Re: simulation of membrane-protein systems

From: Guo Zhi (
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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:57 CST