55907061791913e-02 ), ( -2.09370541899716e-03 , -2.64663879970091e-03 , 4.04063346386015e-02 ), ( -5.77353689472605e-03 , 9.92898655659034e-03 , 3.61127372741654e-02 ), ( 2.68495661875315e-03 , -1.29409636173138e-02 , 1.95929838330084e-02 ), ( 8.95464052648908e-03 , -2.20662135786371e-02 , -2.68667237089156e-02 ), ( 8.66369655000776e-03 , -2.38537280061534e-02 , -1.50453182585348e-02 ), ( 6.53999219691608e-03 , -1.36172289972066e-02 , -3.05455555170775e-02 ), ( 1.50176159970732e-02 , -4.68238119845228e-02 , -2.14130988594834e-03 ), ( 2.76703023716468e-02 , -8.88526582257361e-02 , 7.32763641562824e-03 ), ( 1.43169910754908e-02 , -4.71308548263177e-02 , 8.85056798528954e-03 ), ( 1.42657338744872e-02 , -4.43248724469113e-02 , -2.71006633727086e-03 ), ( 9.36528608667769e-03 , -3.72197152508182e-02 , 3.37223434971325e-02 ), ( -7.21504131285961e-04 , -1.52905347062471e-02 , 7.67810657807838e-02 ), ( -3.72528256564419e-03 , 4.17432885242504e-03 , 3.30593835387062e-02 ), ( -5.78257112165284e-03 , 1.12277726999349e-02 , 3.05594093243620e-02 ), ( -7.28993979152107e-03 , 1.80436025627073e-02 , 2.15242117056218e-02 ), ( -1.63558940654101e-02 , 5.23852695599543e-02 , -3.73915389641006e-03 ), ( -9.81031471026572e-03 , 3.58912916496682e-02 , -2.17857056962443e-02 ), ( -1.38492253162238e-02 , 5.01659601331753e-02 , -2.85612669585644e-02 ), ( -2.05962857627377e-03 , 1.48469797126605e-02 , -3.65378567014534e-02 ), ( 1.04783374291988e-02 , -1.61854613034706e-02 , -7.35606117525263e-02 ), ( 4.31670110681341e-03 , -1.11542447291206e-03 , -5.45771754964243e-02 ), ( 3.27982880802864e-03 , 5.68645760642483e-03 , -7.00314830313078e-02 ), ( 7.12123613458921e-03 , -1.52133335041448e-02 , -3.15734429379239e-02 ), ( 1.31790365397598e-02 , -4.19140962086650e-02 , 1.71795596493782e-03 ), ( 5.62737062255136e-04 , 1.41951133743415e-03 , -1.39560183089450e-02 ), ( 4.98953902161181e-04 , 2.96382598398075e-03 , -1.98286454303239e-02 ), ( -6.47935157763107e-03 , 2.04327935768268e-02 , -8.44654753455294e-05 ), ( -2.05200517884924e-02 , 5.80004004527264e-02 , 2.90662088850963e-02 ), ( -1.89655968658880e-02 , 6.33940538126061e-02 , -1.59219105336480e-02 ), ( -2.26670637582555e-02 , 7.53671927014898e-02 , -1.72837048580550e-02 ), ( -1.69597158830491e-02 , 7.24610787203844e-02 , -8.31859201087093e-02 ), ( -2.00871048374524e-02 , 8.66507978883153e-02 , -1.02144384436106e-01 ), ( -8.66934268082573e-03 , 4.63828731985594e-02 , -8.33650111463786e-02 ), ( -1.86591940279770e-02 , 6.68490223519342e-02 , -3.52456476594086e-02 ), ( -2.45472378440625e-02 , 9.31456187363586e-02 , -6.91082336777466e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 23, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 24, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 24, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 24, atoms_positions[size = 51] = { ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 ), ( 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 ), ( 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 ), ( 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 ), ( 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 ), ( 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 ), ( -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 ), ( -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 ), ( -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 ), ( -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ), ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 ), ( 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 ), ( 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 ), ( 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 ), ( 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 ), ( 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 ), ( 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 ), ( 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 ), ( 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 ), ( 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 ), ( 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 ), ( 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 ), ( 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 ), ( 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 ), ( 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 ), ( 3.75816832389217e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 ), ( 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 ), ( 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 ), ( 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 ), ( -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 ), ( 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 ), ( 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 ), ( -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 ), ( -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 ), ( -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 ), ( -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 ), ( -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 ), ( -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 ), ( -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 ), ( -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 ), ( -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 ), ( -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 ), ( -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 ), ( -2.39101064153575e+00 , -3.23953535315112e-01 , 6.15985323826371e+00 ), ( -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 ), ( -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 ), ( -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 ), ( -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 ), ( -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 ), ( -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 ), ( -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ) } +colvars: Step 24, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756127e-02 , 1.27630697470618e-02 , -1.31113665114322e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 , 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 , 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 , 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 , 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 , 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 , 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 , 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 , 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 , 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 , 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 , 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 , 3.75816832389217e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 , 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 , 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 , -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 , 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 , -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 , -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 , -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 , -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 , -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 , -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 , -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 , -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 , -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -2.39101064153575e+00 , -3.23953535315112e-01 , 6.15985323826371e+00 , -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 , -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 , -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 , -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 , -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 , -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 , -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ). +colvars: Done calculating colvar "main". +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99737489847089e-01 , 1.37893985756127e-02 , 1.27630697470618e-02 , -1.31113665114322e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30620781072974e+00 , 4.18064522247766e-02 , -7.33225507151434e-01 , 6.91729621390874e+00 , -5.57091421586993e-01 , -5.42539046769640e-01 , 7.03553480651868e+00 , -2.05624028923975e+00 , -9.16074940306886e-01 , 6.18276945147063e+00 , -3.89826156087348e-01 , 7.59690073681585e-01 , 4.95289617204130e+00 , -1.46213012029004e-01 , 7.34904596663071e-01 , 6.82539310400490e+00 , -2.75639767176683e-01 , 1.94140476354519e+00 , 6.12094320926949e+00 , -1.96662585526302e-01 , 3.16790854367548e+00 , 7.08522786132224e+00 , -3.47300542704821e-01 , 4.33346934121746e+00 , 5.30707785392009e+00 , 1.07799511411036e+00 , 3.35229212003449e+00 , 4.13171632913018e+00 , 1.01441994836660e+00 , 3.70592953837888e+00 , 5.82493109728095e+00 , 2.25303742013725e+00 , 2.98229845405554e+00 , 5.21724596582048e+00 , 3.57153610169804e+00 , 2.91396224134112e+00 , 6.31885463289814e+00 , 4.49483487133971e+00 , 2.32389983834783e+00 , 3.86506918304834e+00 , 3.68039075583410e+00 , 2.03996008885996e+00 , 2.79218151695552e+00 , 4.16835472600928e+00 , 2.46514108443038e+00 , 3.93788896061010e+00 , 3.22662583199428e+00 , 7.29228688462269e-01 , 2.69897295220978e+00 , 3.01514098347367e+00 , -9.36071484491299e-02 , 3.07835976234139e+00 , 2.67956899161629e+00 , -1.52328204084298e+00 , 1.57939293822308e+00 , 2.16980376694419e+00 , 4.27511622087788e-01 , 3.75816832389217e-01 , 2.60641155854152e+00 , 4.92814457249487e-01 , 2.07188489060301e+00 , 1.12620580223262e+00 , 1.05055888428012e+00 , 1.16978764595701e+00 , 1.16754753422420e-01 , 1.70048610330319e+00 , 2.05774645305050e+00 , -1.09369624273257e+00 , 2.02277003529943e+00 , 5.69446187330118e-01 , 6.17261328693535e-01 , 2.96089545351769e+00 , -5.86253224721710e-01 , 3.51767666048574e-01 , 3.16399575807899e+00 , 1.30172435314309e+00 , 1.35307499052773e+00 , 3.74659621554135e+00 , 8.41701952822355e-01 , 1.98358458626386e+00 , 5.02675309786416e+00 , 2.10784777753045e+00 , 2.72317253015683e+00 , 5.70624440534305e+00 , -3.42493071791099e-01 , 2.91064076461746e+00 , 4.97039709946572e+00 , -1.12267002320403e+00 , 3.06653437701478e+00 , 5.87920539708389e+00 , -5.30349212131165e-01 , 3.51481180424591e+00 , 3.82965146656906e+00 , -1.50982560767739e+00 , 4.51939633455690e+00 , 3.41953453898451e+00 , -7.05086207224982e-01 , 5.42096703604624e+00 , 2.46974615543574e+00 , -2.74704337192707e+00 , 3.92054569822793e+00 , 2.86561601422574e+00 , -3.81294383800873e+00 , 4.53229649264381e+00 , 2.81348674674023e+00 , -2.65085587859970e+00 , 2.65593633751865e+00 , 2.37642390887430e+00 , -3.78508552527350e+00 , 1.80876981687841e+00 , 2.00376231048101e+00 , -3.37440141972859e+00 , 8.80901404713567e-01 , 8.51191758687578e-01 , -4.29385802021457e+00 , 1.06624960554840e+00 , 3.21429864908296e+00 , -5.49347630919106e+00 , 7.90456119038356e-01 , 3.33505708764970e+00 , -3.36460662620379e+00 , 7.09172702823026e-01 , 4.20528043418871e+00 , -3.68005965040029e+00 , 6.78907924099865e-02 , 5.45204135176785e+00 , -2.39101064153575e+00 , -3.23953535315112e-01 , 6.15985323826371e+00 , -4.46120154542664e+00 , 9.52435166612142e-01 , 6.43250575540937e+00 , -5.36375234742093e+00 , 5.92310222524114e-01 , 7.22055877226790e+00 , -6.26714919648178e+00 , 3.62566696511803e+00 , 6.75008262704702e+00 , -6.97235532353079e+00 , 4.29722237284704e+00 , 7.49281451851313e+00 , -6.70569791173069e+00 , 3.16968011174723e+00 , 5.51027846672450e+00 , -4.11765291366207e+00 , 2.24550914938645e+00 , 6.39374465644049e+00 , -4.80598237277264e+00 , 3.23976099423521e+00 , 7.25950275492445e+00 , -4.06523112839317e+00 , 4.55411737637028e+00 , 7.27503613536848e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 24. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 24. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atoms_new_colvar_forces = { ( -7.06413071230504e-02 , 3.03646376177113e-01 , -4.01360271764822e-01 ), ( 1.29135699454975e-02 , 3.05895907970703e-02 , -2.39103012853669e-01 ), ( -4.22727893177430e-02 , 9.48806486655140e-02 , 8.68992202535934e-02 ), ( -9.69353995896309e-02 , 2.50634381681781e-01 , 6.47066866422256e-02 ), ( -1.83397783484814e-02 , 9.85756742630302e-02 , -1.72126442430389e-01 ), ( 7.07728219511373e-02 , -1.85765887475988e-01 , -3.80697774318616e-02 ), ( 9.79094825409427e-03 , -9.88124633185437e-02 , 2.55459166370171e-01 ), ( -4.09551734426115e-02 , 6.10746932338373e-02 , 1.92255054495674e-01 ), ( 6.62713061540428e-02 , -1.91287333337422e-01 , 3.26356316955038e-02 ), ( 1.14308608904662e-01 , -3.92214125425127e-01 , 2.76215371150626e-01 ), ( 2.45725920232996e-02 , -9.95638546443988e-02 , 9.62771812753496e-02 ), ( 2.65546467078899e-02 , -9.74578351767043e-02 , 5.98293143046423e-02 ), ( 1.24049987615565e-02 , -5.57845532030435e-02 , 7.26871465513840e-02 ), ( 1.25488921727912e-02 , -5.36768078818011e-02 , 6.15147514345488e-02 ), ( 5.57889542473557e-03 , -3.49669023596321e-02 , 7.57778613512469e-02 ), ( -8.61511790943968e-03 , 9.84223056552992e-03 , 7.55684853155769e-02 ), ( -2.09705915825774e-03 , -2.64725710136186e-03 , 4.03903767810113e-02 ), ( -5.77488506395000e-03 , 9.93524199145591e-03 , 3.60968052014862e-02 ), ( 2.68555107386697e-03 , -1.29560057336035e-02 , 1.95709202788530e-02 ), ( 8.96558132413490e-03 , -2.21050689084729e-02 , -2.69029309665138e-02 ), ( 8.66766398808848e-03 , -2.38805017462989e-02 , -1.50614381521955e-02 ), ( 6.54848333975447e-03 , -1.36430392009208e-02 , -3.05652148041552e-02 ), ( 1.50134061346635e-02 , -4.68539729865604e-02 , -2.14212405348141e-03 ), ( 2.76535944622938e-02 , -8.88924111111195e-02 , 7.35459163320721e-03 ), ( 1.43063692881742e-02 , -4.71487915327259e-02 , 8.86870857810114e-03 ), ( 1.42567773634181e-02 , -4.43424413314667e-02 , -2.68944979509766e-03 ), ( 9.35108517815968e-03 , -3.72249354736576e-02 , 3.37419691915580e-02 ), ( -7.42093767884172e-04 , -1.52692752516169e-02 , 7.68061137984732e-02 ), ( -3.73289987962753e-03 , 4.18986710243482e-03 , 3.30695277218438e-02 ), ( -5.78995808229407e-03 , 1.12491380714132e-02 , 3.05733940861192e-02 ), ( -7.29041607322480e-03 , 1.80568906634082e-02 , 2.15185307159462e-02 ), ( -1.63414772366860e-02 , 5.23986257872083e-02 , -3.77465749262822e-03 ), ( -9.79832819666987e-03 , 3.58985454533797e-02 , -2.18051356045120e-02 ), ( -1.38341517731008e-02 , 5.01795107928477e-02 , -2.85827133571873e-02 ), ( -2.04790718474561e-03 , 1.48390673158269e-02 , -3.65546209718068e-02 ), ( 1.04926098671793e-02 , -1.62200191491437e-02 , -7.35748831065827e-02 ), ( 4.32610626512208e-03 , -1.12923962307860e-03 , -5.45781232758893e-02 ), ( 3.29291015644962e-03 , 5.67254452054352e-03 , -7.00339106044753e-02 ), ( 7.12187254119930e-03 , -1.52231512708809e-02 , -3.15600301609801e-02 ), ( 1.31643703507535e-02 , -4.19177461698118e-02 , 1.76043709113810e-03 ), ( 5.59193791564009e-04 , 1.43044841286951e-03 , -1.39305256747124e-02 ), ( 4.95289569726373e-04 , 2.97716813520242e-03 , -1.97977791071556e-02 ), ( -6.48138398004286e-03 , 2.04545723962382e-02 , -6.71144154469311e-05 ), ( -2.05210193315769e-02 , 5.80475595770238e-02 , 2.90742990478969e-02 ), ( -1.89565419805277e-02 , 6.34302052679531e-02 , -1.59214405626777e-02 ), ( -2.26568850688841e-02 , 7.54112231480941e-02 , -1.72818588807230e-02 ), ( -1.69327803850088e-02 , 7.24752813498580e-02 , -8.32085865792704e-02 ), ( -2.00533740645507e-02 , 8.66648297314470e-02 , -1.02175971750392e-01 ), ( -8.64801089252043e-03 , 4.63872708123076e-02 , -8.33751561955853e-02 ), ( -1.86433498800995e-02 , 6.68759703471642e-02 , -3.52584071050766e-02 ), ( -2.45160572636472e-02 , 9.31660631528295e-02 , -6.91499678688890e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 24, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 25, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 25, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 25, atoms_positions[size = 51] = { ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 ), ( 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 ), ( 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 ), ( 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 ), ( 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 ), ( 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 ), ( -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 ), ( -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 ), ( -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 ), ( -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ), ( 8.30509683048428e+00 , 4.19726743115742e-02 , -7.29420068900795e-01 ), ( 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 ), ( 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 ), ( 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 ), ( 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 ), ( 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 ), ( 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 ), ( 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 ), ( 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 ), ( 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 ), ( 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 ), ( 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 ), ( 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 ), ( 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 ), ( 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 ), ( 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 ), ( 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 ), ( 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 ), ( 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 ), ( -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 ), ( 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 ), ( 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 ), ( -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 ), ( -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 ), ( -5.34273816020181e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 ), ( -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 ), ( -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 ), ( -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 ), ( -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 ), ( -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 ), ( -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 ), ( -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 ), ( -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 ), ( -2.39001770562880e+00 , -3.24650284743465e-01 , 6.15574359469104e+00 ), ( -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 ), ( -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 ), ( -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 ), ( -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 ), ( -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 ), ( -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 ), ( -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ) } +colvars: Step 25, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876204e-02 , 1.29777530480416e-02 , -1.34613291247889e-02 ). +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30509683048428e+00 , 4.19726743115742e-02 , -7.29420068900795e-01 , 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 , 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 , 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 , 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 , 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 , 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 , 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 , 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 , 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 , 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 , 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 , 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 , 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 , 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 , -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 , 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 , -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 , -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 , -5.34273816020181e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 , -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 , -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 , -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 , -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 , -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 , -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -2.39001770562880e+00 , -3.24650284743465e-01 , 6.15574359469104e+00 , -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 , -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 , -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 , -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 , -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 , -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 , -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ). +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99728636259111e-01 , 1.38933216876204e-02 , 1.29777530480416e-02 , -1.34613291247889e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30509683048428e+00 , 4.19726743115742e-02 , -7.29420068900795e-01 , 6.90858635758027e+00 , -5.60407192347503e-01 , -5.36819646889094e-01 , 7.03096231788356e+00 , -2.05759628372070e+00 , -9.10675140152154e-01 , 6.18256560831461e+00 , -3.89449280476306e-01 , 7.68336493220592e-01 , 4.94918949489411e+00 , -1.43972039804972e-01 , 7.36571172886984e-01 , 6.81980136982472e+00 , -2.78930188770548e-01 , 1.94902243948162e+00 , 6.11062700680115e+00 , -2.04029597893877e-01 , 3.16350955306012e+00 , 7.09011449914290e+00 , -3.45412965332306e-01 , 4.34002419301881e+00 , 5.30626808702853e+00 , 1.07454551036636e+00 , 3.35385567648144e+00 , 4.13151004505906e+00 , 1.01244341565045e+00 , 3.71272619928229e+00 , 5.82363877636823e+00 , 2.25227858979188e+00 , 2.98059851063313e+00 , 5.20802143080252e+00 , 3.56947877976783e+00 , 2.91032118387577e+00 , 6.31741170892816e+00 , 4.49252427379011e+00 , 2.31490075583518e+00 , 3.86259931137073e+00 , 3.67383767030136e+00 , 2.03799865316075e+00 , 2.79436170687385e+00 , 4.16929728906941e+00 , 2.45969835125011e+00 , 3.93444207446705e+00 , 3.22189484664495e+00 , 7.29808113571796e-01 , 2.71077157037530e+00 , 3.02148025757965e+00 , -9.01827391969891e-02 , 3.08519519187245e+00 , 2.67306416894080e+00 , -1.52743548860715e+00 , 1.57152680563267e+00 , 2.17043107982995e+00 , 4.25533836955124e-01 , 3.79297677549126e-01 , 2.61014137245973e+00 , 4.87751923694815e-01 , 2.07488120184109e+00 , 1.13557997747480e+00 , 1.04709733854309e+00 , 1.17414646030816e+00 , 1.17257197841184e-01 , 1.69967540980046e+00 , 2.06189542944388e+00 , -1.09277087517988e+00 , 2.02627464285466e+00 , 5.71112913797729e-01 , 6.17903871356173e-01 , 2.96331702661885e+00 , -5.84407225357038e-01 , 3.52457161361140e-01 , 3.16579506947285e+00 , 1.29808300234100e+00 , 1.35716059408718e+00 , 3.74347085400931e+00 , 8.44142830988299e-01 , 1.98338664214562e+00 , 5.02736607402698e+00 , 2.11051658951145e+00 , 2.73057782434961e+00 , 5.71108290550791e+00 , -3.44946298029435e-01 , 2.90922405427321e+00 , 4.97007105145024e+00 , -1.11995272557718e+00 , 3.06721448509341e+00 , 5.87813983914951e+00 , -5.34273816020181e-01 , 3.51272907056477e+00 , 3.82296040856855e+00 , -1.50447898552173e+00 , 4.51302919656754e+00 , 3.41660146457247e+00 , -7.08938024005226e-01 , 5.42290903996785e+00 , 2.47099945386640e+00 , -2.74524092670153e+00 , 3.92806879262504e+00 , 2.85499848961593e+00 , -3.81166370017355e+00 , 4.53768746639608e+00 , 2.81352561754890e+00 , -2.65804094852500e+00 , 2.65011326083907e+00 , 2.37135654085329e+00 , -3.78761014869642e+00 , 1.81299166598222e+00 , 2.00533985501840e+00 , -3.37135570146038e+00 , 8.78996279269729e-01 , 8.44773411197925e-01 , -4.28429675100875e+00 , 1.06338808313435e+00 , 3.21804046963707e+00 , -5.49174172778968e+00 , 7.83649635099011e-01 , 3.33628874320777e+00 , -3.36554049793186e+00 , 7.13762612627844e-01 , 4.20057492811399e+00 , -3.67692497938528e+00 , 7.24104000983912e-02 , 5.45877291154939e+00 , -2.39001770562880e+00 , -3.24650284743465e-01 , 6.15574359469104e+00 , -4.46316681844048e+00 , 9.43582332211813e-01 , 6.43028464155246e+00 , -5.36368064939316e+00 , 5.90213136234558e-01 , 7.21909765896476e+00 , -6.27626132852270e+00 , 3.62848016964581e+00 , 6.75226337994972e+00 , -6.97608264600132e+00 , 4.29709777016449e+00 , 7.49656462123632e+00 , -6.69443026733839e+00 , 3.16729775660245e+00 , 5.51291958586983e+00 , -4.11463016965820e+00 , 2.24726037200533e+00 , 6.39236656627899e+00 , -4.80734421837152e+00 , 3.24896814727340e+00 , 7.26120990324001e+00 , -4.05668823859352e+00 , 4.55089935416450e+00 , 7.27389451946626e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 25. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 25. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atoms_new_colvar_forces = { ( -7.04600443638351e-02 , 3.03621747458522e-01 , -4.01373682028473e-01 ), ( 1.29420506857990e-02 , 3.08450317799853e-02 , -2.39227221868054e-01 ), ( -4.23355906274467e-02 , 9.50793160624864e-02 , 8.64467007486022e-02 ), ( -9.68894888293516e-02 , 2.50479150966912e-01 , 6.45062578129430e-02 ), ( -1.82393338200141e-02 , 9.84602010337278e-02 , -1.71931658781829e-01 ), ( 7.07263478012350e-02 , -1.85609672059077e-01 , -3.79978980760433e-02 ), ( 9.68400550810402e-03 , -9.87944561148575e-02 , 2.55296819269016e-01 ), ( -4.09399777928876e-02 , 6.07633323078664e-02 , 1.92403592972447e-01 ), ( 6.62674376926361e-02 , -1.91412527838396e-01 , 3.30433713295305e-02 ), ( 1.14140727837322e-01 , -3.92115243802243e-01 , 2.76345875640083e-01 ), ( 2.45303535326015e-02 , -9.95720517518532e-02 , 9.63105281691545e-02 ), ( 2.65278426707223e-02 , -9.74872741208499e-02 , 5.98491237917058e-02 ), ( 1.23800078595191e-02 , -5.57945041990639e-02 , 7.26963423269236e-02 ), ( 1.25256232080886e-02 , -5.36844439703333e-02 , 6.15274102361732e-02 ), ( 5.55871954717284e-03 , -3.49756477161695e-02 , 7.57742636763354e-02 ), ( -8.62458743879690e-03 , 9.83841075458371e-03 , 7.55411808127873e-02 ), ( -2.10133459875127e-03 , -2.65705587569528e-03 , 4.03733078812120e-02 ), ( -5.77739600858532e-03 , 9.93201495398462e-03 , 3.60790735980493e-02 ), ( 2.68726300921176e-03 , -1.29789758403624e-02 , 1.95524417854630e-02 ), ( 8.98170264457942e-03 , -2.21500931356782e-02 , -2.69262680091888e-02 ), ( 8.67464681814414e-03 , -2.39087709180257e-02 , -1.50701443449332e-02 ), ( 6.56074612158967e-03 , -1.36702589485719e-02 , -3.05758637567222e-02 ), ( 1.50111682037605e-02 , -4.68811361083810e-02 , -2.13810104570518e-03 ), ( 2.76377619824813e-02 , -8.89193875459930e-02 , 7.38337491409857e-03 ), ( 1.42956328492329e-02 , -4.71593898002372e-02 , 8.88642649261350e-03 ), ( 1.42480549426660e-02 , -4.43507918114741e-02 , -2.66868998230111e-03 ), ( 9.33487811850630e-03 , -3.72258735497682e-02 , 3.37570127503085e-02 ), ( -7.68369119173247e-04 , -1.52484894295288e-02 , 7.68183269009158e-02 ), ( -3.74332602967186e-03 , 4.20432533857040e-03 , 3.30732666132640e-02 ), ( -5.80058286933925e-03 , 1.12703919993963e-02 , 3.05797902919005e-02 ), ( -7.29234650113122e-03 , 1.80648763741093e-02 , 2.15098284387671e-02 ), ( -1.63260769480337e-02 , 5.23986038060843e-02 , -3.80716611556857e-03 ), ( -9.78497055648197e-03 , 3.59002867510908e-02 , -2.18212967568863e-02 ), ( -1.38177140907221e-02 , 5.01868220910697e-02 , -2.86010179352413e-02 ), ( -2.03339071916587e-03 , 1.48294691070948e-02 , -3.65649683550387e-02 ), ( 1.05127471287825e-02 , -1.62492873763924e-02 , -7.35760043117994e-02 ), ( 4.33869355337769e-03 , -1.13698546157585e-03 , -5.45723770452254e-02 ), ( 3.30989754432303e-03 , 5.66560766362085e-03 , -7.00281639538081e-02 ), ( 7.12381538260144e-03 , -1.52244133889981e-02 , -3.15443190776360e-02 ), ( 1.31478892206905e-02 , -4.19063984404894e-02 , 1.79769937088845e-03 ), ( 5.54388479922564e-04 , 1.45041162698810e-03 , -1.39089157145296e-02 ), ( 4.90214236116315e-04 , 3.00169662343026e-03 , -1.97713882165925e-02 ), ( -6.48554752146524e-03 , 2.04801681670990e-02 , -5.53434019236684e-05 ), ( -2.05264663856608e-02 , 5.80900538781189e-02 , 2.90718102447906e-02 ), ( -1.89490503248258e-02 , 6.34642763608981e-02 , -1.59251829016669e-02 ), ( -2.26487578411400e-02 , 7.54529703717812e-02 , -1.72854851773508e-02 ), ( -1.69021686492795e-02 , 7.24877434965381e-02 , -8.32235613476904e-02 ), ( -2.00147470785519e-02 , 8.66757664758654e-02 , -1.02197102389267e-01 ), ( -8.62297525244983e-03 , 4.63953041892996e-02 , -8.33777736619381e-02 ), ( -1.86270819201375e-02 , 6.68989416403372e-02 , -3.52706493301954e-02 ), ( -2.44812912922878e-02 , 9.31762079245552e-02 , -6.91835824823653e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 25, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 26, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 26, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 26, atoms_positions[size = 51] = { ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 ), ( 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 ), ( 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 ), ( 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 ), ( 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 ), ( 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 ), ( -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 ), ( -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 ), ( -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 ), ( -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ), ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 ), ( 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459834e-01 ), ( 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 ), ( 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 ), ( 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 ), ( 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 ), ( 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 ), ( 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 ), ( 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 ), ( 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 ), ( 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 ), ( 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 ), ( 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 ), ( 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 ), ( 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 ), ( 3.83975554418137e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 ), ( 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 ), ( 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 ), ( 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 ), ( -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 ), ( 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 ), ( 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 ), ( -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 ), ( -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 ), ( -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 ), ( -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 ), ( -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 ), ( -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 ), ( -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 ), ( -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 ), ( -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 ), ( -5.48945484200930e+00 , 7.77049854240671e-01 , 3.33760630244013e+00 ), ( -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 ), ( -2.38839256737455e+00 , -3.24502407433307e-01 , 6.15138672061077e+00 ), ( -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 ), ( -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983190e+00 ), ( -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 ), ( -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 ), ( -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 ), ( -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 ), ( -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ) } +colvars: Step 26, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 , 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459834e-01 , 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 , 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 , 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 , 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 , 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 , 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 , 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 , 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 , 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 , 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 , 3.83975554418137e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 , 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 , 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 , -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 , 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 , -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 , -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 , -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 , -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 , -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 , -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 , -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 , -5.48945484200930e+00 , 7.77049854240671e-01 , 3.33760630244013e+00 , -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -2.38839256737455e+00 , -3.24502407433307e-01 , 6.15138672061077e+00 , -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 , -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983190e+00 , -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 , -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 , -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 , -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 , -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99719415689473e-01 , 1.40430139976915e-02 , 1.31736646150011e-02 , -1.37963115349980e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30368677824060e+00 , 4.21514639867546e-02 , -7.25483239462402e-01 , 6.90102500734281e+00 , -5.64367944466917e-01 , -5.31895472653596e-01 , 7.02631696893803e+00 , -2.05902021594483e+00 , -9.04858631459834e-01 , 6.18027929939676e+00 , -3.87258551997490e-01 , 7.76908533178730e-01 , 4.94635525129989e+00 , -1.42297358459208e-01 , 7.38193464644724e-01 , 6.81478636320642e+00 , -2.82677086748113e-01 , 1.95601664521508e+00 , 6.09988229106924e+00 , -2.11050660963089e-01 , 3.16062127289817e+00 , 7.09533673500577e+00 , -3.43712735060751e-01 , 4.34634932218721e+00 , 5.30391534227458e+00 , 1.07134671305850e+00 , 3.35496523470085e+00 , 4.13150456167252e+00 , 1.01057706977931e+00 , 3.71970989786194e+00 , 5.82299879891212e+00 , 2.25100771330774e+00 , 2.97895941057775e+00 , 5.19776191426564e+00 , 3.56707235622104e+00 , 2.90597508054540e+00 , 6.31558836881746e+00 , 4.48958280947361e+00 , 2.30663083731284e+00 , 3.86079348373964e+00 , 3.66745459732436e+00 , 2.03559542421506e+00 , 2.79725093845983e+00 , 4.16984183248884e+00 , 2.45430299474857e+00 , 3.93011538123333e+00 , 3.21660945421813e+00 , 7.30861396235425e-01 , 2.72244054439072e+00 , 3.02901974791788e+00 , -8.66264111316608e-02 , 3.09176835337043e+00 , 2.66690987352894e+00 , -1.53174182575978e+00 , 1.56367585376442e+00 , 2.17317718188026e+00 , 4.24205684149011e-01 , 3.83975554418137e-01 , 2.61283514762871e+00 , 4.82483676808177e-01 , 2.07612105190919e+00 , 1.14219567399683e+00 , 1.04462002184962e+00 , 1.18043125377318e+00 , 1.18598686751984e-01 , 1.69792049273255e+00 , 2.06604155080176e+00 , -1.09235211238995e+00 , 2.02962454986394e+00 , 5.72511969974605e-01 , 6.18119250873497e-01 , 2.96447453935603e+00 , -5.83440058048653e-01 , 3.53192779370295e-01 , 3.16816645334375e+00 , 1.29468604784806e+00 , 1.36224346130530e+00 , 3.74222980710584e+00 , 8.47820394290413e-01 , 1.98278709727219e+00 , 5.02811433264652e+00 , 2.11103025543746e+00 , 2.73736623031006e+00 , 5.71521863137289e+00 , -3.47516467749870e-01 , 2.90770332308804e+00 , 4.96896590208285e+00 , -1.11767462941623e+00 , 3.06784857995853e+00 , 5.87772301608539e+00 , -5.37619378897362e-01 , 3.51139430435178e+00 , 3.81546413541767e+00 , -1.49808669994827e+00 , 4.50650268249983e+00 , 3.41495694818442e+00 , -7.13712984922438e-01 , 5.42508155429137e+00 , 2.47232083085061e+00 , -2.74418492020547e+00 , 3.93463113198724e+00 , 2.84322901422040e+00 , -3.81029734284168e+00 , 4.54311657416575e+00 , 2.81369239552076e+00 , -2.66521730461956e+00 , 2.64464341625580e+00 , 2.36703818251505e+00 , -3.79019292155199e+00 , 1.81735424155422e+00 , 2.00681437172922e+00 , -3.36859747820250e+00 , 8.77384991456883e-01 , 8.38189657257807e-01 , -4.27504993146447e+00 , 1.05987411004896e+00 , 3.22282745730501e+00 , -5.48945484200930e+00 , 7.77049854240671e-01 , 3.33760630244013e+00 , -3.36681680575928e+00 , 7.18088213962232e-01 , 4.19477821135669e+00 , -3.67441092319199e+00 , 7.60406688373056e-02 , 5.46566218960245e+00 , -2.38839256737455e+00 , -3.24502407433307e-01 , 6.15138672061077e+00 , -4.46583672971628e+00 , 9.35756288775792e-01 , 6.42834013727742e+00 , -5.36309063025825e+00 , 5.87795721969000e-01 , 7.21702085983190e+00 , -6.28488306170113e+00 , 3.63011350154007e+00 , 6.75379914568836e+00 , -6.98022282152255e+00 , 4.29723711842134e+00 , 7.50030943228954e+00 , -6.68273006685559e+00 , 3.16545433156216e+00 , 5.51647699185910e+00 , -4.11170288339109e+00 , 2.24935048324457e+00 , 6.39214102080456e+00 , -4.80897022566677e+00 , 3.25782791559000e+00 , 7.26180238293391e+00 , -4.04812797729058e+00 , 4.54940256274560e+00 , 7.27327687313751e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 26. