Mark,
first of all I think that something wrong in amber and charm simulations because of some fluctuations of the box x-y-z dims during simulation Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Box-X 9.32108 0.0068 0.0360834 0.0289953 (nm) Box-Y 8.89245 0.0064 0.0344241 0.0276619 (nm) Box-Z 9.07051 0.013 0.0702945 -0.0525563 (nm) so due to decreasing of the box dims the overal conformational behaviour of the system is very 'straitjacketed' - its likely my protein placed in the compact crystal environment preventing its dynamics. James 2013/4/9 Mark Abraham <mark.j.abra...@gmail.com> > 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 > -- 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
