[gmx-users] graph rmsd and rmsf(backbone)

Justin Lemkul jalemkul at vt.edu
Mon Sep 15 13:53:14 CEST 2014

On 9/15/14 12:36 AM, RINU KHATTRI wrote:
> http://s48.photobucket.com/user/mittukhattri/library/?view=recent&page=1
> hello gromacs users
> I am working on protein complex with popc membrane i have been plot
> two graph which is between time vs rmsd (backbone) ,rmsf in rmsf file
> i didnt get time its the serial no 1---- to last i made the graph here
> is the link i am not happy with it

By default, g_rmsf computes per-atom RMSF, unless you use the -res option, in 
which case you get per-residue RMSF.  It's not a time series.

> i didnt remove the initila frame in xtc file

You probably should, as well as removing even more frames that likely aren't 
equilibrated.  RMSF is very sensitive to equilibrium sampling.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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