For more experienced users that would like to use the Enlighten2 Python package directly (e.g. to setup simulations for HPC systems), usage examples are provided in the GitHub repository. Further, all intermediate files are conveniently stored in separate folders, allowing an experienced user to introduce any input modifications prior to rerunning the corresponding codes manually (e.g. for setting up periodic boundary simulations or introducing covalent bonds between proteins and cofactors) or upload the input files to run simulations on HPC systems.