On 6/14/16 4:38 AM, Sepideh Momeninezhad wrote:
hello everyone,i want to know how can i make average structure for my
molecule?


gmx rmsf -ox

Whether or not an average structure is at all meaningful or physical is another matter. http://www.gromacs.org/Documentation/Terminology/Average_Structure

-Justin

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==================================================

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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