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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.

Managing the colvars module

Input and output

Accessing collective variables

Accessing biases


next up previous contents index
Next: Alchemical Free Energy Methods1 Up: Collective Variable-based Calculations1 Previous: Biasing and analysis methods   Contents   Index
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