Did you correctly account for the different 1-4 scaling factors in the Berger and Amber lipids (either by obtaining .itp files from the authors of the Berger lipids-Amber protein article or making the changes yourself)? If not, then you are doing your simulation incorrectly (see their paper for why).
Chris. -- original message -- 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 ? James -- 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
