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

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 parallelize
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
CONCENTRATION	the concentration parameter for Von Mises-Fisher distributions
COMPONENT	if your input is a vector field use this to specifiy the component of the input vector field for which you wish to use
TEMP	the temperature at which you are operating

Examples

This is a typical example showing how CONVERT_TO_FES might be used when postprocessing 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

x: DISTANCE ATOMS=1,2
hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
ff: CONVERT_TO_FES GRID=hA1 TEMP=300
DUMPGRID GRID=ff FILE=fes.dat