[gmx-users] npt dynamics generate a lot of pdb files

[Mark Abraham]

By modifying nstlist, you're very likely fixing a symptom, rather than
fixing the problem.

Mark


On Thu, May 8, 2014 at 6:21 PM, Natalia Alveal F. <nalveal at bio.puc.cl>wrote:

> Dear Gromacs users,
> Reducing the nstlist value works for me.
>
> Thanks a lot for yours suggestions.
>
>
> 2014-05-06 22:47 GMT-04:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 5/6/14, 5:23 PM, Riccardo Concu wrote:
> >
> >> Dear Natalia,
> >> that error basicly means your system is not well equilibrated, or it is
> >> exploading and so on. Normally, reducing the nstlist value in your mdp
> >> file
> >> should work.
> >>
> >
> > Usually there are far more catastrophic problems than nstlist, and the
> > only case I've found where anything improves is during EM where nstlist
> > must be 1. Decreasing the value may work, but I would be very surprised,
> > and ultimately there is a price to be paid in terms of performance that
> may
> > not be necessary.
> >
> > The OP should post a full description of prior minimization and
> > equilibration as well as the full .mdp file for the crashing run.
>  Without
> > that information, it's totally guesswork as to what's going on.
> >
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > 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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>
>
> --
> Natalia Alveal Fuentealba
> Ingeniera en Bioinformática
> Laboratory of Membranes Proteins Structure and Signalling
> Departamento de Fisiología
> Pontificia Universidad Católica de Chile
> Alameda 340, Santiago, Chile
> Fono: 56-2-3542877
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