[gmx-users] area per headgroup for lipid

Yuhua Song yhsong at ccb.wustl.edu
Fri Jun 11 01:15:28 CEST 2004

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?

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.



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