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 2013/4/8 Justin Lemkul <jalem...@vt.edu> > On Mon, Apr 8, 2013 at 7:50 AM, James Starlight <jmsstarli...@gmail.com > >wrote: > > > In literature I found that the ussage of 1.0 cutoffs should give good > > results but in the antechamber manual I've seen that usages of 1.2 > cutoofs > > ( with GAFF) should be used. So what cut-offs should I use for > > protein-ligand complexes done in amber ? (assuming that I simulate my > > system in the berger lipids ) > > > > > > > Do a few test runs and see. I would think the cutoff value would more > strongly affect the lipids, not the ligand, whose interactions are > comparatively few and relatively local. If you use the Verlet cutoff scheme > in version 4.6, it's largely irrelevant since there will not be any > "missed" interactions either way. > > -Justin > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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