[gmx-users] Umbrella_pull_simulation

shahid nayeem msnayeem at gmail.com
Tue Feb 28 06:59:20 CET 2012

Thanks. But Does that mean that I should look in pullf.xvg of each window
and see whether the value is converged or not. If not then I should extend
the simulation.
Shahid Nayeem

On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> shahid nayeem wrote:
>> 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.
> As you would any other system.  Look for convergence of observables of
> interest.  Your PMF alone suggests insufficient sampling for these
> simulations, so as I've said several times, you probably need longer
> simulations to do so, but you can start by examining the physical
> properties of each window.  What you're looking for is up to you, based on
> your knowledge of the system at hand.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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