[gmx-users] Umbrella Sampling - Ligand Protein

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 11 23:13:38 CET 2012

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 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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