[gmx-users] Pressure Coupling for Lipid Bilayers

Erik Lindahl lindahl at sbc.su.se
Fri May 12 10:46:11 CEST 2006


On May 11, 2006, at 6:05 PM, Arneh Babakhani wrote:

> Hello,
> Would the following be a reasonable way to implement semiisotropic  
> pressure coupling, for a 128 DMPC membrane:
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = semiisotropic
> tau_p = 1.0 1.0
> compressibility = 4.5e-5 1.0e-30
> ref_p = 1.0 1.0

I would use slower scaling, e.g. tau_p = 10ps.  The inherent  
relaxation is on the order of nanoseconds anyway, so by using a too  
short time you only add noise and risk risk system crashes due to  
excessively hard scaling.

However, you should be aware that semi-isotropic scaling might affect  
the properties if the membrane since it removes the x-y fluctuations.  
On the other hand, anisotropic scaling probably over-estimates them  
due to PBC.

It was a hack I introduced a long time ago when 64 lipid systems were  
common, and I'm still not sure whether it's better or worse than  
anisotropic scaling...



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