[gmx-users] area per lipid with peptide/protein

[Nicolas Michel]

Patrick Fuchs a écrit :

> Hi gmx users,
> does anyone know a simple way to evaluate the area per lipid of a 
> simulation of peptide (or protein) within a lipid bilayer (in other 
> words, how to evaluate the area of the peptide (or of the protein)) ?
> Thanks for your answer,
>
> Patrick
>
Hello,
I think there is no tool for a direct calculation. But you get the area 
per lipid of simple membranes by division of the surface area (xy plane) 
of the simulation box by the number of lipid in a leaflet (quite 
simple). For a protein you could project it along the normal of the 
bilayer (z) and then calculate its surface area on the xy plane. A vmd 
script would do the trick.
Regards
-- 
Nicolas Michel, PhD Organic Chemistry
Chercheur au chomage