Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex..
So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Thanks, Nitin On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/13 8:54 AM, Sainitin Donakonda wrote: > >> Hi , >> >> I want to use g_lie for my protein-drug complex to get binding energy ..i >> read some information that we need take care some issues if we used PME >> electrostatics.. >> >> Indeed i have used PME in my simulation.. >> >> Can any body explain which parameters to be taken care while running g_LIE >> and what is the isssue with PME .. >> >> > The long-range mesh terms are not decomposable in a pairwise manner. LIE > assumes that all of your interactions can be broken down from additive > terms, and this is not the case with PME. > > > and why we should use -rerun option beofre running LIE >> >> > If you evaluate the energies from a PME simulation, the result will be > off. If you use plain cutoffs for the dynamics, the simulation will > probably be junk. So one solution is to run the simulation with PME to get > reasonable dynamics, then post-process via mdrun -rerun while evaluating > energies with plain cutoffs (which one would usually increase beyond normal > values, IIRC, but I do not use LIE myself). > > -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 <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
