Molecular dynamics (MD) simulations have found their applications in science and engineering, such as chemistry and biochemistry, statistical mechanics, condensed matter physics, and material science. In recent years, MD simulations have significantly impacted in studying complex biological processes such as protein folding, drug discovery, receptor-ligand binding and unbinding, protein-membrane interactions, and protein-protein interactions. MD simulations can effectively analyze key mechanistic insights into highly complex dynamics of biological systems of interest in atomistic detail. However, the task of estimating the kinetics and thermodynamics of such systems comes with its own set of challenges.