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.
-Justin
Thanks a lot again for your help.
Best wishes,
Rebeca.
> Date: Tue, 12 Jul 2011 16:53:54 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] number of windows in PMF
>
>
>
> Rebeca García Fandiño wrote:
> > Hello,
> > I am trying to calculate the binding energy between two monomers in
> > three different dimers, using PMF (Umbrella Sampling method) and
> > following Justin's tutorial.
> > Using 100 windows separated 0.05 nm I get the PMFs represented in
> > "pmf_using_100_points.pdf" (attached), and using 50 windows separated
> > 0.1 nm I get different PMF results, represented in
"pmf_using_50_points.pdf"
> > How is it possible to obtain so different results depending on the
> > number of windows used in the Umbrella Sampling Calculation?
>
> You haven't said how long your simulations are or how large the
system is. It
> looks to me like your curves are not well-converged. The energy
minima are not
> at a consistent location along the reaction coordinate, so I suspect
you're not
> yet converged.
>
> g_wham will give you an error estimate; you may find that you have
large error
> bars, so the results may be indistinguishable (within error), but
from the plots
> one cannot tell.
>
> -Justin
>
> > Any help is appreciated.
> > Thanks a lot in advance!
> > Best wishes,
> > Rebeca.
> >
> > Dr. Rebeca Garcia
> > Santiago de Compostela University
> > Spain
> >
>
> --
> ========================================
>
> 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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