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Thanks a lot for your answer.<br>My system have about 29000 atoms, and the simulation time was 1ns. <br>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<br>What should I do, extending the simulation or generating more windows?<br>Thanks a lot again for your help.<br>Best wishes,<br>Rebeca.<br><br><div>> Date: Tue, 12 Jul 2011 16:53:54 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] number of windows in PMF<br>> <br>> <br>> <br>> Rebeca García Fandiño wrote:<br>> > Hello,<br>> > I am trying to calculate the binding energy between two monomers in <br>> > three different dimers, using PMF (Umbrella Sampling method) and <br>> > following Justin's tutorial.<br>> > Using 100 windows separated 0.05 nm I get the PMFs represented in <br>> > "pmf_using_100_points.pdf" (attached), and using 50 windows separated <br>> > 0.1 nm I get different PMF results, represented in "pmf_using_50_points.pdf"<br>> > How is it possible to obtain so different results depending on the <br>> > number of windows used in the Umbrella Sampling Calculation?<br>> <br>> You haven't said how long your simulations are or how large the system is. It <br>> looks to me like your curves are not well-converged. The energy minima are not <br>> at a consistent location along the reaction coordinate, so I suspect you're not <br>> yet converged.<br>> <br>> g_wham will give you an error estimate; you may find that you have large error <br>> bars, so the results may be indistinguishable (within error), but from the plots <br>> one cannot tell.<br>> <br>> -Justin<br>> <br>> > Any help is appreciated.<br>> > Thanks a lot in advance!<br>> > Best wishes,<br>> > Rebeca.<br>> > <br>> > Dr. Rebeca Garcia<br>> > Santiago de Compostela University<br>> > Spain<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div> </div></body>
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