[gmx-users] lipid molecular director axis definition

[Mohsen Ramezanpour]

Thanks, Justin.

I think so. Sure, I will.

On Fri, Nov 10, 2017 at 5:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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