[gmx-users] Umbrella Sampling - Ligand Protein

[Steven Neumann]

On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <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?

Steven


>  --
> ==============================**==========
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> Justin A. Lemkul
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> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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