[gmx-users] how does gmx rms work?

Seera Suryanarayana palusoori at gmail.com
Wed Sep 21 11:50:53 CEST 2016

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.

Graduate student

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