Ivy Zhang

When I hear "protocol" in the context of alchemical free energy calculations, I think of the alchemical protocol, which tells us how we should transform the WT (or lambda =...

Interesting.. so none of the other test functions in `test_relative.py` fail (e.g. `test_HybridTopologyFactory_energies()`)? is it just `test_RepartitionedHybridTopologyFactory()`? If none of the other test functions besides `test_RepartitionedHybridTopologyFactory()` are failing, then I...

I think all of the files in `app/` have constants that need to be included in this constants file (e.g. [relative_point_mutation_setup.py](https://github.com/choderalab/perses/blob/master/perses/app/relative_point_mutation_setup.py#L19-L23))

@jchodera : I'm having trouble parametrizing the A1 guest because the system_generator doesn't recognize the atom type Ho. Note that I get the same problem when using openff 2.0.0 as...

The `a1.mol2` file I'm feeding into the above code was taken directly from supplementary data from [the paper](https://www.ebi.ac.uk/biostudies/studies/S-EPMC4614838?xr=true) we looked at together last perses dev sync -- its present in...

This worked, thanks so much!!

@jchodera : I started investigating this today, and I have 1 finding and 2 questions. Here is the function in `MultiStateSamplerAnalyzer` that generates the equilibration data (n_equilibration_iterations, statistical inefficiency, and...

As a follow up to question 2 above, I tried swapping out `statisticalInefficiency` with `statisticalInefficiencyMultiple` [here](https://github.com/choderalab/openmmtools/blob/0771ddc36f9a7d4cb183cafe3b95bbd1988fd048/openmmtools/multistate/utils.py#L176) and then fed in the state index and d_u/d_lambda timeseries, but both of them...

The only example I contributed to is `protein_fah` and that one can be deleted. It is out of date. The more up-to-date version is [here](https://github.com/choderalab/perses/tree/master/perses/data/barstar-mutation) and is being tested [here](https://github.com/choderalab/perses/blob/master/perses/tests/test_fah.py#L77)

^*small molecule example