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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
.
Next: Configuration syntax for the
Up: General parameters and input/output
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