Thanks Justin. yes, you are right, my simulation is very sensitive to cut-off.
I did not understand what do you meant by '' is the balance of forces correct''? So If I understood you correctly, the cut-off lengths must be chosen from the force filed, yes? Since I am not expert how to choose a force field, could you tell me a proper force field for Benzene all-atom model? Best regards On Thu, Jun 18, 2015 at 1:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/18/15 7:25 AM, Faezeh Pousaneh wrote: > >> thanks David. >> but I am wondering for example if a chosen short cut-off produces correct >> experimental data, should I still make it larger or PME? >> >> > Playing with cutoffs to try to force models to behave a certain way. You > might get a "right" answer, but is the balance of forces correct? Force > fields are generally tuned to be used with specific nonbonded regimes and > shouldn't be altered unless systematic studies of those setups have been > done. > > No that is an all-atom model. >> >> > Just for pedantic sake, GROMOS96 54A7 is indeed a UA force field, but > aromatic H are represented explicitly. So in this case, the electrostatic > treatment is indeed important. PME makes the Coulombic cutoff a bit more > flexible, but van der Waals interactions are going to be significant in a > system like this and can be very sensitive to changes in the cutoff. > > -Justin > > > >> Best regards >> >> >> On Wed, Jun 17, 2015 at 2:50 PM, David van der Spoel < >> sp...@xray.bmc.uu.se> >> wrote: >> >> On 17/06/15 14:22, Faezeh Pousaneh wrote: >>> >>> Hi, >>>> >>>> Does the choice of cut-off length depends on the chosen force filed? or >>>> it >>>> can be chosen such that the simulation produces the experimental values? >>>> >>>> Cutoff should be used consistently, each force field has their setting, >>> however that does not mean these settings are optimal. >>> Here is a recent paper on organic liquids discussing this. >>> http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00190 >>> >>> >>> >>> In my case, I simulation Benzene with Gromos54A7 and I choose 1.2 nm for >>>> both LJ and coul interactions, is that fine? >>>> >>>> Is it united atom? In that case you have no Coulomb. However from our >>> work >>> above it follows that 1.2 nm is too short and for accurate results you >>> need >>> to use PME for both Coulomb and Van der Waals. >>> >>> >>>> thanks >>>> Best regards >>>> >>>> >>>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
