Hi, Making a selection with a tool like gmx select or gmx make_ndx is a good way to select e.g. by atomtype.
Mark On Sat, Aug 11, 2018, 12:58 Mahsa <ebadi.ma...@gmail.com> wrote: > Hello, > > I would like to calculate the RDF between some ions and oxygen atoms of a > polymer. The polymer has ester functional group with two different atom > types O and OS according to GAFF. It has also a side chain with ethereal > oxygen which has the same atom type as the ester part. How can I specify > the O of the side chain in the index file to tell it apart from the other O > atoms? > Besides there are around 500 of this atom in the system so changing > something manually is not a good option either. > > Best regards, > Mahsa > -- > 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.