Hi, It's a periodic box, right? There is only one water region. You can't get steady-state non-equilibrium ion distribution without forcing it, e.g. https://www.mpibpc.mpg.de/grubmueller/compel
Mark On Tue, Jul 14, 2015 at 12:42 PM anu chandra <anu80...@gmail.com> wrote: > Dear Gromacs users, > > I am working with membrane proteins. The system contains CaCl2 ions and I > build the system with calcium ions on one side of the membrane (here, upper > layer) and chloride ions distributed on both side of the membrane, in order > to maintain the physiological condition. Unfortunately, after the very > first minimization, when I visualize the gro file in VMD I have noticed > that the calcium ions entered the opposite side of the membrane (ie, > lower layer) and subsequently get distributed in the lower layer during the > equilibration process. Though I have tried with varying Z-dimension values > of the box size, the same has been noticed when visualizing the output gro > file with VMD. > > Please help me to figure out what is wrong with my simulation box. > > Many thanks > Anu > -- > 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.