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 
ATOMS
the four atoms involved in the torsional angle 
=5,7,9,15 The TORSION action with label phi calculates a single scalar value
psi: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=7,9,15,17 The TORSION action with label psi calculates a single scalar value
bf1: BF_FOURIER 
ORDER
compulsory keyword 
The order of the basis function expansion. 
=5 
MINIMUM
compulsory keyword 
The minimum of the interval on which the basis functions are defined. 
=-pi 
MAXIMUM
compulsory keyword 
The maximum of the interval on which the basis functions are defined. 
=pi The BF_FOURIER action with label bf1
bf2: BF_FOURIER 
ORDER
compulsory keyword 
The order of the basis function expansion. 
=5 
MINIMUM
compulsory keyword 
The minimum of the interval on which the basis functions are defined. 
=-pi 
MAXIMUM
compulsory keyword 
The maximum of the interval on which the basis functions are defined. 
=pi The BF_FOURIER action with label bf2
ves1: VES_LINEAR_EXPANSION ...
   
ARG
the input for this action is the scalar output from one or more other actions. 
=phi,psi 
   
BASIS_FUNCTIONS
compulsory keyword 
the label of the one dimensional basis functions that should be used. 
=bf1,bf2 
   
   
GRID_BINS
the number of bins used for the grid. 
=100,100 
   
PROJ_ARG1
arguments for doing projections of the FES or the target distribution.. 
=phi 
   
PROJ_ARG2
arguments for doing projections of the FES or the target distribution.. 
=psi 
...The VES_LINEAR_EXPANSION action with label ves1 calculates the following quantities:

 Quantity   
 Description  
ves1.bias
the instantaneous value of the bias potential
ves1.force2
the instantaneous value of the squared force due to this bias potential.


VES_OUTPUT_FES ...
   
BIAS
compulsory keyword 
the label of the VES bias for to output the free energy surfaces and the bias files
=ves1 
   
FES_OUTPUT
how often the FES(s) should be written out to file. 
=500 
   
FES_PROJ_OUTPUT
how often the projections of the FES(s) should be written out to file. 
=500 
   
BIAS_OUTPUT
how often the bias(es) should be written out to file. 
=500 
   
COEFFS_INPUT
compulsory keyword 
the name of input coefficient file 
=coeffs.input.data 
...The VES_OUTPUT_FES action with label 

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.