From: Yanni Wang <Yanni.Wang_at_Kvac.UU.SE>
Date: Fri 30 Mar 2001 10:31:34 +0200

Dear AMBER users,

I have a question about lipid bilayer membrane. In those published
papers that I have read, bilayer membranes are described in the form
that lipid staying in the middle of the box and water at the two sides.
However, in the lipid_bilayer example of AMBER
(~/demo/roar/lipid_bilayer), the membrane (I got it from the parm.crd)
is presented in the form that water in the middle of the box and lipid
bilayer at the two sides. I want to know if there are some differences
(or not because of periodic boundary conditions) between the two kinds
of description.

Recently, I did a membrane (64 DPPC and 1472 water) simulation using the
first kind of model (lipid in the middle of box and water at the sides)
as starting point. However, after about 300 ps constant pressure
simulation, the membrane changed into the second form (water in the
middle of box and lipid at the sides). The membrane was built and had
been equilibrated by another group using GROMOS before my equilibration
and simulation with AMBER. What I did is using their equilibrated
membrane as strating point, and producing .top and .crd files with leap,
then doing equilibration and simulation with AMBER using the same
condition but different water model(they use SPC but I use TIP3P) and
force field. Does somebody know what is wrong with my simulation?

Many thanks for your time and help in advance.

Received on Fri Mar 30 2001 - 00:31:34 PST
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