Hi Aswathy You can make a group with Protein and ligand in an index file using make_ndx and pass it with -n in gmx rms.
Ashutosh On Fri, Apr 22, 2016 at 6:46 PM, Aswathy soman <aswathyneehar...@gmail.com> wrote: > Hi, > I have done a 100 ns simulation of protein-ligand complex. I was wondering > is it possible to calculate RMSD of the entire protein-ligand complex. How > to select the complex as such during the calculation of RMSD because there > is no group as protein+ligand. Thanking you in advance > > Regards, > Aswathy > -- > 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.