[gmx-users] number of windows in PMF

[Justin A. Lemkul]

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: jalemkul at vt.edu
>  > To: gmx-users at 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

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