[gmx-users] trajectories files

[Bert de Groot]

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??
> 

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

cheers,

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________