On Tue, Apr 9, 2013 at 9:59 AM, James Starlight <jmsstarli...@gmail.com> wrote: > By the way during simulation of the membrane-protein systems in the > Amber99sb ff (with berger lipids) I've noticed decreased of my system in > the Z-direction ( I've observed the same also during simulation of such > systems in the Charm full atomic ff). In both cases the observed effect was > seen in both GPU and non-gpu regimes with different cutoffs. > > It's intresting that in the gromos-united atom ff ( with vdw 1.2 cutoff > with berger lipids) I didnt observe such decreasing in the Z - dimension of > my bilayer. The only difference was in the water models (spc in the gromos > and tip3p in the amber or charm). Might it be relevant ? Should I switch to > the spc water with the amber ?
On principle, that is a bad idea. The force fields are parametrized to work with a particular water model, and you should only use another one after careful testing that there is a suitable benefit that outweighs any drawback. They are not plug and play. You have observed two different systems show different behaviour contracting in the Z direction. Why do you think one is abnormal and one is not? Mark -- 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