[gmx-users] lipid molecular director axis definition

Justin Lemkul jalemkul at vt.edu
Fri Nov 10 13:56:12 CET 2017

On 11/9/17 6:21 PM, Mohsen Ramezanpour wrote:
> 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.

It appears to be the principal axis of the lipid molecule, but probably 
the authors of that study can tell you how it was done, either via 
GROMACS tools or their own code. I'm not sure how GROMACS tools would 
calculate that quantity.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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