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

Justin Lemkul jalemkul at vt.edu
Wed May 7 04:49:02 CEST 2014

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 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


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