MDAnalysis example

[Barfy007JB1]

Description of work
A full example of how MDMC can be used to work with MDAnalysis

[alexhroom]

reverted the changes from Ang to Angstrom present in this PR as they were causing issues and are out the scope of this PR!

[alexhroom]

can't get this to run. firstly write_H5MD complains about the lack of creator name and email, but when that's fixed I get:

Traceback (most recent call last):
  File "/workspaces/MDMCv0.2_pilot/examples/mdanal.py", line 36, in <module>
    u = mda.Universe(topology_file_name, fn, format="h5md", topology_format='config',
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 436, in __init__
    self.load_new(coordinates, format=format, in_memory=in_memory,
  File "/usr/local/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 665, in load_new
    self.trajectory = reader(filename, format=format, **kwargs)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/MDAnalysis/lib/util.py", line 2701, in wrapper
    return func(self, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/MDAnalysis/coordinates/H5MD.py", line 450, in __init__
    if self._particle_group['box'].attrs['dimension'] != 3:
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/usr/local/lib/python3.12/site-packages/h5py/_hl/attrs.py", line 56, in __getitem__
    attr = h5a.open(self._id, self._e(name))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5a.pyx", line 80, in h5py.h5a.open
KeyError: "Unable to synchronously open attribute (can't locate attribute: 'dimension')"