Dear Subhomoi Thanks for your reply. I was doing the following:- discarding 1 ns trajectory by the following command:- gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o md_1000ps.xtc
Extracting average structure by the following command:- gmx rmsf -s md.tpr -f md_1000ps.xtc -o rmsf1000ps.xvg -ox average1000ps.pdb -res -n index.ndx I am confused between using gmx rmsf and gmx cluster for getting average structure for clustering should I do the following? gmx cluster -f md_1000ps.xtc -s md.tpr -n index.ndx -av average1000ps.pdb Can you please correct me. Thanks in advance. Sadaf -- 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.
