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 ATOMSthe pair of atom that we are calculating the distance between. =1,2
hA1: HISTOGRAM ARGthe input for this action is the scalar output from one or more other actions. =x GRID_MINcompulsory keyword
the lower bounds for the grid =0.0 GRID_MAXcompulsory keyword
the upper bounds for the grid =3.0 GRID_BINthe number of bins for the grid =100 BANDWIDTHcompulsory keyword
the bandwidths for kernel density estimation =0.1
ff: CONVERT_TO_FES GRIDcompulsory keyword
the action that creates the input grid you would like to use =hA1 TEMPthe temperature at which you are operating =300
DUMPGRID GRIDcompulsory keyword
the action that creates the grid you would like to output =ff FILEcompulsory keyword ( default=density )
the file on which to write the grid. =fes.dat

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