[gmx-users] number of windows in PMF

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 12 22:53:54 CEST 2011

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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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