OpenFE RBFE - jacs_set (8 systems) - 2026-09-28-openff3.0.0-alpha2b_opc3-jacs

OverviewRBFE benchmark results prepared from AlchemicalArchive JSON file(s) generated with OpenFE and Alchemiscale. This submission describes the RBFE benchmark covering jacs_set: bace, cdk2, jnk1, mcl1, p38, ptp1b, thrombin, tyk2 prepared with opc3.offxml/openff-3.0.0-alpha2b for proteins and solvents, and openff-3.0.0-alpha2b with nagl_openff-gnn-am1bcc-1.0.0.pt for ligands, solutes, and cofactors. The submission 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/2026-09-11_openff-3.0.0-alpha2b_opc3/alchemiscale_submission.ipynb Submission Snapshot- Submission ID: 2026-09-28-openff3.0.0-alpha2b_opc3-jacs- Date: 2026-09-28- Results file: computational_results.json.bz2- License: CC-BY-4.0- Authors: Jennifer A. Clark- Tags: rbfe, alchemicalarchive, opc3.offxml, openff-3.0.0-alpha2b, jacs_set, bace, cdk2, jnk1, mcl1, p38, ptp1b, thrombin, tyk2, nagl_openff-gnn-am1bcc-1.0.0.pt, pontibus Systems Covered- jacs_set: bace, cdk2, jnk1, mcl1, p38, ptp1b, thrombin, tyk2 Repository Referencehttps://github.com/OpenFreeEnergy/openfe-benchmarks/tree/main/openfe_benchmarks/results/2026-09-28-openff3.0.0-alpha2b_opc3-jacs Software Versions- openfe_version: 1.8.0- openmm_version: 8.2.0- openff_toolkit_version: 0.18- pontibus_version: 0.4.0 Alchemical Network Keys- AlchemicalNetwork-5dc9c9cfdb1cd11f50dffe8ea01d660b: jacs_set/bace- AlchemicalNetwork-c90824fca3b38fad4f0fa88b50ac3e15: jacs_set/cdk2- AlchemicalNetwork-f923711e3af1e04e523547c137f67fed: jacs_set/jnk1- AlchemicalNetwork-77a1bd8a9a8888aabb307df3306cb763: jacs_set/mcl1- AlchemicalNetwork-332dd0d866b70b97b9e0c8c48db020c5: jacs_set/p38- AlchemicalNetwork-5012b5ccb6ab213efdb22238e293130c: jacs_set/ptp1b- AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2: jacs_set/thrombin- AlchemicalNetwork-9ed5fef0e0f4127532ef49599402ccd0: jacs_set/tyk2 Recommended Descriptors- partial_charges: nagl_openff-gnn-am1bcc-1.0.0.pt- mapper: KartografAtomMapper 1.2.0 (LSA)- forcefield: ['opc3.offxml', 'openff-3.0.0-alpha2b']- small_molecule_forcefield: openff-3.0.0-alpha2b BenchmarkData Provenance- source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks benchmark_data: source_repository: https://github.com/OpenFreeEnergy/openfe-benchmarks jacs_set: bace: AlchemicalNetwork-5dc9c9cfdb1cd11f50dffe8ea01d660b cdk2: AlchemicalNetwork-c90824fca3b38fad4f0fa88b50ac3e15 jnk1: AlchemicalNetwork-f923711e3af1e04e523547c137f67fed mcl1: AlchemicalNetwork-77a1bd8a9a8888aabb307df3306cb763 p38: AlchemicalNetwork-332dd0d866b70b97b9e0c8c48db020c5 ptp1b: AlchemicalNetwork-5012b5ccb6ab213efdb22238e293130c thrombin: AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 tyk2: AlchemicalNetwork-9ed5fef0e0f4127532ef49599402ccd0 Protocol Settings- Protocol settings entries: 2 protocol_settings:- protocol: HybridTopProtocol protocol_library: pontibus notes: |- Applies to 283 edges: - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1a, ligand_final=1c, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1a, ligand_final=3b, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1a, ligand_final=5, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1b, ligand_final=1a, solvent={'O'}, cofactors=none, protein={'unknown'} - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1d, ligand_final=1b, solvent={'O'}, cofactors=none, protein={'unknown'} - etc. timestep: 4.0 fs temperature: 298.15 K pressure: 1 bar lambda_functions: default lambda_windows: '11' small_molecule_forcefield: openff-3.0.0-alpha2b forcefields: - opc3.offxml - openff-3.0.0-alpha2b partial_charges: nagl_openff-gnn-am1bcc-1.0.0.pt equilibration_time: 1.0 ns production_time: 5.0 ns- protocol: HybridTopProtocol protocol_library: pontibus notes: |- Detailed protocol settings differ: - solvation_settings.solvent_padding: 1 -> 1.2 Applies to 283 edges: - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1a, ligand_final=1c, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1a, ligand_final=3b, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1a, ligand_final=5, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1b, ligand_final=1a, solvent={'O'}, cofactors=none, protein=none - AlchemicalNetwork-2e24db5f3ed614ab10c499c0ec6165c2 jacs_set-thrombin: ligand_start=1d, ligand_final=1b, solvent={'O'}, cofactors=none, protein=none - etc. timestep: 4.0 fs temperature: 298.15 K pressure: 1 bar lambda_functions: default lambda_windows: '11' small_molecule_forcefield: openff-3.0.0-alpha2b forcefields: - opc3.offxml - openff-3.0.0-alpha2b partial_charges: nagl_openff-gnn-am1bcc-1.0.0.pt equilibration_time: 1.0 ns production_time: 5.0 ns