[gmx-users] Using pull code to keep two monomers near each other
sebastien.cote.4 at umontreal.ca
Tue Mar 11 11:05:23 CET 2014
PLUMED might be useful in this case : http://www.plumed-code.org
You could setup a simulation with http://plumed.github.io/doc-v2.0/user-doc/html/_u_p_p_e_r__w_a_l_l_s.html to achieve your goal.
Or, as Justin suggested, it might be more straightforward for you to slightly modify the current Gromacs code.
> Date: Sat, 8 Mar 2014 08:32:37 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Using pull code to keep two monomers near each other
> 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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