[gmx-users] vapor phase pmf correction

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 27 19:15:46 CET 2010

On 2010-03-27 17.18, Robin C. Underwood wrote:
> 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
The paper you want to read is R. M. Neumann, Am. J. Phys. 48 (1980) p. 354.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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