I am do not want to choose different pulling conditions as I build a model for specific force constant and pulling rate in given force filed. I think restraining would help much more to then exclude the ions impact.
Steven On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thank you a lot! > > > On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 7/31/13 6:52 AM, Steven Neumann wrote: >> >>> But even though on the other hand that could be more realistic free >>> energy >>> which could be compare to experiment which also involves ions. Would >>> Justin >>> please comment on this? >>> >>> >> I can offer you nothing more than a hand-waving explanation of what I >> think might happen here, so take that for what it's worth. Since you >> explicitly asked for my thoughts, such as they are... >> >> The dissociation of the ions may be nothing more than an artifact of the >> pulling conditions. Have you tried different force constants and pull >> rates to see if this behavior is affected? >> >> >> >>> On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann <s.neuman...@gmail.com >>> >wrote: >>> >>> They do not dissociate...Are you sure? My mdp specifies only ligand as a >>>> pull_group1. I think it would change having ions in this group included. >>>> >>>> >> Even though you're not explicitly pulling the ions, they are being forced >> to move due to the biasing potential that you are applying. >> >> I would think that sufficient sampling in each window (i.e. enough time >> that you might see dissociation of the ions) would provide you with enough >> information, but that's hard to predict. My assumption would be that the >> ions will absolutely impact the free energy of binding, but from what you >> said above, maybe that's right. Maybe it's not. Only way to find out >> would be to either exclude the ions or otherwise restrain their initial >> positions so that you get a "clean" reaction coordinate involving only the >> ligand. Then you can decompose the different contributions to the free >> energy of binding. >> >> -Justin >> >> >>>> On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs <lloyd.ri...@gmx.ch> >>>> wrote: >>>> >>>> >>>>> will get the PMF profile for my >>>>>> ligand binding or ligand and two ions binding? >>>>>> >>>>> >>>>> It would be the ligand and two ions unless the ions also at some point >>>>> discossiate from the ligand once in solvent. Could add positional >>>>> restraint >>>>> for them, but dont know how that effects the calculation? >>>>> *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr >>>>> *Von:* "Steven Neumann" <s.neuman...@gmail.com> >>>>> *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org> >>>>> *Betreff:* [gmx-users] Umbrella Sampling >>>>> >>>>> Dear Gmx Users, >>>>> >>>>> I run SMD to extract the windows for US calculations. The system >>>>> involves >>>>> negatively charged ligand and protein. I generated the protein-ligand >>>>> complex within self assembly MD simulations. >>>>> >>>>> I pulled my molecule away and two ions were also detached from the >>>>> protein >>>>> surface being attached to my ligand. >>>>> >>>>> My question: if I run my US caluclation and combine windows by WHAM (I >>>>> specified in my umbrella.mdp my ligand as a pull_group1 and same >>>>> protein >>>>> residues I pulled it from as pull_group0) will get the PMF profile for >>>>> my >>>>> ligand binding or ligand and two ions binding? >>>>> >>>>> Steven >>>>> -- >>>>> 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<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> >>>>> >>>>> >>>> >>>> >> -- >> ==============================**==================== >> >> 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
