[gmx-users] NVT Equilibration error

Justin Lemkul jalemkul at vt.edu
Tue May 5 18:42:05 CEST 2015

On 5/5/15 12:38 PM, Agnivo Gosai wrote:
> Justin & Tsjerk
> So, do you think the equilibration error is because of this long bond ? I
> was thinking as the error message was about water molecules/atoms , the
> source was something else.

Cause and effect.  You have to visualize everything at every step.  Did the 
output of minimization look OK?  Did you investigate the atoms that pdb2gmx 
warned you about?  Or did you just rely on a number in a .log file?  Always 
confirm that things are OK!  The energy and force are merely suggestive that 
things are right, but you still have to check.  Probably you have a distorted 
geometry there, that kicks things around and ultimately causes a water molecule 
to violently crash into something.  It's a bit odd that it took so long, but not 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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