Dear gromacs users I have executed the following command for the calculating the RMSD of a protein.
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 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 gmx-users-requ...@gromacs.org.
