Thanks again for your quick answer! No, I did not prior equilibration, however for the analysis I was considering only the last 0.5 ns. 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? Best wishes, Rebeca.
> Date: Tue, 12 Jul 2011 17:59:44 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] number of windows in PMF > > > > Justin A. Lemkul wrote: > > > > > > Rebeca García Fandiño wrote: > >> 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? > > > > The simulations probably need to be longer. I've gotten good > > convergence in much larger systems using far fewer windows but somewhat > > longer simulations. > > > > Another thing to consider (aside from my offhand guesses of simulation > length) > is that if you're generating velocities at the beginning of each simulation > in > each window in the absence of prior equilibration, you're not *really* > getting 1 > ns of viable data. Some should be discarded as equilibration, if you're not > doing that already. If you've done prior equilibration in each window, then > disregard this thought. > > -Justin > > -- > ======================================== > > 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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