As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-)
Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati <shahab.shari...@gmail.com>wrote: > Dear Mark > > Thank for your reply. > > If I show my system as 4 regions, my system before equilibration is as > fallows: > > region (1): water + drug > region (2): top leaflet of bilayer > region (3): bottom leaflet of bilayer > region (4): water > > After equilibration, drug molecule exits region (1) and enters region (4). > > Please tell me how to fix it? Which options of trjconv are appropriate > for this problem? > > Best wishes > -- > 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