Let us consider the case of a model receptor-ligand complex to understand the steps involved in the SEEKR2 workflow. Initially, a structural (PDB) file containing the receptor protein and the ligand in an explicit solvent is provided as an input file (Figure ). We then identify the ligand in the PDB file through its atom indices. Once the ligand and the receptor protein are identified, we define a collective variable (CV). In most cases, for receptor-ligand binding and unbinding processes, we choose the CV to be the distance between the center of mass (COM) of α-carbon atoms at the binding site of the receptor and the COM of the heavy atoms of the ligand (Figure ). Atomistic simulation details are required for receptor-ligand complexes when the ligand is close to the binding site, and conformational changes in the receptor are observed as the ligand slowly unbinds. In cases where the ligand is far from the receptor-ligand binding site, these two entities can be treated as point charges. Hence, BD is employed beyond a cut-off distance defined by the user. Therefore, the phase space of the receptor-ligand complex is comprised of the MD region and the BD region (Figure ). We further subdivide the MD region into milestones based on a pre-defined CV.