PLUMED-NEST

Project ID: plumID:19.075
Source: regtest/pycv/rt-f1/plumed.dat
Originally used with PLUMED version: 2.5.2-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

# LOAD FILE=PythonCV.dylib

dAB: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,4

The DISTANCE action with label dAB calculates a scalar quantitydAB2: 
PYTHONFUNCTION
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=dAB IMPORT=pythonfunction FUNCTION=square PERIODIC=NO

dAB2n: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=dAB 
POWERS
 the powers to which you are raising each of the arguments in your function
=2.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

DUMPDERIVATIVES
Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dAB2  
FILE
the name of the file on which to output the derivatives
=dAB2_grad    
FMT
 the format with which the derivatives should be output
=%.5f
DUMPDERIVATIVES
Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases). More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dAB2n 
FILE
the name of the file on which to output the derivatives
=dAB2n_grad   
FMT
 the format with which the derivatives should be output
=%.5f

PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=colvar.out 
ARG
the input for this action is the scalar output from one or more other actions