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Subsections
Colvars scripting
Collective variables and biases can be added, queried and deleted through the scripting command
cv, with the following syntax: cv
subcommand
[args...]
for which the available subcommands are listed in the next subsections.
For example, to query the value of a collective variable named myVar,
use the following syntax: set value [cv colvar myVar value].
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. That is, they may be used within the callback procedures
(e.g. calc_colvar_forces) or in the NAMD config file after a run or
minimize statement.
- configfile
file name
: read configuration from a file
- config
string
: read configuration from the given string
- reset : delete all internal configuration
- list : return a list of all variables
- list biases : return a list of all biases
- load
file name
: load a state file (requires configuration)
- update : recalculate colvars and biases
- printframe : return a summary of the current frame
- printframelabels : return labels to annotate printframe's output
- colvar
name
value : return the current value of the colvar
name
- colvar
name
update : recalculate the colvar
name
- colvar
name
delete : delete the colvar
name
- 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
Next: Alchemical Free Energy Methods1
Up: Collective Variable-based Calculations1
Previous: Biasing and analysis methods
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