[gmx-developers] extraction of trj files

Alan Dodd anoddlad at yahoo.com
Sat Dec 29 21:13:11 CET 2007

If you have some basic C skills, template.c (in the folder gromacs/share/template) gives you a platform to extract what you want in the same (efficient) manner as the GROMACS programs do.  It's then up to you to format the output.

----- Original Message ----
From: Dave Segala <segalad at egr.uri.edu>
To: gmx-developers at gromacs.org
Sent: Saturday, December 29, 2007 5:55:55 PM
Subject: [gmx-developers] extraction of trj files

To Gromacs Developers:

  I have simulated my protein and have my trajectory file with both
position and velocity for each atom. What I am trying to do is take
those positions and velocities and store them into their own
arrays/matrices as a matfile (matlab file). The way I am doing this
seems to be not the right or best way. I redirect the output of the trj
using gmxdump to a text file (gmxdump -f file.trj > file.txt). The trj
file is 8GB and the text file is 30GB.
  Is there anyone that can give me the structure of the trj file(I know
its binary) to bypass the text file? Does anyone have a better way of
extracting the pos and vel into matlab arrays/matrices.

With Best Regards,
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