[gmx-users] which tool to use a measure a user-defined angle in a traj

[Arneh Babakhani]

Hi,

Looking through the gmx tools . . . was wondering, which tool would one 
use (if such a tool exists) to measure the fluctuation of a user-defined 
angle in a trajectory.

For instance, I want to measure the angle defined by a carbonyl vector 
(a vector going through a C=O bond) in my molecule and the z-axis of the 
simulation box.  How do I define this angle, and which tool would I use 
to measure it in each frame of my trr?

Thanks,

Arneh