In this work, we have built on the MD-based ABFE protocol of Ge et al. with a special focus on its potential pitfalls. Additionally, we have used harmonic and vdW restraints, both of which are practical for use in MD, unlike the hard-wall potential used in the previous study of Michel et al. (our approach probably mimics that potential to a significant extent). Moreover, we have designed this study to provide a clear and accurate definition of trapped water displacement. We will demonstrate how it can be adapted to be suitable for workflows involving minimal human interac-tion, avoiding the extensive analyses that were required to confirm correctness in the original work. We then further extended the ABFE protocol into an RBFE protocol, where the unfavorable binding mode of ligand A without the trapped water was transformed into a favorable binding mode of ligand B, and the ∆G Complex,W ater A->B was estimated by calculating the ∆G W ater and ∆G Complex A->B (Figure ). To the best of our knowledge, this is the first study of an MD-based separation of states approach being applied to RBFE calculations between ligands involving displacement of trapped waters.