[gmx-users] Nonsymetric molecule across pbc

Justin Lemkul 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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