<div>Thank you Justin! That helped a lot!</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Thank you Justin, now I get what you mean!<br>As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy?<br>
</blockquote><br></div>The free energy minimum should (theoretically) be when the peptides are still interacting, i.e. at time zero. Use this frame and base the spacing off of it.
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Then spacing should be 0.2 nm. Right? But how is it possible to do spacing like this from such results of summary_distances.dat:<br>
<br>189 0.5769072<br><br><a href="tel:190%200.5753590" target="_blank" value="+19005753590">190 0.5753590</a><br><br><a href="tel:191%200.5711223" target="_blank" value="+19105711223">191 0.5711223</a><br><br><a href="tel:192%200.5719844" target="_blank" value="+19205719844">192 0.5719844</a><br>
<br>193 0.5856807<br><br><a href="tel:194%200.5886649" target="_blank" value="+19405886649">194 0.5886649</a><br><br>195 0.5958101<br><br>.......<br><br>211 0.7111782<br><br>212 0.7322708<br><br>213 0.7675126<br><br>...<br>
<br>378 4.2101626<br><br>379 4.1993918<br><br>380 4.2223649<br><br>......<br><br>500 5.48839<br><br>Do you mean the approximate valueof 0.2 nm spacing? As it would be difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until 5nm?<br>
<br></blockquote><br></div>Choose approximate values.<br><br>My protocol of uneven spacing was necessary to refine the energy minimum for the suitable data for the paper. I kept the tutorial simple; you should still achieve a reasonable result. Uneven spacing is uncommon in the literature, so I did not want to give anyone the impression that it was a standard protocol, leaving it as an exercise for the reader to understand the paper and the motivation for uneven spacing.
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<div class="h5"><br><br>-Justin<br><br>-- <br>==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(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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