[gmx-users] Umbrella Sampling - Ligand Protein

[Steven Neumann]

On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>
>>
>>        <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>
>>
>>        <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
>
>
>
Thank you Justin. Is there any way to find out after deltaG the entropic
contribution to binding free energy?

Steven


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