I think this should be rather straightforward:

We should add some more logic to the designation of the trajectory (or structure) file to be used with the MDAnalysis parser, see Block around Line 1694.

I would suggest creating a function find_trajectory_files(), which executes the current block and logic, but then also looks for pdb, gro, etc. if trr and xtc are not found. We have to define an prioritization ordering, I would say: trr, xtc, pdb, gro, ... (I prioritized pdb above gro because it can also hold a trajectory, but maybe this is not right). Other formats that people use with Gromacs?

A small update:

https://userguide.mdanalysis.org/stable/universe.html

If only a single file is provided, MDAnalysis tries to read both topology and trajectory information from it.

• Passing only a *.gro file to MDAnalysis generates a universe with topology information and a single trajectory frame
• Same for passing only a PDB file
• *.gro and PDB are treated as both trajectory and topology formats by MDAnalysis, so this might not hold for other topology formats.

I would suggest making sure that when we generate the MDAnalysis universe, we use the keywords (topology=..., trajectory=...) to make it very clear what kind of information is passed to the current instance.

@Bernadette-Mohr Make sure to follow up HERE once this is addressed