[gmx-developers] tpr format

Xavier Periole x.periole at rug.nl
Thu Apr 20 17:38:00 CEST 2006

nmichaud at jhu.edu wrote:

>Is the tpr format documented anywhere (besides the source). I would like
>to use gromacs' geometric analysis tools for a simulation I did with
>NAMD. The trajectory I can convert from dcd to xtc, (is there also
vmd 1.8.4 can write trajectory in trr format !!

>documentation for the trr/trj format), but require either a tpr, tpb
>or tpa (what is the difference between all these?) for most of the
>analysis tools.
For many of the analysis tools you can use a coordinate file, either gro 
or pdb file.
To get a tpr file is quite easy from a pdb file if your system is a 
protein. Adding
solvent would more problematic, but feasible.

pdb2gmx -f file.pdb gives you a topol.tpr that you can use.


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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