<p>Hey vrk.</p>
<p>You should carefully compare all run parameters that were active in either program. Sending the parameter files to the list might raise some useful suggestions.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Sep 14, 2011 3:53 PM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><br><p><font color="#500050">
vijayaraj ramadoss wrote:
>
> Hello Users,
>
> Previous I have done simulation of small protein us...</font></p>
Did you run replicates of each system, or are you basing your observations on a single trajectory? You need to compare properly sampled systems. A single trajectory is generally not enough to make reliable conclusions.<br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
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Virginia Tech<br>
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