Thank you very much Dr.Justin for your important notes<br> <br><br><div class="gmail_quote">On Wed, Apr 6, 2011 at 8:09 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
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Dear Dr.Justin<br>
I had asked this question before but unfortunately I didn't answered good!<br>
<br>
Instead of Pulling and separating some structures in definite distances,<br>
I located my drug in definite distances along z axis (as my initial structures for doing umbrella sampling).<br>
Am I right?<br>
<br>
</blockquote>
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I have no idea. Presumably, if you've defined the reaction coordinate appropriately and distributed configurations along this vector at adequate intervals to sample the whole coordinate, then yes.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The main problem underlying this question is :<br>
Do we need to know the velocity of drug in every structure we choose for doing umbrella sampling?(do they need to include the velocities too?)<br>
</blockquote>
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PMF is calculated from either the resulting positions (in pullx.xvg) or forces (pullf.xvg) from the harmonically restrained simulations.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
if no,which criteria assures with this K our molecule can cover the length of it's windows?<br>
<br>
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You can't necessarily know a priori if your force constants are adequate. Unfortunately, it's a bit empirical. Run some simulations and analyze the result with g_wham. A smooth PMF with good overlap between the histograms indicates your sampling is (at least) good, if not optimal on the first try.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Because I have chosen windows with different lingthes,And I want now to choose K so that it can sweep the lengthes.<br>
<br>
</blockquote>
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Weaker force constants allow for more oscillation, but again, there is no prescribed way to know what values to choose. If you have some very large window, you assign a weaker force constant, but then you may not cover the entire sampling window without a longer simulation in this window such that your molecule wanders through all of the applicable configuration space.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks in advance for your reply<br>
<br>
<br>
<br>
<br>
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-- <br>
========================================<br>
<br>
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.vt.edu/Pages/Personal/justin</a><br>
<br>
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