<br><br><div class="gmail_quote">On Fri, May 18, 2012 at 12:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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>
I have no idea why you observe the dip, but it's probably irrelevant as you don't need a reaction coordinate that long, if this is the same plot that we've been discussing on the list.<br>
<br>
I must ask that you always post to the mailing list, for your own benefit, especially in the immediate future as I will be traveling for some time and will not reply very quickly to email; you stand a better chance getting help from others. I am also generally unable to dedicate much time debugging others' research on a personal level.<br>
<br>
-Justin<div class="HOEnZb"><div class="h5"><br></div></div></blockquote><div>Thank you Justin. I decreased the reaction coordinate and this dip still occurs:<br><br><a href="http://speedy.sh/2qHNa/Profile2.JPG">http://speedy.sh/2qHNa/Profile2.JPG</a><br>
<br>Its because of the applied weight of WHAM. Any suggestions please?<br><br>Steven<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="HOEnZb">
<div class="h5">
<br>
On 5/18/12 4:17 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin,<br>
<br>
<br>
I run umbrella sampling (pulling ligand away from the protein) simulations to<br>
get deltaG:<br>
<br>
<a href="http://speedy.sh/XpUks/Profile.JPG" target="_blank">http://speedy.sh/XpUks/<u></u>Profile.JPG</a><br>
<br>
<a href="http://speedy.sh/yvJKx/Histogram.JPG" target="_blank">http://speedy.sh/yvJKx/<u></u>Histogram.JPG</a><br>
<br>
I know I need one more window around 1 nm but apart from this histrogram looks<br>
really good. My each window was 50 ns.<br>
<br>
Why the plateau in the end goes down of 0.4 kcal/mol? Would you suggest longer<br>
simulation in each window?<br>
<br>
Thank you and sorry for writing straight to your email,<br>
<br>
Best<br>
<br>
Steven<br>
<br>
<br>
</blockquote>
<br></div></div><span class="HOEnZb"><font color="#888888">
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Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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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