[gmx-users] Remove rotation from rmsd

Mikhail Yustanov mikhailyustanov at gmail.com
Thu Dec 4 04:04:19 CET 2014

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?



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