WHAM

The Weighted Histogram Analysis Method (WHAM) is a standard technique used to compute potentials of mean force (PMFs) from a set of umbrella sampling simulations.

I have largely rewritten and extended the implementation of the Weighted Histogram Analysis Method (WHAM) that is distributed with the GROMACS simulation software. The implementation, is thus freely available when you install the GROMACS package. The particular command is gmx wham.

Note: gmx wham does not require that the umbrella simulations were carried out with GROMACS. Non-GROMACS users can provide ASCII input files and use the wide functionality of gmx wham.

gmx wham supports:

• Robust error analysis using three different bootstrap techniques.
• Cyclic/periodic WHAM, useful for periodic reaction coordinates.
• Non-harmonic umbrella potentials via tabulated potentials.
• Autocorrelation analysis, autocorrelations are incorporated into WHAM.
• Extensive help text provided by command line gmx wham -h.

Examples and more details are provided in the following publication. We kindly ask you to cite this reference when you use results generated by gmx wham for a publication.