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

[Natalia Alveal F.]

But, I modify nstlist only for 500 ps to fix the problem that comming from
NVT. After that, I change nstlist to default value for MD.
Natalia


2014-05-08 12:51 GMT-04:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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-- 
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