Hi, You should create an index file (use gmx make_ndx) that contains a list of the atom you want to perform RMSD calculation on, e.g P atoms, or whatever you want. Then when you run gmx rms, you have to pass the index file from the above step Best,
On Sat, May 25, 2019 at 11:41 AM mmousivand93 <mmousivan...@ut.ac.ir> wrote: > Dear all > > I have been run molecular dynamic simulation between DNA(50bp)and small > ligand,how to calculate RMSD value for > > specified length of DNA during 50ns simulation(for example residues > from 12 to 25)? > > Best Regards > -- > 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. > -- 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.