Another aspect of MD-based free energy calculations is the extreme sensitivity of such calculations to their initial conditions . It has been shown that free energies derived from two independent MD simulations, only varying in their starting velocities, can vary by a substantial amount; the exact figure depends on the type of method used and the system studied . MD-based free energy methods require ensemble averaging across the conformations generated. However, the practice has been to perform time averaging over a single trajectory relying on the ergodic theorem which equates time averaging to ensemble averaging. It is worth mentioning that the ergodic theorem holds true only in the limit of infinite time which is far from the typical length of simulations performed. This explains the observed differences in free energies between repeat simulations. Indeed, a recent study showed that ensembles are required to handle both aleatoric and parametric uncertainty in MD simulation . It has also been shown that running an ensemble of independent simulations varying only in their starting conditions, or in other words, an ensemble simulation yields precise and reproducible results . In particular, methods such as ESMACS and TIES have been developed based on such ensemble simulations so as to ensure reproducibility and hence reliability of the predicted free energies. Recently, we have also shown that the distributions of free energies obtained from such ensemble simulations are in general not Gaussian, as is the common assumption; rather they exhibit non-normality which has interesting and important consequences . Alchemical binding free energy calculations are a class of free energy method which involve the transformation of one or more chemical moieties in the system to another . Alchemical protein-ligand binding calculations can be performed in an absolute or relative fashion .