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

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue Jul 17 02:30:22 CEST 2007

ok, thanks.  I like Chris's suggestion.  I'll try using matlab to parse 
it out (b/c matlab can easily ingest column formatted data),


Tsjerk Wassenaar wrote:
> 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 <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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