From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Wed Dec 13 2006 - 22:00:03 CST
Dear all namd user,
In my test membrane system, I set up the membrane-water system
with vmd plugin. With the default setting, I found that after
equilibration and a short production run, the water molecules indeed
fill in the gap of the lipid head groups. But I also found that some
lipid head groups seem to thrust out of the water layer, is that
normal? How should I set the thickness of water layer, is there a
standard or something can be calculated according certain physics law,
such as surface tension force? Since I am very new to membrane
simulation, any idea is appreciated.
Guo, Zhi
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