[gmx-users] Umbrella Sampling - Ligand Protein

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
>         Hi Justin,
>          As you advised I reduced number of my windows and I obtined
>         histogram:
>          http://speedy.sh/2b9dT/histo.__JPG
>         <http://speedy.sh/2b9dT/histo.JPG>
>          Which looks really good.
>         The corresponding profile:
>          http://speedy.sh/y8Ssz/__profile.JPG
>         <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
> 
> 
>  
> Thank you Justin. In each window I run the simulation of 10 ns. Do you 
> think that making it 20 ns will make the profile more smooth?
>  

It's no use to blindly guess.  It's up to you to assess the convergence of your 
simulations and decide on an appropriate time frame.

-Justin

-- 
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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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