[gmx-users] gmx cluster

Justin Lemkul jalemkul at vt.edu
Tue Sep 20 17:55:52 CEST 2016

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 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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