Colvars scripting

This interface is particularly useful to implement custom biases as scripted colvar forces. See the scriptedColvarForces option in 10.5.7. Note that scripting commands may not be used directly in the NAMD configuration file before the first run or minimize statement. They may be used either within the callback procedures (e.g. calc_colvar_forces) or in the NAMD config file after a run or minimize statement.

Collective variables and biases can be added, queried and deleted through the scripting command cv, with the following syntax: cv $<$ subcommand$>$ [args...]. For example, to query the value of a collective variable named myVar, use the following syntax: set value [cv colvar myVar value]. All subcommands of cv are documented below.

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Managing the colvars module

• 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;
• reset: delete all internal configuration of the colvars module;
• version: return the version of the colvars code.

Input and output

• list: return a list of all currently defined variables;
• 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 simulation;
• 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;
• 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;

Accessing collective variables

• 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$>$ addforce $<$ F$>$ : apply given force on 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).

Accessing biases

• 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$>$ .