Hi Arneh,
I'd sort of do the same, but would use R (http://cran.r-project.org/)
:) Just a matter of taste (and of sticking to free, open-source
software).
Tsjerk
On 7/17/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote:
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),
Arneh
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 <[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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>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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3584 CH Utrecht
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