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 26. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atoms_new_colvar_forces = { ( -7.02759487121496e-02 , 3.03592903297381e-01 , -4.01322595058309e-01 ), ( 1.29777444484041e-02 , 3.11151912550363e-02 , -2.39334291295019e-01 ), ( -4.23984621351551e-02 , 9.52467395890062e-02 , 8.59805584984231e-02 ), ( -9.68508821319136e-02 , 2.50280691303569e-01 , 6.43201527675709e-02 ), ( -1.81394624860405e-02 , 9.83519274233092e-02 , -1.71706731179628e-01 ), ( 7.06861711244202e-02 , -1.85425392448265e-01 , -3.79380381448007e-02 ), ( 9.57471239129273e-03 , -9.87903314213212e-02 , 2.55100464157634e-01 ), ( -4.09347057274910e-02 , 6.04312464191056e-02 , 1.92547924833260e-01 ), ( 6.62631407386996e-02 , -1.91505902765397e-01 , 3.34422263795946e-02 ), ( 1.13975178390395e-01 , -3.91987080180140e-01 , 2.76419259062611e-01 ), ( 2.44850402010076e-02 , -9.95713974916157e-02 , 9.63342285937298e-02 ), ( 2.65010124687372e-02 , -9.75097049166921e-02 , 5.98681079194398e-02 ), ( 1.23528879662618e-02 , -5.58036520957835e-02 , 7.27007292311104e-02 ), ( 1.25005219271507e-02 , -5.36895785441518e-02 , 6.15353199422810e-02 ), ( 5.53611543404054e-03 , -3.49887682495592e-02 , 7.57667076403759e-02 ), ( -8.63700702604888e-03 , 9.82070089447024e-03 , 7.55114158522256e-02 ), ( -2.10659992708687e-03 , -2.67464113977563e-03 , 4.03568019629268e-02 ), ( -5.78123646494341e-03 , 9.92045066551190e-03 , 3.60609548302388e-02 ), ( 2.68984652041441e-03 , -1.30082658740007e-02 , 1.95391125026403e-02 ), ( 9.00226957835600e-03 , -2.21993856296152e-02 , -2.69355681840099e-02 ), ( 8.68438349470702e-03 , -2.39375135194767e-02 , -1.50708149285185e-02 ), ( 6.57630028948226e-03 , -1.36980342382398e-02 , -3.05772297762471e-02 ), ( 1.50111517137013e-02 , -4.69045680137091e-02 , -2.12866950333664e-03 ), ( 2.76239043083305e-02 , -8.89335499142471e-02 , 7.41413710602703e-03 ), ( 1.42854688295579e-02 , -4.71627686040402e-02 , 8.90375783411515e-03 ), ( 1.42402199047629e-02 , -4.43503631938378e-02 , -2.64816707932508e-03 ), ( 9.31746414113780e-03 , -3.72225620105006e-02 , 3.37679174239998e-02 ), ( -7.99308945475898e-04 , -1.52282832043496e-02 , 7.68186726665386e-02 ), ( -3.75619772566364e-03 , 4.21752672172109e-03 , 3.30709088042420e-02 ), ( -5.81406267630256e-03 , 1.12910157251468e-02 , 3.05785957286102e-02 ), ( -7.29582728360609e-03 , 1.80678557646107e-02 , 2.14986330080878e-02 ), ( -1.63107240894460e-02 , 5.23862202541373e-02 , -3.83592521087052e-03 ), ( -9.77096127551217e-03 , 3.58967100268293e-02 , -2.18343387088894e-02 ), ( -1.38007947251377e-02 , 5.01878895330269e-02 , -2.86165861734203e-02 ), ( -2.01670542625997e-03 , 1.48183742544679e-02 , -3.65692494411242e-02 ), ( 1.05381451549542e-02 , -1.62732033203028e-02 , -7.35649265176479e-02 ), ( 4.35413995448840e-03 , -1.13928950370447e-03 , -5.45611871279412e-02 ), ( 3.33031042288600e-03 , 5.66479643420802e-03 , -7.00158856017225e-02 ), ( 7.12723901359866e-03 , -1.52179938195834e-02 , -3.15274406212481e-02 ), ( 1.31306877600108e-02 , -4.18816228571183e-02 , 1.82851326350306e-03 ), ( 5.48734989236875e-04 , 1.47786091102190e-03 , -1.38926182011663e-02 ), ( 4.84204918059289e-04 , 3.03549036454782e-03 , -1.97512896041410e-02 ), ( -6.49162233900807e-03 , 2.05083540598445e-02 , -5.01450680240616e-05 ), ( -2.05364121159090e-02 , 5.81269386311858e-02 , 2.90583664730193e-02 ), ( -1.89435793931410e-02 , 6.34950680085711e-02 , -1.59343341897455e-02 ), ( -2.26431912621753e-02 , 7.54909620571149e-02 , -1.72960215224767e-02 ), ( -1.68692306396098e-02 , 7.24974880057940e-02 , -8.32327838657938e-02 ), ( -1.99729416336030e-02 , 8.66826413894369e-02 , -1.02209969773827e-01 ), ( -8.59518558707570e-03 , 4.64057351138899e-02 , -8.33750094210587e-02 ), ( -1.86112386515312e-02 , 6.69171340762310e-02 , -3.52835165863774e-02 ), ( -2.44447077038081e-02 , 9.31759407762520e-02 , -6.92101336975360e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 26, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 27, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 27, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 27, atoms_positions[size = 51] = { ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 ), ( 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 ), ( 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 ), ( 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 ), ( 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 ), ( 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 ), ( -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 ), ( -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 ), ( -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 ), ( -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 ), ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 ), ( 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 ), ( 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 ), ( 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321919e-01 ), ( 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 ), ( 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 ), ( 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 ), ( 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 ), ( 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 ), ( 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 ), ( 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 ), ( 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 ), ( 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 ), ( 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 ), ( 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 ), ( 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 ), ( 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 ), ( 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 ), ( 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 ), ( -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 ), ( 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 ), ( 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 ), ( -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 ), ( -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 ), ( -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 ), ( -7.19299148831411e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 ), ( -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 ), ( -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 ), ( -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 ), ( -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 ), ( -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 ), ( -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 ), ( -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 ), ( -2.38611115771938e+00 , -3.23414419937697e-01 , 6.14694225305597e+00 ), ( -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 ), ( -5.36207760113481e+00 , 5.84976302002793e-01 , 7.21438869028155e+00 ), ( -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 ), ( -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 ), ( -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 ), ( -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 ), ( -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ) } +colvars: Step 27, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 , 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 , 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 , 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321919e-01 , 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 , 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 , 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 , 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 , 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 , 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 , 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 , 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 , 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 , 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 , 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 , -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 , 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 , -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 , -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 , -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -7.19299148831411e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 , -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 , -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 , -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 , -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 , -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 , -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -2.38611115771938e+00 , -3.23414419937697e-01 , 6.14694225305597e+00 , -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 , -5.36207760113481e+00 , 5.84976302002793e-01 , 7.21438869028155e+00 , -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 , -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 , -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 , -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 , -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99710459485710e-01 , 1.42224334147857e-02 , 1.33386619296679e-02 , -1.40996340576236e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.30182363724857e+00 , 4.23033847418389e-02 , -7.21400787445986e-01 , 6.89480535884200e+00 , -5.68929175311194e-01 , -5.27737889544217e-01 , 7.02178363191361e+00 , -2.06058095177365e+00 , -8.98604872923256e-01 , 6.17577868431634e+00 , -3.83360958205538e-01 , 7.85192846715205e-01 , 4.94440964158963e+00 , -1.41178083239787e-01 , 7.39817177321919e-01 , 6.81036296532508e+00 , -2.86819621209826e-01 , 1.96223127253095e+00 , 6.08896511294321e+00 , -2.17629979481883e-01 , 3.15965827877773e+00 , 7.10063469002883e+00 , -3.42323534272863e-01 , 4.35237461416730e+00 , 5.30010316280696e+00 , 1.06842760393989e+00 , 3.35557598447636e+00 , 4.13167531773833e+00 , 1.00883556966170e+00 , 3.72688033326675e+00 , 5.82296057111492e+00 , 2.24934688461136e+00 , 2.97735414377161e+00 , 5.18687494342800e+00 , 3.56421857471140e+00 , 2.90103074419594e+00 , 6.31331917846389e+00 , 4.48593253591197e+00 , 2.29927856759984e+00 , 3.85955825888546e+00 , 3.66131894331583e+00 , 2.03278600841757e+00 , 2.80077933885735e+00 , 4.16999242407062e+00 , 2.44898486794179e+00 , 3.92523055166032e+00 , 3.21082974943821e+00 , 7.32482778531717e-01 , 2.73341796925126e+00 , 3.03749563462156e+00 , -8.30677331116486e-02 , 3.09799979951845e+00 , 2.66137496967351e+00 , -1.53579915272766e+00 , 1.55670523021595e+00 , 2.17805205587192e+00 , 4.23388545977002e-01 , 3.89479100314829e-01 , 2.61460108547893e+00 , 4.77060338772269e-01 , 2.07550956627473e+00 , 1.14590901357021e+00 , 1.04320723126337e+00 , 1.18862061829614e+00 , 1.20962893998790e-01 , 1.69522128474687e+00 , 2.07010862289247e+00 , -1.09234120872378e+00 , 2.03265349089865e+00 , 5.73569324496314e-01 , 6.17929917552187e-01 , 2.96431663750174e+00 , -5.83327748164648e-01 , 3.53955007103600e-01 , 3.17109091527287e+00 , 1.29164388959859e+00 , 1.36824752100843e+00 , 3.74280995575468e+00 , 8.52667753488682e-01 , 1.98192877897898e+00 , 5.02905378458282e+00 , 2.10934707631138e+00 , 2.74353768275373e+00 , 5.71860821165459e+00 , -3.50056360974471e-01 , 2.90610334262654e+00 , 4.96693608287452e+00 , -1.11588352510823e+00 , 3.06845031587806e+00 , 5.87800063575301e+00 , -5.40243204497706e-01 , 3.51049314791099e+00 , 3.80731509007792e+00 , -1.49093804673477e+00 , 4.50008003628015e+00 , 3.41441980162017e+00 , -7.19299148831411e-01 , 5.42755398209707e+00 , 2.47376335055040e+00 , -2.74383869221506e+00 , 3.93987812389926e+00 , 2.83046548636251e+00 , -3.80885799801257e+00 , 4.54863108691149e+00 , 2.81394049165230e+00 , -2.67221757575862e+00 , 2.63996155014781e+00 , 2.36349767620534e+00 , -3.79291107666568e+00 , 1.82129979059653e+00 , 2.00802852615937e+00 , -3.36608172268383e+00 , 8.76274609882711e-01 , 8.31460857855180e-01 , -4.26675328477590e+00 , 1.05583628187778e+00 , 3.22827705550158e+00 , -5.48638343279106e+00 , 7.70681890163070e-01 , 3.33902980623711e+00 , -3.36817927668349e+00 , 7.21931971122161e-01 , 4.18842129498664e+00 , -3.67239157969653e+00 , 7.86444043011860e-02 , 5.47216870495720e+00 , -2.38611115771938e+00 , -3.23414419937697e-01 , 6.14694225305597e+00 , -4.46909663613207e+00 , 9.29458460112618e-01 , 6.42676568529387e+00 , -5.36207760113481e+00 , 5.84976302002793e-01 , 7.21438869028155e+00 , -6.29250483131455e+00 , 3.63050232814901e+00 , 6.75481892711296e+00 , -6.98486640441327e+00 , 4.29766850361779e+00 , 7.50404366626336e+00 , -6.67095012302785e+00 , 3.16418859499985e+00 , 5.52081720437248e+00 , -4.10904889584743e+00 , 2.25150280196783e+00 , 6.39298384576933e+00 , -4.81061183134772e+00 , 3.26599326572316e+00 , 7.26118632650396e+00 , -4.03982152676735e+00 , 4.54986308783767e+00 , 7.27319364566475e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 27. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 27. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atoms_new_colvar_forces = { ( -7.00918839295065e-02 , 3.03562631602812e-01 , -4.01230929831610e-01 ), ( 1.30228758705242e-02 , 3.13827887370110e-02 , -2.39424491797733e-01 ), ( -4.24616685652879e-02 , 9.53835979703357e-02 , 8.55264993388502e-02 ), ( -9.68240429627762e-02 , 2.50061075123733e-01 , 6.41508540355183e-02 ), ( -1.80414634629806e-02 , 9.82538668968962e-02 , -1.71472514960320e-01 ), ( 7.06557321135335e-02 , -1.85230277861217e-01 , -3.78873518772363e-02 ), ( 9.46350321907656e-03 , -9.87959399798596e-02 , 2.54890867620378e-01 ), ( -4.09425282344281e-02 , 6.01006350600723e-02 , 1.92681282419908e-01 ), ( 6.62602546982739e-02 , -1.91572278981195e-01 , 3.38169510399862e-02 ), ( 1.13816818760197e-01 , -3.91844223708385e-01 , 2.76452516683183e-01 ), ( 2.44388756577774e-02 , -9.95621342458959e-02 , 9.63505584456550e-02 ), ( 2.64755279440645e-02 , -9.75245532058120e-02 , 5.98880018253482e-02 ), ( 1.23248315375857e-02 , -5.58111427214885e-02 , 7.27023861546839e-02 ), ( 1.24747461734146e-02 , -5.36917952096011e-02 , 6.15401343699061e-02 ), ( 5.51192150634254e-03 , -3.50046483383724e-02 , 7.57575991860129e-02 ), ( -8.65227008336139e-03 , 9.79196214590068e-03 , 7.54819945039508e-02 ), ( -2.11286820065884e-03 , -2.69812507500006e-03 , 4.03425028835691e-02 ), ( -5.78649800221507e-03 , 9.90222838177424e-03 , 3.60438978525862e-02 ), ( 2.69299629720131e-03 , -1.30418621694614e-02 , 1.95321561354718e-02 ), ( 9.02626661697226e-03 , -2.22507545160550e-02 , -2.69306034571754e-02 ), ( 8.69644116503099e-03 , -2.39656725403336e-02 , -1.50633697361967e-02 ), ( 6.59446000905698e-03 , -1.37254617346516e-02 , -3.05696631273867e-02 ), ( 1.50134732127959e-02 , -4.69237871938746e-02 , -2.11363340989585e-03 ), ( 2.76130137525994e-02 , -8.89357221272514e-02 , 7.44686468199215e-03 ), ( 1.42765376002831e-02 , -4.71595341482906e-02 , 8.92074709266032e-03 ), ( 1.42338803726940e-02 , -4.43421789389268e-02 , -2.62826389885197e-03 ), ( 9.29972386139693e-03 , -3.72153352269306e-02 , 3.37753908498073e-02 ), ( -8.33599916874229e-04 , -1.52087633395627e-02 , 7.68089093286441e-02 ), ( -3.77100007712009e-03 , 4.22936205944202e-03 , 3.30631726198432e-02 ), ( -5.82983732798802e-03 , 1.13105190175712e-02 , 3.05703186441769e-02 ), ( -7.30086314368950e-03 , 1.80664473965964e-02 , 2.14856482153999e-02 ), ( -1.62964605632924e-02 , 5.23633164766681e-02 , -3.86040699596929e-03 ), ( -9.75706736775823e-03 , 3.58883761599068e-02 , -2.18446064193114e-02 ), ( -1.37843146647957e-02 , 5.01831413928922e-02 , -2.86299893752881e-02 ), ( -1.99861537665628e-03 , 1.48060903079009e-02 , -3.65682156413178e-02 ), ( 1.05678765369071e-02 , -1.62920244012486e-02 , -7.35434253074627e-02 ), ( 4.37194853737756e-03 , -1.13711218922164e-03 , -5.45461735948314e-02 ), ( 3.35345912840900e-03 , 5.66889059294422e-03 , -6.99991598096522e-02 ), ( 7.13223287626544e-03 , -1.52052602553789e-02 , -3.15106149149864e-02 ), ( 1.31139199664390e-02 , -4.18458818185023e-02 , 1.85205753754504e-03 ), ( 5.42706815934922e-04 , 1.51076931287779e-03 , -1.38827152006991e-02 ), ( 4.77805130120433e-04 , 3.07602707525109e-03 , -1.97388884158322e-02 ), ( -6.49926788211309e-03 , 2.05377353834856e-02 , -5.20710086762631e-05 ), ( -2.05506026036694e-02 , 5.81576335292180e-02 , 2.90343421506679e-02 ), ( -1.89404668103573e-02 , 6.35216142070820e-02 , -1.59497126415629e-02 ), ( -2.26405419833073e-02 , 7.55239927482679e-02 , -1.73144238866618e-02 ), ( -1.68354683467430e-02 , 7.25037673134109e-02 , -8.32385599157364e-02 ), ( -1.99298828125146e-02 , 8.66848171303143e-02 , -1.02217297110141e-01 ), ( -8.56576446939230e-03 , 4.64172138931442e-02 , -8.33693617236000e-02 ), ( -1.85966500629948e-02 , 6.69300872459209e-02 , -3.52980902148761e-02 ), ( -2.44082025097931e-02 , 9.31658827650885e-02 , -6.92311193427338e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 27, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 28, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 28, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 28, atoms_positions[size = 51] = { ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 ), ( 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 ), ( 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 ), ( 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 ), ( 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 ), ( 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 ), ( -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 ), ( -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 ), ( -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 ), ( -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 ), ( 8.29937250565104e+00 , 4.23866805000532e-02 , -7.17159057051135e-01 ), ( 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828405e-01 ), ( 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 ), ( 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 ), ( 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 ), ( 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 ), ( 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 ), ( 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 ), ( 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 ), ( 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 ), ( 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 ), ( 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 ), ( 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 ), ( 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 ), ( 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 ), ( 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 ), ( 2.07308013451523e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 ), ( 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 ), ( 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 ), ( -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 ), ( 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 ), ( 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 ), ( -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 ), ( -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 ), ( -5.42011744036734e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 ), ( -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638270e+00 ), ( -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 ), ( -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 ), ( -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 ), ( -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 ), ( -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 ), ( -5.48235415482577e+00 , 7.64556077951690e-01 , 3.34059019506604e+00 ), ( -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 ), ( -2.38315281417863e+00 , -3.21340415243162e-01 , 6.14259769946698e+00 ), ( -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 ), ( -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 ), ( -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 ), ( -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 ), ( -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 ), ( -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 ), ( -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ) } +colvars: Step 28, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092544e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.29937250565104e+00 , 4.23866805000532e-02 , -7.17159057051135e-01 , 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828405e-01 , 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 , 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 , 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 , 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 , 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 , 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 , 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 , 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 , 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 , 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 , 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 , 2.07308013451523e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 , 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 , -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 , 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 , -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 , -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 , -5.42011744036734e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638270e+00 , -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 , -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 , -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 , -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 , -5.48235415482577e+00 , 7.64556077951690e-01 , 3.34059019506604e+00 , -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -2.38315281417863e+00 , -3.21340415243162e-01 , 6.14259769946698e+00 , -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 , -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 , -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 , -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 , -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 , -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 , -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99702390065719e-01 , 1.44141469092544e-02 , 1.34624614843213e-02 , -1.43570817560709e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.29937250565104e+00 , 4.23866805000532e-02 , -7.17159057051135e-01 , 6.89000256039269e+00 , -5.73995173311854e-01 , -5.24255753371141e-01 , 7.01755427318424e+00 , -2.06234245155383e+00 , -8.91919677828405e-01 , 6.16917068389169e+00 , -3.77961802064591e-01 , 7.92972589935611e-01 , 4.94326176408283e+00 , -1.40565596061253e-01 , 7.41482057167653e-01 , 6.80648589638256e+00 , -2.91274006240415e-01 , 1.96754528083343e+00 , 6.07815351698154e+00 , -2.23695305080469e-01 , 3.16090790354205e+00 , 7.10574759806666e+00 , -3.41346148602582e-01 , 4.35805678373588e+00 , 5.29501684891883e+00 , 1.06580064717382e+00 , 3.35566319500964e+00 , 4.13195484920383e+00 , 1.00723739051520e+00 , 3.73424019818000e+00 , 5.82342709693834e+00 , 2.24745667934779e+00 , 2.97575078310822e+00 , 5.17580475150473e+00 , 3.56084302408529e+00 , 2.89560355034289e+00 , 6.31055228919027e+00 , 4.48154391801286e+00 , 2.29300216613779e+00 , 3.85877138923022e+00 , 3.65549703188035e+00 , 2.02961858112419e+00 , 2.80487654007276e+00 , 4.16975906809585e+00 , 2.44377212204315e+00 , 3.92011514316659e+00 , 3.20461705629880e+00 , 7.34759271924921e-01 , 2.74319380247689e+00 , 3.04666876721881e+00 , -7.96605624409483e-02 , 3.10386496411581e+00 , 2.65670996482410e+00 , -1.53924177501772e+00 , 1.55145166053132e+00 , 2.18491961741298e+00 , 4.23005014147477e-01 , 3.95413251157399e-01 , 2.61558107140656e+00 , 4.71527797088319e-01 , 2.07308013451523e+00 , 1.14677801215469e+00 , 1.04281603913899e+00 , 1.19856851069401e+00 , 1.24416836417003e-01 , 1.69166643682566e+00 , 2.07402533188936e+00 , -1.09262776599234e+00 , 2.03520825688421e+00 , 5.74238880265787e-01 , 6.17417335242143e-01 , 2.96288811795818e+00 , -5.84023938555671e-01 , 3.54721279171932e-01 , 3.17452781831106e+00 , 1.28905102860902e+00 , 1.37503236412016e+00 , 3.74504047877424e+00 , 8.58556678635773e-01 , 1.98097410756241e+00 , 5.03025516082682e+00 , 2.10555341980468e+00 , 2.74910647530045e+00 , 5.72123690520925e+00 , -3.52428458418248e-01 , 2.90444642153795e+00 , 4.96390690111647e+00 , -1.11459838472832e+00 , 3.06903018690947e+00 , 5.87897635937020e+00 , -5.42011744036734e-01 , 3.50969756114752e+00 , 3.79867807941688e+00 , -1.48338247127334e+00 , 4.49402441857696e+00 , 3.41475435816862e+00 , -7.25548130489090e-01 , 5.43039068906150e+00 , 2.47535387638270e+00 , -2.74411640600714e+00 , 3.94355654958858e+00 , 2.81693394197724e+00 , -3.80736184767490e+00 , 4.55426428645250e+00 , 2.81421693621005e+00 , -2.67889257251121e+00 , 2.63641946572024e+00 , 2.36071594277034e+00 , -3.79581266069246e+00 , 1.82432534104327e+00 , 2.00885442154012e+00 , -3.36374943647688e+00 , 8.75833801004899e-01 , 8.24619947369579e-01 , -4.25995475355386e+00 , 1.05143272304923e+00 , 3.23395782047305e+00 , -5.48235415482577e+00 , 7.64556077951690e-01 , 3.34059019506604e+00 , -3.36938961615137e+00 , 7.25082383386691e-01 , 4.18205915300837e+00 , -3.67073843017742e+00 , 8.01608924560731e-02 , 5.47777368326127e+00 , -2.38315281417863e+00 , -3.21340415243162e-01 , 6.14259769946698e+00 , -4.47277724305960e+00 , 9.25105422683803e-01 , 6.42561489534223e+00 , -5.36075664156520e+00 , 5.81682160610639e-01 , 7.21128070679280e+00 , -6.29870226923473e+00 , 3.62966169485554e+00 , 6.75553723080767e+00 , -6.99005869147663e+00 , 4.29838076831348e+00 , 7.50772541407111e+00 , -6.65944410663487e+00 , 3.16351677946629e+00 , 5.52576336056901e+00 , -4.10684788604423e+00 , 2.25346145658646e+00 , 6.39478625957321e+00 , -4.81202089485083e+00 , 3.27314869824354e+00 , 7.25929534791218e+00 , -4.03202122474655e+00 , 4.55238970890442e+00 , 7.27362825966242e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 28. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 28. