Showcase notebook incorrectly says we can set box dimensions via the ChemicalSystem

[IAlibay]

Follow up from OpenFreeEnergy/openfe#1032

Section 2.3 says that you can set the box vectors when creating a ChemicalSystem. As far as I'm aware, this is incorrect. We should remove this to avoid confusing users.

[jameseastwood]

Mike pre-approves the PR to resolve this, so please feel free to merge without review