The working_examples directory contains the SEEKR2 tutorials on biomolecular complexes, i.e., the seven βcyclodextrin-guest complexes (Figure ) and the trypsinbenzamidine complex (Figure ). One of the subdirectories, beta_cyclodextrin_guest_complexes, contains the seven hostguest complexes where necessary files and scripts are located for each of the complexes to set up the SEEKR2 calculation, run MD and BD simulations, and analyze SEEKR2 simulations to calculate thermodynamic and kinetic quantities of interest. The tutorial will go through one of the host-guest complexes, i.e., the BCD-1-butanol complex. The user may follow the same instructions to get started with the other six host-guest complexes within the beta_cyclodextrin_guest_complexes directory. Similarly, the other subdirectory, trypsin_benzamidine_complex contains the files and scripts to parameterize the receptor-ligand complex, set up the SEEKR2 simulations, and perform the post-SEEKR2 analysis. The first stage of a SEEKR2 calculation is the preparation phase. This stage involves setting up the necessary input files and defining parameters for the simulation. Let us subdivide the preparation phase further into three stages: