[gmx-users] Turning off nonbonded interactions in protein-DNA

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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