[gmx-users] Relation between bonds and nstlist

Justin Lemkul 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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