It's appeared new question about G_membed<br><br>Does anobody used this algorithm for insertion of their proteins ?<br>In particular I wounder to know how I can to find optimal parameters ( different scaling factors like in the below command) for insertion in my system( single alpha helix in DMPC bilayer system) and how I can measure area per lipid in the output system?<br>
<br> g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100<br><br><br>James<br><br><br><div class="gmail_quote">2011/10/25 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
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<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Justin,<br>
<br>
I've found the same task of MSU's students :) They simulate membrane formation without NPT stage ( after NVT they run production MD). From they reports I've found that simplest membrane system could be formed within 10-30 Ns. But what about try to make such simulation in vacuum at first without any water ? Might the bilayer been formed in such conditions?<br>
<br>
Finally I have small question about pereodic boundaries of such bilayer system.<br>
<br>
E.g I've done simplest system with water consisted of 8 lipid molecules + some water.<br>
This is the representation of the system <a href="http://i1209.photobucket.com/albums/cc394/own11/lipids8.png" target="_blank">http://i1209.photobucket.com/<u></u>albums/cc394/own11/lipids8.png</a><br>
I want to simulate bilayer formation as well as concomitant hydrophobic effect ( removing all water from formed bilayer)<br>
Does the PBC presented in that example ( 2.64196 2.64196 6.85002 for 8 lipids) are enought for such lipid movement? It seems that more free space aree needed for overal turn of lipid molecules. How I can calculate exactly PBC value required for my system ?<br>
<br>
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I agree that your system has insufficient space for any real movement without violating the minimum image convention. Your system must have adequate room for any lipid to rotate in any direction, and be of sufficient size to accommodate a formed membrane, which will have dimensions dictated by the APL for the chosen lipid (and of course, the force field's ability to produce that value).<div>
<div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
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<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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