[gmx-users] Relation between bonds and nstlist
jalemkul at vt.edu
Fri Nov 7 22:25:02 CET 2014
On 11/7/14 8:06 AM, Mario Fernández Pendás wrote:
> Thank you for your reference Nizar, I will read it carefully.
> Justin, the problem is that I am using my own version of the code with
> Hybrid Monte Carlo included. Now I am observing that there is a relation
> between the value of nstlist and the acceptance rate and accuracy of the
> HMC, so I was trying to guess in which part of the simulation this value is
> playing a key role.
So I'm assuming you're using a modified mdrun as your MC engine, then? If
that's the case, I would assume you'd probably have to set nstlist = 1 for
anything to make sense. If you're making MC moves but not updating the
neighborlist every time you do, you'd probably end up calculating a bunch of
> Thank you very much,
> Mario Fernández-Pendás
> El 07/11/2014 13:42, "Justin Lemkul" <jalemkul at vt.edu> escribió:
>> 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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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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