[gmx-users] Silly little question about PMF - g_wham

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 19 01:42:44 CEST 2012

Eudes Fileti wrote:
> Hi gmx-users,
> How do I plot the repulsive part of the PMF between two molecules 
> that are approaching? I have achieved very good curves, but the potential 
> never exceeds the coordinate reaction axis, stopping exactly at 0.

The PMF always starts with zero assigned at the leftmost point, unless you 
specify its position to be elsewhere with the -zprof0 option.  If you want to 
sample more repulsive configurations in general, you'll need to set up windows 
at even smaller distances and perhaps stronger force constants.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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