Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
© 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 43(2022), 17 vom: 30. Juni, Seite 1151-1160 |
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| Weitere Verfasser: | , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2022
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't free energy calculations solvation free energy toolkit |
| Zusammenfassung: | © 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC. We describe the theory of the so-called common-core/serial-atom-insertion (CC/SAI) approach to compute alchemical free energy differences and its practical implementation in a Python package called Transformato. CC/SAI is not tied to a specific biomolecular simulation program and does not rely on special purpose code for alchemical transformations. To calculate the alchemical free energy difference between several small molecules, the physical end-states are mutated into a suitable common core. Since this only requires turning off interactions, the setup of intermediate states is straightforward to automate. Transformato currently supports CHARMM and OpenMM as back ends to carry out the necessary molecular dynamics simulations, as well as post-processing calculations. We validate the method by computing a series of relative solvation free energy differences |
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| Beschreibung: | Date Completed 26.05.2022 Date Revised 07.09.2022 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.26877 |