RE: simulation of membrane-protein systems

From: JC Gumbart (
Date: Wed Dec 13 2006 - 22:28:17 CST

Can you be more specific with what you mean by "thrust out of the water
layer"? Perhaps a screenshot of your system in this configuration would be
most illustrative.

-----Original Message-----
From: Guo Zhi []
Sent: Wednesday, December 13, 2006 10:00 PM
To: JC Gumbart
Cc: Richard Wood;
Subject: Re: namd-l: simulation of membrane-protein systems

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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