[gmx-users] Calculate RMSD for specific residue.

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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