[gmx-users] regarding confout.gro

[Justin Lemkul]

On 10/15/14 6:25 AM, RINU KHATTRI wrote:
> hello justin
> i have been visualized the file of confout.gro file in vmd and the
> position of protein and ligand is ok i know i have to analyze all the
> parameters like energy and rmsd is it sufficient to extend my
> simulation or which file i have to visualized
>

The decision on whether or not to extend the simulation depends on the 
scientific questions being asked, and whether or not analysis of relevant 
quantities leads to you conclude that additional time is needed.  Visualization 
of any single snapshot will not tell you this.

-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

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

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