Free energy perturbation (FEP)

This includes all data and scripts on how I calcualted the PMFs of some important sidechain pairs by using the OpenMM program.

ipynb or html

Please read the fep.ipynb or fep.html file for more details,

$ jupyter-lab fep.ipynb

or

$ firefox fep.html

which can be generated from "jupyter nbconvert fep.ipynb --to html_toc --ExtractOutputPreprocessor.enabled=False"