[gmx-users] number of windows in PMF
Rebeca García Fandiño
regafan at hotmail.com
Wed Jul 13 00:07:46 CEST 2011
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?
> Date: Tue, 12 Jul 2011 17:59:44 -0400
> From: jalemkul at vt.edu
> To: gmx-users at 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 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
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