[gmx-users] number of windows in PMF

[Justin A. Lemkul]

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: 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
>  >
>  > --
>  > ========================================
>  >
>  > 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

========================================