[gmx-users] Relation between bonds and nstlist
jalemkul at vt.edu
Fri Nov 7 13:41:57 CET 2014
On 11/7/14 6:23 AM, Mario Fernández Pendás wrote:
> Dear all,
> Is it possible that the choice of the value of nstlist can have any
> influence in the behaviour of the bonds between atoms?
Highly unlikely. Any atoms participating in bonds or angles have their
nonbonded interactions excluded. Dihedrals (1-4 interactions) are usually
included as normal or scaled nonbonded interactions, but occur at a distance
usually within rlist, so the calculation of those interactions should not be
affected by nstlist.
Can you describe more exactly the problem you're having? There are a number of
variables at play so it's hard to guess.
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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