[gmx-users] Using pull code to keep two monomers near each other

Justin Lemkul jalemkul at vt.edu
Sat Mar 8 14:34:17 CET 2014

On 3/7/14, 7:19 PM, Michael Daily wrote:
> Hi,
> I am trying to use the pull code to keep two peptide monomers near each
> other during a replica exchange simulation of (homo)dimerization.  I do not
> want any bias if the COM distance between the two is less than some value
> r_max, as in umbrella sampling, i.e.
> E = 0  for r_ij <= r_max;
> E = k*(r_ij - r_max) for r_ij > r_max
> Can this be done with the pull code or some other function? Pull=constraint
> appears to essentially fix the COM distance, which I do not want to do
> either.

There is presently no flat-bottom potential implemented in the pull code, but 
one is planned for version 5.1.  In the meantime, it should be relatively easy 
to add yourself, though, especially if you use a harmonic potential rather than 
a linear one beyond r_max, then it's just a very simple extension of the 
existing harmonic potential.



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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