Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in the energies isnt it?
Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M <hmkv...@gmail.com> wrote: > Ok thank you. I thought it was for protein-ligand-water > that needs to be rerun without PME. > > Thanks > Regards > Kavya > > > > On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 11/2/13 12:14 PM, Kavyashree M wrote: >> >>> Sir, >>> >>> Thank you. Should the ligand-water MD be done without PME? >>> >>> >> I already answered this. Please read my previous reply again. >> >> -Justin >> >> >> Thank you >>> Regards >>> >>> Kavya >>> >>> >>> On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 11/2/13 1:22 AM, Kavyashree M wrote: >>>> >>>> Dear Users, >>>>> >>>>> Its mentioned in the list that it would be >>>>> wrong to use g_lie on a simulation which >>>>> uses PME. >>>>> >>>>> So kindly suggest any other way available >>>>> to get the free energy of ligand binding other >>>>> using g_lie? >>>>> >>>>> >>>>> The original simulation should be done with PME, then the energies >>>> recalculated using mdrun -rerun without PME. More detailed methods are >>>> available in the list archive; this topic gets discussed a lot. >>>> >>>> >>>> -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 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> >>>> ================================================== >>>> -- >>>> 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 >>>> >>>> >> -- >> ================================================== >> >> 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 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >> ================================================== >> -- >> 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