[gmx-users] NVT problem

Justin Lemkul jalemkul at vt.edu
Sat Mar 15 23:05:50 CET 2014

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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