WHAM_HISTOGRAM

This is part of the analysis module |

This can be used to output the a histogram using the weighted histogram technique

This shortcut action allows you to calculate a histogram using the weighted histogram analysis technique. For more detail on how this the weights for configurations are computed see REWEIGHT_WHAM

- Examples

The following input can be used to analyze the output from a series of umbrella sampling calculations. The trajectory from each of the simulations run with the different biases should be concatenated into a single trajectory before running the following analysis script on the concatenated trajectory using PLUMED driver. The umbrella sampling simulations that will be analyzed using the script below applied a harmonic restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values. The script below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm to determine a weight for each configuration in the concatenated trajectory. A histogram is then constructed from the configurations visited and their weights. This histogram is then converted into a free energy surface and output to a file called fes.dat

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

The script above must be run with multiple replicas using the following command:

mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4

- Glossary of keywords and components

- Compulsory keywords

ARG | the arguments that you would like to make the histogram for |

BIAS | ( default=*.bias ) the value of the biases to use when performing WHAM |

TEMP | the temperature at which the simulation was run |

STRIDE | ( default=1 ) the frequency with which the data should be stored to perform WHAM |

GRID_MIN | the minimum to use for the grid |

GRID_MAX | the maximum to use for the grid |

GRID_BIN | the number of bins to use for the grid |

- Options

BANDWIDTH | the bandwidth for kernel density estimation |