{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/best-practices-for-alchemical-free-energy","title":"Best Practices for Alchemical Free Energy Calculations","arxiv_id":"2008.03067","date":"2020-08-07","proceeding":null,"authors":["Antonia S. J. S. Mey","Bryce Allen","Hannah E. Bruce Macdonald","John D. Chodera","Maximilian Kuhn","Julien Michel","David L. Mobley","Levi N. Naden","Samarjeet Prasad","Andrea Rizzi","Jenke Scheen","Michael R. Shirts","Gary Tresadern","Huafeng Xu"],"abstract":"Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of \"bridging\" potential energy functions representing \\emph{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. 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. 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.","url_abs":"https://arxiv.org/abs/2008.03067v3","url_pdf":"https://arxiv.org/pdf/2008.03067v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"best-practices-for-alchemical-free-energy","repo_url":"https://github.com/michellab/alchemical-best-practices","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2008.03067","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}