Hi Lara, The cut-offs are pretty much part of the force field. One rule is that the distance between periodic images should be larger than the cutoff. For protein/solute simulations that translates in a minimal distance between the solute and the wall of half the cutoff used. Another rule is based on the solvent ordering. In water, ordering carries through approximately four layers of water, corresponding to 1 nm. So to avoid indirect effects through solvent ordering, it is advisable to use a distance between periodic images of 2 nm, i.e. a distance between solute and box wall of 1 nm.
Hope it helps, Tsjerk On Thu, Mar 22, 2012 at 5:08 PM, Lara Bunte <lara.bu...@yahoo.de> wrote: > Hello > > What size should a box have in that you do your MD? I always read that for > short Lennard Jones interactions one should do a cut off with the half of the > box size but what how to know a good box size? > > Thanks for help > Greetings > Lara > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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