[gmx-users] NVT problem
Andres Ortega Guerrero
og_andres15 at hotmail.com
Sat Mar 15 23:31:52 CET 2014
Thanks Justin for all your Help, i´m going to do all you suggesta and prepare a new structure,
but before that i would like to try with a POSRE for the protein 10000 due to i am using 1000,
also i would like to tell you, that due to the channel , is too big, in order to embebed in a 512 POPC Box,
i deleted some residues located at the terminal (inside the membrane) , so i think this could be
one reasson of the problem.
Thanks Andres Ortega
> Date: Sat, 15 Mar 2014 18:04:07 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] NVT problem
> On 3/15/14, 5:29 PM, Andres Ortega Guerrero wrote:
> > Hi Justin,
> > I have done a 1ns MD with DOX + water + CL ion , the topology didn´t present any problem,
> > i also did what you suggested, a -DFLEXIBLE EM and settle EM, but when i was trying to do my nvt.mdp
> > Step 0, time 0 (ps) LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.003859, max 0.176655 (between atoms 47397 and 47398)
> > bonds that rotated more than 30 degrees:
> > WARNING: Listed nonbonded interaction between particles 7156 and 7175
> > at distance 3f which is larger than the table limit 3f nm.
> > IMPORTANT: This should not happen in a stable simulation, so there is
> > probably something wrong with your system. Only change the table-extension
> > distance in the mdp file if you are really sure that is the reason.
> > this are the warning that appear, so based on this, the main problem seems like to be my structure right?
> > maybe, the DOX is misplaced or something like that, so should i prepare again the .gro files?
> Yes, if the simulation crashes at step 0 there are severe problems with the
> structure. The error messages tell you the problematic atoms, so simple
> visualization should tell you what is 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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