[gmx-users] area per headgroup for lipid

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Jun 11 02:16:01 CEST 2004

On Friday 11 June 2004 12:15 am, Yuhua Song wrote:
> Dear Gromacs user:
> 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?

> Also, I try to use "g_sas" to calculate the hydrophilic solvent
> accesibility area. the Index group that I set include all the lipids in the
> system, the results show at at 0s, the hydrophilic area is 1663.18nm^2, if
> I total have 256 lipids, then the SAS for per lipid is 6.49nm^2. It is far
> from the per lipid headgroup area: ~0.61nm^2.
> So, I am wondering whether someone could give me some suggestion about how
> to calculte the area per headgroup for lipid for a system with ion, lipid,
> water and small molecules?
> Thank you in advance for your help.
> Regards,
> Yuhua
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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."

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