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
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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