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atoms_new_colvar_forces = { ( -6.99105964745414e-02 , 3.03534108224077e-01 , -4.01125198858137e-01 ), ( 1.30792098250531e-02 , 3.16310929373660e-02 , -2.39499701615836e-01 ), ( -4.25255029736803e-02 , 9.54922740032261e-02 , 8.51087057351073e-02 ), ( -9.68128132349850e-02 , 2.49843308955989e-01 , 6.39997898630516e-02 ), ( -1.79464748638226e-02 , 9.81685466429824e-02 , -1.71250102556514e-01 ), ( 7.06379507910651e-02 , -1.85041970185675e-01 , -3.78425579319191e-02 ), ( 9.35083933511791e-03 , -9.88068220395377e-02 , 2.54689455152915e-01 ), ( -4.09659433594162e-02 , 5.97932072032176e-02 , 1.92798200103656e-01 ), ( 6.62605501454588e-02 , -1.91618026165443e-01 , 3.41544371557534e-02 ), ( 1.13670038704103e-01 , -3.91702187892015e-01 , 2.76465205814139e-01 ), ( 2.43941032937985e-02 , -9.95450315112680e-02 , 9.63621500021451e-02 ), ( 2.64526804358145e-02 , -9.75317185173843e-02 , 5.99104372755897e-02 ), ( 1.22970656157735e-02 , -5.58162675354601e-02 , 7.27035002216811e-02 ), ( 1.24494756477064e-02 , -5.36908802348386e-02 , 6.15436432653573e-02 ), ( 5.48704688714377e-03 , -3.50215844750731e-02 , 7.57493863140233e-02 ), ( -8.67012952291996e-03 , 9.75558764555577e-03 , 7.54556612518543e-02 ), ( -2.12010225636094e-03 , -2.72534424138993e-03 , 4.03319038952513e-02 ), ( -5.79320046768153e-03 , 9.87935351909541e-03 , 3.60292720624457e-02 ), ( 2.69638236344813e-03 , -1.30775617081468e-02 , 1.95324137553816e-02 ), ( 9.05251869178125e-03 , -2.23019324748083e-02 , -2.69119622158068e-02 ), ( 8.71027637037679e-03 , -2.39922447972658e-02 , -1.50481952882849e-02 ), ( 6.61441724671005e-03 , -1.37516683392467e-02 , -3.05540177540563e-02 ), ( 1.50181321585705e-02 , -4.69385652870096e-02 , -2.09312910608296e-03 ), ( 2.76059252628942e-02 , -8.89273993060486e-02 , 7.48140988776513e-03 ), ( 1.42694316016934e-02 , -4.71506609950198e-02 , 8.93744511963321e-03 ), ( 1.42295639585641e-02 , -4.43276814589433e-02 , -2.60933393989568e-03 ), ( 9.28254514352052e-03 , -3.72047576822429e-02 , 3.37803143159949e-02 ), ( -8.69775702737456e-04 , -1.51900253011091e-02 , 7.67913363669554e-02 ), ( -3.78712761698226e-03 , 4.23979009716207e-03 , 3.30510708702082e-02 ), ( -5.84723852640200e-03 , 1.13284759700188e-02 , 3.05558632441676e-02 ), ( -7.30738149450516e-03 , 1.80614978519294e-02 , 2.14716730988585e-02 ), ( -1.62842633958380e-02 , 5.23322937967764e-02 , -3.88032006840828e-03 ), ( -9.74404228898785e-03 , 3.58761140757968e-02 , -2.18525871928399e-02 ), ( -1.37691637380410e-02 , 5.01733408163495e-02 , -2.86418995399456e-02 ), ( -1.97994657736163e-03 , 1.47930001175436e-02 , -3.65629037841475e-02 ), ( 1.06008081770661e-02 , -1.63062648103744e-02 , -7.35138432584533e-02 ), ( 4.39151001737963e-03 , -1.13162558162395e-03 , -5.45291484906228e-02 ), ( 3.37852500415075e-03 , 5.67644658806250e-03 , -6.99802892637869e-02 ), ( 7.13880736625239e-03 , -1.51878963709950e-02 , -3.14950444881112e-02 ), ( 1.30987062537573e-02 , -4.18022069940880e-02 , 1.86792386817922e-03 ), ( 5.36790918205766e-04 , 1.54685236917990e-03 , -1.38799100920889e-02 ), ( 4.71571839629198e-04 , 3.12046790390116e-03 , -1.97351320604518e-02 ), ( -6.50806934625516e-03 , 2.05668835560400e-02 , -6.12559491181563e-05 ), ( -2.05685759895296e-02 , 5.81819166560511e-02 , 2.90007198523593e-02 ), ( -1.89399299546582e-02 , 6.35432232945508e-02 , -1.59717550759216e-02 ), ( -2.26410185265841e-02 , 7.55511789495086e-02 , -1.73411688823523e-02 ), ( -1.68024096378493e-02 , 7.25060849069892e-02 , -8.32433362384075e-02 ), ( -1.98875385771560e-02 , 8.66819831532423e-02 , -1.02222056961598e-01 ), ( -8.53590432797545e-03 , 4.64283976982095e-02 , -8.33634418048038e-02 ), ( -1.85840756007226e-02 , 6.69376673267996e-02 , -3.53153210594370e-02 ), ( -2.43736486000415e-02 , 9.31472296453878e-02 , -6.92483050154469e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 28, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 29, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 29, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 29, atoms_positions[size = 51] = { ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 ), ( 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 ), ( 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 ), ( 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 ), ( 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 ), ( 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 ), ( -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 ), ( -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 ), ( -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 ), ( -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 ), ( 8.29622457456575e+00 , 4.23601649414826e-02 , -7.12749794942444e-01 ), ( 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 ), ( 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 ), ( 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 ), ( 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 ), ( 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 ), ( 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 ), ( 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 ), ( 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 ), ( 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 ), ( 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 ), ( 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 ), ( 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 ), ( 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 ), ( 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 ), ( 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 ), ( 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 ), ( 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 ), ( 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 ), ( -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 ), ( 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 ), ( 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 ), ( -3.54512396787448e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 ), ( -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 ), ( -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 ), ( -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 ), ( -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 ), ( -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 ), ( -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 ), ( -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 ), ( -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 ), ( -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 ), ( -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 ), ( -2.37949805223027e+00 , -3.18274942149990e-01 , 6.13855939203602e+00 ), ( -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 ), ( -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 ), ( -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 ), ( -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 ), ( -6.64854667858964e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 ), ( -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 ), ( -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ) } +colvars: Step 29, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601431e-02 , -1.45578300084090e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.29622457456575e+00 , 4.23601649414826e-02 , -7.12749794942444e-01 , 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 , 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 , 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 , 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 , 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 , 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 , 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 , 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 , 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 , 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 , 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 , 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 , 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 , 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 , -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 , 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 , -3.54512396787448e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 , -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 , -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 , -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 , -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 , -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 , -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 , -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 , -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -2.37949805223027e+00 , -3.18274942149990e-01 , 6.13855939203602e+00 , -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 , -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 , -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 , -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 , -6.64854667858964e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 , -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 , -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Calculating fit gradients. +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99695764763452e-01 , 1.46010853136374e-02 , 1.35372008601431e-02 , -1.45578300084090e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.29622457456575e+00 , 4.23601649414826e-02 , -7.12749794942444e-01 , 6.88656791022682e+00 , -5.79423003861446e-01 , -5.21305056754422e-01 , 7.01381775444901e+00 , -2.06436005554257e+00 , -8.84835577623107e-01 , 6.16078756913376e+00 , -3.71350521036279e-01 , 8.00038106794565e-01 , 4.94272105902056e+00 , -1.40378415166676e-01 , 7.43219079550601e-01 , 6.80305391516275e+00 , -2.95937692424434e-01 , 1.97188232737714e+00 , 6.06773515904304e+00 , -2.29201730151599e-01 , 3.16451247293498e+00 , 7.11042598287134e+00 , -3.40856753718405e-01 , 4.36338147582623e+00 , 5.28892375389985e+00 , 1.06346551395894e+00 , 3.35522734939796e+00 , 4.13224158167050e+00 , 1.00580432292170e+00 , 3.74179353237204e+00 , 5.82425492074354e+00 , 2.24551801865086e+00 , 2.97411738229058e+00 , 5.16500012697731e+00 , 3.55690466690155e+00 , 2.88981698169433e+00 , 6.30725184433866e+00 , 4.47643774424445e+00 , 2.28790607210455e+00 , 3.85830231916698e+00 , 3.65004044014566e+00 , 2.02615341789755e+00 , 2.80946920973463e+00 , 4.16915909582234e+00 , 2.43869157601593e+00 , 3.91507936051298e+00 , 3.19802947471393e+00 , 7.37758520042584e-01 , 2.75134638008383e+00 , 3.05634398647319e+00 , -7.65758471367425e-02 , 3.10938158785981e+00 , 2.65311712698750e+00 , -1.54176681781764e+00 , 1.54864318535101e+00 , 2.19352105864929e+00 , 4.23049230119594e-01 , 4.01396747637272e-01 , 2.61593490390238e+00 , 4.65921725596308e-01 , 2.06899800374124e+00 , 1.14505676035432e+00 , 1.04328006776631e+00 , 1.21000364375481e+00 , 1.28904488116783e-01 , 1.68742670026690e+00 , 2.07772754385857e+00 , -1.09310039312942e+00 , 2.03715895658102e+00 , 5.74507903495704e-01 , 6.16716092228219e-01 , 2.96032334562168e+00 , -5.85462651794052e-01 , 3.55466673053487e-01 , 3.17841607851704e+00 , 1.28697865793817e+00 , 1.38240352510723e+00 , 3.74865920957500e+00 , 8.65304397854145e-01 , 1.98009307225916e+00 , 5.03179448147694e+00 , 2.09986059689393e+00 , 2.75410027470479e+00 , 5.72312335617403e+00 , -3.54512396787448e-01 , 2.90275032869623e+00 , 4.95988801772101e+00 , -1.11380683709475e+00 , 3.06959510200747e+00 , 5.88060755912935e+00 , -5.42812907106037e-01 , 3.50868830447576e+00 , 3.78971650007276e+00 , -1.47580707847513e+00 , 4.48857760285961e+00 , 3.41568649817004e+00 , -7.32279484961581e-01 , 5.43365065316136e+00 , 2.47708892356351e+00 , -2.74489903864028e+00 , 3.94553829654744e+00 , 2.80292306654905e+00 , -3.80582168383723e+00 , 4.56002933033252e+00 , 2.81446312544423e+00 , -2.68511933720613e+00 , 2.63425571085101e+00 , 2.35862533752393e+00 , -3.79891829465030e+00 , 1.82602454098356e+00 , 2.00919663553843e+00 , -3.36153437590100e+00 , 8.76187790571700e-01 , 8.17705927414271e-01 , -4.25506456561460e+00 , 1.04683686614356e+00 , 3.23942544526302e+00 , -5.47727300573892e+00 , 7.58666045877806e-01 , 3.34232650518412e+00 , -3.37024287222302e+00 , 7.27351678353787e-01 , 4.17622219444614e+00 , -3.66933507872099e+00 , 8.05977535935301e-02 , 5.48202248684294e+00 , -2.37949805223027e+00 , -3.18274942149990e-01 , 6.13855939203602e+00 , -4.47666076333546e+00 , 9.22996787939354e-01 , 6.42489815273941e+00 , -5.35925399095935e+00 , 5.77855536283983e-01 , 7.20778970449011e+00 , -6.30316163108302e+00 , 3.62768710455914e+00 , 6.75623810716728e+00 , -6.99579453363441e+00 , 4.29932152312625e+00 , 7.51127590605029e+00 , -6.64854667858964e+00 , 3.16343427485194e+00 , 5.53111031503097e+00 , -4.10526539626638e+00 , 2.25501699149421e+00 , 6.39742182068540e+00 , -4.81296950008506e+00 , 3.27902937016757e+00 , 7.25609311672234e+00 , -4.02494838608621e+00 , 4.55696208687055e+00 , 7.27453310355277e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 29. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 29. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atoms_new_colvar_forces = { ( -6.97345673689355e-02 , 3.03510657206574e-01 , -4.01032117490141e-01 ), ( 1.31479927636833e-02 , 3.18452841780117e-02 , -2.39563239519030e-01 ), ( -4.25902939322403e-02 , 9.55764008556159e-02 , 8.47478780569350e-02 ), ( -9.68202824772279e-02 , 2.49649279092987e-01 , 6.38673507909632e-02 ), ( -1.78554209094393e-02 , 9.80978947661689e-02 , -1.71059030797415e-01 ), ( 7.06351339216979e-02 , -1.84876997886692e-01 , -3.78002906708561e-02 ), ( 9.23717210815477e-03 , -9.88186635802034e-02 , 2.54516498207081e-01 ), ( -4.10067185999412e-02 , 5.95284116782758e-02 , 1.92894973903991e-01 ), ( 6.62656509213339e-02 , -1.91650327349242e-01 , 3.44446751551082e-02 ), ( 1.13538570672862e-01 , -3.91576043794114e-01 , 2.76477610737634e-01 ), ( 2.43528011759160e-02 , -9.95212184108119e-02 , 9.63717066493160e-02 ), ( 2.64335990853690e-02 , -9.75315010313772e-02 , 5.99368309122805e-02 ), ( 1.22707479665203e-02 , -5.58185019853083e-02 , 7.27061619717733e-02 ), ( 1.24258135329339e-02 , -5.36868050421805e-02 , 6.15475967226826e-02 ), ( 5.46238658459673e-03 , -3.50379570239896e-02 , 7.57443415325614e-02 ), ( -8.69024268940156e-03 , 9.71509594049825e-03 , 7.54348715011720e-02 ), ( -2.12822387245308e-03 , -2.75410877718617e-03 , 4.03262459211456e-02 ), ( -5.80130253688933e-03 , 9.85391482653323e-03 , 3.60182615787236e-02 ), ( 2.69968905367764e-03 , -1.31132121873079e-02 , 1.95403438129169e-02 ), ( 9.07983140495067e-03 , -2.23508072022709e-02 , -2.68808418768289e-02 ), ( 8.72530906787373e-03 , -2.40163686340764e-02 , -1.50260205641190e-02 ), ( 6.63533929943793e-03 , -1.37758914733351e-02 , -3.05314804783748e-02 ), ( 1.50250412334631e-02 , -4.69489069415382e-02 , -2.06754550118032e-03 ), ( 2.76032855445120e-02 , -8.89104932973903e-02 , 7.51753913090128e-03 ), ( 1.42646426422054e-02 , -4.71373373917235e-02 , 8.95390893414003e-03 ), ( 1.42276919791724e-02 , -4.43085252454197e-02 , -2.59167092550324e-03 ), ( 9.26674921618978e-03 , -3.71915296398978e-02 , 3.37836374872139e-02 ), ( -9.06372128229042e-04 , -1.51721407720698e-02 , 7.67684938038020e-02 ), ( -3.80395529749381e-03 , 4.24883243177135e-03 , 3.30357666004564e-02 ), ( -5.86557141109127e-03 , 1.13445570023479e-02 , 3.05363750307080e-02 ), ( -7.31525519485768e-03 , 1.80539646497407e-02 , 2.14575122079536e-02 ), ( -1.62749765161026e-02 , 5.22957913864255e-02 , -3.89559645051793e-03 ), ( -9.73256717086334e-03 , 3.58608957287872e-02 , -2.18588455272024e-02 ), ( -1.37561356846092e-02 , 5.01594555083328e-02 , -2.86530175657035e-02 ), ( -1.96150471330580e-03 , 1.47795103338105e-02 , -3.65544936694368e-02 ), ( 1.06357415268573e-02 , -1.63166088971694e-02 , -7.34787770018302e-02 ), ( 4.41217592686858e-03 , -1.12407025410038e-03 , -5.45119214454608e-02 ), ( 3.40465355615724e-03 , 5.68596742599340e-03 , -6.99615536721609e-02 ), ( 7.14690794577242e-03 , -1.51676910384938e-02 , -3.14818108612719e-02 ), ( 1.30860440731738e-02 , -4.17538157142369e-02 , 1.87607969243245e-03 ), ( 5.31438886239974e-04 , 1.58382764422031e-03 , -1.38845375267955e-02 ), ( 4.66019431914596e-04 , 3.16597921279863e-03 , -1.97405139078286e-02 ), ( -6.51759358566815e-03 , 2.05944778805003e-02 , -7.74867141769325e-05 ), ( -2.05897522873164e-02 , 5.81998881002601e-02 , 2.89588835151015e-02 ), ( -1.89420811869476e-02 , 6.35594972111328e-02 , -1.60005578066733e-02 ), ( -2.26447048361701e-02 , 7.55719886654577e-02 , -1.73763109801340e-02 ), ( -1.67714821195974e-02 , 7.25041952445796e-02 , -8.32494688284707e-02 ), ( -1.98477539008037e-02 , 8.66741240236254e-02 , -1.02227174905627e-01 ), ( -8.50675931255931e-03 , 4.64380716891990e-02 , -8.33597300696780e-02 ), ( -1.85741622090217e-02 , 6.69400231747561e-02 , -3.53359787198467e-02 ), ( -2.43427495803689e-02 , 9.31215377117312e-02 , -6.92635303807292e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 29, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 30, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 30, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 30, atoms_positions[size = 51] = { ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 ), ( 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 ), ( 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 ), ( 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 ), ( 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 ), ( 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 ), ( -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 ), ( -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 ), ( -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 ), ( -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ), ( 8.29230184427869e+00 , 4.21861224833244e-02 , -7.08174413023012e-01 ), ( 7.01074964451226e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 ), ( 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 ), ( 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 ), ( 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 ), ( 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 ), ( 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 ), ( 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 ), ( 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 ), ( 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 ), ( 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 ), ( 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 ), ( 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 ), ( 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 ), ( 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 ), ( 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 ), ( 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 ), ( 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 ), ( 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 ), ( -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 ), ( 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 ), ( 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 ), ( -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 ), ( -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 ), ( -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 ), ( -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633870e+00 ), ( -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 ), ( -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 ), ( -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 ), ( -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160169e-01 ), ( -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 ), ( -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 ), ( -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 ), ( -2.37512825645771e+00 , -3.14245448646477e-01 , 6.13503886138836e+00 ), ( -4.48049343311408e+00 , 9.23291002542477e-01 , 6.42458367171772e+00 ), ( -5.35769724718959e+00 , 5.73458684568045e-01 , 7.20401421961488e+00 ), ( -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 ), ( -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 ), ( -6.63855361839082e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 ), ( -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 ), ( -4.01878208177307e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ) } +colvars: Step 30, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.29230184427869e+00 , 4.21861224833244e-02 , -7.08174413023012e-01 , 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 7.01074964451226e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 , 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 , 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 , 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 , 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 , 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 , 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 , 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 , 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 , 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 , 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 , 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 , 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 , 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 , -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 , 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 , -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 , -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 , -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633870e+00 , -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 , -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 , -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160169e-01 , -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 , -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 , -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -2.37512825645771e+00 , -3.14245448646477e-01 , 6.13503886138836e+00 , -4.48049343311408e+00 , 9.23291002542477e-01 , 6.42458367171772e+00 , -5.35769724718959e+00 , 5.73458684568045e-01 , 7.20401421961488e+00 , -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 , -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 , -6.63855361839082e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 , -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 , -4.01878208177307e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99691024670381e-01 , 1.47681305092765e-02 , 1.35577849947435e-02 , -1.46950325205982e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.29230184427869e+00 , 4.21861224833244e-02 , -7.08174413023012e-01 , 6.88433768608823e+00 , -5.85031988970297e-01 , -5.18701380641625e-01 , 7.01074964451226e+00 , -2.06667799484640e+00 , -8.77410220331701e-01 , 6.15114970038315e+00 , -3.63878133297209e-01 , 8.06197351527951e-01 , 4.94251543690501e+00 , -1.40510708677694e-01 , 7.45048563918488e-01 , 6.79992012090271e+00 , -3.00695027857678e-01 , 1.97521694021755e+00 , 6.05799636826626e+00 , -2.34131753886315e-01 , 3.17046189080617e+00 , 7.11444324497079e+00 , -3.40906855821913e-01 , 4.36836341881069e+00 , 5.28214643441668e+00 , 1.06141334708731e+00 , 3.35429787082843e+00 , 4.13241195152973e+00 , 1.00456074339840e+00 , 3.74954369686105e+00 , 5.82526058872789e+00 , 2.24371165654507e+00 , 2.97242632850361e+00 , 5.15488118093665e+00 , 3.55240340619033e+00 , 2.88380235902732e+00 , 6.30340094084669e+00 , 4.47068270677413e+00 , 2.28402203467209e+00 , 3.85803273500040e+00 , 3.64498280582325e+00 , 2.02246180259834e+00 , 2.81447850483436e+00 , 4.16821846186158e+00 , 2.43376917328142e+00 , 3.91039560209809e+00 , 3.19111878243301e+00 , 7.41516858499570e-01 , 2.75757204476422e+00 , 3.06638312387520e+00 , -7.39915939492297e-02 , 3.11458968437518e+00 , 2.65072419053096e+00 , -1.54315036055786e+00 , 1.54882751825715e+00 , 2.20350674186856e+00 , 4.23585404624245e-01 , 4.07097611375832e-01 , 2.61582384772097e+00 , 4.60264284797747e-01 , 2.06354427676343e+00 , 1.14117925680900e+00 , 1.04432185889509e+00 , 1.22254045508823e+00 , 1.34251325596785e-01 , 1.68274111244186e+00 , 2.08115970774137e+00 , -1.09365584719555e+00 , 2.03840694210773e+00 , 5.74397604020809e-01 , 6.16002856112884e-01 , 2.95683435306151e+00 , -5.87560732478312e-01 , 3.56165393940748e-01 , 3.18267637842299e+00 , 1.28546964245969e+00 , 1.39012746265796e+00 , 3.75333538136741e+00 , 8.72683225907226e-01 , 1.97944946628699e+00 , 5.03374243876860e+00 , 2.09259184322799e+00 , 2.75856176906628e+00 , 5.72432440543625e+00 , -3.56210094792986e-01 , 2.90102682207210e+00 , 4.95497957291448e+00 , -1.11346528373123e+00 , 3.07014816399522e+00 , 5.88280434124295e+00 , -5.42567027076289e-01 , 3.50717633741907e+00 , 3.78057938137634e+00 , -1.46861076442094e+00 , 4.48394052521373e+00 , 3.41692093674710e+00 , -7.39287825481485e-01 , 5.43738728518914e+00 , 2.47893460633870e+00 , -2.74605140008548e+00 , 3.94583306216151e+00 , 2.78877499543218e+00 , -3.80424145091217e+00 , 4.56591524326093e+00 , 2.81461561847372e+00 , -2.69080709230051e+00 , 2.63357573561514e+00 , 2.35711228280336e+00 , -3.80222370935105e+00 , 1.82611988719659e+00 , 2.00899223099777e+00 , -3.35936924730990e+00 , 8.77417386699183e-01 , 8.10761148160169e-01 , -4.25231790550359e+00 , 1.04222255289584e+00 , 3.24425942007082e+00 , -5.47113898865365e+00 , 7.52988113617580e-01 , 3.34428215649215e+00 , -3.37057799860531e+00 , 7.28591848381977e-01 , 4.17136999507503e+00 , -3.66808902897429e+00 , 8.00192656616483e-02 , 5.48456203544388e+00 , -2.37512825645771e+00 , -3.14245448646477e-01 , 6.13503886138836e+00 , -4.48049343311408e+00 , 9.23291002542477e-01 , 6.42458367171772e+00 , -5.35769724718959e+00 , 5.73458684568045e-01 , 7.20401421961488e+00 , -6.30569540635115e+00 , 3.62474905173293e+00 , 6.75725026343317e+00 , -7.00201774664557e+00 , 4.30039933884636e+00 , 7.51458412965316e+00 , -6.63855361839082e+00 , 3.16391713791105e+00 , 5.53664135733281e+00 , -4.10443590215485e+00 , 2.25602772398803e+00 , 6.40075008511630e+00 , -4.81327049837051e+00 , 3.28343758608336e+00 , 7.25157995314202e+00 , -4.01878208177307e+00 , 4.56344162881051e+00 , 7.27582832133223e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 30. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atoms_new_colvar_forces = { ( -6.95658913699924e-02 , 3.03495304700359e-01 , -4.00976200210173e-01 ), ( 1.32299191340559e-02 , 3.20134991645447e-02 , -2.39619452468060e-01 ), ( -4.26563766265219e-02 , 9.56403093898097e-02 , 8.44596854250562e-02 ), ( -9.68486750504376e-02 , 2.49497835273790e-01 , 6.37529442829732e-02 ), ( -1.77689888890508e-02 , 9.80431135295304e-02 , -1.70915677049662e-01 ), ( 7.06489024165661e-02 , -1.84749376697780e-01 , -3.77573986335530e-02 ), ( 9.12292858715047e-03 , -9.88276270229263e-02 , 2.54389414476489e-01 ), ( -4.10658673366000e-02 , 5.93219876485636e-02 , 1.92969834008387e-01 ), ( 6.62769371505774e-02 , -1.91676334263824e-01 , 3.46813751733084e-02 ), ( 1.13425333979248e-01 , -3.91478967299099e-01 , 2.76508875738693e-01 ), ( 2.43167271106807e-02 , -9.94920033544715e-02 , 9.63817440640523e-02 ), ( 2.64191895603649e-02 , -9.75245060047426e-02 , 5.99683035376167e-02 ), ( 1.22468789126366e-02 , -5.58175258139928e-02 , 7.27121898589340e-02 ), ( 1.24047035902619e-02 , -5.36796957632884e-02 , 6.15535517723070e-02 ), ( 5.43874680066886e-03 , -3.50523789955921e-02 , 7.57443798203502e-02 ), ( -8.71221758731420e-03 , 9.67375370300251e-03 , 7.54216052589434e-02 ), ( -2.13712409634063e-03 , -2.78243053067266e-03 , 4.03264445359764e-02 ), ( -5.81071492969707e-03 , 9.82785816537380e-03 , 3.60117830588854e-02 ), ( 2.70265027945472e-03 , -1.31469274539608e-02 , 1.95560512477302e-02 ), ( 9.10712044392774e-03 , -2.23956228363689e-02 , -2.68388150373632e-02 ), ( 8.74099287762604e-03 , -2.40373952913405e-02 , -1.49977781270839e-02 ), ( 6.65645930329754e-03 , -1.37975462710417e-02 , -3.05033911886318e-02 ), ( 1.50340605582740e-02 , -4.69550160873604e-02 , -2.03743106755413e-03 ), ( 2.76055388989486e-02 , -8.88870722111463e-02 , 7.55498700718658e-03 ), ( 1.42625395994906e-02 , -4.71208094237406e-02 , 8.97020314867175e-03 ), ( 1.42285636033123e-02 , -4.42863738174126e-02 , -2.57548378640847e-03 ), ( 9.25302873951540e-03 , -3.71763907190270e-02 , 3.37862797711345e-02 ), ( -9.42067296947507e-04 , -1.51551450565181e-02 , 7.67428731176359e-02 ), ( -3.82090419229272e-03 , 4.25656589375704e-03 , 3.30184313118940e-02 ), ( -5.88419054784476e-03 , 1.13585528504002e-02 , 3.05130825138278e-02 ), ( -7.32432688702301e-03 , 1.80448026433321e-02 , 2.14438932885341e-02 ), ( -1.62692581172611e-02 , 5.22563759057720e-02 , -3.90636550782251e-03 ), ( -9.72320285482907e-03 , 3.58437115716669e-02 , -2.18639600318727e-02 ), ( -1.37458764867003e-02 , 5.01425240534089e-02 , -2.86640083889571e-02 ), ( -1.94400216674574e-03 , 1.47660014403295e-02 , -3.65441692936174e-02 ), ( 1.06715441245246e-02 , -1.63238233771593e-02 , -7.34407746919613e-02 ), ( 4.43332716670917e-03 , -1.11562187529326e-03 , -5.44961240911918e-02 ), ( 3.43104066974839e-03 , 5.69605899859925e-03 , -6.99449935137132e-02 ), ( 7.15643203676903e-03 , -1.51463397957204e-02 , -3.14717894247689e-02 ), ( 1.30767350430219e-02 , -4.17037479203933e-02 , 1.87680844406152e-03 ), ( 5.27024352117538e-04 , 1.61965138324291e-03 , -1.38965999902881e-02 ), ( 4.61570877233448e-04 , 3.21002571734941e-03 , -1.97551106198276e-02 ), ( -6.52744180540112e-03 , 2.06194280345440e-02 , -1.00291408984651e-04 ), ( -2.06135237907967e-02 , 5.82119164551233e-02 , 2.89103990433041e-02 ), ( -1.89469500756803e-02 , 6.35703291381154e-02 , -1.60359417691587e-02 ), ( -2.26515916333778e-02 , 7.55862445647695e-02 , -1.74195690035389e-02 ), ( -1.67439071198021e-02 , 7.24980841159224e-02 , -8.32590234227902e-02 ), ( -1.98121104958264e-02 , 8.66614672876918e-02 , -1.02235268950251e-01 ), ( -8.47935120434023e-03 , 4.64452483103734e-02 , -8.33603674838263e-02 ), ( -1.85674151530122e-02 , 6.69375262400479e-02 , -3.53606221186804e-02 ), ( -2.43169201023462e-02 , 9.30905017034529e-02 , -6.92785326262130e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 30, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 31, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 31, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 31, atoms_positions[size = 51] = { ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 ), ( 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 ), ( 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 ), ( 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 ), ( 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 ), ( 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 ), ( -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 ), ( -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 ), ( -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 ), ( -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ), ( 8.28755940062026e+00 , 4.18329711611074e-02 , -7.03446891225446e-01 ), ( 7.00850253516803e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 ), ( 6.14090877060161e+00 , -3.55929932388829e-01 , 8.11285689266245e-01 ), ( 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 ), ( 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 ), ( 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 ), ( 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 ), ( 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 ), ( 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 ), ( 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 ), ( 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 ), ( 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 ), ( 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 ), ( 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 ), ( 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 ), ( 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 ), ( 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 ), ( 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 ), ( 5.73958980727404e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 ), ( -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 ), ( 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 ), ( 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 ), ( -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 ), ( -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 ), ( -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 ), ( -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 ), ( -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 ), ( -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 ), ( -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 ), ( -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697042e-01 ), ( -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 ), ( -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 ), ( -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 ), ( -2.37002722947733e+00 , -3.09308532077121e-01 , 6.13223591205862e+00 ), ( -4.48400436751533e+00 , 9.25990621860430e-01 , 6.42460287653144e+00 ), ( -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 ), ( -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 ), ( -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 ), ( -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876726e+00 ), ( -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 ), ( -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ) } +colvars: Step 31, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250315e-02 , -1.47660205688038e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.28755940062026e+00 , 4.18329711611074e-02 , -7.03446891225446e-01 , 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 7.00850253516803e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 , 6.14090877060161e+00 , -3.55929932388829e-01 , 8.11285689266245e-01 , 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 , 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 , 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 , 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 , 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 , 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 , 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 , 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 , 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 , 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 , 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 , 5.73958980727404e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 , -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 , 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 , -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 , -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 , -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 , -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 , -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 , -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697042e-01 , -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 , -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 , -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -2.37002722947733e+00 , -3.09308532077121e-01 , 6.13223591205862e+00 , -4.48400436751533e+00 , 9.25990621860430e-01 , 6.42460287653144e+00 , -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 , -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 , -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 , -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876726e+00 , -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 , -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99688457134107e-01 , 1.49032814185462e-02 , 1.35220380250315e-02 , -1.47660205688038e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.28755940062026e+00 , 4.18329711611074e-02 , -7.03446891225446e-01 , 6.88305511621394e+00 , -5.90617468008672e-01 , -5.16234061590914e-01 , 7.00850253516803e+00 , -2.06932794320294e+00 , -8.69722910522837e-01 , 6.14090877060161e+00 , -3.55929932388829e-01 , 8.11285689266245e-01 , 4.94231821412680e+00 , -1.40843020281338e-01 , 7.46979410912222e-01 , 6.79690698899740e+00 , -3.05423534184035e-01 , 1.97757656514038e+00 , 6.04921300761007e+00 , -2.38491749393912e-01 , 3.17859730802446e+00 , 7.11760562395298e+00 , -3.41523628827855e-01 , 4.37304400357952e+00 , 5.27503164996258e+00 , 1.05963099600571e+00 , 3.35293534044639e+00 , 4.13233444395280e+00 , 1.00353270054482e+00 , 3.75749101754778e+00 , 5.82623396083581e+00 , 2.24219758328472e+00 , 2.97065772396541e+00 , 5.14580826508495e+00 , 3.54738561631143e+00 , 2.87769676972766e+00 , 6.29900452024698e+00 , 4.46438841140731e+00 , 2.28129874033428e+00 , 3.85787474431848e+00 , 3.64033747064021e+00 , 2.01862435821365e+00 , 2.81981811091543e+00 , 4.16697262371355e+00 , 2.42903040434897e+00 , 3.90628246457153e+00 , 3.18392900947549e+00 , 7.46028818802817e-01 , 2.76170636872688e+00 , 3.07670951287403e+00 , -7.20812647747243e-02 , 3.11953027710871e+00 , 2.64956671993818e+00 , -1.54325347415511e+00 , 1.55231542326084e+00 , 2.21447285452126e+00 , 4.24734263892295e-01 , 4.12263390091665e-01 , 2.61539574531479e+00 , 4.54563593253970e-01 , 2.05708466782489e+00 , 1.13573112663273e+00 , 1.04557827864810e+00 , 1.23570080138039e+00 , 1.40179367953644e-01 , 1.67789822155480e+00 , 2.08427650559882e+00 , -1.09420591006727e+00 , 2.03888940175357e+00 , 5.73958980727404e-01 , 6.15481440863442e-01 , 2.95269456291662e+00 , -5.90219883388677e-01 , 3.56792840843423e-01 , 3.18721429456105e+00 , 1.28453749825327e+00 , 1.39794982822720e+00 , 3.75869660403026e+00 , 8.80432280658313e-01 , 1.97918690450671e+00 , 5.03615391666209e+00 , 2.08415896684524e+00 , 2.76255165036180e+00 , 5.72493726322260e+00 , -3.57448186858373e-01 , 2.89928093526509e+00 , 4.94936987829525e+00 , -1.11350161317331e+00 , 3.07068873394765e+00 , 5.88543219225014e+00 , -5.41235843856789e-01 , 3.50492131555572e+00 , 3.77139063021997e+00 , -1.46217700701645e+00 , 4.48025739135793e+00 , 3.41815904965552e+00 , -7.46352560904742e-01 , 5.44164729114344e+00 , 2.48083122144472e+00 , -2.74743809667744e+00 , 3.94458864777565e+00 , 2.77487235153421e+00 , -3.80261261155840e+00 , 4.57188550929123e+00 , 2.81460720459722e+00 , -2.69590126548868e+00 , 2.63434489994104e+00 , 2.35602282859836e+00 , -3.80570088329331e+00 , 1.82448211302758e+00 , 2.00820873291962e+00 , -3.35719119703418e+00 , 8.79560588303698e-01 , 8.03832239697042e-01 , -4.25175384411396e+00 , 1.03774979025516e+00 , 3.24809684550553e+00 , -5.46404937822965e+00 , 7.47481970992989e-01 , 3.34650080754244e+00 , -3.37028421139506e+00 , 7.28708348270999e-01 , 4.16785184497661e+00 , -3.66693895104545e+00 , 7.85341863726528e-02 , 5.48517025875379e+00 , -2.37002722947733e+00 , -3.09308532077121e-01 , 6.13223591205862e+00 , -4.48400436751533e+00 , 9.25990621860430e-01 , 6.42460287653144e+00 , -5.35620501231628e+00 , 5.68477859072128e-01 , 7.20005011337770e+00 , -6.30624759410260e+00 , 3.62108193486571e+00 , 6.75891552422390e+00 , -7.00862480252896e+00 , 4.30148995693843e+00 , 7.51751590253258e+00 , -6.62970400260047e+00 , 3.16492323807539e+00 , 5.54214542876726e+00 , -4.10444906761868e+00 , 2.25643437944328e+00 , 6.40461761488605e+00 , -4.81279567150567e+00 , 3.28625547864269e+00 , 7.24580247456447e+00 , -4.01365077416288e+00 , 4.57159312136737e+00 , 7.27740536337571e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 31. