OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

OpenFF 2.2.1 Relative Binding Free Energy Benchmarks Overview Relative binding free energy benchmarks of the openff-2.2.1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024). Contents Benchmark variants The following benchmark variants were run: * `openff-2.2.1_elf10`: simulations using OpenFF 2.2.1 and AM1BCCELF10 charges using the OpenEye Toolkit. * `openff-2.2.1_nagl`: simulations using OpenFF 2.2.1 and AshGC v0.1rc3 charges * `openff-2.2.1_am1bcc`: simulations using OpenFF 2.2.1 and AM1BCC charges calculated using ambertools. Please note that these charges were not assigned to the input conformer, but rather a conformer that was generated at charge assignment time via RDKit through the OpenFF toolkit. RBFE data The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set. Plots dG (MLE-derived using cinnabar) and ddG plots are present for each system under the `plots` folder. Simulation details * All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following: * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent * 2.5 ps HREX exchange rate * 0.9 nm short range interaction cutoff