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. <nalv...@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 <jalem...@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 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.