simulation of membrane-protein systems

From: L. Michel Espinoza-Fonseca (
Date: Wed Dec 13 2006 - 02:01:41 CST

Hi people,

I have been performing a few simulations of protein-membrane systems
using a flexible cell and PBC. I used the "membrane" plugin to build
the membranes. I subjected such membranes to minimization and
equilibration for a period of 0.5 ns. I get a pretty good equilibrated
slab, so no problem there. The "problem" (I really don't know if
that's a problem) is that after continuing my simulation for about 10
ns, the shape of the lipid bilayer looks more like a "disc" than a
"box". Moreover, water molecules start to surround the Z-axis edges of
the membrane. Now my question is, is that normal? According to what I
believe, it is not. how can I avoid this?
All comments are very appreciated.

Thanks a lot!

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