Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools ..
thanks, nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/17/13 9:21 AM, Sainitin Donakonda wrote: > >> 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? >> >> > Which simulation stage do you normally use to collect data? > > -Justin > > 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 <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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<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 > > 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
