Address warning about neighbour list limit

[jan-janssen]

Currently in the tests we get the following warning:

/home/runner/work/structuretoolkit/structuretoolkit/structuretoolkit/analyse/neighbors.py:270: UserWarning: Number of neighbors found within the cutoff_radius is equal to (estimated) num_neighbors. Increase num_neighbors (or set it to None) or width_buffer to find all neighbors within cutoff_radius.

It is not yet clear to me which tests cause these warnings, but we should take a look to see if we can fix them.