[gmx-users] A. - Vol. / lipid & associated errors

Erik Lindahl lindahl at csb.stanford.edu
Wed Jun 9 14:09:10 CEST 2004


> Why the area per lipid and not the V. per lipid, as I "suggested" 
> above?

Because you can't really change the density of a condensed system 
significantly by scaling. As an example, if you take a water box of 
2*2*2 nanometers and change it to 4*4*4 nanometers the system will 
equilibrate to 'islands' of water with vacuum between, instead of 
uniform 1/8 density.

In other words: you'll have to live with whatever volume/lipid your 
forcefield reproduces.

The area compressiblity is much lower, since the bilayer thickness will 
change simultaneously to keep the volume/lipid constant.

> Yes, the bilayer will be just a "solvent" to a protein.
> BTW, if I first equilibrate a membrane in NAreaPT conditions, with zero
> compressibility in the plane (xy) of the membrane (with the correct
> area/lipid), and then give semi or anisotropically freedom in the xy 
> plane,
> will the assimptotically area-volume per lipid will be the "same", if 
> I turn
> the semi or anisotropically freedom in the xy plane at the begining of 
> the
> equilibration? I suppose so.

No idea what you mean here. I would recommend coupling xy and z 
pressures separately, and let the area/lipid change freely during your 
simulation. That's what happens in reality since the lipids are part of 
a much larger patch.



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