Using the cv command

The colvars module is accessed in VMD through the command cv. The command must be used the first time as cv molid $<$ molid$>$ to set up the collective variables module for a given molecule. In all following uses, the cv command will continue operating on the same molecule, regardless of its ``top'' status. To use the cv command on a different molecule, use cv delete first and then cv molid $<$ molid$>$ . Invoking the cv command with no arguments prints a help screen.

The list of parameters of the cv command is:

• molid $<$ molid$>$ : set up the colvars module, where $<$ molid$>$ is the identifier of a valid VMD molecule as provided e.g. by molinfo: for example, use cv molid top to set the colvars module for the top molecule;
• configfile $<$ file name$>$ : read the colvars configuration from the contents of the specified file; the cv command can be invoked multiple times with this argument and/or with the config argument; see 13.1.2 for the configuration syntax;
• config $<$ string$>$ : read the colvars configuration from the given text string; see 13.1.2 for the configuration syntax;
• reset: delete all internal configuration, while keeping information about the VMD molecule;
• delete: delete the colvars module; after this, the module can be reissued again using cv molid;
• list: return a list of all colvars currently defined (see 13.2, 13.4 and 13.3 for how to configure a collective variable);
• list biases: return a list of all collective variable biases (i.e. sampling and analysis algorithms) currently defined (see 13.5 for how to configure a bias);
• load $<$ file name$>$ : load a collective variables state file, typically produced during a 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;
• 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 to annotate printframe's output;
• frame: return the current frame number, where variables are calculated;
• frame $<$ new frame$>$ : set the frame number (must be a valid frame number of the VMD molecule);
• colvar $<$ name$>$ update: recalculate the colvar $<$ name$>$ ;
• colvar $<$ name$>$ value: return the current value of the colvar $<$ name$>$ ;
• colvar $<$ name$>$ delete: delete the colvar $<$ name$>$ ;
• colvar $<$ name$>$ addforce force: apply the given force on $<$ name$>$ (this option is provided for compatibility with NAMD, but has no effect in VMD);
• bias $<$ name$>$ update: recalculate the bias $<$ name$>$ ;
• bias $<$ name$>$ energy: return the current energy of the bias $<$ name$>$ ;
• bias $<$ name$>$ delete: delete the bias $<$ name$>$ .