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 31. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atoms_new_colvar_forces = { ( -6.94062311976977e-02 , 3.03490162526349e-01 , -4.00977684676539e-01 ), ( 1.33250914292942e-02 , 3.21274159113017e-02 , -2.39673124267053e-01 ), ( -4.27240173299418e-02 , 9.56884710025727e-02 , 8.42538100974747e-02 ), ( -9.68992403195541e-02 , 2.49403270880954e-01 , 6.36550646087563e-02 ), ( -1.76876529227757e-02 , 9.80045407383212e-02 , -1.70832054059996e-01 ), ( 7.06801261970314e-02 , -1.84669520776609e-01 , -3.77111455843509e-02 ), ( 9.00854828343877e-03 , -9.88304975182525e-02 , 2.54321406257577e-01 ), ( -4.11436258006877e-02 , 5.91850265153628e-02 , 1.93022819474710e-01 ), ( 6.62954345819473e-02 , -1.91702333806160e-01 , 3.48621933243010e-02 ), ( 1.13332338741391e-01 , -3.91420878955912e-01 , 2.76575377836213e-01 ), ( 2.42872148797991e-02 , -9.94587130056355e-02 , 9.63943991230486e-02 ), ( 2.64100966633783e-02 , -9.75115436907893e-02 , 6.00056349308210e-02 ), ( 1.22262415576413e-02 , -5.58132199905036e-02 , 7.27230076112159e-02 ), ( 1.23868742972013e-02 , -5.36697943768003e-02 , 6.15627630782520e-02 ), ( 5.41679282312664e-03 , -3.50637919502010e-02 , 7.57509344298476e-02 ), ( -8.73564860535173e-03 , 9.63430126607933e-03 , 7.54172439511873e-02 ), ( -2.14667172436306e-03 , -2.80868609548291e-03 , 4.03330489817440e-02 ), ( -5.82131170575600e-03 , 9.80282071643299e-03 , 3.60104340994009e-02 ), ( 2.70507434291429e-03 , -1.31772377559795e-02 , 1.95793288634017e-02 ), ( 9.13350434142548e-03 , -2.24351165446065e-02 , -2.67876251701295e-02 ), ( 8.75686636115702e-03 , -2.40549319003777e-02 , -1.49644833891818e-02 ), ( 6.67714140247194e-03 , -1.38162687868113e-02 , -3.04710927408924e-02 ), ( 1.50450251745692e-02 , -4.69572561816395e-02 , -2.00341070693012e-03 ), ( 2.76129239088779e-02 , -8.88591444165270e-02 , 7.59350369394596e-03 ), ( 1.42633561864486e-02 , -4.71022538320507e-02 , 8.98640238438215e-03 ), ( 1.42323483168066e-02 , -4.42627395145504e-02 , -2.56087965676217e-03 ), ( 9.24190630524867e-03 , -3.71600388875370e-02 , 3.37890553737085e-02 ), ( -9.75780785785199e-04 , -1.51390239570636e-02 , 7.67166922117844e-02 ), ( -3.83748876882388e-03 , 4.26311527955188e-03 , 3.30001325447189e-02 ), ( -5.90255480909130e-03 , 1.13703876236472e-02 , 3.04871677339910e-02 ), ( -7.33442811574979e-03 , 1.80348763776466e-02 , 2.14314056086946e-02 ), ( -1.62675478976216e-02 , 5.22163018395812e-02 , -3.91292521691018e-03 ), ( -9.71635845312025e-03 , 3.58254697071210e-02 , -2.18684742275428e-02 ), ( -1.37388511966618e-02 , 5.01235438545573e-02 , -2.86754534301744e-02 ), ( -1.92800700867434e-03 , 1.47527874968520e-02 , -3.65330096949882e-02 ), ( 1.07072451090726e-02 , -1.63286881274528e-02 , -7.34020992469166e-02 ), ( 4.45442382316416e-03 , -1.10729458237341e-03 , -5.44830805548990e-02 ), ( 3.45699477161344e-03 , 5.70554105771486e-03 , -6.99322518035784e-02 ), ( 7.16724311301135e-03 , -1.51252971866452e-02 , -3.14655922184140e-02 ), ( 1.30713373800647e-02 , -4.16545922190191e-02 , 1.87064785303078e-03 ), ( 5.23813753763790e-04 , 1.65268772039422e-03 , -1.39158135611629e-02 ), ( 4.58524248322313e-04 , 3.25057971335604e-03 , -1.97786328645290e-02 ), ( -6.53728779931366e-03 , 2.06409550101289e-02 , -1.29023632259628e-04 ), ( -2.06393235201968e-02 , 5.82185808423522e-02 , 2.88568299399628e-02 ), ( -1.89545031374289e-02 , 6.35758809325615e-02 , -1.60775201326768e-02 ), ( -2.26616033796460e-02 , 7.55941014081297e-02 , -1.74704140838847e-02 ), ( -1.67206283762288e-02 , 7.24879315487867e-02 , -8.32736354364718e-02 ), ( -1.97818320480012e-02 , 8.66444186321444e-02 , -1.02248462678572e-01 ), ( -8.45450440118757e-03 , 4.64492240552550e-02 , -8.33670099030260e-02 ), ( -1.85641815327470e-02 , 6.69307057568639e-02 , -3.53895893594843e-02 ), ( -2.42972071567756e-02 , 9.30557656449630e-02 , -6.92948157148458e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 31, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 32, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 32, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 32, atoms_positions[size = 51] = { ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 ), ( 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 ), ( 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 ), ( 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 ), ( 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 ), ( 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 ), ( -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 ), ( -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 ), ( -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 ), ( -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ), ( 8.28198546168908e+00 , 4.12774609412895e-02 , -6.98594743896480e-01 ), ( 7.00719717014730e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 ), ( 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 ), ( 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 ), ( 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 ), ( 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 ), ( 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 ), ( 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 ), ( 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 ), ( 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 ), ( 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 ), ( 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 ), ( 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 ), ( 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 ), ( 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 ), ( 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 ), ( 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 ), ( 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 ), ( 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 ), ( -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 ), ( 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 ), ( 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 ), ( -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013816e+00 ), ( -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 ), ( -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 ), ( -7.53250040458547e-01 , 5.44646798686886e+00 , 2.48270190089129e+00 ), ( -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 ), ( -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 ), ( -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 ), ( -3.35494631132017e+00 , 8.82615575571747e-01 , 7.96973196127046e-01 ), ( -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 ), ( -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 ), ( -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 ), ( -2.36418473395889e+00 , -3.03550327204897e-01 , 6.13032039751401e+00 ), ( -4.48692880047465e+00 , 9.30938001369170e-01 , 6.42485932408154e+00 ), ( -5.35487679866182e+00 , 5.62926127628068e-01 , 7.19598206069251e+00 ), ( -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246736e+00 ), ( -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 ), ( -6.62216635512165e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 ), ( -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 ), ( -4.00962749496155e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ) } +colvars: Step 32, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919957e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.28198546168908e+00 , 4.12774609412895e-02 , -6.98594743896480e-01 , 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 7.00719717014730e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 , 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 , 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 , 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 , 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 , 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 , 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 , 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 , 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 , 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 , 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 , 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 , 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 , 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 , -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 , 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 , -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013816e+00 , -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 , -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -7.53250040458547e-01 , 5.44646798686886e+00 , 2.48270190089129e+00 , -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 , -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 , -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.35494631132017e+00 , 8.82615575571747e-01 , 7.96973196127046e-01 , -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 , -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 , -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -2.36418473395889e+00 , -3.03550327204897e-01 , 6.13032039751401e+00 , -4.48692880047465e+00 , 9.30938001369170e-01 , 6.42485932408154e+00 , -5.35487679866182e+00 , 5.62926127628068e-01 , 7.19598206069251e+00 , -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246736e+00 , -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 , -6.62216635512165e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 , -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 , -4.00962749496155e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99688177857407e-01 , 1.49982495919957e-02 , 1.34307033891384e-02 , -1.47721280723773e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.28198546168908e+00 , 4.12774609412895e-02 , -6.98594743896480e-01 , 6.88240209667101e+00 , -5.95966874017173e-01 , -5.13681889155025e-01 , 7.00719717014730e+00 , -2.07232827742037e+00 , -8.61869492626379e-01 , 6.13077761393558e+00 , -3.47897429601852e-01 , 8.15174808865575e-01 , 4.94178103206282e+00 , -1.41253527166661e-01 , 7.49009469726219e-01 , 6.79382437697347e+00 , -3.10000081686072e-01 , 1.97903925285769e+00 , 6.04164240956982e+00 , -2.42305792435086e-01 , 3.18862568363511e+00 , 7.11975988131612e+00 , -3.42709679956176e-01 , 4.37748604277585e+00 , 5.26791860916905e+00 , 1.05810474242556e+00 , 3.35123239720047e+00 , 4.13188399286401e+00 , 1.00274686040698e+00 , 3.76563020044346e+00 , 5.82695699577678e+00 , 2.24109684021019e+00 , 2.96880145046603e+00 , 5.13805632010478e+00 , 3.54194728508216e+00 , 2.87163746938009e+00 , 6.29409120697750e+00 , 4.45769477201394e+00 , 2.27960199165651e+00 , 3.85778446732623e+00 , 3.63609628698156e+00 , 2.01472890695302e+00 , 2.82539343956937e+00 , 4.16546671822863e+00 , 2.42450059596644e+00 , 3.90289427078530e+00 , 3.17649679858173e+00 , 7.51239344856362e-01 , 2.76373568392669e+00 , 3.08730313019588e+00 , -7.10019126451150e-02 , 3.12422847030328e+00 , 2.64958183407039e+00 , -1.54202204986400e+00 , 1.55914460320919e+00 , 2.22599934083307e+00 , 4.26649084027177e-01 , 4.16743308932159e-01 , 2.61477352488619e+00 , 4.48816090909186e-01 , 2.05003107676073e+00 , 1.12940712488927e+00 , 1.04663693244921e+00 , 1.24894400529371e+00 , 1.46331588126714e-01 , 1.67321437585106e+00 , 2.08704551806050e+00 , -1.09468199757487e+00 , 2.03858009655284e+00 , 5.73264714184023e-01 , 6.15365384579517e-01 , 2.94821926898319e+00 , -5.93328385633697e-01 , 3.57327970254261e-01 , 3.19192420209928e+00 , 1.28416995622961e+00 , 1.40561528233074e+00 , 3.76435757187678e+00 , 8.88270428927635e-01 , 1.97941625973830e+00 , 5.03905886865087e+00 , 2.07502998560500e+00 , 2.76615104928888e+00 , 5.72509643838354e+00 , -3.58177784198763e-01 , 2.89751111606089e+00 , 4.94332433013816e+00 , -1.11382022082063e+00 , 3.07121284869205e+00 , 5.88831831146269e+00 , -5.38829128220319e-01 , 3.50174574950091e+00 , 3.76224175178235e+00 , -1.45684745557273e+00 , 4.47760467576840e+00 , 3.41911641598249e+00 , -7.53250040458547e-01 , 5.44646798686886e+00 , 2.48270190089129e+00 , -2.74893665391071e+00 , 3.94207859486397e+00 , 2.76162166560497e+00 , -3.80091302698539e+00 , 4.57787946059417e+00 , 2.81436850382274e+00 , -2.70038555597256e+00 , 2.63639531401040e+00 , 2.35517091626826e+00 , -3.80929697983861e+00 , 1.82113500670611e+00 , 2.00684106564218e+00 , -3.35494631132017e+00 , 8.82615575571747e-01 , 7.96973196127046e-01 , -4.25321259065413e+00 , 1.03355228978196e+00 , 3.25066014987407e+00 , -5.45619586694312e+00 , 7.42092563021892e-01 , 3.34902231545439e+00 , -3.36930450870410e+00 , 7.27670828195793e-01 , 4.16587805610637e+00 , -3.66585660784361e+00 , 7.62856477282835e-02 , 5.48377527024691e+00 , -2.36418473395889e+00 , -3.03550327204897e-01 , 6.13032039751401e+00 , -4.48692880047465e+00 , 9.30938001369170e-01 , 6.42485932408154e+00 , -5.35487679866182e+00 , 5.62926127628068e-01 , 7.19598206069251e+00 , -6.30488900247528e+00 , 3.61696819331200e+00 , 6.76155373246736e+00 , -7.01547229074162e+00 , 4.30244594153046e+00 , 7.51992640337819e+00 , -6.62216635512165e+00 , 3.16639334613561e+00 , 5.54743399186819e+00 , -4.10534222338303e+00 , 2.25626617172271e+00 , 6.40885804677088e+00 , -4.81148880739297e+00 , 3.28745332275292e+00 , 7.23886417846671e+00 , -4.00962749496155e+00 , 4.58111241438880e+00 , 7.27913592019503e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 32. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 32. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atoms_new_colvar_forces = { ( -6.92568715614584e-02 , 3.03495735434584e-01 , -4.01051034554086e-01 ), ( 1.34329507330978e-02 , 3.21823421820298e-02 , -2.39728800701794e-01 ), ( -4.27932942514773e-02 , 9.57250229757168e-02 , 8.41336611203875e-02 ), ( -9.69721359131866e-02 , 2.49374374044742e-01 , 6.35713681489005e-02 ), ( -1.76117481642180e-02 , 9.79815145584645e-02 , -1.70815129298603e-01 ), ( 7.07288562482510e-02 , -1.84643583954109e-01 , -3.76592985999826e-02 ), ( 8.89458290762093e-03 , -9.88246374575186e-02 , 2.54320588792076e-01 ), ( -4.12394038835747e-02 , 5.91236247152376e-02 , 1.93055401124770e-01 ), ( 6.63217004345558e-02 , -1.91733043548502e-01 , 3.49885686528138e-02 ), ( 1.13260661861210e-01 , -3.91407351480788e-01 , 2.76689535486304e-01 ), ( 2.42651317273264e-02 , -9.94225742000947e-02 , 9.64113282701169e-02 ), ( 2.64066904536132e-02 , -9.74935399270448e-02 , 6.00492513226762e-02 ), ( 1.22093769543052e-02 , -5.58056399140130e-02 , 7.27395848120445e-02 ), ( 1.23728157982682e-02 , -5.36574167094586e-02 , 6.15761281158678e-02 ), ( 5.39702675372180e-03 , -3.50714933498933e-02 , 7.57648994879826e-02 ), ( -8.76013321362389e-03 , 9.59882429321861e-03 , 7.54225173037756e-02 ), ( -2.15671749599581e-03 , -2.83168923198219e-03 , 4.03462312173627e-02 ), ( -5.83293595863409e-03 , 9.78005162701337e-03 , 3.60144735560437e-02 ), ( 2.70685449391101e-03 , -1.32031518159557e-02 , 1.96096956238938e-02 ), ( 9.15834484476424e-03 , -2.24685704740751e-02 , -2.67290524869441e-02 ), ( 8.77257569498755e-03 , -2.40688502387905e-02 , -1.49271558255535e-02 ), ( 6.69690925220351e-03 , -1.38319295185637e-02 , -3.04358373033775e-02 ), ( 1.50577581290483e-02 , -4.69561111251409e-02 , -1.96613008527343e-03 ), ( 2.76254746082904e-02 , -8.88285207379886e-02 , 7.63288568266022e-03 ), ( 1.42671870557170e-02 , -4.70826991952575e-02 , 9.00259338710698e-03 ), ( 1.42390841263955e-02 , -4.42388910447388e-02 , -2.54785637659202e-03 ), ( 9.23371743643695e-03 , -3.71430769112850e-02 , 3.37926316895199e-02 ), ( -1.00671645139511e-03 , -1.51237006633047e-02 , 7.66917667387033e-02 ), ( -3.85333757609560e-03 , 4.26864830346807e-03 , 3.29817680526447e-02 ), ( -5.92025145185636e-03 , 1.13801197645519e-02 , 3.04596874187430e-02 ), ( -7.34538833041085e-03 , 1.80249123828996e-02 , 2.14204667214301e-02 ), ( -1.62700547283456e-02 , 5.21773794390723e-02 , -3.91571878647396e-03 ), ( -9.71227876735541e-03 , 3.58069340024963e-02 , -2.18728681348969e-02 ), ( -1.37353309403861e-02 , 5.01033977158764e-02 , -2.86878254222996e-02 ), ( -1.91392124870543e-03 , 1.47400910989978e-02 , -3.65219256023003e-02 ), ( 1.07420773702121e-02 , -1.63319578513661e-02 , -7.33645921720010e-02 ), ( 4.47502720517408e-03 , -1.09989696158711e-03 , -5.44737391135987e-02 ), ( 3.48196414612036e-03 , 5.71349460324854e-03 , -6.99244915959538e-02 ), ( 7.17917766055985e-03 , -1.51057032137927e-02 , -3.14635424487425e-02 ), ( 1.30701470184094e-02 , -4.16083430400286e-02 , 1.85834248014845e-03 ), ( 5.21954160713208e-04 , 1.68178454324210e-03 , -1.39416476691109e-02 ), ( 4.57038802683104e-04 , 3.28621433002093e-03 , -1.98104713257074e-02 ), ( -6.54689474568868e-03 , 2.06586185232721e-02 , -1.62922115952693e-04 ), ( -2.06666564338070e-02 , 5.82206186454471e-02 , 2.87996216213028e-02 ), ( -1.89646538418560e-02 , 6.35765442851976e-02 , -1.61247498604394e-02 ), ( -2.26746116772884e-02 , 7.55960018013675e-02 , -1.75281356896499e-02 ), ( -1.67022826530015e-02 , 7.24740620594433e-02 , -8.32944414820944e-02 ), ( -1.97577450187155e-02 , 8.66234931154465e-02 , -1.02268290532814e-01 ), ( -8.43281840311428e-03 , 4.64495839359491e-02 , -8.33807577121063e-02 ), ( -1.85646447386543e-02 , 6.69201891596660e-02 , -3.54230015720242e-02 ), ( -2.42842584287525e-02 , 9.30187950246104e-02 , -6.93135803589044e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 32, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 33, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 33, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 33, atoms_positions[size = 51] = { ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 ), ( 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 ), ( 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 ), ( 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 ), ( 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 ), ( 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 ), ( -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 ), ( -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 ), ( -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 ), ( -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 ), ( 8.27559967802095e+00 , 4.05062115642717e-02 , -6.93657807517061e-01 ), ( 7.00691465518315e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 ), ( 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 ), ( 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 ), ( 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 ), ( 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 ), ( 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 ), ( 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 ), ( 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 ), ( 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 ), ( 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 ), ( 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 ), ( 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 ), ( 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 ), ( 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 ), ( 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 ), ( 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 ), ( 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 ), ( 5.72398418120016e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 ), ( -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 ), ( 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 ), ( 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 ), ( -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 ), ( -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 ), ( -5.35408684950862e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 ), ( -7.59767399943053e-01 , 5.45187321071623e+00 , 2.48446362740501e+00 ), ( -2.75044654362178e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 ), ( -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 ), ( -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 ), ( -3.35259279459821e+00 , 8.86544438418596e-01 , 7.90248627130323e-01 ), ( -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 ), ( -5.44785168837973e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 ), ( -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345539e+00 ), ( -2.35760224718148e+00 , -2.97089451023085e-01 , 6.12941517052038e+00 ), ( -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 ), ( -5.35378412302326e+00 , 5.56844942923711e-01 , 7.19187592084459e+00 ), ( -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 ), ( -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 ), ( -6.61603045936865e+00 , 3.16825299393760e+00 , 5.55235673570188e+00 ), ( -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 ), ( -4.00672772214132e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ) } +colvars: Step 33, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_ids[size = 0] = +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: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99690134322554e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Calculating gradients of colvar "one". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.27559967802095e+00 , 4.05062115642717e-02 , -6.93657807517061e-01 , 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 7.00691465518315e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 , 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 , 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 , 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 , 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 , 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 , 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 , 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 , 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 , 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 , 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 , 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 , 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 , 5.72398418120016e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 , -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 , 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 , -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 , -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 , -5.35408684950862e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -7.59767399943053e-01 , 5.45187321071623e+00 , 2.48446362740501e+00 , -2.75044654362178e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 , -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 , -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.35259279459821e+00 , 8.86544438418596e-01 , 7.90248627130323e-01 , -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 , -5.44785168837973e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 , -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345539e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -2.35760224718148e+00 , -2.97089451023085e-01 , 6.12941517052038e+00 , -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 , -5.35378412302326e+00 , 5.56844942923711e-01 , 7.19187592084459e+00 , -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 , -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 , -6.61603045936865e+00 , 3.16825299393760e+00 , 5.55235673570188e+00 , -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 , -4.00672772214132e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99690134322554e-01 , 1.50484589019195e-02 , 1.32873355861170e-02 , -1.47182178219408e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.27559967802095e+00 , 4.05062115642717e-02 , -6.93657807517061e-01 , 6.88203601862936e+00 , -6.00875966473512e-01 , -5.10830478120440e-01 , 7.00691465518315e+00 , -2.07568372459065e+00 , -8.53955790655777e-01 , 6.12145389412972e+00 , -3.40152875865253e-01 , 8.17780620296603e-01 , 4.94056933245282e+00 , -1.41628253816357e-01 , 7.51126829468872e-01 , 6.79048863282767e+00 , -3.14306578502145e-01 , 1.97972725021113e+00 , 6.03551503192261e+00 , -2.45608396916201e-01 , 3.20014388631359e+00 , 7.12079847503097e+00 , -3.44441959310997e-01 , 4.38176605244796e+00 , 5.26110989918230e+00 , 1.05682306741921e+00 , 3.34931330799913e+00 , 4.13095523869723e+00 , 1.00222934027721e+00 , 3.77394771785995e+00 , 5.82722512778535e+00 , 2.24047783014073e+00 , 2.96685775134309e+00 , 5.13179764773230e+00 , 3.53623385031784e+00 , 2.86575204503726e+00 , 6.28871294395244e+00 , 4.45075965841945e+00 , 2.27872525679712e+00 , 3.85776936859013e+00 , 3.63222993396293e+00 , 2.01086803620859e+00 , 2.83110239908888e+00 , 4.16375484623553e+00 , 2.42020501248875e+00 , 3.90031655212963e+00 , 3.16885340824077e+00 , 7.57039802411183e-01 , 2.76379781124030e+00 , 3.09818698844805e+00 , -7.08830949729123e-02 , 3.12868413741721e+00 , 2.65061358973656e+00 , -1.53948505302019e+00 , 1.56906804391941e+00 , 2.23768587142785e+00 , 4.29484578276600e-01 , 4.20500058293997e-01 , 2.61404828855065e+00 , 4.43011464119370e-01 , 2.04280538083483e+00 , 1.12295491710747e+00 , 1.04707866929854e+00 , 1.26170196473021e+00 , 1.52303932016939e-01 , 1.66901068628576e+00 , 2.08945104278475e+00 , -1.09503790833904e+00 , 2.03748645818651e+00 , 5.72398418120016e-01 , 6.15859432573413e-01 , 2.94374414878075e+00 , -5.96762730941521e-01 , 3.57755680706967e-01 , 3.19669380078064e+00 , 1.28433641094083e+00 , 1.41288708977068e+00 , 3.76994803054610e+00 , 8.95909602987325e-01 , 1.98020599204513e+00 , 5.04245560045186e+00 , 2.06569140566051e+00 , 2.76946146512658e+00 , 5.72496430900109e+00 , -3.58371963851417e-01 , 2.89571022722893e+00 , 4.93716600658157e+00 , -1.11430886951430e+00 , 3.07171402181744e+00 , 5.89126136669208e+00 , -5.35408684950862e-01 , 3.49754392121953e+00 , 3.75318899036169e+00 , -1.45289837031122e+00 , 4.47598586490931e+00 , 3.41953908668656e+00 , -7.59767399943053e-01 , 5.45187321071623e+00 , 2.48446362740501e+00 , -2.75044654362178e+00 , 3.93867804128079e+00 , 2.74943371733009e+00 , -3.79910865965421e+00 , 4.58381639155032e+00 , 2.81383029974761e+00 , -2.70428161308211e+00 , 2.63944584901112e+00 , 2.35434915084550e+00 , -3.81293200553924e+00 , 1.81624569183856e+00 , 2.00490808757975e+00 , -3.35259279459821e+00 , 8.86544438418596e-01 , 7.90248627130323e-01 , -4.25635131497264e+00 , 1.02972760449235e+00 , 3.25177612729857e+00 , -5.44785168837973e+00 , 7.36753116755700e-01 , 3.35187924958020e+00 , -3.36763768157317e+00 , 7.25519944052726e-01 , 4.16550487345539e+00 , -3.66484332642688e+00 , 7.34445121413673e-02 , 5.48046255017266e+00 , -2.35760224718148e+00 , -2.97089451023085e-01 , 6.12941517052038e+00 , -4.48903223337168e+00 , 9.37821749229521e-01 , 6.42523994647828e+00 , -5.35378412302326e+00 , 5.56844942923711e-01 , 7.19187592084459e+00 , -6.30180374348640e+00 , 3.61271857275161e+00 , 6.76542757327724e+00 , -7.02238757559323e+00 , 4.30310884060215e+00 , 7.52167470065025e+00 , -6.61603045936865e+00 , 3.16825299393760e+00 , 5.55235673570188e+00 , -4.10710014107789e+00 , 2.25563737604943e+00 , 6.41329347116789e+00 , -4.80937207857509e+00 , 3.28709350636302e+00 , 7.23093439006144e+00 , -4.00672772214132e+00 , 4.59165352398524e+00 , 7.28088548212391e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 33. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 33. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atoms_new_colvar_forces = { ( -6.91188567735980e-02 , 3.03510290930652e-01 , -4.01204144218599e-01 ), ( 1.35521762003069e-02 , 3.21768778512665e-02 , -2.39790134003718e-01 ), ( -4.28639525555756e-02 , 9.57534430612640e-02 , 8.40967235066482e-02 ), ( -9.70663031948216e-02 , 2.49414118682993e-01 , 6.34987583733795e-02 ), ( -1.75415795560572e-02 , 9.79722684267187e-02 , -1.70866696053046e-01 ), ( 7.07942495838554e-02 , -1.84673272750277e-01 , -3.76001166998724e-02 ), ( 8.78184374387509e-03 , -9.88077937155114e-02 , 2.54389666713542e-01 ), ( -4.13517014975361e-02 , 5.91390874827821e-02 , 1.93069939999040e-01 ), ( 6.63557173096009e-02 , -1.91771135913036e-01 , 3.50652281889724e-02 ), ( 1.13210481361609e-01 , -3.91438934081905e-01 , 2.76859144441299e-01 ), ( 2.42508944679388e-02 , -9.93846540337705e-02 , 9.64336947828107e-02 ), ( 2.64090719407573e-02 , -9.74714705706513e-02 , 6.00992361309367e-02 ), ( 1.21965933010758e-02 , -5.57949721748439e-02 , 7.27624373994068e-02 ), ( 1.23627885303054e-02 , -5.36429148072454e-02 , 6.15941847800254e-02 ), ( 5.37979546280222e-03 , -3.50750987052206e-02 , 7.57866353155476e-02 ), ( -8.78526662946196e-03 , 9.56877620746106e-03 , 7.54375158033274e-02 ), ( -2.16709293495136e-03 , -2.85067072987602e-03 , 4.03657995178171e-02 ), ( -5.84539818911867e-03 , 9.76042249153604e-03 , 3.60238306868930e-02 ), ( 2.70796487908088e-03 , -1.32241296979077e-02 , 1.96464215489824e-02 ), ( 9.18123224966560e-03 , -2.24957783523680e-02 , -2.66648685481025e-02 ), ( 8.78786656590287e-03 , -2.40792626679961e-02 , -1.48867932591327e-02 ), ( 6.71543577080716e-03 , -1.38446172953135e-02 , -3.03987599525088e-02 ), ( 1.50720661069986e-02 , -4.69521524401563e-02 , -1.92623704629729e-03 ), ( 2.76430209908363e-02 , -8.87967682589700e-02 , 7.67298256261931e-03 ), ( 1.42739897167352e-02 , -4.70630029142169e-02 , 9.01887453976427e-03 ), ( 1.42486787822643e-02 , -4.42158363168288e-02 , -2.53630561326753e-03 ), ( 9.22861705229513e-03 , -3.71259922873569e-02 , 3.37975218579997e-02 ), ( -1.03434697133723e-03 , -1.51090259593528e-02 , 7.66694860475731e-02 ), ( -3.86818586249688e-03 , 4.27337270826743e-03 , 3.29640520152657e-02 ), ( -5.93698751092329e-03 , 1.13879312616528e-02 , 3.04315529874886e-02 ), ( -7.35703194127185e-03 , 1.80154944915386e-02 , 2.14113196413313e-02 ), ( -1.62767618705796e-02 , 5.21409602254909e-02 , -3.91531965756660e-03 ), ( -9.71104920550146e-03 , 3.57887071932448e-02 , -2.18775513745860e-02 ), ( -1.37353980805760e-02 , 5.00828269242236e-02 , -2.87014844466075e-02 ), ( -1.90198879974780e-03 , 1.47280365461961e-02 , -3.65116461378043e-02 ), ( 1.07754626664859e-02 , -1.63343561723597e-02 , -7.33296483410146e-02 ), ( 4.49479215925102e-03 , -1.09404148493305e-03 , -5.44686669481053e-02 ), ( 3.50552735386580e-03 , 5.71924557998363e-03 , -6.99223907581775e-02 ), ( 7.19204308392410e-03 , -1.50883876037312e-02 , -3.14656795197781e-02 ), ( 1.30732051974002e-02 , -4.15663983506900e-02 , 1.84081814203583e-03 ), ( 5.21478005410681e-04 , 1.70625332202462e-03 , -1.39733493818603e-02 ), ( 4.57140419366889e-04 , 3.31607765582658e-03 , -1.98497263687156e-02 ), ( -6.55610910963488e-03 , 2.06722915485129e-02 , -2.01135264238113e-04 ), ( -2.06950886573350e-02 , 5.82188855341264e-02 , 2.87400696279859e-02 ), ( -1.89772593961475e-02 , 6.35728929566775e-02 , -1.61769549127556e-02 ), ( -2.26904308970780e-02 , 7.55926189084029e-02 , -1.75918705795381e-02 ), ( -1.66892107294848e-02 , 7.24568921030756e-02 , -8.33220787125386e-02 ), ( -1.97402932869575e-02 , 8.65992546836357e-02 , -1.02295692485758e-01 ), ( -8.41467779143527e-03 , 4.64461590623506e-02 , -8.34021574859848e-02 ), ( -1.85688269232122e-02 , 6.69066565879083e-02 , -3.54607731899793e-02 ), ( -2.42783345375781e-02 , 9.29808248567058e-02 , -6.93357136511408e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 33, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 34, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 34, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 34, atoms_positions[size = 51] = { ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 ), ( 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 ), ( 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 ), ( 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 ), ( 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 ), ( 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 ), ( -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 ), ( -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 ), ( -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 ), ( -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ), ( 8.26845026355394e+00 , 3.95164634150697e-02 , -6.88685005072648e-01 ), ( 7.00769008928433e+00 , -2.07938515079511e+00 , -8.46089877311365e-01 ), ( 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548921e-01 ), ( 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 ), ( 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 ), ( 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 ), ( 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 ), ( 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 ), ( 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 ), ( 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 ), ( 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473451e+00 ), ( 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 ), ( 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 ), ( 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 ), ( 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 ), ( 4.23609800543255e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 ), ( 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 ), ( 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 ), ( 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 ), ( -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 ), ( 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 ), ( 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 ), ( -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 ), ( -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 ), ( -5.31089467087468e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 ), ( -7.65716766890362e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 ), ( -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 ), ( -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 ), ( -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 ), ( -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354263e-01 ), ( -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 ), ( -5.43935071235475e+00 , 7.31389248939756e-01 , 3.35509424924392e+00 ), ( -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 ), ( -2.35030078449156e+00 , -2.90079848836035e-01 , 6.12958271650987e+00 ), ( -4.49013169330158e+00 , 9.46193862990714e-01 , 6.42562713694847e+00 ), ( -5.35296372957695e+00 , 5.50304318713274e-01 , 7.18777295484910e+00 ), ( -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 ), ( -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 ), ( -6.61130571979380e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 ), ( -4.10966101472105e+00 , 2.25473453690065e+00 , 6.41773857390378e+00 ), ( -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721326e+00 ) } +colvars: Step 34, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: [2/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "one", components 0 through 1. