[gmx-users] Nonsymetric molecule across pbc
jalemkul at vt.edu
Wed Feb 19 14:38:24 CET 2014
On 2/18/14, 4:04 PM, Steven Neumann wrote:
> Or maybe just 2 of them in the box: so that the one in the cell and another one
> has its quarter in the unit cell edge and the free energy between them? Then
> this PMF take into account all of the others being copied around. Would US mdp
> option wont complain?
Worth a try. This is a very complicated case that I doubt the pull code in
Gromacs will deal with very elegantly. You can easily define two vectors along
which to pull (one tube is pull_group0 and the other two are pull_group1 and
pull_group2, with relevant vectors for the biasing restraint). That's a fairly
simple 2-D PMF that can be done. The problem is in maintaining the equilateral
geometry that you desire. To do that, you have to introduce a third restraint,
which also somehow has to be debiased during WHAM. The problem is it does not
come from the pull code, so I honestly don't know how to deal with it within
Gromacs. You'll probably have to look into Alan Grossfield's WHAM program or
something else entirely, like PLUMED.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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