Thank you! Would you suggest just a cut-off for coulmb? Steven
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/4/13 10:03 AM, Steven Neumann wrote: > >> DEa Users, >> >> My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I >> want >> to use PME in my mdp: >> >> rcoulomb = 2.0 >> coulombtype = PME >> pme_order = 4 >> fourierspacing = 0.12 >> >> The cutoff needs to stay like this, I have my own tables with VDW, bonds, >> angles and dihedrals. >> >> i got the NOTE: >> >> The optimal PME mesh load for parallel simulations is below 0.5 >> and for highly parallel simulations between 0.25 and 0.33, >> for higher performance, increase the cut-off and the PME grid spacing >> >> what setting would you suggest to use on 8 CPUs? >> >> > I would suggest not using PME :) The problem is PME is extremely > inefficient in vacuo because it spends a lot of time doing nothing due to > the empty space. Moreover, you're not likely really simulating in vacuo at > that point because you've got PBC and therefore are really doing a > simulation in more of a diffuse crystal environment, so there are probably > artifacts. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
