Thanks a lot for your answer. My system have about 29000 atoms, and the simulation time was 1ns. I have generated the error bars, and indeed you were right, they are too big. The histograms looked good, so I thought they should be well-converged...:S What should I do, extending the simulation or generating more windows? Thanks a lot again for your help. Best wishes, Rebeca.
> Date: Tue, 12 Jul 2011 16:53:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] number of windows in PMF > > > > Rebeca García Fandiño wrote: > > Hello, > > I am trying to calculate the binding energy between two monomers in > > three different dimers, using PMF (Umbrella Sampling method) and > > following Justin's tutorial. > > Using 100 windows separated 0.05 nm I get the PMFs represented in > > "pmf_using_100_points.pdf" (attached), and using 50 windows separated > > 0.1 nm I get different PMF results, represented in "pmf_using_50_points.pdf" > > How is it possible to obtain so different results depending on the > > number of windows used in the Umbrella Sampling Calculation? > > You haven't said how long your simulations are or how large the system is. > It > looks to me like your curves are not well-converged. The energy minima are > not > at a consistent location along the reaction coordinate, so I suspect you're > not > yet converged. > > g_wham will give you an error estimate; you may find that you have large > error > bars, so the results may be indistinguishable (within error), but from the > plots > one cannot tell. > > -Justin > > > Any help is appreciated. > > Thanks a lot in advance! > > Best wishes, > > Rebeca. > > > > Dr. Rebeca Garcia > > Santiago de Compostela University > > Spain > > > > -- > ======================================== > > 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 > > ======================================== > -- > 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
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