The following directory contains all simulation files and code to reproduce our work, "Characterizing Discrete Binding Conformations of T4 L99A via Markov State Modeling".
Associated code and files for different procedures are separated into distinct directories, outlined below. Each level of organization also contains a separate README.md file that better details what can be found.
simulation_files: starter files to reproduce simulationsmsm_notebooks: Jupyter notebooks to build MSMs for different protein--ligand systemsfigures: contains all figures from the main textSI: contains all figures from the Supporting Information and sample trajectory frames to visualize
The content here relies primarily on open-source tools and we provide files to reproduce the environment we used to run the analyses. Some materials require an OpenEye license, which is free for academics.