[gmx-users] how to apply distance restrains between a residue and an ion
jalemkul at vt.edu
Wed Sep 2 01:20:16 CEST 2015
On 9/1/15 5:57 PM, Victor Ma wrote:
> Thank you Justin.
> Right now I have a sodium with three ligand residue. One of the ligand
> residue is in a not very good position. I would like to apply a soft
> harmonic distant restraint to keep them together and pull the "bad" ligand
> residue a little closer. Mostly I am trying to maintain and optimize this
> sodium-ligand cluster. What would you suggest? I am using Gromacs 5.0.4.
> The "flat bottom restraints" and "intermolecular distance restraints" are
> in the 5.1 version? Is "Any pull rate of zero maintains a specified
> distance using a harmonic biasing potential. " what I need?
What you need is a simple application of the pull code to apply a harmonic
biasing force to these atoms. A pull rate of zero and a pull reference distance
of whatever you want the coordinating distance to be is straightforward. You
can also use the pull code to simultaneously restrain all three distances by
setting them as separate coordinates in the .mdp file.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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