[gmx-users] Relation between bonds and nstlist

[Mario Fernández Pendás]

Hi,

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.

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
>
> --
> ==================================================
>
> 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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