Dear Gromacs users Unfortunately, no one did not answer my previous question about selection of appropriate option for trjconv -pbc to solve pbc problem.
For preparation of initial system, I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC lipid bilayer (black line) as a function of simulation time, using g_traj tool. The related figure is in following link: https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0 Do this state is related to pbc problem? How to solve this issue? Any help will highly appreciated. -- 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.
