From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Mon Feb 05 2007 - 11:50:04 CST
If one generates a POPE membrane using the vmd plugin, the resulting area
per lipid is about 71 A^2 per lipid [example, a 100 x 100 patch has 140
lipids in each leaflet]. This area per lipid is about 17% higher than the
experimentally measured values at 30-40 degree C. However, the average
bilayer thickness (phosphate-to-phosphate) is about 38 A, which is more or
less as expected in experiments.
It this initial membrane setup not too far from equilibrium ? Of course,
one could equilibrate to the correct area per lipid, but that would
require holding the headgroups constrained along the bilayer normal, so
that the bilayer thickness does not increase while the area gets reduced.
However, I have not really come across this method/discusssion/problem in
any articles where VMD's plugins have been used. What am I missing ?
P.S: I think this post is relevant to both vmd and namd forums, and have
copied it to both.
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