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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 16 09:05:14 CEST 2007

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.



On 7/13/07, Arneh Babakhani <ababakha at mccammon.ucsd.edu> 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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