MD Protocol protocol unit output includes a PDB for the NVT equilibrated structure even NVT equil was not run #1298
Description
If we set simulation_settings.equililbration_length_nvt=None, no NVT simulation will be run.
However, the ProtocolUnit output will still contain a path to a non-existant PDB file for the NVT equilibrated structure, because output_settings.equil_nvt_structure is not None by default.