Hi Rajat, Thanks -- but I don't want -pbc mol because that keeps my molecules whole, which I don't want. I actually want to keep the shape of the cubic box for my purposes. Maybe I'll try -pbc atom -ur compact, but I think I tried that and it didn't work -- but will try again.
Mala On Fri, Feb 8, 2019 at 5:19 AM Rajat Desikan <rajatdesi...@gmail.com> wrote: > Hi Mala, > Please combine -center with "-pbc mol -ur compact" and check. > > Regards, > Rajat > > -- > Dr. Rajat Desikan > Invictus Oncology, Delhi > -- > 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. > -- Mala L. Radhakrishnan Whitehead Associate Professor of Critical Thought Associate Professor of Chemistry Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- 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.
