From: Philip Blood (philb_at_hec.utah.edu)
Date: Fri Apr 08 2005 - 11:14:40 CDT
Hi,
I am equilibrating some lipid bilayer configurations (72 lipids) with a
fully flexible cell and I see something rather odd. I start the
configurations at a higher area per lipid than given by experiment and
I expect the bilayer to relax to a lower area per lipid, which it does.
The odd thing is that all the relaxation occurs in the x direction,
while the y dimension of the box stays at about the same average
length. I realize that this could be a result of some weird thing with
the initial conditions, but I have seen this same behavior with two
separate configurations.
So I was wondering if those of you who have simulated lipid bilayers
with anisotropic pressure coupling or who have used anisotropic pressure
coupling in general could comment. These are isotropic systems (in the
x-y plane), so it is strange that the cell would shrink over 8 angtroms
in the x direction and only 1 angstrom in the y direction (this is after
10 ns of simulation time). Could there be anything in the pressure
routine itself that might cause some bias? Again I can't rule out that
this happens by chance, but it might be worthwhile to look into this.
Thanks,
Phil Blood
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