We will explore the three distinct stages of a SEEKR2 calculation: prepare, run, and analyze. Every stage is required to obtain estimates of the kinetics and thermodynamics of a system. This tutorial assumes that we use a computer with one or more graphical processing units (GPUs). If the computer does not have a GPU, we ought to transfer all files to a computer equipped with a GPU (and OpenMM, with the SEEKR2 OpenMM Plugin and SEEKR2 Python API installed) to run MD simulations.