SEEKR2 has emerged as a multiscale simulation tool designed to increase the speed and efficiency of calculating kinetic and thermodynamic properties of receptor-ligand binding and unbinding. This tutorial covers the underlying theory behind SEEKR2, describing how kinetic and thermodynamic properties are calculated. Beginning with the installation and setup, this manuscript guides the readers through the processes of preparing SEEKR2 simulations, highlighting essential options such as equilibration steps and adjusting the speed of HIDR simulations. The subsequent sections then provide a detailed walkthrough of the run and analysis stages, emphasizing the significance of files like model.xml and scripts like run.py and analyze.py.