Dear Justin Thanks for your reply.
I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug molecules) are seen in other side of bilayer (bottom). I really do not know what thing has to be translated. Should I shift all components of my system (DPPC, drug, and water molecules) along z or only drug molecules? The dimensions of my system in final gro file are as follows: 6.46063 6.57889 8.30034 Based on your reply (The exact magnitude depends on the dimensions of the system), should I use following command: trjconv –trans 6.46063 6.57889 8.30034 -- 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.
