Gromacs

Potential of Mean Force

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    The potential of mean force (PMF) is defined as the the potential that gives an average force over all the configurations of a given system.  There are several ways to calculate the PMF in GROMACS, probably the most common of which is to make use of the pull code.  The steps for obtaining a PMF using umbrella sampling, which allows for sampling of statistically-improbable states, are:

    1. Generate a series of configurations along a reaction coordinate (from a steered MD simulation, a normal MD simulation, or from some arbitrarily-created configurations)
    2. Use umbrella sampling to restrain these configurations within sampling windows.
    3. Use g_wham to make use of the WHAM algorithm to reconstruct a PMF curve.  Note that If you are using a GROMACS version in the 4.0.x series, only pull_geometry = distance and position are supported for use with the WHAM algorithm.  Use of direction will cause the WHAM algorithm to fail.  All of these geometries, however, are supported in newer (4.5.x) versions.

    A more detailed tutorial is linked from the Tutorials page.

    Page last modified 12:48, 8 Jun 2011 by JLemkul?