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
