I think it is a dangerous practice to simulate with a cutoff of 0.5 nm. Irrespectively of what you study.
Dr. Vitaly V. Chaban On Fri, Aug 30, 2013 at 11:32 AM, Valentina <valentina.erast...@durham.ac.uk > wrote: > 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 > -- 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