Action: VES_OUTPUT_FES

Module	ves
Description	Usage
Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients.

Details and examples

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

#SETTINGS INPUTFILES=regtest/ves/rt-output-fes-2d-targetdist/coeffs.input.data INPUTFILELINES=1-14
phi:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomspsi:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17

The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomsbf1: BF_FOURIERFourier basis functions. More details ORDERThe order of the basis function expansion=5 MINIMUMThe minimum of the interval on which the basis functions are defined=-pi MAXIMUMThe maximum of the interval on which the basis functions are defined=pi
The BF_FOURIER action with label bf1 calculates somethingbf2: BF_FOURIERFourier basis functions. More details ORDERThe order of the basis function expansion=5 MINIMUMThe minimum of the interval on which the basis functions are defined=-pi MAXIMUMThe maximum of the interval on which the basis functions are defined=pi

The BF_FOURIER action with label bf2 calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ...
 ARGthe labels of the scalars on which the bias will act=phi,psi
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1,bf2
 LABELa label for the action so that its output can be referenced in the input to other actions=ves1
 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_LINEAR_EXPANSION

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 potentialVES_OUTPUT_FESTool to output biases and free energy surfaces for VES biases from previously obtained coefficients. More details ...
  BIASthe 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_INPUTthe name of input coefficient file=
regtest/ves/rt-output-fes-2d-targetdist/coeffs.input.data
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/ves/rt-output-fes-2d-targetdist/coeffs.input.data
    
#! FIELDS idx_phi idx_psi ves1.coeffs ves1.aux_coeffs index
#! SET time 0.000000
#! SET iteration  0
#! SET type LinearBasisSet
#! SET ndimensions  2
#! SET ncoeffs_total  99
#! SET shape_phi  11
#! SET shape_psi  9
       0       0     0.000000     0.000000       0
       1       0     0.000000     0.000000       1
       2       0     0.000000     0.000000       2
       3       0     0.000000     0.000000       3
       4       0     0.000000     0.000000       4
       5       0     0.000000     0.000000       5
  
... VES_OUTPUT_FES

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 driveranalyze trajectories with plumed This action has hidden defaults. More details --plumed specify the name of the plumed input file plumed.dat --igrothe trajectory in gro format configuration.gro

The driver action with label plumed calculates somethingplumed driveranalyze trajectories with plumed This action uses the defaults shown here. More details --plumed specify the name of the plumed input file plumed.dat --igrothe trajectory in gro format configuration.gro
 --timestep the timestep that was used in the calculation that produced this trajectory in picoseconds 1.0 --trajectory-stride the frequency with which frames were output to this trajectory during the simulation (0 means that the number of the step is read from the trajectory file, currently working only for xtc/trr files read with --ixtc/--trr) 1 --multi set number of replicas for multi environment (needs MPI) 0 --dump-forces-fmt the format to use to dump the forces %%f 

Full list of keywords

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

Keyword	Type	Default	Description
BIAS	compulsory	none	the label of the VES bias for to output the free energy surfaces and the bias files
COEFFS_INPUT	compulsory	none	the name of input coefficient file
BIAS_OUTPUT	optional	not used	how often the bias(es) should be written out to file
FES_OUTPUT	optional	not used	how often the FES(s) should be written out to file
FES_PROJ_OUTPUT	optional	not used	how often the projections of the FES(s) should be written out to file