[gmx-users] bilayer simulation, compressibility

[Erik Lindahl]

T. Zaraiskaya wrote:
> question about the simulation published in Biophy.J v79,2000,426-433
> 
> i would appreciate if Erik Lindahl will take it, since he is a
> co-author of the paper.
> 
> What were the values of compressibility (x/y and z) used in that study?
> 

Hi Tanya,

The volume compressibility of a bilayer is almost exactly that of water
(we used 6e-5). Berger et al (Biophys J. 72:2002-2013) determined that 
from simulations too, so it's not only my guess :-)

Remember that the compressibility only affects the speed of the scaling,
and whether the pressure coupling time constant is in the order of 1 or
10 picoseconds doesn't  matter much when you study fluctuations on
nanosecond scales, so as long as it's in the right order of magnitude 
you should be fine.

That's also the reason why there's usually no practical difference 
between Berendsen and Parinello-Rahman pressure coupling; the 
fluctuations on picosecond scales are different, but averaged over
100ps-1ns the systems behave the same.

Cheers,

Erik