perses_protein_mutations

a collection of ipython notebooks attempting to resurrect and complete protein mutations.

the minimal working examples are as follows:

protein_test_mappings.ipynb attempts to generate a 19x19 protein mutation map (including topology proposals, geometry proposals, and hybrid system creations) for dipeptides.

protein_test_mutation.ipynb attempts to run vacuum and tip3p replica exchange free energy simulations from alanine dipeptide to valine dipeptide; both appear to be converging without instabilities

the working PR in https://github.com/choderalab/perses to run this code is found here: choderalab/perses#618