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111080e-02 , 1.30981148586898e-02 , -1.46120262321522e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.26845026355394e+00 , 3.95164634150697e-02 , -6.88685005072648e-01 , 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 7.00769008928433e+00 , -2.07938515079511e+00 , -8.46089877311365e-01 , 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548921e-01 , 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 , 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 , 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 , 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 , 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 , 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473451e+00 , 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 , 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 , 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 , 4.23609800543255e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 , 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 , 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 , -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 , 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 , -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 , -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 , -5.31089467087468e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -7.65716766890362e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 , -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 , -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 , -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354263e-01 , -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 , -5.43935071235475e+00 , 7.31389248939756e-01 , 3.35509424924392e+00 , -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -2.35030078449156e+00 , -2.90079848836035e-01 , 6.12958271650987e+00 , -4.49013169330158e+00 , 9.46193862990714e-01 , 6.42562713694847e+00 , -5.35296372957695e+00 , 5.50304318713274e-01 , 7.18777295484910e+00 , -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 , -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 , -6.61130571979380e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 , -4.10966101472105e+00 , 2.25473453690065e+00 , 6.41773857390378e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 , -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721326e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99694127613340e-01 , 1.50525510111080e-02 , 1.30981148586898e-02 , -1.46120262321522e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.26845026355394e+00 , 3.95164634150697e-02 , -6.88685005072648e-01 , 6.88162662528210e+00 , -6.05163338634998e-01 , -5.07491004213233e-01 , 7.00769008928433e+00 , -2.07938515079511e+00 , -8.46089877311365e-01 , 6.11354544419487e+00 , -3.33028612270975e-01 , 8.19069868548921e-01 , 4.93839670511578e+00 , -1.41869050515915e-01 , 7.53311672839089e-01 , 6.78674100097421e+00 , -3.18235113947914e-01 , 1.97979721093657e+00 , 6.03102463385946e+00 , -2.48437797476193e-01 , 3.21266983009148e+00 , 7.12066227628776e+00 , -3.46670237197429e-01 , 4.38596502898488e+00 , 5.25484799743806e+00 , 1.05577826909590e+00 , 3.34733225226850e+00 , 4.12947334000980e+00 , 1.00200447253813e+00 , 3.78241948546147e+00 , 5.82686752621756e+00 , 2.24034831420636e+00 , 2.96483642223569e+00 , 5.12709539922559e+00 , 3.53043535952245e+00 , 2.86014531059029e+00 , 6.28294147619008e+00 , 4.44374683243144e+00 , 2.27840845052217e+00 , 3.85788830516525e+00 , 3.62869003862892e+00 , 2.00713648473451e+00 , 2.83683791141238e+00 , 4.16189837608551e+00 , 2.41616872649920e+00 , 3.89856735939669e+00 , 3.16102795440246e+00 , 7.63268494494519e-01 , 2.76217123234297e+00 , 3.10940692875268e+00 , -7.18172012547471e-02 , 3.13287108560643e+00 , 2.65242825279430e+00 , -1.53575355120836e+00 , 1.58156876090567e+00 , 2.24918289584663e+00 , 4.33363089292907e-01 , 4.23609800543255e-01 , 2.61327738684354e+00 , 4.37139404143488e-01 , 2.03581292623918e+00 , 1.11711000764289e+00 , 1.04651952756014e+00 , 1.27341573009206e+00 , 1.57682477700770e-01 , 1.66558985042994e+00 , 2.09149854241183e+00 , -1.09525121972805e+00 , 2.03564409406982e+00 , 5.71442939920275e-01 , 6.17141254074948e-01 , 2.93960315530386e+00 , -6.00389484543333e-01 , 3.58068945873233e-01 , 3.20140907854227e+00 , 1.28499745175010e+00 , 1.41956493850939e+00 , 3.77513792345628e+00 , 9.03067744585787e-01 , 1.98157643035722e+00 , 5.04630719287008e+00 , 2.05661055765401e+00 , 2.77260078082547e+00 , 5.72471640094996e+00 , -3.58021696329006e-01 , 2.89386738419899e+00 , 4.93124929482814e+00 , -1.11484676723814e+00 , 3.07218438455739e+00 , 5.89404403088503e+00 , -5.31089467087468e-01 , 3.49228521667944e+00 , 3.74425529482752e+00 , -1.45052168667198e+00 , 4.47533226180279e+00 , 3.41921749123048e+00 , -7.65716766890362e-01 , 5.45786856835413e+00 , 2.48603823833017e+00 , -2.75189356960014e+00 , 3.93482970833437e+00 , 2.73870178659254e+00 , -3.79715795689386e+00 , 4.58960208277965e+00 , 2.81292665230372e+00 , -2.70764563365855e+00 , 2.64313302299388e+00 , 2.35334167709351e+00 , -3.81649743984014e+00 , 1.81010224843688e+00 , 2.00244886672301e+00 , -3.35010261450538e+00 , 8.91277520378448e-01 , 7.83735434354263e-01 , -4.26067699113737e+00 , 1.02633034709206e+00 , 3.25138470928131e+00 , -5.43935071235475e+00 , 7.31389248939756e-01 , 3.35509424924392e+00 , -3.36533929440318e+00 , 7.22368906758605e-01 , 4.16663441022311e+00 , -3.66392163061900e+00 , 7.02059845558158e-02 , 5.47546908453680e+00 , -2.35030078449156e+00 , -2.90079848836035e-01 , 6.12958271650987e+00 , -4.49013169330158e+00 , 9.46193862990714e-01 , 6.42562713694847e+00 , -5.35296372957695e+00 , 5.50304318713274e-01 , 7.18777295484910e+00 , -6.29726878124543e+00 , 3.60864948535656e+00 , 6.77071081330584e+00 , -7.02918198146008e+00 , 4.30332267754961e+00 , 7.52263853972974e+00 , -6.61130571979380e+00 , 3.17041590093055e+00 , 5.55681505986724e+00 , -4.10966101472105e+00 , 2.25473453690065e+00 , 6.41773857390378e+00 , -4.80654536027350e+00 , 3.28533043122667e+00 , 7.22225324814125e+00 , -4.00490846968091e+00 , 4.60284855380208e+00 , 7.28252930721326e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 34. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 34. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atoms_new_colvar_forces = { ( -6.89931515523722e-02 , 3.03529453435325e-01 , -4.01438225063418e-01 ), ( 1.36805804611950e-02 , 3.21123159144447e-02 , -2.39859338329955e-01 ), ( -4.29352667358211e-02 , 9.57764098729455e-02 , 8.41354087339803e-02 ), ( -9.71793493942812e-02 , 2.49519950404404e-01 , 6.34334958307607e-02 ), ( -1.74775293005200e-02 , 9.79738898846051e-02 , -1.70983723879155e-01 ), ( 7.08744938792751e-02 , -1.84756089859670e-01 , -3.75322777943504e-02 ), ( 8.67155116481996e-03 , -9.87778464994403e-02 , 2.54526116207477e-01 ), ( -4.14780086993958e-02 , 5.92285323448909e-02 , 1.93069092917231e-01 ), ( 6.63968084260576e-02 , -1.91817057413589e-01 , 3.50994591677031e-02 ), ( 1.13181130747263e-01 , -3.91510994669006e-01 , 2.77087216958719e-01 ), ( 2.42445286609735e-02 , -9.93458642506380e-02 , 9.64622242692801e-02 ), ( 2.64170912653268e-02 , -9.74463301627498e-02 , 6.01553510528831e-02 ), ( 1.21880001742566e-02 , -5.57814893760357e-02 , 7.27916733558242e-02 ), ( 1.23568551091888e-02 , -5.36266530279977e-02 , 6.16171486908459e-02 ), ( 5.36532119084152e-03 , -3.50744606060441e-02 , 7.58160218574634e-02 ), ( -8.81061897949866e-03 , 9.54511730651304e-03 , 7.54617555207575e-02 ), ( -2.17760511040056e-03 , -2.86518723913950e-03 , 4.03912296616751e-02 ), ( -5.85846868302164e-03 , 9.74450841827337e-03 , 3.60381370606483e-02 ), ( 2.70844461247052e-03 , -1.32399871433099e-02 , 1.96885363244457e-02 ), ( 9.20192687987023e-03 , -2.25169446455836e-02 , -2.65968732719789e-02 ), ( 8.80255120781468e-03 , -2.40864736018276e-02 , -1.48443959207891e-02 ), ( 6.73250208365004e-03 , -1.38545990414471e-02 , -3.03609130906804e-02 ), ( 1.50877199996254e-02 , -4.69460167158573e-02 , -1.88440003463211e-03 ), ( 2.76651864173050e-02 , -8.87652480873047e-02 , 7.71367668824414e-03 ), ( 1.42835896453966e-02 , -4.70438788226700e-02 , 9.03535000251388e-03 ), ( 1.42609120931696e-02 , -4.41943703904301e-02 , -2.52602727794592e-03 ), ( 9.22660325372609e-03 , -3.71091704512848e-02 , 3.38041040625322e-02 ), ( -1.05835313619202e-03 , -1.50947778879150e-02 , 7.66508781959285e-02 ), ( -3.88184605550168e-03 , 4.27753341324616e-03 , 3.29475466990500e-02 ), ( -5.95255522011070e-03 , 1.13941067628747e-02 , 3.04035631838731e-02 ), ( -7.36916549274786e-03 , 1.80070942161375e-02 , 2.14040567647014e-02 ), ( -1.62874444626766e-02 , 5.21080227589862e-02 , -3.91242232744704e-03 ), ( -9.71261338380347e-03 , 3.57712555200730e-02 , -2.18828726157710e-02 ), ( -1.37389641632307e-02 , 5.00624491635394e-02 , -2.87166885471019e-02 ), ( -1.89232631851091e-03 , 1.47166616758053e-02 , -3.65027479143405e-02 ), ( 1.08069515486647e-02 , -1.63365926908086e-02 , -7.32982874652060e-02 ), ( 4.51343606296246e-03 , -1.09019322499420e-03 , -5.44680977153746e-02 ), ( 3.52735490621464e-03 , 5.72230291359508e-03 , -6.99262007192625e-02 ), ( 7.20560809590540e-03 , -1.50739359573486e-02 , -3.14717893114619e-02 ), ( 1.30803256344866e-02 , -4.15296746745539e-02 , 1.81917584866731e-03 ), ( 5.22321157891290e-04 , 1.72577325068763e-03 , -1.40099506251826e-02 ), ( 4.58742355604879e-04 , 3.33977328082308e-03 , -1.98952188702454e-02 ), ( -6.56483596370068e-03 , 2.06820949494386e-02 , -2.42711121581312e-04 ), ( -2.07242020794929e-02 , 5.82143300984995e-02 , 2.86793663983974e-02 ), ( -1.89921052856701e-02 , 6.35656362416375e-02 , -1.62333176260830e-02 ), ( -2.27087976362070e-02 , 7.55847985706018e-02 , -1.76605909183659e-02 ), ( -1.66814979147063e-02 , 7.24368891060879e-02 , -8.33567348746792e-02 ), ( -1.97295924656961e-02 , 8.65722790102330e-02 , -1.02331076952250e-01 ), ( -8.40029022578602e-03 , 4.64389575616804e-02 , -8.34312592396013e-02 ), ( -1.85765957934514e-02 , 6.68908166789611e-02 , -3.55026209993640e-02 ), ( -2.42793529811600e-02 , 9.29428836853372e-02 , -6.93618229473791e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 34, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 35, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 35, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 35, atoms_positions[size = 51] = { ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 ), ( 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 ), ( 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 ), ( 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 ), ( 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 ), ( 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 ), ( -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 ), ( -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 ), ( -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 ), ( -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 ), ( 8.26061045679133e+00 , 3.83159872376033e-02 , -6.83729575836184e-01 ), ( 7.00950811364949e+00 , -2.08340936270183e+00 , -8.38373555072614e-01 ), ( 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 ), ( 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 ), ( 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 ), ( 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 ), ( 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486680e+00 ), ( 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 ), ( 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 ), ( 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 ), ( 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 ), ( 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 ), ( 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 ), ( 3.13674411350812e+00 , 2.65473647538067e+00 , -1.53101934024696e+00 ), ( 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 ), ( 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 ), ( 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 ), ( 2.09321874616617e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 ), ( 5.70469478379834e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 ), ( -6.04067745585491e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 ), ( 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 ), ( 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 ), ( -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233232e+00 ), ( -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 ), ( -5.26037504488994e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 ), ( -7.70948015201459e-01 , 5.46443699617149e+00 , 2.48736122784711e+00 ), ( -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 ), ( -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 ), ( -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 ), ( -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293814e-01 ), ( -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 ), ( -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 ), ( -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306038e+00 ), ( -2.34232995666454e+00 , -2.82710935135204e-01 , 6.13081751615585e+00 ), ( -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958556e+00 ), ( -5.35241375743554e+00 , 5.43401369702618e-01 , 7.18368666862339e+00 ), ( -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 ), ( -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 ), ( -6.60792606081237e+00 , 3.17278933049613e+00 , 5.56077186656671e+00 ), ( -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 ), ( -4.00406811080272e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ) } +colvars: Step 35, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858439e-02 , 1.28715966499479e-02 , -1.44634565196466e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.26061045679133e+00 , 3.83159872376033e-02 , -6.83729575836184e-01 , 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 7.00950811364949e+00 , -2.08340936270183e+00 , -8.38373555072614e-01 , 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 , 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 , 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 , 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486680e+00 , 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 , 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 , 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 , 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 , 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 3.13674411350812e+00 , 2.65473647538067e+00 , -1.53101934024696e+00 , 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 , 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 , 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 2.09321874616617e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 , 5.70469478379834e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 , -6.04067745585491e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 , 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 , -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233232e+00 , -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 , -5.26037504488994e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -7.70948015201459e-01 , 5.46443699617149e+00 , 2.48736122784711e+00 , -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 , -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 , -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293814e-01 , -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 , -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 , -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306038e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -2.34232995666454e+00 , -2.82710935135204e-01 , 6.13081751615585e+00 , -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958556e+00 , -5.35241375743554e+00 , 5.43401369702618e-01 , 7.18368666862339e+00 , -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 , -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 , -6.60792606081237e+00 , 3.17278933049613e+00 , 5.56077186656671e+00 , -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 , -4.00406811080272e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99699846006243e-01 , 1.50116061858439e-02 , 1.28715966499479e-02 , -1.44634565196466e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.26061045679133e+00 , 3.83159872376033e-02 , -6.83729575836184e-01 , 6.88088825477158e+00 , -6.08681901910275e-01 , -5.03519047518402e-01 , 7.00950811364949e+00 , -2.08340936270183e+00 , -8.38373555072614e-01 , 6.10750479906275e+00 , -3.26802144281748e-01 , 8.19065292661057e-01 , 4.93505474399466e+00 , -1.41898809052657e-01 , 7.55538158094108e-01 , 6.78246367587320e+00 , -3.21692683963763e-01 , 1.97942804787509e+00 , 6.02831662068299e+00 , -2.50830987675919e-01 , 3.22567739482300e+00 , 7.11934100658893e+00 , -3.49316151672047e-01 , 4.39015913135325e+00 , 5.24929949982854e+00 , 1.05496676581604e+00 , 3.34546993486680e+00 , 4.12740130983140e+00 , 1.00209357961779e+00 , 3.79100926460535e+00 , 5.82576263193606e+00 , 2.24065328799326e+00 , 2.96275496670661e+00 , 5.12390883909099e+00 , 3.52477572167754e+00 , 2.85488581715929e+00 , 6.27686137080751e+00 , 4.43681555380932e+00 , 2.27836151169341e+00 , 3.85824419324196e+00 , 3.62541328860656e+00 , 2.00362837977509e+00 , 2.84249208877218e+00 , 4.15996331667264e+00 , 2.41241623811687e+00 , 3.89760382511988e+00 , 3.15305128971607e+00 , 7.69715911566150e-01 , 2.75925267840360e+00 , 3.12100816780507e+00 , -7.38515303532892e-02 , 3.13674411350812e+00 , 2.65473647538067e+00 , -1.53101934024696e+00 , 1.59590046216788e+00 , 2.26021519256670e+00 , 4.38342853666811e-01 , 4.26250059050784e-01 , 2.61248712951815e+00 , 4.31197143941255e-01 , 2.02942857092578e+00 , 1.11253025330527e+00 , 1.04464609047151e+00 , 1.28357020686338e+00 , 1.62082532589514e-01 , 1.66321373730640e+00 , 2.09321874616617e+00 , -1.09532372723993e+00 , 2.03311038998544e+00 , 5.70469478379834e-01 , 6.19344693162499e-01 , 2.93610717130991e+00 , -6.04067745585491e-01 , 3.58270481763408e-01 , 3.20595951725001e+00 , 1.28611408556646e+00 , 1.42549973652358e+00 , 3.77965824033291e+00 , 9.09480833412254e-01 , 1.98349849846931e+00 , 5.05054142167207e+00 , 2.04820353401842e+00 , 2.77569499720714e+00 , 5.72452416638457e+00 , -3.57131068332098e-01 , 2.89197056218246e+00 , 4.92592873233232e+00 , -1.11531316047217e+00 , 3.07261605073183e+00 , 5.89644732400387e+00 , -5.26037504488994e-01 , 3.48601201736923e+00 , 3.73543684521893e+00 , -1.44981206383771e+00 , 4.47550964705134e+00 , 3.41799698043975e+00 , -7.70948015201459e-01 , 5.46443699617149e+00 , 2.48736122784711e+00 , -2.75322985558568e+00 , 3.93100283628642e+00 , 2.72977917355420e+00 , -3.79501833460222e+00 , 4.59513716173055e+00 , 2.81159863448638e+00 , -2.71056130519907e+00 , 2.64704919439371e+00 , 2.35193833144522e+00 , -3.81985840872299e+00 , 1.80308223553373e+00 , 1.99951849608793e+00 , -3.34746172045222e+00 , 8.96718520736950e-01 , 7.77521834293814e-01 , -4.26559315753315e+00 , 1.02336865937289e+00 , 3.24953713660205e+00 , -5.43106033830887e+00 , 7.25924056711847e-01 , 3.35867829720771e+00 , -3.36252071459398e+00 , 7.18398475194915e-01 , 4.16902941306038e+00 , -3.66312344819817e+00 , 6.67877799859202e-02 , 5.46916433855245e+00 , -2.34232995666454e+00 , -2.82710935135204e-01 , 6.13081751615585e+00 , -4.49011132336196e+00 , 9.55496875620262e-01 , 6.42591049958556e+00 , -5.35241375743554e+00 , 5.43401369702618e-01 , 7.18368666862339e+00 , -6.29162869878297e+00 , 3.60505879814971e+00 , 6.77746323968115e+00 , -7.03566575609994e+00 , 4.30294750869284e+00 , 7.52272776813223e+00 , -6.60792606081237e+00 , 3.17278933049613e+00 , 5.56077186656671e+00 , -4.11292622985910e+00 , 2.25379570346728e+00 , 6.42200752732932e+00 , -4.80317903895887e+00 , 3.28240651229301e+00 , 7.21313101103288e+00 , -4.00406811080272e+00 , 4.61431678895696e+00 , 7.28396746523970e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 35. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 35. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atoms_new_colvar_forces = { ( -6.88807360946587e-02 , 3.03546174506848e-01 , -4.01748229755430e-01 ), ( 1.38150532480894e-02 , 3.19920050341430e-02 , -2.39936826947338e-01 ), ( -4.30059550048689e-02 , 9.57958483467742e-02 , 8.42381958230143e-02 ), ( -9.73074704360656e-02 , 2.49684520874827e-01 , 6.33713523707341e-02 ), ( -1.74201151791814e-02 , 9.79823778111991e-02 , -1.71159035993790e-01 ), ( 7.09667533396044e-02 , -1.84885894825296e-01 , -3.74547956787869e-02 ), ( 8.56541917378938e-03 , -9.87326138352738e-02 , 2.54722745980557e-01 ), ( -4.16147347248274e-02 , 5.93856644975062e-02 , 1.93055283348347e-01 ), ( 6.64435907168653e-02 , -1.91869163125822e-01 , 3.51002760286789e-02 ), ( 1.13171124872205e-01 , -3.91614114049827e-01 , 2.77372205308533e-01 ), ( 2.42457448834941e-02 , -9.93070224567197e-02 , 9.64972929017528e-02 ), ( 2.64303690231682e-02 , -9.74191373119858e-02 , 6.02170552240258e-02 ), ( 1.21835519220548e-02 , -5.57655192466589e-02 , 7.28270609870343e-02 ), ( 1.23549210045000e-02 , -5.36090050053975e-02 , 6.16449699320789e-02 ), ( 5.35374003500274e-03 , -3.50695784504462e-02 , 7.58525382532428e-02 ), ( -8.83570700232429e-03 , 9.52850693697150e-03 , 7.54942754737820e-02 ), ( -2.18803122140736e-03 , -2.87499821449636e-03 , 4.04217065934371e-02 ), ( -5.87186847068819e-03 , 9.73270279833237e-03 , 3.60567731097607e-02 ), ( 2.70837477367325e-03 , -1.32507681744094e-02 , 1.97348271046725e-02 ), ( 9.22027924498692e-03 , -2.25325482849989e-02 , -2.65269833710352e-02 ), ( 8.81646329246599e-03 , -2.40909194584065e-02 , -1.48010224744675e-02 ), ( 6.74794204665998e-03 , -1.38622651450867e-02 , -3.03233386338982e-02 ), ( 1.51044276345387e-02 , -4.69383939076473e-02 , -1.84135275144506e-03 ), ( 2.76913826852593e-02 , -8.87352085322907e-02 , 7.75483897287110e-03 ), ( 1.42956864003069e-02 , -4.70259579292682e-02 , 9.05211661372034e-03 ), ( 1.42754387286164e-02 , -4.41751623983651e-02 , -2.51675453633897e-03 ), ( 9.22754823332049e-03 , -3.70929337651855e-02 , 3.38126538002124e-02 ), ( -1.07854362508031e-03 , -1.50806771148120e-02 , 7.66367273623761e-02 ), ( -3.89416842781478e-03 , 4.28140636220418e-03 , 3.29327218643407e-02 ), ( -5.96678550441178e-03 , 1.13990052816781e-02 , 3.03764693573409e-02 ), ( -7.38156070100469e-03 , 1.80001190670400e-02 , 2.13986614634107e-02 ), ( -1.63016928856876e-02 , 5.20793173793131e-02 , -3.90783217966120e-03 ), ( -9.71679604441101e-03 , 3.57549618897123e-02 , -2.18891358294395e-02 ), ( -1.37457928463725e-02 , 5.00428092109121e-02 , -2.87336088867498e-02 ), ( -1.88496398780749e-03 , 1.47059454600984e-02 , -3.64957084247095e-02 ), ( 1.08361435000648e-02 , -1.63393854324177e-02 , -7.32712852290432e-02 ), ( 4.53069842551564e-03 , -1.08873278149816e-03 , -5.44720111056568e-02 ), ( 3.54715952514462e-03 , 5.72228164961961e-03 , -6.99358433688927e-02 ), ( 7.21959067154380e-03 , -1.50627862598159e-02 , -3.14814510290332e-02 ), ( 1.30911314699056e-02 , -4.14987884092741e-02 , 1.79469385094998e-03 ), ( 5.24348506408816e-04 , 1.74025786394995e-03 , -1.40502650952513e-02 ), ( 4.61674806489519e-04 , 3.35719489023764e-03 , -1.99454895684731e-02 ), ( -6.57300468365554e-03 , 2.06883139076785e-02 , -2.86564847277578e-04 ), ( -2.07535322945683e-02 , 5.82079798474097e-02 , 2.86187002618328e-02 ), ( -1.90088824990835e-02 , 6.35555827272412e-02 , -1.62928456142045e-02 ), ( -2.27293407292263e-02 , 7.55735124075078e-02 , -1.77330614847094e-02 ), ( -1.66790254550069e-02 , 7.24145550891492e-02 , -8.33982228687755e-02 ), ( -1.97254993582460e-02 , 8.65431509733359e-02 , -1.02374417573546e-01 ), ( -8.38973467101070e-03 , 4.64280970315202e-02 , -8.34677033511890e-02 ), ( -1.85876716559441e-02 , 6.68734057428191e-02 , -3.55480668376697e-02 ), ( -2.42869446603211e-02 , 9.29058765273728e-02 , -6.93922885498936e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 35, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 36, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 36, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 36, atoms_positions[size = 51] = { ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 ), ( 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 ), ( 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 ), ( 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 ), ( 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 ), ( 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 ), ( -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 ), ( -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 ), ( -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 ), ( -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 ), ( 8.25217464544869e+00 , 3.69221958155758e-02 , -6.78843503334926e-01 ), ( 7.01230109825312e+00 , -2.08771896240021e+00 , -8.30893615702844e-01 ), ( 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221475e-01 ), ( 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 ), ( 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 ), ( 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 ), ( 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 ), ( 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 ), ( 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 ), ( 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 ), ( 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981679e+00 ), ( 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 ), ( 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 ), ( 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 ), ( 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 ), ( 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 ), ( 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 ), ( 2.09467021666479e+00 , -1.09528109816072e+00 , 2.02995905011222e+00 ), ( 5.69529133519056e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 ), ( -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 ), ( 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 ), ( 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 ), ( -3.55712677434051e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 ), ( -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 ), ( -5.20464387542566e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 ), ( -7.75358318910477e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 ), ( -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 ), ( -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 ), ( -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 ), ( -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839784e-01 ), ( -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 ), ( -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 ), ( -3.35934410802697e+00 , 7.13844953536181e-01 , 4.17234104677064e+00 ), ( -2.33377676810806e+00 , -2.75203274913510e-01 , 6.13304533363274e+00 ), ( -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 ), ( -5.35209341374793e+00 , 5.36256909713219e-01 , 7.17960272686383e+00 ), ( -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394097e+00 ), ( -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 ), ( -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 ), ( -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 ), ( -4.00404855626915e+00 , 4.62566455159042e+00 , 7.28513526460300e+00 ) } +colvars: Step 36, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [2/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956245e-02 , 1.26183883681986e-02 , -1.42839286474993e-02 ). +colvars: Done calculating gradients of colvar "main". +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.25217464544869e+00 , 3.69221958155758e-02 , -6.78843503334926e-01 , 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 7.01230109825312e+00 , -2.08771896240021e+00 , -8.30893615702844e-01 , 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221475e-01 , 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 , 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 , 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 , 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 , 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 , 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981679e+00 , 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 , 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 , 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 , 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 , 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 2.09467021666479e+00 , -1.09528109816072e+00 , 2.02995905011222e+00 , 5.69529133519056e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 , -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 , 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 , -3.55712677434051e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 , -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 , -5.20464387542566e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -7.75358318910477e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 , -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 , -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 , -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839784e-01 , -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 , -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 , -3.35934410802697e+00 , 7.13844953536181e-01 , 4.17234104677064e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -2.33377676810806e+00 , -2.75203274913510e-01 , 6.13304533363274e+00 , -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 , -5.35209341374793e+00 , 5.36256909713219e-01 , 7.17960272686383e+00 , -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394097e+00 , -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 , -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 , -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 , -4.00404855626915e+00 , 4.62566455159042e+00 , 7.28513526460300e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99706901952671e-01 , 1.49283570956245e-02 , 1.26183883681986e-02 , -1.42839286474993e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.25217464544869e+00 , 3.69221958155758e-02 , -6.78843503334926e-01 , 6.87960405041136e+00 , -6.11326767603932e-01 , -4.98831427460806e-01 , 7.01230109825312e+00 , -2.08771896240021e+00 , -8.30893615702844e-01 , 6.10357970218918e+00 , -3.21686866991033e-01 , 8.17848768221475e-01 , 4.93043530265216e+00 , -1.41663846400487e-01 , 7.57775991108233e-01 , 6.77759207295793e+00 , -3.24605657141308e-01 , 1.97880759089787e+00 , 6.02747530820641e+00 , -2.52820890808462e-01 , 3.23863189075895e+00 , 7.11687159779290e+00 , -3.52274012343781e-01 , 4.39441173957480e+00 , 5.24454811778643e+00 , 1.05438813003332e+00 , 3.34392818640015e+00 , 4.12474350519541e+00 , 1.00251381174941e+00 , 3.79966821082162e+00 , 5.82384634642754e+00 , 2.24127818636718e+00 , 2.96063624952601e+00 , 5.12210967663333e+00 , 3.51949582679000e+00 , 2.84999622902058e+00 , 6.27056020488582e+00 , 4.43011213449652e+00 , 2.27828886695384e+00 , 3.85897010951837e+00 , 3.62232745916840e+00 , 2.00043419981679e+00 , 2.84796171629412e+00 , 4.15801693262510e+00 , 2.40897082492923e+00 , 3.89733307621969e+00 , 3.14495982931050e+00 , 7.76134445544478e-01 , 2.75552414248519e+00 , 3.13301278498989e+00 , -7.69823983643876e-02 , 3.14025225749023e+00 , 2.65721867759519e+00 , -1.52554895674406e+00 , 1.61115119898283e+00 , 2.27059611629814e+00 , 4.44392612632783e-01 , 4.28676388074995e-01 , 2.61167917305116e+00 , 4.25196493436307e-01 , 2.02399290495710e+00 , 1.10973900825139e+00 , 1.04124096557112e+00 , 1.29172434640429e+00 , 1.65185890499649e-01 , 1.66208256397796e+00 , 2.09467021666479e+00 , -1.09528109816072e+00 , 2.02995905011222e+00 , 5.69529133519056e-01 , 6.22545808245189e-01 , 2.93352477220501e+00 , -6.07652484604558e-01 , 3.58373824077312e-01 , 3.21024332904820e+00 , 1.28765432802280e+00 , 1.43060439592395e+00 , 3.78331667884053e+00 , 9.14913692767033e-01 , 1.98589676749277e+00 , 5.05505415452094e+00 , 2.04081245083353e+00 , 2.77886654480213e+00 , 5.72453850731404e+00 , -3.55712677434051e-01 , 2.89000982331657e+00 , 4.92152589921071e+00 , -1.11559572463807e+00 , 3.07300254323846e+00 , 5.89826551998046e+00 , -5.20464387542566e-01 , 3.47883260661645e+00 , 3.72671317932189e+00 , -1.45076077839070e+00 , 4.47633011957852e+00 , 3.41578430939674e+00 , -7.75358318910477e-01 , 5.47153553704757e+00 , 2.48838704872224e+00 , -2.75443038349857e+00 , 3.92764860412772e+00 , 2.72295756569176e+00 , -3.79265383508450e+00 , 4.60032649215763e+00 , 2.80979834353215e+00 , -2.71312910889599e+00 , 2.65078383419146e+00 , 2.34994882589010e+00 , -3.82286114827542e+00 , 1.79561675924995e+00 , 1.99618321075264e+00 , -3.34466927801878e+00 , 9.02750424539248e-01 , 7.71703437839784e-01 , -4.27045625678108e+00 , 1.02080382172400e+00 , 3.24638445434956e+00 , -5.42335067759256e+00 , 7.20283988982482e-01 , 3.36262977574835e+00 , -3.35934410802697e+00 , 7.13844953536181e-01 , 4.17234104677064e+00 , -3.66247706101863e+00 , 6.34272909613138e-02 , 5.46201921848079e+00 , -2.33377676810806e+00 , -2.75203274913510e-01 , 6.13304533363274e+00 , -4.48893072463695e+00 , 9.65099827389133e-01 , 6.42599709055802e+00 , -5.35209341374793e+00 , 5.36256909713219e-01 , 7.17960272686383e+00 , -6.28526779976564e+00 , 3.60220205158113e+00 , 6.78561519394097e+00 , -7.04166356746730e+00 , 4.30187182470643e+00 , 7.52189488204698e+00 , -6.60576072050366e+00 , 3.17528103171988e+00 , 5.56425589688531e+00 , -4.11677132774871e+00 , 2.25308425813436e+00 , 6.42592224633809e+00 , -4.79950128550455e+00 , 3.27864412311331e+00 , 7.20394064252680e+00 , -4.00404855626915e+00 , 4.62566455159042e+00 , 7.28513526460300e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 36. