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. Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
