Try -pbc mol and -ur compact with trjconv command. I think this will help. On Sat, Aug 25, 2018 at 7:53 PM mmousivand93 <mmousivan...@ut.ac.ir> wrote:
> Dear all users > > I have run a molecular dynamic simulation for my aptamer-ligand by > gromacs (50 ns), At the end of simulations,by using VMD,it seems the > molecule is out side the box, but I am not sure, is it possible to check > the attachment and explain how to center it again? > > Thanks a lot > > Maryam-- > 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. -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- 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.