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 36. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atoms_new_colvar_forces = { ( -6.87825515010303e-02 , 3.03551175854197e-01 , -4.02123591707848e-01 ), ( 1.39516159518602e-02 , 3.18209001221919e-02 , -2.40021075355466e-01 ), ( -4.30741931969210e-02 , 9.58131187992768e-02 , 8.43908110464438e-02 ), ( -9.74454677719412e-02 , 2.49896651123009e-01 , 6.33078221622214e-02 ), ( -1.73699557572936e-02 , 9.79928227747052e-02 , -1.71382115313688e-01 ), ( 7.10671728779810e-02 , -1.85053619004943e-01 , -3.73669781672520e-02 ), ( 8.46560683046813e-03 , -9.86698209726457e-02 , 2.54968457116350e-01 ), ( -4.17572287925472e-02 , 5.96014738190170e-02 , 1.93030343635103e-01 ), ( 6.64939874414992e-02 , -1.91924129005421e-01 , 3.50776228827207e-02 ), ( 1.13178124270782e-01 , -3.91734979956620e-01 , 2.77708435582396e-01 ), ( 2.42540016505370e-02 , -9.92689443102836e-02 , 9.65390072894103e-02 ), ( 2.64483115922368e-02 , -9.73909658951079e-02 , 6.02835162651833e-02 ), ( 1.21830809877308e-02 , -5.57474384223472e-02 , 7.28680948982734e-02 ), ( 1.23567667227087e-02 , -5.35903711954581e-02 , 6.16773865701318e-02 ), ( 5.34512949395850e-03 , -3.50605336726781e-02 , 7.58953439322043e-02 ), ( -8.85997764673842e-03 , 9.51947116101915e-03 , 7.55337438274854e-02 ), ( -2.19811885413009e-03 , -2.87995808817898e-03 , 4.04561704955643e-02 ), ( -5.88526593724565e-03 , 9.72531991195741e-03 , 3.60789200428813e-02 ), ( 2.70785417124688e-03 , -1.32566301520370e-02 , 1.97838389513108e-02 ), ( 9.23615813287942e-03 , -2.25432107077569e-02 , -2.64573206711712e-02 ), ( 8.82941764911573e-03 , -2.40931117783055e-02 , -1.47578476036868e-02 ), ( 6.76159384954824e-03 , -1.38680730198555e-02 , -3.02871414148130e-02 ), ( 1.51218095131350e-02 , -4.69300222271671e-02 , -1.79794353022244e-03 ), ( 2.77208071616533e-02 , -8.87078872996009e-02 , 7.79627322118805e-03 ), ( 1.43098597663197e-02 , -4.70098544163797e-02 , 9.06924461340024e-03 ), ( 1.42917926844773e-02 , -4.41588435488001e-02 , -2.50818581251334e-03 ), ( 9.23122439443108e-03 , -3.70775907849662e-02 , 3.38233725284600e-02 ), ( -1.09478835120119e-03 , -1.50664198922653e-02 , 7.66276922034177e-02 ), ( -3.90500816429111e-03 , 4.28528625123975e-03 , 3.29200157247979e-02 ), ( -5.97950807729432e-03 , 1.14030284170730e-02 , 3.03510423802199e-02 ), ( -7.39394176377097e-03 , 1.79949563178355e-02 , 2.13950536392084e-02 ), ( -1.63189362527715e-02 , 5.20555115448216e-02 , -3.90244624481996e-03 ), ( -9.72332312549997e-03 , 3.57401858757540e-02 , -2.18966122390077e-02 ), ( -1.37555195126383e-02 , 5.00244400005668e-02 , -2.87523394191009e-02 ), ( -1.87987996734087e-03 , 1.46958439822277e-02 , -3.64909585650040e-02 ), ( 1.08626211982598e-02 , -1.63434687790130e-02 , -7.32493095287909e-02 ), ( 4.54630977618068e-03 , -1.09000456952993e-03 , -5.44802162169457e-02 ), ( 3.56465799952969e-03 , 5.71884565694859e-03 , -6.99510120052419e-02 ), ( 7.23365133628510e-03 , -1.50553158520898e-02 , -3.14940893290122e-02 ), ( 1.31050916705081e-02 , -4.14742340010639e-02 , 1.76882071273220e-03 ), ( 5.27380256966284e-04 , 1.74973163386151e-03 , -1.40928889578658e-02 ), ( 4.65715758364312e-04 , 3.36837393393763e-03 , -1.99988030791925e-02 ), ( -6.58053681650213e-03 , 2.06913214588559e-02 , -3.31446169875400e-04 ), ( -2.07825151365776e-02 , 5.82009297448728e-02 , 2.85593613051498e-02 ), ( -1.90271656243260e-02 , 6.35436180091860e-02 , -1.63543335215463e-02 ), ( -2.27515526488476e-02 , 7.55598273573979e-02 , -1.78077907924694e-02 ), ( -1.66815106120319e-02 , 7.23904387415432e-02 , -8.34460512800944e-02 ), ( -1.97276671460812e-02 , 8.65124958483397e-02 , -1.02425344852602e-01 ), ( -8.38299757725756e-03 , 4.64137645103610e-02 , -8.35108075184975e-02 ), ( -1.86016314754188e-02 , 6.68552036549514e-02 , -3.55964346198361e-02 ), ( -2.43005014289643e-02 , 9.28706910473661e-02 , -6.94273071096894e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 36, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 37, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 37, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 37, atoms_positions[size = 51] = { ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 ), ( 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 ), ( 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 ), ( 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 ), ( 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 ), ( 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 ), ( -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 ), ( -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 ), ( -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 ), ( -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 ), ( 8.24325423950952e+00 , 3.53606340058551e-02 , -6.74071896755363e-01 ), ( 7.01595064911501e+00 , -2.09226237248072e+00 , -8.23713639498105e-01 ), ( 6.10178478736824e+00 , -3.17827591276146e-01 , 8.15561834792714e-01 ), ( 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 ), ( 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 ), ( 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 ), ( 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 ), ( 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 ), ( 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757519e+00 ), ( 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 ), ( 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 ), ( 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 ), ( 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 ), ( 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 ), ( 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 ), ( 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 ), ( 2.01981272765406e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 ), ( 2.09593922434932e+00 , -1.09517162307366e+00 , 2.02627695012513e+00 ), ( 5.68648106130872e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 ), ( -6.10998899499222e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 ), ( 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 ), ( 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 ), ( -3.53783966258116e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 ), ( -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 ), ( -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 ), ( -7.78897366273473e-01 , 5.47909401918027e+00 , 2.48909074021990e+00 ), ( -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 ), ( -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 ), ( -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 ), ( -3.34173659956129e+00 , 9.09242156894625e-01 , 7.66376749024157e-01 ), ( -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 ), ( -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 ), ( -3.35601110578621e+00 , 7.08982263935927e-01 , 4.17614644200216e+00 ), ( -2.32477219663652e+00 , -2.67799335468032e-01 , 6.13612947330242e+00 ), ( -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 ), ( -5.35192634835997e+00 , 5.29009862298980e-01 , 7.17548197632397e+00 ), ( -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 ), ( -7.04702908508777e+00 , 4.30002272437194e+00 , 7.52014167082679e+00 ), ( -6.60462930316152e+00 , 3.17780650929998e+00 , 5.56735921475797e+00 ), ( -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 ), ( -4.00464293001050e+00 , 4.63648260149376e+00 , 7.28600629551502e+00 ) } +colvars: Step 37, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905549e-02 , -1.40858436164589e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.24325423950952e+00 , 3.53606340058551e-02 , -6.74071896755363e-01 , 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 7.01595064911501e+00 , -2.09226237248072e+00 , -8.23713639498105e-01 , 6.10178478736824e+00 , -3.17827591276146e-01 , 8.15561834792714e-01 , 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 , 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 , 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 , 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 , 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757519e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 , 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 , 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 , 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 , 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 , 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 , 2.01981272765406e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 2.09593922434932e+00 , -1.09517162307366e+00 , 2.02627695012513e+00 , 5.68648106130872e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 , -6.10998899499222e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 , 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 , -3.53783966258116e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 , -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 , -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -7.78897366273473e-01 , 5.47909401918027e+00 , 2.48909074021990e+00 , -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 , -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 , -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.34173659956129e+00 , 9.09242156894625e-01 , 7.66376749024157e-01 , -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 , -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 , -3.35601110578621e+00 , 7.08982263935927e-01 , 4.17614644200216e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -2.32477219663652e+00 , -2.67799335468032e-01 , 6.13612947330242e+00 , -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 , -5.35192634835997e+00 , 5.29009862298980e-01 , 7.17548197632397e+00 , -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 , -7.04702908508777e+00 , 4.30002272437194e+00 , 7.52014167082679e+00 , -6.60462930316152e+00 , 3.17780650929998e+00 , 5.56735921475797e+00 , -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 , -4.00464293001050e+00 , 4.63648260149376e+00 , 7.28600629551502e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99714865026614e-01 , 1.48066563993706e-02 , 1.23507319905549e-02 , -1.40858436164589e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.24325423950952e+00 , 3.53606340058551e-02 , -6.74071896755363e-01 , 6.87764039562635e+00 , -6.13039623935818e-01 , -4.93418615171616e-01 , 7.01595064911501e+00 , -2.09226237248072e+00 , -8.23713639498105e-01 , 6.10178478736824e+00 , -3.17827591276146e-01 , 8.15561834792714e-01 , 4.92454287699673e+00 , -1.41133925883134e-01 , 7.59991434056255e-01 , 6.77212219464218e+00 , -3.26924062641870e-01 , 1.97811919324091e+00 , 6.02851186400459e+00 , -2.54435198438978e-01 , 3.25102349614165e+00 , 7.11333468146805e+00 , -3.55414334664625e-01 , 4.39876800744377e+00 , 5.24059650966949e+00 , 1.05404297790640e+00 , 3.34292215620563e+00 , 4.12154496225479e+00 , 1.00327718001658e+00 , 3.80833594784917e+00 , 5.82111179018167e+00 , 2.24205658805729e+00 , 2.95850617757519e+00 , 5.12150674573125e+00 , 3.51483194082434e+00 , 2.84545181159567e+00 , 6.26411755216551e+00 , 4.42376279489110e+00 , 2.27791119712875e+00 , 3.86021045959326e+00 , 3.61935888194486e+00 , 1.99763722264245e+00 , 2.85315448267103e+00 , 4.15612389498969e+00 , 2.40585364632631e+00 , 3.89762635840233e+00 , 3.13679868389266e+00 , 7.82251857626469e-01 , 2.75151166136377e+00 , 3.14540216276767e+00 , -8.11517568588423e-02 , 3.14335535376885e+00 , 2.65955031448199e+00 , -1.51966823623054e+00 , 1.62632476565743e+00 , 2.28023184217949e+00 , 4.51375776136553e-01 , 4.31189985778254e-01 , 2.61083924649072e+00 , 4.19169024746188e-01 , 2.01981272765406e+00 , 1.10908349476627e+00 , 1.03619842713248e+00 , 1.29753518879670e+00 , 1.66772307296446e-01 , 1.66231666627899e+00 , 2.09593922434932e+00 , -1.09517162307366e+00 , 2.02627695012513e+00 , 5.68648106130872e-01 , 6.26752875040433e-01 , 2.93206632718867e+00 , -6.10998899499222e-01 , 3.58403709929558e-01 , 3.21417245612843e+00 , 1.28959552061232e+00 , 1.43485975951110e+00 , 3.78600759733201e+00 , 9.19169465945246e-01 , 1.98865620676103e+00 , 5.05971586890552e+00 , 2.03469278079062e+00 , 2.78222097271587e+00 , 5.72487648907329e+00 , -3.53783966258116e-01 , 2.88798100868500e+00 , 4.91829761919159e+00 , -1.11559807686627e+00 , 3.07334009617371e+00 , 5.89932024892110e+00 , -5.14618236723049e-01 , 3.47090982261960e+00 , 3.71805939963806e+00 , -1.45325678576191e+00 , 4.47756802299590e+00 , 3.41254980220807e+00 , -7.78897366273473e-01 , 5.47909401918027e+00 , 2.48909074021990e+00 , -2.75548750283942e+00 , 3.92515606943749e+00 , 2.71844784341367e+00 , -3.79004282585256e+00 , 4.60508859241757e+00 , 2.80749269823150e+00 , -2.71545289700286e+00 , 2.65396366733235e+00 , 2.34721559722457e+00 , -3.82534589607282e+00 , 1.78815485009757e+00 , 1.99251483642297e+00 , -3.34173659956129e+00 , 9.09242156894625e-01 , 7.66376749024157e-01 , -4.27463635076915e+00 , 1.01855272127941e+00 , 3.24215827961337e+00 , -5.41656294035798e+00 , 7.14405138192751e-01 , 3.36693402158753e+00 , -3.35601110578621e+00 , 7.08982263935927e-01 , 4.17614644200216e+00 , -3.66199545735369e+00 , 6.03753664064925e-02 , 5.45456574948844e+00 , -2.32477219663652e+00 , -2.67799335468032e-01 , 6.13612947330242e+00 , -4.48662567056949e+00 , 9.74341110344997e-01 , 6.42581921785737e+00 , -5.35192634835997e+00 , 5.29009862298980e-01 , 7.17548197632397e+00 , -6.27858144860994e+00 , 3.60027175877739e+00 , 6.79496390448224e+00 , -7.04702908508777e+00 , 4.30002272437194e+00 , 7.52014167082679e+00 , -6.60462930316152e+00 , 3.17780650929998e+00 , 5.56735921475797e+00 , -4.12105625702076e+00 , 2.25286072278065e+00 , 6.42932006136343e+00 , -4.79578085552801e+00 , 3.27443300712988e+00 , 7.19510333931396e+00 , -4.00464293001050e+00 , 4.63648260149376e+00 , 7.28600629551502e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 37. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 37. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atoms_new_colvar_forces = { ( -6.86992555484975e-02 , 3.03533865507726e-01 , -4.02549057467857e-01 ), ( 1.40856347083699e-02 , 3.16054533617280e-02 , -2.40108723882893e-01 ), ( -4.31377610411099e-02 , 9.58292762145927e-02 , 8.45772221147907e-02 ), ( -9.75869154560515e-02 , 2.50142296885573e-01 , 6.32383876309269e-02 ), ( -1.73276221003674e-02 , 9.79997153046433e-02 , -1.71639856633221e-01 ), ( 7.11709823308419e-02 , -1.85247971867427e-01 , -3.72684595182543e-02 ), ( 8.37449646163001e-03 , -9.85873004139697e-02 , 2.55249027610008e-01 ), ( -4.18999502863234e-02 , 5.98646644222403e-02 , 1.92995396989750e-01 ), ( 6.65453214330516e-02 , -1.91977552169553e-01 , 3.50417318547981e-02 ), ( 1.13198840831002e-01 , -3.91857648237532e-01 , 2.78086587467602e-01 ), ( 2.42685311116601e-02 , -9.92325269053166e-02 , 9.65872421316359e-02 ), ( 2.64701156863432e-02 , -9.73629786194262e-02 , 6.03536160863482e-02 ), ( 1.21863057138768e-02 , -5.57276902573276e-02 , 7.29140401008524e-02 ), ( 1.23620577888413e-02 , -5.35712074899439e-02 , 6.17139569187325e-02 ), ( 5.33950914573622e-03 , -3.50474741441834e-02 , 7.59433411582640e-02 ), ( -8.88281993356185e-03 , 9.51847849516848e-03 , 7.55785515708699e-02 ), ( -2.20759731463679e-03 , -2.87996413681196e-03 , 4.04933637879492e-02 ), ( -5.89828602420450e-03 , 9.72264454596844e-03 , 3.61036089633234e-02 ), ( 2.70697939545163e-03 , -1.32577794042573e-02 , 1.98338955000179e-02 ), ( 9.24941364417825e-03 , -2.25496043655818e-02 , -2.63902426068051e-02 ), ( 8.84119091067348e-03 , -2.40935956604268e-02 , -1.47161864940915e-02 ), ( 6.77327853075886e-03 , -1.38725010943118e-02 , -3.02535239169240e-02 ), ( 1.51393890116988e-02 , -4.69216812545931e-02 , -1.75516266427920e-03 ), ( 2.77524492898462e-02 , -8.86845708413806e-02 , 7.83766833850178e-03 ), ( 1.43255768269100e-02 , -4.69962060586814e-02 , 9.08675655639763e-03 ), ( 1.43093962067837e-02 , -4.41460571780061e-02 , -2.50001761113216e-03 ), ( 9.23731630260703e-03 , -3.70634757084186e-02 , 3.38363984449441e-02 ), ( -1.10699471847071e-03 , -1.50517238825784e-02 , 7.66243735456774e-02 ), ( -3.91421362763153e-03 , 4.28946728051718e-03 , 3.29098700792867e-02 ), ( -5.99053525305984e-03 , 1.14065895810092e-02 , 3.03281077571817e-02 ), ( -7.40598527053741e-03 , 1.79919911555435e-02 , 2.13931244285798e-02 ), ( -1.63384629373081e-02 , 5.20372766884959e-02 , -3.89721869762521e-03 ), ( -9.73183297611764e-03 , 3.57273056791312e-02 , -2.19055389368894e-02 ), ( -1.37676619415743e-02 , 5.00079066655862e-02 , -2.87728945664571e-02 ), ( -1.87701437763674e-03 , 1.46863241700003e-02 , -3.64889093585485e-02 ), ( 1.08859301674394e-02 , -1.63495717571680e-02 , -7.32330047742822e-02 ), ( 4.55998687637413e-03 , -1.09432736090076e-03 , -5.44924110293288e-02 ), ( 3.57956536940767e-03 , 5.71169649747292e-03 , -6.99712434611576e-02 ), ( 7.24739952063043e-03 , -1.50518827154553e-02 , -3.15090206351926e-02 ), ( 1.31215493743308e-02 , -4.14564908669139e-02 , 1.74314223554922e-03 ), ( 5.31212991272958e-04 , 1.75425920777897e-03 , -1.41362226136182e-02 ), ( 4.70616521599421e-04 , 3.37339310139407e-03 , -2.00531767539541e-02 ), ( -6.58732737457219e-03 , 2.06915304154358e-02 , -3.75933503541254e-04 ), ( -2.08104666769917e-02 , 5.81943213728344e-02 , 2.85028017920971e-02 ), ( -1.90464014201955e-02 , 6.35306924938405e-02 , -1.64163462385557e-02 ), ( -2.27747747072921e-02 , 7.55448881774991e-02 , -1.78830097269419e-02 ), ( -1.66885178805266e-02 , 7.23651669999104e-02 , -8.34994688828353e-02 ), ( -1.97355628115302e-02 , 8.64810282483968e-02 , -1.02483200962999e-01 ), ( -8.37997841556812e-03 , 4.63962179161769e-02 , -8.35596291533627e-02 ), ( -1.86179094057264e-02 , 6.68370515009344e-02 , -3.56468487901189e-02 ), ( -2.43191986518237e-02 , 9.28382805005677e-02 , -6.94669041832188e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 37, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 38, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 38, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 38, atoms_positions[size = 51] = { ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 ), ( 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 ), ( 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 ), ( 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 ), ( 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 ), ( 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 ), ( -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 ), ( -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 ), ( -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 ), ( -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 ), ( 8.23397334242518e+00 , 3.36629988416880e-02 , -6.69448059688789e-01 ), ( 7.02029295911993e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 ), ( 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545465e-01 ), ( 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 ), ( 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 ), ( 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 ), ( 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 ), ( 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522921e+00 ), ( 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 ), ( 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 ), ( 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 ), ( 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 ), ( 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868301e-01 ), ( 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 ), ( 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 ), ( 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 ), ( 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 ), ( 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 ), ( 5.67827189361793e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 ), ( -6.13967788582874e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 ), ( 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 ), ( 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 ), ( -3.51365065386001e-01 , 2.88588961715295e+00 , 4.91640875050461e+00 ), ( -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 ), ( -5.08771410005461e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 ), ( -7.81567996234714e-01 , 5.48701616412022e+00 , 2.48946663787882e+00 ), ( -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 ), ( -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 ), ( -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 ), ( -3.33868648611506e+00 , 9.16055538251034e-01 , 7.61631047253218e-01 ), ( -4.27757651872762e+00 , 1.01649290349518e+00 , 3.23714639246471e+00 ), ( -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 ), ( -3.35274399292602e+00 , 7.04100676066045e-01 , 4.17999176321871e+00 ), ( -2.31549361557949e+00 , -2.60750067046287e-01 , 6.13988294900186e+00 ), ( -4.48330176893684e+00 , 9.82575531416185e-01 , 6.42533908148497e+00 ), ( -5.35180750527742e+00 , 5.21809458288690e-01 , 7.17126620866168e+00 ), ( -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304485e+00 ), ( -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 ), ( -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 ), ( -4.12563405115866e+00 , 2.25335610553220e+00 , 6.43205928200358e+00 ), ( -4.00561105971607e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ) } +colvars: Step 38, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_ids[size = 0] = +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: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "one", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865608e-02 , 1.20819700460900e-02 , -1.38821562016639e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.23397334242518e+00 , 3.36629988416880e-02 , -6.69448059688789e-01 , 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 7.02029295911993e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 , 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545465e-01 , 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 , 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 , 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 , 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522921e+00 , 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 , 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 , 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 , 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868301e-01 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 , 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 , 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 , 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 , 5.67827189361793e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 , -6.13967788582874e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 , 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 , -3.51365065386001e-01 , 2.88588961715295e+00 , 4.91640875050461e+00 , -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 , -5.08771410005461e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -7.81567996234714e-01 , 5.48701616412022e+00 , 2.48946663787882e+00 , -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 , -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 , -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.33868648611506e+00 , 9.16055538251034e-01 , 7.61631047253218e-01 , -4.27757651872762e+00 , 1.01649290349518e+00 , 3.23714639246471e+00 , -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 , -3.35274399292602e+00 , 7.04100676066045e-01 , 4.17999176321871e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -2.31549361557949e+00 , -2.60750067046287e-01 , 6.13988294900186e+00 , -4.48330176893684e+00 , 9.82575531416185e-01 , 6.42533908148497e+00 , -5.35180750527742e+00 , 5.21809458288690e-01 , 7.17126620866168e+00 , -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304485e+00 , -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 , -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 , -4.12563405115866e+00 , 2.25335610553220e+00 , 6.43205928200358e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 , -4.00561105971607e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ). +colvars: Calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99723286500429e-01 , 1.46513537865608e-02 , 1.20819700460900e-02 , -1.38821562016639e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.23397334242518e+00 , 3.36629988416880e-02 , -6.69448059688789e-01 , 6.87495146528438e+00 , -6.13810179280311e-01 , -4.87350711114379e-01 , 7.02029295911993e+00 , -2.09697424866983e+00 , -8.16867224790344e-01 , 6.10189750287780e+00 , -3.15299729132043e-01 , 8.12402925545465e-01 , 4.91749577976549e+00 , -1.40300604404045e-01 , 7.62147778441498e-01 , 6.76611237147668e+00 , -3.28625649245759e-01 , 1.97752930645271e+00 , 6.03135502824184e+00 , -2.55695811256309e-01 , 3.26239710996336e+00 , 7.10884951426596e+00 , -3.58590493720709e-01 , 4.40325238239853e+00 , 5.23737604359663e+00 , 1.05392999654092e+00 , 3.34267002830215e+00 , 4.11788691979984e+00 , 1.00438985164907e+00 , 3.81694332522921e+00 , 5.81760126608442e+00 , 2.24278168580790e+00 , 2.95639177799916e+00 , 5.12187465946914e+00 , 3.51099230343068e+00 , 2.84118951825235e+00 , 6.25759501004995e+00 , 4.41786704945890e+00 , 2.27698200468750e+00 , 3.86209947339393e+00 , 3.61644049304222e+00 , 1.99530925186943e+00 , 2.85799527858893e+00 , 4.15434234892396e+00 , 2.40308270028296e+00 , 3.89833504881930e+00 , 3.12862361416268e+00 , 7.87787442868301e-01 , 2.74773948632418e+00 , 3.15810727647984e+00 , -8.62470827556785e-02 , 3.14603981522959e+00 , 2.66142490305053e+00 , -1.51373536771568e+00 , 1.64043269739871e+00 , 2.28911609768493e+00 , 4.59046151148791e-01 , 4.34099529714510e-01 , 2.60994675964043e+00 , 4.13168219645865e-01 , 2.01715907384165e+00 , 1.11071119332182e+00 , 1.02953228839135e+00 , 1.30077517136529e+00 , 1.66741691585175e-01 , 1.66394221975421e+00 , 2.09713602382649e+00 , -1.09506363207455e+00 , 2.02216373350857e+00 , 5.67827189361793e-01 , 6.31901382794820e-01 , 2.93187243096503e+00 , -6.13967788582874e-01 , 3.58395715502606e-01 , 3.21767706019277e+00 , 1.29192182941583e+00 , 1.43831495594354e+00 , 3.78771587713980e+00 , 9.22097757526462e-01 , 1.99163166107716e+00 , 5.06438067679724e+00 , 2.03000872022742e+00 , 2.78583436560323e+00 , 5.72561240280103e+00 , -3.51365065386001e-01 , 2.88588961715295e+00 , 4.91640875050461e+00 , -1.11524582990740e+00 , 3.07362866358296e+00 , 5.89947245140629e+00 , -5.08771410005461e-01 , 3.46244639424936e+00 , 3.70945863553544e+00 , -1.45709473720248e+00 , 4.47897852276886e+00 , 3.40832541281407e+00 , -7.81567996234714e-01 , 5.48701616412022e+00 , 2.48946663787882e+00 , -2.75640498094059e+00 , 3.92381285210018e+00 , 2.71636477219835e+00 , -3.78718457605269e+00 , 4.60936399633531e+00 , 2.80466649499731e+00 , -2.71762546207420e+00 , 2.65628806445677e+00 , 2.34362419710604e+00 , -3.82716365577601e+00 , 1.78113191282633e+00 , 1.98858500377438e+00 , -3.33868648611506e+00 , 9.16055538251034e-01 , 7.61631047253218e-01 , -4.27757651872762e+00 , 1.01649290349518e+00 , 3.23714639246471e+00 , -5.41098004365145e+00 , 7.08239404802630e-01 , 3.37156309238238e+00 , -3.35274399292602e+00 , 7.04100676066045e-01 , 4.17999176321871e+00 , -3.66166853640506e+00 , 5.78854680676899e-02 , 5.44735153195078e+00 , -2.31549361557949e+00 , -2.60750067046287e-01 , 6.13988294900186e+00 , -4.48330176893684e+00 , 9.82575531416185e-01 , 6.42533908148497e+00 , -5.35180750527742e+00 , 5.21809458288690e-01 , 7.17126620866168e+00 , -6.27194845198585e+00 , 3.59938249842601e+00 , 6.80518266304485e+00 , -7.05165719900996e+00 , 4.29737299037050e+00 , 7.51752147267413e+00 , -6.60431920131686e+00 , 3.18029491516661e+00 , 5.57022721273918e+00 , -4.12563405115866e+00 , 2.25335610553220e+00 , 6.43205928200358e+00 , -4.79230652547135e+00 , 3.27021253565706e+00 , 7.18706754003824e+00 , -4.00561105971607e+00 , 4.64635007557036e+00 , 7.28658740660872e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 38. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 38. