[gmx-users] on g_covar to produce average structure

Justin Lemkul jalemkul at vt.edu
Mon May 25 18:30:45 CEST 2015

On 5/25/15 1:44 AM, Brett wrote:
> Dear All,
> The on-line tutorial says, "Warning – Average structures (by g_covar) tend to be crude. Minimization is recommended". Here the minmization should be the "energy minization" step before the NVT and NPT equilibration steps, for our preparation of the files for the production md, right?

Yes, but whether or not an average structure or its minimized form has any 
physical relevance is debatable.



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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