Thanks Justin<div>I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier.</div>
<div>shahid Nayeem <br><br><div class="gmail_quote">On Sat, Feb 18, 2012 at 7:27 PM, 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>
<br>
shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All<br>
<br>
I am doing umbrella sampling for a protein complex. After analysis I am finding that prifle.xvg has not converged. Now I want to extend simulation. I have already pulled one chain to the length of the box. Can I further pull by extending the box size and add more windows to umbrella sampling. Please suggest.<br>
</blockquote>
<br></div>
You would have to use a simple test system to prove that this is a valid approach. Changing the nature of the system for some windows sounds very questionable to me, and likely would be to reviewers.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
How one should ascertain the initial box size so that g_wham gives a converged profile.xvg.<br>
</blockquote>
<br></div>
You should determine the distance needed to sufficiently separate your components, that is, determine the minimum COM distance at which interaction between the two species is negligible. Ideally, they would be non-interacting, but with PME, that is not possible.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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