[gmx-users] Writing out individual coordinates

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 19 22:25:56 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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