[gmx-users] lipid order parameter

[Pedro Alexandre Lapido Loureiro]

> 
> Hi Pedro,
> 
> If your united atom chain contains N atoms, then you will have N-1 order
> parameters.  The reason for this is that with united atoms, you have to use
> C-C bond geometry to extract the angle a C-H (or for deuterium C-D) vector
> would make with a stationary vector in the lab frame (in simulations the
> vector
> is usually taken to be in the z direction) if it existed in the model.
> 
> 
> David
> 
Thanks for your reply, David!

Yes, but you need information (for the i-th CH2) from the i-1 and i+1 CH2. So, 
from a N-atom chain I would get N-2 order parameters.
My question is: does the first reported Scd refers to the "second" CH2 (carbon 
no. 18 n sn-2, according to a widely used convention) of the chain?
..
C = O
|
CH2 (17)
|
CH2 (18)
..

Cheers, 

Pedro.
--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil