Shortcut: EXTRACV

Module	colvar
Description	Usage
Allow PLUMED to use collective variables computed in the MD engine.
output value	type
the value of the CV that was passed from the MD code to PLUMED	scalar

Further details and examples

Allow PLUMED to use collective variables computed in the MD engine.

This feature requires the MD engine to use special instructions to pass to PLUMED the value of some pre-computed collective variable. Check the documentation for the MD code to find out which collective variables can be computed and passed to PLUMED. These variables can then be accessed by name using the EXTRACV action.

This example takes the lambda variable pre-computed in GROMACS and applies a restraint to keep it close to the value 3.

Click on the labels of the actions for more information on what each action computes

lThe EXTRACV action with label l calculates the following quantities:
 Quantity   
 Type   
 Description  
l
scalar
the value of the CV that was passed from the MD code to PLUMED: EXTRACVAllow PLUMED to use collective variables computed in the MD engine. This action is a shortcut. More details NAMEname of the CV as computed by the MD engine=lambda
# PLUMED interprets the command:
# l: EXTRACV NAME=lambda
# as follows (Click the red comment above to revert to the short version of the input):
lambdaThe PUT action with label lambda calculates the following quantities:
 Quantity   
 Type   
 Description  
lambda
scalar
the data that was passed from the MD code: PUTPass data into PLUMED More details UNITthe unit of the quantity that is being passed to PLUMED through this value=number SHAPE the shape of the value that is being passed to PLUMED=0 MUTABLE can plumed change the value of the pointer that is passed from the MD code PERIODICif the value being passed to plumed is periodic then you should specify the periodicity of the function=NO
lThe COMBINE action with label l calculates the following quantities:
 Quantity   
 Type   
 Description  
l
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lambda PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=l KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10 ATthe position of the restraint=3

Syntax

The following table describes the keywords and options that can be used with this action