[gmx-users] Calculate RMSD for specific residue.
jalemkul at vt.edu
Tue Aug 19 14:12:16 CEST 2014
On 8/19/14, 8:10 AM, Dawid das wrote:
> Dear Gromacs experts,
> How can I calculate RMSD as a fucntion of time for one residue in my
> protein? Let's say I have a part of my sequence:
> ...-Phe-Ala-Ser-CH6-Tyr-Met-Cys-Gly-... . Now I want to get a plot of RMSD
> versus time for CH6 (my newly introduced residue).
> I can't find such an option in g_rms and what g_rmsf -od is not what I am
> interested in or I understood something incorrectly.
g_rms will do whatever you want if you provide the right index group.
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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