Yes, there's no way to cheat on the explicit electrostatics to reduce cost, except implicit solvation. The kind of approach used in QM/MM is not useful for MM/MM! The rate-limiting part is still there.
Mark On Apr 8, 2013 12:42 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: > On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban <vvcha...@gmail.com > >wrote: > > > If you do not care about the atoms, which are too far away from the > region > > of interest, is it not reasonable just to cut that "useless" part? Also, > > > > Hear hear. If it's so meaningless, why is it there? ;) > > > > you may want to look towards implicit solvent simulations. > > > > > Indeed. Or use GPU's. Erik was showing us great performance on a laptop > during the webinar, even using (relatively) cheap consumer-grade cards. > Back to the original point (and as I posted before), even if you freeze > some amount of atoms, you don't gain any performance by doing so. > > -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
