<html>
<blockquote type=cite class=cite cite>originally from Tieleman, that has
been simulated for some time. So my<br>
patch does not have very clean edges, meaning some parts of some
lipids<br>
protrude out of my boundaries for the box. Will increasing the
box<br>
dimensions so that all of the lipids totally fit in the box mess up
the<br>
simulation by decreasing the density of the bilayer? And does
protruding<br>
lipids or atoms mess up the periodic boundary
conditions?</blockquote><br>
No, since they are a consequence of the PBC. If you find a chain
that is sticking out one side of the box, go to the opposite side and you
will see a void where it is actually located.<br><br>
VMD can show adjoining boxes to help with PBC visualisation.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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