Thank you for your reply. My box is quite small indeed, so my cut-offs are 0.5
If I make a single layer, I would have to run quite a small system in z-direction. My residue box size: 0.62840 0.54421 1.60000 0.00000 0.00000 -0.31420 0.00000 0.00000 0.00000 My suspect of the problem In my system I have Al, bonded to 6 OH, and Mg, that is non-bonded, so only LJ. My nrexcl is set to 2, as I don't have dihedrals. The Al and Mg form a mesh, that should be infinite in xy- I am guessing what I have to do is to artificially connect those Mg to OH with k=0 bonds & angles (?) and then include [ pairs ] of Mg O and Mg H to be calculated as LJ? I have a non usual FF, hence cannot figure out how to implement it yet. Thank you for help, V -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-missing-interactions-tp5010815p5010851.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
