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Potential of Mean Force  

2011-05-06 22:28:52|  分类: Gromacs |  标签: |举报 |字号 订阅

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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 and position are supported for use with the WHAM algorithm.  If you use direction the WHAM algorithm will fail.

A more detailed tutorial is linked from the Tutorials page.

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