[gmx-developers] Format of Gromacs files

Nicolas Vervelle nvervell at club-internet.fr
Sat Oct 7 22:08:22 CEST 2006


I am totally new to this list, so I am going to introduce myself.

I am working on the Jmol project [1], a Java open-source molecular viewer.
I am also interested in the Folding At Home [2], a distributed computing 
projects about protein folding.
They have just released a client based on Gromacs capable of running on 
a GPU instead of a CPU.

I have done a web page [3] allowing Folding At Home contributors to see 
the proteins they are working on in 3D.
Currently, I can only read the information from the CPU client, not by 
the GPU client because the GPU client outputs less files.

I want to be able to add the proteins that are dealt with by the GPU 
client, so I need to be able to read the files from Jmol.
I have the following files available :
- a .ckp file
- a .dat file
- a .dyn file (small)
- a .edr file (small)
- a .tpr file
- a. trr file (empty)
- a .xtc file

If I understand correctly (correct me if I am wrong), I would need to read:
- the .tpr file containing system topology, coordinates
- eventuallly, the .xtc file containing the trajectories

But, I can't find the description of .tpr file format.
I found a short description of the .xtc file format.

Any help will be appreciated.

[1] http://www.jmol.org/
[2] http://folding.stanford.edu/
[3] http://www.jmol.org/fah/

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