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 Colvars 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.
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.