[gmx-users] vapor phase pmf correction

Robin C. Underwood rcunderw at purdue.edu
Sat Mar 27 17:18:41 CET 2010

Hello Gromacs users,

I have a simple question about whether it is possible to implement a kinetic
energy correction to vapor phase potential of mean force calculations using
g_wham. I have used the umbrella pulling method (outlined in the umbrella
sampling tutorial by Justin on the Gromacs tutorial web page) but for a very
simple system- pulling apart two methanes. When I run g_wham, my resulting pmf
graph is shifted uniformly by about -13 kJ/mol from achieving a baseline of
zero, and has a deeper minimum than I would expect based on the literature.
Thus, I would like to use g_wham on only the potential energy portion, excluding
the kinetic portion from my calculation. Is it possible to do this? 

I have read the entropic effects section 6 in the manual, but do not understand
the statistical mechanical origin of this equation 6.1. I assume r represents
the pull parameter, in my case, distance between the COM of the two groups. If
so, such a correction does not shift my pmf to a baseline of 0.


Robin C. Underwood
Chemistry Department
560 Oval Drive
West Lafayette, IN 47907

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