As suggested by you I added some new window and extended some simulation and I got the attached profile and histo file. Please see these files. Experimentally it is known that wt protein-protein interaction is stronger than the mutants. But I get here is reverse. what could be the possible reason for it. My profile.xvg and histo.xvg are right or they need more improvement.<div>
Shahid Nayeem<br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 7:44 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">
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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">
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. <br>
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I've already made numerous suggestions. The value in pullf.xvg is a consequence of the nature of the system. Looking at the interactions between your proteins, the stability of those proteins, etc. is far more informative, like you would for any simulation (even those that do not make use of the pull code).<div>
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<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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