Rebeca García Fandiño wrote:
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?
Appending should work as it would for any other simulation.
-Justin
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
>
> ========================================
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--
========================================
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
========================================
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