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. <div>Shahid Nayeem<br><br><div class="gmail_quote">On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
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shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.<br>
</blockquote>
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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.<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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