VES_OUTPUT_FES
 This is part of the ves module It is only available if you configure PLUMED with ./configure –enable-modules=ves . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients.

This action can be used to output to file biases and free energy surfaces for VES biases from previously obtained coefficients. It should be used through the driver and can only be used in post processing. The VES bias needs to be defined in the exact same way as during the simulation. At the current moment this action does not support dynamic target distributions (e.g. well-tempered).

Examples

In the following input we define a VES bias and then read in the coefficient file coeffs.input.data and output the FES and bias every 500 iterations.

Click on the labels of the actions for more information on what each action computes
phi: TORSION ATOMSthe four atoms involved in the torsional angle =5,7,9,15
psi: TORSION ATOMSthe four atoms involved in the torsional angle =7,9,15,17
bf1: BF_FOURIER ORDERcompulsory keyword
The order of the basis function expansion. =5 MINIMUMcompulsory keyword
The minimum of the interval on which the basis functions are defined. =-pi MAXIMUMcompulsory keyword
The maximum of the interval on which the basis functions are defined. =pi
bf2: BF_FOURIER ORDERcompulsory keyword
The order of the basis function expansion. =5 MINIMUMcompulsory keyword
The minimum of the interval on which the basis functions are defined. =-pi MAXIMUMcompulsory keyword
The maximum of the interval on which the basis functions are defined. =pi
ves1: VES_LINEAR_EXPANSION ...
ARGthe input for this action is the scalar output from one or more other actions. =phi,psi
BASIS_FUNCTIONScompulsory keyword
the label of the one dimensional basis functions that should be used. =bf1,bf2

GRID_BINSthe number of bins used for the grid. =100,100
PROJ_ARG1arguments for doing projections of the FES or the target distribution.. =phi
PROJ_ARG2arguments for doing projections of the FES or the target distribution.. =psi
...
VES_OUTPUT_FES ...
BIAScompulsory keyword
the label of the VES bias for to output the free energy surfaces and the bias files
=ves1
FES_OUTPUThow often the FES(s) should be written out to file. =500
FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file. =500
BIAS_OUTPUThow often the bias(es) should be written out to file. =500
COEFFS_INPUTcompulsory keyword
the name of input coefficient file =coeffs.input.data
...


The header of coeffs.input.data should look like the following:

#! FIELDS idx_phi idx_psi ves1.coeffs ves1.aux_coeffs index
#! SET time 100.000000
#! SET iteration  10
#! SET type LinearBasisSet
#! SET ndimensions  2
#! SET ncoeffs_total  121
#! SET shape_phi  11
#! SET shape_psi  11


This input should be run through the driver by using a command similar to the following one where the trajectory/configuration file configuration.gro is needed to correctly define the CVs

plumed driver --plumed plumed.dat --igro configuration.gro

Glossary of keywords and components
Compulsory keywords
 BIAS the label of the VES bias for to output the free energy surfaces and the bias files COEFFS_INPUT the name of input coefficient file
Options
 BIAS_OUTPUT how often the bias(es) should be written out to file. Note that the value is given in terms of coefficient iterations. FES_OUTPUT how often the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations. FES_PROJ_OUTPUT how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.