[gmx-users] A. - Vol. / lipid & associated errors
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"
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
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
> 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
> 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.
More information about the gromacs.org_gmx-users