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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