@article{Mey_Allen_Bruce McDonald_Chodera_Hahn_Kuhn_Michel_Mobley_Naden_Prasad_Rizzi_Scheen_Shirts_Tresadern_Xu_2020, place={Boulder, CO, USA}, title={Best Practices for Alchemical Free Energy Calculations [Article v1.0]}, volume={2}, url={https://livecomsjournal.org/index.php/livecoms/article/view/v2i1e18378}, DOI={10.33011/livecoms.2.1.18378}, abstractNote={<p>Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another.</p> <p>The hallmark of these methods is the use of "bridging" potential energy functions representing _alchemical_ intermediate states that cannot exist as real chemical species. The data collected from these bridging alchemical thermodynamic states allows the efficient computation of transfer free energies (or differences in transfer free energies) with orders of magnitude less simulation time than simulating the transfer process directly.</p> <p>While these methods are highly flexible, care must be taken in avoiding common pitfalls to ensure that computed free energy differences can be robust and reproducible for the chosen force field, and that appropriate corrections are included to permit direct comparison with experimental data.</p> <p>In this paper, we review current best practices for several popular application domains of alchemical free energy calculations, including relative and absolute small molecule binding free energy calculations to biomolecular targets.</p>}, number={1}, journal={Living Journal of Computational Molecular Science}, author={Mey, Antonia S. J. S. and Allen, Bryce K. and Bruce McDonald, Hannah E. and Chodera, John D. and Hahn, David F. and Kuhn, Maxmillian and Michel, Julien and Mobley, David L. and Naden, Levi N. and Prasad, Samarjeet and Rizzi, Andrea and Scheen, Jenke and Shirts, Michael R. and Tresadern, Gary and Xu, Huafeng}, year={2020}, month={Dec.}, pages={18378} }