On 9/20/16 5:39 AM, Alex Mathew wrote:
Dear gmx experts,

I would calculate to energetically favoured conformation of my ligand with
protein for 100ns MD traj. I guess I have to use gmx cluster ,Any
assistance on how to proceed .
I need to get at least 10 most favoured conformations.

gmx cluster -f input.xtc -s input.tpr -method gromos -cl out.pdb -g out.log

is it okay?


gmx cluster does RMSD-based clustering. It can show you the most populated states, but there is no energy criterion here.

-Justin

--
==================================================

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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