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atoms_new_colvar_forces = { ( -6.86308206116252e-02 , 3.03483614991524e-01 , -4.03005467230188e-01 ), ( 1.42122004866687e-02 , 3.13538650225891e-02 , -2.40194902047227e-01 ), ( -4.31943237080591e-02 , 9.58453152835205e-02 , 8.47803175901870e-02 ), ( -9.77245156213514e-02 , 2.50405352501500e-01 , 6.31588211970295e-02 ), ( -1.72933931549216e-02 , 9.79973607673579e-02 , -1.71917156945550e-01 ), ( 7.12727321448884e-02 , -1.85456026954594e-01 , -3.71593100693835e-02 ), ( 8.29430983007038e-03 , -9.84834160035740e-02 , 2.55547810067643e-01 ), ( -4.20368158050723e-02 , 6.01617567264364e-02 , 1.92950990770399e-01 ), ( 6.65945023408876e-02 , -1.92024618939844e-01 , 3.50027046417249e-02 ), ( 1.13228932734361e-01 , -3.91964986992019e-01 , 2.78494124440071e-01 ), ( 2.42883201820209e-02 , -9.91987813394095e-02 , 9.66416199757185e-02 ), ( 2.64947648348944e-02 , -9.73364338961822e-02 , 6.04259622476607e-02 ), ( 1.21928076457344e-02 , -5.57068145202949e-02 , 7.29639460351481e-02 ), ( 1.23703282478627e-02 , -5.35520485838742e-02 , 6.17540627985406e-02 ), ( 5.33680830935802e-03 , -3.50306520250387e-02 , 7.59952094602464e-02 ), ( -8.90361352233684e-03 , 9.52588864838625e-03 , 7.56268806698402e-02 ), ( -2.21620231280116e-03 , -2.87498061072686e-03 , 4.05318787135928e-02 ), ( -5.91053580061552e-03 , 9.72490617764340e-03 , 3.61297622980792e-02 ), ( 2.70583315529538e-03 , -1.32544772276848e-02 , 1.98831553338981e-02 ), ( 9.25989089906253e-03 , -2.25524231939904e-02 , -2.63282702430854e-02 ), ( 8.85153296477521e-03 , -2.40929295219061e-02 , -1.46774587577451e-02 ), ( 6.78281666744159e-03 , -1.38760216221009e-02 , -3.02237522299002e-02 ), ( 1.51566055711864e-02 , -4.69141735790476e-02 , -1.71412442695694e-03 ), ( 2.77851147346442e-02 , -8.86665700485733e-02 , 7.87857868564022e-03 ), ( 1.43422027572355e-02 , -4.69856650191699e-02 , 9.10461085344262e-03 ), ( 1.43275767180269e-02 , -4.41374431611392e-02 , -2.49197110163824e-03 ), ( 9.24541543566430e-03 , -3.70509593640707e-02 , 3.38517921818640e-02 ), ( -1.11514134289469e-03 , -1.50363761218496e-02 , 7.66272962861233e-02 ), ( -3.92164379332092e-03 , 4.29421869707043e-03 , 3.29027198923366e-02 ), ( -5.99967910186777e-03 , 1.14100882546170e-02 , 3.03085239625798e-02 ), ( -7.41733786811937e-03 , 1.79915865282469e-02 , 2.13927487362460e-02 ), ( -1.63594388549171e-02 , 5.20252755586254e-02 , -3.89310930664074e-03 ), ( -9.74187732357992e-03 , 3.57167216706750e-02 , -2.19161002769431e-02 ), ( -1.37816216212824e-02 , 4.99938096396475e-02 , -2.87951941243782e-02 ), ( -1.87625613950851e-03 , 1.46773844030486e-02 , -3.64899362824451e-02 ), ( 1.09056209410313e-02 , -1.63583620058829e-02 , -7.32229830172713e-02 ), ( 4.57146300390366e-03 , -1.10195764427398e-03 , -5.45081993441415e-02 ), ( 3.59163170697864e-03 , 5.70061800575523e-03 , -6.99959399808052e-02 ), ( 7.26041751542733e-03 , -1.50528004946293e-02 , -3.15254859290255e-02 ), ( 1.31397398961161e-02 , -4.14460138981812e-02 , 1.71931122698228e-03 ), ( 5.35631856761175e-04 , 1.75395146515923e-03 , -1.41785278298944e-02 ), ( 4.76117787198405e-04 , 3.37239514763842e-03 , -2.01064513441219e-02 ), ( -6.59324679933045e-03 , 2.06893842474070e-02 , -4.18476613147348e-04 ), ( -2.08366128212283e-02 , 5.81893019564110e-02 , 2.84506088586251e-02 ), ( -1.90659163881719e-02 , 6.35178090703330e-02 , -1.64772486067613e-02 ), ( -2.27982067233440e-02 , 7.55299015632438e-02 , -1.79567088892806e-02 ), ( -1.66994361211408e-02 , 7.23394764221847e-02 , -8.35574744904818e-02 ), ( -1.97484391686672e-02 , 8.64495918792104e-02 , -1.02547043382609e-01 ), ( -8.38045756030614e-03 , 4.63758256138757e-02 , -8.36129911674442e-02 ), ( -1.86357970883621e-02 , 6.68198521875454e-02 , -3.56982452867785e-02 ), ( -2.43419891146704e-02 , 9.28096803384051e-02 , -6.95109079997762e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 38, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 39, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 39, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 39, atoms_positions[size = 51] = { ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 ), ( 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 ), ( 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 ), ( 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 ), ( 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 ), ( 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 ), ( -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 ), ( -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 ), ( -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 ), ( -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 ), ( 8.22446419823708e+00 , 3.18649479383647e-02 , -6.64989816298089e-01 ), ( 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 ), ( 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254842e-01 ), ( 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 ), ( 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 ), ( 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 ), ( 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 ), ( 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 ), ( 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 ), ( 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 ), ( 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 ), ( 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991724e+00 ), ( 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 ), ( 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 ), ( 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528188e-01 ), ( 4.37681313203301e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 ), ( 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 ), ( 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 ), ( 5.67045576176347e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 ), ( -6.16431681139152e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 ), ( 1.29461765027048e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 ), ( 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 ), ( -3.48478472967697e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 ), ( -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 ), ( -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 ), ( -7.83422856191325e-01 , 5.49518347305934e+00 , 2.48952532366078e+00 ), ( -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 ), ( -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 ), ( -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 ), ( -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 ), ( -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 ), ( -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 ), ( -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 ), ( -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 ), ( -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 ), ( -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 ), ( -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 ), ( -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 ), ( -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 ), ( -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 ), ( -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ) } +colvars: Step 39, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: [1/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating gradients of colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.22446419823708e+00 , 3.18649479383647e-02 , -6.64989816298089e-01 , 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 , 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254842e-01 , 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 , 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 , 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 , 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 , 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 , 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 , 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991724e+00 , 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 , 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528188e-01 , 4.37681313203301e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 , 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 , 5.67045576176347e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 , -6.16431681139152e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 , 1.29461765027048e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 , -3.48478472967697e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 , -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 , -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -7.83422856191325e-01 , 5.49518347305934e+00 , 2.48952532366078e+00 , -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 , -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 , -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 , -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 , -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 , -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 , -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 , -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 , -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 , -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 , -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 , -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 , -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ). +colvars: Done calculating colvar "main". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99731715211329e-01 , 1.44685704498021e-02 , 1.18258865135862e-02 , -1.36859956861529e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.22446419823708e+00 , 3.18649479383647e-02 , -6.64989816298089e-01 , 6.87157498333425e+00 , -6.13675422114814e-01 , -4.80775874116678e-01 , 7.02512809690057e+00 , -2.10177651263430e+00 , -8.10353649285075e-01 , 6.10347881602634e+00 , -3.14111133215889e-01 , 8.08620807254842e-01 , 4.90951586819433e+00 , -1.39174597408468e-01 , 7.64205571343543e-01 , 6.75967912376300e+00 , -3.29719511254224e-01 , 1.97717689209792e+00 , 6.03584651544874e+00 , -2.56617724209356e-01 , 3.27237784883838e+00 , 7.10356773210695e+00 , -3.61648239935162e-01 , 4.40786888296440e+00 , 5.23476284386090e+00 , 1.05404253320047e+00 , 3.34338065865323e+00 , 4.11387917782663e+00 , 1.00585174822796e+00 , 3.82541674848885e+00 , 5.81339254735295e+00 , 2.24322100046206e+00 , 2.95431975882808e+00 , 5.12298146209666e+00 , 3.50813544845299e+00 , 2.83712709500752e+00 , 6.25102951018724e+00 , 4.41249148876516e+00 , 2.27529791290682e+00 , 3.86473959226473e+00 , 3.61351935232975e+00 , 1.99350561105418e+00 , 2.86243185237433e+00 , 4.15272030722413e+00 , 2.40067179991724e+00 , 3.89930712935003e+00 , 3.12050153326183e+00 , 7.92469627135085e-01 , 2.74468414526742e+00 , 3.17100784708891e+00 , -9.21054029925343e-02 , 3.14832911577605e+00 , 2.66257363037078e+00 , -1.50810562408364e+00 , 1.65258828990459e+00 , 2.29731686737542e+00 , 4.67056353528188e-01 , 4.37681313203301e-01 , 2.60898394417790e+00 , 4.07267809645518e-01 , 2.01625769509659e+00 , 1.11456398060063e+00 , 1.02137791807099e+00 , 1.30134291871749e+00 , 1.65124561639393e-01 , 1.66688264750346e+00 , 2.09838710685538e+00 , -1.09504095669704e+00 , 2.01773344297118e+00 , 5.67045576176347e-01 , 6.37854737588134e-01 , 2.93300732368685e+00 , -6.16431681139152e-01 , 3.58395117129089e-01 , 3.22070919727440e+00 , 1.29461765027048e+00 , 1.44108174336442e+00 , 3.78851433862067e+00 , 9.23601384288891e-01 , 1.99465895288051e+00 , 5.06889704417693e+00 , 2.02683325967789e+00 , 2.78974383813576e+00 , 5.72677334241935e+00 , -3.48478472967697e-01 , 2.88375450522735e+00 , 4.91591248425235e+00 , -1.11449074228904e+00 , 3.07387251773988e+00 , 5.89863103463398e+00 , -5.03205586227219e-01 , 3.45366813907574e+00 , 3.70091297429332e+00 , -1.46198923284115e+00 , 4.48031715232442e+00 , 3.40319926113213e+00 , -7.83422856191325e-01 , 5.49518347305934e+00 , 2.48952532366078e+00 , -2.75719288661495e+00 , 3.92377465660900e+00 , 2.71671681985500e+00 , -3.78410368192332e+00 , 4.61312152041393e+00 , 2.80132425973028e+00 , -2.71971532554703e+00 , 2.65755695955288e+00 , 2.33911063249870e+00 , -3.82819415986158e+00 , 1.77494421812315e+00 , 1.98445990283311e+00 , -3.33555341340174e+00 , 9.23051989092354e-01 , 7.57539942689171e-01 , -4.27884524745475e+00 , 1.01447009982099e+00 , 3.23166589702991e+00 , -5.40680224570339e+00 , 7.01759842820932e-01 , 3.37647557412863e+00 , -3.34976062208996e+00 , 6.99485565685801e-01 , 4.18343622948658e+00 , -3.66146058229158e+00 , 5.61986142826153e-02 , 5.44089379923339e+00 , -2.30616158940055e+00 , -2.54299022897329e-01 , 6.14408467519650e+00 , -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 , -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 , -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 , -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 , -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 , -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 , -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 39. +colvars: colvarmodule::write_traj_files() +colvars: Using colvarproxy_namd::output_stream() +colvars: colvarmodule::end_of_step(), step = 39. +colvars: End of step for colvar "one". +colvars: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atoms_new_colvar_forces = { ( -6.85760792996514e-02 , 3.03391190372132e-01 , -4.03470465038437e-01 ), ( 1.43266319462627e-02 , 3.10765577955413e-02 , -2.40273727195948e-01 ), ( -4.32418115472581e-02 , 9.58623311770647e-02 , 8.49822855712108e-02 ), ( -9.78506393239423e-02 , 2.50668249779756e-01 , 6.30654919349158e-02 ), ( -1.72669714438695e-02 , 9.79803550809251e-02 , -1.72197348799224e-01 ), ( 7.13666644571403e-02 , -1.85663666663477e-01 , -3.70401934232006e-02 ), ( 8.22663282605456e-03 , -9.83576242859786e-02 , 2.55846331786987e-01 ), ( -4.21617012069781e-02 , 6.04769641875639e-02 , 1.92897427331650e-01 ), ( 6.66383033413408e-02 , -1.92060723280848e-01 , 3.49703055971522e-02 ), ( 1.13262969450725e-01 , -3.92040115424842e-01 , 2.78915680074420e-01 ), ( 2.43120615818261e-02 , -9.91687871383143e-02 , 9.67014422689912e-02 ), ( 2.65210286567995e-02 , -9.73126436762223e-02 , 6.04989195122588e-02 ), ( 1.22019876372008e-02 , -5.56854705073975e-02 , 7.30166371651342e-02 ), ( 1.23809460844627e-02 , -5.35335097256021e-02 , 6.17968896446734e-02 ), ( 5.33680866413097e-03 , -3.50104986769917e-02 , 7.60494168987403e-02 ), ( -8.92180929547345e-03 , 9.54178500425501e-03 , 7.56767473291032e-02 ), ( -2.22371115869815e-03 , -2.86513208581138e-03 , 4.05702084627808e-02 ), ( -5.92164461686847e-03 , 9.73218229005274e-03 , 3.61562278670125e-02 ), ( 2.70448252725674e-03 , -1.32471106341959e-02 , 1.99297111740999e-02 ), ( 9.26749253439036e-03 , -2.25524145633818e-02 , -2.62739003345519e-02 ), ( 8.86020893235890e-03 , -2.40916843932129e-02 , -1.46430826543643e-02 ), ( 6.79008106829279e-03 , -1.38790942151789e-02 , -3.01990451011923e-02 ), ( 1.51728533578123e-02 , -4.69082884526167e-02 , -1.67599335757658e-03 ), ( 2.78174735877192e-02 , -8.86550992426879e-02 , 7.91844579743057e-03 ), ( 1.43590192425672e-02 , -4.69788314968345e-02 , 9.12269597050373e-03 ), ( 1.43455946611162e-02 , -4.41335513916129e-02 , -2.48380726608011e-03 ), ( 9.25500305278823e-03 , -3.70404219689551e-02 , 3.38695002708129e-02 ), ( -1.11936165716940e-03 , -1.50202702602189e-02 , 7.66368011977586e-02 ), ( -3.92721222202761e-03 , 4.29975912649859e-03 , 3.28989332702641e-02 ), ( -6.00679980196899e-03 , 1.14138917306432e-02 , 3.02930976450661e-02 ), ( -7.42765119826019e-03 , 1.79940255100833e-02 , 2.13937723184561e-02 ), ( -1.63809278079067e-02 , 5.20200431521571e-02 , -3.89101834427696e-03 ), ( -9.75291630201698e-03 , 3.57088137252074e-02 , -2.19283949849110e-02 ), ( -1.37966814091787e-02 , 4.99827360070345e-02 , -2.88190408100287e-02 ), ( -1.87740684913845e-03 , 1.46690549469220e-02 , -3.64943197340017e-02 ), ( 1.09213485123972e-02 , -1.63703636169440e-02 , -7.32197132080786e-02 ), ( 4.58054909200224e-03 , -1.11301381598286e-03 , -5.45270632193023e-02 ), ( 3.60071564144862e-03 , 5.68556530723009e-03 , -7.00243396038003e-02 ), ( 7.27230082340125e-03 , -1.50582502822534e-02 , -3.15426687678145e-02 ), ( 1.31588021489714e-02 , -4.14431027325794e-02 , 1.69893986732982e-03 ), ( 5.40413457436425e-04 , 1.74904516444122e-03 , -1.42180257520665e-02 ), ( 4.81955385624934e-04 , 3.36568253909036e-03 , -2.01564103345880e-02 ), ( -6.59816426575165e-03 , 2.06853833091742e-02 , -4.57496077723089e-04 ), ( -2.08601693150008e-02 , 5.81869588982627e-02 , 2.84043742803996e-02 ), ( -1.90849481901457e-02 , 6.35059990249224e-02 , -1.65352950682017e-02 ), ( -2.28209467504911e-02 , 7.55161082636293e-02 , -1.80267509733149e-02 ), ( -1.67134328831537e-02 , 7.23142221324330e-02 , -8.36188006345148e-02 ), ( -1.97652753228755e-02 , 8.64191632927915e-02 , -1.02615606437546e-01 ), ( -8.38403595659016e-03 , 4.63531251980092e-02 , -8.36694766979938e-02 ), ( -1.86544506501744e-02 , 6.68045394632732e-02 , -3.57494057868077e-02 ), ( -2.43675801969379e-02 , 9.27859360530459e-02 , -6.95588936316067e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 39, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 } +colvars: Step 40, atoms_masses[size = 51] = { 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 12.011, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 14.007, 12.011, 12.011, 15.999, 12.011, 15.999, 14.007, 14.007, 12.011 } +colvars: Step 40, atoms_charges[size = 51] = { -0.1, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, -0.62, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, -0.47, -0.27, 0.51, -0.51, 0.55, -0.55, -0.62, -0.47, -0.27 } +colvars: Step 40, atoms_positions[size = 51] = { ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 ), ( 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 ), ( 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 ), ( 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 ), ( 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 ), ( 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 ), ( -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 ), ( -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 ), ( -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 ), ( -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ), ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 ), ( 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 ), ( 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 ), ( 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 ), ( 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 ), ( 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 ), ( 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 ), ( 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 ), ( 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 ), ( 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 ), ( 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 ), ( 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 ), ( 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 ), ( 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 ), ( 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 ), ( 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 ), ( 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 ), ( 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 ), ( 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 ), ( -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 ), ( 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 ), ( 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 ), ( -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 ), ( -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 ), ( -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 ), ( -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 ), ( -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 ), ( -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 ), ( -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 ), ( -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 ), ( -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 ), ( -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 ), ( -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 ), ( -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 ), ( -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 ), ( -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 ), ( -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 ), ( -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 ), ( -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 ), ( -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 ), ( -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ) } +colvars: Step 40, atoms_total_forces[size = 51] = { ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ), ( 0.00000000000000e+00 , 0.00000000000000e+00 , 0.00000000000000e+00 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_ids[size = 0] = +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: [3/4]: calc_colvars_items_smp(), first = 1, last = 1, cv = main, cvc = 0 +colvars: Calculating colvar "main", components 0 through 1. +colvars: Calculating colvar components. +colvars: Calculating colvar components. +colvars: [1/4]: calc_colvars_items_smp(), first = 2, last = 2, cv = fitting, cvc = 0 +colvars: Calculating colvar "fitting", components 0 through 1. +colvars: Calculating colvar components. +colvars: Colvar component no. 1 within colvar "main" has value ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ). +colvars: Calculating gradients of colvar "main". +colvars: Done calculating gradients of colvar "main". +colvars: Done calculating colvar "main". +colvars: Colvar component no. 1 within colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629674e-02 , 1.15959419288222e-02 , -1.35102502789137e-02 ). +colvars: Calculating gradients of colvar "one". +colvars: Calculating fit gradients. +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Colvar component no. 1 within colvar "fitting" has value ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 , 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 , 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 , 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 , 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 , 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 , 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 , 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 , 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 , 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 , 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 , 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 , 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 , 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 , 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 , -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 , 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 , -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 , -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 , -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 , -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 , -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 , -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 , -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 , -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 , -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 , -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 , -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 , -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 , -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 , -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 , -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 , -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ). +colvars: ( 0 , 0 , 0 ) +colvars: Calculating gradients of colvar "fitting". +colvars: Done calculating gradients of colvar "fitting". +colvars: Done calculating colvar "fitting". +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: ( 0 , 0 , 0 ) +colvars: Done calculating fit gradients. +colvars: Done calculating gradients of colvar "one". +colvars: Done calculating colvar "one". +colvars: Calculating colvar "one"'s properties. +colvars: Colvar "one" has value ( 9.99739707661452e-01 , 1.42661905629674e-02 , 1.15959419288222e-02 , -1.35102502789137e-02 ). +colvars: Done calculating colvar "one"'s properties. +colvars: Calculating colvar "main"'s properties. +colvars: Colvar "main" has value ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 ). +colvars: Done calculating colvar "main"'s properties. +colvars: Calculating colvar "fitting"'s properties. +colvars: Colvar "fitting" has value ( 8.21486247008991e+00 , 3.00039497048974e-02 , -6.60697462712691e-01 , 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 7.03023272897269e+00 , -2.10658024555681e+00 , -8.04136728435112e-01 , 6.10591660712888e+00 , -3.14205944761017e-01 , 8.04504142528586e-01 , 4.90090775892793e+00 , -1.37782672034107e-01 , 7.66123043173235e-01 , 6.75298740911122e+00 , -3.30248914398086e-01 , 1.97716536336984e+00 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 , 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 , 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 , 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 , 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 , 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 , 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 , 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 , 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 , 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 , 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 , -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 , 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 , -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 , -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 , -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 , -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 , -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 , -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 , -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 , -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 , -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 , -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 , -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 , -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 , -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 , -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 , -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 , -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ). +colvars: Done calculating colvar "fitting"'s properties. +colvars: Updating collective variable biases. +colvars: [0/4]: calc_cv_biases_smp(), first = 0, last = 0, bias = harmonic1 +colvars: Updating the harmonic bias "harmonic1". +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: Updating colvar "main". +colvars: Done updating colvar "main". +colvars: Updating colvar "fitting". +colvars: Done updating colvar "fitting". +colvars: Adding total colvar energy: 0 +colvars: Communicating forces from the colvars to the atoms. +colvars: Communicating forces from colvar "one". +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: 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 applying force on the fitting group of main group: +colvars: Done communicating forces from colvar "one". +colvars: colvarmodule::analyze(), step = 40. +colvars: colvarmodule::write_traj_files() +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: End of step for colvar "main". +colvars: End of step for colvar "fitting". +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atoms_new_colvar_forces = { ( -6.85323667607087e-02 , 3.03250085633828e-01 , -4.03919244566743e-01 ), ( 1.44250120644039e-02 , 3.07866206325814e-02 , -2.40338909060198e-01 ), ( -4.32788268105407e-02 , 9.58815639835369e-02 , 8.51648417941772e-02 ), ( -9.79580001908216e-02 , 2.50912438003103e-01 , 6.29556416781233e-02 ), ( -1.72472401057155e-02 , 9.79440595116233e-02 , -1.72462588377445e-01 ), ( 7.14471883024387e-02 , -1.85855959156371e-01 , -3.69125172216921e-02 ), ( 8.17196163325191e-03 , -9.82110268157001e-02 , 2.56124884008762e-01 ), ( -4.22690273374394e-02 , 6.07920779777388e-02 , 1.92835186870276e-01 ), ( 6.66737009441523e-02 , -1.92081954588494e-01 , 3.49538806817384e-02 ), ( 1.13294551779846e-01 , -3.92067691417467e-01 , 2.79333500624614e-01 ), ( 2.43381070971489e-02 , -9.91435684382055e-02 , 9.67656042693871e-02 ), ( 2.65474804688020e-02 , -9.72928771737139e-02 , 6.05706743700988e-02 ), ( 1.22130220545263e-02 , -5.56644363052378e-02 , 7.30706999847849e-02 ), ( 1.23930794636728e-02 , -5.35162574221356e-02 , 6.18414015927799e-02 ), ( 5.33908232466114e-03 , -3.49877052428895e-02 , 7.61042263482980e-02 ), ( -8.93702422432010e-03 , 9.56574591985604e-03 , 7.57260345722720e-02 ), ( -2.22998076945107e-03 , -2.85083274124681e-03 , 4.06068065590374e-02 ), ( -5.93131133315949e-03 , 9.74426221995694e-03 , 3.61818108984666e-02 ), ( 2.70298600701360e-03 , -1.32362980851642e-02 , 1.99717264345225e-02 ), ( 9.27227028404927e-03 , -2.25504503061480e-02 , -2.62293277894644e-02 ), ( 8.86706074728803e-03 , -2.40904542112200e-02 , -1.46143142955974e-02 ), ( 6.79506980951520e-03 , -1.38821750859600e-02 , -3.01804053172094e-02 ), ( 1.51875404530745e-02 , -4.69047478317859e-02 , -1.64186260049470e-03 ), ( 2.78481343112598e-02 , -8.86510812523362e-02 , 7.95666205544640e-03 ), ( 1.43752539372569e-02 , -4.69761437538033e-02 , 9.14083867651916e-03 ), ( 1.43626830924914e-02 , -4.41347053823264e-02 , -2.47532915565276e-03 ), ( 9.26543336548818e-03 , -3.70321914229108e-02 , 3.38893091282548e-02 ), ( -1.12004885949659e-03 , -1.50034226484375e-02 , 7.66528774929137e-02 ), ( -3.93094451591356e-03 , 4.30623483933488e-03 , 3.28987164124701e-02 ), ( -6.01187124969791e-03 , 1.14183247352518e-02 , 3.02824521939554e-02 ), ( -7.43662755693067e-03 , 1.79994313113881e-02 , 2.13959799540316e-02 ), ( -1.64019199467728e-02 , 5.20217936348420e-02 , -3.89171641232289e-03 ), ( -9.76431618508571e-03 , 3.57038612670259e-02 , -2.19423983487685e-02 ), ( -1.38120095259618e-02 , 4.99751669683367e-02 , -2.88441005754843e-02 ), ( -1.88013590503811e-03 , 1.46613779011853e-02 , -3.65021572613942e-02 ), ( 1.09330016456256e-02 , -1.63858682409413e-02 , -7.32233385220953e-02 ), ( 4.58720889823014e-03 , -1.12738473805356e-03 , -5.45483074608206e-02 ), ( 3.60687333466524e-03 , 5.66676925795172e-03 , -7.00554557812025e-02 ), ( 7.28270763577972e-03 , -1.50681561528744e-02 , -3.15597043389583e-02 ), ( 1.31777917031141e-02 , -4.14476897041726e-02 , 1.68346700673701e-03 ), ( 5.45322168857212e-04 , 1.74002562910157e-03 , -1.42530289183739e-02 ), ( 4.87858268944153e-04 , 3.35386962129516e-03 , -2.02009403001517e-02 ), ( -6.60198593674321e-03 , 2.06801299134617e-02 , -4.91529279330374e-04 ), ( -2.08804561740570e-02 , 5.81882353586720e-02 , 2.83654816899834e-02 ), ( -1.91027000722412e-02 , 6.34962788800136e-02 , -1.65887744997137e-02 ), ( -2.28420590270769e-02 , 7.55047340022036e-02 , -1.80910514907058e-02 ), ( -1.67294107746415e-02 , 7.22903490015903e-02 , -8.36818944736092e-02 ), ( -1.97847172876338e-02 , 8.63908043813335e-02 , -1.02687251415262e-01 ), ( -8.39007040909996e-03 , 4.63288740292679e-02 , -8.37274147395396e-02 ), ( -1.86729126279069e-02 , 6.67920120077291e-02 , -3.57990212161275e-02 ), ( -2.43944182091028e-02 , 9.27679514953860e-02 , -6.96101218792904e-02 ) } +colvars: ---------------------------------------------------------------------- +colvars: Step 40, atom_groups_new_colvar_forces = +colvars: ---------------------------------------------------------------------- +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..05eb9d8b8 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,27 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x ( 0.99973970766145 , 0.014266190562967 , 0.011595941928822 , -0.013510250278914 ) +} + +colvar { + name main + x ( 6.8676208645464 , -0.61271733826672 , -0.47391111954395 , 6.0417423917699 , -0.2572065757875 , 3.280691671575 , 5.1246111101011 , 3.5063531103509 , 2.8331884221988 , 2.7427331318038 , 3.183939270326 , -0.098522041714588 , 1.299268032236 , 0.16207979639779 , 1.6709575658416 , 0.92364152112933 , 1.9975665777803 , 5.0731192588566 , -1.4675941518372 , 4.4813585508814 , 3.3973074276517 , -3.8283620698119 , 1.7699294118509 , 1.9801964665289 , -3.6613128207809 , 0.055525971668209 , 5.4356378032103 , -4.7872153127373 , 3.2636042470594 , 7.1751730326322 ) +} + +colvar { + name fitting + x ( 8.2148624700899 , 0.030003949704897 , -0.66069746271269 , 6.8676208645464 , -0.61271733826672 , -0.47391111954395 , 7.0302327289727 , -2.1065802455568 , -0.80413672843511 , 6.1059166071289 , -0.31420594476102 , 0.80450414252859 , 4.9009077589279 , -0.13778267203411 , 0.76612304317323 , 6.7529874091112 , -0.33024891439809 , 1.9771653633698 , 6.0417423917699 , -0.2572065757875 , 3.280691671575 , 7.0976664348158 , -0.36443719008101 , 4.4126033869916 , 5.2325979411613 , 1.0543652658116 , 3.345239990687 , 4.1096502105894 , 1.0076564480121 , 3.8336836889602 , 5.8085825883195 , 2.2431337878562 , 2.9523153959534 , 5.1246111101011 , 3.5063531103509 , 2.8331884221988 , 6.2444316302188 , 4.4076649760484 , 2.2727031062502 , 3.8681823242069 , 3.6105625251087 , 1.9922597257068 , 2.8664391562608 , 4.1512927538128 , 2.3986297766829 , 3.900402643639 , 3.1125094911486 , 0.79605361698408 , 2.7427331318038 , 3.183939270326 , -0.098522041714588 , 3.1502857891748 , 2.662780648907 , -1.5030953088307 , 1.6620934927936 , 2.3049571979405 , 0.47497903946509 , 0.44214209617904 , 2.6079434547308 , 0.40155618441789 , 2.0172699632204 , 1.1203884493605 , 1.0119885004965 , 1.299268032236 , 0.16207979639779 , 1.6709575658416 , 2.0998237962452 , -1.0951958530446 , 2.0131165512648 , 0.56626839231711 , 0.64441103033332 , 2.9354575894766 , -0.61828128115051 , 0.35845492398582 , 3.2232453783193 , 1.297658748413 , 1.443322963564 , 3.788554519119 , 0.92364152112933 , 1.9975665777803 , 5.0731192588566 , 2.0251501427829 , 2.7939431841391 , 5.7283391503185 , -0.34515060449594 , 2.8816108985945 , 4.916740331129 , -1.1133126917309 , 3.0740803793275 , 5.8967574266384 , -0.4981951970656 , 3.4448064301456 , 3.6924514397354 , -1.4675941518372 , 4.4813585508814 , 3.3973074276517 , -0.784558308208 , 5.5034619834142 , 2.4892899213029 , -2.7578640391705 , 3.9250471855758 , 2.7194020951498 , -3.7808515929938 , 4.6163616235847 , 2.7974905973992 , -2.7217568374415 , 2.6576894477977 , 2.333665549995 , -3.8283620698119 , 1.7699294118509 , 1.9801964665289 , -3.332384494147 , 0.93009845517884 , 0.75415399422761 , -4.2781766964511 , 1.0123082758255 , 3.2260364775698 , -5.404130077644 , 0.69496442496522 , 3.381616475444 , -3.3472467118183 , 0.69539921370932 , 4.186092874279 , -3.6613128207809 , 0.055525971668209 , 5.4356378032103 , -2.2970304216736 , -0.24866623749075 , 6.1484973246134 , -4.474291638219 , 0.99380955494008 , 6.4234730837728 , -5.351210770386 , 0.50813790209854 , 7.1622694572923 , -6.2601316351656 , 3.6007623232274 , 6.82644344781 , -7.0585346267793 , 4.289807293986 , 7.5101346800503 , -6.6052567178241 , 3.1849591257566 , 5.5759990068514 , -4.1350860238649 , 2.2571545644834 , 6.4351156570431 , -4.7872153127373 , 3.2636042470594 , 7.1751730326322 , -4.0076750093925 , 4.6616098154713 , 7.2870028955611 ) +} + +restraint { + 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..3b8b8dacc --- /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 main fitting + 20 ( 9.99758842025952e-01 , 1.40273695003402e-02 , 1.19794087379276e-02 , -1.19157233149254e-02 ) ( -2.33415112386265e-01 , 1.72075525576161e+01 , 1.72731350135756e+01 , 1.80383359267298e+01 ) ( 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 ) ( 8.31090675932249e+00 , 4.18321055369488e-02 , -7.47201521849219e-01 , 6.95697285352072e+00 , -5.49562296849458e-01 , -5.71672875700706e-01 , 7.05013140894045e+00 , -2.05023512296687e+00 , -9.34669806296762e-01 , 6.17240254680718e+00 , -3.74400069980217e-01 , 7.27960689700406e-01 , 4.97289012195966e+00 , -1.59840133025210e-01 , 7.26861478006921e-01 , 6.85143016424651e+00 , -2.67411058958381e-01 , 1.90833777927846e+00 , 6.15419391836547e+00 , -1.66072332719724e-01 , 3.18953674170869e+00 , 7.07360741467198e+00 , -3.53787041278778e-01 , 4.30709519134346e+00 , 5.29707732701665e+00 , 1.09306757774027e+00 , 3.34272989433020e+00 , 4.13343237319073e+00 , 1.02327246245068e+00 , 3.68077579810689e+00 , 5.83633060084645e+00 , 2.25051412758168e+00 , 2.98980695537450e+00 , 5.23832428615246e+00 , 3.57842258438988e+00 , 2.91983903820893e+00 , 6.32251543245755e+00 , 4.50069432109923e+00 , 2.36348825823247e+00 , 3.88157997271048e+00 , 3.70656124620231e+00 , 2.04309444408829e+00 , 2.79198948709314e+00 , 4.16068180386918e+00 , 2.48673203609126e+00 , 3.93792476668629e+00 , 3.23915517733109e+00 , 7.30091374411066e-01 , 2.66118610902653e+00 , 3.00667285732861e+00 , -1.04345678058027e-01 , 3.05165044818937e+00 , 2.70436148716590e+00 , -1.51567333037120e+00 , 1.59708748713844e+00 , 2.18297286920705e+00 , 4.45556770549766e-01 , 3.78584378858993e-01 , 2.58072646353568e+00 , 5.10195570905079e-01 , 2.04711677577995e+00 , 1.07038136373826e+00 , 1.06920675470600e+00 , 1.16848579041049e+00 , 1.16556747429878e-01 , 1.69697630204218e+00 , 2.04253290473041e+00 , -1.10351049600709e+00 , 2.01036748468488e+00 , 5.61949018704076e-01 , 6.11851875225114e-01 , 2.94281324266892e+00 , -6.01976769592518e-01 , 3.49784599309613e-01 , 3.16216490779620e+00 , 1.31635901812368e+00 , 1.34586876738189e+00 , 3.77521128509793e+00 , 8.43402881850553e-01 , 1.97859839718229e+00 , 5.02538632116996e+00 , 2.08041934928527e+00 , 2.68815955986576e+00 , 5.68159299594615e+00 , -3.36606764835887e-01 , 2.91482986504629e+00 , 4.96814896674175e+00 , -1.13628659076044e+00 , 3.06300104606802e+00 , 5.88800075787313e+00 , -5.11355512191276e-01 , 3.53530055398401e+00 , 3.84643710881153e+00 , -1.51785948621973e+00 , 4.53912860111727e+00 , 3.44518171907994e+00 , -6.99851975148663e-01 , 5.41409435697686e+00 , 2.46386423232082e+00 , -2.76016180386143e+00 , 3.88956073346774e+00 , 2.89579336342103e+00 , -3.81734971241040e+00 , 4.51010369961674e+00 , 2.81527737487722e+00 , -2.62539242196120e+00 , 2.67332612766542e+00 , 2.40226199530184e+00 , -3.77324373504424e+00 , 1.80375076631133e+00 , 2.00013505051883e+00 , -3.38950144161652e+00 , 8.86669637663103e-01 , 8.75671332682718e-01 , -4.32272439198799e+00 , 1.07021727915687e+00 , 3.21413036434023e+00 , -5.50013423740763e+00 , 8.18932135050308e-01 , 3.33101661006383e+00 , -3.36888605586921e+00 , 6.91744787444546e-01 , 4.20579009905972e+00 , -3.70041478321665e+00 , 4.62269643354005e-02 , 5.43590659796911e+00 , -2.38952897780255e+00 , -3.16614240925530e-01 , 6.17171197332790e+00 , -4.46079702134748e+00 , 9.87298067706133e-01 , 6.44137425707663e+00 , -5.35797456018837e+00 , 5.99067686148005e-01 , 7.21989553211130e+00 , -6.23692826148947e+00 , 3.60612735076136e+00 , 6.73537968722392e+00 , -6.95882586593268e+00 , 4.29884122192187e+00 , 7.47695539865336e+00 , -6.74039937188414e+00 , 3.18302572187854e+00 , 5.50946750515387e+00 , -4.12767231895083e+00 , 2.24670346730028e+00 , 6.41109099300551e+00 , -4.80736760169664e+00 , 3.20639437683912e+00 , 7.24443119647944e+00 , -4.09378774140924e+00 , 4.57600136508791e+00 , 7.28382984993688e+00 ) + 21 ( 9.99756404916955e-01 , 1.38613245482543e-02 , 1.21390059267497e-02 , -1.21506808205584e-02 ) ( -2.29006853143000e-01 , 1.72135778158611e+01 , 1.72687267375248e+01 , 1.80464864475683e+01 ) ( 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 ) ( 8.30938567525840e+00 , 4.16877375503137e-02 , -7.43912099686806e-01 , 6.94709314955551e+00 , -5.50750166517949e-01 , -5.63762127590062e-01 , 7.04726107924897e+00 , -2.05192460490773e+00 , -9.30315846288022e-01 , 6.17535670611533e+00 , -3.80476568844216e-01 , 7.35176725315256e-01 , 4.96764093565076e+00 , -1.55900883020060e-01 , 7.29163897304371e-01 , 6.84467324603761e+00 , -2.68746534496584e-01 , 1.91663424599716e+00 , 6.14733399319888e+00 , -1.73647393190300e-01 , 3.18472248149620e+00 , 7.07493661684435e+00 , -3.52623525086354e-01 , 4.31345679706143e+00 , 5.30108805722385e+00 , 1.08927608754602e+00 , 3.34548990060171e+00 , 4.13308459458055e+00 , 1.02092392301853e+00 , 3.68673120256419e+00 , 5.83264791576591e+00 , 2.25186118515138e+00 , 2.98785718537116e+00 , 5.23573240036143e+00 , 3.57671066110996e+00 , 2.91978162765071e+00 , 6.32172566366245e+00 , 4.49936864307714e+00 , 2.35338010272974e+00 , 3.87662004161420e+00 , 3.70020460270434e+00 , 2.04301963938042e+00 , 2.79061356054732e+00 , 4.16316684514033e+00 , 2.48142915541731e+00 , 3.94031020925687e+00 , 3.23702505545926e+00 , 7.29507013519662e-01 , 2.66831540932201e+00 , 3.00585853233039e+00 , -1.02206760299319e-01 , 3.05783620756688e+00 , 2.69873728260059e+00 , -1.51560606161625e+00 , 1.59567902070796e+00 , 2.17821554883414e+00 , 4.39182817521267e-01 , 3.75189022300578e-01 , 2.58866479573903e+00 , 5.06329948063377e-01 , 2.05465980474862e+00 , 1.08579439090454e+00 , 1.06449758815532e+00 , 1.16689542722101e+00 , 1.17110302749973e-01 , 1.69846114917935e+00 , 2.04601646564743e+00 , -1.10011844699539e+00 , 2.01295092900353e+00 , 5.63776887207455e-01 , 6.13383382367263e-01 , 2.94796916642678e+00 , -5.96911722844028e-01 , 3.50134284798621e-01 , 3.16190053517762e+00 , 1.31292485383305e+00 , 1.34653819132038e+00 , 3.76617937544043e+00 , 8.41500887378600e-01 , 1.98080044589067e+00 , 5.02552408339577e+00 , 2.08907825224586e+00 , 2.69756964424858e+00 , 5.68831997221198e+00 , -3.37256406076599e-01 , 2.91403587436073e+00 , 4.96879465227115e+00 , -1.13266179246335e+00 , 3.06404541306661e+00 , 5.88536359922020e+00 , -5.16405409226794e-01 , 3.52805084528982e+00 , 3.84382055283056e+00 , -1.51791909165374e+00 , 4.53533951716696e+00 , 3.43678883241073e+00 , -6.99626673160170e-01 , 5.41580553307440e+00 , 2.46562895639193e+00 , -2.75632494832513e+00 , 3.89656736413705e+00 , 2.89001295721714e+00 , -3.81630013573795e+00 , 4.51582971628209e+00 , 2.81449171123103e+00 , -2.63096733040019e+00 , 2.67073990407670e+00 , 2.39522628703764e+00 , -3.77672210246999e+00 , 1.80236075334925e+00 , 2.00026305691032e+00 , -3.38536145757478e+00 , 8.85979881342965e-01 , 8.69609722319221e-01 , -4.31798028391291e+00 , 1.07030829068157e+00 , 3.21181182544835e+00 , -5.49802675844805e+00 , 8.11716401985840e-01 , 3.33186281789443e+00 , -3.36625865953360e+00 , 6.95706014586949e-01 , 4.20881979533729e+00 , -3.69409231538775e+00 , 5.15006269291789e-02 , 5.43762393708684e+00 , -2.39058560242180e+00 , -3.18609476113615e-01 , 6.16957497599152e+00 , -4.45986122800256e+00 , 9.79681061010628e-01 , 6.43946952806521e+00 , -5.36033300781632e+00 , 5.97489992841687e-01 , 7.22100823450474e+00 , -6.24249333378036e+00 , 3.61179529091855e+00 , 6.73971703265567e+00 , -6.96229704469881e+00 , 4.29845684597736e+00 , 7.48116384903755e+00 , -6.73376539314804e+00 , 3.17932487298240e+00 , 5.50831050839436e+00 , -4.12573802887122e+00 , 2.24481370595785e+00 , 6.40507122485745e+00 , -4.80566017170882e+00 , 3.21357888112476e+00 , 7.24906900030056e+00 , -4.08799854722257e+00 , 4.57017086224379e+00 , 7.28115879476838e+00 ) + 22 ( 9.99751825801053e-01 , 1.37668632596691e-02 , 1.23305794072404e-02 , -1.24385326679425e-02 ) ( -2.25354457213011e-01 , 1.72171754135474e+01 , 1.72631618101901e+01 , 1.80562099325717e+01 ) ( 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 5.23130648071420e+00 , 3.57504698402741e+00 , 2.91876106664987e+00 , 2.67724316859312e+00 , 3.00710564945166e+00 , -9.96809435036511e-02 , 1.16638493571971e+00 , 1.17059328374754e-01 , 1.69969339103600e+00 , 8.40474011651061e-01 , 1.98235339414393e+00 , 5.02582499379831e+00 , -1.51662307920245e+00 , 4.53072479871976e+00 , 3.42963791013140e+00 , -3.77977090227983e+00 , 1.80297019533497e+00 , 2.00103128266615e+00 , -3.68858938020335e+00 , 5.71185724985555e-02 , 5.44106122479227e+00 , -4.80495334627875e+00 , 3.22172961108294e+00 , 7.25326380693817e+00 ) ( 8.30819124245833e+00 , 4.16417475787460e-02 , -7.40474698217961e-01 , 6.93692624954704e+00 , -5.52330095724236e-01 , -5.56142746693275e-01 , 7.04381268842703e+00 , -2.05346209285297e+00 , -9.25823056925289e-01 , 6.17855179332584e+00 , -3.85211838386071e-01 , 7.42949176483995e-01 , 4.96236137056383e+00 , -1.52251263556674e-01 , 7.31246313239799e-01 , 6.83796788278979e+00 , -2.70547436959856e-01 , 1.92502453824008e+00 , 6.13944807438661e+00 , -1.81349791614332e-01 , 3.17911135101690e+00 , 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6.14408467519650e+00 , -4.47912226138258e+00 , 9.89222211089516e-01 , 6.42454983767422e+00 , -5.35161281557211e+00 , 5.14805563214696e-01 , 7.16688596353334e+00 , -6.26570637171555e+00 , 3.59956388146635e+00 , 6.81584237022505e+00 , -7.05549269364421e+00 , 4.29394444691956e+00 , 7.51413706834312e+00 , -6.60460337240091e+00 , 3.18269197795597e+00 , 5.57304171930707e+00 , -4.13035777276138e+00 , 2.25474987182156e+00 , 6.43402213231196e+00 , -4.78936447974313e+00 , 3.26644842590913e+00 , 7.18028305985000e+00 , -4.00670158436284e+00 , 4.65485176981042e+00 , 7.28690738849568e+00 ) + 40 ( 9.99739707661452e-01 , 1.42661905629674e-02 , 1.15959419288222e-02 , -1.35102502789137e-02 ) ( -2.01548974416543e-01 , 1.72050238188529e+01 , 1.72904735673894e+01 , 1.80938885690596e+01 ) ( 6.86762086454639e+00 , -6.12717338266719e-01 , -4.73911119543950e-01 , 6.04174239176985e+00 , -2.57206575787504e-01 , 3.28069167157503e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 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7.09766643481576e+00 , -3.64437190081014e-01 , 4.41260338699156e+00 , 5.23259794116129e+00 , 1.05436526581157e+00 , 3.34523999068699e+00 , 4.10965021058945e+00 , 1.00765644801206e+00 , 3.83368368896025e+00 , 5.80858258831952e+00 , 2.24313378785624e+00 , 2.95231539595336e+00 , 5.12461111010113e+00 , 3.50635311035087e+00 , 2.83318842219880e+00 , 6.24443163021879e+00 , 4.40766497604838e+00 , 2.27270310625019e+00 , 3.86818232420693e+00 , 3.61056252510868e+00 , 1.99225972570684e+00 , 2.86643915626076e+00 , 4.15129275381282e+00 , 2.39862977668293e+00 , 3.90040264363905e+00 , 3.11250949114855e+00 , 7.96053616984078e-01 , 2.74273313180385e+00 , 3.18393927032603e+00 , -9.85220417145884e-02 , 3.15028578917481e+00 , 2.66278064890697e+00 , -1.50309530883071e+00 , 1.66209349279360e+00 , 2.30495719794052e+00 , 4.74979039465087e-01 , 4.42142096179045e-01 , 2.60794345473079e+00 , 4.01556184417888e-01 , 2.01726996322042e+00 , 1.12038844936051e+00 , 1.01198850049651e+00 , 1.29926803223596e+00 , 1.62079796397793e-01 , 1.67095756584156e+00 , 2.09982379624525e+00 , -1.09519585304460e+00 , 2.01311655126484e+00 , 5.66268392317114e-01 , 6.44411030333318e-01 , 2.93545758947663e+00 , -6.18281281150510e-01 , 3.58454923985819e-01 , 3.22324537831926e+00 , 1.29765874841298e+00 , 1.44332296356401e+00 , 3.78855451911896e+00 , 9.23641521129327e-01 , 1.99756657778026e+00 , 5.07311925885661e+00 , 2.02515014278286e+00 , 2.79394318413907e+00 , 5.72833915031846e+00 , -3.45150604495941e-01 , 2.88161089859454e+00 , 4.91674033112903e+00 , -1.11331269173090e+00 , 3.07408037932750e+00 , 5.89675742663844e+00 , -4.98195197065596e-01 , 3.44480643014558e+00 , 3.69245143973537e+00 , -1.46759415183722e+00 , 4.48135855088138e+00 , 3.39730742765171e+00 , -7.84558308207997e-01 , 5.50346198341422e+00 , 2.48928992130295e+00 , -2.75786403917046e+00 , 3.92504718557584e+00 , 2.71940209514984e+00 , -3.78085159299383e+00 , 4.61636162358473e+00 , 2.79749059739920e+00 , -2.72175683744148e+00 , 2.65768944779769e+00 , 2.33366554999501e+00 , -3.82836206981185e+00 , 1.76992941185088e+00 , 1.98019646652893e+00 , -3.33238449414696e+00 , 9.30098455178843e-01 , 7.54153994227610e-01 , -4.27817669645113e+00 , 1.01230827582551e+00 , 3.22603647756983e+00 , -5.40413007764400e+00 , 6.94964424965218e-01 , 3.38161647544399e+00 , -3.34724671181829e+00 , 6.95399213709320e-01 , 4.18609287427902e+00 , -3.66131282078092e+00 , 5.55259716682087e-02 , 5.43563780321032e+00 , -2.29703042167362e+00 , -2.48666237490752e-01 , 6.14849732461339e+00 , -4.47429163821902e+00 , 9.93809554940076e-01 , 6.42347308377283e+00 , -5.35121077038599e+00 , 5.08137902098545e-01 , 7.16226945729229e+00 , -6.26013163516562e+00 , 3.60076232322739e+00 , 6.82644344781004e+00 , -7.05853462677926e+00 , 4.28980729398599e+00 , 7.51013468005025e+00 , -6.60525671782407e+00 , 3.18495912575661e+00 , 5.57599900685142e+00 , -4.13508602386485e+00 , 2.25715456448337e+00 , 6.43511565704307e+00 , -4.78721531273728e+00 , 3.26360424705940e+00 , 7.17517303263219e+00 , -4.00767500939247e+00 , 4.66160981547131e+00 , 7.28700289556107e+00 ) diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py new file mode 100644 index 000000000..ced91627c --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/compare_with_pytorch.py @@ -0,0 +1,245 @@ +#!/usr/bin/env python3 +import torch +import re +import numpy as np + +torch.set_printoptions(precision=10) + +ref_main_group = torch.tensor( + [[6.3061, -1.592, -3.585], + [5.4031, -0.784, 0.045] , + [3.8061, 2.804, -0.129] , + [1.2441, 1.799, -2.726] , + [0.5861, -1.803, -1.516], + [-0.2169, -0.926, 2.133], + [-2.1679, 2.13, 1.258] , + [-4.4689, 0.434, -1.263], + [-4.8649, -2.25, 1.46] , + [-5.6269, 0.188, 4.323]], dtype=torch.float64) + +ref_fitting_group = torch.tensor( + [[5.69469, -1.80418, -5.22382] , + [6.37169, -1.08118, -4.10382] , + [6.61169, 0.365824, -4.58082] , + [5.62269, -1.09518, -2.77982] , + [4.39969, -0.986176, -2.72882] , + [6.36569, -1.21018, -1.66282] , + [5.83469, -1.37018, -0.318824] , + [7.00969, -1.45018, 0.678176] , + [4.84269, -0.296176, 0.126176] , + [3.77369, -0.596176, 0.648176] , + [5.15669, 0.991824, -0.113824] , + [4.27869, 2.10682, 0.190176] , + [5.03669, 3.42282, -0.0748235] , + [2.96669, 2.09282, -0.596824] , + [1.89969, 2.39182, -0.0678235] , + [3.01469, 1.69682, -1.88382] , + [1.84869, 1.57082, -2.73482] , + [2.30269, 1.40782, -4.19882] , + [0.962686, 0.399824, -2.31982] , + [-0.255314, 0.522824, -2.22882] , + [1.57569, -0.758176, -2.00882] , + [0.900686, -1.92218, -1.46882] , + [1.91969, -3.07218, -1.33582] , + [0.223686, -1.65518, -0.123824] , + [-0.930314, -2.01818, 0.0891765] , + [0.918686, -0.964176, 0.800176] , + [0.372686, -0.514176, 2.06618] , + [1.49069, 0.164824, 2.88418] , + [-0.814314, 0.435824, 1.92118] , + [-1.84631, 0.257824, 2.56118] , + [-0.707314, 1.45482, 1.04518] , + [-1.78431, 2.37982, 0.745176] , + [-1.24331, 3.48882, -0.178824] , + [-3.00931, 1.72082, 0.109176] , + [-4.14731, 2.02882, 0.455176] , + [-2.80331, 0.769824, -0.821824] , + [-3.86731, -0.00917647, -1.42282], + [-3.28731, -0.820176, -2.59882] , + [-4.57231, -0.946176, -0.440824] , + [-5.78931, -1.10018, -0.475824] , + [-3.81431, -1.58718, 0.469176] , + [-4.35131, -2.44718, 1.50418] , + [-3.19331, -3.25818, 2.12018] , + [-5.10031, -1.70118, 2.61018] , + [-6.15131, -2.13818, 3.07218] , + [-6.33131, 1.19882, 3.62918] , + [-7.08531, 1.74482, 4.44018] , + [-6.45431, 1.44382, 2.30618] , + [-4.56431, -0.557176, 3.07518] , + [-5.19131, 0.240824, 4.11318] , + [-4.10131, 1.05882, 4.83518]], dtype=torch.float64) + +# fitting_group = atom_positions +# main_group = atom_positions[[0, 1, 2, 3]] + + +def get_optimal_rotation(fitting_atoms: torch.tensor, reference_atoms: torch.tensor): + fitting_atoms_centered = fitting_atoms - fitting_atoms.mean(dim=0) + reference_atoms_centered = reference_atoms - reference_atoms.mean(dim=0) + mat_R = torch.linalg.matmul(fitting_atoms_centered.T, reference_atoms_centered) + F00 = mat_R[0][0] + mat_R[1][1] + mat_R[2][2] + F01 = mat_R[1][2] - mat_R[2][1] + F02 = mat_R[2][0] - mat_R[0][2] + F03 = mat_R[0][1] - mat_R[1][0] + F10 = F01 + F11 = mat_R[0][0] - mat_R[1][1] - mat_R[2][2] + F12 = mat_R[0][1] + mat_R[1][0] + F13 = mat_R[0][2] + mat_R[2][0] + F20 = F02 + F21 = F12 + F22 = -mat_R[0][0] + mat_R[1][1] - mat_R[2][2] + F23 = mat_R[1][2] + mat_R[2][1] + F30 = F03 + F31 = F13 + F32 = F23 + F33 = -mat_R[0][0] - mat_R[1][1] + mat_R[2][2] + row0 = torch.stack((F00, F01, F02, F03)) + row1 = torch.stack((F10, F11, F12, F13)) + row2 = torch.stack((F20, F21, F22, F23)) + row3 = torch.stack((F30, F31, F32, F33)) + F = torch.stack((row0, row1, row2, row3)) + w, v = torch.linalg.eigh(F) + q = v[:, -1] + R00 = q[0] * q[0] + q[1] * q[1] - q[2] * q[2] - q[3] * q[3] + R01 = 2.0 * (q[1] * q[2] - q[0] * q[3]) + R02 = 2.0 * (q[1] * q[3] + q[0] * q[2]) + R10 = 2.0 * (q[1] * q[2] + q[0] * q[3]) + R11 = q[0] * q[0] - q[1] * q[1] + q[2] * q[2] - q[3] * q[3] + R12 = 2.0 * (q[2] * q[3] - q[0] * q[1]) + R20 = 2.0 * (q[1] * q[3] - q[0] * q[2]) + R21 = 2.0 * (q[2] * q[3] + q[0] * q[1]) + R22 = q[0] * q[0] - q[1] * q[1] - q[2] * q[2] + q[3] * q[3] + row0 = torch.stack((R00, R01, R02)) + row1 = torch.stack((R10, R11, R12)) + row2 = torch.stack((R20, R21, R22)) + R = torch.stack((row0, row1, row2)) + return w, v, R + + +def test(force, main_group, fitting_group): + # Using all atoms as the fitting group + w, v, R = get_optimal_rotation(fitting_group, ref_fitting_group) + main_group_centered = main_group - main_group.mean(dim=0) + ref_main_group_centered = ref_main_group - ref_main_group.mean(dim=0) + # Rotate the main group + main_group_r = (R @ main_group_centered.T).T + # main_group_r.register_hook(set_grad(main_group_r)) + w2, v2, R2 = get_optimal_rotation(ref_main_group_centered, main_group_r) + q = v2[:, -1] + ref_quat = torch.tensor([1.0, 0.0, 0.0, 0.0], dtype=torch.float64) + q_inner_ref_quat = torch.sum(ref_quat * q) + if (q_inner_ref_quat > 0): + final_q = q + else: + final_q = -1.0 * q + # print('Orientation:\n', final_q) + # Force on q + # force = torch.tensor([3.40697e-06, -8.24548e-05, -5.71708e-05, 5.95895e-05], dtype=torch.float64) + # Apply force + # torch.sum(force * final_q).backward() + (force[0] * final_q[0]).backward(retain_graph=True) + (force[1] * final_q[1]).backward(retain_graph=True) + (force[2] * final_q[2]).backward(retain_graph=True) + (force[3] * final_q[3]).backward(retain_graph=True) + # print('main group force:\n', main_group.grad) + # print('main group (rotated) force:\n', main_group_r.grad) + # print('fitting group force:\n', fitting_group.grad) + return main_group.grad.cpu().detach().numpy(), fitting_group.grad.cpu().detach().numpy() + + +def read_data_from_traj(filename): + main_group_positions = [] + fitting_group_positions = [] + forces = [] + with open(filename, 'r') as f_input: + for line in f_input: + s = line.strip() + if s.startswith('#'): + # skip comment lines + continue + if len(s) > 0: + # skip empty lines + # match the data in parentheses + result = re.findall(r'\(([^)]+)\)', s) + # get the force applied on the orientation + forces.append(torch.tensor(list(map(float, result[1].split(','))), dtype=torch.float64)) + # get the main group position + tmp = np.array(list(map(float, result[2].split(',')))).reshape(-1, 3) + main_group_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + # get the fitting group position + tmp = np.array(list(map(float, result[3].split(',')))).reshape(-1, 3) + fitting_group_positions.append(torch.tensor(tmp, dtype=torch.float64, requires_grad=True)) + return forces, main_group_positions, fitting_group_positions + + +def scan_force_from_log(filename): + main_group_forces = [] + fitting_group_forces = [] + with open(filename, 'r') as f_input: + new_main_group_started = False + main_group_force = [] + new_fitting_group_started = False + fitting_group_force = [] + for line in f_input: + if new_main_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + main_group_force.append(list(map(float, result[0].split(',')))) + else: + new_main_group_started = False + main_group_forces.append(np.array(main_group_force)) + main_group_force = [] + if new_fitting_group_started: + result = re.findall(r'\(([^)]+)\)', line) + if result: + fitting_group_force.append(list(map(float, result[0].split(',')))) + else: + new_fitting_group_started = False + fitting_group_forces.append(np.array(fitting_group_force)) + fitting_group_force = [] + if line.startswith('colvars: Applying force on the fitting group of main group:'): + new_fitting_group_started = True + continue + if line.startswith('colvars: Applying force on main group'): + new_main_group_started = True + continue + return main_group_forces, fitting_group_forces + + +if __name__ == '__main__': + print('Compare AutoDiff/test.colvars.traj and AutoDiff/test.colvars.out') + # read positions from Colvars traj + forces, main_group_positions, fitting_group_positions = read_data_from_traj('AutoDiff/test.colvars.traj') + main_group_forces_pytorch = [] + fitting_group_forces_pytorch = [] + # calculate the forces by pytorch + for f, pm, pf in zip(forces, main_group_positions, fitting_group_positions): + f1, f2 = test(f, pm, pf) + main_group_forces_pytorch.append(f1) + fitting_group_forces_pytorch.append(f2) + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.colvars.out') + # compare the force (calculate the relative error) + for i in range(len(main_group_forces_colvars)): + error_main = np.mean(np.abs(main_group_forces_colvars[i] - main_group_forces_pytorch[i]) / np.abs(main_group_forces_colvars[i])) + error_fitting = np.mean(np.abs(fitting_group_forces_colvars[i] - fitting_group_forces_pytorch[i]) / np.abs(fitting_group_forces_colvars[i])) + print(f'Frame {i}: error of the main group forces {error_main:12.5e} , fitting group forces {error_fitting:12.5e}') + + # Do the same thing with the restart file + print('Compare AutoDiff/test.restart.colvars.traj and AutoDiff/test.restart.colvars.out') + forces, main_group_positions, fitting_group_positions = read_data_from_traj('AutoDiff/test.restart.colvars.traj') + main_group_forces_pytorch = [] + fitting_group_forces_pytorch = [] + # calculate the forces by pytorch + for f, pm, pf in zip(forces, main_group_positions, fitting_group_positions): + f1, f2 = test(f, pm, pf) + main_group_forces_pytorch.append(f1) + fitting_group_forces_pytorch.append(f2) + # read the forces from the debug Colvars log file + main_group_forces_colvars, fitting_group_forces_colvars = scan_force_from_log('AutoDiff/test.restart.colvars.out') + # compare the force (calculate the relative error) + for i in range(len(main_group_forces_colvars)): + error_main = np.mean(np.abs(main_group_forces_colvars[i] - main_group_forces_pytorch[i]) / np.abs(main_group_forces_colvars[i])) + error_fitting = np.mean(np.abs(fitting_group_forces_colvars[i] - fitting_group_forces_pytorch[i]) / np.abs(fitting_group_forces_colvars[i])) + print(f'Frame {i}: error of the main group forces {error_main:12.5e} , fitting group forces {error_fitting:12.5e}') diff --git a/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/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..68d8433c9 --- /dev/null +++ b/namd/tests/library/000_orientation-fitgroup_harmonic-ori-fixed-fit-forces/test.in @@ -0,0 +1,49 @@ +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 + } +} + +colvar { + name main + cartesian { + atoms { + indexGroup RMSD_atoms + } + } +} + +colvar { + name fitting + cartesian { + atoms { + indexGroup heavy_atoms + } + } +} + +harmonic { + colvars one + centers (0.9, 0.5, 0.5, 0.5) + forceConstant 10.0 +} diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp index e15b9301a..745cb0328 100644 --- a/src/colvaratoms.cpp +++ b/src/colvaratoms.cpp @@ -1217,23 +1217,30 @@ void cvm::atom_group::calc_fit_gradients() if (cvm::debug()) cvm::log("Calculating fit gradients.\n"); + cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; + + auto accessor_main = [this](size_t i){return atoms[i].grad;}; + auto accessor_fitting = [&group_for_fit](size_t j, const cvm::rvector& grad){group_for_fit->fit_gradients[j] = grad;}; if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) - calc_fit_gradients_impl(); + calc_fit_forces_impl(accessor_main, accessor_fitting); if (cvm::debug()) cvm::log("Done calculating fit gradients.\n"); } -template -void cvm::atom_group::calc_fit_gradients_impl() { - cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; +template +void cvm::atom_group::calc_fit_forces_impl( + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const { + const cvm::atom_group *group_for_fit = fitting_group ? fitting_group : this; // the center of geometry contribution to the gradients cvm::rvector atom_grad; // the rotation matrix contribution to the gradients @@ -1245,15 +1252,15 @@ void cvm::atom_group::calc_fit_gradients_impl() { for (size_t i = 0; i < size(); i++) { cvm::atom_pos pos_orig; if (B_ag_center) { - atom_grad += atoms[i].grad; + atom_grad += accessor_main(i); if (B_ag_rotate) pos_orig = rot_inv * (atoms[i].pos - ref_pos_cog); } else { - if (B_ag_rotate) pos_orig = atoms[i].pos; + if (B_ag_rotate) pos_orig = rot_inv * atoms[i].pos; } if (B_ag_rotate) { // calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i cvm::quaternion const dxdq = - rot.q.position_derivative_inner(pos_orig, atoms[i].grad); + rot.q.position_derivative_inner(pos_orig, accessor_main(i)); sum_dxdq[0] += dxdq[0]; sum_dxdq[1] += dxdq[1]; sum_dxdq[2] += dxdq[2]; @@ -1261,26 +1268,45 @@ void cvm::atom_group::calc_fit_gradients_impl() { } } if (B_ag_center) { - if (B_ag_rotate) atom_grad = rot.inverse().matrix() * atom_grad; + if (B_ag_rotate) atom_grad = rot_inv * atom_grad; atom_grad *= (-1.0)/(cvm::real(group_for_fit->size())); } // loop 2: iterate over the fitting group if (B_ag_rotate) rot_deriv->prepare_derivative(rotation_derivative_dldq::use_dq); for (size_t j = 0; j < group_for_fit->size(); j++) { + cvm::rvector fitting_force_grad{0, 0, 0}; if (B_ag_center) { - group_for_fit->fit_gradients[j] = atom_grad; + fitting_force_grad += atom_grad; } if (B_ag_rotate) { rot_deriv->calc_derivative_wrt_group1(j, nullptr, &dq0_1); // multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients - group_for_fit->fit_gradients[j] += sum_dxdq[0] * dq0_1[0] + - sum_dxdq[1] * dq0_1[1] + - sum_dxdq[2] * dq0_1[2] + - sum_dxdq[3] * dq0_1[3]; + fitting_force_grad += sum_dxdq[0] * dq0_1[0] + + sum_dxdq[1] * dq0_1[1] + + sum_dxdq[2] * dq0_1[2] + + sum_dxdq[3] * dq0_1[3]; + } + if (cvm::debug()) { + cvm::log(cvm::to_str(fitting_force_grad)); } + accessor_fitting(j, fitting_force_grad); } } +template +void cvm::atom_group::calc_fit_forces( + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const { + if (is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) + calc_fit_forces_impl(accessor_main, accessor_fitting); + if (is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) + calc_fit_forces_impl(accessor_main, accessor_fitting); + if (!is_enabled(f_ag_center) && is_enabled(f_ag_rotate)) + calc_fit_forces_impl(accessor_main, accessor_fitting); + if (!is_enabled(f_ag_center) && !is_enabled(f_ag_rotate)) + calc_fit_forces_impl(accessor_main, accessor_fitting); +} + std::vector cvm::atom_group::positions() const { @@ -1452,17 +1478,72 @@ void cvm::atom_group::apply_force(cvm::rvector const &force) return; } - if (is_enabled(f_ag_rotate)) { + auto ag_force = get_group_force_object(); + for (size_t i = 0; i < size(); ++i) { + ag_force.add_atom_force(i, atoms[i].mass / total_mass * force); + } +} - const auto rot_inv = rot.inverse().matrix(); - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->apply_force(rot_inv * ((ai->mass/total_mass) * force)); +cvm::atom_group::group_force_object cvm::atom_group::get_group_force_object() { + return cvm::atom_group::group_force_object(this); +} + +cvm::atom_group::group_force_object::group_force_object(cvm::atom_group* ag): +m_ag(ag), m_group_for_fit(m_ag->fitting_group ? m_ag->fitting_group : m_ag), +m_has_fitting_force(m_ag->is_enabled(f_ag_center) || m_ag->is_enabled(f_ag_rotate)) { + if (m_has_fitting_force) { + if (m_ag->group_forces.size() != m_ag->size()) { + m_ag->group_forces.assign(m_ag->size(), 0); + } else { + std::fill(m_ag->group_forces.begin(), + m_ag->group_forces.end(), 0); } + } +} +cvm::atom_group::group_force_object::~group_force_object() { + if (m_has_fitting_force) { + apply_force_with_fitting_group(); + } +} + +void cvm::atom_group::group_force_object::add_atom_force(size_t i, const cvm::rvector& force) { + if (m_has_fitting_force) { + m_ag->group_forces[i] += force; } else { + // Apply the force directly if we don't use fitting + (*m_ag)[i].apply_force(force); + } +} - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - ai->apply_force((ai->mass/total_mass) * force); +void cvm::atom_group::group_force_object::apply_force_with_fitting_group() { + const cvm::rmatrix rot_inv = m_ag->rot.inverse().matrix(); + if (cvm::debug()) { + cvm::log("Applying force on main group " + m_ag->name + ":\n"); + } + for (size_t ia = 0; ia < m_ag->size(); ++ia) { + const cvm::rvector f_ia = rot_inv * m_ag->group_forces[ia]; + (*m_ag)[ia].apply_force(f_ia); + if (cvm::debug()) { + cvm::log(cvm::to_str(f_ia)); + } + } + // Gradients are only available with scalar components, so for a scalar component, + // if f_ag_fit_gradients is disabled, then the forces on the fitting group is not + // computed. For a vector component, we can only know the forces on the fitting + // group, but checking this flag can mimic results that the users expect (if + // "enableFitGradients no" then there is no force on the fitting group). + if (m_ag->is_enabled(f_ag_fit_gradients)) { + auto accessor_main = [this](size_t i){return m_ag->group_forces[i];}; + auto accessor_fitting = [this](size_t j, const cvm::rvector& fitting_force){ + (*(m_group_for_fit))[j].apply_force(fitting_force); + }; + if (cvm::debug()) { + cvm::log("Applying force on the fitting group of main group" + m_ag->name + ":\n"); + } + m_ag->calc_fit_forces(accessor_main, accessor_fitting); + if (cvm::debug()) { + cvm::log("Done applying force on the fitting group of main group" + m_ag->name + ":\n"); } } } diff --git a/src/colvaratoms.h b/src/colvaratoms.h index d16ca7bd5..1493046e0 100644 --- a/src/colvaratoms.h +++ b/src/colvaratoms.h @@ -257,8 +257,27 @@ class colvarmodule::atom_group /// \brief Index in the colvarproxy arrays (if the group is scalable) int index; + /// \brief The temporary forces acting on the main group atoms. + /// Currently this is only used for calculating the fitting group forces for + /// non-scalar components. + std::vector group_forces; + public: + class group_force_object { + public: + group_force_object(cvm::atom_group* ag); + ~group_force_object(); + void add_atom_force(size_t i, const cvm::rvector& force); + private: + cvm::atom_group* m_ag; + cvm::atom_group* m_group_for_fit; + bool m_has_fitting_force; + void apply_force_with_fitting_group(); + }; + + group_force_object get_group_force_object(); + inline cvm::atom & operator [] (size_t const i) { return atoms[i]; @@ -497,15 +516,47 @@ class colvarmodule::atom_group /// \brief Calculate the derivatives of the fitting transformation void calc_fit_gradients(); -/*! @brief Actual implementation of `calc_fit_gradients`. The template is +/*! @brief Actual implementation of `calc_fit_gradients` and + * `calc_fit_forces`. The template is * used to avoid branching inside the loops in case that the CPU * branch prediction is broken (or further migration to GPU code). * @tparam B_ag_center Centered the reference to origin? This should follow * the value of `is_enabled(f_ag_center)`. * @tparam B_ag_rotate Calculate the optimal rotation? This should follow * the value of `is_enabled(f_ag_rotate)`. + * @tparam main_force_accessor_T The type of accessor of the main + * group forces or gradients. + * @tparam fitting_force_accessor_T The type of accessor of the fitting group + * forces or gradients. + * @param accessor_main The accessor of the main group forces or gradients. + * accessor_main(i) should return the i-th force or gradient of the + * main group. + * @param accessor_fitting The accessor of the fitting group forces or gradients. + * accessor_fitting(j, v) should store/apply the j-th atom gradient or + * force in the fitting group. + */ + template + void calc_fit_forces_impl( + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const; + +/*! @brief Calculate or apply the fitting group forces from the main group forces. + * @tparam main_force_accessor_T The type of accessor of the main + * group forces or gradients. + * @tparam fitting_force_accessor_T The type of accessor of the fitting group + * forces or gradients. + * @param accessor_main The accessor of the main group forces or gradients. + * accessor_main(i) should return the i-th force or gradient of the + * main group. + * @param accessor_fitting The accessor of the fitting group forces or gradients. + * accessor_fitting(j, v) should store/apply the j-th atom gradient or + * force in the fitting group. */ - template void calc_fit_gradients_impl(); + template + void calc_fit_forces( + main_force_accessor_T accessor_main, + fitting_force_accessor_T accessor_fitting) const; /// \brief Derivatives of the fitting transformation std::vector fit_gradients; diff --git a/src/colvarcomp_distances.cpp b/src/colvarcomp_distances.cpp index 6e97e276e..1c7267f1e 100644 --- a/src/colvarcomp_distances.cpp +++ b/src/colvarcomp_distances.cpp @@ -1401,11 +1401,12 @@ void colvar::cartesian::apply_force(colvarvalue const &force) size_t ia, j; if (!atoms->noforce) { cvm::rvector f; + auto ag_force = atoms->get_group_force_object(); for (ia = 0; ia < atoms->size(); ia++) { for (j = 0; j < dim; j++) { f[axes[j]] = force.vector1d_value[dim*ia + j]; } - (*atoms)[ia].apply_force(f); + ag_force.add_atom_force(ia, f); } } } diff --git a/src/colvarcomp_rotations.cpp b/src/colvarcomp_rotations.cpp index 9f401a5f2..12dd90e33 100644 --- a/src/colvarcomp_rotations.cpp +++ b/src/colvarcomp_rotations.cpp @@ -137,22 +137,14 @@ void colvar::orientation::apply_force(colvarvalue const &force) if (!atoms->noforce) { rot_deriv_impl->prepare_derivative(rotation_derivative_dldq::use_dq); cvm::vector1d dq0_2; - - if (atoms->is_enabled(f_ag_rotate)) { - auto const rot_inv = atoms->rot.inverse().matrix(); - for (size_t ia = 0; ia < atoms->size(); ia++) { - rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); - for (size_t i = 0; i < 4; i++) { - (*atoms)[ia].apply_force(rot_inv * (FQ[i] * dq0_2[i])); - } - } - } else { - for (size_t ia = 0; ia < atoms->size(); ia++) { - rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); - for (size_t i = 0; i < 4; i++) { - (*atoms)[ia].apply_force(FQ[i] * dq0_2[i]); - } - } + auto ag_force = atoms->get_group_force_object(); + for (size_t ia = 0; ia < atoms->size(); ia++) { + rot_deriv_impl->calc_derivative_wrt_group2(ia, nullptr, &dq0_2); + const auto f_ia = FQ[0] * dq0_2[0] + + FQ[1] * dq0_2[1] + + FQ[2] * dq0_2[2] + + FQ[3] * dq0_2[3]; + ag_force.add_atom_force(ia, f_ia); } } }