From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 29 2007 - 13:41:29 CDT
I noticed that at no point during your equilibration do you allow the
lipids to move under conditions where the area is not fixed. Is there
any particular reason for this? It is quite likely that your area is too
big for the lipids if you're using a stock lipid box, since they need to
be further equilibrated, particularly if there is an embedded protein.
You may want to check that you have a realistic surface area per lipid
in your system, and have a look at Feller and Pastor, JCP 111:1281
(1999) for some of the hazards present in dealing with lipid surface
areas in MD.
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