[gmx-users] number of windows in PMF

[Rebeca García Fandiño]

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?
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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