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• molid $<$ molid$>$ : setup the colvars module for the given molecule; $<$ molid$>$ is the identifier of a valid VMD molecule, either an integer or top for the top molecule;
• delete: delete the colvars module; after this, the module can be setup again using cv molid;
• configfile $<$ file name$>$ : read configuration from a file;
• config $<$ string$>$ : read configuration from the given string; both config and configfile subcommands may be invoked multiple times; see 13.1.2 for the configuration syntax;
• reset: delete all internal configuration of the colvars module;
• version: return the version of the colvars code.

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• list: return a list of all currently defined variables; See 13.2, 13.4 and 13.3 for how to configure a collective variable;
• list biases: return a list of all currently defined biases (i.e. sampling and analysis algorithms);
• load $<$ file name$>$ : load a collective variables state file, typically produced during a previous simulation; this parameter requires that the corresponding configuration has already been loaded by configfile or config; see 13.1.4 for a brief description of this file; the contents of this file are not required for as long as the VMD molecule has valid coordinates and cv update is used;
• load $<$ prefix$>$ : same as above, but without the .colvars.state suffix;
• save $<$ prefix$>$ : save the current state in a file whose name begins with the given argument; if any of the biases have additional output files defined, those are saved as well using the same prefix;
• update: recalculate all colvars and biases based on the current atomic coordinates;
• printframe: return a summary of the current frame, in a format equivalent to a line of the collective variables trajectory file;
• printframelabels: return text labels for the columns of printframe's output;
• frame: return the current frame number, from which colvar values are calculated;
• frame $<$ new frame$>$ : set the frame number; returns 0 if successful, nonzero if the requested frame does not exist.

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• colvar $<$ name$>$ value: return the current value of colvar $<$ name$>$ ;
• colvar $<$ name$>$ update: recalculate colvar $<$ name$>$ ;
• colvar $<$ name$>$ type: return the type of colvar $<$ name$>$ ;
• colvar $<$ name$>$ delete: delete colvar $<$ name$>$ ;
• colvar $<$ name$>$ getconfig: return config string of colvar $<$ name$>$ .
• colvar $<$ name$>$ cvcflags $<$ flags$>$ : for a colvar with several cvcs (numbered according to their name string order), set which cvcs are enabled or disabled in subsequent evaluations according to a list of 0/1 flags (one per cvc).

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• bias $<$ name$>$ energy: return the current energy of the bias $<$ name$>$ ;
• bias $<$ name$>$ update: recalculate the bias $<$ name$>$ ;
• bias $<$ name$>$ delete: delete the bias $<$ name$>$ ;
• bias $<$ name$>$ getconfig: return config string of bias $<$ name$>$ .

The following configuration options can modify the behavior of the scripting interface for optimization purposes:

• scriptingAfterBiases $\langle\,$ Scripted colvar forces need updated biases$\,\rangle$
  Context: global
  Acceptable values: boolean
  Default value: on
  Description: This flag specifies that the calc_colvar_forces procedure, when defined, is executed only after all biases have been updated. For example, this allows using the energy of a restraint bias, or the force applied on a colvar, to calculate additional scripted forces, such as boundary constraints. When this flag is set to off, it is assumed that only the values of their colvars (but not their energy or forces) will be used by calc_colvar_forces: this can be used to schedule the calculation of scripted forces and biases concurrently to increase performance.