[gmx-users] how does gmx rms work?

[Justin Lemkul]

On 9/21/16 5:50 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
>
> Previously I posed a problem how to calculate the RMSD of our interested
> region of protein, even though I did simulation for full length protein. I
> got solution from one of our user. Based his suggestion I created index
> file and have executed the following command.
>
> gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx
>
> My index.ndx file has the c alpha numbers which I have to calculate the
> RMSD. Here I am not mentioning any superimposition. How does the gmx rms
> command work? can I do superimposition of my interested residues?   and
> also what is -fit argument?  I request you to answer my question.
>

The first group gmx rms prompts for is the fitting group, applying whatever type 
of fitting is requested in -fit.  The default is rotational and translational 
fitting, which is usually what one wants to avoid spurious global contributions 
to the RMSD.

-Justin

-- 
==================================================

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

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