[gmx-users] lipid molecular director axis definition

[Mohsen Ramezanpour]

Hi Everyone,

I have a system formed of lipids (DOPE). I would like to know the average
angle of the "molecular director axis" with z-direction. Using g_angle it
should be easy. However, my question is regarding the molecular director
axis.

Is there any definition for how to determine a "lipid molecular axis"?

If yes, is this definition applicable to all lipids, e.g. PC, PE, PS
lipids, disregards the angle the headgroups makes with the lipid/water
interface?


I looked at the literature but I could not find any definition.
For instance, such an angle was calculated in the following article.

https://www.ncbi.nlm.nih.gov/pubmed/17598103

However, I could not find how the molecular director axis was defined.

Thanks in advance for your reply

Cheers,
Mohsen


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