Hello, I would like to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40xNa+) above the membrane and water and chloride ions (40 Cl-) beneath it. First, I built up the system, did an energy minimization and then implemented the walls for the npt-equilibration. I didn't change anything in the topology. (Do I have to define the wall-atom-type there?If yes, what exactly do I have to put in the topology?) The interesting part of my nvt.mdp file looks like that:
nwall = 2 wall_type = 10-4 wall_density = 100 100 wall_atomtype = C C wall_r_linpot = 1 1 ; with -1 I got a fatal error, because atoms were beyond the wall wall_ewald_zfac = 3 ewald_geometry= 3dc pbc = xy ; Periodic Boundary Conditions in x/y direction What I see in VMD is the following: as expected some NA-ions are going through the membrane to reach the chloride/water side. But at the same time water molecules (and one chloride-ion) at both sides disappear in z-direction and never come back. In the first 10ps (with a tiny time step of 0.1fs) there were only a few molecules that went outside the box, but after 10 ps it increased dramatically and at some point the equilibration crashed. I already played around with time-steps, atom-types and the density, but couldn't find anything that works to keep the molecules inside the box... Anyone has an idea what I did wrong and how I can correct it? Unfortunately there is not much about that in the manual and I could not find anything that really helped me in the mailing-list archive.... Thanks in advance!!! Cheers, Marianne Schulte -- 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