[gmx-users] area per headgroup for lipid

[Yuhua Song]

> > I am trying to figure out how to calculate the area per headgroup for
> > lipid. I have an equilibrated system with small molecules, lipids, ion
and
> > water. From mailing list dated on May 2, 2002, Nov 9, 2003, David and
Anton
> > had said that simple way to calculate the lipid area is to use the box-x
> > times box-y/#lipids per monolayer. If the system is the pure lipids with
> > water, I understand this way for the calculation of the area per
headgroup
> > for lipid. But if the system has other small molecules and ions, is it
> > still reasonable to calculate the area per headgroup for lipid?
> >
>
> If those small molecules and ions are not "inside" the bilayer, what David
and
> Anton told you, its still true, isn't it?

But the fact is: after a certain time equilibation, some ions are inside the
bilayer, and the small molecules are half-insertion of the bilayer, in this
case, could I still use the way: box_X*box_Y/#lipids per monolayer? If I can
not, what would be the proper way?

Thanks,

Yuhua