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 only pull_geometry = distance is supported for use with the WHAM algorithm.  If you use "distance" or "position" the WHAM algorithm will fail.
    Page last modified 19:52, 29 Oct 2009 by JLemkul?