CONVERT_TO_FES

Convert a histogram, \(H(x)\), to a free energy surface using \(F(x) = -k_B T \ln H(x)\).

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

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 input for this action is the scalar output from one or more other actions. 
=x 
GRID_MIN
compulsory keyword 
the lower bounds for the grid 
=0.0 
GRID_MAX
compulsory keyword 
the upper bounds for the grid 
=3.0 
GRID_BIN
the number of bins for the grid 
=100 
BANDWIDTH
compulsory keyword 
the bandwidths for kernel density estimation 
=0.1 The HISTOGRAM action with label hA1
ff: CONVERT_TO_FES 
GRID
compulsory keyword 
the action that creates the input grid you would like to use 
=hA1 
TEMP
the temperature at which you are operating 
=300 The CONVERT_TO_FES action with label ff
DUMPGRID 
GRID
compulsory keyword 
the action that creates the grid you would like to output 
=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

GRID	the action that creates the input grid you would like to use

Options

SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
MINTOZERO	( default=off ) set the minimum in the free energy to be equal to zero
CONCENTRATION	the concentration parameter for Von Mises-Fisher distributions
COMPONENT	if your input is a vector field use this to specify the component of the input vector field for which you wish to use
TEMP	the temperature at which you are operating