Box vectors not being saved properly in utils/equilibration.py

[zhang-ivy]

In the equilibration module, the equilibrated PDB is saved here: https://github.com/choderalab/openmmtools/blob/main/openmmtools/utils/equilibration.py#L154-L158

The box vectors for the equilibrated PDB are not saved properly, as they are the box vectors for the original solvated input PDB, not the final equilibrated positions.

Before saving the equilibrated PDB, we should add something like this that updates the box vectors in the topology:

box_vectors_formatted = []
for vec in box_vectors:
    box_vectors_formatted.append(openmm.Vec3(*[val.value_in_unit_system(unit.md_unit_system) for val in vec]))
box_vectors_final = unit.Quantity(value=box_vectors_formatted, unit=unit.nanometer)
topology.setPeriodicBoxVectors(box_vectors_final)