Steven Neumann wrote:
Hi Justin,
As you advised I reduced number of my windows and I obtined histogram:
http://speedy.sh/2b9dT/histo.JPG
Which looks really good.
The corresponding profile:
http://speedy.sh/y8Ssz/profile.JPG
I do not understand it. Does my deltaG of binding correspond to
everything above 0 kcal/mol which is 6 kcal/mol?
DeltaG = the free energy difference between the final and initial states. So
that's up to you to decide. Your curve is rather rough and the energy minimum
potentially still ill-defined. The histograms indicate that the sampling
overlap is likely fine, you just may need a bit more sampling in each window to
smooth things out. Also make use of the error estimates that g_wham can
provide; they can be quite informative (and necessary).
-Justin
--
========================================
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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