[gmx-users] Umbrella_pull_simulation

[shahid nayeem]

My protein complex interface has a hydrophobic core and on each side of
this core at the edge are two hydrogen bonds. The Hydrogen bond on one side
is between Arg and Asp and another side it is between Arg and Glu. Its
experimental Kd is in nanomolar regions. How should I decide the length of
the simulation required in each window with this information.
Shahid nayeem

On Fri, Feb 24, 2012 at 7:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shahid nayeem wrote:
>
>> I thought this time to be sufficient without any reasonable basis.
>>
>
> If you pick an arbitrary time frame, you're going to get results with
> arbitrary accuracy.  Your time frame should be decided based on a whole
> host of factors, not the least of which include an assessment of the types
> of interactions in the system and how they may decay as a function of
> distance, as well as the individual convergence of observables in each
> simulation.  This is true of any simulation.  Only after you can conclude
> that each window has converged can you expect to draw any reasonable
> conclusions.
>
>
> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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