Add a warning/note in the setup that protein inputs may need to be equilibrated before running RBFE?

[hannahbaumann]

Simulations can crash (give NaN errors) if the protein has not been equilibrated first. Maybe we could add a warning or note in the documentation that proteins may need to be equilibrated (short minimization and MD simulation) before setting up the free energy calculations

[IAlibay]

Sounds like a good idea to me!