If the box is periodic, then it is everywhere. mdrun makes no promises about its output being mapped to a particular box.
Mark On Thu, Jul 25, 2013 at 9:56 PM, Neha <nshafi...@wesleyan.edu> wrote: > Hi everybody, > > I was wondering if you could answer a quick question I had. Where does the > axis in a box with PBC lie in Gromacs? I thought 0, 0, 0 was the corner of > the box, but if that was true none of the x, y, z values for position should > be negative. However in my trajectory I see a value with a negative sign > before it which implies the axis might be somewhere else. It seems to happen > pretty rarely, so I am not sure why a) more of the values are not in the > negative direction or b) why that would happen in this one particular case? > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Axis-of-the-box-in-Gromacs-tp5010131.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
