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

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

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

phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
rp: RESTRAINT ARG=phi KAPPA=50.0 ...
  AT=@replicas:{
        -3.00000000000000000000
        -2.22580645161290322584
        -1.45161290322580645168
        -.67741935483870967752
        .09677419354838709664
        .87096774193548387080
        1.64516129032258064496
        2.41935483870967741912
     }
...

hh: WHAM_HISTOGRAM ARG=phi BIAS=rp.bias TEMP=300 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=50
fes: CONVERT_TO_FES GRID=hh TEMP=300
DUMPGRID GRID=fes FILE=fes.dat

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

mpirun -np 6 plumed driver --mf_xtc alltraj.xtc --multi 6