[gmx-users] Is there any chance to concatenate (fast) more, than 1000 energy files....

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 22 21:37:00 CET 2008

Wouldn't it be a lot easier to just do:

eneconv -f *.edr

Or am I misunderstanding what you're trying to accomplish?


Quoting Sergio <sgaray at fbcb.unl.edu.ar>:

> Dear Diego I'm not sure whether I am understanding well what you suggest
> me. The fact is that I have 1000 energy files to concatenate in one PC.
> My bash script takes the fist two files and concatenates them to produce
> a temporary output file (using eneconv), after that it concatenates the
> last temporary file with the next one to produce a new temp file, and so
> on. Thank you Diego Enry wrote: I think it would take more time to
> transfer files than doing it on a single machine, but here is what I
> suggest: Assuming you have a cluster of 5 nodes you may concatenate by
> parts than put it all together, something like this: transfer .edr files
> to /tmp/ of each node than eneconv the fragments node1 fragments 1-199
> node2 fragments 200-399 node3 fragments 400-599 node4 fragments 600-799
> node5 fragments 800-1000 transfer all back to your $HOME and eneconv all
> five fragments.
> -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
> ------------------------------
> --
> Alberto Sergio Garay
> Practica Profesional - Departamente de Física
> Facultad de Bioquímica Y Cs. Biológicas
> Santa Fe - 3000 - Ciudad Universitaria
> Santa Fe - Argentina


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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