<div>Thank you Justin, now I get what you mean!</div>
<div>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?</div>
<div>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:</div>
<div> </div>
<div><span lang="EN">
<p>189 0.5769072</p>
<p>190 0.5753590</p>
<p>191 0.5711223</p>
<p>192 0.5719844</p>
<p>193 0.5856807</p>
<p>194 0.5886649</p>
<p>195 0.5958101</p>
<p>.......</p>
<p>211 0.7111782</p>
<p>212 0.7322708</p>
<p>213 0.7675126</p>
<p>...</p>
<p>378 4.2101626</p>
<p>379 4.1993918</p>
<p>380 4.2223649</p>
<p>......</p>
<p>500 5.48839</p>
<p>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? </p>
<p>Thank you,</p>
<p>Steven</p></span><br><br></div>
<div class="gmail_quote">On Wed, Nov 16, 2011 at 2:31 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">Hi GMX Users,<br> I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other?<br>
<br></blockquote><br></div>By pulling on the COM of any molecule, the forces are then redistributed to the other atoms. In the case given in the tutorial, the region you see dissociate first is held together by relatively weak interactions. If you pull directly on a specific residue or atom, that residue will dissociate first in all likelihood. For further discussion pertinent to this specific system, please refer to our paper linked from the tutorial. You're observing what we observed, so there is no problem and I am happy that the behavior is reproducible for others :)
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations:<br>
0 - 0.50<br>50 - 0.52<br>100 - 0.51<br>150 - 0.51<br>200 - 0.62<br>250 - 2.21<br>....<br>500 - 5.48<br> My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary?<br>
</blockquote><br></div>I'm not clear on what you mean here. In constructing a reaction coordinate, you need to sample at finite intervals along the given path. 0.2 nm is a common spacing used for many systems, and if you want to reproduce the tutorial's results, you should use that spacing. Otherwise, I can't guarantee what you will see. The peptide chains remain bound for a long time, until the force applied by the harmonic spring overcomes the intermolecular interactions. This was useful in our study (again, see the paper for why).
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">And the last thing - is it required to use frames till 189 as the COM varies in this area?<br> <br></blockquote>
<br></div>You only need one to represent the center of that particular window, since the COM distance isn't changing much here.<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><br>==============================<u></u>==========<br><font color="#888888">-- <br>
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