[gmx-users] number of windows in PMF
Rebeca García Fandiño
regafan at hotmail.com
Tue Jul 12 23:46:30 CEST 2011
Thanks a lot for your answer.
My system have about 29000 atoms, and the simulation time was 1ns.
have generated the error bars, and indeed you were right, they are too
big. The histograms looked good, so I thought they should be
What should I do, extending the simulation or generating more windows?
Thanks a lot again for your help.
> 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.
> > 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
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