[gmx-users] RMSD plot of the backbone atoms

Justin Lemkul jalemkul at vt.edu
Thu Mar 3 23:04:47 CET 2016

On 3/3/16 7:01 AM, Mahboobeh Eslami wrote:
> hi GMX usersi have done MD simulation for a  protein-protein complex.  i want to get RMSD plot of the backbone atoms for one of the  protein chain. how do i prepare index file?thanks for your help

Use make_ndx.  Type "help" at the prompt if you want examples.  Otherwise, most 
simple tutorials cover this.



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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