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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$>$ .