[gmx-users] Doubt in gmx rms

Seera Suryanarayana palusoori at gmail.com
Wed Sep 21 19:00:49 CEST 2016

Dear gromacs users

I have executed the following command for the calculating the RMSD of a

gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx

My doubt is whether I did correct or wrong I don't know. I have simulation
of 197 residues length protein and I want to calculate the RMSD for 2-27
residues. Then I created the index file which contains the c alpha atoms
numbers and passed it to RMSD calculation with the -n argument. Just tell
me whether my command  is correct or wrong.

Thanks in advance
Graduate student

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