From: Jerome Henin (jerome.henin_at_uhp-nancy.fr)
Date: Fri Apr 08 2005 - 13:44:19 CDT
Hi Philip,
Actually, I did see a similar behaviour on some lipid bilayer I have simulated.
Until now, I assumed it to be a consequence of intrinsic properties of my
system, but I would be interested to know if many people experienced the same
situation, and if it somehow could be linked to the barostat.
Best,
Jerome
> 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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