On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> >> >> On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Steven Neumann wrote: >> >> Hi Justin, >> As you advised I reduced number of my windows and I obtined >> histogram: >> >> http://speedy.sh/2b9dT/histo._**_JPG<http://speedy.sh/2b9dT/histo.__JPG> >> >> <http://speedy.sh/2b9dT/histo.**JPG<http://speedy.sh/2b9dT/histo.JPG> >> > >> Which looks really good. >> The corresponding profile: >> >> http://speedy.sh/y8Ssz/__**profile.JPG<http://speedy.sh/y8Ssz/__profile.JPG> >> >> >> <http://speedy.sh/y8Ssz/**profile.JPG<http://speedy.sh/y8Ssz/profile.JPG> >> > >> I do not understand it. Does my deltaG of binding correspond to >> everything above 0 kcal/mol which is 6 kcal/mol? >> >> >> DeltaG = the free energy difference between the final and initial >> states. So that's up to you to decide. Your curve is rather rough >> and the energy minimum potentially still ill-defined. The >> histograms indicate that the sampling overlap is likely fine, you >> just may need a bit more sampling in each window to smooth things >> out. Also make use of the error estimates that g_wham can provide; >> they can be quite informative (and necessary). >> >> -Justin >> >> >> Thank you Justin. In each window I run the simulation of 10 ns. Do you >> think that making it 20 ns will make the profile more smooth? >> >> > > It's no use to blindly guess. It's up to you to assess the convergence of > your simulations and decide on an appropriate time frame. > > -Justin > > > Thank you Justin. Is there any way to find out after deltaG the entropic contribution to binding free energy? Steven > > -- > ==============================**========== > > 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 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> >
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