Installed the GROMACS 4.6.5 tools via Ubuntu-repository.
With those tools is rather simple to read the files from the working directory. The first learning: there can be more then one protein chain in the WU and sometimes something else (and not only water).
Like in P7505 there is a compound included called POPC (on the left); that one has quite a number of carbon atoms (comes at no surprise: 42

) It looked wired the first times I saw it but it start to make sense.
One problem is that the trajectory provided by the API don't contain those additional information like number of protein chains, the identification of the side chains/residue or additional relevant molecules. GROMAS file has it all. Passthrough would be great as it would allow much simpler and diverse visualisation.
Anyway: I'm getting used to the files and continue my journey into the "boxes" ...
The learning continues ...