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
