Hi Tsjerk, I defined only one box. I mean several atoms in one chain run out of the boundary, and I can see them in the box but not in the chain. So I think maybe they run to the nearby box because of the periodic boundary conditions.
Thanks, Ming -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Sunday, 5 April 2015 7:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] periodic boundary conditions pbc=xyz Hi Ming, You have another box in your (infinite) periodic system? Cheers, Tsjerk On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang <m21.t...@qut.edu.au> wrote: > Dear all, > > I did a simulation using periodic boundary conditions pbc=xyz. It > turns out that the box is defined too small, and some atoms go to another box. > Does this affect the simulation result? If not, how to display the > real model (without separation) in VMD? > > Thanks in advance, > Ming > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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.