[gmx-users] Relation between bonds and nstlist

[Mark Abraham]

Hi,

You'd want to start with section 3.4.2 in the manual.

Mark

On Wed, Nov 19, 2014 at 5:05 PM, Mario Fernández Pendás <mariofp77 at gmail.com
> wrote:

> Hi Justin,
>
> I am sorry to bother you again, can you recommend me any kind of refference
> to understand better how the neighbolist update works?
>
> Thank you very much.
>
> Best regards,
> Mario
>
> 2014-11-08 12:33 GMT+01:00 Mario Fernández Pendás <mariofp77 at gmail.com>:
>
> > Yes, that is exactly the case, I am using a modified mdrun.
> >
> > I was using nstlist = 1, but I was testing with different numbers to see
> > its influence, but I was not sure at wich level it was modifying my
> results.
> >
> > Thank you very much.
> >
> > 2014-11-07 22:24 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> >>
> >>
> >> On 11/7/14 8:06 AM, Mario Fernández Pendás wrote:
> >>
> >>> 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.
> >>>
> >>>
> >> 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 spurious stuff.
> >>
> >> -Justin
> >>
> >>
> >>  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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> >>>>
> >> --
> >> ==================================================
> >>
> >> 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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