HIV RT RBFE calculation results

# unzip the results folders using: tar -xf hiv_rt_rbfe_results.tar.gz # Four folders containing R-modification and Core-hopping series RBFE calculations using Pilot and Adaptive lambda scheme, as stated in the folder names. # In every folder, there is a Juptyer notebook "fep_analysis.ipynb", which is used to obtain ddg values, overlapping matrix plots, and dg_i,0 vs lambda window plots. Users who want to use the notebook need to install all the packages listed in the first cell, and the most important two packages are alchemlyb and pymbar. Users only need to modify the perturbation folders name in the inputs of the "get_ddg" function located in the last cell and run the entire notebook to obtain the results. # In every pilot calculations folder, there is a Juptyer notebook "adaptive_lambda.ipynb", which is primarily used to obtain the adaptive lambda scheme based on the pilot calculation results. Users only need to modify the perturbation folders name in the "system" variable located at the 1st line of the last cell and run the entire notebook to obtain the results.