Justin,<br><br>The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle)<br>
But after nvt simulation this discrepancy occured :)<br><br>I've used pbc size like in the KALP simulation because I have bilayer ( 128 lipids) and the protein (38 a.a) of the same size.<br>My box vectors were 6.500 6.500 6.500<br>
<br>Do you think that I should use smaller pbc? How I could define pbc on the right size for my purely bilayer system?<br><br>I've used<br><font face="Arial"><font size="3"><pre>trjconv -s em.tpr -f dmpc128.gro -o dmpc128_whole.gro -pbc mol -ur compact
<br>at the preequilibrated bilayer and than done anything in accordance to the KALP tutorial<br><br><br>James</pre></font></font><br><div class="gmail_quote">2011/11/11 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">How large of a void exists between your lipids and water prior to starting the simulation? I'm almost certain that you built the unit cell incorrectly - there should never be that much free space.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
By the way I'ts intresting that Gmembed has removed 6 lipids in comparison to the inflateglo ( althought I've done all things in accordance to the KALP tutorial because my protein is the same). <br>
</blockquote>
<br></div>
Different algorithms, different results. Nothing odd about that to me.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><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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