[gmx-users] trajectories files

Bert de Groot bgroot at gwdg.de
Fri Nov 29 10:38:46 CET 2002

Ruben Martinez Buey wrote:
> Hi everybody,
> How can I join a lot of pdb structures generated by concoord into a trajectory file??

cat disco*.pdb > concoord.pdb
will generate a valid NMR pdb file that can be treated as a trajectory in
gromacs. Alernatively, you could have generated a trajectory with concoord
in e.g. the .xtc format using the -ox flag.

> What programs do you suggest to visualize the trajectories/structures??

Usually the visualisation of concoord results is most clearly visible
after an essential dynamics/PCA analysis (ie after g_covar+g_anaeig)



Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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