I have added some new windows in mutant umbrella sampling which removes the sampling gap around 4 nm. Also I sampled more windows in the initial COM distance in the hope that I get energy minimum of profile well defined. I also did boot strapping for error estimates. The files can be assessed at<div>
<a href="http://www.freefilehosting.net/umbrellamut">http://www.freefilehosting.net/umbrellamut</a> </div><div><br><br><div class="gmail_quote">On Wed, Mar 7, 2012 at 4:38 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"><br>
<br>
shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
The attached profile.xvg and histo.xvg are here.<br>
sorry for sending earlier mail without attachments<br>
Shahid Nayeem<br>
<br></div><div class="im">
On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem <<a href="mailto:msnayeem@gmail.com" target="_blank">msnayeem@gmail.com</a> <mailto:<a href="mailto:msnayeem@gmail.com" target="_blank">msnayeem@gmail.com</a>>> wrote:<br>
<br>
As suggested by you I added some new window and extended some<br>
simulation and I got the attached profile and histo file. Please see<br>
these files. Experimentally it is known that wt protein-protein<br>
interaction is stronger than the mutants. But I get here is reverse.<br>
what could be the possible reason for it. My profile.xvg and<br>
histo.xvg are right or they need more improvement.<br>
</div></blockquote>
<br>
I wouldn't base any conclusions off of them. You have a sampling gap at just over 4 nm in the mutant simulations. More importantly, you do not have a defined energy minimum in the mutant windows so it is impossible to calculate a reliable value for DeltaG. Moreover, in the absence of any error estimates, you can't make any conclusions about these data. g_wham can generate error bars for you; I'd suggest you do it.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Shahid Nayeem<br>
<br>
<br>
On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div class="im">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
shahid nayeem wrote:<br>
<br>
Thanks. But Does that mean that I should look in pullf.xvg<br>
of each window and see whether the value is converged or<br>
not. If not then I should extend the simulation.<br>
<br>
<br>
I've already made numerous suggestions. The value in pullf.xvg<br>
is a consequence of the nature of the system. Looking at the<br>
interactions between your proteins, the stability of those<br>
proteins, etc. is far more informative, like you would for any<br>
simulation (even those that do not make use of the pull code).<br>
<br>
<br>
-Justin<br>
<br></div>
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Virginia Tech<br>
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Virginia Tech<br>
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