[gmx-users] pressure coupling for lipid bilayer

[Erik Lindahl]

Shang-Te Danny Hsu wrote:

> After many helpful suggestions, I can obtain a quite stable system. 
> The simulation is still underway (it is stablized after 500ps) but I 
> do notice some differences between anisotropic coupling and 
> semi-isotropic coupling.
>
> For 72 POPC with 2799 water molecules at 300K after 200ps simulation, 
> I got surface areas of:
>
> anisotropic     semi-isotropic
> 61.84 A**2    58.83 A**2
>
> For anisotropic, the thickness of membrane decreases much more than 
> that for semi-isotropic; probably due to the coupled-lateral coupling 
> in x/z dimensions, the width of BOX-X decrease less in the 
> semi-isotropic case compared to the anisotropic case. However, the 
> total box volumes in both cases are very similar through out 200 ps 
> simulation.

Hi Xavier,

Have a look at the scaling paper in BpJ 79, 426 (2000) - you will find 
that there are fluctuations with periods up to 10ns for such a small system!

Cheers,

Erik