Ivy Zhang

Yay, glad its working! The second code snippet you shared is for setting up neq switching calculations. `n_equilibration_iterations` is used here for the repex: https://github.com/choderalab/perses/blob/f3aacde3588e5b90e67a21052d914a033d3c087b/perses/app/setup_relative_calculation.py#L980 `hss_run` is an instance of...

Also, we're super glad that you are using perses -- huge apologies that there aren't any docs. Thanks for your patience / happy to help clarify things whenever we can!