[gmx-users] Umbrella Sampling - Ligand Protein

[Justin A. Lemkul]

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

========================================