Thank you. i am using my own vdw tables so need a cut off.
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/4/13 10:11 AM, Steven Neumann wrote: > >> Thank you! Would you suggest just a cut-off for coulmb? >> >> > Not a finite one. The best in vacuo settings are: > > pbc = no > rlist = 0 > rvdw = 0 > rcoulomb = 0 > nstlist = 0 > vdwtype = cutoff > coulombtype = cutoff > > -Justin > > 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 <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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**==================== > > 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
