[gmx-users] Turning off nonbonded interactions in protein-DNA
jalemkul at vt.edu
Wed Oct 21 23:20:23 CEST 2015
On 10/21/15 2:41 PM, Kartheek wrote:
> Dear all,
> I am now trying to do a simulation of protein-DNA complex by turning off all nonbonded interactions between protein and DNA, as suggested in the mailing list an "exclusions" section has been included in topology file. How do I know when I generate input file for mdrun whether these nonbonded interactions are turned off or not.
You can use gmx dump on the .tpr file to verify what's been excluded. But the
easier (and ultimately much faster) method is to use energygrp_excl in the .mdp
file, specifying Protein and DNA (which are default groups) to be excluded.
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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