[gmx-users] area per headgroup for lipid

[Nuno R. L. Ferreira]

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
Portugal
www.biolchem.qui.uc.pt
**********************************************
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."
                                   emc2