[gmx-users] how to apply distance restrains between a residue and an ion

Justin Lemkul 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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