CONVERT_TO_FES

This is part of the gridtools module

Convert a histogram to a free energy surface.

This action allows you to take a free energy surface that was calculated using the HISTOGRAM action and to convert it to a free energy surface. This transformation performed by doing:

\[ F(x) = -k_B T \ln H(x) \]

The free energy calculated on a grid is output by this action and can be printed using DUMPGRID

Examples

This is a typical example showing how CONVERT_TO_FES might be used when post processing a trajectory. The input below calculates the free energy as a function of the distance between atom 1 and atom 2. This is done by accumulating a histogram as a function of this distance using kernel density estimation and the HISTOGRAM action. All the data within this trajectory is used in the construction of this HISTOGRAM. Finally, once all the data has been read in, the histogram is converted to a free energy using the formula above and the free energy is output to a file called fes.dat

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

contract shortcuts

x: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label x calculates a single scalar value
hA1: HISTOGRAM 
ARG
the quantity that is being averaged 
=x 
GRID_MIN
compulsory keyword ( default=auto )
the lower bounds for the grid 
=0.0 
GRID_MAX
compulsory keyword ( default=auto )
the upper bounds for the grid 
=3.0 
GRID_BIN
the number of bins for the grid 
=100 
BANDWIDTH
the bandwidths for kernel density esimtation 
=0.1 The HISTOGRAM action with label hA1 calculates a single scalar value
ff: CONVERT_TO_FES 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hA1 
TEMP
the temperature at which you are operating 
=300 The CONVERT_TO_FES action with label ff calculates a single scalar value
DUMPGRID 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff 
FILE
compulsory keyword ( default=density )
the file on which to write the grid. 
=fes.dat The DUMPGRID action with label 

x: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label x calculates a single scalar value
hA1_weight: ONES 
SIZE
compulsory keyword 
the number of ones that you would like to create 
=1 The ONES action with label hA1_weight calculates a single scalar value
hA1_kde: KDE 
ARG
the input for this action is the scalar output from one or more other actions. 
=x 
GRID_MIN
compulsory keyword ( default=auto )
the lower bounds for the grid 
=0.0 
GRID_MAX
compulsory keyword ( default=auto )
the upper bounds for the grid 
=3.0 
GRID_BIN
the number of bins for the grid 
=100 
BANDWIDTH
the bandwidths for kernel density esimtation 
=0.1 The KDE action with label hA1_kde calculates a single scalar value
hA1_kdep: CUSTOM 
ARG
the input to this function. 
=hA1_kde,hA1_weight 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x*y 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The CUSTOM action with label hA1_kdep calculates a single scalar value
hA1_u: ACCUMULATE 
ARG
the input for this action is the scalar output from one or more other actions. 
=hA1_kdep 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the data should be collected and added to the quantity being
averaged 
=1 
CLEAR
compulsory keyword ( default=0 )
the frequency with which to clear all the accumulated data. 
=0 The ACCUMULATE action with label hA1_u calculates a single scalar value
hA1_nsum: ACCUMULATE 
ARG
the input for this action is the scalar output from one or more other actions. 
=hA1_weight 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the data should be collected and added to the quantity being
averaged 
=1 
CLEAR
compulsory keyword ( default=0 )
the frequency with which to clear all the accumulated data. 
=0 The ACCUMULATE action with label hA1_nsum calculates a single scalar value
hA1: CUSTOM 
ARG
the input to this function. 
=hA1_u,hA1_nsum 
FUNC
compulsory keyword 
the function you wish to evaluate 
=x/y 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The CUSTOM action with label hA1 calculates a single scalar value
ff: CUSTOM 
ARG
the input to this function. 
=hA1 
FUNC
compulsory keyword 
the function you wish to evaluate 
=-2.49434*log(x) 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The CUSTOM action with label ff calculates a single scalar value
DUMPGRID 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff 
FILE
compulsory keyword ( default=density )
the file on which to write the grid. 
=fes.dat The DUMPGRID action with label 

Glossary of keywords and components

Compulsory keywords

ARG	the histogram that you would like to convert into a free energy surface

Options

MINTOZERO	( default=off ) set the minimum in the free energy to be equal to zero
GRID	the histogram that you would like to convert into a free energy surface (old syntax)
TEMP	the temperature at which you are operating