Feature request: Better support for non-orthogonal simulation boxes

[Ladme]

This issue serves to gather feedback on whether better support for non-orthogonal (e.g. hexagonal) simulation boxes is a widely desired feature. If this functionality is important for your use case, please leave a comment or react to this issue (or write us an e-mail!).

(Note: Non-orthogonal boxes are currently supported, but require manual handling of PBC and ensuring molecules remain whole within the box. See the manual for details.)