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

[Tsjerk Wassenaar]

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 <ababakha at mccammon.ucsd.edu> 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 <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
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