Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist > rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME?
Thank you Regards Kavya On Wed, Nov 6, 2013 at 11:52 AM, Kavyashree M <hmkv...@gmail.com> wrote: > 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
