OpenFE RBFE - jacs_set (8 systems) - 2026-08-04-openff3.0.0-alpha1b_opc3-jacs

OverviewRBFE benchmark results prepared from AlchemicalArchive JSON file(s) generated with OpenFE and Alchemiscale. This submission describes the RBFE benchmark covering the jacs_set benchmark set (bace, cdk2, jnk1,mcl1, p38, ptp1b, thrombin, tyk2) prepared with opc3.offxml/openff-3.0.0-alpha1b for proteins andsolvents, and openff-3.0.0-alpha1b with nagl_openff-gnn-am1bcc-1.0.0.pt for ligands, solutes, andcofactors. The network contains 566 edges across 194 unique ligands. Results are derived fromarchived Alchemiscale workflow data. For scripts to generate this network:github.com/openforcefield/alchemical-benchmark-resources/submissions/2026_07_15_openff-3.0.0-alpha1b_opc3/alchemiscale_submission.ipynb Repository ReferenceThis submission is linked from the OpenFE Benchmarks repository:https://github.com/OpenFreeEnergy/openfe-benchmarks/tree/main/openfe_benchmarks/results/2026-08-04-openff3.0.0-alpha1b_opc3-jacs Software Versionsopenfe_version: 1.8.0openmm_version: 8.2.0openff_toolkit_version: 0.82 Alchemical Network Keys: - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2: jacs_set/ptp1b - AlchemicalNetwork-51caad3a5d3daea240406eb23fa6dad6: jacs_set/tyk2 - AlchemicalNetwork-58ef1baba714145eaddb8f81abf609ce: jacs_set/bace - AlchemicalNetwork-6cea205bc124349b8add8824e2060147: jacs_set/jnk1 - AlchemicalNetwork-7fcf1d4cb0a6af702747de83fc23af69: jacs_set/thrombin - AlchemicalNetwork-8b3e6b25fe046924998a1f520c798b19: jacs_set/cdk2 - AlchemicalNetwork-c613a533bdaa47f92e9a1cf4d58fe6dd: jacs_set/p38 - AlchemicalNetwork-ee5422ba932ced782b51da9bb9eb24ff: jacs_set/mcl1 Recommended Descriptorsforcefield: ["opc3.offxml", "openff-3.0.0-alpha1b"]small_molecule_forcefield: "openff-3.0.0-alpha1b"partial_charges: "nagl_openff-gnn-am1bcc-1.0.0.pt"mapper: "KartografAtomMapper 1.2.0 (LSA)" BenchmarkData provenance (from openfe-benchmarks planning script) with associated network keybenchmark_data: source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks "jacs_set": "bace": AlchemicalNetwork-58ef1baba714145eaddb8f81abf609ce "cdk2": AlchemicalNetwork-8b3e6b25fe046924998a1f520c798b19 "jnk1": AlchemicalNetwork-6cea205bc124349b8add8824e2060147 "mcl1": AlchemicalNetwork-ee5422ba932ced782b51da9bb9eb24ff "p38": AlchemicalNetwork-c613a533bdaa47f92e9a1cf4d58fe6dd "ptp1b": AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 "thrombin": AlchemicalNetwork-7fcf1d4cb0a6af702747de83fc23af69 "tyk2": AlchemicalNetwork-51caad3a5d3daea240406eb23fa6dad6 Protocol Settingsprotocol_settings: - protocol: "HybridTopProtocol" protocol_library: "pontibus" timestep: "4.0 fs" temperature: "298.15 K" pressure: "1 bar" small_molecule_forcefield: "" partial_charges: "nagl_openff-gnn-am1bcc-1.0.0.pt" equilibration_time: "1.0 ns" production_time: "5.0 ns" vacuum_equilibration_time: vacuum_production_time: solvent_equilibration_time: solvent_production_time: lambda_functions: "default" lambda_windows: "11" lambda_schedule: "" notes: | Applies to 283 edges: - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20667, ligand_final=23482, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20667, ligand_final=23485, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20667, ligand_final=23486, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20669, ligand_final=23466, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=23466, ligand_final=20670, solvent={'O'}, cofactors=none, protein=none - etc. - protocol: "HybridTopProtocol" notes: | Detailed protocol settings differ: - solvation_settings.solvent_padding: 1.2 -> 1 Applies to 283 edges: - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20667, ligand_final=23482, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20667, ligand_final=23485, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20667, ligand_final=23486, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=20669, ligand_final=23466, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-3885e858e4b36849e110edbebe348ae2 jacs_set-ptp1b: ligand_start=23466, ligand_final=20670, solvent={'O'}, cofactors=none, protein={'unknown'} - etc.