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:DISTANCEATOMS=1,2the pair of atom that we are calculating the distance between.hA1:HISTOGRAMARG=the input for this action is the scalar output from one or more other actions.xGRID_MIN=0.0compulsory keywordthe lower bounds for the gridGRID_MAX=3.0compulsory keywordthe upper bounds for the gridGRID_BIN=100the number of bins for the gridBANDWIDTH=0.1compulsory keywordthe bandwidths for kernel density estimationff:CONVERT_TO_FESGRID=compulsory keywordthe action that creates the input grid you would like to usehA1TEMP=300 DUMPGRIDthe temperature at which you are operatingGRID=compulsory keywordthe action that creates the grid you would like to outputffFILE=fes.datcompulsory keyword ( default=density )the file on which to write the grid.

- 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 |