OpenFE RBFE - jacs_set (8 systems) - 2026-08-05-openff3.0.0-alpha1b_tip3p-jacs

Overview RBFE 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 openff-3.0.0-alpha1b/tip3p.offxml for proteins and solvents, and openff-3.0.0-alpha1b with nagl_openff-gnn-am1bcc-1.0.0.pt for ligands, solutes, and cofactors. The network contains 566 edges across 194 unique ligands. Results are derived from archived Alchemiscale workflow data. For scripts to generate this network: github.com/openforcefield/alchemical-benchmark- resources/submissions/2026_07_15_openff-3.0.0-alpha1b_tip3p/alchemiscale_submission.ipynb Repository Reference This submission is linked from the OpenFE Benchmarks repository: https://github.com/OpenFreeEnergy/openfe-benchmarks/tree/main/openfe_benchmarks/results/2026-08-05-openff3.0.0-alpha1b_tip3p-jacs Software Versions openfe_version: "1.8.0" openmm_version: "8.2.0" openff_toolkit_version: "0.18" Alchemical Network Keys - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd: jacs_set/cdk2 - AlchemicalNetwork-38e7552634bee5f4d425fe9ed2fb85d9: jacs_set/bace - AlchemicalNetwork-5a1747bd8d2fec35462d32168df71c4f: jacs_set/ptp1b - AlchemicalNetwork-5aca98623a3487f76f1fd7255848a4a9: jacs_set/mcl1 - AlchemicalNetwork-7337defddce50b480590f8c848143d65: jacs_set/p38 - AlchemicalNetwork-79b5a746219163f999ed27182064a7d0: jacs_set/jnk1 - AlchemicalNetwork-8f28971733a4f639c9ba89cba74466f9: jacs_set/thrombin - AlchemicalNetwork-f8388a2e4aa7e6909e505ae1e61b4e12: jacs_set/tyk2 Recommended Descriptors forcefield: ["openff-3.0.0-alpha1b", "tip3p.offxml"] 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 key benchmark_data: source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks "jacs_set": "bace": AlchemicalNetwork-38e7552634bee5f4d425fe9ed2fb85d9 "cdk2": AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd "jnk1": AlchemicalNetwork-79b5a746219163f999ed27182064a7d0 "mcl1": AlchemicalNetwork-5aca98623a3487f76f1fd7255848a4a9 "p38": AlchemicalNetwork-7337defddce50b480590f8c848143d65 "ptp1b": AlchemicalNetwork-5a1747bd8d2fec35462d32168df71c4f "thrombin": AlchemicalNetwork-8f28971733a4f639c9ba89cba74466f9 "tyk2": AlchemicalNetwork-f8388a2e4aa7e6909e505ae1e61b4e12 Protocol Settings protocol_settings: - protocol: "HybridTopProtocol" protocol_library: "pontibus" timestep: "4.0 fs" temperature: "298.15 K" pressure: "1 bar" forcefields: ["TODO"] 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-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=17, ligand_final=1h1q, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=17, ligand_final=1h1r, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=17, ligand_final=1oiu, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=1h1r, ligand_final=1h1q, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=1h1s, ligand_final=31, solvent={'O'}, cofactors=none, protein={'unknown'} - etc. - protocol: "HybridTopProtocol" notes: | Detailed protocol settings differ: - solvation_settings.solvent_padding: 1 -> 1.2 Applies to 283 edges: - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=17, ligand_final=1h1q, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=17, ligand_final=1h1r, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=17, ligand_final=1oiu, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=1h1r, ligand_final=1h1q, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-28ff87e9e98dcc018873a3d0f364c0cd jacs_set-cdk2: ligand_start=1h1s, ligand_final=31, solvent={'O'}, cofactors=none, protein=none - etc.