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

[Natalia Alveal F.]

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
>
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> 20 Penn St.
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>
> 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