[gmx-users] Writing out individual coordinates

[Justin A. Lemkul]

patrick wintrode wrote:
> Hi.
> 
> For each alpha carbon in my protein, I want to write out the x, y and z 
> coordinates as separate time series.
> 
> If I use g_traj with the flags -oxt -x (or y orz) and -n along with an 
> index file selecting the appropriate alpha carbon, will that do the 
> trick? Does anyone know of a less cumbersome way of doing this?
> 

You don't necessarily have to do each alpha carbon separately (though you could 
script all of it, which is relatively easy).  If you use the default C-alpha 
group, all of the chosen x/y/z coordinates are printed in order of the atom 
number, which can then be parsed with something like awk or perl.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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