Thanks a lot for your suggestions. On Mon, Dec 19, 2011 at 21:00, David Mobley <[email protected]> wrote:
> Yes, changing the net charge of the system is something that is rather > complicated in fact (one can plunge ahead and do it while ignoring the > complications, but the results will typically be rather system-size > dependent and essentially wrong). For more details refer to the Kastenholz > and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references > therein. The good news is that for simple spherical ions K&H have worked > out the relevant corrections. The bad news is that if you move away from > simple spherical ions you've got problems. > > David Mobley > > > > On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul <[email protected]> wrote: > >> >> >> bipin singh wrote: >> >>> Hello, >>> >>> I am willing to study the free energy of binding of a cation (Ca++) to >>> the protein and I am following the free energy tutorial >>> provided by Justin >>> (http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >>> gmx-tutorials/free_energy<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy> >>> ). >>> Please let me know whether the settings for this type of study would >>> be same as given in the tutorial for ligand-Protein >>> binding free energy calculation or it need some different approach: >>> >> >> By decoupling a Ca2+ ion, you are removing 2 charges from the system. I >> don't know how to properly treat such a case (perhaps someone else can >> comment), but likely you'll find such topics in the literature. A better >> approach may be umbrella sampling, but again the literature should point >> you to reasonable methodology. I'm sure others have dealt with such >> questions before. >> >> -Justin >> >> >> The setting from the ligand-Protein binding free energy calculation >>> are given as: >>> >>> >>> van der Waals coupling: >>> >>> sc-alpha = 0.5 ; use soft-core for LJ (de)coupling >>> sc-sigma = 0.3 >>> sc-power = 1 >>> couple-moltype = LIG >>> couple-intramol = no >>> couple-lambda0 = none ; non-interacting dummy in state A >>> couple-lambda1 = vdw ; only vdW terms on in state B >>> >>> Coulombic coupling: >>> >>> sc-alpha = 0 ; soft-core during (dis)charging can >>> be unstable! >>> sc-sigma = 0 >>> couple-moltype = LIG >>> couple-intramol = no >>> couple-lambda0 = vdw ; only vdW terms in state A (the >>> previous state B is now A) >>> couple-lambda1 = vdw-q ; all nonbonded interactions are on in >>> state B >>> >>> >>> >> -- >> ==============================**========== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==============================**========== >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > > > -- > David Mobley > [email protected] > 504-383-3662 > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ----------------------- *Regards,* Bipin Singh
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