Hi Arneh,
I think you're out of luck here. However, this is an excellent
exercise to get started with writing custom made analysis tools :)
Alternatively, you could output the coordinates for the C and O using
g_traj and use a script to calculate the angles with the z-axis, in
case it's a single bond you're interested in.
Cheers,
Tsjerk
On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote:
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
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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