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Thanks again for your quick answer!<br>No, I did not prior equilibration, however for the analysis I was considering only the last 0.5 ns. <br>I will try to extend the simulations and see what happens. Is it possible to do it using tpbconv as in a typical simulation? Should I create different files for pullf*.xvg and pullx*.xvg and then join them for the analysis?<br>Best wishes,<br>Rebeca.<br><br><div>> Date: Tue, 12 Jul 2011 17:59:44 -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>> Justin A. Lemkul wrote:<br>> > <br>> > <br>> > Rebeca García Fandiño wrote:<br>> >> 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 <br>> >> too big. The histograms looked good, so I thought they should be <br>> >> well-converged...:S<br>> >> What should I do, extending the simulation or generating more windows?<br>> > <br>> > The simulations probably need to be longer. I've gotten good <br>> > convergence in much larger systems using far fewer windows but somewhat <br>> > longer simulations.<br>> > <br>> <br>> Another thing to consider (aside from my offhand guesses of simulation length) <br>> is that if you're generating velocities at the beginning of each simulation in <br>> each window in the absence of prior equilibration, you're not *really* getting 1 <br>> ns of viable data. Some should be discarded as equilibration, if you're not <br>> doing that already. If you've done prior equilibration in each window, then <br>> disregard this thought.<br>> <br>> -Justin<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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