[gmx-users] Remove rotation from rmsd

Justin Lemkul jalemkul at vt.edu
Thu Dec 4 04:07:51 CET 2014

On 12/3/14 10:04 PM, Mikhail Yustanov wrote:
> Hi all,
> I am trying to remove rotation from the output trajectories and rmsd plots.
> I used:
> gmx trjconv -fit rot+trans -s step5.tpr -f step5_noPBC.xtc -o OUTPUT.xtc
> I selected protein for fitting and system for output.
> Then I visualized OUTPUT.xtc, it seems rotation has been removed.
> However, then I use
> gmx rms -s step5.tpr -f OUTPUT.xtc -o rmsd.xvg -tu ns
> to generate rmsd for c-alpha, but rmsd plot shows no change from original.
> How do I remove the rotation in the rmsd plot?

Fitting is done within gmx rms, so there probably won't be a difference if you 
do rotational fitting via trjconv.



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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