Indeed, it is unlikely that averaged coordinates of certain structure
versus time correspond to something physically meaningful.
How do you average them, by the way? And what for, please?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Tue, Sep 30, 2014 at 12:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/30/14 3:36 AM, Mahboobeh Eslami wrote:
hi GMX users
i have simulated the protein-ligand complex by gromacs for 20ns.
The average for the final structure of 18 to 20 nanoseconds has been
achieved.is minimization for the final average structure required?Sincerely.
An average structure might be totally unphysical. Energy minimization of an
unphysical structure leads you to something that is probably useless. I'd
suggest doing clustering if you're interested in the predominant
conformation(s) during a certain time period of the simulation.
-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
==
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